# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 01:34:56 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: (7R)-2-amino-7-[4-fluoro-2-(6-methoxypyridin-2-yl)phenyl]-4-methyl-7,8-dihydropyrido[4,3-d]pyrimidin-5(6H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(n1)c2cc(F)ccc2[C@H]3Cc4nc(N)nc(C)c4C(=O)N3
#
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
 990  990  (7R)-2-amino-7-[4-fluoro-2-(6-methoxypyridin-2-yl)phenyl]-4-methyl-7,8-dihydropyrido[4,3-d]pyrimidin-5(6H)-one  ligand  46  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_990
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
 990  F17  F  F     0  -0.314   0.6803  -4.8151   0.6648
 990  C16  C  CR6   0   0.541   0.5575  -3.4821   0.7590
 990  C18  C  CR16  0  -0.455   1.4775  -2.6817   0.1143
 990  C8   C  CR6   0   0.077   1.3736  -1.2958   0.2056
 990  C21  C  CR6   0   0.161   2.4009  -0.4992  -0.5117
 990  N26  N  N     0  -0.476   3.0241   0.4627   0.1764
 990  C25  C  CR6   0   0.522   3.9517   1.1758  -0.4213
 990  O27  O  O2    0  -0.471   4.5788   2.1389   0.2549
 990  C28  C  CH3   0  -0.420   4.1949   2.3730   1.6024
 990  C24  C  CR16  0  -0.388   4.3329   0.9808  -1.7556
 990  C23  C  CR16  0  -0.147   3.6864  -0.0094  -2.4590
 990  C22  C  CR16  0  -0.341   2.6983  -0.7705  -1.8363
 990  C19  C  CR16  0  -0.403  -0.4715  -2.9472   1.5006
 990  C20  C  CR16  0  -0.296  -0.5713  -1.5651   1.5823
 990  C7   C  CR6   0   0.106   0.3283  -0.7174   0.9466
 990  C6   C  CH1   0  -0.182   0.1543   0.7964   1.0108
 990  N9   N  NH1   0  -0.634  -0.8302   1.2243   1.9776
 990  C1   C  C     0   0.489  -2.1597   1.3153   1.7475
 990  O2   O  O     0  -0.479  -2.9397   1.6377   2.6358
 990  C5   C  CH2   0  -0.537  -0.2294   1.3802  -0.3476
 990  C4   C  CR6   0   0.321  -1.6492   1.0482  -0.6709
 990  N15  N  N     0  -0.480  -1.9634   0.8319  -1.9316
 990  C13  C  CR6   0   0.552  -3.2508   0.5596  -2.1812
 990  N14  N  NH2   0  -0.815  -3.5943   0.3433  -3.4535
 990  N12  N  N     0  -0.480  -4.2206   0.4710  -1.2623
 990  C10  C  CR6   0   0.303  -3.9057   0.6970   0.0019
 990  C3   C  CR6   0  -0.231  -2.5848   1.0091   0.3673
 990  C11  C  CH3   0  -0.723  -5.0325   0.5733   0.9782
 990  H1   H  HCR6  0   0.281   2.2885  -3.1343  -0.4422
 990  H2   H  HCH3  0   0.231   3.1489   2.6741   1.6791
 990  H3   H  HCH3  0   0.231   4.3516   1.4935   2.2278
 990  H4   H  HCH3  0   0.249   4.8272   3.1834   1.9553
 990  H5   H  HCR6  0   0.276   5.1020   1.5928  -2.2065
 990  H6   H  HCR6  0   0.277   3.9399  -0.1917  -3.4948
 990  H7   H  HCR6  0   0.273   2.1674  -1.5407  -2.3779
 990  H8   H  HCR6  0   0.282  -1.1839  -3.5850   2.0063
 990  H9   H  HCR6  0   0.268  -1.3805  -1.1557   2.1698
 990  H10  H  HCH1  0   0.303   1.1025   1.2356   1.3133
 990  H11  H  HNH1  0   0.400  -0.5223   1.3994   2.9226
 990  H12  H  HCH2  0   0.290  -0.1227   2.4691  -0.3073
 990  H13  H  HCH2  0   0.276   0.4249   1.0259  -1.1423
 990  H14  H  HNH2  0   0.404  -2.9158   0.4413  -4.1878
 990  H15  H  HNH2  0   0.404  -4.5521   0.1676  -3.7001
 990  H16  H  HCH3  0   0.260  -5.2959   1.5452   1.3940
 990  H17  H  HCH3  0   0.246  -5.9033   0.1616   0.4735
 990  H18  H  HCH3  0   0.251  -4.7699  -0.0686   1.8172

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
 990  O2   C1   double    1.225  0.020  1.225
 990  C19  C20  aromatic  1.388  0.020  1.388
 990  C19  C16  aromatic  1.377  0.020  1.377
 990  C20  C7   aromatic  1.390  0.020  1.390
 990  C1   N9   single    1.352  0.020  1.352
 990  C1   C3   single    1.476  0.020  1.476
 990  C11  C10  single    1.496  0.020  1.496
 990  N9   C6   single    1.445  0.020  1.445
 990  F17  C16  single    1.342  0.020  1.342
 990  C10  C3   aromatic  1.406  0.020  1.406
 990  C10  N12  aromatic  1.322  0.020  1.322
 990  C3   C4   aromatic  1.398  0.020  1.398
 990  C16  C18  aromatic  1.379  0.020  1.379
 990  C7   C6   single    1.525  0.020  1.525
 990  C7   C8   aromatic  1.406  0.020  1.406
 990  N12  C13  aromatic  1.339  0.020  1.339
 990  C4   C5   single    1.494  0.020  1.494
 990  C4   N15  aromatic  1.317  0.020  1.317
 990  C5   C6   single    1.528  0.020  1.528
 990  C13  N15  aromatic  1.339  0.020  1.339
 990  C13  N14  single    1.336  0.020  1.336
 990  C18  C8   aromatic  1.393  0.020  1.393
 990  C8   C21  single    1.485  0.020  1.485
 990  C21  N26  aromatic  1.337  0.020  1.337
 990  C21  C22  aromatic  1.384  0.020  1.384
 990  N26  C25  aromatic  1.314  0.020  1.314
 990  C22  C23  aromatic  1.394  0.020  1.394
 990  C28  O27  single    1.421  0.020  1.421
 990  C25  O27  single    1.333  0.020  1.333
 990  C25  C24  aromatic  1.401  0.020  1.401
 990  C23  C24  aromatic  1.376  0.020  1.376
 990  C18  H1   single    0.930  0.020  1.080
 990  C28  H2   single    0.970  0.020  1.090
 990  C28  H3   single    0.970  0.020  1.090
 990  C28  H4   single    0.970  0.020  1.090
 990  C24  H5   single    0.930  0.020  1.080
 990  C23  H6   single    0.930  0.020  1.080
 990  C22  H7   single    0.930  0.020  1.080
 990  C19  H8   single    0.930  0.020  1.080
 990  C20  H9   single    0.930  0.020  1.080
 990  C6   H10  single    0.970  0.020  1.090
 990  N9   H11  single    0.860  0.020  1.020
 990  C5   H12  single    0.970  0.020  1.090
 990  C5   H13  single    0.970  0.020  1.090
 990  N14  H14  single    0.860  0.020  1.020
 990  N14  H15  single    0.860  0.020  1.020
 990  C11  H16  single    0.970  0.020  1.090
 990  C11  H17  single    0.970  0.020  1.090
 990  C11  H18  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
 990  C19  C16  C18  121.66  3.000
 990  C18  C16  F17  118.85  3.000
 990  C19  C16  F17  119.49  3.000
 990  H1   C18  C8   120.37  3.000
 990  H1   C18  C16  119.82  3.000
 990  C8   C18  C16  119.80  3.000
 990  C7   C8   C21  123.25  3.000
 990  C21  C8   C18  116.78  3.000
 990  C7   C8   C18  119.97  3.000
 990  C22  C21  N26  122.23  3.000
 990  C22  C21  C8   120.38  3.000
 990  N26  C21  C8   117.39  3.000
 990  C25  N26  C21  119.05  3.000
 990  C24  C25  O27  117.10  3.000
 990  C24  C25  N26  123.34  3.000
 990  O27  C25  N26  119.56  3.000
 990  C28  O27  C25  118.23  3.000
 990  H4   C28  H3   109.37  3.000
 990  H4   C28  H2   109.21  3.000
 990  H3   C28  H2   108.66  3.000
 990  H4   C28  O27  105.89  3.000
 990  H3   C28  O27  111.86  3.000
 990  H2   C28  O27  111.79  3.000
 990  H5   C24  C23  121.89  3.000
 990  H5   C24  C25  120.78  3.000
 990  C23  C24  C25  117.33  3.000
 990  H6   C23  C22  120.12  3.000
 990  H6   C23  C24  120.04  3.000
 990  C22  C23  C24  119.84  3.000
 990  H7   C22  C23  120.88  3.000
 990  H7   C22  C21  120.90  3.000
 990  C23  C22  C21  118.21  3.000
 990  H8   C19  C20  120.81  3.000
 990  H8   C19  C16  121.00  3.000
 990  C20  C19  C16  118.19  3.000
 990  H9   C20  C7   120.15  3.000
 990  H9   C20  C19  117.59  3.000
 990  C7   C20  C19  122.26  3.000
 990  C6   C7   C20  120.81  3.000
 990  C6   C7   C8   121.03  3.000
 990  C20  C7   C8   118.12  3.000
 990  H10  C6   C5   108.17  3.000
 990  H10  C6   N9   106.75  3.000
 990  C5   C6   N9   108.11  3.000
 990  H10  C6   C7   108.24  3.000
 990  C5   C6   C7   111.75  3.000
 990  N9   C6   C7   113.58  3.000
 990  H11  N9   C1   116.59  3.000
 990  H11  N9   C6   118.05  3.000
 990  C1   N9   C6   125.17  3.000
 990  C3   C1   O2   123.30  3.000
 990  C3   C1   N9   115.35  3.000
 990  O2   C1   N9   121.34  3.000
 990  H13  C5   H12  106.98  3.000
 990  H13  C5   C4   109.93  3.000
 990  H12  C5   C4   108.77  3.000
 990  H13  C5   C6   111.95  3.000
 990  H12  C5   C6   108.84  3.000
 990  C4   C5   C6   110.26  3.000
 990  C3   C4   N15  123.13  3.000
 990  N15  C4   C5   118.07  3.000
 990  C3   C4   C5   118.79  3.000
 990  C13  N15  C4   116.17  3.000
 990  N12  C13  N14  117.18  3.000
 990  N14  C13  N15  117.24  3.000
 990  N12  C13  N15  125.57  3.000
 990  H15  N14  H14  118.79  3.000
 990  H15  N14  C13  120.49  3.000
 990  H14  N14  C13  120.45  3.000
 990  C10  N12  C13  118.19  3.000
 990  C11  C10  C3   123.81  3.000
 990  C3   C10  N12  120.68  3.000
 990  C11  C10  N12  115.49  3.000
 990  C10  C3   C4   116.23  3.000
 990  C4   C3   C1   119.72  3.000
 990  C10  C3   C1   124.04  3.000
 990  H18  C11  H17  109.13  3.000
 990  H18  C11  H16  106.87  3.000
 990  H17  C11  H16  108.74  3.000
 990  H18  C11  C10  111.72  3.000
 990  H17  C11  C10  109.37  3.000
 990  H16  C11  C10  110.94  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
 990  CONST_01  C7   C20  C19  C16     0.00   0.0  0
 990  CONST_02  C7   C8   C18  C16     0.00   0.0  0
 990  CONST_03  C21  C8   C18  C16   180.00   0.0  0
 990  CONST_04  C20  C19  C16  C18     0.00   0.0  0
 990  CONST_05  C20  C7   C8   C18     0.00   0.0  0
 990  CONST_08  C19  C20  C7   C8      0.00   0.0  0
 990  CONST_09  C19  C16  C18  C8      0.00   0.0  0
 990  CONST_10  C25  N26  C21  C8    180.00   0.0  0
 990  CONST_11  C23  C22  C21  C8    180.00   0.0  0
 990  CONST_12  C20  C7   C8   C21   180.00   0.0  0
 990  CONST_13  C24  C25  N26  C21     0.00   0.0  0
 990  CONST_14  C24  C23  C22  C21     0.00   0.0  0
 990  CONST_16  C23  C22  C21  N26     0.00   0.0  0
 990  CONST_17  C23  C24  C25  N26     0.00   0.0  0
 990  CONST_18  C22  C21  N26  C25     0.00   0.0  0
 990  CONST_19  C22  C23  C24  C25     0.00   0.0  0
 990  CONST_21  N12  C10  C3   C4      0.00   0.0  0
 990  CONST_22  N12  C13  N15  C4      0.00   0.0  0
 990  CONST_23  C10  C3   C4   N15     0.00   0.0  0
 990  CONST_24  C10  N12  C13  N15     0.00   0.0  0
 990  CONST_25  C3   C10  N12  C13     0.00   0.0  0
 990  CONST_26  C3   C4   N15  C13     0.00   0.0  0
 990  CONST_27  C6   C7   C8   C18   180.00   0.0  0
 990  CONST_28  C6   C7   C8   C21     0.00   0.0  0
 990  CONST_29  C6   C7   C20  C19   180.00   0.0  0
 990  CONST_30  C3   C1   N9   C6      0.00   0.0  0
 990  CONST_31  C20  C19  C16  F17   180.00   0.0  0
 990  CONST_32  C8   C18  C16  F17   180.00   0.0  0
 990  CONST_33  O27  C25  N26  C21   180.00   0.0  0
 990  CONST_34  C23  C24  C25  O27   180.00   0.0  0
 990  CONST_35  C11  C10  C3   C1      0.00   0.0  0
 990  CONST_36  C11  C10  C3   C4    180.00   0.0  0
 990  CONST_37  N14  C13  N15  C4    180.00   0.0  0
 990  CONST_38  C11  C10  N12  C13   180.00   0.0  0
 990  CONST_39  C10  N12  C13  N14   180.00   0.0  0
 990  CONST_40  O2   C1   N9   C6    180.00   0.0  0
 990  CONST_41  H9   C20  C19  C16   180.00   0.0  0
 990  CONST_42  H8   C19  C16  C18   180.00   0.0  0
 990  CONST_43  H7   C22  C21  C8      0.00   0.0  0
 990  CONST_44  H1   C18  C8   C21     0.00   0.0  0
 990  CONST_45  H6   C23  C22  C21   180.00   0.0  0
 990  CONST_46  H5   C24  C25  N26   180.00   0.0  0
 990  CONST_47  H11  N9   C1   C3    180.00   0.0  0
 990  CONST_48  H14  N14  C13  N15     0.00   0.0  0
 990  CONST_49  H15  N14  C13  N15   180.00   0.0  0
 990  Var_01    C3   C4   C5   C6     35.45  30.0  1
 990  Var_02    C10  C3   C1   N9    162.31  30.0  1
 990  Var_03    C24  C25  O27  C28   178.92  30.0  1
 990  Var_04    H16  C11  C10  N12  -111.28  30.0  2
 990  Var_05    H2   C28  O27  C25   -61.42  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 990  chir_01  C6  N9  C7  C5  negativ

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
 990  plan-1  C8   0.020
 990  plan-1  C21  0.020
 990  plan-1  N26  0.020
 990  plan-1  C25  0.020
 990  plan-1  O27  0.020
 990  plan-1  C24  0.020
 990  plan-1  C23  0.020
 990  plan-1  C22  0.020
 990  plan-1  H5   0.020
 990  plan-1  H6   0.020
 990  plan-1  H7   0.020
 990  plan-2  F17  0.020
 990  plan-2  C16  0.020
 990  plan-2  C18  0.020
 990  plan-2  C8   0.020
 990  plan-2  C21  0.020
 990  plan-2  C19  0.020
 990  plan-2  C20  0.020
 990  plan-2  C7   0.020
 990  plan-2  C6   0.020
 990  plan-2  H1   0.020
 990  plan-2  H8   0.020
 990  plan-2  H9   0.020
 990  plan-3  C13  0.020
 990  plan-3  N14  0.020
 990  plan-3  H14  0.020
 990  plan-3  H15  0.020
 990  plan-4  C1   0.020
 990  plan-4  C5   0.020
 990  plan-4  C4   0.020
 990  plan-4  N15  0.020
 990  plan-4  C13  0.020
 990  plan-4  N14  0.020
 990  plan-4  N12  0.020
 990  plan-4  C10  0.020
 990  plan-4  C3   0.020
 990  plan-4  C11  0.020
 990  plan-5  C6   0.020
 990  plan-5  N9   0.020
 990  plan-5  C1   0.020
 990  plan-5  O2   0.020
 990  plan-5  C3   0.020
 990  plan-5  H11  0.020

