# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 06:28:41 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  46  30  .  2022-07-22  2022-11-17
;
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   0.397   6.3812   1.7701  -0.2650
 N1H  C2    C  CR16   0  -0.389   6.7253   0.5397   0.3580
 N1H  C3    C  CR16   0  -0.208   5.7531  -0.3923   0.6302
 N1H  C4    C  CR56   0   0.269   4.4503  -0.0587   0.2726
 N1H  C5    C  CR56   0   0.175   4.1919   1.1822  -0.3342
 N1H  N6    N  N      0  -0.492   5.1454   2.0844  -0.6087
 N1H  N7    N  NH2    0  -0.844   7.3602   2.7084  -0.4815
 N1H  N3    N  NR15   0  -0.717   3.2628  -0.7263   0.3808
 N1H  CN4   C  CR15   0  -0.480   2.7907   1.2384  -0.5781
 N1H  C8    C  CR5    0   0.306   2.2589   0.0488  -0.1213
 N1H  C1'   C  CR6    0  -0.040   0.8787  -0.4358  -0.1410
 N1H  C2'   C  CR16   0  -0.349   0.6031  -1.7481  -0.5186
 N1H  C3'   C  CR6    0   0.160  -0.6929  -2.2372  -0.5602
 N1H  CV'   C  CH2    0  -0.697  -0.9712  -3.6516  -0.9671
 N1H  CW'   C  C      0   0.558  -0.7635  -4.6361   0.1584
 N1H  OX'   O  OH1    0  -0.593  -1.1030  -5.8664  -0.2091
 N1H  OY'   O  O      0  -0.433  -0.3399  -4.3619   1.2513
 N1H  C4'   C  CR16   0  -0.339  -1.7269  -1.3819  -0.2067
 N1H  C5'   C  CR6    0  -0.021  -1.4939  -0.0721   0.1988
 N1H  C6'   C  CR6    0   0.276  -0.1804   0.4065   0.2289
 N1H  O6'   O  OH1    0  -0.607   0.0079   1.6803   0.6090
 N1H  C1B   C  CR6    0   0.094  -2.6336   0.7911   0.5779
 N1H  C2B   C  CR16   0  -0.263  -2.6764   1.4514   1.8069
 N1H  C3B   C  CR16   0  -0.236  -3.7731   2.2211   2.1621
 N1H  C4B   C  CR16   0  -0.278  -4.8514   2.3533   1.3025
 N1H  C5B   C  CR6    0   0.275  -4.8020   1.6926   0.0852
 N1H  N5B   N  N      1   0.327  -5.9238   1.8169  -0.8348
 N1H  O51   O  O     -1  -0.377  -6.8629   2.4978  -0.4967
 N1H  O52   O  O      0  -0.378  -5.8613   1.2331  -1.8911
 N1H  C6B   C  CR16   0  -0.328  -3.7133   0.9182  -0.2884
 N1H  H2    H  HCR6   0   0.267   7.7577   0.3409   0.6137
 N1H  H3    H  HCR6   0   0.274   6.0010  -1.3361   1.0988
 N1H  HN71  H  HNH2   0   0.384   8.3021   2.3646  -0.5726
 N1H  HN72  H  HNH2   0   0.375   7.1332   3.4183  -1.1594
 N1H  HN3   H  HNR5   0   0.415   3.1262  -1.6026   0.8588
 N1H  HN4   H  HCR5   0   0.274   2.2611   2.0195  -1.1023
 N1H  H2'   H  HCR6   0   0.263   1.4251  -2.3912  -0.8125
 N1H  H311  H  HCH2   0   0.305  -1.9959  -3.7570  -1.3324
 N1H  H312  H  HCH2   0   0.307  -0.3293  -3.9557  -1.7996
 N1H  H33'  H  HOH1   0   0.482  -0.9504  -6.4861   0.5201
 N1H  H4'   H  HCR6   0   0.262  -2.7483  -1.7445  -0.2283
 N1H  H6'   H  HOH1   0   0.476   0.9509   1.8683   0.7201
 N1H  H2B   H  HCR6   0   0.271  -1.8551   1.3500   2.5028
 N1H  H3B   H  HCR6   0   0.279  -3.7920   2.7208   3.1207
 N1H  H4B   H  HCR6   0   0.299  -5.7023   2.9553   1.5850
 N1H  H6B   H  HCR6   0   0.295  -3.6931   0.4197  -1.2476

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    1.373  0.020  1.373
 N1H  C2   C3    aromatic  1.374  0.020  1.374
 N1H  C2   H2    single    0.930  0.020  1.080
 N1H  C3   C4    aromatic  1.392  0.020  1.392
 N1H  C3   H3    single    0.930  0.020  1.080
 N1H  C4   C5    aromatic  1.405  0.020  1.405
 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  1.393  0.020  1.393
 N1H  C1'  C6'   aromatic  1.403  0.020  1.403
 N1H  C2'  C3'   aromatic  1.386  0.020  1.386
 N1H  C2'  H2'   single    0.930  0.020  1.080
 N1H  C3'  CV'   single    1.498  0.020  1.498
 N1H  C3'  C4'   aromatic  1.388  0.020  1.388
 N1H  CV'  CW'   single    1.510  0.020  1.510
 N1H  CV'  H311  single    0.970  0.020  1.090
 N1H  CV'  H312  single    0.970  0.020  1.090
 N1H  CW'  OX'   single    1.328  0.020  1.328
 N1H  CW'  OY'   double    1.204  0.020  1.204
 N1H  OX'  H33'  single    0.850  0.020  0.980
 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    1.343  0.020  1.343
 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    1.208  0.020  1.208
 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    117.61  3.000
 N1H  N7    C1   C2    119.21  3.000
 N1H  N6    C1   C2    123.14  3.000
 N1H  H2    C2   C3    120.24  3.000
 N1H  H2    C2   C1    119.58  3.000
 N1H  C3    C2   C1    120.18  3.000
 N1H  H3    C3   C4    122.32  3.000
 N1H  H3    C3   C2    121.01  3.000
 N1H  C4    C3   C2    116.67  3.000
 N1H  N3    C4   C5    107.80  3.000
 N1H  N3    C4   C3    132.53  3.000
 N1H  C5    C4   C3    119.66  3.000
 N1H  CN4   C5   N6    129.66  3.000
 N1H  CN4   C5   C4    106.85  3.000
 N1H  N6    C5   C4    123.48  3.000
 N1H  C5    N6   C1    116.87  3.000
 N1H  HN72  N7   HN71  112.99  3.000
 N1H  HN72  N7   C1    115.27  3.000
 N1H  HN71  N7   C1    116.61  3.000
 N1H  HN3   N3   C8    124.69  3.000
 N1H  HN3   N3   C4    125.47  3.000
 N1H  C8    N3   C4    109.43  3.000
 N1H  HN4   CN4  C8    126.52  3.000
 N1H  HN4   CN4  C5    126.49  3.000
 N1H  C8    CN4  C5    106.76  3.000
 N1H  C1'   C8   CN4   130.11  3.000
 N1H  C1'   C8   N3    120.73  3.000
 N1H  CN4   C8   N3    109.14  3.000
 N1H  C6'   C1'  C2'   119.19  3.000
 N1H  C6'   C1'  C8    120.65  3.000
 N1H  C2'   C1'  C8    120.16  3.000
 N1H  H2'   C2'  C3'   119.44  3.000
 N1H  H2'   C2'  C1'   118.83  3.000
 N1H  C3'   C2'  C1'   121.71  3.000
 N1H  C4'   C3'  CV'   120.84  3.000
 N1H  C4'   C3'  C2'   118.14  3.000
 N1H  CV'   C3'  C2'   121.01  3.000
 N1H  H312  CV'  H311  105.59  3.000
 N1H  H312  CV'  CW'   107.77  3.000
 N1H  H311  CV'  CW'   108.38  3.000
 N1H  H312  CV'  C3'   111.11  3.000
 N1H  H311  CV'  C3'   110.86  3.000
 N1H  CW'   CV'  C3'   112.81  3.000
 N1H  OY'   CW'  OX'   123.52  3.000
 N1H  OY'   CW'  CV'   125.22  3.000
 N1H  OX'   CW'  CV'   111.26  3.000
 N1H  H33'  OX'  CW'   110.11  3.000
 N1H  H4'   C4'  C5'   118.60  3.000
 N1H  H4'   C4'  C3'   119.40  3.000
 N1H  C5'   C4'  C3'   122.00  3.000
 N1H  C1B   C5'  C6'   121.23  3.000
 N1H  C1B   C5'  C4'   119.69  3.000
 N1H  C6'   C5'  C4'   119.08  3.000
 N1H  O6'   C6'  C5'   117.55  3.000
 N1H  O6'   C6'  C1'   122.58  3.000
 N1H  C5'   C6'  C1'   119.87  3.000
 N1H  H6'   O6'  C6'   110.69  3.000
 N1H  C6B   C1B  C2B   118.79  3.000
 N1H  C6B   C1B  C5'   119.48  3.000
 N1H  C2B   C1B  C5'   121.70  3.000
 N1H  H2B   C2B  C3B   119.22  3.000
 N1H  H2B   C2B  C1B   119.93  3.000
 N1H  C3B   C2B  C1B   120.84  3.000
 N1H  H3B   C3B  C4B   119.50  3.000
 N1H  H3B   C3B  C2B   119.84  3.000
 N1H  C4B   C3B  C2B   120.65  3.000
 N1H  H4B   C4B  C5B   121.58  3.000
 N1H  H4B   C4B  C3B   120.27  3.000
 N1H  C5B   C4B  C3B   118.15  3.000
 N1H  C6B   C5B  N5B   118.82  3.000
 N1H  C6B   C5B  C4B   122.05  3.000
 N1H  N5B   C5B  C4B   119.13  3.000
 N1H  O52   N5B  O51   123.85  3.000
 N1H  O52   N5B  C5B   118.11  3.000
 N1H  O51   N5B  C5B   118.04  3.000
 N1H  H6B   C6B  C5B   120.73  3.000
 N1H  H6B   C6B  C1B   119.74  3.000
 N1H  C5B   C6B  C1B   119.52  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  CONST_72  H33'  OX'  CW'  CV'  180.00   0.0  0
 N1H  Var_01    CW'   CV'  C3'  C2'   81.21  30.0  2
 N1H  Var_02    OX'   CW'  CV'  C3'  175.86  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
 N1H  plan-6  H33'  0.020

