# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 05:08:23 2020
#   Inital geometry file: a 144 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-cyanophenyl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]cc(Cc3ccc(cc3)C(=O)Nc4cc(ccc4CC(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
 OFD  OFD  '[2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)-4-cyanophenyl]acetic 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_OFD
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
 OFD  O1   O  O     0  -0.477   4.4505  -1.9570  -0.1339
 OFD  C1   C  CR6   0   0.675   6.0165   0.3532   2.0515
 OFD  O2   O  O     0  -0.459  -2.4522  -2.2980  -1.0232
 OFD  C2   C  CR56  0   0.500   5.2802   1.5039   0.2970
 OFD  C3   C  CR56  0  -0.239   4.7189   0.4029  -0.3490
 OFD  C4   C  CR6   0   0.496   4.8409  -0.8710   0.2717
 OFD  C5   C  CR5   0   0.036   4.1555   0.8629  -1.5814
 OFD  C6   C  CR15  0  -0.093   4.3994   2.2039  -1.6250
 OFD  C7   C  CH2   0  -0.622   3.4011   0.0599  -2.5914
 OFD  C8   C  CR6   0   0.151   1.9970  -0.2560  -2.1374
 OFD  C9   C  CR16  0  -0.301   1.5941  -1.5615  -1.8769
 OFD  C10  C  CR16  0  -0.252   0.2975  -1.8385  -1.4735
 OFD  C11  C  CR6   0  -0.063  -0.6260  -0.8110  -1.3024
 OFD  C12  C  CR16  0  -0.284  -0.2265   0.5003  -1.5652
 OFD  O3   O  O     0  -0.444  -2.7704   2.5060   0.9411
 OFD  C13  C  CR16  0  -0.275   1.0670   0.7687  -1.9764
 OFD  C14  C  C     0   0.532  -2.0080  -1.1726  -0.8795
 OFD  C15  C  CR6   0   0.322  -4.0639  -0.2762   0.0989
 OFD  C16  C  CR6   0   0.115  -4.4372   0.1705   1.3720
 OFD  C17  C  CR16  0  -0.292  -5.7770   0.1053   1.7434
 OFD  C18  C  CR16  0  -0.236  -6.7368  -0.4173   0.8979
 OFD  C19  C  CR6   0  -0.005  -6.3464  -0.8770  -0.3577
 OFD  C20  C  CR16  0  -0.264  -5.0183  -0.8010  -0.7628
 OFD  C21  C  CSP   0   0.057  -7.3200  -1.4206  -1.2490
 OFD  C22  C  CH2   0  -0.688  -3.4284   0.6826   2.3613
 OFD  C23  C  C     0   0.578  -2.9522   2.0830   2.0588
 OFD  N1   N  NR16  0  -0.722   5.5119  -0.7879   1.4973
 OFD  N2   N  N     0  -0.508   5.9205   1.5239   1.4821
 OFD  N3   N  NR15  0  -0.664   5.0773   2.5821  -0.4846
 OFD  N5   N  NH1   0  -0.785  -2.7261  -0.1696  -0.3085
 OFD  N6   N  NS    0  -0.248  -8.1079  -1.8599  -1.9656
 OFD  O4   O  OH1   0  -0.574  -2.7196   2.7836   3.1517
 OFD  H1   H  HCR5  0   0.282   4.1429   2.9312  -2.3782
 OFD  H2   H  HCH2  0   0.267   3.3519   0.6212  -3.5280
 OFD  H3   H  HCH2  0   0.261   3.9284  -0.8699  -2.8101
 OFD  H4   H  HCR6  0   0.253   2.3031  -2.3712  -1.9862
 OFD  H5   H  HCR6  0   0.259   0.0052  -2.8620  -1.2806
 OFD  H6   H  HCR6  0   0.253  -0.9208   1.3281  -1.4876
 OFD  H7   H  HCR6  0   0.254   1.3565   1.7923  -2.1817
 OFD  H8   H  HCR6  0   0.277  -6.0714   0.4570   2.7235
 OFD  H9   H  HCR6  0   0.284  -7.7717  -0.4701   1.2059
 OFD  H10  H  HCR6  0   0.293  -4.7388  -1.1313  -1.7527
 OFD  H11  H  HCH2  0   0.309  -3.8376   0.6372   3.3694
 OFD  H12  H  HCH2  0   0.323  -2.5399   0.0406   2.3599
 OFD  H13  H  HNR6  0   0.419   5.6409  -1.6620   1.9905
 OFD  H14  H  HNR5  0   0.409   5.3848   3.5174  -0.2723
 OFD  H15  H  HNH2  0   0.409   6.5640  -0.6093   3.7740
 OFD  H16  H  HNH2  0   0.407   6.8752   1.0664   3.7276
 OFD  H17  H  HNH1  0   0.418  -2.2782   0.7132  -0.1118
 OFD  H18  H  HOH1  0   0.487  -2.3626   3.6560   2.9225
 OFD  N4   N  NH2   0  -0.834   6.6728   0.2224   3.2189

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
 OFD  N4   C1   single    1.346  0.020  1.346
 OFD  N2   C1   double    1.305  0.020  1.305
 OFD  N2   C2   single    1.347  0.020  1.347
 OFD  C1   N1   single    1.365  0.020  1.365
 OFD  N3   C2   aromatic  1.347  0.020  1.347
 OFD  N3   C6   aromatic  1.380  0.020  1.380
 OFD  C2   C3   aromatic  1.394  0.020  1.394
 OFD  O2   C14  double    1.218  0.020  1.218
 OFD  N1   C4   single    1.400  0.020  1.400
 OFD  C10  C9   aromatic  1.386  0.020  1.386
 OFD  C10  C11  aromatic  1.392  0.020  1.392
 OFD  C6   C5   aromatic  1.364  0.020  1.364
 OFD  C22  C16  single    1.503  0.020  1.503
 OFD  C22  C23  single    1.510  0.020  1.510
 OFD  C3   C4   single    1.422  0.020  1.422
 OFD  C3   C5   aromatic  1.431  0.020  1.431
 OFD  C9   C8   aromatic  1.391  0.020  1.391
 OFD  C14  C11  single    1.490  0.020  1.490
 OFD  C14  N5   single    1.359  0.020  1.359
 OFD  C4   O1   double    1.223  0.020  1.223
 OFD  O3   C23  double    1.209  0.020  1.209
 OFD  C17  C16  aromatic  1.392  0.020  1.392
 OFD  C17  C18  aromatic  1.382  0.020  1.382
 OFD  C16  C15  aromatic  1.400  0.020  1.400
 OFD  C5   C7   single    1.495  0.020  1.495
 OFD  C23  O4   single    1.319  0.020  1.319
 OFD  C11  C12  aromatic  1.396  0.020  1.396
 OFD  C18  C19  aromatic  1.393  0.020  1.393
 OFD  C15  N5   single    1.403  0.020  1.403
 OFD  C15  C20  aromatic  1.389  0.020  1.389
 OFD  C8   C7   single    1.509  0.020  1.509
 OFD  C8   C13  aromatic  1.393  0.020  1.393
 OFD  C19  C20  aromatic  1.391  0.020  1.391
 OFD  C19  C21  single    1.428  0.020  1.428
 OFD  C12  C13  aromatic  1.384  0.020  1.384
 OFD  C21  N6   triple    1.152  0.020  1.152
 OFD  C6   H1   single    0.930  0.020  1.080
 OFD  C7   H2   single    0.970  0.020  1.090
 OFD  C7   H3   single    0.970  0.020  1.090
 OFD  C9   H4   single    0.930  0.020  1.080
 OFD  C10  H5   single    0.930  0.020  1.080
 OFD  C12  H6   single    0.930  0.020  1.080
 OFD  C13  H7   single    0.930  0.020  1.080
 OFD  C17  H8   single    0.930  0.020  1.080
 OFD  C18  H9   single    0.930  0.020  1.080
 OFD  C20  H10  single    0.930  0.020  1.080
 OFD  C22  H11  single    0.970  0.020  1.090
 OFD  C22  H12  single    0.970  0.020  1.090
 OFD  N1   H13  single    0.860  0.020  1.020
 OFD  N3   H14  single    0.860  0.020  1.020
 OFD  N4   H15  single    0.890  0.020  1.040
 OFD  N4   H16  single    0.890  0.020  1.040
 OFD  N5   H17  single    0.860  0.020  1.020
 OFD  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
 OFD  N4   C1   N2   120.10  3.000
 OFD  N2   C1   N1   123.05  3.000
 OFD  N4   C1   N1   116.82  3.000
 OFD  N3   C2   N2   124.76  3.000
 OFD  N3   C2   C3   107.61  3.000
 OFD  N2   C2   C3   127.63  3.000
 OFD  C5   C3   C4   134.23  3.000
 OFD  C5   C3   C2   107.68  3.000
 OFD  C4   C3   C2   118.06  3.000
 OFD  N1   C4   C3   111.72  3.000
 OFD  C3   C4   O1   128.54  3.000
 OFD  N1   C4   O1   119.74  3.000
 OFD  C7   C5   C6   126.65  3.000
 OFD  C7   C5   C3   127.44  3.000
 OFD  C6   C5   C3   105.86  3.000
 OFD  H1   C6   N3   120.63  3.000
 OFD  H1   C6   C5   130.04  3.000
 OFD  N3   C6   C5   109.33  3.000
 OFD  H3   C7   H2   106.72  3.000
 OFD  H3   C7   C8   109.36  3.000
 OFD  H2   C7   C8   108.87  3.000
 OFD  H3   C7   C5   110.45  3.000
 OFD  H2   C7   C5   109.02  3.000
 OFD  C8   C7   C5   112.26  3.000
 OFD  C13  C8   C9   118.38  3.000
 OFD  C13  C8   C7   120.12  3.000
 OFD  C9   C8   C7   121.49  3.000
 OFD  H4   C9   C10  119.53  3.000
 OFD  H4   C9   C8   119.59  3.000
 OFD  C10  C9   C8   120.88  3.000
 OFD  H5   C10  C11  119.81  3.000
 OFD  H5   C10  C9   119.59  3.000
 OFD  C11  C10  C9   120.59  3.000
 OFD  C14  C11  C12  123.16  3.000
 OFD  C12  C11  C10  118.71  3.000
 OFD  C14  C11  C10  118.11  3.000
 OFD  H6   C12  C13  118.18  3.000
 OFD  H6   C12  C11  121.40  3.000
 OFD  C13  C12  C11  120.38  3.000
 OFD  H7   C13  C12  119.30  3.000
 OFD  H7   C13  C8   119.65  3.000
 OFD  C12  C13  C8   121.05  3.000
 OFD  N5   C14  C11  115.48  3.000
 OFD  N5   C14  O2   122.58  3.000
 OFD  C11  C14  O2   121.93  3.000
 OFD  N5   C15  C20  120.26  3.000
 OFD  C20  C15  C16  120.11  3.000
 OFD  N5   C15  C16  119.62  3.000
 OFD  C22  C16  C17  119.11  3.000
 OFD  C17  C16  C15  118.97  3.000
 OFD  C22  C16  C15  121.90  3.000
 OFD  H8   C17  C18  119.22  3.000
 OFD  H8   C17  C16  119.23  3.000
 OFD  C18  C17  C16  121.54  3.000
 OFD  H9   C18  C19  120.59  3.000
 OFD  H9   C18  C17  120.61  3.000
 OFD  C19  C18  C17  118.80  3.000
 OFD  C21  C19  C20  119.36  3.000
 OFD  C21  C19  C18  119.83  3.000
 OFD  C20  C19  C18  120.81  3.000
 OFD  H10  C20  C19  119.83  3.000
 OFD  H10  C20  C15  120.41  3.000
 OFD  C19  C20  C15  119.75  3.000
 OFD  N6   C21  C19  180.00  3.000
 OFD  H12  C22  H11  106.34  3.000
 OFD  H12  C22  C23  106.70  3.000
 OFD  H11  C22  C23  110.04  3.000
 OFD  H12  C22  C16  110.10  3.000
 OFD  H11  C22  C16  110.06  3.000
 OFD  C23  C22  C16  113.32  3.000
 OFD  O4   C23  C22  112.48  3.000
 OFD  O4   C23  O3   123.62  3.000
 OFD  C22  C23  O3   123.87  3.000
 OFD  H13  N1   C4   115.89  3.000
 OFD  H13  N1   C1   118.49  3.000
 OFD  C4   N1   C1   125.61  3.000
 OFD  C2   N2   C1   113.91  3.000
 OFD  H14  N3   C6   125.37  3.000
 OFD  H14  N3   C2   125.10  3.000
 OFD  C6   N3   C2   109.53  3.000
 OFD  H17  N5   C15  115.67  3.000
 OFD  H17  N5   C14  119.53  3.000
 OFD  C15  N5   C14  124.74  3.000
 OFD  H18  O4   C23  110.29  3.000
 OFD  H16  N4   H15  115.87  3.000
 OFD  H16  N4   C1   117.08  3.000
 OFD  H15  N4   C1   120.43  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
 OFD  CONST_01  C5   C6   N3   C2      0.00   0.0  0
 OFD  CONST_02  C6   C5   C3   C2      0.00   0.0  0
 OFD  CONST_03  C6   N3   C2   C3      0.00   0.0  0
 OFD  CONST_04  N3   C6   C5   C3      0.00   0.0  0
 OFD  CONST_05  N3   C2   C3   C5      0.00   0.0  0
 OFD  CONST_06  C11  C10  C9   C8      0.00   0.0  0
 OFD  CONST_07  C11  C12  C13  C8      0.00   0.0  0
 OFD  CONST_08  C12  C11  C10  C9      0.00   0.0  0
 OFD  CONST_09  C12  C13  C8   C9      0.00   0.0  0
 OFD  CONST_10  C13  C8   C9   C10     0.00   0.0  0
 OFD  CONST_11  C13  C12  C11  C10     0.00   0.0  0
 OFD  CONST_12  C18  C17  C16  C15     0.00   0.0  0
 OFD  CONST_13  C18  C19  C20  C15     0.00   0.0  0
 OFD  CONST_14  C19  C18  C17  C16     0.00   0.0  0
 OFD  CONST_15  C19  C20  C15  C16     0.00   0.0  0
 OFD  CONST_16  C20  C15  C16  C17     0.00   0.0  0
 OFD  CONST_17  C20  C19  C18  C17     0.00   0.0  0
 OFD  CONST_18  C3   C4   N1   C1      0.00   0.0  0
 OFD  CONST_19  N1   C1   N2   C2      0.00   0.0  0
 OFD  CONST_20  N2   C1   N1   C4      0.00   0.0  0
 OFD  CONST_21  C7   C5   C3   C2    180.00   0.0  0
 OFD  CONST_22  C7   C5   C3   C4      0.00   0.0  0
 OFD  CONST_23  N3   C6   C5   C7    180.00   0.0  0
 OFD  CONST_24  C10  C9   C8   C7    180.00   0.0  0
 OFD  CONST_25  C12  C13  C8   C7    180.00   0.0  0
 OFD  CONST_26  C14  C11  C10  C9    180.00   0.0  0
 OFD  CONST_27  C14  C11  C12  C13   180.00   0.0  0
 OFD  CONST_28  C21  C19  C20  C15   180.00   0.0  0
 OFD  CONST_29  N5   C15  C16  C17   180.00   0.0  0
 OFD  CONST_30  C21  C19  C18  C17   180.00   0.0  0
 OFD  CONST_31  C22  C16  C17  C18   180.00   0.0  0
 OFD  CONST_32  N5   C15  C20  C19   180.00   0.0  0
 OFD  CONST_33  C22  C16  C15  C20   180.00   0.0  0
 OFD  CONST_34  C1   N1   C4   O1    180.00   0.0  0
 OFD  CONST_35  N4   C1   N2   C2    180.00   0.0  0
 OFD  CONST_36  N4   C1   N1   C4    180.00   0.0  0
 OFD  CONST_37  H1   C6   N3   C2    180.00   0.0  0
 OFD  CONST_38  H14  N3   C2   C3    180.00   0.0  0
 OFD  CONST_39  H5   C10  C9   C8    180.00   0.0  0
 OFD  CONST_40  H6   C12  C13  C8    180.00   0.0  0
 OFD  CONST_41  H7   C13  C8   C9    180.00   0.0  0
 OFD  CONST_42  H4   C9   C10  C11   180.00   0.0  0
 OFD  CONST_43  H8   C17  C16  C15   180.00   0.0  0
 OFD  CONST_44  H9   C18  C17  C16   180.00   0.0  0
 OFD  CONST_45  H10  C20  C15  C16   180.00   0.0  0
 OFD  CONST_46  H13  N1   C4   C3    180.00   0.0  0
 OFD  CONST_47  C15  N5   C14  C11   180.00   0.0  0
 OFD  CONST_52  H16  N4   C1   N1    180.00   0.0  0
 OFD  CONST_53  C15  N5   C14  O2      0.00   0.0  0
 OFD  CONST_54  H18  O4   C23  O3      0.00   0.0  0
 OFD  Var_01    C8   C7   C5   C3     74.98  30.0  2
 OFD  Var_02    C9   C8   C7   C5   -114.40  30.0  2
 OFD  Var_03    C10  C11  C14  O2    -19.97  30.0  2
 OFD  Var_04    C23  C22  C16  C15    76.69  30.0  2
 OFD  Var_05    C16  C22  C23  O3    -36.98  30.0  1

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
 OFD  plan-1  C7   0.020
 OFD  plan-1  C8   0.020
 OFD  plan-1  C9   0.020
 OFD  plan-1  C10  0.020
 OFD  plan-1  C11  0.020
 OFD  plan-1  C12  0.020
 OFD  plan-1  C13  0.020
 OFD  plan-1  C14  0.020
 OFD  plan-1  H4   0.020
 OFD  plan-1  H5   0.020
 OFD  plan-1  H6   0.020
 OFD  plan-1  H7   0.020
 OFD  plan-2  C15  0.020
 OFD  plan-2  C16  0.020
 OFD  plan-2  C17  0.020
 OFD  plan-2  C18  0.020
 OFD  plan-2  C19  0.020
 OFD  plan-2  C20  0.020
 OFD  plan-2  C21  0.020
 OFD  plan-2  C22  0.020
 OFD  plan-2  N5   0.020
 OFD  plan-2  N6   0.020
 OFD  plan-2  H8   0.020
 OFD  plan-2  H9   0.020
 OFD  plan-2  H10  0.020
 OFD  plan-3  O1   0.020
 OFD  plan-3  C1   0.020
 OFD  plan-3  C2   0.020
 OFD  plan-3  C3   0.020
 OFD  plan-3  C4   0.020
 OFD  plan-3  C5   0.020
 OFD  plan-3  C6   0.020
 OFD  plan-3  C7   0.020
 OFD  plan-3  N1   0.020
 OFD  plan-3  N2   0.020
 OFD  plan-3  N3   0.020
 OFD  plan-3  H1   0.020
 OFD  plan-3  H13  0.020
 OFD  plan-3  H14  0.020
 OFD  plan-3  H15  0.020
 OFD  plan-3  H16  0.020
 OFD  plan-3  N4   0.020
 OFD  plan-4  O2   0.020
 OFD  plan-4  C11  0.020
 OFD  plan-4  C14  0.020
 OFD  plan-4  C15  0.020
 OFD  plan-4  N5   0.020
 OFD  plan-4  H17  0.020
 OFD  plan-5  O3   0.020
 OFD  plan-5  C22  0.020
 OFD  plan-5  C23  0.020
 OFD  plan-5  O4   0.020
 OFD  plan-5  H18  0.020

