# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 23:45:36 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 1-benzyl-4-(benzyloxy)-3-bromopyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: BrC1=C(OCc2ccccc2)C=CN(Cc3ccccc3)C1=O
#
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
 P36  P36  1-benzyl-4-(benzyloxy)-3-bromopyridin-2(1H)-one  ligand  39  23  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P36
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
 P36  C1    C   CR16  0  -0.242  -5.6185   0.0253  -1.6675
 P36  C2    C   CR16  0  -0.262  -5.8486  -1.3317  -1.8509
 P36  C3    C   CR16  0  -0.242  -5.3367  -2.2465  -0.9397
 P36  C4    C   CR16  0  -0.306  -4.5964  -1.8027   0.1470
 P36  C5    C   CR6   0   0.152  -4.3539  -0.4439   0.3337
 P36  C6    C   CR16  0  -0.291  -4.8742   0.4667  -0.5816
 P36  C7    C   CH2   0  -0.451  -3.5274   0.0177   1.5053
 P36  N8    N   NR6   0  -0.506  -2.0900  -0.0428   1.2164
 P36  C9    C   CR6   0   0.606  -1.4959   1.0457   0.5789
 P36  C10   C   CR6   0  -0.457  -0.1058   0.8688   0.2762
 P36  C11   C   CR6   0   0.578   0.5938  -0.2769   0.5773
 P36  C12   C   CR16  0  -0.508  -0.0920  -1.3314   1.2306
 P36  C13   C   CR16  0   0.072  -1.4061  -1.1655   1.5179
 P36  O14   O   O     0  -0.491  -2.1469   2.0509   0.3217
 P36  O15   O   O2    0  -0.434   1.8739  -0.3345   0.2403
 P36  C16   C   CH2   0  -0.282   2.6363  -1.5073   0.5502
 P36  C17   C   CR6   0   0.102   4.0326  -1.2617   0.0702
 P36  C18   C   CR16  0  -0.282   4.8816  -0.4208   0.7857
 P36  C19   C   CR16  0  -0.242   6.1678  -0.1707   0.3318
 P36  C20   C   CR16  0  -0.260   6.6194  -0.7628  -0.8422
 P36  C21   C   CR16  0  -0.241   5.7797  -1.6032  -1.5595
 P36  C22   C   CR16  0  -0.298   4.4899  -1.8478  -1.1049
 P36  BR23  BR  BR    0  -0.024   0.7474   2.2973  -0.5798
 P36  H1    H   HCR6  0   0.257  -6.0194   0.7431  -2.3716
 P36  H2    H   HCR6  0   0.259  -6.4274  -1.6754  -2.6984
 P36  H3    H   HCR6  0   0.259  -5.5194  -3.3051  -1.0712
 P36  H4    H   HCR6  0   0.252  -4.2120  -2.5243   0.8591
 P36  H6    H   HCR6  0   0.256  -4.6936   1.5249  -0.4454
 P36  H7    H   HCH2  0   0.295  -3.7795   1.0365   1.7882
 P36  H7A   H   HCH2  0   0.294  -3.7079  -0.6145   2.3742
 P36  H12   H   HCR6  0   0.310   0.3914  -2.2536   1.5127
 P36  H13   H   HCR6  0   0.316  -1.9648  -1.9445   2.0163
 P36  H16   H   HCH2  0   0.258   2.6200  -1.6832   1.6289
 P36  H16A  H   HCH2  0   0.260   2.2029  -2.3787   0.0523
 P36  H18   H   HCR6  0   0.256   4.5386   0.0371   1.7060
 P36  H19   H   HCR6  0   0.260   6.8203   0.4841   0.8942
 P36  H20   H   HCR6  0   0.260   7.6251  -0.5712  -1.1932
 P36  H21   H   HCR6  0   0.260   6.1261  -2.0685  -2.4730
 P36  H22   H   HCR6  0   0.257   3.8366  -2.5046  -1.6666

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
 P36  C6    C1    aromatic  1.389  0.020  1.389
 P36  C1    C2    aromatic  1.389  0.020  1.389
 P36  C1    H1    single    0.930  0.020  1.080
 P36  C2    C3    aromatic  1.389  0.020  1.389
 P36  C2    H2    single    0.930  0.020  1.080
 P36  C4    C3    aromatic  1.388  0.020  1.388
 P36  C3    H3    single    0.930  0.020  1.080
 P36  C5    C4    aromatic  1.393  0.020  1.393
 P36  C4    H4    single    0.930  0.020  1.080
 P36  C7    C5    single    1.506  0.020  1.506
 P36  C6    C5    aromatic  1.392  0.020  1.392
 P36  C6    H6    single    0.930  0.020  1.080
 P36  N8    C7    single    1.467  0.020  1.467
 P36  C7    H7    single    0.970  0.020  1.090
 P36  C7    H7A   single    0.970  0.020  1.090
 P36  C9    N8    single    1.394  0.020  1.394
 P36  C13   N8    single    1.349  0.020  1.349
 P36  C10   C9    single    1.434  0.020  1.434
 P36  C9    O14   double    1.225  0.020  1.225
 P36  BR23  C10   single    1.871  0.020  1.871
 P36  C11   C10   double    1.376  0.020  1.376
 P36  O15   C11   single    1.325  0.020  1.325
 P36  C11   C12   single    1.417  0.020  1.417
 P36  C12   C13   double    1.355  0.020  1.355
 P36  C12   H12   single    0.930  0.020  1.080
 P36  C13   H13   single    0.930  0.020  1.080
 P36  C16   O15   single    1.433  0.020  1.433
 P36  C17   C16   single    1.497  0.020  1.497
 P36  C16   H16   single    0.970  0.020  1.090
 P36  C16   H16A  single    0.970  0.020  1.090
 P36  C18   C17   aromatic  1.393  0.020  1.393
 P36  C22   C17   aromatic  1.391  0.020  1.391
 P36  C19   C18   aromatic  1.387  0.020  1.387
 P36  C18   H18   single    0.930  0.020  1.080
 P36  C20   C19   aromatic  1.390  0.020  1.390
 P36  C19   H19   single    0.930  0.020  1.080
 P36  C20   C21   aromatic  1.388  0.020  1.388
 P36  C20   H20   single    0.930  0.020  1.080
 P36  C21   C22   aromatic  1.389  0.020  1.389
 P36  C21   H21   single    0.930  0.020  1.080
 P36  C22   H22   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
 P36  H1    C1   C6   119.76  3.000
 P36  H1    C1   C2   120.05  3.000
 P36  C6    C1   C2   120.19  3.000
 P36  H2    C2   C3   120.11  3.000
 P36  H2    C2   C1   120.16  3.000
 P36  C3    C2   C1   119.73  3.000
 P36  H3    C3   C4   119.87  3.000
 P36  H3    C3   C2   120.15  3.000
 P36  C4    C3   C2   119.98  3.000
 P36  H4    C4   C5   119.96  3.000
 P36  H4    C4   C3   119.38  3.000
 P36  C5    C4   C3   120.65  3.000
 P36  C7    C5   C6   121.07  3.000
 P36  C6    C5   C4   119.01  3.000
 P36  C7    C5   C4   119.92  3.000
 P36  H6    C6   C5   119.64  3.000
 P36  H6    C6   C1   119.92  3.000
 P36  C5    C6   C1   120.44  3.000
 P36  H7A   C7   H7   107.33  3.000
 P36  H7A   C7   N8   107.18  3.000
 P36  H7    C7   N8   108.49  3.000
 P36  H7A   C7   C5   110.58  3.000
 P36  H7    C7   C5   111.25  3.000
 P36  N8    C7   C5   111.82  3.000
 P36  C13   N8   C9   122.41  3.000
 P36  C13   N8   C7   119.15  3.000
 P36  C9    N8   C7   118.37  3.000
 P36  O14   C9   C10  124.91  3.000
 P36  O14   C9   N8   120.68  3.000
 P36  C10   C9   N8   114.42  3.000
 P36  BR23  C10  C11  120.26  3.000
 P36  C11   C10  C9   123.35  3.000
 P36  BR23  C10  C9   116.39  3.000
 P36  O15   C11  C12  123.53  3.000
 P36  C12   C11  C10  118.32  3.000
 P36  O15   C11  C10  118.15  3.000
 P36  H12   C12  C13  118.93  3.000
 P36  H12   C12  C11  122.66  3.000
 P36  C13   C12  C11  118.41  3.000
 P36  H13   C13  C12  120.72  3.000
 P36  H13   C13  N8   116.17  3.000
 P36  C12   C13  N8   123.11  3.000
 P36  C16   O15  C11  119.65  3.000
 P36  H16A  C16  H16  108.38  3.000
 P36  H16A  C16  C17  110.77  3.000
 P36  H16   C16  C17  110.90  3.000
 P36  H16A  C16  O15  110.06  3.000
 P36  H16   C16  O15  109.71  3.000
 P36  C17   C16  O15  107.02  3.000
 P36  C22   C17  C18  119.22  3.000
 P36  C22   C17  C16  120.57  3.000
 P36  C18   C17  C16  120.20  3.000
 P36  H18   C18  C19  119.70  3.000
 P36  H18   C18  C17  119.89  3.000
 P36  C19   C18  C17  120.40  3.000
 P36  H19   C19  C20  120.05  3.000
 P36  H19   C19  C18  119.88  3.000
 P36  C20   C19  C18  120.06  3.000
 P36  H20   C20  C21  120.12  3.000
 P36  H20   C20  C19  120.02  3.000
 P36  C21   C20  C19  119.86  3.000
 P36  H21   C21  C22  119.85  3.000
 P36  H21   C21  C20  120.20  3.000
 P36  C22   C21  C20  119.95  3.000
 P36  H22   C22  C21  119.80  3.000
 P36  H22   C22  C17  119.70  3.000
 P36  C21   C22  C17  120.51  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
 P36  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 P36  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 P36  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 P36  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 P36  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 P36  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 P36  CONST_07  C20  C19  C18  C17     0.00   0.0  0
 P36  CONST_08  C20  C21  C22  C17     0.00   0.0  0
 P36  CONST_09  C21  C22  C17  C18     0.00   0.0  0
 P36  CONST_10  C21  C20  C19  C18     0.00   0.0  0
 P36  CONST_11  C22  C17  C18  C19     0.00   0.0  0
 P36  CONST_12  C22  C21  C20  C19     0.00   0.0  0
 P36  CONST_13  C13  N8   C9   C10     0.00   0.0  0
 P36  CONST_14  C7   C5   C6   C1    180.00   0.0  0
 P36  CONST_15  C7   C5   C4   C3    180.00   0.0  0
 P36  CONST_16  C19  C18  C17  C16   180.00   0.0  0
 P36  CONST_17  C21  C22  C17  C16   180.00   0.0  0
 P36  CONST_18  C10  C9   N8   C7    180.00   0.0  0
 P36  CONST_19  O14  C9   N8   C13   180.00   0.0  0
 P36  CONST_20  H3   C3   C2   C1    180.00   0.0  0
 P36  CONST_21  H6   C6   C1   C2    180.00   0.0  0
 P36  CONST_22  H4   C4   C3   C2    180.00   0.0  0
 P36  CONST_23  H1   C1   C2   C3    180.00   0.0  0
 P36  CONST_24  H2   C2   C3   C4    180.00   0.0  0
 P36  CONST_25  H19  C19  C18  C17   180.00   0.0  0
 P36  CONST_26  H21  C21  C22  C17   180.00   0.0  0
 P36  CONST_27  H22  C22  C17  C18   180.00   0.0  0
 P36  CONST_28  H20  C20  C19  C18   180.00   0.0  0
 P36  CONST_29  H18  C18  C19  C20   180.00   0.0  0
 P36  CONST_30  O14  C9   N8   C7      0.00   0.0  0
 P36  Var_01    N8   C7   C5   C4     84.19  30.0  2
 P36  Var_02    C9   N8   C7   C5     85.84  30.0  2
 P36  Var_03    C17  C16  O15  C11  -179.08  30.0  2
 P36  Var_04    C18  C17  C16  O15    75.57  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
 P36  plan-1  C1    0.020
 P36  plan-1  C2    0.020
 P36  plan-1  C3    0.020
 P36  plan-1  C4    0.020
 P36  plan-1  C5    0.020
 P36  plan-1  C6    0.020
 P36  plan-1  C7    0.020
 P36  plan-1  H1    0.020
 P36  plan-1  H2    0.020
 P36  plan-1  H3    0.020
 P36  plan-1  H4    0.020
 P36  plan-1  H6    0.020
 P36  plan-2  C7    0.020
 P36  plan-2  N8    0.020
 P36  plan-2  C9    0.020
 P36  plan-2  C10   0.020
 P36  plan-2  C11   0.020
 P36  plan-2  C12   0.020
 P36  plan-2  C13   0.020
 P36  plan-2  O14   0.020
 P36  plan-2  O15   0.020
 P36  plan-2  BR23  0.020
 P36  plan-2  H12   0.020
 P36  plan-2  H13   0.020
 P36  plan-3  C16   0.020
 P36  plan-3  C17   0.020
 P36  plan-3  C18   0.020
 P36  plan-3  C19   0.020
 P36  plan-3  C20   0.020
 P36  plan-3  C21   0.020
 P36  plan-3  C22   0.020
 P36  plan-3  H18   0.020
 P36  plan-3  H19   0.020
 P36  plan-3  H20   0.020
 P36  plan-3  H21   0.020
 P36  plan-3  H22   0.020

