# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 19:12:19 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (1S,2S,5R,6S)-2-aminobicyclo[3.1.0]hexane-2,6-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@]1(CC[C@H]2[C@@H]([C@@H]12)C(O)=O)C(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
 40F  40F  '(1S,2S,5R,6S)-2-aminobicyclo[3.1.0]hexane-2,6-dicarboxylic acid'  ligand  24  13  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_40F
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
 40F  O1   O  OH1   0  -0.594  -3.3225   0.6019  -0.6128
 40F  C7   C  CH2   0  -0.427  -1.4438  -1.5828   0.4238
 40F  O2   O  OH1   0  -0.598   3.5306   0.2887  -1.0514
 40F  C6   C  CH2   0  -0.451  -0.0755  -2.2054   0.7249
 40F  C1   C  CT    0  -0.021  -1.1352  -0.2278  -0.2624
 40F  C5   C  CH1   0  -0.230   0.8277  -1.0096   0.9844
 40F  C3   C  CH1   0  -0.394   1.4536  -0.3771  -0.2337
 40F  C2   C  CH1   0  -0.234   0.1935   0.1885   0.3765
 40F  O3   O  O     0  -0.457   2.9344   1.0645   0.9548
 40F  N    N  NH2   0  -0.786  -0.9983  -0.4349  -1.6907
 40F  C    C  C     0   0.559  -2.2325   0.7627   0.1259
 40F  O    O  O     0  -0.436  -2.1598   1.5668   1.0220
 40F  H1   H  HOH1  0   0.484  -4.0184   1.2081  -0.3171
 40F  H2   H  HCH2  0   0.250  -2.0880  -2.2139  -0.1905
 40F  H3   H  HCH2  0   0.246  -1.9629  -1.4080   1.3696
 40F  H4   H  HOH1  0   0.480   4.3321   0.8043  -0.8763
 40F  H5   H  HCH2  0   0.254  -0.1202  -2.8639   1.5916
 40F  H6   H  HCH2  0   0.244   0.2826  -2.8035  -0.1147
 40F  H7   H  HCH1  0   0.268   1.3660  -0.9396   1.9217
 40F  H8   H  HCH1  0   0.285   1.3703  -0.9067  -1.1744
 40F  H9   H  HCH1  0   0.272   0.2686   1.1600   0.8459
 40F  H10  H  HNH2  0   0.356  -1.8707  -0.7446  -2.0991
 40F  H11  H  HNH2  0   0.355  -0.7407   0.4264  -2.1572
 40F  C4   C  C     0   0.576   2.6916   0.4012  -0.0267

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
 40F  O   C    double  1.206  0.020  1.206
 40F  N   C1   single  1.450  0.020  1.450
 40F  C   C1   single  1.528  0.020  1.528
 40F  C   O1   single  1.326  0.020  1.326
 40F  C1  C2   single  1.532  0.020  1.532
 40F  C1  C7   single  1.550  0.020  1.550
 40F  C2  C3   single  1.510  0.020  1.510
 40F  C2  C5   single  1.486  0.020  1.486
 40F  C7  C6   single  1.533  0.020  1.533
 40F  C3  C4   single  1.477  0.020  1.477
 40F  C3  C5   single  1.509  0.020  1.509
 40F  C4  O3   double  1.209  0.020  1.209
 40F  C4  O2   single  1.329  0.020  1.329
 40F  C5  C6   single  1.521  0.020  1.521
 40F  O1  H1   single  0.850  0.020  0.980
 40F  C7  H2   single  0.970  0.020  1.090
 40F  C7  H3   single  0.970  0.020  1.090
 40F  O2  H4   single  0.850  0.020  0.980
 40F  C6  H5   single  0.970  0.020  1.090
 40F  C6  H6   single  0.970  0.020  1.090
 40F  C5  H7   single  0.970  0.020  1.090
 40F  C3  H8   single  0.970  0.020  1.090
 40F  C2  H9   single  0.970  0.020  1.090
 40F  N   H10  single  0.890  0.020  1.040
 40F  N   H11  single  0.890  0.020  1.040

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
 40F  H1   O1  C    110.14  3.000
 40F  H3   C7  H2   107.41  3.000
 40F  H3   C7  C1   109.75  3.000
 40F  H2   C7  C1   111.96  3.000
 40F  H3   C7  C6   108.60  3.000
 40F  H2   C7  C6   113.74  3.000
 40F  C1   C7  C6   105.33  3.000
 40F  H4   O2  C4   109.74  3.000
 40F  H6   C6  H5   107.12  3.000
 40F  H6   C6  C5   111.55  3.000
 40F  H5   C6  C5   111.33  3.000
 40F  H6   C6  C7   111.37  3.000
 40F  H5   C6  C7   111.41  3.000
 40F  C5   C6  C7   104.13  3.000
 40F  C    C1  N    114.25  3.000
 40F  C    C1  C2   109.92  3.000
 40F  N    C1  C2   111.58  3.000
 40F  C2   C1  C7   103.04  3.000
 40F  C    C1  C7   108.12  3.000
 40F  N    C1  C7   109.27  3.000
 40F  H7   C5  C2   120.94  3.000
 40F  H7   C5  C3   117.74  3.000
 40F  C2   C5  C3    60.57  3.000
 40F  H7   C5  C6   119.58  3.000
 40F  C3   C5  C6   115.99  3.000
 40F  C2   C5  C6   108.11  3.000
 40F  H8   C3  C2   118.04  3.000
 40F  H8   C3  C4   116.36  3.000
 40F  C2   C3  C4   116.45  3.000
 40F  H8   C3  C5   117.68  3.000
 40F  C4   C3  C5   117.10  3.000
 40F  C2   C3  C5    58.97  3.000
 40F  H9   C2  C3   117.00  3.000
 40F  H9   C2  C5   121.14  3.000
 40F  C3   C2  C5    60.47  3.000
 40F  H9   C2  C1   119.03  3.000
 40F  C5   C2  C1   108.77  3.000
 40F  C3   C2  C1   116.96  3.000
 40F  H11  N   H10  107.08  3.000
 40F  H11  N   C1   110.87  3.000
 40F  H10  N   C1   111.09  3.000
 40F  O    C   C1   125.28  3.000
 40F  C1   C   O1   111.71  3.000
 40F  O    C   O1   122.96  3.000
 40F  O3   C4  C3   124.83  3.000
 40F  O3   C4  O2   123.06  3.000
 40F  C3   C4  O2   112.12  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
 40F  CONST_01  H1  O1  C   C1  180.00   0.0  0
 40F  CONST_02  H4  O2  C4  C3  180.00   0.0  0
 40F  Var_01    C2  C5  C6  C7  -20.26  30.0  1
 40F  Var_02    C1  C2  C5  C6    0.80  30.0  1
 40F  Var_03    C5  C3  C2  C1  -97.28  30.0  1
 40F  Var_04    C5  C6  C7  C1   31.83  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 40F  chir_01  C1  C   C2  C7  negativ
 40F  chir_02  C5  C2  C3  C6  both
 40F  chir_03  C3  C5  C4  C2  both
 40F  chir_04  C2  C5  C3  C1  both

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
 40F  plan-1  O1  0.020
 40F  plan-1  C1  0.020
 40F  plan-1  C   0.020
 40F  plan-1  O   0.020
 40F  plan-1  H1  0.020
 40F  plan-2  O2  0.020
 40F  plan-2  C3  0.020
 40F  plan-2  O3  0.020
 40F  plan-2  H4  0.020
 40F  plan-2  C4  0.020

