# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 11:46:28 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (1R,2S,4R,5R,6R)-2-amino-4-(1H-1,2,4-triazol-3-ylsulfanyl)bicyclo[3.1.0]hexane-2,6-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@]1(C[C@@H](Sc2n[nH]cn2)[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
 52Q  52Q  '(1R,2S,4R,5R,6R)-2-amino-4-(1H-1,2,4-triazol-3-ylsulfanyl)bicyclo[3.1.0]hexane-2,6-dicarboxylic acid'  ligand  29  19  .  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_52Q
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
 52Q  C7   C  CH1    0  -0.230   1.1795  -0.4970   0.8229
 52Q  C6   C  CH1    0  -0.407   2.0233  -0.9602  -0.3383
 52Q  C1   C  CR15   0   0.115  -4.5059   0.3566   0.3492
 52Q  C5   C  CH2    0  -0.458  -0.1470   0.8195  -0.7039
 52Q  C4   C  C      0   0.410   1.1068   2.7845   0.2302
 52Q  C3   C  C      0   0.429   3.2038  -1.8597  -0.0417
 52Q  C2   C  CR5    0   0.173  -2.8445  -0.8768   0.0940
 52Q  C8   C  CH1    0  -0.221   2.0751   0.4675   0.1357
 52Q  C9   C  CH1    0  -0.345  -0.2391  -0.0892   0.5217
 52Q  C10  C  CT     0  -0.004   1.2468   1.4904  -0.6207
 52Q  N11  N  NR15   0  -0.413  -4.8221  -0.6488  -0.4616
 52Q  N12  N  N      0  -0.266  -3.7666  -1.4471  -0.6500
 52Q  N13  N  N      0  -0.446  -3.2536   0.2420   0.7328
 52Q  N14  N  NH2    0  -0.799   1.7819   1.7109  -1.9576
 52Q  O15  O  OC    -1  -0.623   3.4766  -2.7202  -0.9048
 52Q  O16  O  OC    -1  -0.605   1.2002   3.8755  -0.3673
 52Q  O17  O  O      0  -0.612   3.8117  -1.6730   1.0332
 52Q  O18  O  O      0  -0.599   0.8721   2.6275   1.4456
 52Q  S19  S  S2     0   0.022  -1.2552  -1.5845   0.2596
 52Q  H1   H  HCH1   0   0.246   1.4126  -0.8785   1.8095
 52Q  H2   H  HCH1   0   0.226   1.5195  -1.1586  -1.2794
 52Q  H4   H  HCH2   0   0.238  -0.1924   0.2286  -1.6210
 52Q  H5   H  HCH2   0   0.249  -0.9705   1.5340  -0.7447
 52Q  H6   H  HCH1   0   0.239   2.9917   0.7945   0.6139
 52Q  H7   H  HCH1   0   0.286  -0.6526   0.4471   1.3736
 52Q  H8   H  HNR5   0   0.436  -5.7006  -0.8339  -0.9213
 52Q  H9   H  HNH2   0   0.326   1.3356   2.5400  -2.3342
 52Q  H10  H  HNH2   0   0.329   2.7558   1.9800  -1.8690
 52Q  H3   H  HCR5   0   0.304  -5.1988   1.1331   0.6331

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
 52Q  C1   N11  aromatic  1.330  0.020  1.330
 52Q  C1   N13  aromatic  1.315  0.020  1.315
 52Q  N11  N12  aromatic  1.337  0.020  1.337
 52Q  N13  C2   aromatic  1.352  0.020  1.352
 52Q  N12  C2   aromatic  1.315  0.020  1.315
 52Q  C2   S19  single    1.748  0.020  1.748
 52Q  S19  C9   single    1.827  0.020  1.827
 52Q  C9   C7   single    1.506  0.020  1.506
 52Q  C9   C5   single    1.528  0.020  1.528
 52Q  C7   C6   single    1.508  0.020  1.508
 52Q  C7   C8   single    1.485  0.020  1.485
 52Q  O17  C3   deloc     1.249  0.020  1.249
 52Q  O15  C3   deloc     1.249  0.020  1.249
 52Q  C3   C6   single    1.513  0.020  1.513
 52Q  C6   C8   single    1.505  0.020  1.505
 52Q  C5   C10  single    1.549  0.020  1.549
 52Q  C8   C10  single    1.518  0.020  1.518
 52Q  O18  C4   deloc     1.248  0.020  1.248
 52Q  C10  C4   single    1.555  0.020  1.555
 52Q  C10  N14  single    1.457  0.020  1.457
 52Q  C4   O16  deloc     1.247  0.020  1.247
 52Q  C7   H1   single    0.970  0.020  1.090
 52Q  C6   H2   single    0.970  0.020  1.090
 52Q  C1   H3   single    0.930  0.020  1.080
 52Q  C5   H4   single    0.970  0.020  1.090
 52Q  C5   H5   single    0.970  0.020  1.090
 52Q  C8   H6   single    0.970  0.020  1.090
 52Q  C9   H7   single    0.970  0.020  1.090
 52Q  N11  H8   single    0.860  0.020  1.020
 52Q  N14  H9   single    0.890  0.020  1.040
 52Q  N14  H10  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
 52Q  H1   C7   C9   118.69  3.000
 52Q  H1   C7   C8   121.37  3.000
 52Q  C9   C7   C8   107.43  3.000
 52Q  H1   C7   C6   118.21  3.000
 52Q  C8   C7   C6    60.38  3.000
 52Q  C9   C7   C6   117.13  3.000
 52Q  H2   C6   C8   117.53  3.000
 52Q  H2   C6   C3   115.03  3.000
 52Q  C8   C6   C3   118.37  3.000
 52Q  H2   C6   C7   117.64  3.000
 52Q  C8   C6   C7    59.04  3.000
 52Q  C3   C6   C7   117.90  3.000
 52Q  H3   C1   N13  126.71  3.000
 52Q  H3   C1   N11  123.50  3.000
 52Q  N13  C1   N11  109.79  3.000
 52Q  H5   C5   H4   106.95  3.000
 52Q  H5   C5   C10  113.42  3.000
 52Q  H4   C5   C10  108.48  3.000
 52Q  H5   C5   C9   111.95  3.000
 52Q  H4   C5   C9   110.44  3.000
 52Q  C10  C5   C9   105.58  3.000
 52Q  O18  C4   O16  126.21  3.000
 52Q  O16  C4   C10  117.32  3.000
 52Q  O18  C4   C10  116.43  3.000
 52Q  O17  C3   O15  126.26  3.000
 52Q  O15  C3   C6   116.39  3.000
 52Q  O17  C3   C6   117.35  3.000
 52Q  S19  C2   N13  124.45  3.000
 52Q  S19  C2   N12  121.04  3.000
 52Q  N13  C2   N12  114.47  3.000
 52Q  H6   C8   C10  118.54  3.000
 52Q  H6   C8   C6   117.00  3.000
 52Q  C10  C8   C6   117.61  3.000
 52Q  H6   C8   C7   120.11  3.000
 52Q  C10  C8   C7   109.83  3.000
 52Q  C6   C8   C7    60.58  3.000
 52Q  H7   C9   S19  107.71  3.000
 52Q  H7   C9   C5   110.96  3.000
 52Q  S19  C9   C5   113.90  3.000
 52Q  H7   C9   C7   109.55  3.000
 52Q  C5   C9   C7   105.34  3.000
 52Q  S19  C9   C7   109.32  3.000
 52Q  N14  C10  C8   111.02  3.000
 52Q  N14  C10  C4   114.16  3.000
 52Q  C8   C10  C4   109.71  3.000
 52Q  N14  C10  C5   110.29  3.000
 52Q  C4   C10  C5   107.99  3.000
 52Q  C8   C10  C5   103.05  3.000
 52Q  H8   N11  N12  120.92  3.000
 52Q  H8   N11  C1   128.60  3.000
 52Q  N12  N11  C1   110.47  3.000
 52Q  N11  N12  C2   102.41  3.000
 52Q  C2   N13  C1   102.86  3.000
 52Q  H10  N14  H9   103.77  3.000
 52Q  H10  N14  C10  108.22  3.000
 52Q  H9   N14  C10  107.63  3.000
 52Q  C9   S19  C2   100.83  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
 52Q  CONST_01  C2   N12  N11  C1     0.00   0.0  0
 52Q  CONST_02  N12  C2   N13  C1     0.00   0.0  0
 52Q  CONST_03  N11  C1   N13  C2     0.00   0.0  0
 52Q  CONST_04  N13  C2   N12  N11    0.00   0.0  0
 52Q  CONST_05  N13  C1   N11  N12    0.00   0.0  0
 52Q  CONST_06  S19  C2   N13  C1   180.00   0.0  0
 52Q  CONST_07  S19  C2   N12  N11  180.00   0.0  0
 52Q  CONST_08  H3   C1   N13  C2   180.00   0.0  0
 52Q  CONST_09  H8   N11  N12  C2   180.00   0.0  0
 52Q  Var_01    C10  C8   C6   C7   -98.31  30.0  1
 52Q  Var_02    N13  C2   S19  C9   -32.48  30.0  1
 52Q  Var_03    O17  C3   C6   C7   -33.93  30.0  2

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
 52Q  chir_04  C9   S19  C7  C5   negativ
 52Q  chir_05  C10  C5   C8  C4   positiv
 52Q  chir_06  C7   C9   C6  C8   both
 52Q  chir_07  C6   C7   C3  C8   both
 52Q  chir_08  C8   C7   C6  C10  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
 52Q  plan-1  C1   0.020
 52Q  plan-1  C2   0.020
 52Q  plan-1  N11  0.020
 52Q  plan-1  N12  0.020
 52Q  plan-1  N13  0.020
 52Q  plan-1  S19  0.020
 52Q  plan-1  H8   0.020
 52Q  plan-1  H3   0.020
 52Q  plan-2  C4   0.020
 52Q  plan-2  C10  0.020
 52Q  plan-2  O16  0.020
 52Q  plan-2  O18  0.020
 52Q  plan-3  C6   0.020
 52Q  plan-3  C3   0.020
 52Q  plan-3  O15  0.020
 52Q  plan-3  O17  0.020

