# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:29:19 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: 7-nitro-9H-fluoren-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc2c(Cc3cc(ccc23)[N+]([O-])=O)c1
#
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
 HNF  HNF  '7-nitro-9H-fluoren-2-ol  '  ligand  26  17  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HNF
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
 HNF  H15'  H  HOH1   0   0.478  -5.6470   1.1872   0.1442
 HNF  O1    O  OH1    0  -0.626  -5.4632   0.2412   0.1195
 HNF  C1    C  CR6    0   0.371  -4.1377   0.0191   0.0894
 HNF  C2    C  CR16   0  -0.339  -3.7134  -1.3150   0.0504
 HNF  C3    C  CR16   0  -0.322  -2.3653  -1.6197   0.0180
 HNF  C4    C  CR56   0   0.102  -1.4352  -0.5853   0.0245
 HNF  C5    C  CR56   0   0.061  -1.8641   0.7459   0.0628
 HNF  C6    C  CR16   0  -0.454  -3.2088   1.0601   0.0954
 HNF  C7    C  CR56   0   0.145   0.0171  -0.6023  -0.0021
 HNF  C8    C  CR56   0   0.044   0.4768   0.7238   0.0195
 HNF  C9    C  CH2    0  -0.519  -0.6845   1.6757   0.0605
 HNF  C10   C  CR16   0  -0.348   0.9172  -1.6613  -0.0418
 HNF  C11   C  CR16   0  -0.266   2.2741  -1.3904  -0.0598
 HNF  C12   C  CR6    0   0.244   2.7106  -0.0688  -0.0383
 HNF  C13   C  CR16   0  -0.345   1.8231   1.0057   0.0014
 HNF  N1    N  N      1   0.326   4.1329   0.2022  -0.0576
 HNF  O2    O  O     -1  -0.388   4.8978  -0.7357  -0.0862
 HNF  O3    O  O      0  -0.387   4.4947   1.3577  -0.0443
 HNF  H25'  H  HCR6   0   0.270  -4.4535  -2.1048   0.0454
 HNF  H4'   H  HCR6   0   0.255  -2.0508  -2.6557  -0.0126
 HNF  H1'   H  HCR6   0   0.273  -3.5388   2.0931   0.1262
 HNF  H12'  H  HCH2   0   0.289  -0.6930   2.3454  -0.8034
 HNF  H22'  H  HCH2   0   0.289  -0.6615   2.3119   0.9493
 HNF  H3'   H  HCR6   0   0.262   0.5760  -2.6882  -0.0583
 HNF  HO3'  H  HCR6   0   0.295   2.9814  -2.2059  -0.0904
 HNF  H3    H  HCR6   0   0.289   2.1764   2.0274   0.0179

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
 HNF  O1   H15'  single    0.850  0.020  0.980
 HNF  C1   C2    aromatic  1.400  0.020  1.400
 HNF  C1   O1    single    1.344  0.020  1.344
 HNF  C2   H25'  single    0.930  0.020  1.080
 HNF  C3   C2    aromatic  1.383  0.020  1.383
 HNF  C3   H4'   single    0.930  0.020  1.080
 HNF  C4   C3    aromatic  1.391  0.020  1.391
 HNF  C5   C4    aromatic  1.399  0.020  1.399
 HNF  C5   C6    aromatic  1.381  0.020  1.381
 HNF  C6   C1    aromatic  1.395  0.020  1.395
 HNF  C6   H1'   single    0.930  0.020  1.080
 HNF  C7   C10   aromatic  1.390  0.020  1.390
 HNF  C7   C4    aromatic  1.453  0.020  1.453
 HNF  C8   C9    single    1.502  0.020  1.502
 HNF  C8   C7    aromatic  1.404  0.020  1.404
 HNF  C9   C5    single    1.502  0.020  1.502
 HNF  C9   H12'  single    0.970  0.020  1.090
 HNF  C9   H22'  single    0.970  0.020  1.090
 HNF  C10  H3'   single    0.930  0.020  1.080
 HNF  C11  C10   aromatic  1.384  0.020  1.384
 HNF  C11  HO3'  single    0.930  0.020  1.080
 HNF  C12  C11   aromatic  1.392  0.020  1.392
 HNF  C13  C12   aromatic  1.394  0.020  1.394
 HNF  C13  C8    aromatic  1.376  0.020  1.376
 HNF  C13  H3    single    0.930  0.020  1.080
 HNF  N1   O2    single    1.211  0.020  1.211
 HNF  N1   C12   single    1.448  0.020  1.448
 HNF  O3   N1    double    1.211  0.020  1.211

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
 HNF  C1    O1   H15'  110.53  3.000
 HNF  C6    C1   C2    120.61  3.000
 HNF  C6    C1   O1    122.21  3.000
 HNF  C2    C1   O1    117.18  3.000
 HNF  H25'  C2   C3    120.38  3.000
 HNF  C3    C2   C1    120.40  3.000
 HNF  H25'  C2   C1    119.22  3.000
 HNF  H4'   C3   C4    121.15  3.000
 HNF  C4    C3   C2    119.21  3.000
 HNF  H4'   C3   C2    119.65  3.000
 HNF  C7    C4   C5    108.55  3.000
 HNF  C7    C4   C3    131.28  3.000
 HNF  C5    C4   C3    120.18  3.000
 HNF  C9    C5   C6    128.60  3.000
 HNF  C9    C5   C4    110.38  3.000
 HNF  C6    C5   C4    121.03  3.000
 HNF  H1'   C6   C5    120.89  3.000
 HNF  H1'   C6   C1    120.53  3.000
 HNF  C5    C6   C1    118.58  3.000
 HNF  C10   C7   C8    120.53  3.000
 HNF  C8    C7   C4    108.43  3.000
 HNF  C10   C7   C4    131.04  3.000
 HNF  C13   C8   C9    128.84  3.000
 HNF  C13   C8   C7    120.92  3.000
 HNF  C9    C8   C7    110.24  3.000
 HNF  H22'  C9   H12'  106.62  3.000
 HNF  H22'  C9   C8    112.00  3.000
 HNF  H12'  C9   C8    111.88  3.000
 HNF  H22'  C9   C5    112.06  3.000
 HNF  H12'  C9   C5    111.98  3.000
 HNF  C8    C9   C5    102.41  3.000
 HNF  H3'   C10  C11   119.65  3.000
 HNF  C11   C10  C7    119.08  3.000
 HNF  H3'   C10  C7    121.27  3.000
 HNF  HO3'  C11  C12   120.80  3.000
 HNF  C12   C11  C10   119.54  3.000
 HNF  HO3'  C11  C10   119.65  3.000
 HNF  N1    C12  C13   118.78  3.000
 HNF  N1    C12  C11   119.04  3.000
 HNF  C13   C12  C11   122.18  3.000
 HNF  H3    C13  C12   121.38  3.000
 HNF  H3    C13  C8    120.88  3.000
 HNF  C12   C13  C8    117.74  3.000
 HNF  O3    N1   O2    123.43  3.000
 HNF  O3    N1   C12   118.16  3.000
 HNF  O2    N1   C12   118.42  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
 HNF  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 HNF  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 HNF  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 HNF  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 HNF  CONST_05  C7    C4   C3   C2   180.00   0.0  0
 HNF  CONST_06  C6    C1   C2   C3     0.00   0.0  0
 HNF  CONST_07  C6    C5   C4   C3     0.00   0.0  0
 HNF  CONST_08  C10   C7   C4   C3     0.00   0.0  0
 HNF  CONST_09  C8    C7   C4   C3   180.00   0.0  0
 HNF  CONST_10  C11   C10  C7   C4   180.00   0.0  0
 HNF  CONST_11  C13   C8   C7   C4   180.00   0.0  0
 HNF  CONST_12  C10   C7   C4   C5   180.00   0.0  0
 HNF  CONST_13  C8    C7   C4   C5     0.00   0.0  0
 HNF  CONST_14  C7    C4   C5   C6   180.00   0.0  0
 HNF  CONST_15  C12   C11  C10  C7     0.00   0.0  0
 HNF  CONST_16  C12   C13  C8   C7     0.00   0.0  0
 HNF  CONST_17  C11   C10  C7   C8     0.00   0.0  0
 HNF  CONST_18  C11   C12  C13  C8     0.00   0.0  0
 HNF  CONST_19  C13   C8   C7   C10    0.00   0.0  0
 HNF  CONST_20  C13   C12  C11  C10    0.00   0.0  0
 HNF  CONST_21  C3    C2   C1   O1   180.00   0.0  0
 HNF  CONST_22  C5    C6   C1   O1   180.00   0.0  0
 HNF  CONST_23  N1    C12  C13  C8   180.00   0.0  0
 HNF  CONST_24  N1    C12  C11  C10  180.00   0.0  0
 HNF  CONST_25  H4'   C3   C2   C1   180.00   0.0  0
 HNF  CONST_26  H1'   C6   C1   C2   180.00   0.0  0
 HNF  CONST_27  H25'  C2   C3   C4   180.00   0.0  0
 HNF  CONST_28  H3'   C10  C7   C4     0.00   0.0  0
 HNF  CONST_29  HO3'  C11  C10  C7   180.00   0.0  0
 HNF  CONST_30  H3    C13  C8   C7   180.00   0.0  0
 HNF  CONST_31  O2    N1   C12  C11    0.00   0.0  0
 HNF  CONST_32  O3    N1   C12  C11  180.00   0.0  0
 HNF  CONST_33  O2    N1   C12  C13  180.00   0.0  0
 HNF  CONST_34  O3    N1   C12  C13    0.00   0.0  0
 HNF  Var_01    H12'  C9   C5   C4   119.90  30.0  1

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
 HNF  plan-1  O1    0.020
 HNF  plan-1  C1    0.020
 HNF  plan-1  C2    0.020
 HNF  plan-1  C3    0.020
 HNF  plan-1  C4    0.020
 HNF  plan-1  C5    0.020
 HNF  plan-1  C6    0.020
 HNF  plan-1  C7    0.020
 HNF  plan-1  C8    0.020
 HNF  plan-1  C9    0.020
 HNF  plan-1  C10   0.020
 HNF  plan-1  C11   0.020
 HNF  plan-1  C12   0.020
 HNF  plan-1  C13   0.020
 HNF  plan-1  N1    0.020
 HNF  plan-1  H25'  0.020
 HNF  plan-1  H4'   0.020
 HNF  plan-1  H1'   0.020
 HNF  plan-1  H3'   0.020
 HNF  plan-1  HO3'  0.020
 HNF  plan-1  H3    0.020
 HNF  plan-2  C12   0.020
 HNF  plan-2  N1    0.020
 HNF  plan-2  O2    0.020
 HNF  plan-2  O3    0.020

