# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 11:50:36 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 3-[2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)phenyl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]cc(Cc3ccc(cc3)C(=O)Nc4ccccc4CCC(O)=O)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
 OG4  OG4  '3-[2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)phenyl]propanoic acid'  ligand  53  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_OG4
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
 OG4  C1   C  CR56  0   0.503  -4.8757  -1.5045   0.6175
 OG4  C10  C  CR16  0  -0.249  -0.3712   1.9797  -0.8195
 OG4  C11  C  CR6   0  -0.064   0.8084   1.3137  -1.1498
 OG4  C12  C  CR16  0  -0.283   0.7292   0.1542  -1.9178
 OG4  C13  C  CR16  0  -0.305  -0.5023  -0.3367  -2.3241
 OG4  C14  C  C     0   0.526   2.1007   1.9011  -0.6947
 OG4  C15  C  CR6   0   0.291   4.4415   1.3631  -0.1870
 OG4  C16  C  CR6   0   0.100   5.0662   0.6193   0.8203
 OG4  C17  C  CR16  0  -0.318   6.3725   0.9513   1.1707
 OG4  C18  C  CR16  0  -0.246   7.0412   2.0020   0.5622
 OG4  C19  C  CR16  0  -0.274   6.4054   2.7355  -0.4302
 OG4  C2   C  CR56  0  -0.246  -4.5558  -0.4614  -0.2531
 OG4  C20  C  CR16  0  -0.271   5.1126   2.4131  -0.8087
 OG4  C21  C  CH2   0  -0.536   4.3733  -0.5296   1.5007
 OG4  C22  C  CH2   0  -0.585   4.5247  -1.8270   0.7099
 OG4  C23  C  C     0   0.558   3.8292  -2.9967   1.3521
 OG4  C3   C  CR6   0   0.511  -5.1598   0.8057  -0.0204
 OG4  C4   C  CR6   0   0.674  -6.2152  -0.2893   1.9106
 OG4  C5   C  CR5   0   0.031  -3.6792  -0.9869  -1.2555
 OG4  C6   C  CR15  0  -0.083  -3.5090  -2.3045  -0.9472
 OG4  C7   C  CH2   0  -0.632  -3.0206  -0.2522  -2.3843
 OG4  C8   C  CR6   0   0.147  -1.6825   0.3123  -1.9763
 OG4  C9   C  CR16  0  -0.294  -1.5975   1.4812  -1.2214
 OG4  N1   N  N     0  -0.507  -5.6852  -1.4615   1.6932
 OG4  N2   N  NR16  0  -0.721  -5.9824   0.7915   1.1095
 OG4  N3   N  NR15  0  -0.662  -4.2328  -2.6064   0.1866
 OG4  N4   N  NH2   0  -0.834  -7.0006  -0.0891   2.9850
 OG4  N5   N  NH1   0  -0.766   3.1330   1.0239  -0.5860
 OG4  O1   O  O     0  -0.488  -5.0419   1.8383  -0.6688
 OG4  O2   O  O     0  -0.460   2.2082   3.0846  -0.4261
 OG4  O3   O  O     0  -0.441   3.2858  -2.9711   2.4277
 OG4  O4   O  OH1   0  -0.594   3.8881  -4.0832   0.5911
 OG4  H1   H  HCR6  0   0.259  -0.3297   2.8915  -0.2383
 OG4  H2   H  HCR6  0   0.258   1.6211  -0.3681  -2.2424
 OG4  H3   H  HCR6  0   0.255  -0.5391  -1.2337  -2.9303
 OG4  H4   H  HCR6  0   0.253   6.8670   0.3794   1.9470
 OG4  H5   H  HCR6  0   0.258   8.0529   2.2448   0.8593
 OG4  H6   H  HCR6  0   0.259   6.9185   3.5528  -0.9196
 OG4  H7   H  HCR6  0   0.266   4.6314   2.9681  -1.6020
 OG4  H8   H  HCH2  0   0.272   4.8025  -0.6650   2.4940
 OG4  H9   H  HCH2  0   0.258   3.3165  -0.3004   1.6530
 OG4  H10  H  HCH2  0   0.274   4.1558  -1.7261  -0.3155
 OG4  H11  H  HCH2  0   0.302   5.5841  -2.0787   0.6009
 OG4  H12  H  HCR5  0   0.281  -2.9201  -3.0605  -1.4406
 OG4  H13  H  HCH2  0   0.266  -2.8809  -0.9329  -3.2260
 OG4  H14  H  HCH2  0   0.268  -3.6682   0.5539  -2.7319
 OG4  H15  H  HCR6  0   0.263  -2.5045   2.0066  -0.9503
 OG4  H16  H  HNR6  0   0.419  -6.4371   1.6671   1.3341
 OG4  H17  H  HNR5  0   0.410  -4.2916  -3.5157   0.6158
 OG4  H18  H  HNH2  0   0.410  -7.6074   0.7118   3.0311
 OG4  H19  H  HNH2  0   0.408  -7.3133  -0.9058   3.4820
 OG4  H20  H  HNH1  0   0.401   2.9209   0.0439  -0.6726
 OG4  H21  H  HOH1  0   0.480   3.4366  -4.8205   1.0288

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
 OG4  N4   C4   single    1.346  0.020  1.346
 OG4  N1   C4   double    1.305  0.020  1.305
 OG4  N1   C1   single    1.347  0.020  1.347
 OG4  C4   N2   single    1.365  0.020  1.365
 OG4  N3   C1   aromatic  1.346  0.020  1.346
 OG4  N3   C6   aromatic  1.379  0.020  1.379
 OG4  C1   C2   aromatic  1.396  0.020  1.396
 OG4  O2   C14  double    1.218  0.020  1.218
 OG4  N2   C3   single    1.398  0.020  1.398
 OG4  C12  C13  aromatic  1.387  0.020  1.387
 OG4  C12  C11  aromatic  1.393  0.020  1.393
 OG4  C6   C5   aromatic  1.364  0.020  1.364
 OG4  C13  C8   aromatic  1.391  0.020  1.391
 OG4  C2   C3   single    1.423  0.020  1.423
 OG4  C2   C5   aromatic  1.432  0.020  1.432
 OG4  C22  C21  single    1.527  0.020  1.527
 OG4  C22  C23  single    1.505  0.020  1.505
 OG4  O3   C23  double    1.205  0.020  1.205
 OG4  C3   O1   double    1.225  0.020  1.225
 OG4  C14  C11  single    1.491  0.020  1.491
 OG4  C14  N5   single    1.359  0.020  1.359
 OG4  C5   C7   single    1.499  0.020  1.499
 OG4  C21  C16  single    1.504  0.020  1.504
 OG4  C11  C10  aromatic  1.394  0.020  1.394
 OG4  C23  O4   single    1.328  0.020  1.328
 OG4  C16  C17  aromatic  1.393  0.020  1.393
 OG4  C16  C15  aromatic  1.399  0.020  1.399
 OG4  C17  C18  aromatic  1.386  0.020  1.386
 OG4  C8   C7   single    1.508  0.020  1.508
 OG4  C8   C9   aromatic  1.394  0.020  1.394
 OG4  N5   C15  single    1.409  0.020  1.409
 OG4  C15  C20  aromatic  1.393  0.020  1.393
 OG4  C18  C19  aromatic  1.388  0.020  1.388
 OG4  C10  C9   aromatic  1.383  0.020  1.383
 OG4  C20  C19  aromatic  1.385  0.020  1.385
 OG4  C10  H1   single    0.930  0.020  1.080
 OG4  C12  H2   single    0.930  0.020  1.080
 OG4  C13  H3   single    0.930  0.020  1.080
 OG4  C17  H4   single    0.930  0.020  1.080
 OG4  C18  H5   single    0.930  0.020  1.080
 OG4  C19  H6   single    0.930  0.020  1.080
 OG4  C20  H7   single    0.930  0.020  1.080
 OG4  C21  H8   single    0.970  0.020  1.090
 OG4  C21  H9   single    0.970  0.020  1.090
 OG4  C22  H10  single    0.970  0.020  1.090
 OG4  C22  H11  single    0.970  0.020  1.090
 OG4  C6   H12  single    0.930  0.020  1.080
 OG4  C7   H13  single    0.970  0.020  1.090
 OG4  C7   H14  single    0.970  0.020  1.090
 OG4  C9   H15  single    0.930  0.020  1.080
 OG4  N2   H16  single    0.860  0.020  1.020
 OG4  N3   H17  single    0.860  0.020  1.020
 OG4  N4   H18  single    0.890  0.020  1.040
 OG4  N4   H19  single    0.890  0.020  1.040
 OG4  N5   H20  single    0.860  0.020  1.020
 OG4  O4   H21  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
 OG4  N3   C1   N1   124.66  3.000
 OG4  N3   C1   C2   107.61  3.000
 OG4  N1   C1   C2   127.73  3.000
 OG4  H1   C10  C9   119.58  3.000
 OG4  H1   C10  C11  119.82  3.000
 OG4  C9   C10  C11  120.60  3.000
 OG4  C14  C11  C12  123.06  3.000
 OG4  C14  C11  C10  118.22  3.000
 OG4  C12  C11  C10  118.69  3.000
 OG4  H2   C12  C13  118.21  3.000
 OG4  H2   C12  C11  121.31  3.000
 OG4  C13  C12  C11  120.44  3.000
 OG4  H3   C13  C8   119.83  3.000
 OG4  H3   C13  C12  119.16  3.000
 OG4  C8   C13  C12  121.00  3.000
 OG4  O2   C14  N5   122.85  3.000
 OG4  N5   C14  C11  115.38  3.000
 OG4  O2   C14  C11  121.77  3.000
 OG4  N5   C15  C20  120.17  3.000
 OG4  C20  C15  C16  120.46  3.000
 OG4  N5   C15  C16  119.36  3.000
 OG4  C21  C16  C17  120.03  3.000
 OG4  C17  C16  C15  118.24  3.000
 OG4  C21  C16  C15  121.73  3.000
 OG4  H4   C17  C18  119.63  3.000
 OG4  H4   C17  C16  118.85  3.000
 OG4  C18  C17  C16  121.52  3.000
 OG4  H5   C18  C19  120.40  3.000
 OG4  H5   C18  C17  120.04  3.000
 OG4  C19  C18  C17  119.56  3.000
 OG4  H6   C19  C20  119.66  3.000
 OG4  H6   C19  C18  120.35  3.000
 OG4  C20  C19  C18  119.99  3.000
 OG4  C5   C2   C3   134.54  3.000
 OG4  C5   C2   C1   107.62  3.000
 OG4  C3   C2   C1   117.79  3.000
 OG4  H7   C20  C19  119.76  3.000
 OG4  H7   C20  C15  120.00  3.000
 OG4  C19  C20  C15  120.22  3.000
 OG4  H9   C21  H8   106.25  3.000
 OG4  H9   C21  C22  110.27  3.000
 OG4  H8   C21  C22  109.10  3.000
 OG4  H9   C21  C16  110.40  3.000
 OG4  H8   C21  C16  109.00  3.000
 OG4  C22  C21  C16  111.65  3.000
 OG4  H11  C22  H10  104.72  3.000
 OG4  H11  C22  C23  108.13  3.000
 OG4  H10  C22  C23  108.41  3.000
 OG4  H11  C22  C21  110.06  3.000
 OG4  H10  C22  C21  111.93  3.000
 OG4  C23  C22  C21  113.18  3.000
 OG4  O4   C23  O3   123.28  3.000
 OG4  O4   C23  C22  111.77  3.000
 OG4  O3   C23  C22  124.94  3.000
 OG4  O1   C3   N2   119.54  3.000
 OG4  O1   C3   C2   128.55  3.000
 OG4  N2   C3   C2   111.90  3.000
 OG4  N4   C4   N2   116.75  3.000
 OG4  N2   C4   N1   122.97  3.000
 OG4  N4   C4   N1   120.25  3.000
 OG4  C7   C5   C6   126.07  3.000
 OG4  C7   C5   C2   128.04  3.000
 OG4  C6   C5   C2   105.83  3.000
 OG4  H12  C6   N3   120.64  3.000
 OG4  H12  C6   C5   129.97  3.000
 OG4  N3   C6   C5   109.39  3.000
 OG4  H14  C7   H13  106.92  3.000
 OG4  H14  C7   C8   109.65  3.000
 OG4  H13  C7   C8   109.18  3.000
 OG4  H14  C7   C5   109.95  3.000
 OG4  H13  C7   C5   109.34  3.000
 OG4  C8   C7   C5   111.68  3.000
 OG4  C9   C8   C7   120.95  3.000
 OG4  C9   C8   C13  118.35  3.000
 OG4  C7   C8   C13  120.69  3.000
 OG4  H15  C9   C8   119.44  3.000
 OG4  H15  C9   C10  119.67  3.000
 OG4  C8   C9   C10  120.89  3.000
 OG4  C4   N1   C1   113.95  3.000
 OG4  H16  N2   C4   118.56  3.000
 OG4  H16  N2   C3   115.80  3.000
 OG4  C4   N2   C3   125.64  3.000
 OG4  H17  N3   C6   125.37  3.000
 OG4  H17  N3   C1   125.06  3.000
 OG4  C6   N3   C1   109.55  3.000
 OG4  H19  N4   H18  115.87  3.000
 OG4  H19  N4   C4   117.07  3.000
 OG4  H18  N4   C4   120.47  3.000
 OG4  H20  N5   C15  117.03  3.000
 OG4  H20  N5   C14  117.49  3.000
 OG4  C15  N5   C14  124.92  3.000
 OG4  H21  O4   C23  110.06  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
 OG4  CONST_01  C5   C6   N3   C1      0.00   0.0  0
 OG4  CONST_02  C6   C5   C2   C1      0.00   0.0  0
 OG4  CONST_03  C13  C12  C11  C10     0.00   0.0  0
 OG4  CONST_04  C13  C8   C9   C10     0.00   0.0  0
 OG4  CONST_05  C8   C13  C12  C11     0.00   0.0  0
 OG4  CONST_06  C8   C9   C10  C11     0.00   0.0  0
 OG4  CONST_07  C9   C8   C13  C12     0.00   0.0  0
 OG4  CONST_08  C9   C10  C11  C12     0.00   0.0  0
 OG4  CONST_09  C18  C17  C16  C15     0.00   0.0  0
 OG4  CONST_10  C18  C19  C20  C15     0.00   0.0  0
 OG4  CONST_11  C19  C18  C17  C16     0.00   0.0  0
 OG4  CONST_12  C19  C20  C15  C16     0.00   0.0  0
 OG4  CONST_13  C20  C15  C16  C17     0.00   0.0  0
 OG4  CONST_14  C20  C19  C18  C17     0.00   0.0  0
 OG4  CONST_15  C6   N3   C1   C2      0.00   0.0  0
 OG4  CONST_16  N3   C6   C5   C2      0.00   0.0  0
 OG4  CONST_17  N3   C1   C2   C5      0.00   0.0  0
 OG4  CONST_18  N2   C4   N1   C1      0.00   0.0  0
 OG4  CONST_19  C4   N2   C3   C2      0.00   0.0  0
 OG4  CONST_20  N1   C4   N2   C3      0.00   0.0  0
 OG4  CONST_21  C7   C5   C2   C1    180.00   0.0  0
 OG4  CONST_22  C7   C8   C9   C10   180.00   0.0  0
 OG4  CONST_23  C7   C8   C13  C12   180.00   0.0  0
 OG4  CONST_24  C14  C11  C12  C13   180.00   0.0  0
 OG4  CONST_25  C9   C10  C11  C14   180.00   0.0  0
 OG4  CONST_26  N5   C15  C16  C17   180.00   0.0  0
 OG4  CONST_27  C21  C16  C17  C18   180.00   0.0  0
 OG4  CONST_28  N5   C15  C20  C19   180.00   0.0  0
 OG4  CONST_29  C21  C16  C15  C20   180.00   0.0  0
 OG4  CONST_30  C7   C5   C2   C3      0.00   0.0  0
 OG4  CONST_31  N3   C6   C5   C7    180.00   0.0  0
 OG4  CONST_32  N4   C4   N1   C1    180.00   0.0  0
 OG4  CONST_33  N4   C4   N2   C3    180.00   0.0  0
 OG4  CONST_34  O1   C3   N2   C4    180.00   0.0  0
 OG4  CONST_35  H12  C6   N3   C1    180.00   0.0  0
 OG4  CONST_36  H2   C12  C11  C10   180.00   0.0  0
 OG4  CONST_37  H3   C13  C12  C11   180.00   0.0  0
 OG4  CONST_38  H15  C9   C10  C11   180.00   0.0  0
 OG4  CONST_39  H1   C10  C11  C12   180.00   0.0  0
 OG4  CONST_40  H4   C17  C16  C15   180.00   0.0  0
 OG4  CONST_41  H6   C19  C20  C15   180.00   0.0  0
 OG4  CONST_42  H5   C18  C17  C16   180.00   0.0  0
 OG4  CONST_43  H7   C20  C15  C16   180.00   0.0  0
 OG4  CONST_44  H17  N3   C1   C2    180.00   0.0  0
 OG4  CONST_45  H16  N2   C3   C2    180.00   0.0  0
 OG4  CONST_46  C15  N5   C14  C11   180.00   0.0  0
 OG4  CONST_51  H19  N4   C4   N1      0.00   0.0  0
 OG4  CONST_52  O2   C14  N5   C15     0.00   0.0  0
 OG4  CONST_53  H21  O4   C23  C22   180.00   0.0  0
 OG4  Var_01    C5   C7   C8   C13   100.36  30.0  2
 OG4  Var_02    C8   C7   C5   C2     89.11  30.0  2
 OG4  Var_03    O2   C14  C11  C10   -22.80  30.0  2
 OG4  Var_04    C22  C21  C16  C15    84.86  30.0  2
 OG4  Var_05    C23  C22  C21  C16  -179.30  30.0  1
 OG4  Var_06    O3   C23  C22  C21    -5.33  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
 OG4  plan-1  C10  0.020
 OG4  plan-1  C11  0.020
 OG4  plan-1  C12  0.020
 OG4  plan-1  C13  0.020
 OG4  plan-1  C14  0.020
 OG4  plan-1  C7   0.020
 OG4  plan-1  C8   0.020
 OG4  plan-1  C9   0.020
 OG4  plan-1  H1   0.020
 OG4  plan-1  H2   0.020
 OG4  plan-1  H3   0.020
 OG4  plan-1  H15  0.020
 OG4  plan-2  C15  0.020
 OG4  plan-2  C16  0.020
 OG4  plan-2  C17  0.020
 OG4  plan-2  C18  0.020
 OG4  plan-2  C19  0.020
 OG4  plan-2  C20  0.020
 OG4  plan-2  C21  0.020
 OG4  plan-2  N5   0.020
 OG4  plan-2  H4   0.020
 OG4  plan-2  H5   0.020
 OG4  plan-2  H6   0.020
 OG4  plan-2  H7   0.020
 OG4  plan-3  C1   0.020
 OG4  plan-3  C2   0.020
 OG4  plan-3  C3   0.020
 OG4  plan-3  C4   0.020
 OG4  plan-3  C5   0.020
 OG4  plan-3  C6   0.020
 OG4  plan-3  C7   0.020
 OG4  plan-3  N1   0.020
 OG4  plan-3  N2   0.020
 OG4  plan-3  N3   0.020
 OG4  plan-3  N4   0.020
 OG4  plan-3  O1   0.020
 OG4  plan-3  H12  0.020
 OG4  plan-3  H16  0.020
 OG4  plan-3  H17  0.020
 OG4  plan-3  H18  0.020
 OG4  plan-3  H19  0.020
 OG4  plan-4  C11  0.020
 OG4  plan-4  C14  0.020
 OG4  plan-4  C15  0.020
 OG4  plan-4  N5   0.020
 OG4  plan-4  O2   0.020
 OG4  plan-4  H20  0.020
 OG4  plan-5  C22  0.020
 OG4  plan-5  C23  0.020
 OG4  plan-5  O3   0.020
 OG4  plan-5  O4   0.020
 OG4  plan-5  H21  0.020

