# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 09:42:43 2020
#   Inital geometry file: a 137 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)phenyl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]cc(Cc3ccc(cc3)C(=O)Nc4ccccc4CC(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
 OF7  OF7  '[2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)phenyl]acetic acid'  ligand  50  31  .  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_OF7
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
 OF7  N1   N  N     0  -0.507   6.3089  -0.0673   1.6321
 OF7  C1   C  CR56  0   0.500   5.5640   0.5369   0.6859
 OF7  O1   O  O     0  -0.480   3.6201  -2.1535  -0.6694
 OF7  N2   N  NR16  0  -0.721   5.1692  -2.0115   0.9804
 OF7  C2   C  CR56  0  -0.242   4.5985  -0.0419  -0.1389
 OF7  O2   O  O     0  -0.466  -2.5492   2.1883   1.1432
 OF7  N3   N  NR15  0  -0.662   5.6406   1.8437   0.3695
 OF7  C3   C  CR6   0   0.503   4.3760  -1.4422  -0.0211
 OF7  O3   O  O     0  -0.447  -3.8729  -2.0650  -1.5238
 OF7  C10  C  CR16  0  -0.254  -0.1716   2.2362  -0.3954
 OF7  C11  C  CR6   0  -0.060  -0.9167   1.0791  -0.1716
 OF7  C12  C  CR16  0  -0.284  -0.3707  -0.1483  -0.5396
 OF7  C13  C  CR16  0  -0.297   0.8826  -0.2147  -1.1297
 OF7  C14  C  C     0   0.523  -2.2572   1.2155   0.4681
 OF7  C15  C  CR6   0   0.293  -4.4296   0.1162   0.7378
 OF7  C16  C  CR6   0   0.103  -5.4969  -0.0892  -0.1417
 OF7  C17  C  CR16  0  -0.305  -6.7780  -0.2220   0.3850
 OF7  C18  C  CR16  0  -0.246  -7.0093  -0.1311   1.7490
 OF7  C19  C  CR16  0  -0.272  -5.9439   0.0886   2.6110
 OF7  C20  C  CR16  0  -0.270  -4.6583   0.2060   2.1075
 OF7  C21  C  CH2   0  -0.685  -5.3050  -0.1364  -1.6329
 OF7  C22  C  C     0   0.574  -4.7107  -1.4332  -2.1247
 OF7  C4   C  CR6   0   0.673   6.0778  -1.3458   1.7512
 OF7  C5   C  CR5   0   0.039   4.0813   0.9874  -0.9887
 OF7  C6   C  CR15  0  -0.091   4.7504   2.1250  -0.6452
 OF7  C7   C  CH2   0  -0.631   2.9882   0.8798  -2.0060
 OF7  C8   C  CR6   0   0.151   1.6194   0.9394  -1.3729
 OF7  C9   C  CR16  0  -0.293   1.0736   2.1646  -0.9936
 OF7  N4   N  NH2   0  -0.833   6.7799  -2.0834   2.6330
 OF7  N5   N  NH1   0  -0.775  -3.1216   0.2005   0.2242
 OF7  O4   O  OH1   0  -0.577  -5.1777  -1.7888  -3.3080
 OF7  H1   H  HNR6  0   0.419   5.0518  -3.0062   1.1217
 OF7  H2   H  HNR5  0   0.410   6.2713   2.5056   0.7920
 OF7  H3   H  HCR6  0   0.259  -0.5749   3.1996  -0.1134
 OF7  H4   H  HCR6  0   0.255  -0.8963  -1.0763  -0.3488
 OF7  H5   H  HCR6  0   0.260   1.2965  -1.1783  -1.3931
 OF7  H6   H  HCR6  0   0.259  -7.6099  -0.3837  -0.2897
 OF7  H7   H  HCR6  0   0.259  -8.0152  -0.2311   2.1348
 OF7  H8   H  HCR6  0   0.261  -6.1087   0.1573   3.6782
 OF7  H9   H  HCR6  0   0.266  -3.8257   0.3454   2.7835
 OF7  H10  H  HCH2  0   0.302  -6.2523   0.0524  -2.1372
 OF7  H11  H  HCH2  0   0.314  -4.6250   0.6603  -1.9574
 OF7  H12  H  HCR5  0   0.281   4.6628   3.1248  -1.0389
 OF7  H13  H  HCH2  0   0.267   3.0875   1.7008  -2.7194
 OF7  H14  H  HCH2  0   0.263   3.0883  -0.0457  -2.5747
 OF7  H15  H  HCR6  0   0.251   1.6291   3.0782  -1.1705
 OF7  H16  H  HNH2  0   0.407   7.3031  -1.5806   3.3301
 OF7  H17  H  HNH2  0   0.409   6.4413  -2.9881   2.9147
 OF7  H18  H  HNH1  0   0.413  -2.8684  -0.5185  -0.4374
 OF7  H19  H  HOH1  0   0.486  -4.7333  -2.5942  -3.6161

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
 OF7  C6   N3   aromatic  1.379  0.020  1.379
 OF7  C6   C5   aromatic  1.364  0.020  1.364
 OF7  C7   C5   single    1.497  0.020  1.497
 OF7  C7   C8   single    1.509  0.020  1.509
 OF7  N3   C1   aromatic  1.347  0.020  1.347
 OF7  C5   C2   aromatic  1.431  0.020  1.431
 OF7  C1   C2   aromatic  1.395  0.020  1.395
 OF7  C1   N1   single    1.347  0.020  1.347
 OF7  C2   C3   single    1.423  0.020  1.423
 OF7  C8   C9   aromatic  1.394  0.020  1.394
 OF7  C8   C13  aromatic  1.391  0.020  1.391
 OF7  N1   C4   double    1.305  0.020  1.305
 OF7  C9   C10  aromatic  1.383  0.020  1.383
 OF7  C3   O1   double    1.224  0.020  1.224
 OF7  C3   N2   single    1.399  0.020  1.399
 OF7  C4   N2   single    1.365  0.020  1.365
 OF7  C4   N4   single    1.347  0.020  1.347
 OF7  C13  C12  aromatic  1.387  0.020  1.387
 OF7  C10  C11  aromatic  1.394  0.020  1.394
 OF7  C12  C11  aromatic  1.393  0.020  1.393
 OF7  C11  C14  single    1.492  0.020  1.492
 OF7  C14  O2   double    1.220  0.020  1.220
 OF7  C14  N5   single    1.355  0.020  1.355
 OF7  N5   C15  single    1.408  0.020  1.408
 OF7  O3   C22  double    1.209  0.020  1.209
 OF7  C22  O4   single    1.321  0.020  1.321
 OF7  C22  C21  single    1.509  0.020  1.509
 OF7  C15  C20  aromatic  1.392  0.020  1.392
 OF7  C15  C16  aromatic  1.398  0.020  1.398
 OF7  C20  C19  aromatic  1.386  0.020  1.386
 OF7  C21  C16  single    1.504  0.020  1.504
 OF7  C16  C17  aromatic  1.392  0.020  1.392
 OF7  C19  C18  aromatic  1.388  0.020  1.388
 OF7  C17  C18  aromatic  1.386  0.020  1.386
 OF7  N2   H1   single    0.860  0.020  1.020
 OF7  N3   H2   single    0.860  0.020  1.020
 OF7  C10  H3   single    0.930  0.020  1.080
 OF7  C12  H4   single    0.930  0.020  1.080
 OF7  C13  H5   single    0.930  0.020  1.080
 OF7  C17  H6   single    0.930  0.020  1.080
 OF7  C18  H7   single    0.930  0.020  1.080
 OF7  C19  H8   single    0.930  0.020  1.080
 OF7  C20  H9   single    0.930  0.020  1.080
 OF7  C21  H10  single    0.970  0.020  1.090
 OF7  C21  H11  single    0.970  0.020  1.090
 OF7  C6   H12  single    0.930  0.020  1.080
 OF7  C7   H13  single    0.970  0.020  1.090
 OF7  C7   H14  single    0.970  0.020  1.090
 OF7  C9   H15  single    0.930  0.020  1.080
 OF7  N4   H16  single    0.890  0.020  1.040
 OF7  N4   H17  single    0.890  0.020  1.040
 OF7  N5   H18  single    0.860  0.020  1.020
 OF7  O4   H19  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
 OF7  C4   N1   C1   113.93  3.000
 OF7  N3   C1   C2   107.63  3.000
 OF7  C2   C1   N1   127.71  3.000
 OF7  N3   C1   N1   124.66  3.000
 OF7  H1   N2   C4   118.56  3.000
 OF7  H1   N2   C3   115.75  3.000
 OF7  C4   N2   C3   125.69  3.000
 OF7  C5   C2   C3   134.45  3.000
 OF7  C3   C2   C1   117.87  3.000
 OF7  C5   C2   C1   107.62  3.000
 OF7  H2   N3   C6   125.37  3.000
 OF7  H2   N3   C1   125.09  3.000
 OF7  C6   N3   C1   109.52  3.000
 OF7  C2   C3   N2   111.79  3.000
 OF7  N2   C3   O1   119.54  3.000
 OF7  C2   C3   O1   128.67  3.000
 OF7  H3   C10  C9   119.63  3.000
 OF7  H3   C10  C11  119.86  3.000
 OF7  C9   C10  C11  120.50  3.000
 OF7  C14  C11  C12  123.11  3.000
 OF7  C14  C11  C10  118.24  3.000
 OF7  C12  C11  C10  118.65  3.000
 OF7  H4   C12  C13  118.19  3.000
 OF7  H4   C12  C11  121.21  3.000
 OF7  C13  C12  C11  120.59  3.000
 OF7  H5   C13  C8   119.62  3.000
 OF7  H5   C13  C12  119.48  3.000
 OF7  C8   C13  C12  120.89  3.000
 OF7  N5   C14  C11  115.31  3.000
 OF7  N5   C14  O2   122.97  3.000
 OF7  C11  C14  O2   121.71  3.000
 OF7  N5   C15  C20  120.53  3.000
 OF7  C20  C15  C16  120.21  3.000
 OF7  N5   C15  C16  119.25  3.000
 OF7  C21  C16  C17  119.32  3.000
 OF7  C17  C16  C15  118.60  3.000
 OF7  C21  C16  C15  122.06  3.000
 OF7  H6   C17  C18  119.63  3.000
 OF7  H6   C17  C16  119.04  3.000
 OF7  C18  C17  C16  121.32  3.000
 OF7  H7   C18  C19  120.45  3.000
 OF7  H7   C18  C17  119.99  3.000
 OF7  C19  C18  C17  119.56  3.000
 OF7  H8   C19  C20  119.62  3.000
 OF7  H8   C19  C18  120.38  3.000
 OF7  C20  C19  C18  120.00  3.000
 OF7  H9   C20  C19  119.88  3.000
 OF7  H9   C20  C15  119.80  3.000
 OF7  C19  C20  C15  120.30  3.000
 OF7  H11  C21  H10  106.04  3.000
 OF7  H11  C21  C22  106.48  3.000
 OF7  H10  C21  C22  109.91  3.000
 OF7  H11  C21  C16  110.47  3.000
 OF7  H10  C21  C16  110.03  3.000
 OF7  C22  C21  C16  113.60  3.000
 OF7  O4   C22  C21  112.59  3.000
 OF7  C21  C22  O3   124.05  3.000
 OF7  O4   C22  O3   123.33  3.000
 OF7  N4   C4   N2   116.72  3.000
 OF7  N4   C4   N1   120.26  3.000
 OF7  N2   C4   N1   122.98  3.000
 OF7  C7   C5   C6   126.11  3.000
 OF7  C7   C5   C2   127.99  3.000
 OF7  C6   C5   C2   105.84  3.000
 OF7  H12  C6   C5   129.92  3.000
 OF7  H12  C6   N3   120.69  3.000
 OF7  C5   C6   N3   109.38  3.000
 OF7  H14  C7   H13  106.80  3.000
 OF7  H14  C7   C8   109.60  3.000
 OF7  H13  C7   C8   109.07  3.000
 OF7  H14  C7   C5   110.38  3.000
 OF7  H13  C7   C5   108.87  3.000
 OF7  C8   C7   C5   111.98  3.000
 OF7  C9   C8   C7   120.27  3.000
 OF7  C9   C8   C13  118.32  3.000
 OF7  C7   C8   C13  121.40  3.000
 OF7  H15  C9   C8   119.73  3.000
 OF7  H15  C9   C10  119.23  3.000
 OF7  C8   C9   C10  121.04  3.000
 OF7  H17  N4   H16  115.48  3.000
 OF7  H17  N4   C4   120.01  3.000
 OF7  H16  N4   C4   116.80  3.000
 OF7  H18  N5   C15  115.44  3.000
 OF7  H18  N5   C14  119.43  3.000
 OF7  C15  N5   C14  124.88  3.000
 OF7  H19  O4   C22  110.25  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
 OF7  CONST_01  C5   C6   N3   C1     0.00   0.0  0
 OF7  CONST_02  C6   C5   C2   C1     0.00   0.0  0
 OF7  CONST_03  N3   C6   C5   C2     0.00   0.0  0
 OF7  CONST_04  C6   N3   C1   C2     0.00   0.0  0
 OF7  CONST_05  C5   C2   C1   N3     0.00   0.0  0
 OF7  CONST_06  C13  C8   C9   C10    0.00   0.0  0
 OF7  CONST_07  C13  C12  C11  C10    0.00   0.0  0
 OF7  CONST_08  C8   C9   C10  C11    0.00   0.0  0
 OF7  CONST_09  C8   C13  C12  C11    0.00   0.0  0
 OF7  CONST_10  C9   C8   C13  C12    0.00   0.0  0
 OF7  CONST_11  C9   C10  C11  C12    0.00   0.0  0
 OF7  CONST_12  C18  C19  C20  C15    0.00   0.0  0
 OF7  CONST_13  C18  C17  C16  C15    0.00   0.0  0
 OF7  CONST_14  C19  C20  C15  C16    0.00   0.0  0
 OF7  CONST_15  C19  C18  C17  C16    0.00   0.0  0
 OF7  CONST_16  C20  C15  C16  C17    0.00   0.0  0
 OF7  CONST_17  C20  C19  C18  C17    0.00   0.0  0
 OF7  CONST_18  C3   N2   C4   N1     0.00   0.0  0
 OF7  CONST_19  N2   C4   N1   C1     0.00   0.0  0
 OF7  CONST_20  C4   N2   C3   C2     0.00   0.0  0
 OF7  CONST_21  C7   C5   C2   C1   180.00   0.0  0
 OF7  CONST_22  C7   C5   C6   N3   180.00   0.0  0
 OF7  CONST_23  C7   C5   C2   C3     0.00   0.0  0
 OF7  CONST_24  C7   C8   C9   C10  180.00   0.0  0
 OF7  CONST_25  C7   C8   C13  C12  180.00   0.0  0
 OF7  CONST_26  C14  C11  C12  C13  180.00   0.0  0
 OF7  CONST_27  C9   C10  C11  C14  180.00   0.0  0
 OF7  CONST_28  N5   C15  C16  C17  180.00   0.0  0
 OF7  CONST_29  C21  C16  C17  C18  180.00   0.0  0
 OF7  CONST_30  N5   C15  C20  C19  180.00   0.0  0
 OF7  CONST_31  C21  C16  C15  C20  180.00   0.0  0
 OF7  CONST_32  N4   C4   N1   C1   180.00   0.0  0
 OF7  CONST_33  C4   N2   C3   O1   180.00   0.0  0
 OF7  CONST_34  N4   C4   N2   C3   180.00   0.0  0
 OF7  CONST_35  H2   N3   C1   N1     0.00   0.0  0
 OF7  CONST_36  H12  C6   N3   C1   180.00   0.0  0
 OF7  CONST_37  H4   C12  C11  C10  180.00   0.0  0
 OF7  CONST_38  H15  C9   C10  C11  180.00   0.0  0
 OF7  CONST_39  H5   C13  C12  C11  180.00   0.0  0
 OF7  CONST_40  H3   C10  C11  C12  180.00   0.0  0
 OF7  CONST_41  H8   C19  C20  C15  180.00   0.0  0
 OF7  CONST_42  H6   C17  C16  C15  180.00   0.0  0
 OF7  CONST_43  H9   C20  C15  C16  180.00   0.0  0
 OF7  CONST_44  H7   C18  C17  C16  180.00   0.0  0
 OF7  CONST_45  H1   N2   C4   N1   180.00   0.0  0
 OF7  CONST_46  C15  N5   C14  C11  180.00   0.0  0
 OF7  CONST_50  H16  N4   C4   N1     0.00   0.0  0
 OF7  CONST_52  C15  N5   C14  O2     0.00   0.0  0
 OF7  CONST_53  H19  O4   C22  O3     0.00   0.0  0
 OF7  Var_01    C8   C7   C5   C2    80.29  30.0  2
 OF7  Var_02    C5   C7   C8   C13  -99.65  30.0  2
 OF7  Var_03    C10  C11  C14  O2   -22.22  30.0  2
 OF7  Var_04    C22  C21  C16  C15   76.45  30.0  2
 OF7  Var_05    C16  C21  C22  O3   -36.28  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
 OF7  plan-1  C15  0.020
 OF7  plan-1  C16  0.020
 OF7  plan-1  C17  0.020
 OF7  plan-1  C18  0.020
 OF7  plan-1  C19  0.020
 OF7  plan-1  C20  0.020
 OF7  plan-1  C21  0.020
 OF7  plan-1  N5   0.020
 OF7  plan-1  H6   0.020
 OF7  plan-1  H7   0.020
 OF7  plan-1  H8   0.020
 OF7  plan-1  H9   0.020
 OF7  plan-2  C10  0.020
 OF7  plan-2  C11  0.020
 OF7  plan-2  C12  0.020
 OF7  plan-2  C13  0.020
 OF7  plan-2  C14  0.020
 OF7  plan-2  C7   0.020
 OF7  plan-2  C8   0.020
 OF7  plan-2  C9   0.020
 OF7  plan-2  H3   0.020
 OF7  plan-2  H4   0.020
 OF7  plan-2  H5   0.020
 OF7  plan-2  H15  0.020
 OF7  plan-3  N1   0.020
 OF7  plan-3  C1   0.020
 OF7  plan-3  O1   0.020
 OF7  plan-3  N2   0.020
 OF7  plan-3  C2   0.020
 OF7  plan-3  N3   0.020
 OF7  plan-3  C3   0.020
 OF7  plan-3  C4   0.020
 OF7  plan-3  C5   0.020
 OF7  plan-3  C6   0.020
 OF7  plan-3  C7   0.020
 OF7  plan-3  N4   0.020
 OF7  plan-3  H1   0.020
 OF7  plan-3  H2   0.020
 OF7  plan-3  H12  0.020
 OF7  plan-3  H16  0.020
 OF7  plan-3  H17  0.020
 OF7  plan-4  O2   0.020
 OF7  plan-4  C11  0.020
 OF7  plan-4  C14  0.020
 OF7  plan-4  C15  0.020
 OF7  plan-4  N5   0.020
 OF7  plan-4  H18  0.020
 OF7  plan-5  O3   0.020
 OF7  plan-5  C21  0.020
 OF7  plan-5  C22  0.020
 OF7  plan-5  O4   0.020
 OF7  plan-5  H19  0.020

