# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 20:10:42 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  22  13  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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  OC    -1  -0.609  -3.2357   0.8852  -0.7176
 40F  C7   C  CH2    0  -0.416  -1.4251  -1.5819   0.4832
 40F  O2   O  OC    -1  -0.628   3.4982   0.4248  -1.1397
 40F  C6   C  CH2    0  -0.444  -0.0369  -2.1748   0.7561
 40F  C1   C  CT     0  -0.003  -1.1766  -0.2447  -0.2541
 40F  C5   C  CH1    0  -0.246   0.8552  -0.9563   0.9471
 40F  C3   C  CH1    0  -0.394   1.4395  -0.3387  -0.2937
 40F  C2   C  CH1    0  -0.251   0.1707   0.2078   0.3128
 40F  O3   O  O      0  -0.616   2.8629   1.1519   0.8673
 40F  N    N  NH2    0  -0.803  -1.0850  -0.5143  -1.6883
 40F  C    C  C      0   0.400  -2.3146   0.7477   0.1142
 40F  O    O  O      0  -0.607  -2.2503   1.2937   1.2342
 40F  H2   H  HCH2   0   0.212  -2.0795  -2.2495  -0.0837
 40F  H3   H  HCH2   0   0.216  -1.9119  -1.3807   1.4406
 40F  H5   H  HCH2   0   0.226  -0.0383  -2.8171   1.6386
 40F  H6   H  HCH2   0   0.216   0.3013  -2.7911  -0.0808
 40F  H7   H  HCH1   0   0.227   1.4029  -0.8411   1.8754
 40F  H8   H  HCH1   0   0.220   1.3398  -0.9167  -1.2071
 40F  H9   H  HCH1   0   0.226   0.2350   1.1882   0.7652
 40F  H10  H  HNH2   0   0.326  -2.0350  -0.5490  -2.0417
 40F  H11  H  HNH2   0   0.327  -0.6712   0.2923  -2.1432
 40F  C4   C  C      0   0.422   2.7035   0.4828  -0.1760

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    deloc   1.248  0.020  1.248
 40F  N   C1   single  1.462  0.020  1.462
 40F  C   C1   single  1.554  0.020  1.554
 40F  C   O1   deloc   1.249  0.020  1.249
 40F  C1  C2   single  1.530  0.020  1.530
 40F  C1  C7   single  1.547  0.020  1.547
 40F  C2  C3   single  1.509  0.020  1.509
 40F  C2  C5   single  1.492  0.020  1.492
 40F  C7  C6   single  1.534  0.020  1.534
 40F  C3  C4   single  1.512  0.020  1.512
 40F  C3  C5   single  1.504  0.020  1.504
 40F  C4  O3   deloc   1.250  0.020  1.250
 40F  C4  O2   deloc   1.250  0.020  1.250
 40F  C5  C6   single  1.522  0.020  1.522
 40F  C7  H2   single  0.970  0.020  1.090
 40F  C7  H3   single  0.970  0.020  1.090
 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  H3   C7  H2   107.46  3.000
 40F  H3   C7  C1   109.27  3.000
 40F  H2   C7  C1   112.13  3.000
 40F  H3   C7  C6   108.57  3.000
 40F  H2   C7  C6   113.45  3.000
 40F  C1   C7  C6   105.87  3.000
 40F  H6   C6  H5   106.71  3.000
 40F  H6   C6  C5   111.48  3.000
 40F  H5   C6  C5   111.74  3.000
 40F  H6   C6  C7   111.20  3.000
 40F  H5   C6  C7   111.72  3.000
 40F  C5   C6  C7   104.08  3.000
 40F  C    C1  N    113.33  3.000
 40F  C    C1  C2   111.60  3.000
 40F  N    C1  C2   111.27  3.000
 40F  C2   C1  C7   102.73  3.000
 40F  C    C1  C7   108.74  3.000
 40F  N    C1  C7   108.55  3.000
 40F  H7   C5  C2   120.86  3.000
 40F  H7   C5  C3   117.81  3.000
 40F  C2   C5  C3    60.47  3.000
 40F  H7   C5  C6   119.25  3.000
 40F  C3   C5  C6   116.92  3.000
 40F  C2   C5  C6   107.60  3.000
 40F  H8   C3  C2   117.00  3.000
 40F  H8   C3  C4   115.56  3.000
 40F  C2   C3  C4   118.35  3.000
 40F  H8   C3  C5   116.10  3.000
 40F  C4   C3  C5   118.92  3.000
 40F  C2   C3  C5    59.37  3.000
 40F  H9   C2  C3   116.52  3.000
 40F  H9   C2  C5   120.14  3.000
 40F  C3   C2  C5    60.16  3.000
 40F  H9   C2  C1   118.38  3.000
 40F  C5   C2  C1   109.31  3.000
 40F  C3   C2  C1   118.97  3.000
 40F  H11  N   H10  104.66  3.000
 40F  H11  N   C1   108.60  3.000
 40F  H10  N   C1   106.83  3.000
 40F  O    C   C1   117.03  3.000
 40F  C1   C   O1   116.91  3.000
 40F  O    C   O1   126.00  3.000
 40F  O3   C4  C3   117.55  3.000
 40F  O3   C4  O2   125.96  3.000
 40F  C3   C4  O2   116.49  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  Var_01  C2  C5  C6  C7  -20.51  30.0  1
 40F  Var_02  C1  C2  C5  C6    1.51  30.0  1
 40F  Var_03  C5  C3  C2  C1  -96.79  30.0  1
 40F  Var_04  C5  C6  C7  C1   31.82  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-2  O2  0.020
 40F  plan-2  C3  0.020
 40F  plan-2  O3  0.020
 40F  plan-2  C4  0.020

