# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 04:08:19 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 1-methyl-3-oxidanyl-5-phenyl-pyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C=C(C=C(O)C1=O)c2ccccc2
#
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
 7JR  7JR  1-methyl-3-oxidanyl-5-phenyl-pyridin-2-one  ligand  26  15  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7JR
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
 7JR  N1    N  NR6   0  -0.507   1.8812  -1.1418   0.0473
 7JR  C4    C  CR16  0  -0.286   0.5292   1.2544   0.0381
 7JR  C5    C  CR6   0  -0.034  -0.1951   0.0286   0.0213
 7JR  C6    C  CR16  0  -0.012   0.5162  -1.1283   0.0313
 7JR  C7    C  CH3   0  -0.546   2.5408  -2.4433   0.0612
 7JR  C10   C  CR6   0   0.086  -1.6688   0.0147   0.0049
 7JR  C13   C  CR16  0  -0.267  -4.4713  -0.0114  -0.0045
 7JR  C15   C  CR16  0  -0.318  -2.3725  -0.9560  -0.7113
 7JR  C2    C  CR6   0   0.472   2.6348  -0.0012   0.0595
 7JR  C3    C  CR6   0   0.219   1.8836   1.2409   0.0586
 7JR  O8    O  O     0  -0.523   3.8685   0.0039   0.0683
 7JR  O9    O  OH1   0  -0.624   2.6101   2.3667   0.0645
 7JR  C11   C  CR16  0  -0.314  -2.3953   0.9768   0.7090
 7JR  C12   C  CR16  0  -0.239  -3.7825   0.9645   0.7035
 7JR  C14   C  CR16  0  -0.239  -3.7594  -0.9723  -0.7109
 7JR  H41   H  HCR6  0   0.275   0.0002   2.1995   0.0154
 7JR  H61   H  HCR6  0   0.299   0.0458  -2.1012   0.0481
 7JR  H71   H  HCH3  0   0.275   3.6147  -2.3110   0.1093
 7JR  H72   H  HCH3  0   0.267   2.2121  -3.0117   0.9286
 7JR  H73   H  HCH3  0   0.267   2.2900  -2.9938  -0.8432
 7JR  H131  H  HCR6  0   0.258  -5.5535  -0.0210  -0.0091
 7JR  H151  H  HCR6  0   0.253  -1.8339  -1.6956  -1.2907
 7JR  H91   H  HOH1  0   0.468   3.5467   2.1163   0.0638
 7JR  H111  H  HCR6  0   0.255  -1.8763   1.7350   1.2825
 7JR  H121  H  HCR6  0   0.258  -4.3263   1.7176   1.2591
 7JR  H141  H  HCR6  0   0.258  -4.2853  -1.7324  -1.2740

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
 7JR  C14  C13   aromatic  1.389  0.020  1.389
 7JR  C14  C15   aromatic  1.387  0.020  1.387
 7JR  C13  C12   aromatic  1.389  0.020  1.389
 7JR  C15  C10   aromatic  1.397  0.020  1.397
 7JR  C12  C11   aromatic  1.387  0.020  1.387
 7JR  C10  C11   aromatic  1.396  0.020  1.396
 7JR  C10  C5    single    1.474  0.020  1.474
 7JR  C5   C6    double    1.358  0.020  1.358
 7JR  C5   C4    single    1.424  0.020  1.424
 7JR  C6   N1    single    1.365  0.020  1.365
 7JR  C4   C3    double    1.355  0.020  1.355
 7JR  N1   C7    single    1.459  0.020  1.459
 7JR  N1   C2    single    1.367  0.020  1.367
 7JR  C3   C2    single    1.452  0.020  1.452
 7JR  C3   O9    single    1.340  0.020  1.340
 7JR  C2   O8    double    1.234  0.020  1.234
 7JR  C4   H41   single    0.930  0.020  1.080
 7JR  C6   H61   single    0.930  0.020  1.080
 7JR  C7   H71   single    0.970  0.020  1.090
 7JR  C7   H72   single    0.970  0.020  1.090
 7JR  C7   H73   single    0.970  0.020  1.090
 7JR  C13  H131  single    0.930  0.020  1.080
 7JR  C15  H151  single    0.930  0.020  1.080
 7JR  O9   H91   single    0.850  0.020  0.980
 7JR  C11  H111  single    0.930  0.020  1.080
 7JR  C12  H121  single    0.930  0.020  1.080
 7JR  C14  H141  single    0.930  0.020  1.080

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
 7JR  C2    N1   C7   119.66  3.000
 7JR  C2    N1   C6   122.89  3.000
 7JR  C7    N1   C6   117.45  3.000
 7JR  H41   C4   C3   119.81  3.000
 7JR  H41   C4   C5   120.16  3.000
 7JR  C3    C4   C5   120.01  3.000
 7JR  C10   C5   C6   121.05  3.000
 7JR  C6    C5   C4   117.83  3.000
 7JR  C10   C5   C4   121.12  3.000
 7JR  H61   C6   C5   122.61  3.000
 7JR  H61   C6   N1   115.22  3.000
 7JR  C5    C6   N1   122.16  3.000
 7JR  H73   C7   H72  109.19  3.000
 7JR  H73   C7   H71  109.10  3.000
 7JR  H72   C7   H71  109.14  3.000
 7JR  H73   C7   N1   109.83  3.000
 7JR  H72   C7   N1   109.70  3.000
 7JR  H71   C7   N1   109.86  3.000
 7JR  C11   C10  C15  118.39  3.000
 7JR  C11   C10  C5   120.54  3.000
 7JR  C15   C10  C5   121.07  3.000
 7JR  H131  C13  C14  120.28  3.000
 7JR  H131  C13  C12  120.29  3.000
 7JR  C14   C13  C12  119.43  3.000
 7JR  H151  C15  C14  119.31  3.000
 7JR  H151  C15  C10  119.89  3.000
 7JR  C14   C15  C10  120.79  3.000
 7JR  O8    C2   C3   120.93  3.000
 7JR  O8    C2   N1   123.69  3.000
 7JR  C3    C2   N1   115.38  3.000
 7JR  O9    C3   C2   116.00  3.000
 7JR  O9    C3   C4   122.27  3.000
 7JR  C2    C3   C4   121.73  3.000
 7JR  H91   O9   C3   107.87  3.000
 7JR  H111  C11  C12  119.17  3.000
 7JR  H111  C11  C10  120.01  3.000
 7JR  C12   C11  C10  120.81  3.000
 7JR  H121  C12  C11  119.62  3.000
 7JR  H121  C12  C13  120.10  3.000
 7JR  C11   C12  C13  120.28  3.000
 7JR  H141  C14  C15  119.60  3.000
 7JR  H141  C14  C13  120.09  3.000
 7JR  C15   C14  C13  120.30  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
 7JR  CONST_01  C13   C14  C15  C10     0.00   0.0  0
 7JR  CONST_02  C13   C12  C11  C10     0.00   0.0  0
 7JR  CONST_03  C12   C13  C14  C15     0.00   0.0  0
 7JR  CONST_04  C12   C11  C10  C15     0.00   0.0  0
 7JR  CONST_05  C14   C13  C12  C11     0.00   0.0  0
 7JR  CONST_06  C14   C15  C10  C11     0.00   0.0  0
 7JR  CONST_07  C14   C15  C10  C5    180.00   0.0  0
 7JR  CONST_08  C12   C11  C10  C5    180.00   0.0  0
 7JR  CONST_09  C3    C2   N1   C6      0.00   0.0  0
 7JR  CONST_10  O8    C2   N1   C6    180.00   0.0  0
 7JR  CONST_11  C3    C2   N1   C7    180.00   0.0  0
 7JR  CONST_12  H151  C15  C10  C5      0.00   0.0  0
 7JR  CONST_13  H111  C11  C10  C5      0.00   0.0  0
 7JR  CONST_14  H141  C14  C15  C10   180.00   0.0  0
 7JR  CONST_15  H121  C12  C11  C10   180.00   0.0  0
 7JR  CONST_16  H131  C13  C14  C15   180.00   0.0  0
 7JR  CONST_17  O8    C2   N1   C7      0.00   0.0  0
 7JR  Var_01    C15   C10  C5   C4    144.10  30.0  2
 7JR  Var_02    H71   C7   N1   C6   -177.96  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
 7JR  plan-1  N1    0.020
 7JR  plan-1  C4    0.020
 7JR  plan-1  C5    0.020
 7JR  plan-1  C6    0.020
 7JR  plan-1  C7    0.020
 7JR  plan-1  C10   0.020
 7JR  plan-1  C2    0.020
 7JR  plan-1  C3    0.020
 7JR  plan-1  O8    0.020
 7JR  plan-1  O9    0.020
 7JR  plan-1  H41   0.020
 7JR  plan-1  H61   0.020
 7JR  plan-2  C5    0.020
 7JR  plan-2  C10   0.020
 7JR  plan-2  C13   0.020
 7JR  plan-2  C15   0.020
 7JR  plan-2  C11   0.020
 7JR  plan-2  C12   0.020
 7JR  plan-2  C14   0.020
 7JR  plan-2  H131  0.020
 7JR  plan-2  H151  0.020
 7JR  plan-2  H111  0.020
 7JR  plan-2  H121  0.020
 7JR  plan-2  H141  0.020

