# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 04:00:57 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (2~{R})-2-diethoxyphosphoryl-5-phenyl-pentane-1-thiol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCO[P](=O)(OCC)[C@@H](CS)CCCc1ccccc1
#
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
 8SH  8SH  (2~{R})-2-diethoxyphosphoryl-5-phenyl-pentane-1-thiol  ligand  45  20  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8SH
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
 8SH  CAA   C  CH3   0  -0.684  -1.1236  -2.8502   2.2754
 8SH  CAB   C  CH2   0  -0.178  -0.9212  -2.4509   0.8342
 8SH  OAC   O  O2    0  -0.607  -1.8520  -1.4047   0.5181
 8SH  PAD   P  P     0   1.430  -1.6198  -0.3758  -0.6989
 8SH  OAE   O  O     0  -0.714  -0.7122  -0.8918  -1.7560
 8SH  OAF   O  O2    0  -0.580  -3.1202  -0.0659  -1.1533
 8SH  CAG   C  CH2   0  -0.171  -3.9213  -1.0604  -1.8142
 8SH  CAH   C  CH3   0  -0.679  -5.2573  -0.4480  -2.1556
 8SH  CAI   C  CH1   0  -0.496  -1.1374   1.1947   0.0808
 8SH  CAJ   C  CH2   0  -0.573  -2.2867   1.8275   0.8726
 8SH  SAK   S  S2    0  -0.224  -3.5607   2.6286  -0.1682
 8SH  CAL   C  CH2   0  -0.449   0.0855   1.0069   0.9946
 8SH  CAM   C  CH2   0  -0.431   1.3823   0.6149   0.2940
 8SH  CAN   C  CH2   0  -0.507   2.5590   0.5821   1.2716
 8SH  CAO   C  CR6   0   0.138   3.8331   0.1631   0.5943
 8SH  CAP   C  CR16  0  -0.311   4.6455   1.1006  -0.0408
 8SH  CAQ   C  CR16  0  -0.239   5.7978   0.7094  -0.7095
 8SH  CAR   C  CR16  0  -0.275   6.1565  -0.6320  -0.7545
 8SH  CAS   C  CR16  0  -0.240   5.3553  -1.5760  -0.1253
 8SH  CAT   C  CR16  0  -0.314   4.2042  -1.1789   0.5424
 8SH  HAA3  H  HCH3  0   0.238  -0.4397  -3.6609   2.5262
 8SH  HAA1  H  HCH3  0   0.234  -0.9195  -2.0190   2.9511
 8SH  HAA2  H  HCH3  0   0.237  -2.1402  -3.2003   2.4536
 8SH  HAB1  H  HCH2  0   0.222   0.1075  -2.1179   0.6748
 8SH  HAB2  H  HCH2  0   0.242  -1.0971  -3.2977   0.1681
 8SH  HAG1  H  HCH2  0   0.232  -3.4106  -1.4007  -2.7175
 8SH  HAG2  H  HCH2  0   0.232  -4.0506  -1.9220  -1.1554
 8SH  HAH2  H  HCH3  0   0.235  -5.1466   0.3928  -2.8396
 8SH  HAH1  H  HCH3  0   0.236  -5.8815  -1.1986  -2.6399
 8SH  HAH3  H  HCH3  0   0.235  -5.7762  -0.1026  -1.2617
 8SH  HAI1  H  HCH1  0   0.289  -0.8565   1.8715  -0.7327
 8SH  HAJ1  H  HCH2  0   0.278  -2.7683   1.1001   1.5266
 8SH  HAJ2  H  HCH2  0   0.295  -1.8749   2.6030   1.5162
 8SH  HAK1  H  HSH1  0   0.211  -3.4031   3.8623   0.3231
 8SH  HAL1  H  HCH2  0   0.255   0.2494   1.9629   1.5005
 8SH  HAL2  H  HCH2  0   0.239  -0.1448   0.2895   1.7885
 8SH  HAM2  H  HCH2  0   0.234   1.2973  -0.3632  -0.1840
 8SH  HAM1  H  HCH2  0   0.236   1.5922   1.3292  -0.5076
 8SH  HAN2  H  HCH2  0   0.243   2.6831   1.5690   1.7256
 8SH  HAN1  H  HCH2  0   0.239   2.3291  -0.1112   2.0855
 8SH  HAP1  H  HCR6  0   0.245   4.3738   2.1497  -0.0078
 8SH  HAQ1  H  HCR6  0   0.252   6.4184   1.4529  -1.1935
 8SH  HAR1  H  HCR6  0   0.253   7.0561  -0.9389  -1.2722
 8SH  HAS1  H  HCR6  0   0.253   5.6287  -2.6232  -0.1512
 8SH  HAT1  H  HCR6  0   0.243   3.5876  -1.9224   1.0354

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
 8SH  SAK  CAJ   single    1.830  0.020  1.830
 8SH  CAJ  CAI   single    1.532  0.020  1.532
 8SH  CAI  CAL   single    1.538  0.020  1.538
 8SH  CAI  PAD   single    1.819  0.020  1.819
 8SH  CAN  CAO   single    1.503  0.020  1.503
 8SH  CAN  CAM   single    1.530  0.020  1.530
 8SH  OAE  PAD   double    1.486  0.020  1.486
 8SH  CAO  CAP   aromatic  1.394  0.020  1.394
 8SH  CAO  CAT   aromatic  1.393  0.020  1.393
 8SH  CAL  CAM   single    1.525  0.020  1.525
 8SH  CAP  CAQ   aromatic  1.388  0.020  1.388
 8SH  CAT  CAS   aromatic  1.389  0.020  1.389
 8SH  PAD  OAF   single    1.598  0.020  1.598
 8SH  PAD  OAC   single    1.611  0.020  1.611
 8SH  CAQ  CAR   aromatic  1.389  0.020  1.389
 8SH  CAS  CAR   aromatic  1.389  0.020  1.389
 8SH  OAF  CAG   single    1.438  0.020  1.438
 8SH  CAH  CAG   single    1.509  0.020  1.509
 8SH  OAC  CAB   single    1.435  0.020  1.435
 8SH  CAB  CAA   single    1.509  0.020  1.509
 8SH  CAA  HAA3  single    0.970  0.020  1.090
 8SH  CAA  HAA1  single    0.970  0.020  1.090
 8SH  CAA  HAA2  single    0.970  0.020  1.090
 8SH  CAB  HAB1  single    0.970  0.020  1.090
 8SH  CAB  HAB2  single    0.970  0.020  1.090
 8SH  CAG  HAG1  single    0.970  0.020  1.090
 8SH  CAG  HAG2  single    0.970  0.020  1.090
 8SH  CAH  HAH2  single    0.970  0.020  1.090
 8SH  CAH  HAH1  single    0.970  0.020  1.090
 8SH  CAH  HAH3  single    0.970  0.020  1.090
 8SH  CAI  HAI1  single    0.970  0.020  1.090
 8SH  CAJ  HAJ1  single    0.970  0.020  1.090
 8SH  CAJ  HAJ2  single    0.970  0.020  1.090
 8SH  SAK  HAK1  single    1.200  0.020  1.300
 8SH  CAL  HAL1  single    0.970  0.020  1.090
 8SH  CAL  HAL2  single    0.970  0.020  1.090
 8SH  CAM  HAM2  single    0.970  0.020  1.090
 8SH  CAM  HAM1  single    0.970  0.020  1.090
 8SH  CAN  HAN2  single    0.970  0.020  1.090
 8SH  CAN  HAN1  single    0.970  0.020  1.090
 8SH  CAP  HAP1  single    0.930  0.020  1.080
 8SH  CAQ  HAQ1  single    0.930  0.020  1.080
 8SH  CAR  HAR1  single    0.930  0.020  1.080
 8SH  CAS  HAS1  single    0.930  0.020  1.080
 8SH  CAT  HAT1  single    0.930  0.020  1.080

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
 8SH  HAA2  CAA  HAA1  108.55  3.000
 8SH  HAA2  CAA  HAA3  107.98  3.000
 8SH  HAA1  CAA  HAA3  107.88  3.000
 8SH  HAA2  CAA  CAB   111.48  3.000
 8SH  HAA1  CAA  CAB   111.41  3.000
 8SH  HAA3  CAA  CAB   109.42  3.000
 8SH  HAB2  CAB  HAB1  107.40  3.000
 8SH  HAB2  CAB  OAC   109.05  3.000
 8SH  HAB1  CAB  OAC   110.86  3.000
 8SH  HAB2  CAB  CAA   110.85  3.000
 8SH  HAB1  CAB  CAA   110.25  3.000
 8SH  OAC   CAB  CAA   108.43  3.000
 8SH  PAD   OAC  CAB   122.58  3.000
 8SH  CAI   PAD  OAF   101.74  3.000
 8SH  OAF   PAD  OAE   116.02  3.000
 8SH  CAI   PAD  OAE   116.29  3.000
 8SH  OAF   PAD  OAC   101.74  3.000
 8SH  OAE   PAD  OAC   113.82  3.000
 8SH  CAI   PAD  OAC   105.42  3.000
 8SH  CAG   OAF  PAD   121.31  3.000
 8SH  HAG2  CAG  HAG1  107.97  3.000
 8SH  HAG2  CAG  CAH   110.60  3.000
 8SH  HAG1  CAG  CAH   110.70  3.000
 8SH  HAG2  CAG  OAF   109.53  3.000
 8SH  HAG1  CAG  OAF   109.58  3.000
 8SH  CAH   CAG  OAF   108.46  3.000
 8SH  HAH3  CAH  HAH1  108.07  3.000
 8SH  HAH3  CAH  HAH2  108.58  3.000
 8SH  HAH1  CAH  HAH2  108.10  3.000
 8SH  HAH3  CAH  CAG   111.39  3.000
 8SH  HAH1  CAH  CAG   109.16  3.000
 8SH  HAH2  CAH  CAG   111.43  3.000
 8SH  HAI1  CAI  CAL   108.24  3.000
 8SH  HAI1  CAI  CAJ   108.73  3.000
 8SH  CAL   CAI  CAJ   109.86  3.000
 8SH  HAI1  CAI  PAD   106.46  3.000
 8SH  CAL   CAI  PAD   111.11  3.000
 8SH  CAJ   CAI  PAD   112.28  3.000
 8SH  HAJ2  CAJ  HAJ1  106.72  3.000
 8SH  HAJ2  CAJ  SAK   106.72  3.000
 8SH  HAJ1  CAJ  SAK   109.02  3.000
 8SH  HAJ2  CAJ  CAI   108.41  3.000
 8SH  HAJ1  CAJ  CAI   111.46  3.000
 8SH  SAK   CAJ  CAI   114.14  3.000
 8SH  HAK1  SAK  CAJ    96.48  3.000
 8SH  HAL2  CAL  HAL1  105.60  3.000
 8SH  HAL2  CAL  CAM   110.09  3.000
 8SH  HAL1  CAL  CAM   108.04  3.000
 8SH  HAL2  CAL  CAI   110.11  3.000
 8SH  HAL1  CAL  CAI   106.69  3.000
 8SH  CAM   CAL  CAI   115.75  3.000
 8SH  HAM1  CAM  HAM2  106.20  3.000
 8SH  HAM1  CAM  CAN   109.54  3.000
 8SH  HAM2  CAM  CAN   108.69  3.000
 8SH  HAM1  CAM  CAL   109.38  3.000
 8SH  HAM2  CAM  CAL   111.41  3.000
 8SH  CAN   CAM  CAL   111.46  3.000
 8SH  HAN1  CAN  HAN2  106.68  3.000
 8SH  HAN1  CAN  CAO   109.69  3.000
 8SH  HAN2  CAN  CAO   110.04  3.000
 8SH  HAN1  CAN  CAM   109.11  3.000
 8SH  HAN2  CAN  CAM   109.47  3.000
 8SH  CAO   CAN  CAM   111.72  3.000
 8SH  CAT   CAO  CAP   118.41  3.000
 8SH  CAT   CAO  CAN   120.75  3.000
 8SH  CAP   CAO  CAN   120.80  3.000
 8SH  HAP1  CAP  CAQ   119.69  3.000
 8SH  HAP1  CAP  CAO   119.40  3.000
 8SH  CAQ   CAP  CAO   120.91  3.000
 8SH  HAQ1  CAQ  CAR   120.04  3.000
 8SH  HAQ1  CAQ  CAP   119.84  3.000
 8SH  CAR   CAQ  CAP   120.13  3.000
 8SH  HAR1  CAR  CAS   120.23  3.000
 8SH  HAR1  CAR  CAQ   120.26  3.000
 8SH  CAS   CAR  CAQ   119.51  3.000
 8SH  HAS1  CAS  CAT   119.83  3.000
 8SH  HAS1  CAS  CAR   120.06  3.000
 8SH  CAT   CAS  CAR   120.11  3.000
 8SH  HAT1  CAT  CAS   119.59  3.000
 8SH  HAT1  CAT  CAO   119.47  3.000
 8SH  CAS   CAT  CAO   120.93  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
 8SH  CONST_01  CAR   CAQ  CAP  CAO     0.00   0.0  0
 8SH  CONST_02  CAR   CAS  CAT  CAO     0.00   0.0  0
 8SH  CONST_03  CAS   CAT  CAO  CAP     0.00   0.0  0
 8SH  CONST_04  CAS   CAR  CAQ  CAP     0.00   0.0  0
 8SH  CONST_05  CAT   CAO  CAP  CAQ     0.00   0.0  0
 8SH  CONST_06  CAT   CAS  CAR  CAQ     0.00   0.0  0
 8SH  CONST_07  CAQ   CAP  CAO  CAN   180.00   0.0  0
 8SH  CONST_08  CAS   CAT  CAO  CAN   180.00   0.0  0
 8SH  CONST_09  HAQ1  CAQ  CAP  CAO   180.00   0.0  0
 8SH  CONST_10  HAS1  CAS  CAT  CAO   180.00   0.0  0
 8SH  CONST_11  HAT1  CAT  CAO  CAP   180.00   0.0  0
 8SH  CONST_12  HAR1  CAR  CAQ  CAP   180.00   0.0  0
 8SH  CONST_13  HAP1  CAP  CAQ  CAR   180.00   0.0  0
 8SH  Var_01    CAP   CAO  CAN  CAM    86.65  30.0  2
 8SH  Var_02    CAO   CAN  CAM  CAL   178.57  30.0  2
 8SH  Var_03    CAI   PAD  OAC  CAB  -105.69  30.0  1
 8SH  Var_04    CAH   CAG  OAF  PAD  -177.94  30.0  3
 8SH  Var_05    CAN   CAM  CAL  CAI   174.68  30.0  3
 8SH  Var_06    HAA3  CAA  CAB  OAC   178.69  30.0  3
 8SH  Var_07    HAB1  CAB  OAC  PAD    36.57  30.0  3
 8SH  Var_08    HAH2  CAH  CAG  OAF    61.78  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
 8SH  chir_01  CAI  CAJ  CAL  PAD  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
 8SH  plan-1  CAN   0.020
 8SH  plan-1  CAO   0.020
 8SH  plan-1  CAP   0.020
 8SH  plan-1  CAQ   0.020
 8SH  plan-1  CAR   0.020
 8SH  plan-1  CAS   0.020
 8SH  plan-1  CAT   0.020
 8SH  plan-1  HAP1  0.020
 8SH  plan-1  HAQ1  0.020
 8SH  plan-1  HAR1  0.020
 8SH  plan-1  HAS1  0.020
 8SH  plan-1  HAT1  0.020

