# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 13:34:20 2021
#   Inital geometry file: a 93 line input string
#   Ligand name: (3-methoxy-5-nitro-4-oxidanyl-phenyl)-(4-methylphenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(c1O)[N+]([O-])=O)C(=O)c2ccc(C)cc2
#
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
 LVE  LVE  (3-methoxy-5-nitro-4-oxidanyl-phenyl)-(4-methylphenyl)methanone  ligand  34  21  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LVE
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
 LVE  C2   C  CR6    0   0.346  23.2034  43.7753  35.4365
 LVE  C4   C  CR6    0  -0.022  22.4834  43.3191  37.7021
 LVE  C6   C  CR6    0   0.207  21.1969  42.5002  35.8571
 LVE  C12  C  C      0   0.371  22.6959  43.5513  39.1541
 LVE  C14  C  CR6    0  -0.057  22.1757  42.5669  40.1342
 LVE  C15  C  CR16   0  -0.253  21.7510  43.0185  41.3835
 LVE  C16  C  CR16   0  -0.291  21.3038  42.1217  42.3379
 LVE  O13  O  O      0  -0.393  23.2883  44.5447  39.5290
 LVE  C3   C  CR16   0  -0.403  23.3787  43.9099  36.7918
 LVE  C21  C  CH3    0  -0.445  25.1442  45.0123  34.9039
 LVE  O7   O  O2     0  -0.457  24.0092  44.2714  34.4918
 LVE  C1   C  CR6    0   0.287  22.0858  43.0610  34.9305
 LVE  C5   C  CR16   0  -0.376  21.3951  42.6223  37.2344
 LVE  N9   N  N      1   0.365  20.0419  41.7731  35.4039
 LVE  O11  O  O     -1  -0.423  19.8698  41.6528  34.1986
 LVE  O10  O  O      0  -0.356  19.2871  41.3073  36.2170
 LVE  C19  C  CR16   0  -0.271  22.1685  41.1956  39.8768
 LVE  C18  C  CR16   0  -0.279  21.7431  40.3027  40.8462
 LVE  C17  C  CR6    0   0.101  21.2980  40.7493  42.0894
 LVE  C20  C  CH3    0  -0.724  20.8514  39.7750  43.1370
 LVE  H1   H  HOH1   0   0.489  21.1827  42.4810  33.3947
 LVE  H2   H  HCR6   0   0.262  21.7493  44.0782  41.6036
 LVE  H3   H  HCR6   0   0.257  20.9545  42.4927  43.2936
 LVE  H4   H  HCR6   0   0.304  24.2238  44.4607  37.1817
 LVE  H5   H  HCH3   0   0.269  25.6633  45.3059  33.9959
 LVE  H6   H  HCH3   0   0.237  24.8599  45.9107  35.4569
 LVE  H7   H  HCH3   0   0.237  25.8177  44.4121  35.5206
 LVE  H8   H  HCR6   0   0.309  20.6783  42.1895  37.9164
 LVE  H9   H  HCR6   0   0.274  22.5222  40.8146  38.9275
 LVE  H10  H  HCR6   0   0.257  21.7581  39.2410  40.6315
 LVE  H11  H  HCH3   0   0.256  21.7121  39.3027  43.6144
 LVE  H12  H  HCH3   0   0.248  20.2704  40.2634  43.9176
 LVE  H13  H  HCH3   0   0.250  20.2450  38.9774  42.7078
 LVE  O8   O  OH1    0  -0.576  21.9856  42.9900  33.6194

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
 LVE  O8   C1   single    1.317  0.020  1.317
 LVE  O11  N9   single    1.223  0.020  1.223
 LVE  O7   C21  single    1.417  0.020  1.417
 LVE  O7   C2   single    1.337  0.020  1.337
 LVE  C1   C2   aromatic  1.420  0.020  1.420
 LVE  C1   C6   aromatic  1.401  0.020  1.401
 LVE  C2   C3   aromatic  1.373  0.020  1.373
 LVE  N9   C6   single    1.438  0.020  1.438
 LVE  N9   O10  double    1.203  0.020  1.203
 LVE  C6   C5   aromatic  1.397  0.020  1.397
 LVE  C3   C4   aromatic  1.407  0.020  1.407
 LVE  C5   C4   aromatic  1.374  0.020  1.374
 LVE  C4   C12  single    1.486  0.020  1.486
 LVE  C12  O13  double    1.216  0.020  1.216
 LVE  C12  C14  single    1.483  0.020  1.483
 LVE  C19  C14  aromatic  1.395  0.020  1.395
 LVE  C19  C18  aromatic  1.385  0.020  1.385
 LVE  C14  C15  aromatic  1.395  0.020  1.395
 LVE  C18  C17  aromatic  1.394  0.020  1.394
 LVE  C15  C16  aromatic  1.384  0.020  1.384
 LVE  C17  C16  aromatic  1.395  0.020  1.395
 LVE  C17  C20  single    1.499  0.020  1.499
 LVE  O8   H1   single    0.850  0.020  0.980
 LVE  C15  H2   single    0.930  0.020  1.080
 LVE  C16  H3   single    0.930  0.020  1.080
 LVE  C3   H4   single    0.930  0.020  1.080
 LVE  C21  H5   single    0.970  0.020  1.090
 LVE  C21  H6   single    0.970  0.020  1.090
 LVE  C21  H7   single    0.970  0.020  1.090
 LVE  C5   H8   single    0.930  0.020  1.080
 LVE  C19  H9   single    0.930  0.020  1.080
 LVE  C18  H10  single    0.930  0.020  1.080
 LVE  C20  H11  single    0.970  0.020  1.090
 LVE  C20  H12  single    0.970  0.020  1.090
 LVE  C20  H13  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
 LVE  C1   C2   O7   114.17  3.000
 LVE  C1   C2   C3   120.10  3.000
 LVE  O7   C2   C3   125.73  3.000
 LVE  C5   C4   C3   119.78  3.000
 LVE  C5   C4   C12  121.67  3.000
 LVE  C3   C4   C12  118.41  3.000
 LVE  N9   C6   C5   117.96  3.000
 LVE  C5   C6   C1   121.80  3.000
 LVE  N9   C6   C1   120.23  3.000
 LVE  O13  C12  C14  120.62  3.000
 LVE  C14  C12  C4   119.46  3.000
 LVE  O13  C12  C4   119.92  3.000
 LVE  C19  C14  C15  118.81  3.000
 LVE  C15  C14  C12  118.94  3.000
 LVE  C19  C14  C12  122.15  3.000
 LVE  H2   C15  C16  119.59  3.000
 LVE  H2   C15  C14  119.98  3.000
 LVE  C16  C15  C14  120.42  3.000
 LVE  H3   C16  C17  119.53  3.000
 LVE  H3   C16  C15  119.39  3.000
 LVE  C17  C16  C15  121.07  3.000
 LVE  H4   C3   C4   118.55  3.000
 LVE  H4   C3   C2   120.36  3.000
 LVE  C4   C3   C2   121.08  3.000
 LVE  H7   C21  H6   109.05  3.000
 LVE  H7   C21  H5   109.01  3.000
 LVE  H6   C21  H5   108.97  3.000
 LVE  H7   C21  O7   111.76  3.000
 LVE  H6   C21  O7   111.64  3.000
 LVE  H5   C21  O7   106.32  3.000
 LVE  C21  O7   C2   118.12  3.000
 LVE  O8   C1   C6   126.05  3.000
 LVE  C6   C1   C2   117.72  3.000
 LVE  O8   C1   C2   116.22  3.000
 LVE  H8   C5   C6   119.57  3.000
 LVE  H8   C5   C4   120.92  3.000
 LVE  C6   C5   C4   119.49  3.000
 LVE  O10  N9   O11  122.65  3.000
 LVE  O10  N9   C6   119.11  3.000
 LVE  O11  N9   C6   118.24  3.000
 LVE  H9   C19  C18  119.17  3.000
 LVE  H9   C19  C14  120.40  3.000
 LVE  C18  C19  C14  120.41  3.000
 LVE  H10  C18  C17  119.68  3.000
 LVE  H10  C18  C19  119.27  3.000
 LVE  C17  C18  C19  121.05  3.000
 LVE  C20  C17  C18  120.68  3.000
 LVE  C20  C17  C16  121.09  3.000
 LVE  C18  C17  C16  118.22  3.000
 LVE  H13  C20  H12  108.29  3.000
 LVE  H13  C20  H11  107.11  3.000
 LVE  H12  C20  H11  107.53  3.000
 LVE  H13  C20  C17  111.49  3.000
 LVE  H12  C20  C17  111.63  3.000
 LVE  H11  C20  C17  110.61  3.000
 LVE  H1   O8   C1   108.65  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
 LVE  CONST_01  C5   C6   C1   C2      0.00   0.0  0
 LVE  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 LVE  CONST_03  C1   C2   C3   C4      0.00   0.0  0
 LVE  CONST_04  C1   C6   C5   C4      0.00   0.0  0
 LVE  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 LVE  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 LVE  CONST_07  C17  C18  C19  C14     0.00   0.0  0
 LVE  CONST_08  C17  C16  C15  C14     0.00   0.0  0
 LVE  CONST_09  C18  C19  C14  C15     0.00   0.0  0
 LVE  CONST_10  C18  C17  C16  C15     0.00   0.0  0
 LVE  CONST_11  C19  C14  C15  C16     0.00   0.0  0
 LVE  CONST_12  C19  C18  C17  C16     0.00   0.0  0
 LVE  CONST_13  N9   C6   C1   C2    180.00   0.0  0
 LVE  CONST_14  C12  C4   C3   C2    180.00   0.0  0
 LVE  CONST_15  O7   C2   C3   C4    180.00   0.0  0
 LVE  CONST_16  N9   C6   C5   C4    180.00   0.0  0
 LVE  CONST_17  O7   C2   C1   C6    180.00   0.0  0
 LVE  CONST_18  C12  C4   C5   C6    180.00   0.0  0
 LVE  CONST_19  C3   C2   C1   O8    180.00   0.0  0
 LVE  CONST_20  C5   C6   C1   O8    180.00   0.0  0
 LVE  CONST_21  C18  C19  C14  C12   180.00   0.0  0
 LVE  CONST_22  C16  C15  C14  C12   180.00   0.0  0
 LVE  CONST_23  C20  C17  C16  C15   180.00   0.0  0
 LVE  CONST_24  C20  C17  C18  C19   180.00   0.0  0
 LVE  CONST_25  H10  C18  C19  C14   180.00   0.0  0
 LVE  CONST_26  H3   C16  C15  C14   180.00   0.0  0
 LVE  CONST_27  H9   C19  C14  C15   180.00   0.0  0
 LVE  CONST_28  H8   C5   C4   C3    180.00   0.0  0
 LVE  CONST_29  H4   C3   C2   C1    180.00   0.0  0
 LVE  CONST_30  H2   C15  C14  C19   180.00   0.0  0
 LVE  CONST_31  O11  N9   C6   C1      0.00   0.0  0
 LVE  CONST_32  O10  N9   C6   C1    180.00   0.0  0
 LVE  CONST_33  O11  N9   C6   C5    180.00   0.0  0
 LVE  CONST_34  O10  N9   C6   C5      0.00   0.0  0
 LVE  Var_01    C19  C14  C12  C4     36.00  30.0  2
 LVE  Var_02    C3   C4   C12  C14  -155.24  30.0  2
 LVE  Var_03    C1   C2   O7   C21   179.34  30.0  2
 LVE  Var_04    H11  C20  C17  C16  -101.72  30.0  2
 LVE  Var_05    H5   C21  O7   C2    179.13  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
 LVE  plan-1  C2   0.020
 LVE  plan-1  C4   0.020
 LVE  plan-1  C6   0.020
 LVE  plan-1  C12  0.020
 LVE  plan-1  C3   0.020
 LVE  plan-1  O7   0.020
 LVE  plan-1  C1   0.020
 LVE  plan-1  C5   0.020
 LVE  plan-1  N9   0.020
 LVE  plan-1  H4   0.020
 LVE  plan-1  H8   0.020
 LVE  plan-1  O8   0.020
 LVE  plan-2  C12  0.020
 LVE  plan-2  C14  0.020
 LVE  plan-2  C15  0.020
 LVE  plan-2  C16  0.020
 LVE  plan-2  C19  0.020
 LVE  plan-2  C18  0.020
 LVE  plan-2  C17  0.020
 LVE  plan-2  C20  0.020
 LVE  plan-2  H2   0.020
 LVE  plan-2  H3   0.020
 LVE  plan-2  H9   0.020
 LVE  plan-2  H10  0.020
 LVE  plan-3  C6   0.020
 LVE  plan-3  N9   0.020
 LVE  plan-3  O11  0.020
 LVE  plan-3  O10  0.020
 LVE  plan-4  C4   0.020
 LVE  plan-4  C12  0.020
 LVE  plan-4  C14  0.020
 LVE  plan-4  O13  0.020

