# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 19 10:39:03 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 5-[(3aS,4S,6aR)-1-acetyl-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1[C@H]2CS[C@@H](CCCCC(O)=O)[C@H]2NC1=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
 NVZ  NVZ  '5-[(3aS,4S,6aR)-1-acetyl-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid'  ligand  37  19  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NVZ
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
 NVZ  N1    N  NR5   0  -0.557   3.4043  -0.3222   0.0112
 NVZ  S1    S  S2    0  -0.004   0.5624   1.2072  -1.0805
 NVZ  C2    C  CH1   0  -0.368   0.1222   0.7568   0.6282
 NVZ  N2    N  NR15  0  -0.662   1.5387  -1.2762   0.6940
 NVZ  C3    C  CR5   0   0.703   2.6832  -1.5286   0.0337
 NVZ  O3    O  O     0  -0.475   3.0322  -2.5900  -0.4304
 NVZ  C4    C  CR15  0  -0.045   1.3793   0.0678   1.1714
 NVZ  C5    C  CR15  0  -0.098   2.6288   0.7723   0.5819
 NVZ  C6    C  CH2   0  -0.570   2.1662   1.7850  -0.4756
 NVZ  C7    C  CH2   0  -0.428  -1.1463  -0.0710   0.7198
 NVZ  C8    C  CH2   0  -0.418  -2.3789   0.6515   0.1899
 NVZ  C9    C  CH2   0  -0.419  -3.6563  -0.1482   0.4106
 NVZ  C10   C  CH2   0  -0.581  -4.8632   0.5482  -0.1948
 NVZ  C11   C  C     0   0.550  -6.1583  -0.1855   0.0126
 NVZ  O11   O  O     0  -0.446  -6.2848  -1.2224   0.6155
 NVZ  O12   O  OH1   0  -0.598  -7.1812   0.4485  -0.5551
 NVZ  C17   C  C     0   0.527   4.7271  -0.2154  -0.3702
 NVZ  C18   C  CH3   0  -0.809   5.3914   1.1016  -0.0611
 NVZ  O19   O  O     0  -0.437   5.3250  -1.1267  -0.8968
 NVZ  H2    H  HCH1  0   0.285  -0.0141   1.6859   1.1922
 NVZ  HN2   H  HNR5  0   0.414   0.9043  -2.0238   0.9236
 NVZ  H4    H  HCR5  0   0.293   1.3692   0.0993   2.2642
 NVZ  H5    H  HCR5  0   0.309   3.1950   1.2762   1.3644
 NVZ  H6    H  HCH2  0   0.295   2.8600   1.8715  -1.3094
 NVZ  H6A   H  HCH2  0   0.288   2.0572   2.7704  -0.0203
 NVZ  H7    H  HCH2  0   0.234  -1.0188  -1.0121   0.1773
 NVZ  H7A   H  HCH2  0   0.246  -1.3029  -0.3315   1.7721
 NVZ  H8    H  HCH2  0   0.225  -2.4701   1.6291   0.6742
 NVZ  H8A   H  HCH2  0   0.224  -2.2548   0.8498  -0.8795
 NVZ  H9    H  HCH2  0   0.229  -3.5430  -1.1434  -0.0279
 NVZ  H9A   H  HCH2  0   0.230  -3.8108  -0.2968   1.4823
 NVZ  H10   H  HCH2  0   0.277  -4.9767   1.5551   0.2202
 NVZ  H10A  H  HCH2  0   0.276  -4.7239   0.6925  -1.2708
 NVZ  HO12  H  HOH1  0   0.478  -8.0001  -0.0469  -0.4054
 NVZ  H18   H  HCH3  0   0.277   5.3806   1.3027   1.0112
 NVZ  H18A  H  HCH3  0   0.281   6.4246   1.0630  -0.3946
 NVZ  H18B  H  HCH3  0   0.274   4.9031   1.9422  -0.5534

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
 NVZ  N1   C3    single  1.406  0.020  1.406
 NVZ  N1   C5    single  1.458  0.020  1.458
 NVZ  N1   C17   single  1.381  0.020  1.381
 NVZ  S1   C2    single  1.821  0.020  1.821
 NVZ  S1   C6    single  1.809  0.020  1.809
 NVZ  C2   C4    single  1.533  0.020  1.533
 NVZ  C2   C7    single  1.517  0.020  1.517
 NVZ  N2   C3    single  1.345  0.020  1.345
 NVZ  N2   C4    single  1.435  0.020  1.435
 NVZ  C3   O3    double  1.210  0.020  1.210
 NVZ  C4   C5    single  1.551  0.020  1.551
 NVZ  C5   C6    single  1.536  0.020  1.536
 NVZ  C7   C8    single  1.524  0.020  1.524
 NVZ  C8   C9    single  1.523  0.020  1.523
 NVZ  C9   C10   single  1.519  0.020  1.519
 NVZ  C10  C11   single  1.503  0.020  1.503
 NVZ  C11  O11   double  1.206  0.020  1.206
 NVZ  C11  O12   single  1.331  0.020  1.331
 NVZ  C17  C18   single  1.507  0.020  1.507
 NVZ  C17  O19   double  1.211  0.020  1.211
 NVZ  C2   H2    single  0.970  0.020  1.090
 NVZ  N2   HN2   single  0.860  0.020  1.020
 NVZ  C4   H4    single  0.970  0.020  1.090
 NVZ  C5   H5    single  0.970  0.020  1.090
 NVZ  C6   H6    single  0.970  0.020  1.090
 NVZ  C6   H6A   single  0.970  0.020  1.090
 NVZ  C7   H7    single  0.970  0.020  1.090
 NVZ  C7   H7A   single  0.970  0.020  1.090
 NVZ  C8   H8    single  0.970  0.020  1.090
 NVZ  C8   H8A   single  0.970  0.020  1.090
 NVZ  C9   H9    single  0.970  0.020  1.090
 NVZ  C9   H9A   single  0.970  0.020  1.090
 NVZ  C10  H10   single  0.970  0.020  1.090
 NVZ  C10  H10A  single  0.970  0.020  1.090
 NVZ  O12  HO12  single  0.850  0.020  0.980
 NVZ  C18  H18   single  0.970  0.020  1.090
 NVZ  C18  H18A  single  0.970  0.020  1.090
 NVZ  C18  H18B  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
 NVZ  C17   N1   C5    124.03  3.000
 NVZ  C17   N1   C3    124.21  3.000
 NVZ  C5    N1   C3    111.42  3.000
 NVZ  C6    S1   C2     88.83  3.000
 NVZ  H2    C2   C7    109.12  3.000
 NVZ  H2    C2   C4    107.51  3.000
 NVZ  C7    C2   C4    114.77  3.000
 NVZ  H2    C2   S1    107.66  3.000
 NVZ  C7    C2   S1    113.18  3.000
 NVZ  C4    C2   S1    104.20  3.000
 NVZ  HN2   N2   C4    123.33  3.000
 NVZ  HN2   N2   C3    120.57  3.000
 NVZ  C4    N2   C3    115.69  3.000
 NVZ  O3    C3   N2    126.75  3.000
 NVZ  O3    C3   N1    126.78  3.000
 NVZ  N2    C3   N1    106.46  3.000
 NVZ  H4    C4   C5    111.98  3.000
 NVZ  H4    C4   N2    111.13  3.000
 NVZ  C5    C4   N2    102.09  3.000
 NVZ  H4    C4   C2    109.49  3.000
 NVZ  C5    C4   C2    108.77  3.000
 NVZ  N2    C4   C2    113.21  3.000
 NVZ  H5    C5   C6    110.26  3.000
 NVZ  H5    C5   C4    110.84  3.000
 NVZ  C6    C5   C4    108.58  3.000
 NVZ  H5    C5   N1    110.61  3.000
 NVZ  C6    C5   N1    112.70  3.000
 NVZ  C4    C5   N1    103.67  3.000
 NVZ  H6A   C6   H6    108.17  3.000
 NVZ  H6A   C6   C5    109.78  3.000
 NVZ  H6    C6   C5    112.83  3.000
 NVZ  H6A   C6   S1    109.84  3.000
 NVZ  H6    C6   S1    109.54  3.000
 NVZ  C5    C6   S1    106.66  3.000
 NVZ  H7A   C7   H7    106.77  3.000
 NVZ  H7A   C7   C8    109.34  3.000
 NVZ  H7    C7   C8    109.26  3.000
 NVZ  H7A   C7   C2    107.89  3.000
 NVZ  H7    C7   C2    110.00  3.000
 NVZ  C8    C7   C2    113.36  3.000
 NVZ  H8A   C8   H8    106.25  3.000
 NVZ  H8A   C8   C9    109.37  3.000
 NVZ  H8    C8   C9    109.57  3.000
 NVZ  H8A   C8   C7    109.50  3.000
 NVZ  H8    C8   C7    109.69  3.000
 NVZ  C9    C8   C7    112.28  3.000
 NVZ  H9A   C9   H9    106.51  3.000
 NVZ  H9A   C9   C10   109.92  3.000
 NVZ  H9    C9   C10   109.87  3.000
 NVZ  H9A   C9   C8    109.39  3.000
 NVZ  H9    C9   C8    109.44  3.000
 NVZ  C10   C9   C8    111.58  3.000
 NVZ  H10A  C10  H10   105.34  3.000
 NVZ  H10A  C10  C11   108.04  3.000
 NVZ  H10   C10  C11   107.90  3.000
 NVZ  H10A  C10  C9    110.55  3.000
 NVZ  H10   C10  C9    110.67  3.000
 NVZ  C11   C10  C9    113.94  3.000
 NVZ  O12   C11  O11   122.84  3.000
 NVZ  O12   C11  C10   111.77  3.000
 NVZ  O11   C11  C10   125.39  3.000
 NVZ  HO12  O12  C11   109.89  3.000
 NVZ  O19   C17  C18   121.96  3.000
 NVZ  O19   C17  N1    122.35  3.000
 NVZ  C18   C17  N1    115.67  3.000
 NVZ  H18B  C18  H18A  108.36  3.000
 NVZ  H18B  C18  H18   107.30  3.000
 NVZ  H18A  C18  H18   108.52  3.000
 NVZ  H18B  C18  C17   112.58  3.000
 NVZ  H18A  C18  C17   108.98  3.000
 NVZ  H18   C18  C17   110.99  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
 NVZ  CONST_01  C4    N2   C3   N1      0.00   0.0  0
 NVZ  CONST_02  C5    N1   C3   N2      0.00   0.0  0
 NVZ  CONST_03  C17   N1   C3   N2    180.00   0.0  0
 NVZ  CONST_04  C5    N1   C3   O3    180.00   0.0  0
 NVZ  CONST_05  C4    N2   C3   O3    180.00   0.0  0
 NVZ  CONST_06  HN2   N2   C3   N1    180.00   0.0  0
 NVZ  CONST_07  C18   C17  N1   C3    180.00   0.0  0
 NVZ  CONST_08  O19   C17  N1   C3      0.00   0.0  0
 NVZ  CONST_09  C18   C17  N1   C5      0.00   0.0  0
 NVZ  CONST_10  O19   C17  N1   C5    180.00   0.0  0
 NVZ  CONST_11  C17   N1   C3   O3      0.00   0.0  0
 NVZ  CONST_12  HO12  O12  C11  C10   180.00   0.0  0
 NVZ  Var_01    C5    C6   S1   C2     40.29  30.0  1
 NVZ  Var_02    C9    C8   C7   C2   -174.72  30.0  3
 NVZ  Var_03    H18   C18  C17  N1     59.91  30.0  3
 NVZ  Var_04    C10   C9   C8   C7   -176.68  30.0  3
 NVZ  Var_05    C11   C10  C9   C8   -179.03  30.0  3
 NVZ  Var_06    O11   C11  C10  C9      1.20  30.0  3

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
 NVZ  chir_01  C2  S1  C4  C7  positiv
 NVZ  chir_02  C4  N2  C5  C2  negativ
 NVZ  chir_03  C5  N1  C4  C6  positiv

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
 NVZ  plan-1  N1    0.020
 NVZ  plan-1  N2    0.020
 NVZ  plan-1  C3    0.020
 NVZ  plan-1  O3    0.020
 NVZ  plan-1  C4    0.020
 NVZ  plan-1  C5    0.020
 NVZ  plan-1  C17   0.020
 NVZ  plan-1  C18   0.020
 NVZ  plan-1  O19   0.020
 NVZ  plan-1  HN2   0.020
 NVZ  plan-2  C10   0.020
 NVZ  plan-2  C11   0.020
 NVZ  plan-2  O11   0.020
 NVZ  plan-2  O12   0.020
 NVZ  plan-2  HO12  0.020

