# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 03:22:43 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)-4-cyanobenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]cc(Cc3ccc(cc3)C(=O)Nc4cc(ccc4C(O)=O)C#N)c2C(=O)N1
#
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
 OG1  OG1  '2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)-4-cyanobenzoic acid'  ligand  48  32  .  2022-11-17  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_OG1
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
 OG1  C1   C  CR56  0   0.500   5.5272   0.7762   0.8629
 OG1  C10  C  CR16  0  -0.248   0.2022  -1.1491  -1.5918
 OG1  C11  C  CR6   0  -0.063  -0.6546  -0.3134  -0.8805
 OG1  C12  C  CR16  0  -0.281  -0.2253   0.9748  -0.5587
 OG1  C13  C  CR16  0  -0.281   1.0297   1.4095  -0.9470
 OG1  C14  C  C     0   0.537  -1.9758  -0.8540  -0.4568
 OG1  C15  C  CR6   0   0.421  -4.2555  -0.0676   0.1226
 OG1  C16  C  CR16  0  -0.314  -4.7021  -1.2529   0.7139
 OG1  C17  C  CR6   0   0.035  -6.0166  -1.3648   1.1414
 OG1  C18  C  CR16  0  -0.247  -6.9268  -0.3222   0.9976
 OG1  C19  C  CR16  0  -0.253  -6.4883   0.8477   0.4165
 OG1  C2   C  CR56  0  -0.239   4.8366   0.1821  -0.1936
 OG1  C20  C  CR6   0  -0.173  -5.1726   1.0013  -0.0229
 OG1  C21  C  C     0   0.594  -4.7648   2.2948  -0.6284
 OG1  C22  C  CSP   0   0.063  -6.4379  -2.5888   1.7489
 OG1  C3   C  CR6   0   0.498   4.9637  -1.2242  -0.3675
 OG1  C4   C  CR6   0   0.674   6.3902  -1.1222   1.6339
 OG1  C5   C  CR5   0   0.036   4.1641   1.2216  -0.9111
 OG1  C6   C  CR15  0  -0.093   4.4757   2.3819  -0.2659
 OG1  C7   C  CH2   0  -0.624   3.2482   1.0789  -2.0848
 OG1  C8   C  CR6   0   0.152   1.8829   0.5835  -1.6751
 OG1  C9   C  CR16  0  -0.298   1.4504  -0.7001  -1.9924
 OG1  N1   N  N     0  -0.508   6.3020   0.1710   1.7841
 OG1  N2   N  NR16  0  -0.721   5.7659  -1.7979   0.6256
 OG1  N3   N  NR15  0  -0.663   5.2974   2.1023   0.8059
 OG1  N4   N  NH2   0  -0.834   7.0874  -1.8610   2.5178
 OG1  N5   N  NH1   0  -0.794  -2.9485   0.0929  -0.3012
 OG1  N6   N  NS    0  -0.237  -6.7813  -3.5697   2.2444
 OG1  O1   O  O     0  -0.477   4.4817  -1.9322  -1.2406
 OG1  O2   O  O     0  -0.449  -2.1512  -2.0461  -0.2870
 OG1  O3   O  OH1   0  -0.578  -5.7683   3.1323  -0.7910
 OG1  O4   O  O     0  -0.455  -3.6266   2.5736  -0.9481
 OG1  H1   H  HCR6  0   0.260  -0.1098  -2.1537  -1.8453
 OG1  H2   H  HCR6  0   0.259  -0.8457   1.6432   0.0253
 OG1  H3   H  HCR6  0   0.254   1.3524   2.4062  -0.6707
 OG1  H4   H  HCR6  0   0.315  -4.0299  -2.0833   0.8461
 OG1  H5   H  HCR6  0   0.290  -7.9487  -0.4233   1.3331
 OG1  H6   H  HCR6  0   0.292  -7.1907   1.6604   0.3078
 OG1  H7   H  HCR5  0   0.282   4.1747   3.3947  -0.4790
 OG1  H8   H  HCH2  0   0.267   3.1444   2.0509  -2.5734
 OG1  H9   H  HCH2  0   0.262   3.6775   0.4001  -2.8231
 OG1  H10  H  HCR6  0   0.254   2.0999  -1.3586  -2.5530
 OG1  H11  H  HNR6  0   0.419   5.8891  -2.8003   0.5676
 OG1  H12  H  HNR5  0   0.409   5.6733   2.7836   1.4452
 OG1  H13  H  HNH2  0   0.409   7.3877  -2.7902   2.2763
 OG1  H14  H  HNH2  0   0.407   7.6834  -1.3628   3.1575
 OG1  H15  H  HNH1  0   0.445  -2.7458   1.0309  -0.6320
 OG1  H16  H  HOH1  0   0.498  -5.4530   3.9596  -1.1869

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
 OG1  N6   C22  triple    1.151  0.020  1.151
 OG1  C22  C17  single    1.430  0.020  1.430
 OG1  C18  C17  aromatic  1.392  0.020  1.392
 OG1  C18  C19  aromatic  1.378  0.020  1.378
 OG1  C17  C16  aromatic  1.387  0.020  1.387
 OG1  C19  C20  aromatic  1.396  0.020  1.396
 OG1  C16  C15  aromatic  1.398  0.020  1.398
 OG1  O2   C14  double    1.217  0.020  1.217
 OG1  N4   C4   single    1.347  0.020  1.347
 OG1  C20  C15  aromatic  1.416  0.020  1.416
 OG1  C20  C21  single    1.485  0.020  1.485
 OG1  C15  N5   single    1.383  0.020  1.383
 OG1  C14  N5   single    1.366  0.020  1.366
 OG1  C14  C11  single    1.489  0.020  1.489
 OG1  C21  O4   double    1.215  0.020  1.215
 OG1  C21  O3   single    1.317  0.020  1.317
 OG1  C4   N2   single    1.365  0.020  1.365
 OG1  C4   N1   double    1.305  0.020  1.305
 OG1  N2   C3   single    1.400  0.020  1.400
 OG1  C12  C11  aromatic  1.395  0.020  1.395
 OG1  C12  C13  aromatic  1.384  0.020  1.384
 OG1  C11  C10  aromatic  1.392  0.020  1.392
 OG1  N1   C1   single    1.347  0.020  1.347
 OG1  C3   O1   double    1.223  0.020  1.223
 OG1  C3   C2   single    1.423  0.020  1.423
 OG1  C13  C8   aromatic  1.393  0.020  1.393
 OG1  C10  C9   aromatic  1.386  0.020  1.386
 OG1  C1   C2   aromatic  1.395  0.020  1.395
 OG1  C1   N3   aromatic  1.347  0.020  1.347
 OG1  C2   C5   aromatic  1.431  0.020  1.431
 OG1  C9   C8   aromatic  1.391  0.020  1.391
 OG1  C8   C7   single    1.509  0.020  1.509
 OG1  N3   C6   aromatic  1.379  0.020  1.379
 OG1  C5   C6   aromatic  1.364  0.020  1.364
 OG1  C5   C7   single    1.496  0.020  1.496
 OG1  C10  H1   single    0.930  0.020  1.080
 OG1  C12  H2   single    0.930  0.020  1.080
 OG1  C13  H3   single    0.930  0.020  1.080
 OG1  C16  H4   single    0.930  0.020  1.080
 OG1  C18  H5   single    0.930  0.020  1.080
 OG1  C19  H6   single    0.930  0.020  1.080
 OG1  C6   H7   single    0.930  0.020  1.080
 OG1  C7   H8   single    0.970  0.020  1.090
 OG1  C7   H9   single    0.970  0.020  1.090
 OG1  C9   H10  single    0.930  0.020  1.080
 OG1  N2   H11  single    0.860  0.020  1.020
 OG1  N3   H12  single    0.860  0.020  1.020
 OG1  N4   H13  single    0.890  0.020  1.040
 OG1  N4   H14  single    0.890  0.020  1.040
 OG1  N5   H15  single    0.860  0.020  1.020
 OG1  O3   H16  single    0.850  0.020  0.980

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
 OG1  N3   C1   N1   124.70  3.000
 OG1  N3   C1   C2   107.62  3.000
 OG1  N1   C1   C2   127.68  3.000
 OG1  H1   C10  C9   119.53  3.000
 OG1  H1   C10  C11  119.97  3.000
 OG1  C9   C10  C11  120.50  3.000
 OG1  C14  C11  C12  122.85  3.000
 OG1  C12  C11  C10  118.86  3.000
 OG1  C14  C11  C10  118.26  3.000
 OG1  H2   C12  C13  118.49  3.000
 OG1  H2   C12  C11  121.19  3.000
 OG1  C13  C12  C11  120.29  3.000
 OG1  H3   C13  C8   119.76  3.000
 OG1  H3   C13  C12  119.18  3.000
 OG1  C8   C13  C12  121.06  3.000
 OG1  O2   C14  N5   124.09  3.000
 OG1  N5   C14  C11  114.36  3.000
 OG1  O2   C14  C11  121.55  3.000
 OG1  N5   C15  C20  119.53  3.000
 OG1  N5   C15  C16  121.99  3.000
 OG1  C20  C15  C16  118.47  3.000
 OG1  H4   C16  C17  119.45  3.000
 OG1  H4   C16  C15  120.43  3.000
 OG1  C17  C16  C15  120.11  3.000
 OG1  C22  C17  C18  119.51  3.000
 OG1  C18  C17  C16  121.85  3.000
 OG1  C22  C17  C16  118.64  3.000
 OG1  H5   C18  C19  120.76  3.000
 OG1  H5   C18  C17  121.10  3.000
 OG1  C19  C18  C17  118.14  3.000
 OG1  H6   C19  C20  119.92  3.000
 OG1  H6   C19  C18  118.33  3.000
 OG1  C20  C19  C18  121.75  3.000
 OG1  C5   C2   C3   134.33  3.000
 OG1  C5   C2   C1   107.64  3.000
 OG1  C3   C2   C1   117.99  3.000
 OG1  C21  C20  C19  118.88  3.000
 OG1  C21  C20  C15  121.43  3.000
 OG1  C19  C20  C15  119.68  3.000
 OG1  O4   C21  O3   122.38  3.000
 OG1  O3   C21  C20  113.26  3.000
 OG1  O4   C21  C20  124.36  3.000
 OG1  N6   C22  C17  180.00  3.000
 OG1  O1   C3   N2   119.67  3.000
 OG1  O1   C3   C2   128.63  3.000
 OG1  N2   C3   C2   111.70  3.000
 OG1  N4   C4   N2   116.76  3.000
 OG1  N2   C4   N1   123.00  3.000
 OG1  N4   C4   N1   120.21  3.000
 OG1  C7   C5   C6   126.33  3.000
 OG1  C7   C5   C2   127.73  3.000
 OG1  C6   C5   C2   105.87  3.000
 OG1  H7   C6   N3   120.70  3.000
 OG1  H7   C6   C5   129.95  3.000
 OG1  N3   C6   C5   109.35  3.000
 OG1  H9   C7   H8   106.75  3.000
 OG1  H9   C7   C8   109.60  3.000
 OG1  H8   C7   C8   109.11  3.000
 OG1  H9   C7   C5   110.46  3.000
 OG1  H8   C7   C5   108.92  3.000
 OG1  C8   C7   C5   111.86  3.000
 OG1  C9   C8   C7   121.48  3.000
 OG1  C7   C8   C13  120.09  3.000
 OG1  C9   C8   C13  118.42  3.000
 OG1  H10  C9   C8   119.56  3.000
 OG1  H10  C9   C10  119.57  3.000
 OG1  C8   C9   C10  120.87  3.000
 OG1  C4   N1   C1   113.91  3.000
 OG1  H11  N2   C4   118.50  3.000
 OG1  H11  N2   C3   115.80  3.000
 OG1  C4   N2   C3   125.69  3.000
 OG1  H12  N3   C6   125.35  3.000
 OG1  H12  N3   C1   125.13  3.000
 OG1  C6   N3   C1   109.52  3.000
 OG1  H14  N4   H13  115.67  3.000
 OG1  H14  N4   C4   116.89  3.000
 OG1  H13  N4   C4   120.24  3.000
 OG1  H15  N5   C15  113.31  3.000
 OG1  H15  N5   C14  117.45  3.000
 OG1  C15  N5   C14  128.84  3.000
 OG1  H16  O3   C21  110.19  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
 OG1  CONST_01  C6   C5   C2   C1     0.00   0.0  0
 OG1  CONST_02  C5   C6   N3   C1     0.00   0.0  0
 OG1  CONST_03  C13  C12  C11  C10    0.00   0.0  0
 OG1  CONST_04  C13  C8   C9   C10    0.00   0.0  0
 OG1  CONST_05  C8   C13  C12  C11    0.00   0.0  0
 OG1  CONST_06  C8   C9   C10  C11    0.00   0.0  0
 OG1  CONST_07  C9   C10  C11  C12    0.00   0.0  0
 OG1  CONST_08  C9   C8   C13  C12    0.00   0.0  0
 OG1  CONST_09  C18  C17  C16  C15    0.00   0.0  0
 OG1  CONST_10  C18  C19  C20  C15    0.00   0.0  0
 OG1  CONST_11  C19  C18  C17  C16    0.00   0.0  0
 OG1  CONST_12  C19  C20  C15  C16    0.00   0.0  0
 OG1  CONST_13  C20  C19  C18  C17    0.00   0.0  0
 OG1  CONST_14  C20  C15  C16  C17    0.00   0.0  0
 OG1  CONST_15  C6   N3   C1   C2     0.00   0.0  0
 OG1  CONST_16  N3   C6   C5   C2     0.00   0.0  0
 OG1  CONST_17  N3   C1   C2   C5     0.00   0.0  0
 OG1  CONST_18  N2   C4   N1   C1     0.00   0.0  0
 OG1  CONST_19  C4   N2   C3   C2     0.00   0.0  0
 OG1  CONST_20  N1   C4   N2   C3     0.00   0.0  0
 OG1  CONST_21  C7   C5   C2   C1   180.00   0.0  0
 OG1  CONST_22  C7   C8   C9   C10  180.00   0.0  0
 OG1  CONST_23  C7   C8   C13  C12  180.00   0.0  0
 OG1  CONST_24  C14  C11  C12  C13  180.00   0.0  0
 OG1  CONST_25  C9   C10  C11  C14  180.00   0.0  0
 OG1  CONST_26  C22  C17  C16  C15  180.00   0.0  0
 OG1  CONST_27  C21  C20  C15  C16  180.00   0.0  0
 OG1  CONST_28  N5   C15  C16  C17  180.00   0.0  0
 OG1  CONST_29  C21  C20  C19  C18  180.00   0.0  0
 OG1  CONST_30  C22  C17  C18  C19  180.00   0.0  0
 OG1  CONST_31  N5   C15  C20  C19  180.00   0.0  0
 OG1  CONST_32  C7   C5   C2   C3     0.00   0.0  0
 OG1  CONST_33  N3   C6   C5   C7   180.00   0.0  0
 OG1  CONST_34  N4   C4   N1   C1   180.00   0.0  0
 OG1  CONST_35  N4   C4   N2   C3   180.00   0.0  0
 OG1  CONST_36  O1   C3   N2   C4   180.00   0.0  0
 OG1  CONST_37  H7   C6   N3   C1   180.00   0.0  0
 OG1  CONST_38  H2   C12  C11  C10  180.00   0.0  0
 OG1  CONST_39  H3   C13  C12  C11  180.00   0.0  0
 OG1  CONST_40  H10  C9   C10  C11  180.00   0.0  0
 OG1  CONST_41  H1   C10  C11  C12  180.00   0.0  0
 OG1  CONST_42  H6   C19  C20  C15  180.00   0.0  0
 OG1  CONST_43  H5   C18  C17  C16  180.00   0.0  0
 OG1  CONST_44  H4   C16  C17  C18  180.00   0.0  0
 OG1  CONST_45  H12  N3   C1   C2   180.00   0.0  0
 OG1  CONST_46  H11  N2   C3   C2   180.00   0.0  0
 OG1  CONST_47  C15  N5   C14  C11  180.00   0.0  0
 OG1  CONST_48  C16  C15  N5   C14    0.00   0.0  0
 OG1  CONST_49  C20  C15  N5   C14  180.00   0.0  0
 OG1  CONST_50  H15  N5   C15  C16  180.00   0.0  0
 OG1  CONST_52  H14  N4   C4   N1     0.00   0.0  0
 OG1  CONST_53  O2   C14  N5   C15    0.00   0.0  0
 OG1  CONST_54  H16  O3   C21  C20  180.00   0.0  0
 OG1  Var_01    C5   C7   C8   C13   69.72  30.0  2
 OG1  Var_02    C8   C7   C5   C2    76.02  30.0  2
 OG1  Var_03    O2   C14  C11  C10   25.80  30.0  2
 OG1  Var_04    O4   C21  C20  C15   -5.58  30.0  2

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
 OG1  plan-1  C10  0.020
 OG1  plan-1  C11  0.020
 OG1  plan-1  C12  0.020
 OG1  plan-1  C13  0.020
 OG1  plan-1  C14  0.020
 OG1  plan-1  C7   0.020
 OG1  plan-1  C8   0.020
 OG1  plan-1  C9   0.020
 OG1  plan-1  H1   0.020
 OG1  plan-1  H2   0.020
 OG1  plan-1  H3   0.020
 OG1  plan-1  H10  0.020
 OG1  plan-2  C15  0.020
 OG1  plan-2  C16  0.020
 OG1  plan-2  C17  0.020
 OG1  plan-2  C18  0.020
 OG1  plan-2  C19  0.020
 OG1  plan-2  C20  0.020
 OG1  plan-2  C21  0.020
 OG1  plan-2  C22  0.020
 OG1  plan-2  N5   0.020
 OG1  plan-2  N6   0.020
 OG1  plan-2  H4   0.020
 OG1  plan-2  H5   0.020
 OG1  plan-2  H6   0.020
 OG1  plan-3  C1   0.020
 OG1  plan-3  C2   0.020
 OG1  plan-3  C3   0.020
 OG1  plan-3  C4   0.020
 OG1  plan-3  C5   0.020
 OG1  plan-3  C6   0.020
 OG1  plan-3  C7   0.020
 OG1  plan-3  N1   0.020
 OG1  plan-3  N2   0.020
 OG1  plan-3  N3   0.020
 OG1  plan-3  N4   0.020
 OG1  plan-3  O1   0.020
 OG1  plan-3  H7   0.020
 OG1  plan-3  H11  0.020
 OG1  plan-3  H12  0.020
 OG1  plan-3  H13  0.020
 OG1  plan-3  H14  0.020
 OG1  plan-4  C11  0.020
 OG1  plan-4  C14  0.020
 OG1  plan-4  C15  0.020
 OG1  plan-4  N5   0.020
 OG1  plan-4  O2   0.020
 OG1  plan-4  H15  0.020
 OG1  plan-5  C20  0.020
 OG1  plan-5  C21  0.020
 OG1  plan-5  O3   0.020
 OG1  plan-5  O4   0.020
 OG1  plan-5  H16  0.020

