# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 17:27:22 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)methyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]cc(Cc3ccc(cc3)C(=O)NCc4ccccc4C(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
 OF4  OF4  '2-[({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)methyl]benzoic 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_OF4
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
 OF4  C10  C  CR16  0  -0.280   0.5222  -0.0585  -0.8620
 OF4  C11  C  CR6   0  -0.045   0.8506  -1.0968   0.0053
 OF4  C21  C  CR16  0  -0.294   5.8373  -1.1868   0.3001
 OF4  C1   C  CR56  0   0.500  -5.6812  -0.5110   0.4531
 OF4  C12  C  CR16  0  -0.258  -0.0682  -2.1279   0.1951
 OF4  C13  C  CR16  0  -0.278  -1.2934  -2.1023  -0.4464
 OF4  C14  C  C     0   0.528   2.1683  -1.1778   0.7035
 OF4  C15  C  CH2   0  -0.407   4.0961   0.1073   1.5054
 OF4  C16  C  CR6   0   0.153   5.1457   0.0147   0.4202
 OF4  C17  C  CR6   0  -0.114   5.4656   1.0590  -0.4644
 OF4  C18  C  CR16  0  -0.249   6.4527   0.8653  -1.4337
 OF4  C19  C  CR16  0  -0.253   7.1149  -0.3452  -1.5466
 OF4  C2   C  CR56  0  -0.239  -4.5885  -0.0332  -0.2688
 OF4  C20  C  CR16  0  -0.229   6.8088  -1.3751  -0.6711
 OF4  C3   C  CR6   0   0.494  -4.1960   1.3201  -0.0752
 OF4  C4   C  CR6   0   0.671  -6.0550   1.3958   1.5334
 OF4  C5   C  CR5   0   0.034  -4.1207  -1.0959  -1.1043
 OF4  C6   C  CR15  0  -0.096  -4.9403  -2.1561  -0.8521
 OF4  C8   C  CR6   0   0.150  -1.6276  -1.0640  -1.3145
 OF4  C9   C  CR16  0  -0.299  -0.7031  -0.0457  -1.5131
 OF4  N1   N  N     0  -0.507  -6.4321   0.1605   1.3480
 OF4  N2   N  NR16  0  -0.721  -5.0004   1.9602   0.8754
 OF4  N3   N  NR15  0  -0.664  -5.8793  -1.7935   0.0913
 OF4  N5   N  NH1   0  -0.635   2.7508  -0.0020   0.9901
 OF4  O1   O  O     0  -0.474  -3.2917   1.9348  -0.6221
 OF4  O2   O  O     0  -0.488   2.6605  -2.2576   1.0056
 OF4  O3   O  OH1   0  -0.588   5.4516   3.3394  -0.9980
 OF4  O4   O  O     0  -0.446   3.6899   2.5631   0.1079
 OF4  H1   H  HCR6  0   0.246   1.2259   0.7397  -1.0668
 OF4  H2   H  HCR6  0   0.261   5.6060  -1.9927   0.9846
 OF4  H3   H  HCR6  0   0.255   0.1755  -2.9504   0.8549
 OF4  H4   H  HCR6  0   0.250  -2.0034  -2.9028  -0.2744
 OF4  H5   H  HCH2  0   0.273   4.2636  -0.6951   2.2223
 OF4  H6   H  HCH2  0   0.276   4.1717   1.0401   2.0602
 OF4  H7   H  HCR6  0   0.271   6.7045   1.6614  -2.1198
 OF4  H8   H  HCR6  0   0.267   7.8681  -0.4772  -2.3115
 OF4  H9   H  HCR6  0   0.267   7.3237  -2.3243  -0.7416
 OF4  H10  H  HCR5  0   0.281  -4.9329  -3.1504  -1.2685
 OF4  H11  H  HCH2  0   0.265  -3.0002  -1.9483  -2.6851
 OF4  H12  H  HCH2  0   0.258  -3.0112  -0.1968  -2.6887
 OF4  H13  H  HCR6  0   0.250  -0.9373   0.7661  -2.1894
 OF4  H14  H  HNR6  0   0.419  -4.7670   2.9243   1.0749
 OF4  H15  H  HNR5  0   0.409  -6.6036  -2.3925   0.4530
 OF4  H16  H  HNH2  0   0.408  -6.5987   3.1690   2.3950
 OF4  H17  H  HNH2  0   0.406  -7.5730   1.8291   2.7783
 OF4  H18  H  HNH1  0   0.409   2.3080   0.8592   0.7182
 OF4  H19  H  HOH1  0   0.489   4.9423   4.1634  -0.9720
 OF4  C7   C  CH2   0  -0.613  -2.9534  -1.0696  -2.0362
 OF4  N4   N  NH2   0  -0.833  -6.6887   2.1677   2.4380
 OF4  C22  C  C     0   0.521   4.7673   2.3699  -0.4074

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
 OF4  C20  C21  aromatic  1.387  0.020  1.387
 OF4  C20  C19  aromatic  1.386  0.020  1.386
 OF4  C21  C16  aromatic  1.392  0.020  1.392
 OF4  O2   C14  double    1.225  0.020  1.225
 OF4  C19  C18  aromatic  1.384  0.020  1.384
 OF4  C16  C15  single    1.513  0.020  1.513
 OF4  C16  C17  aromatic  1.405  0.020  1.405
 OF4  C15  N5   single    1.445  0.020  1.445
 OF4  O4   C22  double    1.210  0.020  1.210
 OF4  N4   C4   single    1.348  0.020  1.348
 OF4  C18  C17  aromatic  1.397  0.020  1.397
 OF4  C17  C22  single    1.486  0.020  1.486
 OF4  C22  O3   single    1.326  0.020  1.326
 OF4  C14  N5   single    1.343  0.020  1.343
 OF4  C14  C11  single    1.493  0.020  1.493
 OF4  C4   N2   single    1.365  0.020  1.365
 OF4  C4   N1   double    1.305  0.020  1.305
 OF4  N2   C3   single    1.400  0.020  1.400
 OF4  C11  C12  aromatic  1.394  0.020  1.394
 OF4  C11  C10  aromatic  1.392  0.020  1.392
 OF4  C12  C13  aromatic  1.383  0.020  1.383
 OF4  N1   C1   single    1.347  0.020  1.347
 OF4  C3   O1   double    1.223  0.020  1.223
 OF4  C3   C2   single    1.422  0.020  1.422
 OF4  C10  C9   aromatic  1.388  0.020  1.388
 OF4  C13  C8   aromatic  1.394  0.020  1.394
 OF4  C1   C2   aromatic  1.394  0.020  1.394
 OF4  C1   N3   aromatic  1.347  0.020  1.347
 OF4  C2   C5   aromatic  1.430  0.020  1.430
 OF4  C9   C8   aromatic  1.390  0.020  1.390
 OF4  C8   C7   single    1.509  0.020  1.509
 OF4  N3   C6   aromatic  1.380  0.020  1.380
 OF4  C5   C6   aromatic  1.364  0.020  1.364
 OF4  C5   C7   single    1.494  0.020  1.494
 OF4  C10  H1   single    0.930  0.020  1.080
 OF4  C21  H2   single    0.930  0.020  1.080
 OF4  C12  H3   single    0.930  0.020  1.080
 OF4  C13  H4   single    0.930  0.020  1.080
 OF4  C15  H5   single    0.970  0.020  1.090
 OF4  C15  H6   single    0.970  0.020  1.090
 OF4  C18  H7   single    0.930  0.020  1.080
 OF4  C19  H8   single    0.930  0.020  1.080
 OF4  C20  H9   single    0.930  0.020  1.080
 OF4  C6   H10  single    0.930  0.020  1.080
 OF4  C7   H11  single    0.970  0.020  1.090
 OF4  C7   H12  single    0.970  0.020  1.090
 OF4  C9   H13  single    0.930  0.020  1.080
 OF4  N2   H14  single    0.860  0.020  1.020
 OF4  N3   H15  single    0.860  0.020  1.020
 OF4  N4   H16  single    0.890  0.020  1.040
 OF4  N4   H17  single    0.890  0.020  1.040
 OF4  N5   H18  single    0.860  0.020  1.020
 OF4  O3   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
 OF4  H1   C10  C9   118.56  3.000
 OF4  H1   C10  C11  120.92  3.000
 OF4  C9   C10  C11  120.49  3.000
 OF4  C14  C11  C12  118.54  3.000
 OF4  C12  C11  C10  118.75  3.000
 OF4  C14  C11  C10  122.67  3.000
 OF4  H2   C21  C20  119.45  3.000
 OF4  H2   C21  C16  118.83  3.000
 OF4  C20  C21  C16  121.73  3.000
 OF4  N3   C1   N1   124.81  3.000
 OF4  N3   C1   C2   107.60  3.000
 OF4  N1   C1   C2   127.58  3.000
 OF4  H3   C12  C13  119.76  3.000
 OF4  H3   C12  C11  119.78  3.000
 OF4  C13  C12  C11  120.46  3.000
 OF4  H4   C13  C8   119.47  3.000
 OF4  H4   C13  C12  119.54  3.000
 OF4  C8   C13  C12  120.99  3.000
 OF4  O2   C14  N5   123.02  3.000
 OF4  N5   C14  C11  115.78  3.000
 OF4  O2   C14  C11  121.19  3.000
 OF4  H6   C15  H5   106.58  3.000
 OF4  H6   C15  N5   108.15  3.000
 OF4  H5   C15  N5   108.80  3.000
 OF4  H6   C15  C16  111.72  3.000
 OF4  H5   C15  C16  108.69  3.000
 OF4  N5   C15  C16  112.69  3.000
 OF4  C17  C16  C15  124.33  3.000
 OF4  C17  C16  C21  118.31  3.000
 OF4  C15  C16  C21  117.36  3.000
 OF4  C18  C17  C16  119.64  3.000
 OF4  C18  C17  C22  118.74  3.000
 OF4  C16  C17  C22  121.62  3.000
 OF4  H7   C18  C19  118.75  3.000
 OF4  H7   C18  C17  120.20  3.000
 OF4  C19  C18  C17  121.05  3.000
 OF4  H8   C19  C20  120.66  3.000
 OF4  H8   C19  C18  119.83  3.000
 OF4  C20  C19  C18  119.51  3.000
 OF4  C5   C2   C3   134.12  3.000
 OF4  C5   C2   C1   107.71  3.000
 OF4  C3   C2   C1   118.16  3.000
 OF4  H9   C20  C19  120.37  3.000
 OF4  H9   C20  C21  119.88  3.000
 OF4  C19  C20  C21  119.76  3.000
 OF4  O1   C3   N2   119.92  3.000
 OF4  O1   C3   C2   128.44  3.000
 OF4  N2   C3   C2   111.65  3.000
 OF4  N4   C4   N2   116.74  3.000
 OF4  N2   C4   N1   123.11  3.000
 OF4  N4   C4   N1   120.12  3.000
 OF4  C7   C5   C6   126.77  3.000
 OF4  C7   C5   C2   127.36  3.000
 OF4  C6   C5   C2   105.85  3.000
 OF4  H10  C6   N3   120.74  3.000
 OF4  H10  C6   C5   129.91  3.000
 OF4  N3   C6   C5   109.34  3.000
 OF4  C9   C8   C7   121.25  3.000
 OF4  C7   C8   C13  120.37  3.000
 OF4  C9   C8   C13  118.38  3.000
 OF4  H13  C9   C8   119.67  3.000
 OF4  H13  C9   C10  119.42  3.000
 OF4  C8   C9   C10  120.91  3.000
 OF4  C4   N1   C1   113.89  3.000
 OF4  H14  N2   C4   118.51  3.000
 OF4  H14  N2   C3   115.91  3.000
 OF4  C4   N2   C3   125.59  3.000
 OF4  H15  N3   C6   125.37  3.000
 OF4  H15  N3   C1   125.13  3.000
 OF4  C6   N3   C1   109.50  3.000
 OF4  H18  N5   C15  116.20  3.000
 OF4  H18  N5   C14  120.06  3.000
 OF4  C15  N5   C14  123.11  3.000
 OF4  H19  O3   C22  109.79  3.000
 OF4  H12  C7   H11  106.60  3.000
 OF4  H12  C7   C8   109.23  3.000
 OF4  H11  C7   C8   108.93  3.000
 OF4  H12  C7   C5   110.22  3.000
 OF4  H11  C7   C5   108.82  3.000
 OF4  C8   C7   C5   112.84  3.000
 OF4  H17  N4   H16  115.34  3.000
 OF4  H17  N4   C4   116.59  3.000
 OF4  H16  N4   C4   119.95  3.000
 OF4  O4   C22  O3   122.19  3.000
 OF4  O3   C22  C17  112.67  3.000
 OF4  O4   C22  C17  125.14  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
 OF4  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 OF4  CONST_02  C13  C8   C9   C10     0.00   0.0  0
 OF4  CONST_03  C8   C13  C12  C11     0.00   0.0  0
 OF4  CONST_04  C8   C9   C10  C11     0.00   0.0  0
 OF4  CONST_05  C18  C19  C20  C21     0.00   0.0  0
 OF4  CONST_06  C18  C17  C16  C21     0.00   0.0  0
 OF4  CONST_07  C6   C5   C2   C1      0.00   0.0  0
 OF4  CONST_08  C5   C6   N3   C1      0.00   0.0  0
 OF4  CONST_09  C9   C10  C11  C12     0.00   0.0  0
 OF4  CONST_10  C9   C8   C13  C12     0.00   0.0  0
 OF4  CONST_11  C19  C20  C21  C16     0.00   0.0  0
 OF4  CONST_12  C19  C18  C17  C16     0.00   0.0  0
 OF4  CONST_13  C20  C21  C16  C17     0.00   0.0  0
 OF4  CONST_14  C20  C19  C18  C17     0.00   0.0  0
 OF4  CONST_15  C6   N3   C1   C2      0.00   0.0  0
 OF4  CONST_16  N3   C6   C5   C2      0.00   0.0  0
 OF4  CONST_17  N3   C1   C2   C5      0.00   0.0  0
 OF4  CONST_18  N2   C4   N1   C1      0.00   0.0  0
 OF4  CONST_19  C4   N2   C3   C2      0.00   0.0  0
 OF4  CONST_20  N1   C4   N2   C3      0.00   0.0  0
 OF4  CONST_21  C7   C8   C9   C10   180.00   0.0  0
 OF4  CONST_22  C22  C17  C16  C21   180.00   0.0  0
 OF4  CONST_23  C19  C18  C17  C22   180.00   0.0  0
 OF4  CONST_24  C7   C5   C2   C1    180.00   0.0  0
 OF4  CONST_25  C7   C8   C13  C12   180.00   0.0  0
 OF4  CONST_26  C14  C11  C12  C13   180.00   0.0  0
 OF4  CONST_27  C9   C10  C11  C14   180.00   0.0  0
 OF4  CONST_28  C20  C21  C16  C15   180.00   0.0  0
 OF4  CONST_29  C18  C17  C16  C15   180.00   0.0  0
 OF4  CONST_30  C7   C5   C2   C3      0.00   0.0  0
 OF4  CONST_31  N3   C6   C5   C7    180.00   0.0  0
 OF4  CONST_32  N4   C4   N1   C1    180.00   0.0  0
 OF4  CONST_33  N4   C4   N2   C3    180.00   0.0  0
 OF4  CONST_34  O1   C3   N2   C4    180.00   0.0  0
 OF4  CONST_35  H3   C12  C11  C10   180.00   0.0  0
 OF4  CONST_36  H4   C13  C12  C11   180.00   0.0  0
 OF4  CONST_37  H13  C9   C10  C11   180.00   0.0  0
 OF4  CONST_38  H8   C19  C20  C21   180.00   0.0  0
 OF4  CONST_39  H10  C6   N3   C1    180.00   0.0  0
 OF4  CONST_40  H1   C10  C11  C12   180.00   0.0  0
 OF4  CONST_41  H9   C20  C21  C16   180.00   0.0  0
 OF4  CONST_42  H7   C18  C17  C16   180.00   0.0  0
 OF4  CONST_43  H2   C21  C16  C17   180.00   0.0  0
 OF4  CONST_44  H15  N3   C1   C2    180.00   0.0  0
 OF4  CONST_45  H14  N2   C3   C2    180.00   0.0  0
 OF4  CONST_47  H17  N4   C4   N1      0.00   0.0  0
 OF4  CONST_48  C15  N5   C14  C11   180.00   0.0  0
 OF4  CONST_49  H18  N5   C14  C11     0.00   0.0  0
 OF4  CONST_50  H19  O3   C22  C17   180.00   0.0  0
 OF4  CONST_51  O2   C14  N5   C15     0.00   0.0  0
 OF4  Var_01    C5   C7   C8   C13    58.93  30.0  2
 OF4  Var_02    C8   C7   C5   C2     71.67  30.0  2
 OF4  Var_03    O2   C14  C11  C10  -150.48  30.0  2
 OF4  Var_04    N5   C15  C16  C21  -103.37  30.0  2
 OF4  Var_05    O4   C22  C17  C16   -20.14  30.0  2
 OF4  Var_06    C16  C15  N5   C14    81.34  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
 OF4  plan-1  C10  0.020
 OF4  plan-1  C11  0.020
 OF4  plan-1  C12  0.020
 OF4  plan-1  C13  0.020
 OF4  plan-1  C14  0.020
 OF4  plan-1  C8   0.020
 OF4  plan-1  C9   0.020
 OF4  plan-1  H1   0.020
 OF4  plan-1  H3   0.020
 OF4  plan-1  H4   0.020
 OF4  plan-1  H13  0.020
 OF4  plan-1  C7   0.020
 OF4  plan-2  C21  0.020
 OF4  plan-2  C15  0.020
 OF4  plan-2  C16  0.020
 OF4  plan-2  C17  0.020
 OF4  plan-2  C18  0.020
 OF4  plan-2  C19  0.020
 OF4  plan-2  C20  0.020
 OF4  plan-2  H2   0.020
 OF4  plan-2  H7   0.020
 OF4  plan-2  H8   0.020
 OF4  plan-2  H9   0.020
 OF4  plan-2  C22  0.020
 OF4  plan-3  C1   0.020
 OF4  plan-3  C2   0.020
 OF4  plan-3  C3   0.020
 OF4  plan-3  C4   0.020
 OF4  plan-3  C5   0.020
 OF4  plan-3  C6   0.020
 OF4  plan-3  N1   0.020
 OF4  plan-3  N2   0.020
 OF4  plan-3  N3   0.020
 OF4  plan-3  O1   0.020
 OF4  plan-3  H10  0.020
 OF4  plan-3  H14  0.020
 OF4  plan-3  H15  0.020
 OF4  plan-3  H16  0.020
 OF4  plan-3  H17  0.020
 OF4  plan-3  C7   0.020
 OF4  plan-3  N4   0.020
 OF4  plan-4  C11  0.020
 OF4  plan-4  C14  0.020
 OF4  plan-4  C15  0.020
 OF4  plan-4  N5   0.020
 OF4  plan-4  O2   0.020
 OF4  plan-4  H18  0.020
 OF4  plan-5  C17  0.020
 OF4  plan-5  O3   0.020
 OF4  plan-5  O4   0.020
 OF4  plan-5  H19  0.020
 OF4  plan-5  C22  0.020

