# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 17:19:55 2022
#   Inital geometry file: a 120 line input string
#   Ligand name: S-[(2R)-2-methyl-1,1-diphenylbutyl]-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](C)C(SC[C@H](N)C(O)=O)(c1ccccc1)c2ccccc2
#
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
 X2O  X2O  S-[(2R)-2-methyl-1,1-diphenylbutyl]-L-cysteine  ligand  48  24  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_X2O
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
 X2O  CAL   C  CR16   0  -0.288   2.1171  -2.1833  -0.0083
 X2O  CAH   C  CR16   0  -0.246   2.2089  -3.5693   0.0160
 X2O  CAF   C  CR16   0  -0.272   1.0639  -4.3462   0.1018
 X2O  CAI   C  CR16   0  -0.241  -0.1719  -3.7179   0.1740
 X2O  CAM   C  CR16   0  -0.303  -0.2572  -2.3335   0.1509
 X2O  CAT   C  CR6    0   0.197   0.8822  -1.5367   0.0480
 X2O  CAX   C  CT     0  -0.350   0.7846  -0.0109   0.0954
 X2O  SAR   S  S2     0   0.008  -0.5411   0.6194  -1.0666
 X2O  CB    C  CH2    0  -0.587  -2.1884   0.3519  -0.3344
 X2O  CA    C  CH1    0  -0.206  -3.1430   1.4567  -0.8269
 X2O  C     C  C      0   0.412  -4.5572   1.0863  -0.3083
 X2O  OXT   O  OC    -1  -0.613  -5.1241   0.1471  -0.8987
 X2O  O     O  O      0  -0.598  -4.9840   1.7241   0.6719
 X2O  N     N  NH2    0  -0.792  -2.7758   2.8017  -0.4373
 X2O  CAW   C  CH1    0  -0.210   0.4621   0.4172   1.5558
 X2O  CAB   C  CH3    0  -0.685   0.1045   1.8991   1.7228
 X2O  CAP   C  CH2    0  -0.433   1.5108  -0.0390   2.5894
 X2O  CAA   C  CH3    0  -0.663   0.8972  -0.2429   3.9695
 X2O  CAU   C  C      0   0.142   2.0178   0.6180  -0.5516
 X2O  CAN   C  C1     0  -0.258   2.3155   0.2732  -1.8763
 X2O  CAJ   C  C1     0  -0.242   3.4087   0.8089  -2.5358
 X2O  CAG   C  C1     0  -0.270   4.2467   1.7067  -1.8854
 X2O  CAK   C  C1     0  -0.240   3.9720   2.0522  -0.5731
 X2O  CAO   C  C1     0  -0.328   2.8692   1.5154   0.0844
 X2O  HAL   H  HCR6   0   0.257   3.0304  -1.6066  -0.0658
 X2O  HAH   H  HCR6   0   0.253   3.1835  -4.0380  -0.0320
 X2O  HAF   H  HCR6   0   0.254   1.1322  -5.4261   0.1158
 X2O  HAI   H  HCR6   0   0.254  -1.0774  -4.3064   0.2471
 X2O  HAM   H  HCR6   0   0.264  -1.2374  -1.8838   0.2126
 X2O  HAW   H  HCH1   0   0.243  -0.4392  -0.1516   1.8127
 X2O  HB1C  H  HCH2   0   0.269  -2.5771  -0.6197  -0.6372
 X2O  HB2C  H  HCH2   0   0.264  -2.1251   0.3733   0.7549
 X2O  HA    H  HCH1   0   0.221  -3.1674   1.4051  -1.9213
 X2O  HN1   H  HNH2   0   0.332  -2.9711   2.9161   0.5495
 X2O  HN2   H  HNH2   0   0.336  -1.7777   2.9311  -0.5592
 X2O  HAB1  H  HCH3   0   0.234   0.7130   2.5614   1.1108
 X2O  HAB2  H  HCH3   0   0.228  -0.9328   2.0973   1.4612
 X2O  HAB3  H  HCH3   0   0.238   0.2334   2.2049   2.7620
 X2O  HAP1  H  HCH2   0   0.242   1.9727  -0.9768   2.2776
 X2O  HAP2  H  HCH2   0   0.225   2.3229   0.6857   2.6685
 X2O  HAA1  H  HCH3   0   0.231   1.6559  -0.5500   4.6901
 X2O  HAA2  H  HCH3   0   0.222   0.4355   0.6690   4.3519
 X2O  HAA3  H  HCH3   0   0.220   0.1285  -1.0173   3.9447
 X2O  HAN   H  H      0   0.259   1.6869  -0.4358  -2.4009
 X2O  HAO   H  H      0   0.253   2.6992   1.8155   1.1055
 X2O  HAJ   H  H      0   0.255   3.6085   0.5196  -3.5594
 X2O  HAG   H  H      0   0.255   5.1031   2.1270  -2.3964
 X2O  HAK   H  H      0   0.256   4.6148   2.7450  -0.0455

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
 X2O  CAL  CAH   aromatic  1.389  0.020  1.389
 X2O  CAL  CAT   aromatic  1.395  0.020  1.395
 X2O  CAH  CAF   aromatic  1.386  0.020  1.386
 X2O  CAF  CAI   aromatic  1.388  0.020  1.388
 X2O  CAI  CAM   aromatic  1.387  0.020  1.387
 X2O  CAM  CAT   aromatic  1.394  0.020  1.394
 X2O  CAT  CAX   single    1.530  0.020  1.530
 X2O  CAX  SAR   single    1.872  0.020  1.872
 X2O  CAX  CAW   single    1.556  0.020  1.556
 X2O  CAX  CAU   single    1.528  0.020  1.528
 X2O  SAR  CB    single    1.822  0.020  1.822
 X2O  CB   CA    single    1.541  0.020  1.541
 X2O  CA   C     single    1.551  0.020  1.551
 X2O  CA   N     single    1.448  0.020  1.448
 X2O  C    OXT   deloc     1.246  0.020  1.246
 X2O  C    O     deloc     1.245  0.020  1.245
 X2O  CAW  CAB   single    1.534  0.020  1.534
 X2O  CAW  CAP   single    1.542  0.020  1.542
 X2O  CAP  CAA   single    1.524  0.020  1.524
 X2O  CAU  CAN   aromatic  1.401  0.020  1.401
 X2O  CAU  CAO   aromatic  1.391  0.020  1.391
 X2O  CAN  CAJ   aromatic  1.385  0.020  1.385
 X2O  CAJ  CAG   aromatic  1.390  0.020  1.390
 X2O  CAG  CAK   aromatic  1.385  0.020  1.385
 X2O  CAK  CAO   aromatic  1.392  0.020  1.392
 X2O  CAL  HAL   single    0.930  0.020  1.080
 X2O  CAH  HAH   single    0.930  0.020  1.080
 X2O  CAF  HAF   single    0.930  0.020  1.080
 X2O  CAI  HAI   single    0.930  0.020  1.080
 X2O  CAM  HAM   single    0.930  0.020  1.080
 X2O  CAW  HAW   single    0.970  0.020  1.090
 X2O  CB   HB1C  single    0.970  0.020  1.090
 X2O  CB   HB2C  single    0.970  0.020  1.090
 X2O  CA   HA    single    0.970  0.020  1.090
 X2O  N    HN1   single    0.890  0.020  1.040
 X2O  N    HN2   single    0.890  0.020  1.040
 X2O  CAB  HAB1  single    0.970  0.020  1.090
 X2O  CAB  HAB2  single    0.970  0.020  1.090
 X2O  CAB  HAB3  single    0.970  0.020  1.090
 X2O  CAP  HAP1  single    0.970  0.020  1.090
 X2O  CAP  HAP2  single    0.970  0.020  1.090
 X2O  CAA  HAA1  single    0.970  0.020  1.090
 X2O  CAA  HAA2  single    0.970  0.020  1.090
 X2O  CAA  HAA3  single    0.970  0.020  1.090
 X2O  CAN  HAN   single    0.930  0.020  1.080
 X2O  CAO  HAO   single    0.930  0.020  1.080
 X2O  CAJ  HAJ   single    0.930  0.020  1.080
 X2O  CAG  HAG   single    0.930  0.020  1.080
 X2O  CAK  HAK   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
 X2O  HAL   CAL  CAT   120.16  3.000
 X2O  HAL   CAL  CAH   118.50  3.000
 X2O  CAT   CAL  CAH   121.34  3.000
 X2O  HAH   CAH  CAF   120.25  3.000
 X2O  HAH   CAH  CAL   119.38  3.000
 X2O  CAF   CAH  CAL   120.37  3.000
 X2O  HAF   CAF  CAI   120.47  3.000
 X2O  HAF   CAF  CAH   120.52  3.000
 X2O  CAI   CAF  CAH   119.00  3.000
 X2O  HAI   CAI  CAM   119.49  3.000
 X2O  HAI   CAI  CAF   120.14  3.000
 X2O  CAM   CAI  CAF   120.37  3.000
 X2O  HAM   CAM  CAT   120.52  3.000
 X2O  HAM   CAM  CAI   118.06  3.000
 X2O  CAT   CAM  CAI   121.42  3.000
 X2O  CAX   CAT  CAM   121.04  3.000
 X2O  CAX   CAT  CAL   121.34  3.000
 X2O  CAM   CAT  CAL   117.48  3.000
 X2O  CAU   CAX  CAW   116.84  3.000
 X2O  CAU   CAX  SAR    99.80  3.000
 X2O  CAW   CAX  SAR   110.07  3.000
 X2O  CAU   CAX  CAT   110.23  3.000
 X2O  CAW   CAX  CAT   108.47  3.000
 X2O  SAR   CAX  CAT   111.21  3.000
 X2O  CB    SAR  CAX   109.96  3.000
 X2O  HB2C  CB   HB1C  108.40  3.000
 X2O  HB2C  CB   CA    109.93  3.000
 X2O  HB1C  CB   CA    109.25  3.000
 X2O  HB2C  CB   SAR   110.22  3.000
 X2O  HB1C  CB   SAR   109.98  3.000
 X2O  CA    CB   SAR   109.04  3.000
 X2O  HA    CA   N     108.55  3.000
 X2O  HA    CA   C     107.60  3.000
 X2O  N     CA   C     111.29  3.000
 X2O  HA    CA   CB    107.41  3.000
 X2O  N     CA   CB    115.03  3.000
 X2O  C     CA   CB    106.66  3.000
 X2O  O     C    OXT   127.11  3.000
 X2O  O     C    CA    116.97  3.000
 X2O  OXT   C    CA    115.88  3.000
 X2O  HN2   N    HN1   107.01  3.000
 X2O  HN2   N    CA    109.63  3.000
 X2O  HN1   N    CA    108.56  3.000
 X2O  HAW   CAW  CAP   104.39  3.000
 X2O  HAW   CAW  CAB   106.51  3.000
 X2O  CAP   CAW  CAB   111.81  3.000
 X2O  HAW   CAW  CAX   104.34  3.000
 X2O  CAP   CAW  CAX   114.02  3.000
 X2O  CAB   CAW  CAX   114.62  3.000
 X2O  HAB3  CAB  HAB2  106.90  3.000
 X2O  HAB3  CAB  HAB1  107.41  3.000
 X2O  HAB2  CAB  HAB1  106.68  3.000
 X2O  HAB3  CAB  CAW   110.31  3.000
 X2O  HAB2  CAB  CAW   111.85  3.000
 X2O  HAB1  CAB  CAW   113.37  3.000
 X2O  HAP2  CAP  HAP1  106.05  3.000
 X2O  HAP2  CAP  CAA   108.84  3.000
 X2O  HAP1  CAP  CAA   108.31  3.000
 X2O  HAP2  CAP  CAW   111.00  3.000
 X2O  HAP1  CAP  CAW   110.53  3.000
 X2O  CAA   CAP  CAW   111.89  3.000
 X2O  HAA3  CAA  HAA2  107.63  3.000
 X2O  HAA3  CAA  HAA1  107.77  3.000
 X2O  HAA2  CAA  HAA1  107.34  3.000
 X2O  HAA3  CAA  CAP   110.98  3.000
 X2O  HAA2  CAA  CAP   112.08  3.000
 X2O  HAA1  CAA  CAP   110.85  3.000
 X2O  CAO   CAU  CAN   117.46  3.000
 X2O  CAO   CAU  CAX   124.47  3.000
 X2O  CAN   CAU  CAX   118.07  3.000
 X2O  HAN   CAN  CAJ   118.74  3.000
 X2O  HAN   CAN  CAU   119.72  3.000
 X2O  CAJ   CAN  CAU   121.53  3.000
 X2O  HAJ   CAJ  CAG   120.26  3.000
 X2O  HAJ   CAJ  CAN   119.53  3.000
 X2O  CAG   CAJ  CAN   120.21  3.000
 X2O  HAG   CAG  CAK   120.51  3.000
 X2O  HAG   CAG  CAJ   120.47  3.000
 X2O  CAK   CAG  CAJ   119.02  3.000
 X2O  HAK   CAK  CAO   119.16  3.000
 X2O  HAK   CAK  CAG   120.26  3.000
 X2O  CAO   CAK  CAG   120.59  3.000
 X2O  HAO   CAO  CAK   117.72  3.000
 X2O  HAO   CAO  CAU   121.08  3.000
 X2O  CAK   CAO  CAU   121.19  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
 X2O  CONST_01  CAI   CAF  CAH  CAL     0.00   0.0  0
 X2O  CONST_02  CAI   CAM  CAT  CAL     0.00   0.0  0
 X2O  CONST_03  CAM   CAT  CAL  CAH     0.00   0.0  0
 X2O  CONST_04  CAM   CAI  CAF  CAH     0.00   0.0  0
 X2O  CONST_05  CAT   CAL  CAH  CAF     0.00   0.0  0
 X2O  CONST_06  CAT   CAM  CAI  CAF     0.00   0.0  0
 X2O  CONST_07  CAG   CAJ  CAN  CAU     0.00   0.0  0
 X2O  CONST_08  CAG   CAK  CAO  CAU     0.00   0.0  0
 X2O  CONST_09  CAK   CAO  CAU  CAN     0.00   0.0  0
 X2O  CONST_10  CAK   CAG  CAJ  CAN     0.00   0.0  0
 X2O  CONST_11  CAO   CAU  CAN  CAJ     0.00   0.0  0
 X2O  CONST_12  CAO   CAK  CAG  CAJ     0.00   0.0  0
 X2O  CONST_13  CAX   CAT  CAL  CAH   180.00   0.0  0
 X2O  CONST_14  CAX   CAT  CAM  CAI   180.00   0.0  0
 X2O  CONST_15  CAJ   CAN  CAU  CAX   180.00   0.0  0
 X2O  CONST_16  CAK   CAO  CAU  CAX   180.00   0.0  0
 X2O  CONST_17  HAF   CAF  CAH  CAL   180.00   0.0  0
 X2O  CONST_18  HAM   CAM  CAT  CAL   180.00   0.0  0
 X2O  CONST_19  HAI   CAI  CAF  CAH   180.00   0.0  0
 X2O  CONST_20  HAL   CAL  CAH  CAF   180.00   0.0  0
 X2O  CONST_21  HAH   CAH  CAF  CAI   180.00   0.0  0
 X2O  CONST_22  HAJ   CAJ  CAN  CAU   180.00   0.0  0
 X2O  CONST_23  HAK   CAK  CAO  CAU   180.00   0.0  0
 X2O  CONST_24  HAO   CAO  CAU  CAN   180.00   0.0  0
 X2O  CONST_25  HAG   CAG  CAJ  CAN   180.00   0.0  0
 X2O  CONST_26  HAN   CAN  CAJ  CAG   180.00   0.0  0
 X2O  Var_01    CAU   CAX  CAT  CAL    25.95  30.0  2
 X2O  Var_02    CAN   CAU  CAX  CAT    56.98  30.0  2
 X2O  Var_03    CA    CB   SAR  CAX   149.69  30.0  3
 X2O  Var_04    HAA1  CAA  CAP  CAW  -179.11  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
 X2O  chir_01  CA   CB   C    N    negativ
 X2O  chir_02  CAW  CAP  CAB  CAX  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
 X2O  plan-1  CAL  0.020
 X2O  plan-1  CAH  0.020
 X2O  plan-1  CAF  0.020
 X2O  plan-1  CAI  0.020
 X2O  plan-1  CAM  0.020
 X2O  plan-1  CAT  0.020
 X2O  plan-1  CAX  0.020
 X2O  plan-1  HAL  0.020
 X2O  plan-1  HAH  0.020
 X2O  plan-1  HAF  0.020
 X2O  plan-1  HAI  0.020
 X2O  plan-1  HAM  0.020
 X2O  plan-2  CAX  0.020
 X2O  plan-2  CAU  0.020
 X2O  plan-2  CAN  0.020
 X2O  plan-2  CAJ  0.020
 X2O  plan-2  CAG  0.020
 X2O  plan-2  CAK  0.020
 X2O  plan-2  CAO  0.020
 X2O  plan-2  HAN  0.020
 X2O  plan-2  HAO  0.020
 X2O  plan-2  HAJ  0.020
 X2O  plan-2  HAG  0.020
 X2O  plan-2  HAK  0.020
 X2O  plan-3  CA   0.020
 X2O  plan-3  C    0.020
 X2O  plan-3  OXT  0.020
 X2O  plan-3  O    0.020

