# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 13:03:00 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  31  19  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.213   1.1269  -0.5070   0.8722
 52Q  C6   C  CH1   0  -0.413   2.0070  -0.9656  -0.2700
 52Q  C1   C  CR15  0   0.121  -4.4871   0.3867   0.1312
 52Q  C5   C  CH2   0  -0.483  -0.1244   0.8080  -0.7197
 52Q  C4   C  C     0   0.568   1.0842   2.7060   0.3069
 52Q  C3   C  C     0   0.581   3.1464  -1.8355   0.0904
 52Q  C2   C  CR5   0   0.191  -2.8671  -0.9183   0.0486
 52Q  C8   C  CH1   0  -0.196   2.0604   0.4510   0.2369
 52Q  C9   C  CH1   0  -0.374  -0.2786  -0.1074   0.4967
 52Q  C10  C  CT    0  -0.020   1.2724   1.4668  -0.5729
 52Q  N11  N  NR15  0  -0.412  -4.8977  -0.8006  -0.2995
 52Q  N12  N  N     0  -0.272  -3.8722  -1.6564  -0.3659
 52Q  N13  N  N     0  -0.452  -3.1925   0.3515   0.3680
 52Q  N14  N  NH2   0  -0.785   1.8652   1.7035  -1.8669
 52Q  O15  O  OH1   0  -0.595   3.4162  -2.7207  -0.8608
 52Q  O16  O  OH1   0  -0.588   0.9211   3.8143  -0.3994
 52Q  O17  O  O     0  -0.452   3.7671  -1.7608   1.1244
 52Q  O18  O  O     0  -0.434   1.0418   2.6767   1.5121
 52Q  S19  S  S2    0   0.060  -1.2642  -1.6025   0.1873
 52Q  H1   H  HCH1  0   0.289   1.3106  -0.9115   1.8594
 52Q  H2   H  HCH1  0   0.292   1.5605  -1.1572  -1.2385
 52Q  H4   H  HCH2  0   0.275  -0.1263   0.2318  -1.6466
 52Q  H5   H  HCH2  0   0.288  -0.9375   1.5293  -0.7941
 52Q  H6   H  HCH1  0   0.290   2.9642   0.7710   0.7413
 52Q  H7   H  HCH1  0   0.311  -0.7306   0.4239   1.3344
 52Q  H8   H  HNR5  0   0.438  -5.8283  -1.0883  -0.5614
 52Q  H9   H  HNH2  0   0.357   1.2847   2.3151  -2.4269
 52Q  H10  H  HNH2  0   0.355   2.7631   2.1627  -1.7726
 52Q  H12  H  HOH1  0   0.483   4.1661  -3.2730  -0.5932
 52Q  H13  H  HOH1  0   0.483   0.7582   4.5631   0.1943
 52Q  H3   H  HCR5  0   0.307  -5.1413   1.2346   0.2583

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  1.328  0.020  1.328
 52Q  C1   N13  aromatic  1.317  0.020  1.317
 52Q  N11  N12  aromatic  1.337  0.020  1.337
 52Q  N13  C2   aromatic  1.349  0.020  1.349
 52Q  N12  C2   aromatic  1.314  0.020  1.314
 52Q  C2   S19  single    1.748  0.020  1.748
 52Q  S19  C9   single    1.817  0.020  1.817
 52Q  C9   C7   single    1.509  0.020  1.509
 52Q  C9   C5   single    1.530  0.020  1.530
 52Q  C7   C6   single    1.513  0.020  1.513
 52Q  C7   C8   single    1.481  0.020  1.481
 52Q  O17  C3   double    1.208  0.020  1.208
 52Q  O15  C3   single    1.327  0.020  1.327
 52Q  C3   C6   single    1.478  0.020  1.478
 52Q  C6   C8   single    1.505  0.020  1.505
 52Q  C5   C10  single    1.551  0.020  1.551
 52Q  C8   C10  single    1.519  0.020  1.519
 52Q  O18  C4   double    1.206  0.020  1.206
 52Q  C10  C4   single    1.531  0.020  1.531
 52Q  C10  N14  single    1.443  0.020  1.443
 52Q  C4   O16  single    1.324  0.020  1.324
 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
 52Q  O15  H12  single    0.850  0.020  0.980
 52Q  O16  H13  single    0.850  0.020  0.980

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   118.95  3.000
 52Q  H1   C7   C8   121.73  3.000
 52Q  C9   C7   C8   108.01  3.000
 52Q  H1   C7   C6   118.45  3.000
 52Q  C8   C7   C6    60.36  3.000
 52Q  C9   C7   C6   115.74  3.000
 52Q  H2   C6   C8   118.82  3.000
 52Q  H2   C6   C3   115.56  3.000
 52Q  C8   C6   C3   116.38  3.000
 52Q  H2   C6   C7   119.25  3.000
 52Q  C8   C6   C7    58.76  3.000
 52Q  C3   C6   C7   116.27  3.000
 52Q  H3   C1   N13  126.60  3.000
 52Q  H3   C1   N11  123.61  3.000
 52Q  N13  C1   N11  109.78  3.000
 52Q  H5   C5   H4   106.87  3.000
 52Q  H5   C5   C10  113.41  3.000
 52Q  H4   C5   C10  107.83  3.000
 52Q  H5   C5   C9   112.03  3.000
 52Q  H4   C5   C9   111.04  3.000
 52Q  C10  C5   C9   105.64  3.000
 52Q  O18  C4   O16  123.28  3.000
 52Q  O16  C4   C10  112.71  3.000
 52Q  O18  C4   C10  123.96  3.000
 52Q  O17  C3   O15  123.38  3.000
 52Q  O15  C3   C6   111.99  3.000
 52Q  O17  C3   C6   124.62  3.000
 52Q  S19  C2   N13  124.79  3.000
 52Q  S19  C2   N12  120.43  3.000
 52Q  N13  C2   N12  114.76  3.000
 52Q  H6   C8   C10  118.91  3.000
 52Q  H6   C8   C6   117.66  3.000
 52Q  C10  C8   C6   115.54  3.000
 52Q  H6   C8   C7   121.15  3.000
 52Q  C10  C8   C7   109.53  3.000
 52Q  C6   C8   C7    60.88  3.000
 52Q  H7   C9   S19  107.88  3.000
 52Q  H7   C9   C5   111.17  3.000
 52Q  S19  C9   C5   114.30  3.000
 52Q  H7   C9   C7   108.91  3.000
 52Q  C5   C9   C7   105.21  3.000
 52Q  S19  C9   C7   109.25  3.000
 52Q  N14  C10  C8   112.00  3.000
 52Q  N14  C10  C4   115.65  3.000
 52Q  C8   C10  C4   107.37  3.000
 52Q  N14  C10  C5   110.78  3.000
 52Q  C4   C10  C5   106.70  3.000
 52Q  C8   C10  C5   103.50  3.000
 52Q  H8   N11  N12  120.81  3.000
 52Q  H8   N11  C1   128.64  3.000
 52Q  N12  N11  C1   110.55  3.000
 52Q  N11  N12  C2   102.21  3.000
 52Q  C2   N13  C1   102.69  3.000
 52Q  H10  N14  H9   106.62  3.000
 52Q  H10  N14  C10  110.80  3.000
 52Q  H9   N14  C10  111.08  3.000
 52Q  H12  O15  C3   109.85  3.000
 52Q  H13  O16  C4   109.91  3.000
 52Q  C9   S19  C2   100.88  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  CONST_10  H12  O15  C3   C6   180.00   0.0  0
 52Q  CONST_11  H13  O16  C4   C10  180.00   0.0  0
 52Q  Var_01    C10  C8   C6   C7   -99.08  30.0  1
 52Q  Var_02    N13  C2   S19  C9   -11.02  30.0  1
 52Q  Var_03    O17  C3   C6   C7   -33.20  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-2  H13  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
 52Q  plan-3  H12  0.020

