# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 20:33:07 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: (1R,4S,5S,6S)-4-aminospiro[bicyclo[3.1.0]hexane-2,1'-cyclopropane]-4,6-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@]1(CC2(CC2)[C@H]3[C@@H]([C@@H]13)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
 40H  40H  '(1R,4S,5S,6S)-4-aminospiro[bicyclo[3.1.0]hexane-2,1'-cyclopropane]-4,6-dicarboxylic acid'  ligand  26  15  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_40H
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
 40H  O1   O  OC    -1  -0.627  -3.4075  -1.1197  -1.1645
 40H  C7   C  CH2    0  -0.502  -0.1294   3.2703   0.6451
 40H  O2   O  O      0  -0.605   2.1774  -1.3408   1.6657
 40H  C6   C  CH2    0  -0.475  -0.4046   2.8976  -0.7841
 40H  C1   C  CT     0  -0.008   1.2109  -0.2547  -0.2418
 40H  C5   C  CT     0   0.040   0.0568   1.8587   0.1892
 40H  C4   C  CH1    0  -0.269  -0.8623   0.7559   0.6442
 40H  C3   C  CH1    0  -0.383  -1.3921  -0.1594  -0.4261
 40H  C2   C  CH1    0  -0.252  -0.1670  -0.5344   0.3663
 40H  C9   C  C      0   0.400   2.3288  -1.0786   0.4555
 40H  N    N  NH2    0  -0.798   1.1884  -0.4287  -1.6926
 40H  C8   C  C      0   0.424  -2.6755  -0.9158  -0.1715
 40H  O    O  O      0  -0.616  -2.9109  -1.2765   1.0018
 40H  C    C  CH2    0  -0.421   1.4408   1.2415   0.0823
 40H  H2   H  HCH2   0   0.236   0.7563   3.8587   0.8587
 40H  H3   H  HCH2   0   0.238  -0.9744   3.4966   1.2853
 40H  H4   H  HCH2   0   0.235  -1.4367   2.8650  -1.1139
 40H  H5   H  HCH2   0   0.234   0.2945   3.2355  -1.5404
 40H  H6   H  HCH1   0   0.226  -1.4576   0.8895   1.5410
 40H  H7   H  HCH1   0   0.225  -1.2301   0.1674  -1.4471
 40H  H8   H  HCH1   0   0.225  -0.2658  -1.3607   1.0571
 40H  H10  H  HNH2   0   0.325   2.1542  -0.4762  -1.9991
 40H  H11  H  HNH2   0   0.326   0.8066  -1.3452  -1.9013
 40H  H13  H  HCH2   0   0.217   1.9410   1.3325   1.0514
 40H  H14  H  HCH2   0   0.216   2.0763   1.7328  -0.6598
 40H  O3   O  OC    -1  -0.612   3.3251  -1.3677  -0.2401

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
 40H  C6  C7   single  1.502  0.020  1.502
 40H  C6  C5   single  1.496  0.020  1.496
 40H  C7  C5   single  1.495  0.020  1.495
 40H  O   C8   deloc   1.250  0.020  1.250
 40H  C4  C5   single  1.506  0.020  1.506
 40H  C4  C3   single  1.505  0.020  1.505
 40H  C4  C2   single  1.492  0.020  1.492
 40H  C5  C    single  1.519  0.020  1.519
 40H  C8  O1   deloc   1.250  0.020  1.250
 40H  C8  C3   single  1.511  0.020  1.511
 40H  C3  C2   single  1.506  0.020  1.506
 40H  C2  C1   single  1.532  0.020  1.532
 40H  C   C1   single  1.548  0.020  1.548
 40H  O2  C9   deloc   1.247  0.020  1.247
 40H  C1  C9   single  1.554  0.020  1.554
 40H  C1  N    single  1.461  0.020  1.461
 40H  C9  O3   deloc   1.249  0.020  1.249
 40H  C7  H2   single  0.970  0.020  1.090
 40H  C7  H3   single  0.970  0.020  1.090
 40H  C6  H4   single  0.970  0.020  1.090
 40H  C6  H5   single  0.970  0.020  1.090
 40H  C4  H6   single  0.970  0.020  1.090
 40H  C3  H7   single  0.970  0.020  1.090
 40H  C2  H8   single  0.970  0.020  1.090
 40H  N   H10  single  0.890  0.020  1.040
 40H  N   H11  single  0.890  0.020  1.040
 40H  C   H13  single  0.970  0.020  1.090
 40H  C   H14  single  0.970  0.020  1.090

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
 40H  H3   C7  H2   114.02  3.000
 40H  H3   C7  C5   118.31  3.000
 40H  H2   C7  C5   118.07  3.000
 40H  H3   C7  C6   118.09  3.000
 40H  H2   C7  C6   118.13  3.000
 40H  C5   C7  C6    59.90  3.000
 40H  H5   C6  H4   114.28  3.000
 40H  H5   C6  C5   118.12  3.000
 40H  H4   C6  C5   118.07  3.000
 40H  H5   C6  C7   117.92  3.000
 40H  H4   C6  C7   118.12  3.000
 40H  C5   C6  C7    59.81  3.000
 40H  C    C1  N    108.98  3.000
 40H  N    C1  C9   113.17  3.000
 40H  C    C1  C9   108.16  3.000
 40H  N    C1  C2   111.01  3.000
 40H  C9   C1  C2   111.84  3.000
 40H  C    C1  C2   103.12  3.000
 40H  C    C5  C4   106.25  3.000
 40H  C    C5  C6   121.14  3.000
 40H  C4   C5  C6   121.11  3.000
 40H  C    C5  C7   121.23  3.000
 40H  C4   C5  C7   121.55  3.000
 40H  C6   C5  C7    60.29  3.000
 40H  H6   C4  C2   121.08  3.000
 40H  H6   C4  C3   118.02  3.000
 40H  C2   C4  C3    60.36  3.000
 40H  H6   C4  C5   119.64  3.000
 40H  C2   C4  C5   107.02  3.000
 40H  C3   C4  C5   116.45  3.000
 40H  H7   C3  C8   115.87  3.000
 40H  H7   C3  C2   116.67  3.000
 40H  C8   C3  C2   118.51  3.000
 40H  H7   C3  C4   115.71  3.000
 40H  C2   C3  C4    59.40  3.000
 40H  C8   C3  C4   118.93  3.000
 40H  H8   C2  C3   116.87  3.000
 40H  H8   C2  C4   119.95  3.000
 40H  C3   C2  C4    60.24  3.000
 40H  H8   C2  C1   118.38  3.000
 40H  C3   C2  C1   118.50  3.000
 40H  C4   C2  C1   109.58  3.000
 40H  O3   C9  C1   116.53  3.000
 40H  O3   C9  O2   126.05  3.000
 40H  C1   C9  O2   117.35  3.000
 40H  H11  N   H10  104.70  3.000
 40H  H11  N   C1   108.52  3.000
 40H  H10  N   C1   106.92  3.000
 40H  O    C8  C3   117.55  3.000
 40H  C3   C8  O1   116.42  3.000
 40H  O    C8  O1   126.03  3.000
 40H  H14  C   H13  107.33  3.000
 40H  H14  C   C5   113.24  3.000
 40H  H13  C   C5   108.68  3.000
 40H  H14  C   C1   112.24  3.000
 40H  H13  C   C1   109.49  3.000
 40H  C5   C   C1   105.79  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
 40H  Var_01  C4  C5  C6  C7  111.06  30.0  3
 40H  Var_02  C3  C4  C5  C7  132.39  30.0  1
 40H  Var_03  C1  C   C5  C7  173.08  30.0  1
 40H  Var_04  C5  C4  C2  C1    1.13  30.0  1
 40H  Var_05  C2  C3  C4  C5   95.34  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
 40H  chir_01  C1  C   C2  N   negativ
 40H  chir_02  C4  C5  C3  C2  both
 40H  chir_03  C3  C4  C8  C2  both
 40H  chir_04  C2  C4  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
 40H  plan-1  O2  0.020
 40H  plan-1  C1  0.020
 40H  plan-1  C9  0.020
 40H  plan-1  O3  0.020
 40H  plan-2  O1  0.020
 40H  plan-2  C3  0.020
 40H  plan-2  C8  0.020
 40H  plan-2  O   0.020

