# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 11:17:10 2020
#   Inital geometry file: a 131 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-chlorobenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]cc(Cc3ccc(cc3)C(=O)Nc4cc(Cl)ccc4C(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
 OE7  OE7  '2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)-4-chlorobenzoic acid'  ligand  47  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_OE7
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
 OE7  N1   N   N     0  -0.507  -5.8901  -0.1114   2.1405
 OE7  C1   C   CR56  0   0.500  -5.3151  -0.8724   1.1886
 OE7  O1   O   O     0  -0.474  -4.3354   1.5163  -1.2981
 OE7  N2   N   NR16  0  -0.721  -5.3621   1.6818   0.7210
 OE7  C2   C   CR56  0  -0.239  -4.7374  -0.4470  -0.0070
 OE7  O2   O   O     0  -0.451   2.4469   0.8030  -2.5223
 OE7  N3   N   NR15  0  -0.664  -5.2047  -2.2142   1.2397
 OE7  C3   C   CR6   0   0.495  -4.7583   0.9439  -0.3038
 OE7  O3   O   OH1   0  -0.582   4.0685  -1.0624   3.3573
 OE7  N4   N   NH2   0  -0.833  -6.4813   2.0364   2.7095
 OE7  C4   C   CR6   0   0.672  -5.8938   1.1644   1.8667
 OE7  O4   O   O     0  -0.464   2.3178  -1.1042   1.9962
 OE7  C5   C   CR5   0   0.037  -4.2627  -1.6067  -0.6972
 OE7  N5   N   NH1   0  -0.795   2.6329  -0.1579  -0.4589
 OE7  C6   C   CR15  0  -0.094  -4.5703  -2.6679   0.1019
 OE7  C10  C   CR16  0  -0.250  -0.3446   0.3674  -2.4633
 OE7  C11  C   CR6   0  -0.061   0.5572  -0.3213  -1.6560
 OE7  C12  C   CR16  0  -0.282   0.1156  -1.4543  -0.9711
 OE7  C13  C   CR16  0  -0.278  -1.1982  -1.8739  -1.0873
 OE7  C14  C   C     0   0.538   1.9653   0.1629  -1.6053
 OE7  C15  C   CR6   0   0.401   3.9557   0.0702  -0.1205
 OE7  C16  C   CR16  0  -0.275   4.8728   0.6089  -1.0284
 OE7  C17  C   CR6   0  -0.022   6.1856   0.8021  -0.6460
 OE7  C18  C   CR16  0  -0.220   6.6438   0.4858   0.6229
 OE7  C19  C   CR16  0  -0.268   5.7395  -0.0447   1.5186
 OE7  C20  C   CR6   0  -0.185   4.4023  -0.2645   1.1819
 OE7  C21  C   C     0   0.590   3.4903  -0.8441   2.1915
 OE7  C7   C   CH2   0  -0.620  -3.5333  -1.6551  -2.0006
 OE7  C8   C   CR6   0   0.153  -2.1067  -1.1784  -1.8814
 OE7  C9   C   CR16  0  -0.299  -1.6615  -0.0507  -2.5632
 OE7  CL1  CL  CL    0  -0.103   7.2904   1.4602  -1.7996
 OE7  H1   H   HNR6  0   0.419  -5.4208   2.6802   0.5694
 OE7  H2   H   HNR5  0   0.409  -5.5434  -2.7953   1.9892
 OE7  H3   H   HOH1  0   0.495   3.4268  -1.4380   3.9789
 OE7  H4   H   HNH2  0   0.406  -6.7045   1.6933   3.6288
 OE7  H5   H   HNH2  0   0.408  -6.2566   3.0160   2.6572
 OE7  H6   H   HNH1  0   0.446   2.0944  -0.5725   0.2964
 OE7  H7   H   HCR5  0   0.282  -4.3836  -3.7196  -0.0431
 OE7  H8   H   HCR6  0   0.259  -0.0207   1.2453  -3.0066
 OE7  H9   H   HCR6  0   0.256   0.7917  -2.0451  -0.3661
 OE7  H10  H   HCR6  0   0.255  -1.5199  -2.7620  -0.5561
 OE7  H11  H   HCR6  0   0.314   4.5631   0.8757  -2.0240
 OE7  H12  H   HCR6  0   0.288   7.6745   0.6451   0.9050
 OE7  H13  H   HCR6  0   0.286   6.0931  -0.2960   2.5077
 OE7  H14  H   HCH2  0   0.267  -3.5331  -2.6844  -2.3683
 OE7  H15  H   HCH2  0   0.260  -4.0515  -1.0538  -2.7491
 OE7  H16  H   HCR6  0   0.252  -2.3526   0.5062  -3.1819

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
 OE7  O4   C21  double    1.217  0.020  1.217
 OE7  C19  C18  aromatic  1.379  0.020  1.379
 OE7  C19  C20  aromatic  1.396  0.020  1.396
 OE7  C21  O3   single    1.320  0.020  1.320
 OE7  C21  C20  single    1.479  0.020  1.479
 OE7  C18  C17  aromatic  1.386  0.020  1.386
 OE7  C20  C15  aromatic  1.417  0.020  1.417
 OE7  N4   C4   single    1.348  0.020  1.348
 OE7  C17  CL1  single    1.728  0.020  1.728
 OE7  C17  C16  aromatic  1.381  0.020  1.381
 OE7  C4   N1   double    1.305  0.020  1.305
 OE7  C4   N2   single    1.365  0.020  1.365
 OE7  N1   C1   single    1.348  0.020  1.348
 OE7  C15  C16  aromatic  1.398  0.020  1.398
 OE7  C15  N5   single    1.384  0.020  1.384
 OE7  N2   C3   single    1.400  0.020  1.400
 OE7  N5   C14  single    1.365  0.020  1.365
 OE7  C1   N3   aromatic  1.347  0.020  1.347
 OE7  C1   C2   aromatic  1.394  0.020  1.394
 OE7  N3   C6   aromatic  1.379  0.020  1.379
 OE7  C12  C13  aromatic  1.384  0.020  1.384
 OE7  C12  C11  aromatic  1.396  0.020  1.396
 OE7  C3   C2   single    1.422  0.020  1.422
 OE7  C3   O1   double    1.223  0.020  1.223
 OE7  C2   C5   aromatic  1.431  0.020  1.431
 OE7  C14  C11  single    1.490  0.020  1.490
 OE7  C14  O2   double    1.218  0.020  1.218
 OE7  C13  C8   aromatic  1.393  0.020  1.393
 OE7  C6   C5   aromatic  1.364  0.020  1.364
 OE7  C11  C10  aromatic  1.393  0.020  1.393
 OE7  C5   C7   single    1.494  0.020  1.494
 OE7  C8   C7   single    1.509  0.020  1.509
 OE7  C8   C9   aromatic  1.391  0.020  1.391
 OE7  C10  C9   aromatic  1.385  0.020  1.385
 OE7  N2   H1   single    0.860  0.020  1.020
 OE7  N3   H2   single    0.860  0.020  1.020
 OE7  O3   H3   single    0.850  0.020  0.980
 OE7  N4   H4   single    0.890  0.020  1.040
 OE7  N4   H5   single    0.890  0.020  1.040
 OE7  N5   H6   single    0.860  0.020  1.020
 OE7  C6   H7   single    0.930  0.020  1.080
 OE7  C10  H8   single    0.930  0.020  1.080
 OE7  C12  H9   single    0.930  0.020  1.080
 OE7  C13  H10  single    0.930  0.020  1.080
 OE7  C16  H11  single    0.930  0.020  1.080
 OE7  C18  H12  single    0.930  0.020  1.080
 OE7  C19  H13  single    0.930  0.020  1.080
 OE7  C7   H14  single    0.970  0.020  1.090
 OE7  C7   H15  single    0.970  0.020  1.090
 OE7  C9   H16  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
 OE7  C4   N1   C1   113.90  3.000
 OE7  N3   C1   C2   107.60  3.000
 OE7  C2   C1   N1   127.60  3.000
 OE7  N3   C1   N1   124.79  3.000
 OE7  H1   N2   C4   118.51  3.000
 OE7  H1   N2   C3   115.82  3.000
 OE7  C4   N2   C3   125.64  3.000
 OE7  C5   C2   C3   134.18  3.000
 OE7  C5   C2   C1   107.69  3.000
 OE7  C3   C2   C1   118.11  3.000
 OE7  H2   N3   C6   125.36  3.000
 OE7  H2   N3   C1   125.12  3.000
 OE7  C6   N3   C1   109.51  3.000
 OE7  C2   C3   N2   111.66  3.000
 OE7  C2   C3   O1   128.49  3.000
 OE7  N2   C3   O1   119.85  3.000
 OE7  H3   O3   C21  109.91  3.000
 OE7  H5   N4   H4   115.39  3.000
 OE7  H5   N4   C4   120.00  3.000
 OE7  H4   N4   C4   116.58  3.000
 OE7  N4   C4   N2   116.71  3.000
 OE7  N2   C4   N1   123.07  3.000
 OE7  N4   C4   N1   120.18  3.000
 OE7  C7   C5   C6   126.59  3.000
 OE7  C7   C5   C2   127.52  3.000
 OE7  C6   C5   C2   105.86  3.000
 OE7  H6   N5   C15  113.08  3.000
 OE7  H6   N5   C14  117.45  3.000
 OE7  C15  N5   C14  129.34  3.000
 OE7  H7   C6   C5   129.89  3.000
 OE7  H7   C6   N3   120.76  3.000
 OE7  C5   C6   N3   109.34  3.000
 OE7  H8   C10  C9   119.56  3.000
 OE7  H8   C10  C11  119.90  3.000
 OE7  C9   C10  C11  120.54  3.000
 OE7  C14  C11  C12  123.11  3.000
 OE7  C14  C11  C10  118.10  3.000
 OE7  C12  C11  C10  118.76  3.000
 OE7  H9   C12  C13  118.31  3.000
 OE7  H9   C12  C11  121.31  3.000
 OE7  C13  C12  C11  120.35  3.000
 OE7  H10  C13  C8   119.68  3.000
 OE7  H10  C13  C12  119.28  3.000
 OE7  C8   C13  C12  121.04  3.000
 OE7  C11  C14  N5   114.49  3.000
 OE7  C11  C14  O2   121.27  3.000
 OE7  N5   C14  O2   124.24  3.000
 OE7  C20  C15  C16  118.75  3.000
 OE7  C16  C15  N5   122.11  3.000
 OE7  C20  C15  N5   119.14  3.000
 OE7  H11  C16  C17  119.67  3.000
 OE7  H11  C16  C15  120.49  3.000
 OE7  C17  C16  C15  119.84  3.000
 OE7  CL1  C17  C18  119.14  3.000
 OE7  CL1  C17  C16  118.45  3.000
 OE7  C18  C17  C16  122.41  3.000
 OE7  H12  C18  C19  120.85  3.000
 OE7  H12  C18  C17  121.39  3.000
 OE7  C19  C18  C17  117.76  3.000
 OE7  H13  C19  C20  119.85  3.000
 OE7  H13  C19  C18  118.01  3.000
 OE7  C20  C19  C18  122.14  3.000
 OE7  C21  C20  C19  119.19  3.000
 OE7  C21  C20  C15  121.71  3.000
 OE7  C19  C20  C15  119.10  3.000
 OE7  C20  C21  O4   124.65  3.000
 OE7  C20  C21  O3   113.44  3.000
 OE7  O4   C21  O3   121.92  3.000
 OE7  H15  C7   H14  106.76  3.000
 OE7  H15  C7   C8   109.22  3.000
 OE7  H14  C7   C8   108.90  3.000
 OE7  H15  C7   C5   110.41  3.000
 OE7  H14  C7   C5   108.90  3.000
 OE7  C8   C7   C5   112.48  3.000
 OE7  C9   C8   C7   121.33  3.000
 OE7  C9   C8   C13  118.40  3.000
 OE7  C7   C8   C13  120.27  3.000
 OE7  H16  C9   C8   119.56  3.000
 OE7  H16  C9   C10  119.54  3.000
 OE7  C8   C9   C10  120.90  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
 OE7  CONST_01  C5   C6   N3   C1     0.00   0.0  0
 OE7  CONST_02  C6   C5   C2   C1     0.00   0.0  0
 OE7  CONST_03  C6   N3   C1   C2     0.00   0.0  0
 OE7  CONST_04  N3   C6   C5   C2     0.00   0.0  0
 OE7  CONST_05  C5   C2   C1   N3     0.00   0.0  0
 OE7  CONST_06  C13  C12  C11  C10    0.00   0.0  0
 OE7  CONST_07  C13  C8   C9   C10    0.00   0.0  0
 OE7  CONST_08  C8   C13  C12  C11    0.00   0.0  0
 OE7  CONST_09  C8   C9   C10  C11    0.00   0.0  0
 OE7  CONST_10  C9   C8   C13  C12    0.00   0.0  0
 OE7  CONST_11  C9   C10  C11  C12    0.00   0.0  0
 OE7  CONST_12  C18  C19  C20  C15    0.00   0.0  0
 OE7  CONST_13  C18  C17  C16  C15    0.00   0.0  0
 OE7  CONST_14  C19  C18  C17  C16    0.00   0.0  0
 OE7  CONST_15  C19  C20  C15  C16    0.00   0.0  0
 OE7  CONST_16  C20  C19  C18  C17    0.00   0.0  0
 OE7  CONST_17  C20  C15  C16  C17    0.00   0.0  0
 OE7  CONST_18  C3   N2   C4   N1     0.00   0.0  0
 OE7  CONST_19  N2   C4   N1   C1     0.00   0.0  0
 OE7  CONST_20  C4   N2   C3   C2     0.00   0.0  0
 OE7  CONST_21  C7   C5   C2   C1   180.00   0.0  0
 OE7  CONST_22  C7   C5   C6   N3   180.00   0.0  0
 OE7  CONST_23  C7   C5   C2   C3     0.00   0.0  0
 OE7  CONST_24  C19  C20  C15  N5   180.00   0.0  0
 OE7  CONST_25  C17  C16  C15  N5   180.00   0.0  0
 OE7  CONST_26  C7   C8   C9   C10  180.00   0.0  0
 OE7  CONST_27  C7   C8   C13  C12  180.00   0.0  0
 OE7  CONST_28  C14  C11  C12  C13  180.00   0.0  0
 OE7  CONST_29  C9   C10  C11  C14  180.00   0.0  0
 OE7  CONST_30  CL1  C17  C16  C15  180.00   0.0  0
 OE7  CONST_31  C21  C20  C15  C16  180.00   0.0  0
 OE7  CONST_32  C21  C20  C19  C18  180.00   0.0  0
 OE7  CONST_33  CL1  C17  C18  C19  180.00   0.0  0
 OE7  CONST_34  N4   C4   N1   C1   180.00   0.0  0
 OE7  CONST_35  C4   N2   C3   O1   180.00   0.0  0
 OE7  CONST_36  N4   C4   N2   C3   180.00   0.0  0
 OE7  CONST_37  H2   N3   C1   N1     0.00   0.0  0
 OE7  CONST_38  H7   C6   N3   C1   180.00   0.0  0
 OE7  CONST_39  H9   C12  C11  C10  180.00   0.0  0
 OE7  CONST_40  H10  C13  C12  C11  180.00   0.0  0
 OE7  CONST_41  H16  C9   C10  C11  180.00   0.0  0
 OE7  CONST_42  H8   C10  C11  C12  180.00   0.0  0
 OE7  CONST_43  H13  C19  C20  C15  180.00   0.0  0
 OE7  CONST_44  H12  C18  C17  C16  180.00   0.0  0
 OE7  CONST_45  H11  C16  C17  C18  180.00   0.0  0
 OE7  CONST_46  H1   N2   C4   N1   180.00   0.0  0
 OE7  CONST_47  C15  N5   C14  C11  180.00   0.0  0
 OE7  CONST_48  C20  C15  N5   C14  180.00   0.0  0
 OE7  CONST_49  C16  C15  N5   C14    0.00   0.0  0
 OE7  CONST_50  H6   N5   C15  C16  180.00   0.0  0
 OE7  CONST_51  H4   N4   C4   N1     0.00   0.0  0
 OE7  CONST_53  C15  N5   C14  O2     0.00   0.0  0
 OE7  CONST_54  H3   O3   C21  C20  180.00   0.0  0
 OE7  Var_01    C8   C7   C5   C2    73.08  30.0  2
 OE7  Var_02    C13  C8   C7   C5    63.55  30.0  2
 OE7  Var_03    C12  C11  C14  O2   153.01  30.0  2
 OE7  Var_04    C19  C20  C21  O3     1.75  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
 OE7  plan-1  C10  0.020
 OE7  plan-1  C11  0.020
 OE7  plan-1  C12  0.020
 OE7  plan-1  C13  0.020
 OE7  plan-1  C14  0.020
 OE7  plan-1  C7   0.020
 OE7  plan-1  C8   0.020
 OE7  plan-1  C9   0.020
 OE7  plan-1  H8   0.020
 OE7  plan-1  H9   0.020
 OE7  plan-1  H10  0.020
 OE7  plan-1  H16  0.020
 OE7  plan-2  N5   0.020
 OE7  plan-2  C15  0.020
 OE7  plan-2  C16  0.020
 OE7  plan-2  C17  0.020
 OE7  plan-2  C18  0.020
 OE7  plan-2  C19  0.020
 OE7  plan-2  C20  0.020
 OE7  plan-2  C21  0.020
 OE7  plan-2  CL1  0.020
 OE7  plan-2  H11  0.020
 OE7  plan-2  H12  0.020
 OE7  plan-2  H13  0.020
 OE7  plan-3  N1   0.020
 OE7  plan-3  C1   0.020
 OE7  plan-3  O1   0.020
 OE7  plan-3  N2   0.020
 OE7  plan-3  C2   0.020
 OE7  plan-3  N3   0.020
 OE7  plan-3  C3   0.020
 OE7  plan-3  N4   0.020
 OE7  plan-3  C4   0.020
 OE7  plan-3  C5   0.020
 OE7  plan-3  C6   0.020
 OE7  plan-3  C7   0.020
 OE7  plan-3  H1   0.020
 OE7  plan-3  H2   0.020
 OE7  plan-3  H4   0.020
 OE7  plan-3  H5   0.020
 OE7  plan-3  H7   0.020
 OE7  plan-4  O2   0.020
 OE7  plan-4  N5   0.020
 OE7  plan-4  C11  0.020
 OE7  plan-4  C14  0.020
 OE7  plan-4  C15  0.020
 OE7  plan-4  H6   0.020
 OE7  plan-5  O3   0.020
 OE7  plan-5  O4   0.020
 OE7  plan-5  C20  0.020
 OE7  plan-5  C21  0.020
 OE7  plan-5  H3   0.020

