# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 20:08:56 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  28  15  .  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_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  OH1   0  -0.597  -3.3775  -1.1360  -1.0875
 40H  C7   C  CH2   0  -0.494  -0.1193   3.2394   0.6058
 40H  O2   O  O     0  -0.436   2.2479  -1.5288   1.5557
 40H  C6   C  CH2   0  -0.472  -0.4274   2.8288  -0.8038
 40H  C1   C  CT    0  -0.020   1.2236  -0.2805  -0.2581
 40H  C5   C  CT    0   0.022   0.0729   1.8199   0.1819
 40H  C4   C  CH1   0  -0.246  -0.8163   0.7173   0.6895
 40H  C3   C  CH1   0  -0.387  -1.3640  -0.2153  -0.3653
 40H  C2   C  CH1   0  -0.234  -0.1251  -0.5689   0.4180
 40H  C9   C  C     0   0.552   2.3215  -1.0883   0.4351
 40H  N    N  NH2   0  -0.782   1.1486  -0.4681  -1.6914
 40H  C8   C  C     0   0.578  -2.5942  -0.9589  -0.0290
 40H  O    O  O     0  -0.458  -2.8767  -1.3617   1.0758
 40H  C    C  CH2   0  -0.432   1.4618   1.2182   0.0591
 40H  H1   H  HOH1  0   0.480  -4.1764  -1.6189  -0.8275
 40H  H2   H  HCH2  0   0.249   0.7669   3.8375   0.7838
 40H  H3   H  HCH2  0   0.250  -0.9481   3.4665   1.2657
 40H  H4   H  HCH2  0   0.247  -1.4670   2.7733  -1.1042
 40H  H5   H  HCH2  0   0.247   0.2481   3.1500  -1.5875
 40H  H6   H  HCH1  0   0.268  -1.3976   0.8613   1.5927
 40H  H7   H  HCH1  0   0.289  -1.2416   0.0799  -1.3994
 40H  H8   H  HCH1  0   0.273  -0.2000  -1.3954   1.1117
 40H  H9   H  HOH1  0   0.484   4.0944  -1.6900   0.1615
 40H  H10  H  HNH2  0   0.355   2.0277  -0.2365  -2.1349
 40H  H11  H  HNH2  0   0.353   0.9465  -1.4342  -1.9178
 40H  H13  H  HCH2  0   0.249   1.9744   1.3166   1.0207
 40H  H14  H  HCH2  0   0.253   2.0857   1.7041  -0.6940
 40H  O3   O  OH1   0  -0.592   3.4042  -1.2090  -0.3197

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  1.500  0.020  1.500
 40H  C6  C5   single  1.497  0.020  1.497
 40H  C7  C5   single  1.494  0.020  1.494
 40H  O   C8   double  1.209  0.020  1.209
 40H  C4  C5   single  1.505  0.020  1.505
 40H  C4  C3   single  1.511  0.020  1.511
 40H  C4  C2   single  1.485  0.020  1.485
 40H  C5  C    single  1.519  0.020  1.519
 40H  C8  O1   single  1.329  0.020  1.329
 40H  C8  C3   single  1.476  0.020  1.476
 40H  C3  C2   single  1.508  0.020  1.508
 40H  C2  C1   single  1.536  0.020  1.536
 40H  C   C1   single  1.550  0.020  1.550
 40H  O2  C9   double  1.206  0.020  1.206
 40H  C1  C9   single  1.529  0.020  1.529
 40H  C1  N    single  1.447  0.020  1.447
 40H  C9  O3   single  1.325  0.020  1.325
 40H  O1  H1   single  0.850  0.020  0.980
 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  O3  H9   single  0.850  0.020  0.980
 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  H1   O1  C8   109.80  3.000
 40H  H3   C7  H2   114.19  3.000
 40H  H3   C7  C5   118.06  3.000
 40H  H2   C7  C5   117.76  3.000
 40H  H3   C7  C6   118.20  3.000
 40H  H2   C7  C6   118.25  3.000
 40H  C5   C7  C6    59.98  3.000
 40H  H5   C6  H4   114.38  3.000
 40H  H5   C6  C5   117.90  3.000
 40H  H4   C6  C5   117.96  3.000
 40H  H5   C6  C7   118.06  3.000
 40H  H4   C6  C7   118.14  3.000
 40H  C5   C6  C7    59.80  3.000
 40H  C    C1  N    109.62  3.000
 40H  N    C1  C9   114.68  3.000
 40H  C    C1  C9   107.91  3.000
 40H  N    C1  C2   111.47  3.000
 40H  C9   C1  C2   109.37  3.000
 40H  C    C1  C2   103.08  3.000
 40H  C    C5  C4   106.11  3.000
 40H  C    C5  C6   121.30  3.000
 40H  C4   C5  C6   121.24  3.000
 40H  C    C5  C7   121.14  3.000
 40H  C4   C5  C7   121.64  3.000
 40H  C6   C5  C7    60.22  3.000
 40H  H6   C4  C2   121.13  3.000
 40H  H6   C4  C3   118.00  3.000
 40H  C2   C4  C3    60.43  3.000
 40H  H6   C4  C5   120.05  3.000
 40H  C2   C4  C5   107.34  3.000
 40H  C3   C4  C5   115.54  3.000
 40H  H7   C3  C8   116.70  3.000
 40H  H7   C3  C2   117.87  3.000
 40H  C8   C3  C2   116.63  3.000
 40H  H7   C3  C4   117.24  3.000
 40H  C2   C3  C4    58.95  3.000
 40H  C8   C3  C4   117.00  3.000
 40H  H8   C2  C3   117.10  3.000
 40H  H8   C2  C4   120.82  3.000
 40H  C3   C2  C4    60.63  3.000
 40H  H8   C2  C1   119.11  3.000
 40H  C3   C2  C1   116.66  3.000
 40H  C4   C2  C1   109.06  3.000
 40H  O3   C9  C1   112.12  3.000
 40H  O3   C9  O2   123.06  3.000
 40H  C1   C9  O2   124.76  3.000
 40H  H11  N   H10  107.09  3.000
 40H  H11  N   C1   110.82  3.000
 40H  H10  N   C1   111.07  3.000
 40H  O    C8  C3   124.79  3.000
 40H  C3   C8  O1   112.14  3.000
 40H  O    C8  O1   123.07  3.000
 40H  H14  C   H13  107.37  3.000
 40H  H14  C   C5   113.70  3.000
 40H  H13  C   C5   108.77  3.000
 40H  H14  C   C1   112.14  3.000
 40H  H13  C   C1   109.80  3.000
 40H  C5   C   C1   105.01  3.000
 40H  H9   O3  C9   110.13  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  CONST_01  H9  O3  C9  C1  180.00   0.0  0
 40H  CONST_02  H1  O1  C8  C3  180.00   0.0  0
 40H  Var_01    C4  C5  C6  C7  111.09  30.0  3
 40H  Var_02    C3  C4  C5  C7  131.79  30.0  1
 40H  Var_03    C1  C   C5  C7  174.52  30.0  1
 40H  Var_04    C5  C4  C2  C1    0.51  30.0  1
 40H  Var_05    C2  C3  C4  C5   96.23  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  H9  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
 40H  plan-2  H1  0.020

