# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 23:04:59 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 5-[(3aS,4S,6aR)-1,3-dimethyl-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@H]2CS[C@@H](CCCCC(O)=O)[C@H]2N(C)C1=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
 VHH  VHH  '5-[(3aS,4S,6aR)-1,3-dimethyl-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid'  ligand  38  18  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VHH
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
 VHH  N1    N  NR5   0  -0.491   3.6595  -0.2182  -0.4067
 VHH  S1    S  S2    0  -0.022   1.0669   1.6944  -0.7715
 VHH  C2    C  CH1   0  -0.367   0.6265   0.7664   0.7368
 VHH  N2    N  NR5   0  -0.486   1.9931  -1.3377   0.5051
 VHH  C3    C  CR5   0   0.709   3.0415  -1.4302  -0.3560
 VHH  O3    O  O     0  -0.532   3.3665  -2.4341  -0.9722
 VHH  C4    C  CR15  0  -0.050   1.8894  -0.0353   1.1163
 VHH  C5    C  CR15  0  -0.078   3.1386   0.7075   0.5670
 VHH  C6    C  CH2   0  -0.561   2.6896   2.0276  -0.0501
 VHH  C7    C  CH2   0  -0.421  -0.6350  -0.0560   0.5518
 VHH  C8    C  CH2   0  -0.413  -1.8820   0.7765   0.2848
 VHH  C9    C  CH2   0  -0.419  -3.1256  -0.0973   0.1681
 VHH  C10   C  CH2   0  -0.581  -4.3763   0.7265  -0.0852
 VHH  C11   C  C     0   0.550  -5.6268  -0.0960  -0.2231
 VHH  O11   O  OH1   0  -0.598  -6.7023   0.6664  -0.4047
 VHH  O12   O  O     0  -0.446  -5.6780  -1.3002  -0.1845
 VHH  C17   C  CH3   0  -0.525   1.3137  -2.5077   1.0002
 VHH  C18   C  CH3   0  -0.518   4.9397  -0.0151  -1.0246
 VHH  H2    H  HCH1  0   0.275   0.4612   1.5000   1.5332
 VHH  H4    H  HCR5  0   0.276   1.9158  -0.1347   2.2056
 VHH  H5    H  HCR5  0   0.275   3.8849   0.9003   1.3469
 VHH  H6    H  HCH2  0   0.287   3.3791   2.4025  -0.8055
 VHH  H6A   H  HCH2  0   0.278   2.5961   2.7866   0.7282
 VHH  H7    H  HCH2  0   0.235  -0.4897  -0.7706  -0.2634
 VHH  H7A   H  HCH2  0   0.238  -0.7927  -0.6451   1.4610
 VHH  H8    H  HCH2  0   0.223  -2.0158   1.5084   1.0881
 VHH  H8A   H  HCH2  0   0.223  -1.7571   1.3515  -0.6385
 VHH  H9    H  HCH2  0   0.229  -2.9822  -0.8170  -0.6421
 VHH  H9A   H  HCH2  0   0.228  -3.2466  -0.6845   1.0825
 VHH  H10   H  HCH2  0   0.276  -4.5298   1.4500   0.7219
 VHH  H10A  H  HCH2  0   0.277  -4.2614   1.3240  -0.9955
 VHH  HO11  H  HOH1  0   0.478  -7.4899   0.1088  -0.4913
 VHH  H17   H  HCH3  0   0.251   1.9970  -3.3548   1.0555
 VHH  H17A  H  HCH3  0   0.245   0.9459  -2.3125   2.0062
 VHH  H17B  H  HCH3  0   0.235   0.4618  -2.7976   0.3824
 VHH  H18   H  HCH3  0   0.256   5.1504  -0.8414  -1.6981
 VHH  H18A  H  HCH3  0   0.236   4.9537   0.9051  -1.6095
 VHH  H18B  H  HCH3  0   0.231   5.7413   0.0423  -0.2827

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
 VHH  N1   C3    single  1.361  0.020  1.361
 VHH  N1   C5    single  1.441  0.020  1.441
 VHH  N1   C18   single  1.436  0.020  1.436
 VHH  S1   C2    single  1.825  0.020  1.825
 VHH  S1   C6    single  1.807  0.020  1.807
 VHH  C2   C4    single  1.543  0.020  1.543
 VHH  C2   C7    single  1.517  0.020  1.517
 VHH  N2   C3    single  1.360  0.020  1.360
 VHH  N2   C4    single  1.442  0.020  1.442
 VHH  N2   C17   single  1.441  0.020  1.441
 VHH  C3   O3    double  1.222  0.020  1.222
 VHH  C4   C5    single  1.554  0.020  1.554
 VHH  C5   C6    single  1.525  0.020  1.525
 VHH  C7   C8    single  1.523  0.020  1.523
 VHH  C8   C9    single  1.524  0.020  1.524
 VHH  C9   C10   single  1.519  0.020  1.519
 VHH  C10  C11   single  1.503  0.020  1.503
 VHH  C11  O11   single  1.331  0.020  1.331
 VHH  C11  O12   double  1.206  0.020  1.206
 VHH  C2   H2    single  0.970  0.020  1.090
 VHH  C4   H4    single  0.970  0.020  1.090
 VHH  C5   H5    single  0.970  0.020  1.090
 VHH  C6   H6    single  0.970  0.020  1.090
 VHH  C6   H6A   single  0.970  0.020  1.090
 VHH  C7   H7    single  0.970  0.020  1.090
 VHH  C7   H7A   single  0.970  0.020  1.090
 VHH  C8   H8    single  0.970  0.020  1.090
 VHH  C8   H8A   single  0.970  0.020  1.090
 VHH  C9   H9    single  0.970  0.020  1.090
 VHH  C9   H9A   single  0.970  0.020  1.090
 VHH  C10  H10   single  0.970  0.020  1.090
 VHH  C10  H10A  single  0.970  0.020  1.090
 VHH  O11  HO11  single  0.850  0.020  0.980
 VHH  C17  H17   single  0.970  0.020  1.090
 VHH  C17  H17A  single  0.970  0.020  1.090
 VHH  C17  H17B  single  0.970  0.020  1.090
 VHH  C18  H18   single  0.970  0.020  1.090
 VHH  C18  H18A  single  0.970  0.020  1.090
 VHH  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
 VHH  C18   N1   C5    121.48  3.000
 VHH  C18   N1   C3    123.13  3.000
 VHH  C5    N1   C3    112.50  3.000
 VHH  C6    S1   C2     88.88  3.000
 VHH  H2    C2   C7    109.04  3.000
 VHH  H2    C2   C4    107.01  3.000
 VHH  C7    C2   C4    115.39  3.000
 VHH  H2    C2   S1    107.26  3.000
 VHH  C7    C2   S1    112.06  3.000
 VHH  C4    C2   S1    105.66  3.000
 VHH  C17   N2   C4    123.62  3.000
 VHH  C17   N2   C3    121.73  3.000
 VHH  C4    N2   C3    112.65  3.000
 VHH  O3    C3   N2    125.47  3.000
 VHH  O3    C3   N1    126.29  3.000
 VHH  N2    C3   N1    108.24  3.000
 VHH  H4    C4   C5    112.08  3.000
 VHH  H4    C4   N2    109.76  3.000
 VHH  C5    C4   N2    102.95  3.000
 VHH  H4    C4   C2    108.16  3.000
 VHH  C5    C4   C2    108.82  3.000
 VHH  N2    C4   C2    115.07  3.000
 VHH  H5    C5   C6    109.64  3.000
 VHH  H5    C5   C4    112.32  3.000
 VHH  C6    C5   C4    108.68  3.000
 VHH  H5    C5   N1    110.34  3.000
 VHH  C6    C5   N1    112.90  3.000
 VHH  C4    C5   N1    102.85  3.000
 VHH  H6A   C6   H6    108.02  3.000
 VHH  H6A   C6   C5    109.80  3.000
 VHH  H6    C6   C5    113.09  3.000
 VHH  H6A   C6   S1    109.64  3.000
 VHH  H6    C6   S1    110.79  3.000
 VHH  C5    C6   S1    105.45  3.000
 VHH  H7A   C7   H7    106.65  3.000
 VHH  H7A   C7   C8    108.77  3.000
 VHH  H7    C7   C8    109.59  3.000
 VHH  H7A   C7   C2    108.07  3.000
 VHH  H7    C7   C2    109.55  3.000
 VHH  C8    C7   C2    113.95  3.000
 VHH  H8A   C8   H8    106.35  3.000
 VHH  H8A   C8   C9    109.24  3.000
 VHH  H8    C8   C9    109.86  3.000
 VHH  H8A   C8   C7    109.97  3.000
 VHH  H8    C8   C7    109.68  3.000
 VHH  C9    C8   C7    111.60  3.000
 VHH  H9A   C9   H9    106.31  3.000
 VHH  H9A   C9   C10   109.85  3.000
 VHH  H9    C9   C10   109.96  3.000
 VHH  H9A   C9   C8    109.52  3.000
 VHH  H9    C9   C8    109.10  3.000
 VHH  C10   C9   C8    111.94  3.000
 VHH  H10A  C10  H10   105.48  3.000
 VHH  H10A  C10  C11   108.04  3.000
 VHH  H10   C10  C11   108.22  3.000
 VHH  H10A  C10  C9    110.38  3.000
 VHH  H10   C10  C9    110.55  3.000
 VHH  C11   C10  C9    113.80  3.000
 VHH  O12   C11  O11   122.83  3.000
 VHH  O12   C11  C10   125.37  3.000
 VHH  O11   C11  C10   111.80  3.000
 VHH  HO11  O11  C11   109.84  3.000
 VHH  H17B  C17  H17A  107.88  3.000
 VHH  H17B  C17  H17   108.16  3.000
 VHH  H17A  C17  H17   107.71  3.000
 VHH  H17B  C17  N2    112.90  3.000
 VHH  H17A  C17  N2    109.35  3.000
 VHH  H17   C17  N2    110.67  3.000
 VHH  H18B  C18  H18A  108.06  3.000
 VHH  H18B  C18  H18   108.56  3.000
 VHH  H18A  C18  H18   107.86  3.000
 VHH  H18B  C18  N1    111.65  3.000
 VHH  H18A  C18  N1    111.20  3.000
 VHH  H18   C18  N1    109.40  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
 VHH  CONST_01  C4    N2   C3   N1      0.00   0.0  0
 VHH  CONST_02  C5    N1   C3   N2      0.00   0.0  0
 VHH  CONST_03  C17   N2   C3   N1    180.00   0.0  0
 VHH  CONST_04  C18   N1   C3   N2    180.00   0.0  0
 VHH  CONST_05  C5    N1   C3   O3    180.00   0.0  0
 VHH  CONST_06  C4    N2   C3   O3    180.00   0.0  0
 VHH  CONST_07  C18   N1   C3   O3      0.00   0.0  0
 VHH  CONST_08  C17   N2   C3   O3      0.00   0.0  0
 VHH  CONST_09  HO11  O11  C11  C10   180.00   0.0  0
 VHH  Var_01    C5    C6   S1   C2     43.55  30.0  1
 VHH  Var_02    H18   C18  N1   C3     18.88  30.0  3
 VHH  Var_03    H17   C17  N2   C3     29.90  30.0  3
 VHH  Var_04    C9    C8   C7   C2   -177.52  30.0  3
 VHH  Var_05    C10   C9   C8   C7    179.46  30.0  3
 VHH  Var_06    C11   C10  C9   C8    179.34  30.0  3
 VHH  Var_07    O11   C11  C10  C9    178.17  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
 VHH  chir_01  C2  S1  C4  C7  positiv
 VHH  chir_02  C4  N2  C2  C5  positiv
 VHH  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
 VHH  plan-1  N1    0.020
 VHH  plan-1  N2    0.020
 VHH  plan-1  C3    0.020
 VHH  plan-1  O3    0.020
 VHH  plan-1  C4    0.020
 VHH  plan-1  C5    0.020
 VHH  plan-1  C17   0.020
 VHH  plan-1  C18   0.020
 VHH  plan-2  C10   0.020
 VHH  plan-2  C11   0.020
 VHH  plan-2  O11   0.020
 VHH  plan-2  O12   0.020
 VHH  plan-2  HO11  0.020

