# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 14:07:51 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: [5-(5-amino-1H-pyrrolo[3,2-b]pyridin-2-yl)-6-hydroxy-3'-nitrobiphenyl-3-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc2[nH]c(cc2n1)c3cc(CC(O)=O)cc(c3O)c4cccc(c4)[N+]([O-])=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 N1H  N1H  '[5-(5-amino-1H-pyrrolo[3,2-b]pyridin-2-yl)-6-hydroxy-3'-nitrobiphenyl-3-yl]acetic acid'  ligand  45  30  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_N1H
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 N1H  C1    C  CR6    0   0.394   6.4093   1.7491  -0.3457
 N1H  C2    C  CR16   0  -0.389   6.7538   0.5181   0.2739
 N1H  C3    C  CR16   0  -0.209   5.7799  -0.4120   0.5507
 N1H  C4    C  CR56   0   0.269   4.4773  -0.0787   0.1932
 N1H  C5    C  CR56   0   0.174   4.2184   1.1651  -0.4081
 N1H  N6    N  N      0  -0.492   5.1716   2.0687  -0.6779
 N1H  N7    N  NH2    0  -0.843   7.4033   2.6429  -0.6664
 N1H  N3    N  NR15   0  -0.717   3.2881  -0.7430   0.3058
 N1H  CN4   C  CR15   0  -0.482   2.8161   1.2260  -0.6435
 N1H  C8    C  CR5    0   0.305   2.2831   0.0361  -0.1887
 N1H  C1'   C  CR6    0  -0.037   0.9016  -0.4452  -0.2012
 N1H  C2'   C  CR16   0  -0.370   0.6213  -1.7589  -0.5777
 N1H  C3'   C  CR6    0   0.204  -0.6723  -2.2559  -0.6135
 N1H  CV'   C  CH2    0  -0.707  -0.9521  -3.6712  -1.0052
 N1H  CW'   C  C      0   0.424  -0.9371  -4.6772   0.1736
 N1H  OX'   O  OC    -1  -0.625  -1.1323  -5.8673  -0.1435
 N1H  OY'   O  O      0  -0.597  -0.7416  -4.2275   1.3156
 N1H  C4'   C  CR16   0  -0.353  -1.6993  -1.3923  -0.2523
 N1H  C5'   C  CR6    0  -0.019  -1.4651  -0.0817   0.1508
 N1H  C6'   C  CR6    0   0.260  -0.1521   0.3989   0.1736
 N1H  O6'   O  OH1    0  -0.613   0.0394   1.6768   0.5516
 N1H  C1B   C  C      0   0.095  -2.6032   0.7800   0.5374
 N1H  C2B   C  C1     0  -0.264  -2.6349   1.4495   1.7622
 N1H  C3B   C  C1     0  -0.236  -3.7303   2.2175   2.1255
 N1H  C4B   C  C1     0  -0.280  -4.8195   2.3400   1.2784
 N1H  C5B   C  C      0   0.275  -4.7819   1.6704   0.0654
 N1H  N5B   N  N      1   0.327  -5.9149   1.7848  -0.8420
 N1H  O51   O  O     -1  -0.378  -6.8519   2.4660  -0.4979
 N1H  O52   O  O      0  -0.378  -5.8636   1.1940  -1.8949
 N1H  C6B   C  C1     0  -0.330  -3.6949   0.8974  -0.3157
 N1H  H2    H  HCR6   0   0.266   7.7871   0.3155   0.5229
 N1H  H3    H  HCR6   0   0.274   6.0272  -1.3545   1.0222
 N1H  HN71  H  HNH2   0   0.382   8.2419   2.5973  -0.1109
 N1H  HN72  H  HNH2   0   0.374   7.0897   3.5881  -0.8197
 N1H  HN3   H  HNR5   0   0.415   3.1507  -1.6225   0.7775
 N1H  HN4   H  HCR5   0   0.272   2.2852   2.0110  -1.1605
 N1H  H2'   H  HCR6   0   0.252   1.4429  -2.4022  -0.8740
 N1H  H311  H  HCH2   0   0.247  -1.9300  -3.7368  -1.4924
 N1H  H312  H  HCH2   0   0.245  -0.2278  -4.0072  -1.7533
 N1H  H4'   H  HCR6   0   0.251  -2.7220  -1.7526  -0.2671
 N1H  H6'   H  HOH1   0   0.473   0.9827   1.8584   0.6667
 N1H  H2B   H  H      0   0.270  -1.8051   1.3561   2.4490
 N1H  H3B   H  H      0   0.278  -3.7394   2.7238   3.0808
 N1H  H4B   H  H      0   0.298  -5.6691   2.9409   1.5668
 N1H  H6B   H  H      0   0.293  -3.6847   0.3914  -1.2711

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 N1H  C1   C2    aromatic  1.421  0.020  1.421
 N1H  C1   N6    aromatic  1.321  0.020  1.321
 N1H  C1   N7    single    1.375  0.020  1.375
 N1H  C2   C3    aromatic  1.375  0.020  1.375
 N1H  C2   H2    single    0.930  0.020  1.080
 N1H  C3   C4    aromatic  1.391  0.020  1.391
 N1H  C3   H3    single    0.930  0.020  1.080
 N1H  C4   C5    aromatic  1.406  0.020  1.406
 N1H  C4   N3    aromatic  1.367  0.020  1.367
 N1H  C5   N6    aromatic  1.341  0.020  1.341
 N1H  C5   CN4   aromatic  1.423  0.020  1.423
 N1H  N7   HN71  single    0.890  0.020  1.040
 N1H  N7   HN72  single    0.890  0.020  1.040
 N1H  N3   C8    aromatic  1.364  0.020  1.364
 N1H  N3   HN3   single    0.860  0.020  1.020
 N1H  CN4  C8    aromatic  1.381  0.020  1.381
 N1H  CN4  HN4   single    0.930  0.020  1.080
 N1H  C8   C1'   single    1.463  0.020  1.463
 N1H  C1'  C2'   aromatic  1.395  0.020  1.395
 N1H  C1'  C6'   aromatic  1.401  0.020  1.401
 N1H  C2'  C3'   aromatic  1.386  0.020  1.386
 N1H  C2'  H2'   single    0.930  0.020  1.080
 N1H  C3'  CV'   single    1.495  0.020  1.495
 N1H  C3'  C4'   aromatic  1.390  0.020  1.390
 N1H  CV'  CW'   single    1.550  0.020  1.550
 N1H  CV'  H311  single    0.970  0.020  1.090
 N1H  CV'  H312  single    0.970  0.020  1.090
 N1H  CW'  OX'   deloc     1.247  0.020  1.247
 N1H  CW'  OY'   deloc     1.243  0.020  1.243
 N1H  C4'  C5'   aromatic  1.391  0.020  1.391
 N1H  C4'  H4'   single    0.930  0.020  1.080
 N1H  C5'  C6'   aromatic  1.398  0.020  1.398
 N1H  C5'  C1B   single    1.479  0.020  1.479
 N1H  C6'  O6'   single    1.346  0.020  1.346
 N1H  O6'  H6'   single    0.850  0.020  0.980
 N1H  C1B  C2B   aromatic  1.396  0.020  1.396
 N1H  C1B  C6B   aromatic  1.390  0.020  1.390
 N1H  C2B  C3B   aromatic  1.386  0.020  1.386
 N1H  C2B  H2B   single    0.930  0.020  1.080
 N1H  C3B  C4B   aromatic  1.385  0.020  1.385
 N1H  C3B  H3B   single    0.930  0.020  1.080
 N1H  C4B  C5B   aromatic  1.386  0.020  1.386
 N1H  C4B  H4B   single    0.930  0.020  1.080
 N1H  C5B  N5B   single    1.456  0.020  1.456
 N1H  C5B  C6B   aromatic  1.387  0.020  1.387
 N1H  N5B  O51   single    1.208  0.020  1.208
 N1H  N5B  O52   double    1.209  0.020  1.209
 N1H  C6B  H6B   single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 N1H  N7    C1   N6    117.49  3.000
 N1H  N7    C1   C2    119.33  3.000
 N1H  N6    C1   C2    123.14  3.000
 N1H  H2    C2   C3    120.24  3.000
 N1H  H2    C2   C1    119.62  3.000
 N1H  C3    C2   C1    120.15  3.000
 N1H  H3    C3   C4    122.30  3.000
 N1H  H3    C3   C2    120.99  3.000
 N1H  C4    C3   C2    116.71  3.000
 N1H  N3    C4   C5    107.76  3.000
 N1H  N3    C4   C3    132.61  3.000
 N1H  C5    C4   C3    119.63  3.000
 N1H  CN4   C5   N6    129.67  3.000
 N1H  CN4   C5   C4    106.87  3.000
 N1H  N6    C5   C4    123.46  3.000
 N1H  C5    N6   C1    116.91  3.000
 N1H  HN72  N7   HN71  112.68  3.000
 N1H  HN72  N7   C1    114.86  3.000
 N1H  HN71  N7   C1    116.37  3.000
 N1H  HN3   N3   C8    124.59  3.000
 N1H  HN3   N3   C4    125.56  3.000
 N1H  C8    N3   C4    109.48  3.000
 N1H  HN4   CN4  C8    126.48  3.000
 N1H  HN4   CN4  C5    126.51  3.000
 N1H  C8    CN4  C5    106.79  3.000
 N1H  C1'   C8   CN4   130.17  3.000
 N1H  C1'   C8   N3    120.72  3.000
 N1H  CN4   C8   N3    109.09  3.000
 N1H  C6'   C1'  C2'   119.23  3.000
 N1H  C6'   C1'  C8    120.65  3.000
 N1H  C2'   C1'  C8    120.12  3.000
 N1H  H2'   C2'  C3'   119.15  3.000
 N1H  H2'   C2'  C1'   118.69  3.000
 N1H  C3'   C2'  C1'   122.14  3.000
 N1H  C4'   C3'  CV'   121.21  3.000
 N1H  C4'   C3'  C2'   117.40  3.000
 N1H  CV'   C3'  C2'   121.39  3.000
 N1H  H312  CV'  H311  105.58  3.000
 N1H  H312  CV'  CW'   108.32  3.000
 N1H  H311  CV'  CW'   107.96  3.000
 N1H  H312  CV'  C3'   110.24  3.000
 N1H  H311  CV'  C3'   109.91  3.000
 N1H  CW'   CV'  C3'   114.43  3.000
 N1H  OY'   CW'  OX'   127.13  3.000
 N1H  OY'   CW'  CV'   117.74  3.000
 N1H  OX'   CW'  CV'   115.13  3.000
 N1H  H4'   C4'  C5'   118.41  3.000
 N1H  H4'   C4'  C3'   119.14  3.000
 N1H  C5'   C4'  C3'   122.44  3.000
 N1H  C1B   C5'  C6'   121.20  3.000
 N1H  C1B   C5'  C4'   119.68  3.000
 N1H  C6'   C5'  C4'   119.12  3.000
 N1H  O6'   C6'  C5'   117.67  3.000
 N1H  O6'   C6'  C1'   122.68  3.000
 N1H  C5'   C6'  C1'   119.65  3.000
 N1H  H6'   O6'  C6'   110.50  3.000
 N1H  C6B   C1B  C2B   118.68  3.000
 N1H  C6B   C1B  C5'   119.53  3.000
 N1H  C2B   C1B  C5'   121.75  3.000
 N1H  H2B   C2B  C3B   119.20  3.000
 N1H  H2B   C2B  C1B   119.89  3.000
 N1H  C3B   C2B  C1B   120.90  3.000
 N1H  H3B   C3B  C4B   119.49  3.000
 N1H  H3B   C3B  C2B   119.84  3.000
 N1H  C4B   C3B  C2B   120.67  3.000
 N1H  H4B   C4B  C5B   121.59  3.000
 N1H  H4B   C4B  C3B   120.30  3.000
 N1H  C5B   C4B  C3B   118.11  3.000
 N1H  C6B   C5B  N5B   118.84  3.000
 N1H  C6B   C5B  C4B   122.06  3.000
 N1H  N5B   C5B  C4B   119.10  3.000
 N1H  O52   N5B  O51   123.82  3.000
 N1H  O52   N5B  C5B   118.13  3.000
 N1H  O51   N5B  C5B   118.05  3.000
 N1H  H6B   C6B  C5B   120.73  3.000
 N1H  H6B   C6B  C1B   119.69  3.000
 N1H  C5B   C6B  C1B   119.58  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 N1H  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 N1H  CONST_02  C4   C5   N6   C1      0.00   0.0  0
 N1H  CONST_03  CN4  C5   N6   C1    180.00   0.0  0
 N1H  CONST_04  C5   N6   C1   C2      0.00   0.0  0
 N1H  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 N1H  CONST_06  N3   C4   C3   C2    180.00   0.0  0
 N1H  CONST_07  N6   C1   C2   C3      0.00   0.0  0
 N1H  CONST_08  N6   C5   C4   C3      0.00   0.0  0
 N1H  CONST_09  CN4  C5   C4   C3    180.00   0.0  0
 N1H  CONST_10  C8   N3   C4   C3    180.00   0.0  0
 N1H  CONST_11  C8   CN4  C5   C4      0.00   0.0  0
 N1H  CONST_12  CN4  C8   N3   C4      0.00   0.0  0
 N1H  CONST_13  C1'  C8   N3   C4    180.00   0.0  0
 N1H  CONST_14  C8   N3   C4   C5      0.00   0.0  0
 N1H  CONST_15  N3   C8   CN4  C5      0.00   0.0  0
 N1H  CONST_16  C1'  C8   CN4  C5    180.00   0.0  0
 N1H  CONST_17  N3   C4   C5   N6    180.00   0.0  0
 N1H  CONST_18  C8   CN4  C5   N6    180.00   0.0  0
 N1H  CONST_19  CN4  C5   C4   N3      0.00   0.0  0
 N1H  CONST_24  C3'  C2'  C1'  C8    180.00   0.0  0
 N1H  CONST_25  C5'  C6'  C1'  C8    180.00   0.0  0
 N1H  CONST_26  C4'  C3'  C2'  C1'     0.00   0.0  0
 N1H  CONST_27  C4'  C5'  C6'  C1'     0.00   0.0  0
 N1H  CONST_28  C1B  C5'  C6'  C1'   180.00   0.0  0
 N1H  CONST_29  C5'  C6'  C1'  C2'     0.00   0.0  0
 N1H  CONST_30  C5'  C4'  C3'  C2'     0.00   0.0  0
 N1H  CONST_31  C6'  C1'  C2'  C3'     0.00   0.0  0
 N1H  CONST_32  C6'  C5'  C4'  C3'     0.00   0.0  0
 N1H  CONST_33  C1B  C5'  C4'  C3'   180.00   0.0  0
 N1H  CONST_36  C3B  C2B  C1B  C5'   180.00   0.0  0
 N1H  CONST_37  C5B  C6B  C1B  C5'   180.00   0.0  0
 N1H  CONST_40  C4B  C3B  C2B  C1B     0.00   0.0  0
 N1H  CONST_41  C4B  C5B  C6B  C1B     0.00   0.0  0
 N1H  CONST_42  C5B  C6B  C1B  C2B     0.00   0.0  0
 N1H  CONST_43  C5B  C4B  C3B  C2B     0.00   0.0  0
 N1H  CONST_44  C6B  C1B  C2B  C3B     0.00   0.0  0
 N1H  CONST_45  C6B  C5B  C4B  C3B     0.00   0.0  0
 N1H  CONST_46  N7   C1   C2   C3    180.00   0.0  0
 N1H  CONST_47  N7   C1   N6   C5    180.00   0.0  0
 N1H  CONST_48  O6'  C6'  C1'  C8      0.00   0.0  0
 N1H  CONST_49  CV'  C3'  C2'  C1'   180.00   0.0  0
 N1H  CONST_50  O6'  C6'  C1'  C2'   180.00   0.0  0
 N1H  CONST_51  C5'  C4'  C3'  CV'   180.00   0.0  0
 N1H  CONST_52  O6'  C6'  C5'  C4'   180.00   0.0  0
 N1H  CONST_53  C1B  C5'  C6'  O6'     0.00   0.0  0
 N1H  CONST_54  N5B  C5B  C6B  C1B   180.00   0.0  0
 N1H  CONST_55  N5B  C5B  C4B  C3B   180.00   0.0  0
 N1H  CONST_56  H3   C3   C2   C1    180.00   0.0  0
 N1H  CONST_57  HN3  N3   C4   C3      0.00   0.0  0
 N1H  CONST_58  H2   C2   C3   C4    180.00   0.0  0
 N1H  CONST_59  HN4  CN4  C5   C4    180.00   0.0  0
 N1H  CONST_60  H2'  C2'  C1'  C8      0.00   0.0  0
 N1H  CONST_61  H4'  C4'  C3'  C2'   180.00   0.0  0
 N1H  CONST_62  H2B  C2B  C1B  C5'     0.00   0.0  0
 N1H  CONST_63  H6B  C6B  C1B  C5'     0.00   0.0  0
 N1H  CONST_64  H3B  C3B  C2B  C1B   180.00   0.0  0
 N1H  CONST_65  H4B  C4B  C3B  C2B   180.00   0.0  0
 N1H  CONST_66  O51  N5B  C5B  C4B     0.00   0.0  0
 N1H  CONST_67  O52  N5B  C5B  C4B   180.00   0.0  0
 N1H  CONST_68  C6B  C5B  N5B  O51   180.00   0.0  0
 N1H  CONST_69  C6B  C5B  N5B  O52     0.00   0.0  0
 N1H  Var_01    CW'  CV'  C3'  C2'    89.16  30.0  2
 N1H  Var_02    OX'  CW'  CV'  C3'  -178.10  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 N1H  plan-1  C8    0.020
 N1H  plan-1  C1'   0.020
 N1H  plan-1  C2'   0.020
 N1H  plan-1  C3'   0.020
 N1H  plan-1  CV'   0.020
 N1H  plan-1  C4'   0.020
 N1H  plan-1  C5'   0.020
 N1H  plan-1  C6'   0.020
 N1H  plan-1  O6'   0.020
 N1H  plan-1  C1B   0.020
 N1H  plan-1  H2'   0.020
 N1H  plan-1  H4'   0.020
 N1H  plan-2  C5'   0.020
 N1H  plan-2  C1B   0.020
 N1H  plan-2  C2B   0.020
 N1H  plan-2  C3B   0.020
 N1H  plan-2  C4B   0.020
 N1H  plan-2  C5B   0.020
 N1H  plan-2  N5B   0.020
 N1H  plan-2  C6B   0.020
 N1H  plan-2  H2B   0.020
 N1H  plan-2  H3B   0.020
 N1H  plan-2  H4B   0.020
 N1H  plan-2  H6B   0.020
 N1H  plan-3  C1    0.020
 N1H  plan-3  C2    0.020
 N1H  plan-3  C3    0.020
 N1H  plan-3  C4    0.020
 N1H  plan-3  C5    0.020
 N1H  plan-3  N6    0.020
 N1H  plan-3  N7    0.020
 N1H  plan-3  N3    0.020
 N1H  plan-3  CN4   0.020
 N1H  plan-3  C8    0.020
 N1H  plan-3  C1'   0.020
 N1H  plan-3  H2    0.020
 N1H  plan-3  H3    0.020
 N1H  plan-3  HN3   0.020
 N1H  plan-3  HN4   0.020
 N1H  plan-4  C1    0.020
 N1H  plan-4  N7    0.020
 N1H  plan-4  HN71  0.020
 N1H  plan-4  HN72  0.020
 N1H  plan-5  C5B   0.020
 N1H  plan-5  N5B   0.020
 N1H  plan-5  O51   0.020
 N1H  plan-5  O52   0.020
 N1H  plan-6  CV'   0.020
 N1H  plan-6  CW'   0.020
 N1H  plan-6  OX'   0.020
 N1H  plan-6  OY'   0.020

