data_N5P
#
_chem_comp.id N5P
_chem_comp.name
;1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO
-1H-INDOLE
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H17 N2 O14 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-TRIPHOSPHATE"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2007-03-21
_chem_comp.pdbx_modified_date 2020-06-17
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 518.200
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code N5P
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
N5P OR2 OR2 O 0 1 N N N N N N -11.998 65.837 38.494 -9.522 2.250 1.175 OR2 N5P 1
N5P NRO NRO N 1 1 N N N N N N -12.083 64.841 39.197 -8.869 2.213 0.148 NRO N5P 2
N5P OR1 OR1 O -1 1 N N N N N N -11.065 64.372 39.684 -9.295 2.739 -0.865 OR1 N5P 3
N5P CZ3 CZ3 C 0 1 Y N N N N N -13.379 64.215 39.448 -7.553 1.535 0.131 CZ3 N5P 4
N5P CE3 CE3 C 0 1 Y N N N N N -13.435 63.087 40.255 -6.822 1.502 -1.023 CE3 N5P 5
N5P CD2 CD2 C 0 1 Y N N N N N -14.689 62.505 40.486 -5.581 0.862 -1.039 CD2 N5P 6
N5P CH2 CH2 C 0 1 Y N N N N N -14.522 64.788 38.877 -7.070 0.942 1.289 CH2 N5P 7
N5P CZ2 CZ2 C 0 1 Y N N N N N -15.762 64.242 39.088 -5.848 0.306 1.296 CZ2 N5P 8
N5P CE2 CE2 C 0 1 Y N N N N N -15.834 63.091 39.891 -5.089 0.255 0.130 CE2 N5P 9
N5P NE1 NE1 N 0 1 Y N N N N N -16.913 62.339 40.275 -3.863 -0.289 -0.179 NE1 N5P 10
N5P CD1 CD1 C 0 1 Y N N N N N -16.491 61.309 41.080 -3.566 -0.049 -1.493 CD1 N5P 11
N5P CG CG C 0 1 Y N N N N N -15.136 61.368 41.238 -4.563 0.642 -2.069 CG N5P 12
N5P "C1'" "C1'" C 0 1 N N R N N N -18.346 62.553 39.911 -3.004 -1.017 0.758 "C1'" N5P 13
N5P "O4'" "O4'" O 0 1 N N N N N N -19.140 61.497 40.459 -1.641 -0.977 0.304 "O4'" N5P 14
N5P "C4'" "C4'" C 0 1 N N R N N N -19.839 60.808 39.424 -1.035 -2.233 0.679 "C4'" N5P 15
N5P "C3'" "C3'" C 0 1 N N S N N N -19.933 61.809 38.279 -2.150 -3.271 0.398 "C3'" N5P 16
N5P "O3'" "O3'" O 0 1 N N N N N N -21.050 62.687 38.470 -1.975 -4.438 1.204 "O3'" N5P 17
N5P "C2'" "C2'" C 0 1 N N N N N N -18.617 62.561 38.407 -3.425 -2.498 0.813 "C2'" N5P 18
N5P "C5'" "C5'" C 0 1 N N N N N N -19.116 59.497 39.113 0.196 -2.516 -0.185 "C5'" N5P 19
N5P "O5'" "O5'" O 0 1 N N N N N N -19.882 58.704 38.212 1.212 -1.553 0.103 "O5'" N5P 20
N5P PA PA P 0 1 N N N N N N -19.480 57.178 37.897 2.648 -1.549 -0.626 PA N5P 21
N5P O1A O1A O 0 1 N N N N N N -18.003 57.138 37.578 3.289 -2.873 -0.459 O1A N5P 22
N5P O2A O2A O 0 1 N N N N N N -20.008 56.330 39.030 2.453 -1.241 -2.194 O2A N5P 23
N5P O3A O3A O 0 1 N N N N N N -20.269 56.735 36.564 3.581 -0.414 0.033 O3A N5P 24
N5P PB PB P 0 1 N N N N N N -21.441 57.639 35.922 5.159 -0.101 -0.008 PB N5P 25
N5P O1B O1B O 0 1 N N N N N N -20.892 58.294 34.677 5.649 -0.216 -1.400 O1B N5P 26
N5P O2B O2B O 0 1 N N N N N N -22.078 58.503 36.990 5.940 -1.156 0.924 O2B N5P 27
N5P O3B O3B O 0 1 N N N N N N -22.512 56.523 35.471 5.425 1.392 0.532 O3B N5P 28
N5P PG PG P 0 1 N N N N N N -23.685 56.000 36.449 6.640 2.437 0.380 PG N5P 29
N5P O3G O3G O 0 1 N N N N N N -23.759 54.517 36.153 6.146 3.903 0.824 O3G N5P 30
N5P O2G O2G O 0 1 N N N N N N -23.229 56.314 37.860 7.864 1.977 1.319 O2G N5P 31
N5P O1G O1G O 0 1 N N N N N N -24.900 56.779 35.998 7.087 2.472 -1.030 O1G N5P 32
N5P HE3 HE3 H 0 1 N N N N N N -12.539 62.670 40.692 -7.203 1.969 -1.919 HE3 N5P 33
N5P HH2 HH2 H 0 1 N N N N N N -14.426 65.671 38.263 -7.657 0.980 2.195 HH2 N5P 34
N5P HZ2 HZ2 H 0 1 N N N N N N -16.649 64.680 38.654 -5.480 -0.152 2.202 HZ2 N5P 35
N5P HD1 HD1 H 0 1 N N N N N N -17.135 60.563 41.522 -2.663 -0.368 -1.993 HD1 N5P 36
N5P HG HG H 0 1 N N N N N N -14.522 60.692 41.815 -4.606 0.973 -3.096 HG N5P 37
N5P "H1'" "H1'" H 0 1 N N N N N N -18.602 63.544 40.315 -3.079 -0.573 1.751 "H1'" N5P 38
N5P "H4'" "H4'" H 0 1 N N N N N N -20.859 60.488 39.683 -0.770 -2.230 1.737 "H4'" N5P 39
N5P "H3'" "H3'" H 0 1 N N N N N N -20.084 61.350 37.291 -2.181 -3.532 -0.660 "H3'" N5P 40
N5P "HO3'" "HO3'" H 0 0 N N N N N N -21.095 63.304 37.749 -2.649 -5.117 1.064 "HO3'" N5P 41
N5P "H2'1" "H2'1" H 0 0 N N N N N N -18.699 63.586 38.017 -3.725 -2.772 1.825 "H2'1" N5P 42
N5P "H2'2" "H2'2" H 0 0 N N N N N N -17.811 62.061 37.849 -4.235 -2.691 0.109 "H2'2" N5P 43
N5P "H5'1" "H5'1" H 0 0 N N N N N N -18.142 59.723 38.655 0.571 -3.516 0.034 "H5'1" N5P 44
N5P "H5'2" "H5'2" H 0 0 N N N N N N -18.968 58.937 40.048 -0.077 -2.453 -1.238 "H5'2" N5P 45
N5P HO2A HO2A H 0 0 N N N N N N -19.292 55.846 39.424 2.038 -0.387 -2.378 HO2A N5P 46
N5P HO2B HO2B H 0 0 N N N N N N -22.049 59.414 36.721 5.670 -1.137 1.852 HO2B N5P 47
N5P HOG3 HOG3 H 0 0 N N N N N N -24.582 54.321 35.721 6.828 4.585 0.758 HOG3 N5P 48
N5P HOG2 HOG2 H 0 0 N N N N N N -23.801 56.970 38.240 7.643 1.931 2.260 HOG2 N5P 49
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
N5P OR2 NRO DOUB N N 1
N5P NRO CZ3 SING N N 2
N5P NRO OR1 SING N N 3
N5P CZ3 CH2 SING Y N 4
N5P CZ3 CE3 DOUB Y N 5
N5P CE3 CD2 SING Y N 6
N5P CE3 HE3 SING N N 7
N5P CD2 CE2 DOUB Y N 8
N5P CD2 CG SING Y N 9
N5P CH2 CZ2 DOUB Y N 10
N5P CH2 HH2 SING N N 11
N5P CZ2 CE2 SING Y N 12
N5P CZ2 HZ2 SING N N 13
N5P CE2 NE1 SING Y N 14
N5P NE1 "C1'" SING N N 15
N5P NE1 CD1 SING Y N 16
N5P CD1 CG DOUB Y N 17
N5P CD1 HD1 SING N N 18
N5P CG HG SING N N 19
N5P "C1'" "C2'" SING N N 20
N5P "C1'" "O4'" SING N N 21
N5P "C1'" "H1'" SING N N 22
N5P "O4'" "C4'" SING N N 23
N5P "C4'" "C3'" SING N N 24
N5P "C4'" "C5'" SING N N 25
N5P "C4'" "H4'" SING N N 26
N5P "C3'" "C2'" SING N N 27
N5P "C3'" "O3'" SING N N 28
N5P "C3'" "H3'" SING N N 29
N5P "O3'" "HO3'" SING N N 30
N5P "C2'" "H2'1" SING N N 31
N5P "C2'" "H2'2" SING N N 32
N5P "C5'" "O5'" SING N N 33
N5P "C5'" "H5'1" SING N N 34
N5P "C5'" "H5'2" SING N N 35
N5P "O5'" PA SING N N 36
N5P PA O3A SING N N 37
N5P PA O1A DOUB N N 38
N5P PA O2A SING N N 39
N5P O2A HO2A SING N N 40
N5P O3A PB SING N N 41
N5P PB O1B DOUB N N 42
N5P PB O3B SING N N 43
N5P PB O2B SING N N 44
N5P O2B HO2B SING N N 45
N5P O3B PG SING N N 46
N5P PG O1G DOUB N N 47
N5P PG O3G SING N N 48
N5P PG O2G SING N N 49
N5P O3G HOG3 SING N N 50
N5P O2G HOG2 SING N N 51
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
N5P SMILES ACDLabs 12.01 "[O-][N+](=O)c2cc1ccn(c1cc2)C3OC(C(O)C3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O"
N5P InChI InChI 1.03 InChI=1S/C13H17N2O14P3/c16-11-6-13(14-4-3-8-5-9(15(17)18)1-2-10(8)14)27-12(11)7-26-31(22,23)29-32(24,25)28-30(19,20)21/h1-5,11-13,16H,6-7H2,(H,22,23)(H,24,25)(H2,19,20,21)/t11-,12+,13+/m0/s1
N5P InChIKey InChI 1.03 JJJBDAFRCKSXDR-YNEHKIRRSA-N
N5P SMILES_CANONICAL CACTVS 3.370 O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2ccc3cc(ccc23)[N+]([O-])=O
N5P SMILES CACTVS 3.370 O[CH]1C[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2ccc3cc(ccc23)[N+]([O-])=O
N5P SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 c1cc2c(ccn2C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)cc1[N+](=O)[O-]
N5P SMILES "OpenEye OEToolkits" 1.7.2 c1cc2c(ccn2C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)cc1[N+](=O)[O-]
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
N5P "SYSTEMATIC NAME" ACDLabs 12.01 1-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-5-nitro-1H-indole
N5P "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "[[5-(5-nitroindol-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
N5P 'Create component' 2007-03-21 RCSB
N5P 'Modify descriptor' 2011-06-04 RCSB
N5P 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id N5P
_pdbx_chem_comp_synonyms.name "5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-TRIPHOSPHATE"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id N5P
_pdbe_chem_comp_synonyms.name "5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-TRIPHOSPHATE"
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
N5P OR2 O 3.000 3.315 1
N5P NRO N 4.299 4.065 2
N5P OR1 O 4.299 5.565 3
N5P CZ3 C 5.598 3.315 4
N5P CE3 C 6.897 4.065 5
N5P CD2 C 8.196 3.315 6
N5P CH2 C 5.598 1.815 7
N5P CZ2 C 6.897 1.065 8
N5P CE2 C 8.196 1.815 9
N5P NE1 N 9.616 1.358 10
N5P CD1 C 10.491 2.565 11
N5P CG C 9.616 3.772 12
N5P "C1'" C 10.082 -0.068 13
N5P "O4'" O 11.509 -0.529 14
N5P "C4'" C 11.511 -2.029 15
N5P "C3'" C 10.086 -2.495 16
N5P "O3'" O 9.625 -3.922 17
N5P "C2'" C 9.202 -1.283 18
N5P "C5'" C 12.726 -2.908 19
N5P "O5'" O 14.096 -2.296 20
N5P PA P 15.311 -3.175 21
N5P O1A O 16.190 -1.960 22
N5P O2A O 14.431 -4.391 23
N5P O3A O 16.526 -4.055 24
N5P PB P 17.895 -3.442 25
N5P O1B O 18.508 -4.812 26
N5P O2B O 17.283 -2.073 27
N5P O3B O 19.264 -2.830 28
N5P PG P 20.480 -3.710 29
N5P O3G O 21.359 -2.495 30
N5P O2G O 19.600 -4.925 31
N5P O1G O 21.695 -4.589 32
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
N5P OR2 NRO DOUBLE NONE 1
N5P NRO CZ3 SINGLE NONE 2
N5P NRO OR1 SINGLE NONE 3
N5P CZ3 CH2 DOUBLE NONE 4
N5P CZ3 CE3 SINGLE NONE 5
N5P CE3 CD2 DOUBLE NONE 6
N5P CD2 CE2 SINGLE NONE 7
N5P CD2 CG SINGLE NONE 8
N5P CH2 CZ2 SINGLE NONE 9
N5P CZ2 CE2 DOUBLE NONE 10
N5P CE2 NE1 SINGLE NONE 11
N5P "C1'" NE1 SINGLE BEGINDASH 12
N5P NE1 CD1 SINGLE NONE 13
N5P CD1 CG DOUBLE NONE 14
N5P "C1'" "C2'" SINGLE NONE 15
N5P "C1'" "O4'" SINGLE NONE 16
N5P "O4'" "C4'" SINGLE NONE 17
N5P "C4'" "C3'" SINGLE NONE 18
N5P "C4'" "C5'" SINGLE BEGINDASH 19
N5P "C3'" "C2'" SINGLE NONE 20
N5P "C3'" "O3'" SINGLE BEGINWEDGE 21
N5P "C5'" "O5'" SINGLE NONE 22
N5P "O5'" PA SINGLE NONE 23
N5P PA O3A SINGLE NONE 24
N5P PA O1A DOUBLE NONE 25
N5P PA O2A SINGLE BEGINWEDGE 26
N5P O3A PB SINGLE NONE 27
N5P PB O1B DOUBLE NONE 28
N5P PB O3B SINGLE NONE 29
N5P PB O2B SINGLE BEGINWEDGE 30
N5P O3B PG SINGLE NONE 31
N5P PG O1G DOUBLE NONE 32
N5P PG O3G SINGLE NONE 33
N5P PG O2G SINGLE NONE 34
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
N5P MurckoScaffold S1 scaffold 'c1ccc2c(c1)ccn2[C@H]1CCCO1' InChI=1S/C12H13NO/c1-2-5-11-10(4-1)7-8-13(11)12-6-3-9-14-12/h1-2,4-5,7-8,12H,3,6,9H2/t12-/m1/s1 UTEDPNLNJBYVSG-GFCCVEGCSA-N
N5P deoxyribose F1 fragment 'OCC1OC[CH2]C1O' InChI=1S/C5H10O3/c6-3-5-4(7)1-2-8-5/h4-7H,1-3H2 NSMOSDAEGJTOIQ-UHFFFAOYSA-N
N5P indole F2 fragment 'c1ccc2[nH]ccc2c1' InChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9H SIKJAQJRHWYJAI-UHFFFAOYSA-N
N5P phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
N5P phosphate F4 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
N5P pyrrole F5 fragment 'c1cc[nH]c1' InChI=1S/C4H5N/c1-2-4-5-3-1/h1-5H KAESVJOAVNADME-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
N5P CZ3 S1 1
N5P CE3 S1 1
N5P CD2 S1 1
N5P CH2 S1 1
N5P CZ2 S1 1
N5P CE2 S1 1
N5P NE1 S1 1
N5P CD1 S1 1
N5P CG S1 1
N5P "C1'" S1 1
N5P "O4'" S1 1
N5P "C4'" S1 1
N5P "C3'" S1 1
N5P "C2'" S1 1
N5P "C1'" F1 1
N5P "C2'" F1 1
N5P "C3'" F1 1
N5P "O3'" F1 1
N5P "C4'" F1 1
N5P "O4'" F1 1
N5P "C5'" F1 1
N5P "O5'" F1 1
N5P CE2 F2 1
N5P CD2 F2 1
N5P CG F2 1
N5P CD1 F2 1
N5P NE1 F2 1
N5P CE3 F2 1
N5P CZ3 F2 1
N5P CH2 F2 1
N5P CZ2 F2 1
N5P CZ3 F3 1
N5P CH2 F3 1
N5P CZ2 F3 1
N5P CE2 F3 1
N5P CD2 F3 1
N5P CE3 F3 1
N5P "O5'" F4 1
N5P PA F4 1
N5P O1A F4 1
N5P O3A F4 1
N5P O2A F4 1
N5P O3A F4 2
N5P PB F4 2
N5P O1B F4 2
N5P O3B F4 2
N5P O2B F4 2
N5P O3B F4 3
N5P PG F4 3
N5P O1G F4 3
N5P O3G F4 3
N5P O2G F4 3
N5P CE2 F5 1
N5P CD2 F5 1
N5P CG F5 1
N5P CD1 F5 1
N5P NE1 F5 1
#
_pdbe_chem_comp_rdkit_properties.comp_id N5P
_pdbe_chem_comp_rdkit_properties.exactmw 517.989
_pdbe_chem_comp_rdkit_properties.amw 518.201
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 16
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 14
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 15
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 32
_pdbe_chem_comp_rdkit_properties.NumAtoms 49
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 19
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.385
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 5
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 202.396
_pdbe_chem_comp_rdkit_properties.tpsa 237.350
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.732
_pdbe_chem_comp_rdkit_properties.CrippenMR 99.913
_pdbe_chem_comp_rdkit_properties.chi0v 17.135
_pdbe_chem_comp_rdkit_properties.chi1v 11.649
_pdbe_chem_comp_rdkit_properties.chi2v 6.472
_pdbe_chem_comp_rdkit_properties.chi3v 6.472
_pdbe_chem_comp_rdkit_properties.chi4v 4.599
_pdbe_chem_comp_rdkit_properties.chi0n 31.452
_pdbe_chem_comp_rdkit_properties.chi1n 15.308
_pdbe_chem_comp_rdkit_properties.chi2n 2.957
_pdbe_chem_comp_rdkit_properties.chi3n 2.957
_pdbe_chem_comp_rdkit_properties.chi4n 1.924
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.510
_pdbe_chem_comp_rdkit_properties.kappa1 10.826
_pdbe_chem_comp_rdkit_properties.kappa2 9.028
_pdbe_chem_comp_rdkit_properties.kappa3 6.293
_pdbe_chem_comp_rdkit_properties.Phi 3.054
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
N5P UniChem ZINC ZINC000059142887
N5P UniChem PubChem 15374177
N5P UniChem BindingDb 36319
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
N5P OR2 6.136 3.520 2.958 ETKDGv3 1
N5P NRO 5.417 2.557 3.297 ETKDGv3 2
N5P OR1 5.213 2.321 4.637 ETKDGv3 3
N5P CZ3 4.810 1.703 2.311 ETKDGv3 4
N5P CE3 3.952 0.559 2.747 ETKDGv3 5
N5P CD2 3.414 -0.213 1.802 ETKDGv3 6
N5P CH2 5.002 1.922 0.982 ETKDGv3 7
N5P CZ2 4.373 1.039 -0.036 ETKDGv3 8
N5P CE2 3.622 0.023 0.400 ETKDGv3 9
N5P NE1 2.910 -0.955 -0.353 ETKDGv3 10
N5P CD1 2.235 -1.743 0.646 ETKDGv3 11
N5P CG 2.519 -1.355 1.893 ETKDGv3 12
N5P "C1'" 2.504 -0.841 -1.758 ETKDGv3 13
N5P "O4'" 1.249 -0.202 -1.828 ETKDGv3 14
N5P "C4'" 0.378 -1.032 -2.563 ETKDGv3 15
N5P "C3'" 0.952 -2.446 -2.587 ETKDGv3 16
N5P "O3'" 0.680 -3.091 -3.804 ETKDGv3 17
N5P "C2'" 2.426 -2.211 -2.428 ETKDGv3 18
N5P "C5'" -1.018 -0.995 -1.935 ETKDGv3 19
N5P "O5'" -1.510 0.323 -1.984 ETKDGv3 20
N5P PA -3.029 0.357 -1.211 ETKDGv3 21
N5P O1A -3.573 1.766 -1.301 ETKDGv3 22
N5P O2A -4.084 -0.706 -2.002 ETKDGv3 23
N5P O3A -2.832 -0.109 0.417 ETKDGv3 24
N5P PB -4.303 0.167 1.231 ETKDGv3 25
N5P O1B -4.170 -0.414 2.621 ETKDGv3 26
N5P O2B -5.577 -0.618 0.434 ETKDGv3 27
N5P O3B -4.587 1.847 1.320 ETKDGv3 28
N5P PG -5.933 2.105 2.333 ETKDGv3 29
N5P O3G -6.298 3.757 2.330 ETKDGv3 30
N5P O2G -5.572 1.635 3.919 ETKDGv3 31
N5P O1G -7.139 1.338 1.836 ETKDGv3 32
N5P HE3 3.759 0.360 3.793 ETKDGv3 33
N5P HH2 5.617 2.744 0.639 ETKDGv3 34
N5P HZ2 4.531 1.222 -1.090 ETKDGv3 35
N5P HD1 1.551 -2.548 0.415 ETKDGv3 36
N5P HG 2.117 -1.794 2.797 ETKDGv3 37
N5P "H1'" 3.246 -0.227 -2.310 ETKDGv3 38
N5P "H4'" 0.315 -0.637 -3.602 ETKDGv3 39
N5P "H3'" 0.584 -3.057 -1.729 ETKDGv3 40
N5P "HO3'" -0.268 -3.382 -3.763 ETKDGv3 41
N5P "H2'1" 2.906 -3.015 -1.829 ETKDGv3 42
N5P "H2'2" 2.921 -2.165 -3.424 ETKDGv3 43
N5P "H5'1" -1.682 -1.678 -2.511 ETKDGv3 44
N5P "H5'2" -0.937 -1.351 -0.881 ETKDGv3 45
N5P HO2A -4.100 -0.393 -2.942 ETKDGv3 46
N5P HO2B -5.933 0.050 -0.205 ETKDGv3 47
N5P HOG3 -6.418 3.987 1.374 ETKDGv3 48
N5P HOG2 -6.376 1.878 4.444 ETKDGv3 49
#