# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 04:40:21 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (3aS,4S,6aR)-4-(hex-5-yn-1-yl)tetrahydro-1H-thieno[3,4-d]imidazol-2(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1N[C@H]2CS[C@@H](CCCCC#C)[C@H]2N1
#
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
 BC4  BC4  (3aS,4S,6aR)-4-(hex-5-yn-1-yl)tetrahydro-1H-thieno[3,4-d]imidazol-2(3H)-one  ligand  31  15  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BC4
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
 BC4  CAA  C  CSP1  0  -0.570  -6.7271   0.8475   0.1226
 BC4  CAC  C  CSP   0   0.285  -5.7242   0.1831   0.1149
 BC4  CAD  C  CH2   0  -0.575  -4.4996  -0.6066   0.1008
 BC4  CAE  C  CH2   0  -0.422  -3.2542   0.2352  -0.1877
 BC4  CAF  C  CH2   0  -0.421  -1.9883  -0.6111  -0.2041
 BC4  CAG  C  CH2   0  -0.422  -0.7479   0.2203  -0.5076
 BC4  CAM  C  CH1   0  -0.362   0.5220  -0.6031  -0.6213
 BC4  SAK  S  S2    0  -0.023   1.0123  -1.3713   0.9572
 BC4  CAH  C  CH2   0  -0.571   2.6170  -1.7902   0.2283
 BC4  CAN  C  CR15  0  -0.043   3.0316  -0.5923  -0.6361
 BC4  CAO  C  CR15  0  -0.067   1.7561   0.1946  -1.0575
 BC4  NAJ  N  NR15  0  -0.656   1.9033   1.4403  -0.3472
 BC4  CAL  C  CR5   0   0.641   3.1110   1.5670   0.2705
 BC4  OAB  O  O     0  -0.528   3.5136   2.5483   0.8762
 BC4  NAI  N  NR15  0  -0.661   3.7843   0.4054   0.0775
 BC4  H1   H  H     0   0.277  -7.6174   1.4331   0.1359
 BC4  H2   H  HCH2  0   0.266  -4.3909  -1.1115   1.0649
 BC4  H3   H  HCH2  0   0.266  -4.5936  -1.3969  -0.6495
 BC4  H4   H  HCH2  0   0.231  -3.3743   0.7394  -1.1503
 BC4  H5   H  HCH2  0   0.232  -3.1653   1.0198   0.5681
 BC4  H6   H  HCH2  0   0.225  -1.8768  -1.1136   0.7622
 BC4  H7   H  HCH2  0   0.224  -2.0868  -1.4034  -0.9533
 BC4  H8   H  HCH2  0   0.241  -0.8945   0.7433  -1.4592
 BC4  H9   H  HCH2  0   0.235  -0.6199   0.9915   0.2566
 BC4  H10  H  HCH1  0   0.275   0.3685  -1.4035  -1.3533
 BC4  H11  H  HCH2  0   0.289   3.3439  -2.0018   1.0119
 BC4  H12  H  HCH2  0   0.275   2.5164  -2.6824  -0.3915
 BC4  H13  H  HCR5  0   0.278   3.5877  -0.9525  -1.5041
 BC4  H14  H  HCR5  0   0.281   1.7166   0.3571  -2.1385
 BC4  H15  H  HNR5  0   0.399   1.3851   2.2618  -0.6105
 BC4  H16  H  HNR5  0   0.399   4.6255   0.1918   0.5864

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
 BC4  CAC  CAA  triple  1.203  0.020  1.203
 BC4  CAC  CAD  single  1.457  0.020  1.457
 BC4  CAD  CAE  single  1.531  0.020  1.531
 BC4  CAE  CAF  single  1.523  0.020  1.523
 BC4  CAF  CAG  single  1.524  0.020  1.524
 BC4  CAG  CAM  single  1.518  0.020  1.518
 BC4  CAM  CAO  single  1.533  0.020  1.533
 BC4  CAM  SAK  single  1.823  0.020  1.823
 BC4  CAO  NAJ  single  1.441  0.020  1.441
 BC4  CAO  CAN  single  1.557  0.020  1.557
 BC4  NAJ  CAL  single  1.362  0.020  1.362
 BC4  SAK  CAH  single  1.812  0.020  1.812
 BC4  CAN  CAH  single  1.534  0.020  1.534
 BC4  CAN  NAI  single  1.439  0.020  1.439
 BC4  CAL  NAI  single  1.356  0.020  1.356
 BC4  CAL  OAB  double  1.221  0.020  1.221
 BC4  CAA  H1   single  0.913  0.020  1.066
 BC4  CAD  H2   single  0.939  0.020  1.096
 BC4  CAD  H3   single  0.939  0.020  1.096
 BC4  CAE  H4   single  0.939  0.020  1.096
 BC4  CAE  H5   single  0.939  0.020  1.096
 BC4  CAF  H6   single  0.939  0.020  1.096
 BC4  CAF  H7   single  0.939  0.020  1.096
 BC4  CAG  H8   single  0.939  0.020  1.096
 BC4  CAG  H9   single  0.939  0.020  1.096
 BC4  CAM  H10  single  0.939  0.020  1.096
 BC4  CAH  H11  single  0.939  0.020  1.096
 BC4  CAH  H12  single  0.939  0.020  1.096
 BC4  CAN  H13  single  0.939  0.020  1.096
 BC4  CAO  H14  single  0.939  0.020  1.096
 BC4  NAJ  H15  single  0.868  0.020  1.013
 BC4  NAI  H16  single  0.868  0.020  1.013

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
 BC4  H1   CAA  CAC  180.00  3.000
 BC4  CAD  CAC  CAA  180.00  3.000
 BC4  H3   CAD  H2   106.24  3.000
 BC4  H3   CAD  CAE  109.76  3.000
 BC4  H2   CAD  CAE  109.82  3.000
 BC4  H3   CAD  CAC  109.02  3.000
 BC4  H2   CAD  CAC  108.98  3.000
 BC4  CAE  CAD  CAC  112.80  3.000
 BC4  H5   CAE  H4   106.66  3.000
 BC4  H5   CAE  CAF  109.80  3.000
 BC4  H4   CAE  CAF  109.76  3.000
 BC4  H5   CAE  CAD  109.31  3.000
 BC4  H4   CAE  CAD  109.28  3.000
 BC4  CAF  CAE  CAD  111.89  3.000
 BC4  H7   CAF  H6   106.32  3.000
 BC4  H7   CAF  CAG  109.38  3.000
 BC4  H6   CAF  CAG  110.08  3.000
 BC4  H7   CAF  CAE  109.56  3.000
 BC4  H6   CAF  CAE  109.28  3.000
 BC4  CAG  CAF  CAE  112.06  3.000
 BC4  H9   CAG  H8   106.62  3.000
 BC4  H9   CAG  CAM  109.70  3.000
 BC4  H8   CAG  CAM  107.81  3.000
 BC4  H9   CAG  CAF  109.94  3.000
 BC4  H8   CAG  CAF  108.94  3.000
 BC4  CAM  CAG  CAF  113.58  3.000
 BC4  H10  CAM  CAO  107.63  3.000
 BC4  H10  CAM  SAK  107.96  3.000
 BC4  CAO  CAM  SAK  104.43  3.000
 BC4  H10  CAM  CAG  109.22  3.000
 BC4  SAK  CAM  CAG  112.88  3.000
 BC4  CAO  CAM  CAG  114.37  3.000
 BC4  CAH  SAK  CAM   89.27  3.000
 BC4  H12  CAH  H11  108.13  3.000
 BC4  H12  CAH  CAN  110.08  3.000
 BC4  H11  CAH  CAN  112.11  3.000
 BC4  H12  CAH  SAK  109.63  3.000
 BC4  H11  CAH  SAK  110.28  3.000
 BC4  CAN  CAH  SAK  106.59  3.000
 BC4  H13  CAN  NAI  110.88  3.000
 BC4  H13  CAN  CAO  111.64  3.000
 BC4  NAI  CAN  CAO  102.26  3.000
 BC4  H13  CAN  CAH  109.14  3.000
 BC4  NAI  CAN  CAH  113.78  3.000
 BC4  CAO  CAN  CAH  109.01  3.000
 BC4  H14  CAO  NAJ  111.24  3.000
 BC4  H14  CAO  CAN  111.85  3.000
 BC4  NAJ  CAO  CAN  102.69  3.000
 BC4  H14  CAO  CAM  109.23  3.000
 BC4  CAN  CAO  CAM  108.64  3.000
 BC4  NAJ  CAO  CAM  113.06  3.000
 BC4  H15  NAJ  CAL  119.94  3.000
 BC4  H15  NAJ  CAO  121.60  3.000
 BC4  CAL  NAJ  CAO  113.23  3.000
 BC4  NAI  CAL  OAB  126.51  3.000
 BC4  OAB  CAL  NAJ  126.28  3.000
 BC4  NAI  CAL  NAJ  107.21  3.000
 BC4  H16  NAI  CAL  121.66  3.000
 BC4  H16  NAI  CAN  122.75  3.000
 BC4  CAL  NAI  CAN  113.87  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
 BC4  CONST_01  NAJ  CAL  NAI  CAN     0.00   0.0  0
 BC4  CONST_02  NAI  CAL  NAJ  CAO     0.00   0.0  0
 BC4  CONST_03  OAB  CAL  NAI  CAN   180.00   0.0  0
 BC4  CONST_04  OAB  CAL  NAJ  CAO   180.00   0.0  0
 BC4  CONST_05  H16  NAI  CAL  NAJ   180.00   0.0  0
 BC4  Var_01    CAN  CAH  SAK  CAM    39.39  30.0  1
 BC4  Var_02    CAM  CAG  CAF  CAE  -176.26  30.0  3
 BC4  Var_03    CAE  CAD  CAC  CAA     3.08  30.0  3
 BC4  Var_04    CAF  CAE  CAD  CAC  -179.72  30.0  3
 BC4  Var_05    CAG  CAF  CAE  CAD   179.31  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
 BC4  chir_01  CAM  CAG  CAO  SAK  negativ
 BC4  chir_02  CAN  NAI  CAH  CAO  negativ
 BC4  chir_03  CAO  NAJ  CAM  CAN  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
 BC4  plan-1  CAN  0.020
 BC4  plan-1  CAO  0.020
 BC4  plan-1  NAJ  0.020
 BC4  plan-1  CAL  0.020
 BC4  plan-1  OAB  0.020
 BC4  plan-1  NAI  0.020
 BC4  plan-1  H15  0.020
 BC4  plan-1  H16  0.020

