# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:46:32 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: 6-(2-methylpyridin-3-yl)-8-oxidanyl-3~{H}-quinazolin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncccc1c2cc(O)c3N=CNC(=O)c3c2
#
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
 7JM  7JM  6-(2-methylpyridin-3-yl)-8-oxidanyl-3~{H}-quinazolin-4-one  ligand  30  19  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7JM
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
 7JM  C4   C  CR6   0   0.313   1.2569   1.3884   0.8852
 7JM  C6   C  CR66  0  -0.076   1.6237  -0.4938  -0.5838
 7JM  C7   C  CR66  0   0.165   2.1544   0.5317   0.2100
 7JM  C13  C  CR6   0  -0.017  -2.0832  -0.0016  -0.1994
 7JM  C15  C  CR16  0  -0.326  -4.0070  -0.1639  -1.6300
 7JM  C1   C  CR16  0  -0.371   0.2461  -0.6756  -0.7129
 7JM  C2   C  CR6   0   0.057  -0.6226   0.1654  -0.0449
 7JM  C3   C  CR16  0  -0.415  -0.1037   1.1994   0.7475
 7JM  O5   O  OH1   0  -0.609   1.7921   2.3594   1.6382
 7JM  N8   N  N     0  -0.438   3.5037   0.7386   0.3628
 7JM  C9   C  CR16  0   0.142   4.2841  -0.0605  -0.2626
 7JM  N10  N  NR16  0  -0.660   3.8680  -1.0805  -1.0559
 7JM  C11  C  CR6   0   0.561   2.5462  -1.3863  -1.2831
 7JM  O12  O  O     0  -0.452   2.2204  -2.3151  -1.9992
 7JM  C14  C  CR16  0  -0.173  -2.6392  -0.0168  -1.4744
 7JM  C16  C  CR16  0  -0.073  -4.7754  -0.2902  -0.4860
 7JM  N17  N  N     0  -0.422  -4.2600  -0.2996   0.7367
 7JM  C18  C  CR6   0   0.219  -2.9463  -0.1639   0.8967
 7JM  C19  C  CH3   0  -0.745  -2.4412  -0.2327   2.3081
 7JM  H1   H  HCR6  0   0.270  -4.4647  -0.1760  -2.6094
 7JM  H2   H  HCR6  0   0.263  -0.1336  -1.4848  -1.3226
 7JM  H3   H  HCR6  0   0.280  -0.7841   1.8774   1.2508
 7JM  H4   H  HOH1  0   0.480   1.0972   2.8953   2.0376
 7JM  H5   H  HCR6  0   0.300   5.3584   0.0499  -0.1806
 7JM  H6   H  HNR6  0   0.433   4.5677  -1.6636  -1.4965
 7JM  H7   H  HCR6  0   0.270  -1.9992   0.0999  -2.3404
 7JM  H8   H  HCR6  0   0.263  -5.8524  -0.3959  -0.5565
 7JM  H9   H  HCH3  0   0.249  -1.5129  -0.7991   2.3798
 7JM  H10  H  HCH3  0   0.255  -2.2448   0.7601   2.7168
 7JM  H11  H  HCH3  0   0.257  -3.1887  -0.7044   2.9429

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
 7JM  C19  C18  single    1.501  0.020  1.501
 7JM  N17  C16  aromatic  1.327  0.020  1.327
 7JM  N17  C18  aromatic  1.330  0.020  1.330
 7JM  C16  C15  aromatic  1.384  0.020  1.384
 7JM  C18  C13  aromatic  1.404  0.020  1.404
 7JM  C15  C14  aromatic  1.384  0.020  1.384
 7JM  C13  C14  aromatic  1.391  0.020  1.391
 7JM  C13  C2   single    1.478  0.020  1.478
 7JM  C2   C1   aromatic  1.381  0.020  1.381
 7JM  C2   C3   aromatic  1.402  0.020  1.402
 7JM  C1   C6   aromatic  1.396  0.020  1.396
 7JM  C3   C4   aromatic  1.381  0.020  1.381
 7JM  C6   C11  single    1.462  0.020  1.462
 7JM  C6   C7   aromatic  1.401  0.020  1.401
 7JM  C4   C7   aromatic  1.413  0.020  1.413
 7JM  C4   O5   single    1.340  0.020  1.340
 7JM  O12  C11  double    1.217  0.020  1.217
 7JM  C11  N10  single    1.376  0.020  1.376
 7JM  C7   N8   single    1.374  0.020  1.374
 7JM  N10  C9   single    1.357  0.020  1.357
 7JM  N8   C9   double    1.280  0.020  1.280
 7JM  C15  H1   single    0.930  0.020  1.080
 7JM  C1   H2   single    0.930  0.020  1.080
 7JM  C3   H3   single    0.930  0.020  1.080
 7JM  O5   H4   single    0.850  0.020  0.980
 7JM  C9   H5   single    0.930  0.020  1.080
 7JM  N10  H6   single    0.860  0.020  1.020
 7JM  C14  H7   single    0.930  0.020  1.080
 7JM  C16  H8   single    0.930  0.020  1.080
 7JM  C19  H9   single    0.970  0.020  1.090
 7JM  C19  H10  single    0.970  0.020  1.090
 7JM  C19  H11  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
 7JM  O5   C4   C3   123.29  3.000
 7JM  O5   C4   C7   117.02  3.000
 7JM  C3   C4   C7   119.70  3.000
 7JM  C11  C6   C1   119.95  3.000
 7JM  C11  C6   C7   118.61  3.000
 7JM  C1   C6   C7   121.44  3.000
 7JM  N8   C7   C6   123.05  3.000
 7JM  N8   C7   C4   118.65  3.000
 7JM  C6   C7   C4   118.30  3.000
 7JM  C18  C13  C14  117.93  3.000
 7JM  C14  C13  C2   119.47  3.000
 7JM  C18  C13  C2   122.59  3.000
 7JM  H1   C15  C16  120.85  3.000
 7JM  H1   C15  C14  121.42  3.000
 7JM  C16  C15  C14  117.73  3.000
 7JM  H2   C1   C2   120.47  3.000
 7JM  H2   C1   C6   119.74  3.000
 7JM  C2   C1   C6   119.79  3.000
 7JM  C3   C2   C1   119.30  3.000
 7JM  C3   C2   C13  120.53  3.000
 7JM  C1   C2   C13  120.14  3.000
 7JM  H3   C3   C2   119.41  3.000
 7JM  H3   C3   C4   119.11  3.000
 7JM  C2   C3   C4   121.47  3.000
 7JM  H4   O5   C4   110.34  3.000
 7JM  C9   N8   C7   116.77  3.000
 7JM  H5   C9   N10  115.15  3.000
 7JM  H5   C9   N8   120.27  3.000
 7JM  N10  C9   N8   124.59  3.000
 7JM  H6   N10  C11  117.68  3.000
 7JM  H6   N10  C9   118.39  3.000
 7JM  C11  N10  C9   123.92  3.000
 7JM  O12  C11  N10  121.60  3.000
 7JM  N10  C11  C6   113.06  3.000
 7JM  O12  C11  C6   125.34  3.000
 7JM  H7   C14  C15  120.35  3.000
 7JM  H7   C14  C13  119.70  3.000
 7JM  C15  C14  C13  119.94  3.000
 7JM  H8   C16  N17  116.42  3.000
 7JM  H8   C16  C15  120.44  3.000
 7JM  N17  C16  C15  123.14  3.000
 7JM  C18  N17  C16  119.58  3.000
 7JM  C19  C18  N17  116.16  3.000
 7JM  N17  C18  C13  121.65  3.000
 7JM  C19  C18  C13  122.17  3.000
 7JM  H11  C19  H10  107.42  3.000
 7JM  H11  C19  H9   108.75  3.000
 7JM  H10  C19  H9   107.15  3.000
 7JM  H11  C19  C18  109.71  3.000
 7JM  H10  C19  C18  111.78  3.000
 7JM  H9   C19  C18  111.87  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
 7JM  CONST_01  C13  C2   C3   C4   180.00   0.0  0
 7JM  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 7JM  CONST_03  C1   C6   C7   C4     0.00   0.0  0
 7JM  CONST_04  C13  C2   C1   C6   180.00   0.0  0
 7JM  CONST_05  C3   C2   C1   C6     0.00   0.0  0
 7JM  CONST_06  C3   C4   C7   C6     0.00   0.0  0
 7JM  CONST_07  C2   C1   C6   C7     0.00   0.0  0
 7JM  CONST_08  C2   C3   C4   C7     0.00   0.0  0
 7JM  CONST_09  C16  N17  C18  C13    0.00   0.0  0
 7JM  CONST_10  C16  C15  C14  C13    0.00   0.0  0
 7JM  CONST_11  C18  N17  C16  C15    0.00   0.0  0
 7JM  CONST_12  C18  C13  C14  C15    0.00   0.0  0
 7JM  CONST_13  C2   C13  C14  C15  180.00   0.0  0
 7JM  CONST_16  N17  C18  C13  C2   180.00   0.0  0
 7JM  CONST_19  N17  C16  C15  C14    0.00   0.0  0
 7JM  CONST_20  N17  C18  C13  C14    0.00   0.0  0
 7JM  CONST_21  C9   N10  C11  C6     0.00   0.0  0
 7JM  CONST_22  N10  C9   N8   C7     0.00   0.0  0
 7JM  CONST_23  C11  N10  C9   N8     0.00   0.0  0
 7JM  CONST_24  O5   C4   C7   C6   180.00   0.0  0
 7JM  CONST_25  C19  C18  C13  C2     0.00   0.0  0
 7JM  CONST_26  O5   C4   C3   C2   180.00   0.0  0
 7JM  CONST_27  N8   C7   C4   O5     0.00   0.0  0
 7JM  CONST_28  C19  C18  C13  C14  180.00   0.0  0
 7JM  CONST_29  C19  C18  N17  C16  180.00   0.0  0
 7JM  CONST_30  O12  C11  N10  C9   180.00   0.0  0
 7JM  CONST_31  H2   C1   C6   C7   180.00   0.0  0
 7JM  CONST_32  H3   C3   C4   C7   180.00   0.0  0
 7JM  CONST_33  H1   C15  C14  C13  180.00   0.0  0
 7JM  CONST_34  H7   C14  C13  C2     0.00   0.0  0
 7JM  CONST_35  H8   C16  C15  C14  180.00   0.0  0
 7JM  CONST_36  H6   N10  C11  C6   180.00   0.0  0
 7JM  CONST_37  H5   C9   N8   C7   180.00   0.0  0
 7JM  Var_01    H9   C19  C18  C13  -39.02  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
 7JM  plan-1  C13  0.020
 7JM  plan-1  C15  0.020
 7JM  plan-1  C2   0.020
 7JM  plan-1  C14  0.020
 7JM  plan-1  C16  0.020
 7JM  plan-1  N17  0.020
 7JM  plan-1  C18  0.020
 7JM  plan-1  C19  0.020
 7JM  plan-1  H1   0.020
 7JM  plan-1  H7   0.020
 7JM  plan-1  H8   0.020
 7JM  plan-2  C4   0.020
 7JM  plan-2  C6   0.020
 7JM  plan-2  C7   0.020
 7JM  plan-2  C13  0.020
 7JM  plan-2  C1   0.020
 7JM  plan-2  C2   0.020
 7JM  plan-2  C3   0.020
 7JM  plan-2  O5   0.020
 7JM  plan-2  N8   0.020
 7JM  plan-2  C9   0.020
 7JM  plan-2  N10  0.020
 7JM  plan-2  C11  0.020
 7JM  plan-2  O12  0.020
 7JM  plan-2  H2   0.020
 7JM  plan-2  H3   0.020
 7JM  plan-2  H5   0.020
 7JM  plan-2  H6   0.020

