# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:36:13 2022
#   Inital geometry file: a 67 line input string
#   Ligand name: 9H-fluoren-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc2c(Cc3ccccc23)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
 AF  AF  '9H-fluoren-2-amine       '  ligand  25  14  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AF
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
 AF  N    N  NH2   0  -0.860  3.0317   4.8370  4.4748
 AF  C2   C  CR6   0   0.311  3.1804   3.5225  4.0894
 AF  C3   C  CR16  0  -0.324  4.4435   3.0266  3.7246
 AF  C4   C  CR16  0  -0.339  4.6213   1.6955  3.3868
 AF  C4A  C  CR56  0   0.084  3.5328   0.8331  3.4069
 AF  C4B  C  CR56  0   0.135  3.4145  -0.5885  3.1020
 AF  C5   C  CR16  0  -0.356  4.3640  -1.5176  2.6959
 AF  C6   C  CR16  0  -0.255  3.9635  -2.8292  2.4679
 AF  C7   C  CR16  0  -0.268  2.6358  -3.2074  2.6432
 AF  C8   C  CR16  0  -0.320  1.6839  -2.2756  3.0512
 AF  C8A  C  CR56  0   0.030  2.0771  -0.9697  3.2783
 AF  C9   C  CH2   0  -0.527  1.2542   0.2131  3.7136
 AF  C9A  C  CR56  0   0.054  2.2714   1.3208  3.7678
 AF  C1   C  CR16  0  -0.397  2.0853   2.6456  4.1055
 AF  HN1  H  HNH2  0   0.378  3.7311   5.4780  4.1358
 AF  HN2  H  HNH2  0   0.378  2.1024   5.2174  4.3929
 AF  H3   H  HCR6  0   0.253  5.2913   3.7016  3.7093
 AF  H4   H  HCR6  0   0.243  5.6071   1.3424  3.1079
 AF  H5   H  HCR6  0   0.242  5.3994  -1.2306  2.5567
 AF  H6   H  HCR6  0   0.250  4.6920  -3.5640  2.1494
 AF  H7   H  HCR6  0   0.248  2.3407  -4.2327  2.4603
 AF  H8   H  HCR6  0   0.246  0.6513  -2.5754  3.1857
 AF  H91  H  HCH2  0   0.272  0.7794   0.0475  4.6849
 AF  H92  H  HCH2  0   0.272  0.4475   0.4320  3.0083
 AF  H1   H  HCR6  0   0.249  1.1036   3.0152  4.3821

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
 AF  N    C2   single    1.378  0.020  1.378
 AF  N    HN1  single    0.890  0.020  1.040
 AF  N    HN2  single    0.890  0.020  1.040
 AF  C2   C3   aromatic  1.405  0.020  1.405
 AF  C2   C1   aromatic  1.403  0.020  1.403
 AF  C3   C4   aromatic  1.385  0.020  1.385
 AF  C3   H3   single    0.930  0.020  1.080
 AF  C4   C4A  aromatic  1.389  0.020  1.389
 AF  C4   H4   single    0.930  0.020  1.080
 AF  C4A  C4B  aromatic  1.459  0.020  1.459
 AF  C4A  C9A  aromatic  1.400  0.020  1.400
 AF  C4B  C5   aromatic  1.389  0.020  1.389
 AF  C4B  C8A  aromatic  1.402  0.020  1.402
 AF  C5   C6   aromatic  1.390  0.020  1.390
 AF  C5   H5   single    0.930  0.020  1.080
 AF  C6   C7   aromatic  1.392  0.020  1.392
 AF  C6   H6   single    0.930  0.020  1.080
 AF  C7   C8   aromatic  1.393  0.020  1.393
 AF  C7   H7   single    0.930  0.020  1.080
 AF  C8   C8A  aromatic  1.383  0.020  1.383
 AF  C8   H8   single    0.930  0.020  1.080
 AF  C8A  C9   single    1.505  0.020  1.505
 AF  C9   C9A  single    1.505  0.020  1.505
 AF  C9   H91  single    0.970  0.020  1.090
 AF  C9   H92  single    0.970  0.020  1.090
 AF  C9A  C1   aromatic  1.380  0.020  1.380
 AF  C1   H1   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
 AF  HN2  N    HN1  111.89  3.000
 AF  HN2  N    C2   115.92  3.000
 AF  HN1  N    C2   115.97  3.000
 AF  C1   C2   C3   118.95  3.000
 AF  C1   C2   N    120.58  3.000
 AF  C3   C2   N    120.42  3.000
 AF  H3   C3   C4   119.66  3.000
 AF  H3   C3   C2   119.14  3.000
 AF  C4   C3   C2   121.20  3.000
 AF  H4   C4   C4A  120.95  3.000
 AF  H4   C4   C3   119.53  3.000
 AF  C4A  C4   C3   119.52  3.000
 AF  C9A  C4A  C4B  108.69  3.000
 AF  C9A  C4A  C4   119.58  3.000
 AF  C4B  C4A  C4   131.73  3.000
 AF  C8A  C4B  C5   120.46  3.000
 AF  C8A  C4B  C4A  108.43  3.000
 AF  C5   C4B  C4A  131.11  3.000
 AF  H5   C5   C6   120.27  3.000
 AF  H5   C5   C4B  120.91  3.000
 AF  C6   C5   C4B  118.82  3.000
 AF  H6   C6   C7   119.64  3.000
 AF  H6   C6   C5   119.65  3.000
 AF  C7   C6   C5   120.70  3.000
 AF  H7   C7   C8   119.79  3.000
 AF  H7   C7   C6   119.75  3.000
 AF  C8   C7   C6   120.46  3.000
 AF  H8   C8   C8A  120.79  3.000
 AF  H8   C8   C7   120.16  3.000
 AF  C8A  C8   C7   119.05  3.000
 AF  C9   C8A  C8   129.37  3.000
 AF  C9   C8A  C4B  110.13  3.000
 AF  C8   C8A  C4B  120.50  3.000
 AF  H92  C9   H91  106.43  3.000
 AF  H92  C9   C9A  112.00  3.000
 AF  H91  C9   C9A  111.90  3.000
 AF  H92  C9   C8A  111.96  3.000
 AF  H91  C9   C8A  112.03  3.000
 AF  C9A  C9   C8A  102.67  3.000
 AF  C1   C9A  C9   128.64  3.000
 AF  C1   C9A  C4A  121.28  3.000
 AF  C9   C9A  C4A  110.08  3.000
 AF  H1   C1   C9A  120.77  3.000
 AF  H1   C1   C2   119.75  3.000
 AF  C9A  C1   C2   119.48  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
 AF  CONST_01  C4A  C4   C3   C2     0.00   0.0  0
 AF  CONST_02  C4A  C9A  C1   C2     0.00   0.0  0
 AF  CONST_03  C9A  C1   C2   C3     0.00   0.0  0
 AF  CONST_04  C4B  C4A  C4   C3   180.00   0.0  0
 AF  CONST_05  C9A  C4A  C4   C3     0.00   0.0  0
 AF  CONST_06  C1   C2   C3   C4     0.00   0.0  0
 AF  CONST_07  C5   C4B  C4A  C4     0.00   0.0  0
 AF  CONST_08  C8A  C4B  C4A  C4   180.00   0.0  0
 AF  CONST_09  C1   C9A  C4A  C4     0.00   0.0  0
 AF  CONST_10  C6   C5   C4B  C4A  180.00   0.0  0
 AF  CONST_11  C8   C8A  C4B  C4A  180.00   0.0  0
 AF  CONST_12  C1   C9A  C4A  C4B  180.00   0.0  0
 AF  CONST_13  C7   C6   C5   C4B    0.00   0.0  0
 AF  CONST_14  C7   C8   C8A  C4B    0.00   0.0  0
 AF  CONST_15  C9A  C4A  C4B  C5   180.00   0.0  0
 AF  CONST_16  C8   C8A  C4B  C5     0.00   0.0  0
 AF  CONST_17  C8   C7   C6   C5     0.00   0.0  0
 AF  CONST_18  C8A  C4B  C5   C6     0.00   0.0  0
 AF  CONST_19  C8A  C8   C7   C6     0.00   0.0  0
 AF  CONST_20  C9A  C4A  C4B  C8A    0.00   0.0  0
 AF  CONST_21  C4   C3   C2   N    180.00   0.0  0
 AF  CONST_22  C9A  C1   C2   N    180.00   0.0  0
 AF  CONST_23  H4   C4   C3   C2   180.00   0.0  0
 AF  CONST_24  H1   C1   C2   C3   180.00   0.0  0
 AF  CONST_25  H3   C3   C4   C4A  180.00   0.0  0
 AF  CONST_26  H5   C5   C4B  C4A    0.00   0.0  0
 AF  CONST_27  H6   C6   C5   C4B  180.00   0.0  0
 AF  CONST_28  H8   C8   C8A  C4B  180.00   0.0  0
 AF  CONST_29  H7   C7   C6   C5   180.00   0.0  0
 AF  Var_01    H91  C9   C9A  C4A  120.27  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
 AF  plan-1  N    0.020
 AF  plan-1  C2   0.020
 AF  plan-1  C3   0.020
 AF  plan-1  C4   0.020
 AF  plan-1  C4A  0.020
 AF  plan-1  C4B  0.020
 AF  plan-1  C5   0.020
 AF  plan-1  C6   0.020
 AF  plan-1  C7   0.020
 AF  plan-1  C8   0.020
 AF  plan-1  C8A  0.020
 AF  plan-1  C9   0.020
 AF  plan-1  C9A  0.020
 AF  plan-1  C1   0.020
 AF  plan-1  H3   0.020
 AF  plan-1  H4   0.020
 AF  plan-1  H5   0.020
 AF  plan-1  H6   0.020
 AF  plan-1  H7   0.020
 AF  plan-1  H8   0.020
 AF  plan-1  H1   0.020
 AF  plan-2  N    0.020
 AF  plan-2  C2   0.020
 AF  plan-2  HN1  0.020
 AF  plan-2  HN2  0.020

