# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:02:10 2022
#   Inital geometry file: a 81 line input string
#   Ligand name: (3,4-dihydroxy-2-nitrophenyl)(phenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(C(=O)c2ccccc2)c(c1O)[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
 BIE  BIE  (3,4-dihydroxy-2-nitrophenyl)(phenyl)methanone  ligand  28  19  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BIE
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
 BIE  O5   O  O      0  -0.373  -1.1310   1.5552   2.1643
 BIE  C7   C  C      0   0.382  -0.9343   1.0191   1.0965
 BIE  C4   C  CR6    0  -0.061   0.4646   0.8500   0.5935
 BIE  C5   C  CR16   0  -0.304   1.2828   1.9604   0.5411
 BIE  C6   C  CR16   0  -0.349   2.5701   1.8689   0.0212
 BIE  C3   C  CR6    0   0.134   0.9688  -0.3698   0.1268
 BIE  N1   N  N      1   0.335   0.1435  -1.5529   0.2570
 BIE  O4   O  O      0  -0.358   0.1183  -2.3422  -0.6538
 BIE  O3   O  O     -1  -0.368  -0.4895  -1.6678   1.2826
 BIE  C2   C  CR6    0   0.312   2.2504  -0.4945  -0.3914
 BIE  O2   O  OH1    0  -0.594   2.7237  -1.6756  -0.7847
 BIE  C1   C  CR6    0   0.276   3.0542   0.6630  -0.4411
 BIE  O1   O  OH1    0  -0.629   4.2810   0.4707  -0.9474
 BIE  C8   C  CR6    0  -0.043  -2.0488   0.5969   0.2127
 BIE  C9   C  CR16   0  -0.260  -3.3008   0.3336   0.7703
 BIE  C13  C  CR16   0  -0.281  -1.8777   0.5060  -1.1679
 BIE  C12  C  CR16   0  -0.239  -2.9459   0.1543  -1.9812
 BIE  C11  C  CR16   0  -0.245  -4.1831  -0.1239  -1.4189
 BIE  C10  C  CR16   0  -0.244  -4.3587  -0.0360  -0.0414
 BIE  H5   H  HCR6   0   0.286   0.9122   2.9201   0.8735
 BIE  H6   H  HCR6   0   0.299   3.1951   2.7523  -0.0244
 BIE  H2   H  HOH1   0   0.489   3.6616  -1.6049  -1.0078
 BIE  H1   H  HOH1   0   0.495   4.8026   1.2821  -0.9385
 BIE  H9   H  HCR6   0   0.267  -3.4390   0.4002   1.8415
 BIE  H13  H  HCR6   0   0.271  -0.9224   0.7386  -1.6215
 BIE  H12  H  HCR6   0   0.268  -2.8099   0.0993  -3.0530
 BIE  H11  H  HCR6   0   0.269  -5.0138  -0.4069  -2.0522
 BIE  H10  H  HCR6   0   0.266  -5.3232  -0.2568   0.3963

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
 BIE  O5   C7   double    1.211  0.020  1.211
 BIE  C7   C4   single    1.496  0.020  1.496
 BIE  C7   C8   single    1.484  0.020  1.484
 BIE  C4   C5   aromatic  1.380  0.020  1.380
 BIE  C4   C3   aromatic  1.400  0.020  1.400
 BIE  C5   C6   aromatic  1.391  0.020  1.391
 BIE  C5   H5   single    0.930  0.020  1.080
 BIE  C6   C1   aromatic  1.379  0.020  1.379
 BIE  C6   H6   single    0.930  0.020  1.080
 BIE  C3   N1   single    1.448  0.020  1.448
 BIE  C3   C2   aromatic  1.388  0.020  1.388
 BIE  N1   O4   double    1.205  0.020  1.205
 BIE  N1   O3   single    1.211  0.020  1.211
 BIE  C2   O2   single    1.332  0.020  1.332
 BIE  C2   C1   aromatic  1.410  0.020  1.410
 BIE  O2   H2   single    0.850  0.020  0.980
 BIE  C1   O1   single    1.341  0.020  1.341
 BIE  O1   H1   single    0.850  0.020  0.980
 BIE  C8   C9   aromatic  1.396  0.020  1.396
 BIE  C8   C13  aromatic  1.394  0.020  1.394
 BIE  C9   C10  aromatic  1.384  0.020  1.384
 BIE  C9   H9   single    0.930  0.020  1.080
 BIE  C13  C12  aromatic  1.388  0.020  1.388
 BIE  C13  H13  single    0.930  0.020  1.080
 BIE  C12  C11  aromatic  1.387  0.020  1.387
 BIE  C12  H12  single    0.930  0.020  1.080
 BIE  C11  C10  aromatic  1.391  0.020  1.391
 BIE  C11  H11  single    0.930  0.020  1.080
 BIE  C10  H10  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
 BIE  C8   C7   C4   118.03  3.000
 BIE  C8   C7   O5   121.95  3.000
 BIE  C4   C7   O5   119.89  3.000
 BIE  C3   C4   C5   118.34  3.000
 BIE  C3   C4   C7   123.18  3.000
 BIE  C5   C4   C7   118.43  3.000
 BIE  H5   C5   C6   119.37  3.000
 BIE  H5   C5   C4   119.95  3.000
 BIE  C6   C5   C4   120.65  3.000
 BIE  H6   C6   C1   119.77  3.000
 BIE  H6   C6   C5   119.73  3.000
 BIE  C1   C6   C5   120.50  3.000
 BIE  C2   C3   N1   119.10  3.000
 BIE  C2   C3   C4   122.37  3.000
 BIE  N1   C3   C4   118.46  3.000
 BIE  O3   N1   O4   124.55  3.000
 BIE  O3   N1   C3   116.84  3.000
 BIE  O4   N1   C3   118.61  3.000
 BIE  C1   C2   O2   121.00  3.000
 BIE  C1   C2   C3   117.75  3.000
 BIE  O2   C2   C3   121.20  3.000
 BIE  H2   O2   C2   110.37  3.000
 BIE  O1   C1   C2   114.65  3.000
 BIE  O1   C1   C6   124.96  3.000
 BIE  C2   C1   C6   120.39  3.000
 BIE  H1   O1   C1   111.75  3.000
 BIE  C13  C8   C9   119.57  3.000
 BIE  C13  C8   C7   121.08  3.000
 BIE  C9   C8   C7   119.31  3.000
 BIE  H9   C9   C10  119.97  3.000
 BIE  H9   C9   C8   119.90  3.000
 BIE  C10  C9   C8   120.12  3.000
 BIE  H13  C13  C12  119.20  3.000
 BIE  H13  C13  C8   120.61  3.000
 BIE  C12  C13  C8   120.16  3.000
 BIE  H12  C12  C11  120.23  3.000
 BIE  H12  C12  C13  119.79  3.000
 BIE  C11  C12  C13  119.98  3.000
 BIE  H11  C11  C10  119.93  3.000
 BIE  H11  C11  C12  119.99  3.000
 BIE  C10  C11  C12  120.08  3.000
 BIE  H10  C10  C11  120.01  3.000
 BIE  H10  C10  C9   119.92  3.000
 BIE  C11  C10  C9   120.08  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
 BIE  CONST_01  C1   C6   C5   C4     0.00   0.0  0
 BIE  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 BIE  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 BIE  CONST_04  C2   C1   C6   C5     0.00   0.0  0
 BIE  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 BIE  CONST_06  C3   C2   C1   C6     0.00   0.0  0
 BIE  CONST_07  C11  C10  C9   C8     0.00   0.0  0
 BIE  CONST_08  C11  C12  C13  C8     0.00   0.0  0
 BIE  CONST_09  C12  C13  C8   C9     0.00   0.0  0
 BIE  CONST_10  C12  C11  C10  C9     0.00   0.0  0
 BIE  CONST_11  C10  C9   C8   C13    0.00   0.0  0
 BIE  CONST_12  C10  C11  C12  C13    0.00   0.0  0
 BIE  CONST_13  C6   C5   C4   C7   180.00   0.0  0
 BIE  CONST_14  C2   C3   C4   C7   180.00   0.0  0
 BIE  CONST_15  C10  C9   C8   C7   180.00   0.0  0
 BIE  CONST_16  C12  C13  C8   C7   180.00   0.0  0
 BIE  CONST_17  O2   C2   C3   C4   180.00   0.0  0
 BIE  CONST_18  N1   C3   C4   C5   180.00   0.0  0
 BIE  CONST_19  O1   C1   C6   C5   180.00   0.0  0
 BIE  CONST_20  O2   C2   C1   C6   180.00   0.0  0
 BIE  CONST_21  O1   C1   C2   C3   180.00   0.0  0
 BIE  CONST_22  C1   C2   C3   N1   180.00   0.0  0
 BIE  CONST_23  H6   C6   C5   C4   180.00   0.0  0
 BIE  CONST_24  H5   C5   C4   C3   180.00   0.0  0
 BIE  CONST_25  H10  C10  C9   C8   180.00   0.0  0
 BIE  CONST_26  H12  C12  C13  C8   180.00   0.0  0
 BIE  CONST_27  H13  C13  C8   C9   180.00   0.0  0
 BIE  CONST_28  H11  C11  C10  C9   180.00   0.0  0
 BIE  CONST_29  H9   C9   C8   C13  180.00   0.0  0
 BIE  Var_01    C9   C8   C7   C4   159.66  30.0  2
 BIE  Var_02    C8   C7   C4   C5   123.45  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
 BIE  plan-1  C7   0.020
 BIE  plan-1  C4   0.020
 BIE  plan-1  C5   0.020
 BIE  plan-1  C6   0.020
 BIE  plan-1  C3   0.020
 BIE  plan-1  N1   0.020
 BIE  plan-1  C2   0.020
 BIE  plan-1  O2   0.020
 BIE  plan-1  C1   0.020
 BIE  plan-1  O1   0.020
 BIE  plan-1  H5   0.020
 BIE  plan-1  H6   0.020
 BIE  plan-2  C7   0.020
 BIE  plan-2  C8   0.020
 BIE  plan-2  C9   0.020
 BIE  plan-2  C13  0.020
 BIE  plan-2  C12  0.020
 BIE  plan-2  C11  0.020
 BIE  plan-2  C10  0.020
 BIE  plan-2  H9   0.020
 BIE  plan-2  H13  0.020
 BIE  plan-2  H12  0.020
 BIE  plan-2  H11  0.020
 BIE  plan-2  H10  0.020
 BIE  plan-3  C3   0.020
 BIE  plan-3  N1   0.020
 BIE  plan-3  O4   0.020
 BIE  plan-3  O3   0.020
 BIE  plan-4  O5   0.020
 BIE  plan-4  C7   0.020
 BIE  plan-4  C4   0.020
 BIE  plan-4  C8   0.020

