# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 22:59:48 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: (2R)-2-amino-3-[(4-chlorophenyl)-diphenyl-methyl]sulfanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSC(c1ccccc1)(c2ccccc2)c3ccc(Cl)cc3)C(O)=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
 2XA  2XA  '(2R)-2-amino-3-[(4-chlorophenyl)-diphenyl-methyl]sulfanyl-propanoic acid'  L-peptide  46  27  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_2XA
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
 2XA  N     N   NH2    0  -0.781  14.2853  10.3175  -72.8549
 2XA  CA    C   CH1    0  -0.210  15.4343  10.9012  -72.1850
 2XA  CB    C   CH2    0  -0.548  16.5488  11.1295  -73.2003
 2XA  C     C   C      0   0.388  15.1842  12.2400  -71.4333
 2XA  OXT   O   OC    -1  -0.593  14.1183  12.8354  -71.6752
 2XA  O     O   O      0  -0.610  16.0982  12.6048  -70.6667
 2XA  SG    S   S2     0   0.033  16.8168   9.5918  -74.1359
 2XA  CAM   C   CR16   0  -0.302  19.1960  12.3133  -75.0067
 2XA  CAG   C   CR16   0  -0.197  19.0910  13.5811  -75.5680
 2XA  CAD   C   CR6    0  -0.055  18.2428  13.7782  -76.6398
 2XA  CAH   C   CR16   0  -0.204  17.4886  12.7287  -77.1478
 2XA  CAN   C   CR16   0  -0.266  17.5995  11.4776  -76.5705
 2XA  CAV   C   CR6    0   0.155  18.4669  11.2391  -75.5009
 2XA  CAF   C   CR16   0  -0.277  18.3980   7.4137  -75.4869
 2XA  CAL   C   CR16   0  -0.241  18.6270   6.3516  -76.3475
 2XA  CAR   C   CR16   0  -0.265  19.1709   6.5750  -77.6060
 2XA  CAX   C   CR16   0  -0.240  19.4870   7.8697  -77.9860
 2XA  CAQ   C   CR16   0  -0.310  19.2503   8.9347  -77.1249
 2XA  CAK   C   CR6    0   0.180  18.6922   8.7243  -75.8673
 2XA  CAE   C   CR16   0  -0.329  19.4262   9.4258  -72.4948
 2XA  CAJ   C   CR16   0  -0.236  20.5016   9.2702  -71.6247
 2XA  CAP   C   CR16   0  -0.268  21.8015   9.3939  -72.0858
 2XA  CAW   C   CR16   0  -0.237  22.0215   9.6744  -73.4299
 2XA  CAO   C   CR16   0  -0.273  20.9497   9.8282  -74.2925
 2XA  CAI   C   CR6    0   0.181  19.6331   9.7122  -73.8375
 2XA  CAZ   C   CT     0  -0.439  18.5009   9.8594  -74.8568
 2XA  HN1   H   HNH2   0   0.341  13.5939  10.0653  -72.1593
 2XA  HN2   H   HNH2   0   0.328  13.8399  11.0401  -73.4099
 2XA  HA    H   HCH1   0   0.226  15.7974  10.1693  -71.4556
 2XA  HB1C  H   HCH2   0   0.263  16.2805  11.9281  -73.8974
 2XA  HB2C  H   HCH2   0   0.272  17.4670  11.4225  -72.6934
 2XA  HAG   H   HCR6   0   0.276  19.6685  14.4006  -75.1620
 2XA  HAH   H   HCR6   0   0.277  16.8153  12.8858  -77.9798
 2XA  HAN   H   HCR6   0   0.266  16.9884  10.6732  -76.9590
 2XA  HAF   H   HCR6   0   0.253  17.9957   7.2108  -74.5018
 2XA  HAL   H   HCR6   0   0.255  18.3852   5.3457  -76.0294
 2XA  HAR   H   HCR6   0   0.254  19.3521   5.7469  -78.2788
 2XA  HAX   H   HCR6   0   0.254  19.9225   8.0602  -78.9585
 2XA  HAQ   H   HCR6   0   0.261  19.5171   9.9326  -77.4462
 2XA  HAE   H   HCR6   0   0.262  18.4200   9.3052  -72.1160
 2XA  HAJ   H   HCR6   0   0.253  20.3131   9.0478  -70.5822
 2XA  HAP   H   HCR6   0   0.254  22.6373   9.2703  -71.4094
 2XA  HAW   H   HCR6   0   0.254  23.0311   9.7696  -73.8085
 2XA  HAO   H   HCR6   0   0.258  21.1431  10.0416  -75.3368
 2XA  CL    CL  CL     0  -0.131  18.1081  15.3519  -77.3533
 2XA  HAM   H   HCR6   0   0.267  19.8607  12.1869  -74.1637

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
 2XA  N    CA    single    1.458  0.019  1.458
 2XA  CA   CB    single    1.530  0.020  1.530
 2XA  CA   C     single    1.525  0.021  1.525
 2XA  CB   SG    single    1.820  0.020  1.820
 2XA  C    OXT   deloc     1.245  0.020  1.245
 2XA  C    O     deloc     1.231  0.020  1.231
 2XA  SG   CAZ   single    1.851  0.020  1.851
 2XA  CAM  CAG   aromatic  1.391  0.020  1.391
 2XA  CAM  CAV   aromatic  1.389  0.020  1.389
 2XA  CAG  CAD   aromatic  1.381  0.020  1.381
 2XA  CAD  CAH   aromatic  1.389  0.020  1.389
 2XA  CAD  CL    single    1.733  0.020  1.733
 2XA  CAH  CAN   aromatic  1.382  0.020  1.382
 2XA  CAN  CAV   aromatic  1.398  0.020  1.398
 2XA  CAV  CAZ   single    1.523  0.020  1.523
 2XA  CAF  CAL   aromatic  1.386  0.020  1.386
 2XA  CAF  CAK   aromatic  1.396  0.020  1.396
 2XA  CAL  CAR   aromatic  1.389  0.020  1.389
 2XA  CAR  CAX   aromatic  1.386  0.020  1.386
 2XA  CAX  CAQ   aromatic  1.390  0.020  1.390
 2XA  CAQ  CAK   aromatic  1.392  0.020  1.392
 2XA  CAK  CAZ   single    1.532  0.020  1.532
 2XA  CAE  CAJ   aromatic  1.392  0.020  1.392
 2XA  CAE  CAI   aromatic  1.388  0.020  1.388
 2XA  CAJ  CAP   aromatic  1.385  0.020  1.385
 2XA  CAP  CAW   aromatic  1.391  0.020  1.391
 2XA  CAW  CAO   aromatic  1.384  0.020  1.384
 2XA  CAO  CAI   aromatic  1.398  0.020  1.398
 2XA  CAI  CAZ   single    1.531  0.020  1.531
 2XA  N    HN1   single    0.890  0.020  1.040
 2XA  N    HN2   single    0.890  0.020  1.040
 2XA  CA   HA    single    0.970  0.020  0.970
 2XA  CB   HB1C  single    0.970  0.020  1.090
 2XA  CB   HB2C  single    0.970  0.020  1.090
 2XA  CAM  HAM   single    0.930  0.020  1.080
 2XA  CAG  HAG   single    0.930  0.020  1.080
 2XA  CAH  HAH   single    0.930  0.020  1.080
 2XA  CAN  HAN   single    0.930  0.020  1.080
 2XA  CAF  HAF   single    0.930  0.020  1.080
 2XA  CAL  HAL   single    0.930  0.020  1.080
 2XA  CAR  HAR   single    0.930  0.020  1.080
 2XA  CAX  HAX   single    0.930  0.020  1.080
 2XA  CAQ  HAQ   single    0.930  0.020  1.080
 2XA  CAE  HAE   single    0.930  0.020  1.080
 2XA  CAJ  HAJ   single    0.930  0.020  1.080
 2XA  CAP  HAP   single    0.930  0.020  1.080
 2XA  CAW  HAW   single    0.930  0.020  1.080
 2XA  CAO  HAO   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
 2XA  HN2   N    HN1   104.68  3.000
 2XA  HN2   N    CA    108.27  3.000
 2XA  HN1   N    CA    108.87  3.000
 2XA  HA    CA   C     109.00  3.000
 2XA  HA    CA   CB    109.00  3.000
 2XA  C     CA   CB    110.10  1.900
 2XA  HA    CA   N     110.00  3.000
 2XA  C     CA   N     111.00  2.800
 2XA  CB    CA   N     110.50  1.700
 2XA  HB2C  CB   HB1C  107.89  3.000
 2XA  HB2C  CB   SG    110.03  3.000
 2XA  HB1C  CB   SG    109.00  3.000
 2XA  HB2C  CB   CA    110.28  3.000
 2XA  HB1C  CB   CA    110.76  3.000
 2XA  SG    CB   CA    108.87  3.000
 2XA  O     C    OXT   127.37  3.000
 2XA  O     C    CA    120.80  1.700
 2XA  OXT   C    CA    117.10  3.000
 2XA  CAZ   SG   CB    102.24  3.000
 2XA  HAM   CAM  CAV   120.65  3.000
 2XA  HAM   CAM  CAG   117.89  3.000
 2XA  CAV   CAM  CAG   121.45  3.000
 2XA  HAG   CAG  CAD   120.74  3.000
 2XA  HAG   CAG  CAM   119.94  3.000
 2XA  CAD   CAG  CAM   119.33  3.000
 2XA  CL    CAD  CAH   119.57  3.000
 2XA  CL    CAD  CAG   119.79  3.000
 2XA  CAH   CAD  CAG   120.64  3.000
 2XA  HAH   CAH  CAN   120.17  3.000
 2XA  HAH   CAH  CAD   120.64  3.000
 2XA  CAN   CAH  CAD   119.19  3.000
 2XA  HAN   CAN  CAV   119.88  3.000
 2XA  HAN   CAN  CAH   118.52  3.000
 2XA  CAV   CAN  CAH   121.60  3.000
 2XA  CAZ   CAV  CAN   119.48  3.000
 2XA  CAZ   CAV  CAM   122.57  3.000
 2XA  CAN   CAV  CAM   117.78  3.000
 2XA  HAF   CAF  CAK   120.13  3.000
 2XA  HAF   CAF  CAL   118.85  3.000
 2XA  CAK   CAF  CAL   121.02  3.000
 2XA  HAL   CAL  CAR   120.21  3.000
 2XA  HAL   CAL  CAF   119.52  3.000
 2XA  CAR   CAL  CAF   120.27  3.000
 2XA  HAR   CAR  CAX   120.40  3.000
 2XA  HAR   CAR  CAL   120.39  3.000
 2XA  CAX   CAR  CAL   119.21  3.000
 2XA  HAX   CAX  CAQ   119.36  3.000
 2XA  HAX   CAX  CAR   120.17  3.000
 2XA  CAQ   CAX  CAR   120.47  3.000
 2XA  HAQ   CAQ  CAK   120.45  3.000
 2XA  HAQ   CAQ  CAX   118.74  3.000
 2XA  CAK   CAQ  CAX   120.81  3.000
 2XA  CAZ   CAK  CAQ   122.28  3.000
 2XA  CAZ   CAK  CAF   119.32  3.000
 2XA  CAQ   CAK  CAF   118.21  3.000
 2XA  HAE   CAE  CAI   120.01  3.000
 2XA  HAE   CAE  CAJ   119.15  3.000
 2XA  CAI   CAE  CAJ   120.83  3.000
 2XA  HAJ   CAJ  CAP   120.16  3.000
 2XA  HAJ   CAJ  CAE   119.37  3.000
 2XA  CAP   CAJ  CAE   120.47  3.000
 2XA  HAP   CAP  CAW   120.33  3.000
 2XA  HAP   CAP  CAJ   120.44  3.000
 2XA  CAW   CAP  CAJ   119.23  3.000
 2XA  HAW   CAW  CAO   119.63  3.000
 2XA  HAW   CAW  CAP   120.23  3.000
 2XA  CAO   CAW  CAP   120.14  3.000
 2XA  HAO   CAO  CAI   119.88  3.000
 2XA  HAO   CAO  CAW   118.97  3.000
 2XA  CAI   CAO  CAW   121.15  3.000
 2XA  CAZ   CAI  CAO   118.16  3.000
 2XA  CAZ   CAI  CAE   123.62  3.000
 2XA  CAO   CAI  CAE   118.18  3.000
 2XA  CAI   CAZ  CAK   106.00  3.000
 2XA  CAI   CAZ  CAV   112.66  3.000
 2XA  CAK   CAZ  CAV   113.27  3.000
 2XA  CAI   CAZ  SG    113.56  3.000
 2XA  CAK   CAZ  SG    105.27  3.000
 2XA  CAV   CAZ  SG    105.98  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
 2XA  CONST_01  CAH   CAD  CAG  CAM     0.00   0.0  0
 2XA  CONST_02  CAH   CAN  CAV  CAM     0.00   0.0  0
 2XA  CONST_03  CAN   CAV  CAM  CAG     0.00   0.0  0
 2XA  CONST_04  CAN   CAH  CAD  CAG     0.00   0.0  0
 2XA  CONST_05  CAV   CAM  CAG  CAD     0.00   0.0  0
 2XA  CONST_06  CAV   CAN  CAH  CAD     0.00   0.0  0
 2XA  CONST_07  CAX   CAR  CAL  CAF     0.00   0.0  0
 2XA  CONST_08  CAX   CAQ  CAK  CAF     0.00   0.0  0
 2XA  CONST_09  CAQ   CAK  CAF  CAL     0.00   0.0  0
 2XA  CONST_10  CAQ   CAX  CAR  CAL     0.00   0.0  0
 2XA  CONST_11  CAK   CAF  CAL  CAR     0.00   0.0  0
 2XA  CONST_12  CAK   CAQ  CAX  CAR     0.00   0.0  0
 2XA  CONST_13  CAW   CAP  CAJ  CAE     0.00   0.0  0
 2XA  CONST_14  CAW   CAO  CAI  CAE     0.00   0.0  0
 2XA  CONST_15  CAO   CAI  CAE  CAJ     0.00   0.0  0
 2XA  CONST_16  CAO   CAW  CAP  CAJ     0.00   0.0  0
 2XA  CONST_17  CAI   CAE  CAJ  CAP     0.00   0.0  0
 2XA  CONST_18  CAI   CAO  CAW  CAP     0.00   0.0  0
 2XA  CONST_19  CL    CAD  CAG  CAM   180.00   0.0  0
 2XA  CONST_20  CAZ   CAV  CAM  CAG   180.00   0.0  0
 2XA  CONST_21  CAZ   CAV  CAN  CAH   180.00   0.0  0
 2XA  CONST_22  CL    CAD  CAH  CAN   180.00   0.0  0
 2XA  CONST_23  CAZ   CAK  CAF  CAL   180.00   0.0  0
 2XA  CONST_24  CAZ   CAK  CAQ  CAX   180.00   0.0  0
 2XA  CONST_25  CAZ   CAI  CAE  CAJ   180.00   0.0  0
 2XA  CONST_26  CAZ   CAI  CAO  CAW   180.00   0.0  0
 2XA  CONST_27  HAN   CAN  CAV  CAM   180.00   0.0  0
 2XA  CONST_28  HAH   CAH  CAD  CAG   180.00   0.0  0
 2XA  CONST_29  HAM   CAM  CAG  CAD   180.00   0.0  0
 2XA  CONST_30  HAG   CAG  CAD  CAH   180.00   0.0  0
 2XA  CONST_31  HAR   CAR  CAL  CAF   180.00   0.0  0
 2XA  CONST_32  HAQ   CAQ  CAK  CAF   180.00   0.0  0
 2XA  CONST_33  HAX   CAX  CAR  CAL   180.00   0.0  0
 2XA  CONST_34  HAF   CAF  CAL  CAR   180.00   0.0  0
 2XA  CONST_35  HAL   CAL  CAR  CAX   180.00   0.0  0
 2XA  CONST_36  HAP   CAP  CAJ  CAE   180.00   0.0  0
 2XA  CONST_37  HAO   CAO  CAI  CAE   180.00   0.0  0
 2XA  CONST_38  HAW   CAW  CAP  CAJ   180.00   0.0  0
 2XA  CONST_39  HAE   CAE  CAJ  CAP   180.00   0.0  0
 2XA  CONST_40  HAJ   CAJ  CAP  CAW   180.00   0.0  0
 2XA  Var_01    CAK   CAZ  CAV  CAM  -133.16  30.0  2
 2XA  Var_02    CAF   CAK  CAZ  CAV  -163.38  30.0  2
 2XA  Var_03    CAE   CAI  CAZ  CAV   119.57  30.0  1
 2XA  Var_04    CAV   CAZ  SG   CB    -49.54  30.0  3
 2XA  Var_05    HB1C  CB   SG   CAZ    77.52  30.0  1

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
 2XA  chir_01  CA  N  CB  C  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
 2XA  plan-1  CAM  0.020
 2XA  plan-1  CAG  0.020
 2XA  plan-1  CAD  0.020
 2XA  plan-1  CAH  0.020
 2XA  plan-1  CAN  0.020
 2XA  plan-1  CAV  0.020
 2XA  plan-1  CAZ  0.020
 2XA  plan-1  HAG  0.020
 2XA  plan-1  HAH  0.020
 2XA  plan-1  HAN  0.020
 2XA  plan-1  CL   0.020
 2XA  plan-1  HAM  0.020
 2XA  plan-2  CAF  0.020
 2XA  plan-2  CAL  0.020
 2XA  plan-2  CAR  0.020
 2XA  plan-2  CAX  0.020
 2XA  plan-2  CAQ  0.020
 2XA  plan-2  CAK  0.020
 2XA  plan-2  CAZ  0.020
 2XA  plan-2  HAF  0.020
 2XA  plan-2  HAL  0.020
 2XA  plan-2  HAR  0.020
 2XA  plan-2  HAX  0.020
 2XA  plan-2  HAQ  0.020
 2XA  plan-3  CAE  0.020
 2XA  plan-3  CAJ  0.020
 2XA  plan-3  CAP  0.020
 2XA  plan-3  CAW  0.020
 2XA  plan-3  CAO  0.020
 2XA  plan-3  CAI  0.020
 2XA  plan-3  CAZ  0.020
 2XA  plan-3  HAE  0.020
 2XA  plan-3  HAJ  0.020
 2XA  plan-3  HAP  0.020
 2XA  plan-3  HAW  0.020
 2XA  plan-3  HAO  0.020
 2XA  plan-4  CA   0.020
 2XA  plan-4  C    0.020
 2XA  plan-4  OXT  0.020
 2XA  plan-4  O    0.020

