# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 07:24:15 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: ~{N}-[6-(phenylmethyl)-7,8-dihydro-5~{H}-pyrido[4,3-d]pyrimidin-2-yl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1ncc2CN(CCc2n1)Cc3ccccc3
#
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
 QWK  QWK  "~{N}-[6-(phenylmethyl)-7,8-dihydro-5~{H}-pyrido[4,3-d]pyrimidin-2-yl]propanamide"
  ligand  42  22  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_QWK
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
 QWK  C2   C  CR6   0   0.576  -22.5616  14.2789  13.1665
 QWK  C8   C  CH2   0  -0.326  -28.8008  14.9233  12.7186
 QWK  C9   C  CR6   0   0.091  -29.7948  14.1372  13.5326
 QWK  C10  C  CR16  0  -0.285  -29.6474  14.0383  14.9153
 QWK  C11  C  CR16  0  -0.240  -30.5675  13.3320  15.6749
 QWK  C12  C  CR16  0  -0.269  -31.6500  12.7095  15.0625
 QWK  C13  C  CR16  0  -0.239  -31.8031  12.7999  13.6868
 QWK  C14  C  CR16  0  -0.308  -30.8778  13.5084  12.9286
 QWK  C15  C  C     0  -0.302  -27.1379  13.1831  12.5329
 QWK  C16  C  C     0  -0.512  -25.8375  12.6980  13.1512
 QWK  N18  N  N     0  -0.475  -23.5075  13.3520  13.2623
 QWK  C19  C  C     0   0.544  -20.0727  14.4325  13.4201
 QWK  C20  C  CH2   0  -0.589  -18.9326  13.4896  13.7497
 QWK  C21  C  CH3   0  -0.657  -17.5646  14.1407  13.6741
 QWK  N1   N  NH1   0  -0.720  -21.2898  13.7948  13.4152
 QWK  N3   N  N     0  -0.419  -22.7481  15.5534  12.8657
 QWK  C4   C  CR16  0  -0.037  -24.0048  15.9157  12.6452
 QWK  C5   C  CR66  0  -0.059  -25.0774  15.0443  12.7138
 QWK  C6   C  C     0  -0.310  -26.4897  15.4745  12.4472
 QWK  N7   N  NR6   0  -0.427  -27.4347  14.5263  12.9981
 QWK  C17  C  CR66  0   0.278  -24.7590  13.7275  13.0361
 QWK  O22  O  O     0  -0.430  -19.9167  15.6109  13.1952
 QWK  H1   H  HCH2  0   0.254  -28.8971  15.9846  12.9682
 QWK  H2   H  HCH2  0   0.219  -29.0477  14.8363  11.6477
 QWK  H3   H  HCR6  0   0.243  -28.8019  14.5146  15.3965
 QWK  H4   H  HCR6  0   0.251  -30.4417  13.2654  16.7482
 QWK  H5   H  HCR6  0   0.252  -32.3673  12.1568  15.6555
 QWK  H6   H  HCR6  0   0.252  -32.6395  12.3150  13.1997
 QWK  H7   H  HCR6  0   0.248  -30.9989  13.5686  11.8531
 QWK  H8   H  H     0   0.211  -27.0755  13.1425  11.4325
 QWK  H9   H  H     0   0.257  -27.9454  12.5122  12.8270
 QWK  H10  H  H     0   0.266  -25.9929  12.4783  14.2116
 QWK  H11  H  H     0   0.261  -25.5092  11.7684  12.6831
 QWK  H12  H  HCH2  0   0.270  -18.9841  12.6301  13.0744
 QWK  H13  H  HCH2  0   0.274  -19.1070  13.0827  14.7508
 QWK  H14  H  HCH3  0   0.236  -16.7945  13.4105  13.9193
 QWK  H15  H  HCH3  0   0.230  -17.3539  14.5204  12.6750
 QWK  H16  H  HCH3  0   0.230  -17.4714  14.9688  14.3753
 QWK  H17  H  HNH1  0   0.415  -21.2805  12.8074  13.6277
 QWK  H18  H  HCR6  0   0.269  -24.1647  16.9628  12.4044
 QWK  H19  H  H     0   0.259  -26.6648  16.4566  12.8952
 QWK  H20  H  H     0   0.221  -26.6257  15.6013  11.3584

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
 QWK  C15  C16  single    1.519  0.020  1.519
 QWK  C15  N7   single    1.452  0.020  1.452
 QWK  C8   N7   single    1.450  0.020  1.450
 QWK  C8   C9   single    1.506  0.020  1.506
 QWK  C6   C5   single    1.500  0.020  1.500
 QWK  C6   N7   single    1.448  0.020  1.448
 QWK  C14  C9   aromatic  1.390  0.020  1.390
 QWK  C14  C13  aromatic  1.390  0.020  1.390
 QWK  C5   C4   aromatic  1.384  0.020  1.384
 QWK  C5   C17  aromatic  1.393  0.020  1.393
 QWK  C4   N3   aromatic  1.326  0.020  1.326
 QWK  C17  C16  single    1.495  0.020  1.495
 QWK  C17  N18  aromatic  1.326  0.020  1.326
 QWK  N3   C2   aromatic  1.323  0.020  1.323
 QWK  N18  C2   aromatic  1.328  0.020  1.328
 QWK  C2   N1   single    1.383  0.020  1.383
 QWK  O22  C19  double    1.210  0.020  1.210
 QWK  N1   C19  single    1.374  0.020  1.374
 QWK  C21  C20  single    1.517  0.020  1.517
 QWK  C19  C20  single    1.516  0.020  1.516
 QWK  C9   C10  aromatic  1.394  0.020  1.394
 QWK  C13  C12  aromatic  1.387  0.020  1.387
 QWK  C10  C11  aromatic  1.387  0.020  1.387
 QWK  C12  C11  aromatic  1.391  0.020  1.391
 QWK  C8   H1   single    0.970  0.020  1.090
 QWK  C8   H2   single    0.970  0.020  1.090
 QWK  C10  H3   single    0.930  0.020  1.080
 QWK  C11  H4   single    0.930  0.020  1.080
 QWK  C12  H5   single    0.930  0.020  1.080
 QWK  C13  H6   single    0.930  0.020  1.080
 QWK  C14  H7   single    0.930  0.020  1.080
 QWK  C15  H8   single    0.970  0.020  1.090
 QWK  C15  H9   single    0.970  0.020  1.090
 QWK  C16  H10  single    0.970  0.020  1.090
 QWK  C16  H11  single    0.970  0.020  1.090
 QWK  C20  H12  single    0.970  0.020  1.090
 QWK  C20  H13  single    0.970  0.020  1.090
 QWK  C21  H14  single    0.970  0.020  1.090
 QWK  C21  H15  single    0.970  0.020  1.090
 QWK  C21  H16  single    0.970  0.020  1.090
 QWK  N1   H17  single    0.860  0.020  1.020
 QWK  C4   H18  single    0.930  0.020  1.080
 QWK  C6   H19  single    0.970  0.020  1.090
 QWK  C6   H20  single    0.970  0.020  1.090

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
 QWK  N3   C2   N1   120.51  3.000
 QWK  N1   C2   N18  113.43  3.000
 QWK  N3   C2   N18  126.06  3.000
 QWK  H2   C8   H1   106.16  3.000
 QWK  H2   C8   N7   112.13  3.000
 QWK  H1   C8   N7   107.72  3.000
 QWK  H2   C8   C9   109.63  3.000
 QWK  H1   C8   C9   108.96  3.000
 QWK  N7   C8   C9   112.01  3.000
 QWK  C14  C9   C10  118.76  3.000
 QWK  C10  C9   C8   120.22  3.000
 QWK  C14  C9   C8   121.02  3.000
 QWK  H3   C10  C11  119.90  3.000
 QWK  H3   C10  C9   119.47  3.000
 QWK  C11  C10  C9   120.62  3.000
 QWK  H4   C11  C12  119.96  3.000
 QWK  H4   C11  C10  119.82  3.000
 QWK  C12  C11  C10  120.21  3.000
 QWK  H5   C12  C13  120.23  3.000
 QWK  H5   C12  C11  120.20  3.000
 QWK  C13  C12  C11  119.57  3.000
 QWK  H6   C13  C14  119.81  3.000
 QWK  H6   C13  C12  120.15  3.000
 QWK  C14  C13  C12  120.04  3.000
 QWK  H7   C14  C13  119.68  3.000
 QWK  H7   C14  C9   119.53  3.000
 QWK  C13  C14  C9   120.79  3.000
 QWK  H9   C15  H8   106.77  3.000
 QWK  H9   C15  N7   109.36  3.000
 QWK  H8   C15  N7   111.43  3.000
 QWK  H9   C15  C16  109.12  3.000
 QWK  H8   C15  C16  110.23  3.000
 QWK  N7   C15  C16  109.87  3.000
 QWK  H11  C16  H10  106.70  3.000
 QWK  H11  C16  C17  109.66  3.000
 QWK  H10  C16  C17  108.38  3.000
 QWK  H11  C16  C15  110.79  3.000
 QWK  H10  C16  C15  109.70  3.000
 QWK  C17  C16  C15  111.48  3.000
 QWK  C17  N18  C2   117.53  3.000
 QWK  O22  C19  N1   124.45  3.000
 QWK  N1   C19  C20  112.22  3.000
 QWK  O22  C19  C20  123.33  3.000
 QWK  H13  C20  H12  105.37  3.000
 QWK  H13  C20  C21  110.41  3.000
 QWK  H12  C20  C21  110.42  3.000
 QWK  H13  C20  C19  108.07  3.000
 QWK  H12  C20  C19  108.61  3.000
 QWK  C21  C20  C19  113.60  3.000
 QWK  H16  C21  H15  107.99  3.000
 QWK  H16  C21  H14  107.72  3.000
 QWK  H15  C21  H14  107.66  3.000
 QWK  H16  C21  C20  111.81  3.000
 QWK  H15  C21  C20  111.70  3.000
 QWK  H14  C21  C20  109.80  3.000
 QWK  H17  N1   C19  116.41  3.000
 QWK  H17  N1   C2   112.86  3.000
 QWK  C19  N1   C2   130.73  3.000
 QWK  C4   N3   C2   115.76  3.000
 QWK  H18  C4   C5   120.26  3.000
 QWK  H18  C4   N3   116.08  3.000
 QWK  C5   C4   N3   123.66  3.000
 QWK  C17  C5   C6   121.84  3.000
 QWK  C17  C5   C4   115.45  3.000
 QWK  C6   C5   C4   122.71  3.000
 QWK  H20  C6   H19  106.32  3.000
 QWK  H20  C6   N7   111.71  3.000
 QWK  H19  C6   N7   109.13  3.000
 QWK  H20  C6   C5   108.91  3.000
 QWK  H19  C6   C5   109.60  3.000
 QWK  N7   C6   C5   111.04  3.000
 QWK  C6   N7   C15  110.52  3.000
 QWK  C6   N7   C8   111.25  3.000
 QWK  C15  N7   C8   112.59  3.000
 QWK  C5   C17  N18  121.53  3.000
 QWK  N18  C17  C16  118.20  3.000
 QWK  C5   C17  C16  120.26  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
 QWK  CONST_01  C5   C4   N3   C2      0.00   0.0  0
 QWK  CONST_02  C5   C17  N18  C2      0.00   0.0  0
 QWK  CONST_03  C12  C13  C14  C9      0.00   0.0  0
 QWK  CONST_04  C12  C11  C10  C9      0.00   0.0  0
 QWK  CONST_05  C13  C14  C9   C10     0.00   0.0  0
 QWK  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 QWK  CONST_07  C14  C9   C10  C11     0.00   0.0  0
 QWK  CONST_08  C14  C13  C12  C11     0.00   0.0  0
 QWK  CONST_09  C4   C5   C17  N18     0.00   0.0  0
 QWK  CONST_10  C4   N3   C2   N18     0.00   0.0  0
 QWK  CONST_11  C17  C5   C4   N3      0.00   0.0  0
 QWK  CONST_12  C17  N18  C2   N3      0.00   0.0  0
 QWK  CONST_13  C13  C14  C9   C8    180.00   0.0  0
 QWK  CONST_14  C11  C10  C9   C8    180.00   0.0  0
 QWK  CONST_15  C4   N3   C2   N1    180.00   0.0  0
 QWK  CONST_16  C17  N18  C2   N1    180.00   0.0  0
 QWK  CONST_17  H18  C4   N3   C2    180.00   0.0  0
 QWK  CONST_18  H6   C13  C14  C9    180.00   0.0  0
 QWK  CONST_19  H4   C11  C10  C9    180.00   0.0  0
 QWK  CONST_20  H7   C14  C9   C10   180.00   0.0  0
 QWK  CONST_21  H5   C12  C11  C10   180.00   0.0  0
 QWK  CONST_22  H6   C13  C12  C11   180.00   0.0  0
 QWK  CONST_23  H7   C14  C13  C12   180.00   0.0  0
 QWK  CONST_24  H3   C10  C11  C12   180.00   0.0  0
 QWK  CONST_25  H4   C11  C12  C13   180.00   0.0  0
 QWK  CONST_26  H3   C10  C9   C14   180.00   0.0  0
 QWK  CONST_27  H5   C12  C13  C14   180.00   0.0  0
 QWK  CONST_28  H18  C4   C5   C6      0.00   0.0  0
 QWK  CONST_29  H18  C4   C5   C17   180.00   0.0  0
 QWK  CONST_30  C19  N1   C2   N18   180.00   0.0  0
 QWK  CONST_31  N3   C2   N1   C19     0.00   0.0  0
 QWK  CONST_32  H17  N1   C2   N18     0.00   0.0  0
 QWK  CONST_33  H17  N1   C2   N3    180.00   0.0  0
 QWK  CONST_34  O22  C19  N1   C2      0.00   0.0  0
 QWK  CONST_35  C20  C19  N1   C2    180.00   0.0  0
 QWK  CONST_36  H17  N1   C19  C20     0.00   0.0  0
 QWK  CONST_37  H17  N1   C19  O22   180.00   0.0  0
 QWK  Var_01    C5   C17  C16  C15    15.04  30.0  1
 QWK  Var_02    N18  C17  C16  C15  -165.66  30.0  1
 QWK  Var_03    C5   C6   N7   C15   -52.96  30.0  1
 QWK  Var_04    C6   N7   C15  C16    69.13  30.0  1
 QWK  Var_05    N7   C6   C5   C4   -161.19  30.0  1
 QWK  Var_06    C17  C16  C15  N7    -47.69  30.0  1
 QWK  Var_07    C17  C5   C6   N7     19.46  30.0  1
 QWK  Var_08    C16  C15  N7   C8   -165.79  30.0  1
 QWK  Var_09    C5   C6   N7   C8   -178.80  30.0  1
 QWK  Var_10    C15  N7   C8   C9     68.15  30.0  3
 QWK  Var_11    C6   N7   C8   C9   -167.17  30.0  3
 QWK  Var_12    N7   C8   C9   C10    51.49  30.0  2
 QWK  Var_13    N7   C8   C9   C14  -129.07  30.0  2
 QWK  Var_14    H19  C6   N7   C15  -173.89  30.0  1
 QWK  Var_15    H20  C6   N7   C15    68.84  30.0  1
 QWK  Var_16    H10  C16  C17  N18    73.52  30.0  1
 QWK  Var_17    H11  C16  C17  N18   -42.60  30.0  1
 QWK  Var_18    H19  C6   C5   C4    -40.54  30.0  1
 QWK  Var_19    H20  C6   C5   C4     75.39  30.0  1
 QWK  Var_20    H10  C16  C17  C5   -105.78  30.0  1
 QWK  Var_21    H11  C16  C17  C5    138.10  30.0  1
 QWK  Var_22    H8   C15  N7   C6    -53.34  30.0  1
 QWK  Var_23    H9   C15  N7   C6   -171.13  30.0  1
 QWK  Var_24    H10  C16  C15  N7     72.36  30.0  1
 QWK  Var_25    H11  C16  C15  N7   -170.10  30.0  1
 QWK  Var_26    H19  C6   C5   C17   140.11  30.0  1
 QWK  Var_27    H20  C6   C5   C17  -103.96  30.0  1
 QWK  Var_28    H8   C15  C16  C17    75.48  30.0  1
 QWK  Var_29    H9   C15  C16  C17  -167.57  30.0  1
 QWK  Var_30    H8   C15  N7   C8     71.74  30.0  1
 QWK  Var_31    H9   C15  N7   C8    -46.05  30.0  1
 QWK  Var_32    H19  C6   N7   C8     60.28  30.0  1
 QWK  Var_33    H20  C6   N7   C8    -57.00  30.0  1
 QWK  Var_34    H1   C8   C9   C10   -67.59  30.0  2
 QWK  Var_35    H2   C8   C9   C10   176.62  30.0  2
 QWK  Var_36    H1   C8   C9   C14   111.86  30.0  2
 QWK  Var_37    H2   C8   C9   C14    -3.93  30.0  2
 QWK  Var_38    H1   C8   N7   C15  -172.05  30.0  2
 QWK  Var_39    H2   C8   N7   C15   -55.60  30.0  2
 QWK  Var_40    H1   C8   N7   C6    -47.37  30.0  2
 QWK  Var_41    H2   C8   N7   C6     69.08  30.0  2
 QWK  Var_42    O22  C19  C20  C21    -4.13  30.0  1
 QWK  Var_43    N1   C19  C20  C21   176.19  30.0  1
 QWK  Var_44    H14  C21  C20  C19  -179.89  30.0  3
 QWK  Var_45    H15  C21  C20  C19   -60.54  30.0  3
 QWK  Var_46    H16  C21  C20  C19    60.62  30.0  3
 QWK  Var_47    H12  C20  C19  N1     52.91  30.0  3
 QWK  Var_48    H13  C20  C19  N1    -60.92  30.0  3
 QWK  Var_49    H12  C20  C19  O22  -127.42  30.0  3
 QWK  Var_50    H13  C20  C19  O22   118.76  30.0  3

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
 QWK  plan-1  C8   0.020
 QWK  plan-1  C9   0.020
 QWK  plan-1  C10  0.020
 QWK  plan-1  C11  0.020
 QWK  plan-1  C12  0.020
 QWK  plan-1  C13  0.020
 QWK  plan-1  C14  0.020
 QWK  plan-1  H3   0.020
 QWK  plan-1  H4   0.020
 QWK  plan-1  H5   0.020
 QWK  plan-1  H6   0.020
 QWK  plan-1  H7   0.020
 QWK  plan-2  C2   0.020
 QWK  plan-2  C19  0.020
 QWK  plan-2  C20  0.020
 QWK  plan-2  N1   0.020
 QWK  plan-2  O22  0.020
 QWK  plan-2  H17  0.020
 QWK  plan-3  C2   0.020
 QWK  plan-3  C16  0.020
 QWK  plan-3  N18  0.020
 QWK  plan-3  N1   0.020
 QWK  plan-3  N3   0.020
 QWK  plan-3  C4   0.020
 QWK  plan-3  C5   0.020
 QWK  plan-3  C6   0.020
 QWK  plan-3  C17  0.020
 QWK  plan-3  H18  0.020

