# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 19:35:30 2020
#   Inital geometry file: a 142 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-carbamoylbenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(C(O)=O)c(NC(=O)c2ccc(Cc3c[nH]c4N=C(N)NC(=O)c34)cc2)c1
#
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
 OFJ  OFJ  '2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)-4-carbamoylbenzoic acid'  ligand  51  33  .  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_OFJ
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
 OFJ  C1   C  CR56  0   0.500   5.6320   1.1388   0.3787
 OFJ  C2   C  CR56  0  -0.239   4.9644   0.0950  -0.2614
 OFJ  C3   C  CR6   0   0.496   4.9392  -1.1751   0.3783
 OFJ  C4   C  CR6   0   0.674   6.2048  -0.0549   2.1651
 OFJ  N5   N  NH2   0  -0.833   6.7426  -0.2135   3.3893
 OFJ  C6   C  CR15  0  -0.095   4.8603   1.9003  -1.5667
 OFJ  C9   C  CR16  0  -0.279   1.3863   0.7265  -1.9151
 OFJ  C10  C  CR16  0  -0.282   0.0715   0.5456  -1.5223
 OFJ  C11  C  CR6   0  -0.062  -0.4274  -0.7385  -1.2983
 OFJ  C21  C  C     0   0.495  -7.0485  -1.6885  -0.1952
 OFJ  C22  C  C     0   0.591  -3.1745   2.3165   1.3121
 OFJ  C13  C  CR16  0  -0.299   1.7371  -1.6382  -1.8677
 OFJ  C14  C  C     0   0.536  -1.8441  -1.0049  -0.9188
 OFJ  C15  C  CR6   0   0.419  -3.7701   0.1436   0.1558
 OFJ  C16  C  CR16  0  -0.348  -4.7500  -0.7931  -0.1833
 OFJ  C17  C  CR6   0  -0.012  -6.0620  -0.6406   0.2342
 OFJ  C12  C  CR16  0  -0.250   0.4189  -1.8281  -1.4873
 OFJ  C18  C  CR16  0  -0.289  -6.4358   0.4690   0.9852
 OFJ  C19  C  CR16  0  -0.247  -5.4821   1.4085   1.3163
 OFJ  C20  C  CR6   0  -0.192  -4.1504   1.2711   0.9235
 OFJ  C5   C  CR5   0   0.038   4.4732   0.5940  -1.5094
 OFJ  C8   C  CR6   0   0.154   2.2393  -0.3604  -2.0918
 OFJ  N1   N  N     0  -0.508   6.2556   1.1069   1.5727
 OFJ  N2   N  NR16  0  -0.722   5.5875  -1.1426   1.6185
 OFJ  N3   N  NR15  0  -0.664   5.5582   2.2207  -0.4207
 OFJ  N4   N  NH1   0  -0.795  -2.4510   0.0183  -0.2517
 OFJ  N6   N  NH2   0  -0.809  -8.1271  -1.8294   0.5851
 OFJ  O1   O  O     0  -0.452  -2.3813  -2.0642  -1.1879
 OFJ  O2   O  O     0  -0.476   4.4486  -2.2211  -0.0226
 OFJ  O3   O  O     0  -0.473  -6.8563  -2.3538  -1.2025
 OFJ  O4   O  OH1   0  -0.581  -3.6989   3.2733   2.0528
 OFJ  O5   O  O     0  -0.461  -2.0006   2.3178   0.9943
 OFJ  H1   H  HNH2  0   0.409   6.9222  -1.1357   3.7492
 OFJ  H2   H  HNH2  0   0.407   7.3666   0.5081   3.7085
 OFJ  H3   H  HCR5  0   0.282   4.6960   2.6391  -2.3342
 OFJ  H4   H  HCH2  0   0.267   3.6674   0.4279  -3.4613
 OFJ  H5   H  HCH2  0   0.261   4.1272  -1.1072  -2.7517
 OFJ  H6   H  HCR6  0   0.253   1.7510   1.7305  -2.0955
 OFJ  H7   H  HCR6  0   0.255  -0.5636   1.4177  -1.4302
 OFJ  H8   H  HCR6  0   0.252   2.3851  -2.4956  -1.9913
 OFJ  H9   H  HCR6  0   0.297  -4.4876  -1.6546  -0.7733
 OFJ  H10  H  HCR6  0   0.258   0.0501  -2.8319  -1.3243
 OFJ  H11  H  HCR6  0   0.269  -7.4599   0.6304   1.2926
 OFJ  H12  H  HCR6  0   0.282  -5.7871   2.2723   1.8881
 OFJ  H13  H  HNR6  0   0.419   5.6074  -2.0155   2.1293
 OFJ  H14  H  HNR5  0   0.409   5.9667   3.1189  -0.2182
 OFJ  H15  H  HNH1  0   0.445  -1.8643   0.7891   0.0520
 OFJ  H16  H  HNH2  0   0.417  -8.2180  -1.3690   1.4739
 OFJ  H17  H  HNH2  0   0.409  -8.8277  -2.5142   0.3518
 OFJ  H18  H  HOH1  0   0.496  -3.0207   3.9292   2.2755
 OFJ  C7   C  CH2   0  -0.621   3.6668  -0.1430  -2.5293

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
 OFJ  N5   C4   single    1.347  0.020  1.347
 OFJ  O3   C21  double    1.222  0.020  1.222
 OFJ  C4   N2   single    1.365  0.020  1.365
 OFJ  C4   N1   double    1.305  0.020  1.305
 OFJ  N2   C3   single    1.400  0.020  1.400
 OFJ  N6   C21  single    1.339  0.020  1.339
 OFJ  C21  C17  single    1.502  0.020  1.502
 OFJ  N1   C1   single    1.347  0.020  1.347
 OFJ  O2   C3   double    1.223  0.020  1.223
 OFJ  C3   C2   single    1.422  0.020  1.422
 OFJ  C17  C16  aromatic  1.385  0.020  1.385
 OFJ  C17  C18  aromatic  1.391  0.020  1.391
 OFJ  C16  C15  aromatic  1.397  0.020  1.397
 OFJ  C1   C2   aromatic  1.395  0.020  1.395
 OFJ  C1   N3   aromatic  1.347  0.020  1.347
 OFJ  C2   C5   aromatic  1.431  0.020  1.431
 OFJ  C18  C19  aromatic  1.379  0.020  1.379
 OFJ  O1   C14  double    1.218  0.020  1.218
 OFJ  C15  N4   single    1.386  0.020  1.386
 OFJ  C15  C20  aromatic  1.416  0.020  1.416
 OFJ  C14  N4   single    1.364  0.020  1.364
 OFJ  C14  C11  single    1.491  0.020  1.491
 OFJ  N3   C6   aromatic  1.380  0.020  1.380
 OFJ  C11  C12  aromatic  1.393  0.020  1.393
 OFJ  C11  C10  aromatic  1.396  0.020  1.396
 OFJ  C12  C13  aromatic  1.385  0.020  1.385
 OFJ  C5   C7   single    1.495  0.020  1.495
 OFJ  C5   C6   aromatic  1.364  0.020  1.364
 OFJ  C10  C9   aromatic  1.384  0.020  1.384
 OFJ  C13  C8   aromatic  1.391  0.020  1.391
 OFJ  C19  C20  aromatic  1.395  0.020  1.395
 OFJ  C9   C8   aromatic  1.393  0.020  1.393
 OFJ  C8   C7   single    1.509  0.020  1.509
 OFJ  C20  C22  single    1.482  0.020  1.482
 OFJ  C22  O5   double    1.216  0.020  1.216
 OFJ  C22  O4   single    1.319  0.020  1.319
 OFJ  N5   H1   single    0.890  0.020  1.040
 OFJ  N5   H2   single    0.890  0.020  1.040
 OFJ  C6   H3   single    0.930  0.020  1.080
 OFJ  C7   H4   single    0.970  0.020  1.090
 OFJ  C7   H5   single    0.970  0.020  1.090
 OFJ  C9   H6   single    0.930  0.020  1.080
 OFJ  C10  H7   single    0.930  0.020  1.080
 OFJ  C13  H8   single    0.930  0.020  1.080
 OFJ  C16  H9   single    0.930  0.020  1.080
 OFJ  C12  H10  single    0.930  0.020  1.080
 OFJ  C18  H11  single    0.930  0.020  1.080
 OFJ  C19  H12  single    0.930  0.020  1.080
 OFJ  N2   H13  single    0.860  0.020  1.020
 OFJ  N3   H14  single    0.860  0.020  1.020
 OFJ  N4   H15  single    0.860  0.020  1.020
 OFJ  N6   H16  single    0.860  0.020  1.020
 OFJ  N6   H17  single    0.860  0.020  1.020
 OFJ  O4   H18  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
 OFJ  N3   C1   N1   124.76  3.000
 OFJ  N3   C1   C2   107.61  3.000
 OFJ  N1   C1   C2   127.63  3.000
 OFJ  C5   C2   C3   134.23  3.000
 OFJ  C5   C2   C1   107.68  3.000
 OFJ  C3   C2   C1   118.06  3.000
 OFJ  O2   C3   N2   119.74  3.000
 OFJ  O2   C3   C2   128.57  3.000
 OFJ  N2   C3   C2   111.69  3.000
 OFJ  N2   C4   N1   123.04  3.000
 OFJ  N1   C4   N5   120.13  3.000
 OFJ  N2   C4   N5   116.80  3.000
 OFJ  H2   N5   H1   115.67  3.000
 OFJ  H2   N5   C4   116.86  3.000
 OFJ  H1   N5   C4   120.30  3.000
 OFJ  H3   C6   N3   120.62  3.000
 OFJ  H3   C6   C5   130.04  3.000
 OFJ  N3   C6   C5   109.34  3.000
 OFJ  H6   C9   C8   119.72  3.000
 OFJ  H6   C9   C10  119.23  3.000
 OFJ  C8   C9   C10  121.05  3.000
 OFJ  H7   C10  C11  121.18  3.000
 OFJ  H7   C10  C9   118.43  3.000
 OFJ  C11  C10  C9   120.36  3.000
 OFJ  C12  C11  C14  118.19  3.000
 OFJ  C12  C11  C10  118.74  3.000
 OFJ  C14  C11  C10  123.03  3.000
 OFJ  O3   C21  N6   123.35  3.000
 OFJ  N6   C21  C17  115.85  3.000
 OFJ  O3   C21  C17  120.80  3.000
 OFJ  O5   C22  O4   121.99  3.000
 OFJ  O4   C22  C20  113.41  3.000
 OFJ  O5   C22  C20  124.60  3.000
 OFJ  H8   C13  C8   119.56  3.000
 OFJ  H8   C13  C12  119.53  3.000
 OFJ  C8   C13  C12  120.91  3.000
 OFJ  O1   C14  N4   124.35  3.000
 OFJ  N4   C14  C11  114.42  3.000
 OFJ  O1   C14  C11  121.23  3.000
 OFJ  N4   C15  C20  119.13  3.000
 OFJ  C20  C15  C16  118.49  3.000
 OFJ  N4   C15  C16  122.37  3.000
 OFJ  H9   C16  C17  118.96  3.000
 OFJ  H9   C16  C15  119.90  3.000
 OFJ  C17  C16  C15  121.14  3.000
 OFJ  C18  C17  C16  120.34  3.000
 OFJ  C18  C17  C21  122.30  3.000
 OFJ  C16  C17  C21  117.33  3.000
 OFJ  H10  C12  C13  119.54  3.000
 OFJ  H10  C12  C11  119.89  3.000
 OFJ  C13  C12  C11  120.56  3.000
 OFJ  H11  C18  C19  119.02  3.000
 OFJ  H11  C18  C17  121.81  3.000
 OFJ  C19  C18  C17  119.15  3.000
 OFJ  H12  C19  C20  119.83  3.000
 OFJ  H12  C19  C18  118.47  3.000
 OFJ  C20  C19  C18  121.70  3.000
 OFJ  C19  C20  C15  119.16  3.000
 OFJ  C19  C20  C22  119.03  3.000
 OFJ  C15  C20  C22  121.81  3.000
 OFJ  C7   C5   C6   126.65  3.000
 OFJ  C6   C5   C2   105.86  3.000
 OFJ  C7   C5   C2   127.47  3.000
 OFJ  C13  C8   C9   118.37  3.000
 OFJ  C9   C8   C7   120.25  3.000
 OFJ  C13  C8   C7   121.37  3.000
 OFJ  C4   N1   C1   113.91  3.000
 OFJ  H13  N2   C4   118.46  3.000
 OFJ  H13  N2   C3   115.88  3.000
 OFJ  C4   N2   C3   125.64  3.000
 OFJ  H14  N3   C6   125.40  3.000
 OFJ  H14  N3   C1   125.07  3.000
 OFJ  C6   N3   C1   109.52  3.000
 OFJ  H15  N4   C15  113.16  3.000
 OFJ  H15  N4   C14  117.31  3.000
 OFJ  C15  N4   C14  129.42  3.000
 OFJ  H17  N6   H16  116.97  3.000
 OFJ  H17  N6   C21  119.80  3.000
 OFJ  H16  N6   C21  122.69  3.000
 OFJ  H18  O4   C22  109.98  3.000
 OFJ  H5   C7   H4   106.71  3.000
 OFJ  H5   C7   C8   109.33  3.000
 OFJ  H4   C7   C8   108.84  3.000
 OFJ  H5   C7   C5   110.31  3.000
 OFJ  H4   C7   C5   108.91  3.000
 OFJ  C8   C7   C5   112.56  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
 OFJ  CONST_01  C6   C5   C2   C1     0.00   0.0  0
 OFJ  CONST_02  C5   C6   N3   C1     0.00   0.0  0
 OFJ  CONST_03  C6   N3   C1   C2     0.00   0.0  0
 OFJ  CONST_04  N3   C6   C5   C2     0.00   0.0  0
 OFJ  CONST_05  C12  C11  C10  C9     0.00   0.0  0
 OFJ  CONST_06  C12  C13  C8   C9     0.00   0.0  0
 OFJ  CONST_07  C13  C12  C11  C10    0.00   0.0  0
 OFJ  CONST_08  C13  C8   C9   C10    0.00   0.0  0
 OFJ  CONST_09  C8   C13  C12  C11    0.00   0.0  0
 OFJ  CONST_10  C8   C9   C10  C11    0.00   0.0  0
 OFJ  CONST_11  C18  C17  C16  C15    0.00   0.0  0
 OFJ  CONST_12  C18  C19  C20  C15    0.00   0.0  0
 OFJ  CONST_13  C19  C18  C17  C16    0.00   0.0  0
 OFJ  CONST_14  C19  C20  C15  C16    0.00   0.0  0
 OFJ  CONST_15  C20  C15  C16  C17    0.00   0.0  0
 OFJ  CONST_16  C20  C19  C18  C17    0.00   0.0  0
 OFJ  CONST_17  N3   C1   C2   C5     0.00   0.0  0
 OFJ  CONST_18  N2   C4   N1   C1     0.00   0.0  0
 OFJ  CONST_19  C4   N2   C3   C2     0.00   0.0  0
 OFJ  CONST_20  N1   C4   N2   C3     0.00   0.0  0
 OFJ  CONST_21  C7   C5   C2   C1   180.00   0.0  0
 OFJ  CONST_22  C7   C5   C2   C3     0.00   0.0  0
 OFJ  CONST_23  N3   C6   C5   C7   180.00   0.0  0
 OFJ  CONST_24  C12  C13  C8   C7   180.00   0.0  0
 OFJ  CONST_25  C10  C9   C8   C7   180.00   0.0  0
 OFJ  CONST_26  C14  C11  C10  C9   180.00   0.0  0
 OFJ  CONST_27  C15  C16  C17  C21  180.00   0.0  0
 OFJ  CONST_28  C19  C18  C17  C21  180.00   0.0  0
 OFJ  CONST_29  C16  C15  C20  C22  180.00   0.0  0
 OFJ  CONST_30  C18  C19  C20  C22  180.00   0.0  0
 OFJ  CONST_31  C14  C11  C12  C13  180.00   0.0  0
 OFJ  CONST_32  N4   C15  C16  C17  180.00   0.0  0
 OFJ  CONST_33  N4   C15  C20  C19  180.00   0.0  0
 OFJ  CONST_34  N5   C4   N1   C1   180.00   0.0  0
 OFJ  CONST_35  N5   C4   N2   C3   180.00   0.0  0
 OFJ  CONST_36  O2   C3   N2   C4   180.00   0.0  0
 OFJ  CONST_37  H3   C6   N3   C1   180.00   0.0  0
 OFJ  CONST_38  H14  N3   C1   C2   180.00   0.0  0
 OFJ  CONST_39  H8   C13  C8   C9   180.00   0.0  0
 OFJ  CONST_40  H10  C12  C11  C10  180.00   0.0  0
 OFJ  CONST_41  H6   C9   C10  C11  180.00   0.0  0
 OFJ  CONST_42  H12  C19  C20  C15  180.00   0.0  0
 OFJ  CONST_43  H11  C18  C17  C16  180.00   0.0  0
 OFJ  CONST_44  H7   C10  C11  C12  180.00   0.0  0
 OFJ  CONST_45  H9   C16  C17  C18  180.00   0.0  0
 OFJ  CONST_46  H13  N2   C3   C2   180.00   0.0  0
 OFJ  CONST_47  C15  N4   C14  C11  180.00   0.0  0
 OFJ  CONST_48  C16  C15  N4   C14    0.00   0.0  0
 OFJ  CONST_49  C20  C15  N4   C14  180.00   0.0  0
 OFJ  CONST_50  H15  N4   C15  C16  180.00   0.0  0
 OFJ  CONST_52  H2   N5   C4   N1     0.00   0.0  0
 OFJ  CONST_53  O1   C14  N4   C15    0.00   0.0  0
 OFJ  CONST_54  H16  N6   C21  C17    0.00   0.0  0
 OFJ  CONST_55  H17  N6   C21  C17  180.00   0.0  0
 OFJ  CONST_56  H18  O4   C22  C20  180.00   0.0  0
 OFJ  Var_01    C8   C7   C5   C2    73.21  30.0  2
 OFJ  Var_02    C5   C7   C8   C9    65.23  30.0  2
 OFJ  Var_03    O1   C14  C11  C10  153.20  30.0  2
 OFJ  Var_04    O5   C22  C20  C15    1.58  30.0  2
 OFJ  Var_05    O3   C21  C17  C16  -24.87  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
 OFJ  plan-1  C9   0.020
 OFJ  plan-1  C10  0.020
 OFJ  plan-1  C11  0.020
 OFJ  plan-1  C13  0.020
 OFJ  plan-1  C14  0.020
 OFJ  plan-1  C12  0.020
 OFJ  plan-1  C8   0.020
 OFJ  plan-1  H6   0.020
 OFJ  plan-1  H7   0.020
 OFJ  plan-1  H8   0.020
 OFJ  plan-1  H10  0.020
 OFJ  plan-1  C7   0.020
 OFJ  plan-2  C22  0.020
 OFJ  plan-2  C20  0.020
 OFJ  plan-2  O4   0.020
 OFJ  plan-2  O5   0.020
 OFJ  plan-2  H18  0.020
 OFJ  plan-3  C21  0.020
 OFJ  plan-3  C22  0.020
 OFJ  plan-3  C15  0.020
 OFJ  plan-3  C16  0.020
 OFJ  plan-3  C17  0.020
 OFJ  plan-3  C18  0.020
 OFJ  plan-3  C19  0.020
 OFJ  plan-3  C20  0.020
 OFJ  plan-3  N4   0.020
 OFJ  plan-3  H9   0.020
 OFJ  plan-3  H11  0.020
 OFJ  plan-3  H12  0.020
 OFJ  plan-4  C1   0.020
 OFJ  plan-4  C2   0.020
 OFJ  plan-4  C3   0.020
 OFJ  plan-4  C4   0.020
 OFJ  plan-4  N5   0.020
 OFJ  plan-4  C6   0.020
 OFJ  plan-4  C5   0.020
 OFJ  plan-4  N1   0.020
 OFJ  plan-4  N2   0.020
 OFJ  plan-4  N3   0.020
 OFJ  plan-4  O2   0.020
 OFJ  plan-4  H1   0.020
 OFJ  plan-4  H2   0.020
 OFJ  plan-4  H3   0.020
 OFJ  plan-4  H13  0.020
 OFJ  plan-4  H14  0.020
 OFJ  plan-4  C7   0.020
 OFJ  plan-5  C21  0.020
 OFJ  plan-5  C17  0.020
 OFJ  plan-5  N6   0.020
 OFJ  plan-5  O3   0.020
 OFJ  plan-5  H16  0.020
 OFJ  plan-5  H17  0.020
 OFJ  plan-6  C11  0.020
 OFJ  plan-6  C14  0.020
 OFJ  plan-6  C15  0.020
 OFJ  plan-6  N4   0.020
 OFJ  plan-6  O1   0.020
 OFJ  plan-6  H15  0.020

