# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 14:38:56 2022
#   Inital geometry file: a 94 line input string
#   Ligand name: methyl (2S)-(2-chlorophenyl)(6,7-dihydrothieno[3,2-c]pyridin-5(4H)-yl)ethanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](N1CCc2sccc2C1)c3ccccc3Cl
#
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
 CGE  CGE  'methyl (2S)-(2-chlorophenyl)(6,7-dihydrothieno[3,2-c]pyridin-5(4H)-yl)ethanoate'  ligand  37  21  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CGE
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
 CGE  C     C   C     0   0.580   1.0559  -1.6299   0.7304
 CGE  N     N   NT    0  -0.434  -0.6325  -0.0186  -0.0477
 CGE  O     O   O     0  -0.433   0.5867  -1.7723   1.8292
 CGE  CL1   CL  CL    0  -0.129   3.2661  -0.0330  -1.9972
 CGE  CA    C   CH1   0  -0.173   0.7324  -0.4740  -0.2130
 CGE  CAA   C   CH3   0  -0.427   2.4906  -3.4714   1.0181
 CGE  CAD   C   CR16  0  -0.272   3.5522   2.5650   0.9954
 CGE  CAE   C   CR16  0  -0.230   2.4051   2.3205   1.7389
 CGE  CAF   C   CR15  0  -0.474  -5.3006  -0.6360  -0.1692
 CGE  CAG   C   CR16  0  -0.196   3.7998   1.8312  -0.1521
 CGE  CAH   C   CR16  0  -0.272   1.5136   1.3452   1.3279
 CGE  CAI   C   CR15  0  -0.212  -4.1627  -1.3788  -0.1982
 CGE  CAJ   C   CH2   0  -0.481  -2.2148   1.8073  -0.4518
 CGE  CAK   C   CH2   0  -0.311  -0.9166   1.1420  -0.8884
 CGE  CAL   C   CH2   0  -0.323  -1.5820  -1.0881  -0.3379
 CGE  OAM   O   O2    0  -0.438   1.9805  -2.4117   0.2054
 CGE  SAN   S   S2    0   0.199  -4.9577   1.0461  -0.2571
 CGE  CAP   C   CR6   0  -0.117   2.8960   0.8551  -0.5524
 CGE  CAQ   C   CR5   0   0.138  -2.9881  -0.5760  -0.2924
 CGE  CAR   C   CR5   0  -0.241  -3.2635   0.7550  -0.3373
 CGE  CAS   C   CR6   0   0.120   1.7346   0.5995   0.1702
 CGE  HA    H   HCH1  0   0.264   0.9225  -0.8085  -1.2428
 CGE  HAA   H   HCH3  0   0.255   3.2313  -3.9811   0.4099
 CGE  HAAA  H   HCH3  0   0.242   2.9653  -3.0849   1.9196
 CGE  HAAB  H   HCH3  0   0.243   1.7034  -4.1722   1.2946
 CGE  HAD   H   HCR6  0   0.270   4.2576   3.3241   1.3058
 CGE  HAE   H   HCR6  0   0.265   2.2063   2.8874   2.6385
 CGE  HAF   H   HCR5  0   0.291  -6.3199  -0.9824  -0.0974
 CGE  HAG   H   HCR6  0   0.282   4.6920   2.0136  -0.7355
 CGE  HAH   H   HCR6  0   0.267   0.6135   1.1613   1.9000
 CGE  HAI   H   HCR5  0   0.262  -4.1548  -2.4592  -0.1500
 CGE  HAJ   H   HCH2  0   0.254  -2.0701   2.3185   0.5041
 CGE  HAJA  H   HCH2  0   0.257  -2.4921   2.5719  -1.1804
 CGE  HAK   H   HCH2  0   0.265  -0.1061   1.8638  -0.8055
 CGE  HAKA  H   HCH2  0   0.221  -0.9839   0.8563  -1.9502
 CGE  HAL   H   HCH2  0   0.223  -1.3852  -1.5374  -1.3265
 CGE  HALA  H   HCH2  0   0.264  -1.4758  -1.8883   0.3954

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
 CGE  C    O     double    1.203  0.020  1.203
 CGE  C    CA    single    1.527  0.020  1.527
 CGE  C    OAM   single    1.320  0.020  1.320
 CGE  N    CA    single    1.448  0.020  1.448
 CGE  N    CAK   single    1.461  0.020  1.461
 CGE  N    CAL   single    1.459  0.020  1.459
 CGE  CL1  CAP   single    1.736  0.020  1.736
 CGE  CA   CAS   single    1.518  0.020  1.518
 CGE  CAA  OAM   single    1.430  0.020  1.430
 CGE  CAD  CAE   aromatic  1.389  0.020  1.389
 CGE  CAD  CAG   aromatic  1.384  0.020  1.384
 CGE  CAE  CAH   aromatic  1.384  0.020  1.384
 CGE  CAF  CAI   aromatic  1.359  0.020  1.359
 CGE  CAF  SAN   aromatic  1.719  0.020  1.719
 CGE  CAG  CAP   aromatic  1.389  0.020  1.389
 CGE  CAH  CAS   aromatic  1.395  0.020  1.395
 CGE  CAI  CAQ   aromatic  1.426  0.020  1.426
 CGE  CAJ  CAK   single    1.523  0.020  1.523
 CGE  CAJ  CAR   single    1.490  0.020  1.490
 CGE  CAL  CAQ   single    1.497  0.020  1.497
 CGE  SAN  CAR   aromatic  1.721  0.020  1.721
 CGE  CAP  CAS   aromatic  1.391  0.020  1.391
 CGE  CAQ  CAR   aromatic  1.360  0.020  1.360
 CGE  CA   HA    single    0.970  0.020  1.090
 CGE  CAA  HAA   single    0.970  0.020  1.090
 CGE  CAA  HAAA  single    0.970  0.020  1.090
 CGE  CAA  HAAB  single    0.970  0.020  1.090
 CGE  CAD  HAD   single    0.930  0.020  1.080
 CGE  CAE  HAE   single    0.930  0.020  1.080
 CGE  CAF  HAF   single    0.930  0.020  1.080
 CGE  CAG  HAG   single    0.930  0.020  1.080
 CGE  CAH  HAH   single    0.930  0.020  1.080
 CGE  CAI  HAI   single    0.930  0.020  1.080
 CGE  CAJ  HAJ   single    0.970  0.020  1.090
 CGE  CAJ  HAJA  single    0.970  0.020  1.090
 CGE  CAK  HAK   single    0.970  0.020  1.090
 CGE  CAK  HAKA  single    0.970  0.020  1.090
 CGE  CAL  HAL   single    0.970  0.020  1.090
 CGE  CAL  HALA  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
 CGE  OAM   C    CA    110.56  3.000
 CGE  OAM   C    O     124.50  3.000
 CGE  CA    C    O     124.83  3.000
 CGE  CAL   N    CAK   109.95  3.000
 CGE  CAL   N    CA    111.11  3.000
 CGE  CAK   N    CA    111.55  3.000
 CGE  HA    CA   CAS   109.73  3.000
 CGE  HA    CA   N     111.44  3.000
 CGE  CAS   CA   N     111.78  3.000
 CGE  HA    CA   C     108.17  3.000
 CGE  CAS   CA   C     103.86  3.000
 CGE  N     CA   C     111.55  3.000
 CGE  HAAB  CAA  HAAA  109.44  3.000
 CGE  HAAB  CAA  HAA   109.46  3.000
 CGE  HAAA  CAA  HAA   109.44  3.000
 CGE  HAAB  CAA  OAM   111.30  3.000
 CGE  HAAA  CAA  OAM   111.28  3.000
 CGE  HAA   CAA  OAM   105.84  3.000
 CGE  HAD   CAD  CAG   119.54  3.000
 CGE  HAD   CAD  CAE   120.57  3.000
 CGE  CAG   CAD  CAE   119.89  3.000
 CGE  HAE   CAE  CAH   119.87  3.000
 CGE  HAE   CAE  CAD   120.32  3.000
 CGE  CAH   CAE  CAD   119.82  3.000
 CGE  HAF   CAF  SAN   120.40  3.000
 CGE  HAF   CAF  CAI   128.09  3.000
 CGE  SAN   CAF  CAI   111.51  3.000
 CGE  HAG   CAG  CAP   119.99  3.000
 CGE  HAG   CAG  CAD   120.35  3.000
 CGE  CAP   CAG  CAD   119.66  3.000
 CGE  HAH   CAH  CAS   118.67  3.000
 CGE  HAH   CAH  CAE   119.91  3.000
 CGE  CAS   CAH  CAE   121.42  3.000
 CGE  HAI   CAI  CAQ   124.01  3.000
 CGE  HAI   CAI  CAF   123.44  3.000
 CGE  CAQ   CAI  CAF   112.54  3.000
 CGE  HAJA  CAJ  HAJ   106.83  3.000
 CGE  HAJA  CAJ  CAR   111.53  3.000
 CGE  HAJ   CAJ  CAR   110.86  3.000
 CGE  HAJA  CAJ  CAK   109.34  3.000
 CGE  HAJ   CAJ  CAK   110.01  3.000
 CGE  CAR   CAJ  CAK   108.27  3.000
 CGE  HAKA  CAK  HAK   106.91  3.000
 CGE  HAKA  CAK  CAJ   109.73  3.000
 CGE  HAK   CAK  CAJ   108.86  3.000
 CGE  HAKA  CAK  N     111.13  3.000
 CGE  HAK   CAK  N     109.76  3.000
 CGE  CAJ   CAK  N     110.36  3.000
 CGE  HALA  CAL  HAL   106.63  3.000
 CGE  HALA  CAL  CAQ   108.78  3.000
 CGE  HAL   CAL  CAQ   109.51  3.000
 CGE  HALA  CAL  N     109.92  3.000
 CGE  HAL   CAL  N     111.13  3.000
 CGE  CAQ   CAL  N     110.76  3.000
 CGE  CAA   OAM  C     117.58  3.000
 CGE  CAR   SAN  CAF    91.91  3.000
 CGE  CAS   CAP  CAG   121.50  3.000
 CGE  CAS   CAP  CL1   121.08  3.000
 CGE  CAG   CAP  CL1   117.42  3.000
 CGE  CAR   CAQ  CAL   121.60  3.000
 CGE  CAR   CAQ  CAI   112.73  3.000
 CGE  CAL   CAQ  CAI   125.67  3.000
 CGE  CAQ   CAR  SAN   111.31  3.000
 CGE  CAQ   CAR  CAJ   123.45  3.000
 CGE  SAN   CAR  CAJ   125.24  3.000
 CGE  CAP   CAS  CAH   117.71  3.000
 CGE  CAP   CAS  CA    123.36  3.000
 CGE  CAH   CAS  CA    118.89  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
 CGE  CONST_01  CAS  CAH  CAE  CAD     0.00   0.0  0
 CGE  CONST_02  CAS  CAP  CAG  CAD     0.00   0.0  0
 CGE  CONST_03  CAP  CAG  CAD  CAE     0.00   0.0  0
 CGE  CONST_04  CAP  CAS  CAH  CAE     0.00   0.0  0
 CGE  CONST_05  CAR  CAQ  CAI  CAF     0.00   0.0  0
 CGE  CONST_06  CAQ  CAR  SAN  CAF     0.00   0.0  0
 CGE  CONST_07  CAH  CAE  CAD  CAG     0.00   0.0  0
 CGE  CONST_08  CAH  CAS  CAP  CAG     0.00   0.0  0
 CGE  CONST_09  CAR  SAN  CAF  CAI     0.00   0.0  0
 CGE  CONST_10  SAN  CAR  CAQ  CAI     0.00   0.0  0
 CGE  CONST_11  CAQ  CAI  CAF  SAN     0.00   0.0  0
 CGE  CONST_12  CAD  CAG  CAP  CL1   180.00   0.0  0
 CGE  CONST_13  CAH  CAS  CAP  CL1   180.00   0.0  0
 CGE  CONST_14  CAE  CAH  CAS  CA    180.00   0.0  0
 CGE  CONST_15  CAG  CAP  CAS  CA    180.00   0.0  0
 CGE  CONST_16  HAH  CAH  CAE  CAD   180.00   0.0  0
 CGE  CONST_17  HAG  CAG  CAD  CAE   180.00   0.0  0
 CGE  CONST_18  HAE  CAE  CAD  CAG   180.00   0.0  0
 CGE  CONST_19  HAD  CAD  CAE  CAH   180.00   0.0  0
 CGE  CONST_20  HAI  CAI  CAQ  CAL     0.00   0.0  0
 CGE  CONST_21  HAF  CAF  CAI  CAQ   180.00   0.0  0
 CGE  Var_01    CAR  CAJ  CAK  N     -49.57  30.0  1
 CGE  Var_02    CAI  CAQ  CAL  N    -163.62  30.0  1
 CGE  Var_03    CAL  N    CAK  CAJ    70.36  30.0  1
 CGE  Var_04    CAQ  CAL  N    CAK   -50.61  30.0  1
 CGE  Var_05    SAN  CAR  CAJ  CAK  -164.05  30.0  1
 CGE  Var_06    HAA  CAA  OAM  C    -179.67  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
 CGE  chir_01  CA  C  N  CAS  negativ

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
 CGE  plan-1  CL1  0.020
 CGE  plan-1  CA   0.020
 CGE  plan-1  CAD  0.020
 CGE  plan-1  CAE  0.020
 CGE  plan-1  CAG  0.020
 CGE  plan-1  CAH  0.020
 CGE  plan-1  CAP  0.020
 CGE  plan-1  CAS  0.020
 CGE  plan-1  HAD  0.020
 CGE  plan-1  HAE  0.020
 CGE  plan-1  HAG  0.020
 CGE  plan-1  HAH  0.020
 CGE  plan-2  CAF  0.020
 CGE  plan-2  CAI  0.020
 CGE  plan-2  CAJ  0.020
 CGE  plan-2  CAL  0.020
 CGE  plan-2  SAN  0.020
 CGE  plan-2  CAQ  0.020
 CGE  plan-2  CAR  0.020
 CGE  plan-2  HAF  0.020
 CGE  plan-2  HAI  0.020
 CGE  plan-3  C    0.020
 CGE  plan-3  O    0.020
 CGE  plan-3  CA   0.020
 CGE  plan-3  OAM  0.020

