# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 12:23:01 2021
#   Inital geometry file: a 85 line input string
#   Ligand name: (4-methylphenyl)-(3-nitro-4-oxidanyl-phenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)C(=O)c2ccc(O)c(c2)[N+]([O-])=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
 LVB  LVB  (4-methylphenyl)-(3-nitro-4-oxidanyl-phenyl)methanone  ligand  30  19  .  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_LVB
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
 LVB  C1   C  CR6    0   0.377  21.3140  42.8425  42.8529
 LVB  C2   C  CR16   0  -0.335  21.5686  43.8842  41.9537
 LVB  C3   C  CR16   0  -0.251  21.5899  43.6609  40.5987
 LVB  C4   C  CR6    0  -0.045  21.3447  42.3868  40.0664
 LVB  C5   C  CR16   0  -0.324  21.0653  41.3516  40.9373
 LVB  C6   C  CR6    0   0.188  21.0635  41.5636  42.3110
 LVB  O10  O  O      0  -0.358  20.5989  39.3587  42.6784
 LVB  N9   N  N      1   0.367  20.7885  40.4409  43.1684
 LVB  O11  O  O     -1  -0.422  20.7574  40.6347  44.3755
 LVB  O8   O  OH1    0  -0.590  21.3252  43.1356  44.1389
 LVB  C12  C  C      0   0.365  21.2967  42.1231  38.6043
 LVB  O13  O  O      0  -0.393  20.5837  41.2408  38.1670
 LVB  C14  C  CR6    0  -0.053  22.1250  42.9510  37.6952
 LVB  C15  C  CR16   0  -0.254  21.6755  43.1888  36.3960
 LVB  C16  C  CR16   0  -0.287  22.4436  43.9256  35.5125
 LVB  C17  C  CR6    0   0.100  23.6918  44.4241  35.8873
 LVB  C20  C  CH3    0  -0.722  24.5105  45.2443  34.9373
 LVB  C18  C  CR16   0  -0.281  24.1484  44.1579  37.1767
 LVB  C19  C  CR16   0  -0.271  23.3749  43.4404  38.0741
 LVB  H1   H  HCR6   0   0.296  21.7466  44.8750  42.3498
 LVB  H2   H  HCR6   0   0.293  21.7748  44.4994  39.9409
 LVB  H3   H  HCR6   0   0.307  20.8559  40.3650  40.5481
 LVB  H4   H  HOH1   0   0.487  21.1200  42.3319  44.6533
 LVB  H5   H  HCR6   0   0.263  20.7135  42.8068  36.0804
 LVB  H6   H  HCR6   0   0.256  22.0712  44.1129  34.5125
 LVB  H7   H  HCH3   0   0.256  24.3083  46.3083  35.0778
 LVB  H8   H  HCH3   0   0.249  25.5777  45.0942  35.0963
 LVB  H9   H  HCH3   0   0.249  24.2814  45.0049  33.8998
 LVB  H10  H  HCR6   0   0.258  25.1230  44.5175  37.4832
 LVB  H11  H  HCR6   0   0.274  23.7676  43.2382  39.0626

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
 LVB  C20  C17  single    1.499  0.020  1.499
 LVB  C16  C17  aromatic  1.395  0.020  1.395
 LVB  C16  C15  aromatic  1.383  0.020  1.383
 LVB  C17  C18  aromatic  1.394  0.020  1.394
 LVB  C15  C14  aromatic  1.395  0.020  1.395
 LVB  C18  C19  aromatic  1.385  0.020  1.385
 LVB  C14  C19  aromatic  1.395  0.020  1.395
 LVB  C14  C12  single    1.483  0.020  1.483
 LVB  O13  C12  double    1.216  0.020  1.216
 LVB  C12  C4   single    1.486  0.020  1.486
 LVB  C4   C3   aromatic  1.402  0.020  1.402
 LVB  C4   C5   aromatic  1.381  0.020  1.381
 LVB  C3   C2   aromatic  1.373  0.020  1.373
 LVB  C5   C6   aromatic  1.390  0.020  1.390
 LVB  O10  N9   double    1.203  0.020  1.203
 LVB  C2   C1   aromatic  1.399  0.020  1.399
 LVB  C6   N9   single    1.439  0.020  1.439
 LVB  C6   C1   aromatic  1.411  0.020  1.411
 LVB  N9   O11  single    1.223  0.020  1.223
 LVB  C1   O8   single    1.319  0.020  1.319
 LVB  C2   H1   single    0.930  0.020  1.080
 LVB  C3   H2   single    0.930  0.020  1.080
 LVB  C5   H3   single    0.930  0.020  1.080
 LVB  O8   H4   single    0.850  0.020  0.980
 LVB  C15  H5   single    0.930  0.020  1.080
 LVB  C16  H6   single    0.930  0.020  1.080
 LVB  C20  H7   single    0.970  0.020  1.090
 LVB  C20  H8   single    0.970  0.020  1.090
 LVB  C20  H9   single    0.970  0.020  1.090
 LVB  C18  H10  single    0.930  0.020  1.080
 LVB  C19  H11  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
 LVB  O8   C1   C6   125.25  3.000
 LVB  O8   C1   C2   117.36  3.000
 LVB  C6   C1   C2   117.39  3.000
 LVB  H1   C2   C3   120.50  3.000
 LVB  H1   C2   C1   118.45  3.000
 LVB  C3   C2   C1   121.05  3.000
 LVB  H2   C3   C4   120.22  3.000
 LVB  H2   C3   C2   118.46  3.000
 LVB  C4   C3   C2   121.29  3.000
 LVB  C12  C4   C5   118.73  3.000
 LVB  C5   C4   C3   118.48  3.000
 LVB  C12  C4   C3   122.69  3.000
 LVB  H3   C5   C6   119.65  3.000
 LVB  H3   C5   C4   119.74  3.000
 LVB  C6   C5   C4   120.60  3.000
 LVB  N9   C6   C5   118.04  3.000
 LVB  N9   C6   C1   120.80  3.000
 LVB  C5   C6   C1   121.16  3.000
 LVB  O11  N9   O10  122.73  3.000
 LVB  O11  N9   C6   117.99  3.000
 LVB  O10  N9   C6   119.29  3.000
 LVB  H4   O8   C1   109.21  3.000
 LVB  C14  C12  O13  120.82  3.000
 LVB  O13  C12  C4   120.10  3.000
 LVB  C14  C12  C4   119.08  3.000
 LVB  C19  C14  C15  118.81  3.000
 LVB  C19  C14  C12  122.01  3.000
 LVB  C15  C14  C12  119.09  3.000
 LVB  H5   C15  C16  119.69  3.000
 LVB  H5   C15  C14  119.86  3.000
 LVB  C16  C15  C14  120.44  3.000
 LVB  H6   C16  C17  119.58  3.000
 LVB  H6   C16  C15  119.39  3.000
 LVB  C17  C16  C15  121.03  3.000
 LVB  C18  C17  C20  120.81  3.000
 LVB  C18  C17  C16  118.26  3.000
 LVB  C20  C17  C16  120.93  3.000
 LVB  H9   C20  H8   108.35  3.000
 LVB  H9   C20  H7   107.32  3.000
 LVB  H8   C20  H7   107.27  3.000
 LVB  H9   C20  C17  111.63  3.000
 LVB  H8   C20  C17  111.54  3.000
 LVB  H7   C20  C17  110.52  3.000
 LVB  H10  C18  C19  119.42  3.000
 LVB  H10  C18  C17  119.56  3.000
 LVB  C19  C18  C17  121.03  3.000
 LVB  H11  C19  C18  119.06  3.000
 LVB  H11  C19  C14  120.50  3.000
 LVB  C18  C19  C14  120.41  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
 LVB  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 LVB  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 LVB  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 LVB  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 LVB  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 LVB  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 LVB  CONST_07  C17  C16  C15  C14     0.00   0.0  0
 LVB  CONST_08  C17  C18  C19  C14     0.00   0.0  0
 LVB  CONST_09  C18  C17  C16  C15     0.00   0.0  0
 LVB  CONST_10  C18  C19  C14  C15     0.00   0.0  0
 LVB  CONST_11  C19  C18  C17  C16     0.00   0.0  0
 LVB  CONST_12  C19  C14  C15  C16     0.00   0.0  0
 LVB  CONST_13  C12  C4   C3   C2    180.00   0.0  0
 LVB  CONST_14  N9   C6   C1   C2    180.00   0.0  0
 LVB  CONST_15  O8   C1   C2   C3    180.00   0.0  0
 LVB  CONST_16  N9   C6   C5   C4    180.00   0.0  0
 LVB  CONST_17  O8   C1   C6   C5    180.00   0.0  0
 LVB  CONST_18  C12  C4   C5   C6    180.00   0.0  0
 LVB  CONST_19  C16  C15  C14  C12   180.00   0.0  0
 LVB  CONST_20  C18  C19  C14  C12   180.00   0.0  0
 LVB  CONST_21  C20  C17  C16  C15   180.00   0.0  0
 LVB  CONST_22  C19  C18  C17  C20   180.00   0.0  0
 LVB  CONST_23  H2   C3   C2   C1    180.00   0.0  0
 LVB  CONST_24  H3   C5   C6   C1    180.00   0.0  0
 LVB  CONST_25  H1   C2   C3   C4    180.00   0.0  0
 LVB  CONST_26  H6   C16  C15  C14   180.00   0.0  0
 LVB  CONST_27  H10  C18  C19  C14   180.00   0.0  0
 LVB  CONST_28  H11  C19  C14  C15   180.00   0.0  0
 LVB  CONST_29  H5   C15  C16  C17   180.00   0.0  0
 LVB  CONST_30  O10  N9   C6   C1    180.00   0.0  0
 LVB  CONST_31  O11  N9   C6   C1      0.00   0.0  0
 LVB  CONST_32  O10  N9   C6   C5      0.00   0.0  0
 LVB  CONST_33  O11  N9   C6   C5    180.00   0.0  0
 LVB  Var_01    C14  C12  C4   C3     30.34  30.0  2
 LVB  Var_02    C15  C14  C12  C4   -149.77  30.0  2
 LVB  Var_03    H7   C20  C17  C16    92.63  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
 LVB  plan-1  C1   0.020
 LVB  plan-1  C2   0.020
 LVB  plan-1  C3   0.020
 LVB  plan-1  C4   0.020
 LVB  plan-1  C5   0.020
 LVB  plan-1  C6   0.020
 LVB  plan-1  N9   0.020
 LVB  plan-1  O8   0.020
 LVB  plan-1  C12  0.020
 LVB  plan-1  H1   0.020
 LVB  plan-1  H2   0.020
 LVB  plan-1  H3   0.020
 LVB  plan-2  C12  0.020
 LVB  plan-2  C14  0.020
 LVB  plan-2  C15  0.020
 LVB  plan-2  C16  0.020
 LVB  plan-2  C17  0.020
 LVB  plan-2  C20  0.020
 LVB  plan-2  C18  0.020
 LVB  plan-2  C19  0.020
 LVB  plan-2  H5   0.020
 LVB  plan-2  H6   0.020
 LVB  plan-2  H10  0.020
 LVB  plan-2  H11  0.020
 LVB  plan-3  C6   0.020
 LVB  plan-3  O10  0.020
 LVB  plan-3  N9   0.020
 LVB  plan-3  O11  0.020
 LVB  plan-4  C4   0.020
 LVB  plan-4  C12  0.020
 LVB  plan-4  O13  0.020
 LVB  plan-4  C14  0.020

