# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 18:40:45 2021
#   Inital geometry file: a 109 line input string
#   Ligand name: N-{[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)phenyl]methyl}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCc1ccc(cc1)c2ncnc3[nH]ccc23)c4ccccc4
#
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
 RQS  RQS  N-{[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)phenyl]methyl}benzamide  ligand  41  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RQS
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
 RQS  N1   N  N     0  -0.422  18.1125   -5.0995   0.4199
 RQS  N3   N  NH1   0  -0.654  12.7865   -9.1797   6.8291
 RQS  C4   C  CR56  0  -0.002  15.8847   -6.0505   0.6727
 RQS  C5   C  CR6   0   0.211  16.1218   -6.1712   2.0454
 RQS  C6   C  CR6   0   0.047  15.1391   -6.7249   2.9922
 RQS  C7   C  CR16  0  -0.269  15.5714   -7.4410   4.1063
 RQS  C8   C  CR16  0  -0.282  14.6608   -7.9846   4.9999
 RQS  C13  C  CR16  0  -0.298  14.3160  -10.8322   8.6511
 RQS  C15  C  CR16  0  -0.251  14.6946  -11.3652  10.9661
 RQS  C17  C  CR16  0  -0.270  13.5986   -9.3097  10.3673
 RQS  C20  C  CR16  0   0.025  18.2166   -5.2853   1.7235
 RQS  C1   C  CR56  0   0.496  16.9490   -5.4945  -0.0749
 RQS  C11  C  C     0   0.524  13.1620   -8.6654   8.0147
 RQS  C12  C  CR6   0  -0.025  13.6970   -9.6381   9.0167
 RQS  C14  C  CR16  0  -0.240  14.8147  -11.6893   9.6217
 RQS  C16  C  CR16  0  -0.242  14.0850  -10.1729  11.3365
 RQS  C18  C  CR16  0  -0.271  12.8622   -7.0743   3.7145
 RQS  C19  C  CR16  0  -0.301  13.7668   -6.5448   2.8112
 RQS  C2   C  CR15  0   0.009  15.3177   -5.9996  -1.4887
 RQS  C3   C  CR15  0  -0.471  14.8532   -6.3733  -0.2632
 RQS  C9   C  CR6   0   0.078  13.2946   -7.8076   4.8173
 RQS  N2   N  NR15  0  -0.659  16.5748   -5.4655  -1.3733
 RQS  N4   N  N     0  -0.444  17.2984   -5.7929   2.5415
 RQS  O1   O  O     0  -0.478  13.0670   -7.4747   8.2755
 RQS  H1   H  HNH1  0   0.414  12.8096  -10.1757   6.6880
 RQS  H2   H  HCR6  0   0.254  16.6309   -7.5872   4.2698
 RQS  H3   H  HCR6  0   0.246  15.0305   -8.5533   5.8431
 RQS  H4   H  HCH2  0   0.269  11.6723   -7.5559   6.1829
 RQS  H5   H  HCH2  0   0.279  11.5604   -8.9917   5.1943
 RQS  H7   H  HCR6  0   0.265  15.0782  -12.0374  11.7226
 RQS  H8   H  HCR6  0   0.261  13.1327   -8.3789  10.6619
 RQS  H9   H  HCR6  0   0.252  19.1536   -4.9890   2.1817
 RQS  H10  H  HCR6  0   0.265  15.3008  -12.6092   9.3247
 RQS  H11  H  HCR6  0   0.263  13.9911   -9.9129  12.3826
 RQS  H12  H  HCR6  0   0.255  11.8020   -6.9131   3.5572
 RQS  H13  H  HCR6  0   0.259  13.3958   -5.9641   1.9772
 RQS  H14  H  HCR5  0   0.296  14.8469   -6.0791  -2.4547
 RQS  H15  H  HCR5  0   0.262  13.8968   -6.8287  -0.0696
 RQS  H16  H  HNR5  0   0.419  17.1436   -5.1389  -2.1384
 RQS  C10  C  CH2   0  -0.330  12.2586   -8.3741   5.7607
 RQS  H6   H  HCR6  0   0.260  14.4406  -11.1011   7.6095

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
 RQS  C2   N2   aromatic  1.371  0.020  1.371
 RQS  C2   C3   aromatic  1.363  0.020  1.363
 RQS  N2   C1   aromatic  1.352  0.020  1.352
 RQS  C3   C4   aromatic  1.430  0.020  1.430
 RQS  C1   N1   aromatic  1.325  0.020  1.325
 RQS  C1   C4   aromatic  1.414  0.020  1.414
 RQS  N1   C20  aromatic  1.321  0.020  1.321
 RQS  C4   C5   aromatic  1.398  0.020  1.398
 RQS  C20  N4   aromatic  1.330  0.020  1.330
 RQS  C5   N4   aromatic  1.332  0.020  1.332
 RQS  C5   C6   single    1.473  0.020  1.473
 RQS  C19  C6   aromatic  1.396  0.020  1.396
 RQS  C19  C18  aromatic  1.384  0.020  1.384
 RQS  C6   C7   aromatic  1.393  0.020  1.393
 RQS  C18  C9   aromatic  1.393  0.020  1.393
 RQS  C7   C8   aromatic  1.387  0.020  1.387
 RQS  C9   C8   aromatic  1.390  0.020  1.390
 RQS  C9   C10  single    1.511  0.020  1.511
 RQS  C10  N3   single    1.438  0.020  1.438
 RQS  N3   C11  single    1.346  0.020  1.346
 RQS  C11  O1   double    1.223  0.020  1.223
 RQS  C11  C12  single    1.495  0.020  1.495
 RQS  C13  C12  aromatic  1.394  0.020  1.394
 RQS  C13  C14  aromatic  1.388  0.020  1.388
 RQS  C12  C17  aromatic  1.393  0.020  1.393
 RQS  C14  C15  aromatic  1.388  0.020  1.388
 RQS  C17  C16  aromatic  1.386  0.020  1.386
 RQS  C15  C16  aromatic  1.389  0.020  1.389
 RQS  N3   H1   single    0.860  0.020  1.020
 RQS  C7   H2   single    0.930  0.020  1.080
 RQS  C8   H3   single    0.930  0.020  1.080
 RQS  C10  H4   single    0.970  0.020  1.090
 RQS  C10  H5   single    0.970  0.020  1.090
 RQS  C13  H6   single    0.930  0.020  1.080
 RQS  C15  H7   single    0.930  0.020  1.080
 RQS  C17  H8   single    0.930  0.020  1.080
 RQS  C20  H9   single    0.930  0.020  1.080
 RQS  C14  H10  single    0.930  0.020  1.080
 RQS  C16  H11  single    0.930  0.020  1.080
 RQS  C18  H12  single    0.930  0.020  1.080
 RQS  C19  H13  single    0.930  0.020  1.080
 RQS  C2   H14  single    0.930  0.020  1.080
 RQS  C3   H15  single    0.930  0.020  1.080
 RQS  N2   H16  single    0.860  0.020  1.020

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
 RQS  C1   N1   C20  113.32  3.000
 RQS  H1   N3   C11  119.70  3.000
 RQS  H1   N3   C10  117.30  3.000
 RQS  C11  N3   C10  122.87  3.000
 RQS  C3   C4   C1   106.60  3.000
 RQS  C1   C4   C5   115.16  3.000
 RQS  C3   C4   C5   138.20  3.000
 RQS  N4   C5   C6   117.18  3.000
 RQS  C6   C5   C4   123.40  3.000
 RQS  N4   C5   C4   119.41  3.000
 RQS  C19  C6   C7   118.37  3.000
 RQS  C7   C6   C5   120.02  3.000
 RQS  C19  C6   C5   121.61  3.000
 RQS  H2   C7   C8   119.51  3.000
 RQS  H2   C7   C6   119.62  3.000
 RQS  C8   C7   C6   120.87  3.000
 RQS  H3   C8   C9   120.34  3.000
 RQS  H3   C8   C7   118.93  3.000
 RQS  C9   C8   C7   120.72  3.000
 RQS  H6   C13  C14  118.56  3.000
 RQS  H6   C13  C12  121.07  3.000
 RQS  C14  C13  C12  120.35  3.000
 RQS  H7   C15  C16  120.14  3.000
 RQS  H7   C15  C14  120.09  3.000
 RQS  C16  C15  C14  119.77  3.000
 RQS  H8   C17  C16  119.78  3.000
 RQS  H8   C17  C12  119.81  3.000
 RQS  C16  C17  C12  120.41  3.000
 RQS  H9   C20  N4   116.16  3.000
 RQS  H9   C20  N1   116.53  3.000
 RQS  N4   C20  N1   127.31  3.000
 RQS  N2   C1   C4   107.93  3.000
 RQS  C4   C1   N1   125.50  3.000
 RQS  N2   C1   N1   126.56  3.000
 RQS  O1   C11  C12  121.22  3.000
 RQS  C12  C11  N3   116.20  3.000
 RQS  O1   C11  N3   122.58  3.000
 RQS  C11  C12  C17  118.09  3.000
 RQS  C17  C12  C13  119.18  3.000
 RQS  C11  C12  C13  122.71  3.000
 RQS  H10  C14  C15  120.21  3.000
 RQS  H10  C14  C13  119.65  3.000
 RQS  C15  C14  C13  120.15  3.000
 RQS  H11  C16  C17  119.73  3.000
 RQS  H11  C16  C15  120.13  3.000
 RQS  C17  C16  C15  120.13  3.000
 RQS  H12  C18  C9   119.78  3.000
 RQS  H12  C18  C19  119.20  3.000
 RQS  C9   C18  C19  121.02  3.000
 RQS  H13  C19  C18  118.98  3.000
 RQS  H13  C19  C6   120.42  3.000
 RQS  C18  C19  C6   120.57  3.000
 RQS  H14  C2   N2   120.33  3.000
 RQS  H14  C2   C3   129.57  3.000
 RQS  N2   C2   C3   110.10  3.000
 RQS  H15  C3   C2   125.47  3.000
 RQS  H15  C3   C4   128.21  3.000
 RQS  C2   C3   C4   106.31  3.000
 RQS  C18  C9   C10  118.60  3.000
 RQS  C10  C9   C8   122.96  3.000
 RQS  C18  C9   C8   118.44  3.000
 RQS  H16  N2   C2   125.45  3.000
 RQS  H16  N2   C1   125.45  3.000
 RQS  C2   N2   C1   109.05  3.000
 RQS  C20  N4   C5   119.28  3.000
 RQS  H5   C10  H4   106.35  3.000
 RQS  H5   C10  C9   109.07  3.000
 RQS  H4   C10  C9   109.19  3.000
 RQS  H5   C10  N3   107.67  3.000
 RQS  H4   C10  N3   109.25  3.000
 RQS  C9   C10  N3   114.96  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
 RQS  CONST_01  C2   N2   C1   N1   180.00   0.0  0
 RQS  CONST_02  C3   C4   C1   N1   180.00   0.0  0
 RQS  CONST_03  C5   C4   C1   N1     0.00   0.0  0
 RQS  CONST_04  C5   N4   C20  N1     0.00   0.0  0
 RQS  CONST_05  N2   C2   C3   C4     0.00   0.0  0
 RQS  CONST_06  C2   N2   C1   C4     0.00   0.0  0
 RQS  CONST_07  C20  N1   C1   C4     0.00   0.0  0
 RQS  CONST_08  C20  N4   C5   C4     0.00   0.0  0
 RQS  CONST_11  C2   C3   C4   C5   180.00   0.0  0
 RQS  CONST_12  N2   C1   C4   C5   180.00   0.0  0
 RQS  CONST_13  C18  C19  C6   C5   180.00   0.0  0
 RQS  CONST_14  C8   C7   C6   C5   180.00   0.0  0
 RQS  CONST_15  C3   C4   C5   C6     0.00   0.0  0
 RQS  CONST_16  C1   C4   C5   C6   180.00   0.0  0
 RQS  CONST_17  C20  N4   C5   C6   180.00   0.0  0
 RQS  CONST_18  C9   C18  C19  C6     0.00   0.0  0
 RQS  CONST_19  C9   C8   C7   C6     0.00   0.0  0
 RQS  CONST_21  C18  C19  C6   C7     0.00   0.0  0
 RQS  CONST_22  C18  C9   C8   C7     0.00   0.0  0
 RQS  CONST_23  C19  C6   C7   C8     0.00   0.0  0
 RQS  CONST_24  C19  C18  C9   C8     0.00   0.0  0
 RQS  CONST_25  C16  C17  C12  C13    0.00   0.0  0
 RQS  CONST_26  C16  C15  C14  C13    0.00   0.0  0
 RQS  CONST_27  C12  C13  C14  C15    0.00   0.0  0
 RQS  CONST_28  C12  C17  C16  C15    0.00   0.0  0
 RQS  CONST_29  C14  C13  C12  C17    0.00   0.0  0
 RQS  CONST_30  C14  C15  C16  C17    0.00   0.0  0
 RQS  CONST_31  N2   C1   N1   C20  180.00   0.0  0
 RQS  CONST_32  C3   C2   N2   C1     0.00   0.0  0
 RQS  CONST_33  N4   C20  N1   C1     0.00   0.0  0
 RQS  CONST_34  C2   C3   C4   C1     0.00   0.0  0
 RQS  CONST_35  N4   C5   C4   C1     0.00   0.0  0
 RQS  CONST_37  N2   C1   C4   C3     0.00   0.0  0
 RQS  CONST_38  N4   C5   C4   C3   180.00   0.0  0
 RQS  CONST_39  C10  C9   C8   C7   180.00   0.0  0
 RQS  CONST_40  C19  C18  C9   C10  180.00   0.0  0
 RQS  CONST_41  C14  C13  C12  C11  180.00   0.0  0
 RQS  CONST_42  C16  C17  C12  C11  180.00   0.0  0
 RQS  CONST_43  H16  N2   C1   N1     0.00   0.0  0
 RQS  CONST_44  H14  C2   C3   C4   180.00   0.0  0
 RQS  CONST_45  H15  C3   C4   C5     0.00   0.0  0
 RQS  CONST_46  H9   C20  N4   C5   180.00   0.0  0
 RQS  CONST_47  H13  C19  C6   C5     0.00   0.0  0
 RQS  CONST_48  H2   C7   C6   C5     0.00   0.0  0
 RQS  CONST_49  H12  C18  C19  C6   180.00   0.0  0
 RQS  CONST_50  H3   C8   C7   C6   180.00   0.0  0
 RQS  CONST_51  H8   C17  C12  C13  180.00   0.0  0
 RQS  CONST_52  H7   C15  C14  C13  180.00   0.0  0
 RQS  CONST_53  H6   C13  C14  C15  180.00   0.0  0
 RQS  CONST_54  H10  C14  C13  C12  180.00   0.0  0
 RQS  CONST_55  H11  C16  C17  C12  180.00   0.0  0
 RQS  CONST_56  C12  C11  N3   C10  180.00   0.0  0
 RQS  CONST_57  H1   N3   C11  C12    0.00   0.0  0
 RQS  CONST_58  O1   C11  N3   C10    0.00   0.0  0
 RQS  Var_01    C18  C9   C10  N3   176.66  30.0  1
 RQS  Var_02    C13  C12  C11  N3    26.92  30.0  2
 RQS  Var_03    C9   C10  N3   C11   88.98  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
 RQS  plan-1  C13  0.020
 RQS  plan-1  C15  0.020
 RQS  plan-1  C17  0.020
 RQS  plan-1  C11  0.020
 RQS  plan-1  C12  0.020
 RQS  plan-1  C14  0.020
 RQS  plan-1  C16  0.020
 RQS  plan-1  H7   0.020
 RQS  plan-1  H8   0.020
 RQS  plan-1  H10  0.020
 RQS  plan-1  H11  0.020
 RQS  plan-1  H6   0.020
 RQS  plan-2  C5   0.020
 RQS  plan-2  C6   0.020
 RQS  plan-2  C7   0.020
 RQS  plan-2  C8   0.020
 RQS  plan-2  C18  0.020
 RQS  plan-2  C19  0.020
 RQS  plan-2  C9   0.020
 RQS  plan-2  H2   0.020
 RQS  plan-2  H3   0.020
 RQS  plan-2  H12  0.020
 RQS  plan-2  H13  0.020
 RQS  plan-2  C10  0.020
 RQS  plan-3  N1   0.020
 RQS  plan-3  C4   0.020
 RQS  plan-3  C5   0.020
 RQS  plan-3  C6   0.020
 RQS  plan-3  C20  0.020
 RQS  plan-3  C1   0.020
 RQS  plan-3  C2   0.020
 RQS  plan-3  C3   0.020
 RQS  plan-3  N2   0.020
 RQS  plan-3  N4   0.020
 RQS  plan-3  H9   0.020
 RQS  plan-3  H14  0.020
 RQS  plan-3  H15  0.020
 RQS  plan-3  H16  0.020
 RQS  plan-4  N3   0.020
 RQS  plan-4  C11  0.020
 RQS  plan-4  C12  0.020
 RQS  plan-4  O1   0.020
 RQS  plan-4  H1   0.020
 RQS  plan-4  C10  0.020

