# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 13:29:12 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: (3,4-dihydroxy-5-nitrophenyl)(4-methylphenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)C(=O)c2cc(O)c(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
 TCW  TCW  (3,4-dihydroxy-5-nitrophenyl)(4-methylphenyl)methanone  ligand  31  20  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TCW
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
 TCW  O13   O  O      0  -0.393  -1.0954  -2.8418  -0.4157
 TCW  C12   C  C      0   0.371  -0.9388  -1.6584  -0.1851
 TCW  C4    C  CR6    0  -0.030   0.4338  -1.0959  -0.1007
 TCW  C3    C  CR16   0  -0.390   1.4967  -1.9595   0.2116
 TCW  C2    C  CR6    0   0.307   2.7930  -1.5105   0.2464
 TCW  O7    O  OH1    0  -0.612   3.8518  -2.2719   0.5561
 TCW  C5    C  CR16   0  -0.376   0.6991   0.2185  -0.4108
 TCW  C6    C  CR6    0   0.208   2.0168   0.6783  -0.3959
 TCW  N9    N  N      1   0.364   2.2530   2.0565  -0.7355
 TCW  O11   O  O     -1  -0.357   1.3190   2.7546  -1.0324
 TCW  O10   O  O      0  -0.421   3.4034   2.4695  -0.7069
 TCW  C1    C  CR6    0   0.298   3.0897  -0.1613  -0.0640
 TCW  O8    O  OH1    0  -0.579   4.3620   0.1790  -0.0109
 TCW  C14   C  CR6    0  -0.056  -2.1080  -0.7647   0.0017
 TCW  C19   C  CR16   0  -0.254  -3.2801  -1.0327  -0.7060
 TCW  C18   C  CR16   0  -0.287  -4.4010  -0.2411  -0.5321
 TCW  C17   C  CR6    0   0.099  -4.3997   0.8188   0.3755
 TCW  C20   C  CH3    0  -0.721  -5.6285   1.6504   0.5883
 TCW  C16   C  CR16   0  -0.282  -3.2340   1.0657   1.0979
 TCW  C15   C  CR16   0  -0.272  -2.0993   0.2927   0.9110
 TCW  H3    H  HCR6   0   0.296   1.2908  -2.9981   0.4423
 TCW  HO7   H  HOH1   0   0.485   3.5724  -3.1732   0.7553
 TCW  H5    H  HCR6   0   0.309  -0.0957   0.8928  -0.6923
 TCW  HO8   H  HOH1   0   0.488   4.4484   1.1240  -0.2374
 TCW  H19   H  HCR6   0   0.263  -3.3080  -1.8508  -1.4140
 TCW  H18   H  HCR6   0   0.256  -5.2929  -0.4494  -1.1106
 TCW  H20   H  HCH3   0   0.256  -6.2262   1.2488   1.4093
 TCW  H20A  H  HCH3   0   0.249  -5.3779   2.6793   0.8435
 TCW  H20B  H  HCH3   0   0.248  -6.2609   1.6617  -0.2982
 TCW  H16   H  HCR6   0   0.258  -3.2106   1.8750   1.8172
 TCW  H15   H  HCR6   0   0.274  -1.2143   0.5053   1.4973

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
 TCW  O13  C12   double    1.216  0.020  1.216
 TCW  C12  C4    single    1.486  0.020  1.486
 TCW  C12  C14   single    1.483  0.020  1.483
 TCW  C4   C3    aromatic  1.405  0.020  1.405
 TCW  C4   C5    aromatic  1.376  0.020  1.376
 TCW  C3   C2    aromatic  1.372  0.020  1.372
 TCW  C2   O7    single    1.340  0.020  1.340
 TCW  C2   C1    aromatic  1.416  0.020  1.416
 TCW  C5   C6    aromatic  1.396  0.020  1.396
 TCW  C6   N9    single    1.439  0.020  1.439
 TCW  C6   C1    aromatic  1.402  0.020  1.402
 TCW  N9   O11   single    1.203  0.020  1.203
 TCW  N9   O10   double    1.223  0.020  1.223
 TCW  C1   O8    single    1.318  0.020  1.318
 TCW  C14  C19   aromatic  1.395  0.020  1.395
 TCW  C14  C15   aromatic  1.395  0.020  1.395
 TCW  C19  C18   aromatic  1.383  0.020  1.383
 TCW  C18  C17   aromatic  1.395  0.020  1.395
 TCW  C17  C20   single    1.499  0.020  1.499
 TCW  C17  C16   aromatic  1.393  0.020  1.393
 TCW  C16  C15   aromatic  1.386  0.020  1.386
 TCW  C3   H3    single    0.930  0.020  1.080
 TCW  O7   HO7   single    0.850  0.020  0.980
 TCW  C5   H5    single    0.930  0.020  1.080
 TCW  O8   HO8   single    0.850  0.020  0.980
 TCW  C19  H19   single    0.930  0.020  1.080
 TCW  C18  H18   single    0.930  0.020  1.080
 TCW  C20  H20   single    0.970  0.020  1.090
 TCW  C20  H20A  single    0.970  0.020  1.090
 TCW  C20  H20B  single    0.970  0.020  1.090
 TCW  C16  H16   single    0.930  0.020  1.080
 TCW  C15  H15   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
 TCW  C14   C12  C4    119.53  3.000
 TCW  C14   C12  O13   120.58  3.000
 TCW  C4    C12  O13   119.88  3.000
 TCW  C5    C4   C3    119.44  3.000
 TCW  C5    C4   C12   121.79  3.000
 TCW  C3    C4   C12   118.61  3.000
 TCW  H3    C3   C2    119.19  3.000
 TCW  H3    C3   C4    119.53  3.000
 TCW  C2    C3   C4    121.28  3.000
 TCW  C1    C2   O7    115.24  3.000
 TCW  C1    C2   C3    120.28  3.000
 TCW  O7    C2   C3    124.48  3.000
 TCW  HO7   O7   C2    110.48  3.000
 TCW  H5    C5   C6    119.47  3.000
 TCW  H5    C5   C4    120.89  3.000
 TCW  C6    C5   C4    119.62  3.000
 TCW  C1    C6   N9    120.25  3.000
 TCW  C1    C6   C5    121.85  3.000
 TCW  N9    C6   C5    117.91  3.000
 TCW  O10   N9   O11   122.69  3.000
 TCW  O10   N9   C6    118.20  3.000
 TCW  O11   N9   C6    119.11  3.000
 TCW  O8    C1   C6    126.41  3.000
 TCW  O8    C1   C2    116.07  3.000
 TCW  C6    C1   C2    117.53  3.000
 TCW  HO8   O8   C1    109.04  3.000
 TCW  C15   C14  C19   118.79  3.000
 TCW  C15   C14  C12   122.27  3.000
 TCW  C19   C14  C12   118.85  3.000
 TCW  H19   C19  C18   119.61  3.000
 TCW  H19   C19  C14   119.91  3.000
 TCW  C18   C19  C14   120.47  3.000
 TCW  H18   C18  C17   119.61  3.000
 TCW  H18   C18  C19   119.34  3.000
 TCW  C17   C18  C19   121.05  3.000
 TCW  C16   C17  C20   120.93  3.000
 TCW  C16   C17  C18   118.20  3.000
 TCW  C20   C17  C18   120.86  3.000
 TCW  H20B  C20  H20A  108.33  3.000
 TCW  H20B  C20  H20   107.34  3.000
 TCW  H20A  C20  H20   107.28  3.000
 TCW  H20B  C20  C17   111.49  3.000
 TCW  H20A  C20  C17   111.63  3.000
 TCW  H20   C20  C17   110.57  3.000
 TCW  H16   C16  C15   119.26  3.000
 TCW  H16   C16  C17   119.66  3.000
 TCW  C15   C16  C17   121.09  3.000
 TCW  H15   C15  C16   119.13  3.000
 TCW  H15   C15  C14   120.47  3.000
 TCW  C16   C15  C14   120.38  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
 TCW  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 TCW  CONST_02  C1   C6   C5   C4     0.00   0.0  0
 TCW  CONST_03  C6   C5   C4   C3     0.00   0.0  0
 TCW  CONST_04  C6   C1   C2   C3     0.00   0.0  0
 TCW  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 TCW  CONST_06  C5   C6   C1   C2     0.00   0.0  0
 TCW  CONST_07  C17  C18  C19  C14    0.00   0.0  0
 TCW  CONST_08  C17  C16  C15  C14    0.00   0.0  0
 TCW  CONST_09  C16  C15  C14  C19    0.00   0.0  0
 TCW  CONST_10  C16  C17  C18  C19    0.00   0.0  0
 TCW  CONST_11  C15  C14  C19  C18    0.00   0.0  0
 TCW  CONST_12  C15  C16  C17  C18    0.00   0.0  0
 TCW  CONST_13  C2   C3   C4   C12  180.00   0.0  0
 TCW  CONST_14  C6   C5   C4   C12  180.00   0.0  0
 TCW  CONST_15  C18  C19  C14  C12  180.00   0.0  0
 TCW  CONST_16  C16  C15  C14  C12  180.00   0.0  0
 TCW  CONST_17  O7   C2   C3   C4   180.00   0.0  0
 TCW  CONST_18  N9   C6   C5   C4   180.00   0.0  0
 TCW  CONST_19  O8   C1   C2   C3   180.00   0.0  0
 TCW  CONST_20  N9   C6   C1   C2   180.00   0.0  0
 TCW  CONST_21  C6   C1   C2   O7   180.00   0.0  0
 TCW  CONST_22  O8   C1   C6   C5   180.00   0.0  0
 TCW  CONST_23  C20  C17  C18  C19  180.00   0.0  0
 TCW  CONST_24  C15  C16  C17  C20  180.00   0.0  0
 TCW  CONST_25  H5   C5   C4   C3   180.00   0.0  0
 TCW  CONST_26  H3   C3   C4   C5   180.00   0.0  0
 TCW  CONST_27  H18  C18  C19  C14  180.00   0.0  0
 TCW  CONST_28  H16  C16  C15  C14  180.00   0.0  0
 TCW  CONST_29  H15  C15  C14  C19  180.00   0.0  0
 TCW  CONST_30  H19  C19  C18  C17  180.00   0.0  0
 TCW  CONST_31  O11  N9   C6   C5     0.00   0.0  0
 TCW  CONST_32  O10  N9   C6   C5   180.00   0.0  0
 TCW  CONST_33  C1   C6   N9   O11  180.00   0.0  0
 TCW  CONST_34  C1   C6   N9   O10    0.00   0.0  0
 TCW  Var_01    C19  C14  C12  C4   147.09  30.0  2
 TCW  Var_02    C14  C12  C4   C3   156.94  30.0  3
 TCW  Var_03    H20  C20  C17  C18   92.06  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
 TCW  plan-1  C12  0.020
 TCW  plan-1  C4   0.020
 TCW  plan-1  C3   0.020
 TCW  plan-1  C2   0.020
 TCW  plan-1  O7   0.020
 TCW  plan-1  C5   0.020
 TCW  plan-1  C6   0.020
 TCW  plan-1  N9   0.020
 TCW  plan-1  C1   0.020
 TCW  plan-1  O8   0.020
 TCW  plan-1  H3   0.020
 TCW  plan-1  H5   0.020
 TCW  plan-2  C12  0.020
 TCW  plan-2  C14  0.020
 TCW  plan-2  C19  0.020
 TCW  plan-2  C18  0.020
 TCW  plan-2  C17  0.020
 TCW  plan-2  C20  0.020
 TCW  plan-2  C16  0.020
 TCW  plan-2  C15  0.020
 TCW  plan-2  H19  0.020
 TCW  plan-2  H18  0.020
 TCW  plan-2  H16  0.020
 TCW  plan-2  H15  0.020
 TCW  plan-3  C6   0.020
 TCW  plan-3  N9   0.020
 TCW  plan-3  O11  0.020
 TCW  plan-3  O10  0.020
 TCW  plan-4  O13  0.020
 TCW  plan-4  C12  0.020
 TCW  plan-4  C4   0.020
 TCW  plan-4  C14  0.020

