# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 09:34:37 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: S-trityl-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSC(c1ccccc1)(c2ccccc2)c3ccccc3)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
 ZZD  ZZD  'S-trityl-L-cysteine      '  L-peptide  46  26  .  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_ZZD
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
 ZZD  N     N  NH2    0  -0.781   2.2783  -17.5032  53.6991
 ZZD  CA    C  CH1    0  -0.213   2.1681  -18.8165  54.3102
 ZZD  CB    C  CH2    0  -0.547   1.7618  -19.8354  53.2527
 ZZD  C     C  C      0   0.389   3.4387  -19.3474  55.0334
 ZZD  O     O  O      0  -0.610   3.2777  -20.3903  55.6989
 ZZD  OXT   O  OC    -1  -0.593   4.4944  -18.7088  54.8713
 ZZD  SG    S  S2     0   0.029   0.2891  -19.2296  52.3706
 ZZD  CAM   C  CR16   0  -0.311  -1.6757  -20.9282  49.4728
 ZZD  CAG   C  CR16   0  -0.241  -2.7230  -20.5464  48.6422
 ZZD  CAD   C  CR16   0  -0.266  -3.6390  -19.5943  49.0606
 ZZD  CAH   C  CR16   0  -0.241  -3.5081  -19.0372  50.3266
 ZZD  CAN   C  CR16   0  -0.276  -2.4682  -19.4249  51.1566
 ZZD  CAV   C  CR6    0   0.178  -1.5241  -20.3637  50.7355
 ZZD  CAZ   C  CT     0  -0.440  -0.4260  -20.8043  51.7071
 ZZD  CAX   C  CR6    0   0.149   0.7234  -21.5408  51.0263
 ZZD  CAQ   C  CR16   0  -0.260   1.3682  -20.9443  49.9385
 ZZD  CAK   C  CR16   0  -0.246   2.4538  -21.5496  49.3305
 ZZD  CAF   C  CR16   0  -0.266   2.9370  -22.7647  49.8059
 ZZD  CAL   C  CR16   0  -0.242   2.3202  -23.3563  50.8941
 ZZD  CAR   C  CR16   0  -0.299   1.2239  -22.7480  51.4995
 ZZD  CAW   C  CR6    0   0.180  -1.1151  -21.6519  52.7796
 ZZD  CAO   C  CR16   0  -0.331  -1.1473  -21.3149  54.1263
 ZZD  CAI   C  CR16   0  -0.236  -1.8024  -22.1239  55.0501
 ZZD  CAE   C  CR16   0  -0.268  -2.4429  -23.2812  54.6402
 ZZD  CAJ   C  CR16   0  -0.238  -2.4285  -23.6234  53.2925
 ZZD  CAP   C  CR16   0  -0.272  -1.7747  -22.8166  52.3767
 ZZD  HN1   H  HNH2   0   0.340   2.4025  -16.8107  54.4273
 ZZD  HN2   H  HNH2   0   0.328   3.1394  -17.4710  53.1648
 ZZD  HA    H  HCH1   0   0.227   1.3599  -18.7676  55.0487
 ZZD  HB1C  H  HCH2   0   0.263   2.5689  -19.9919  52.5319
 ZZD  HB2C  H  HCH2   0   0.273   1.5411  -20.7944  53.7180
 ZZD  HAD   H  HCR6   0   0.254  -4.4508  -19.2926  48.4115
 ZZD  HAH   H  HCR6   0   0.254  -4.2221  -18.3015  50.6738
 ZZD  HAN   H  HCR6   0   0.253  -2.4002  -18.9952  52.1487
 ZZD  HAQ   H  HCR6   0   0.254   1.0231  -19.9876  49.5669
 ZZD  HAR   H  HCR6   0   0.257   0.7737  -23.2316  52.3552
 ZZD  HAK   H  HCR6   0   0.253   2.9308  -21.0680  48.4865
 ZZD  HAF   H  HCR6   0   0.253   3.7890  -23.2368  49.3341
 ZZD  HAL   H  HCR6   0   0.253   2.6894  -24.2953  51.2863
 ZZD  HAO   H  HCR6   0   0.264  -0.6710  -20.4057  54.4683
 ZZD  HAP   H  HCR6   0   0.257  -1.7762  -23.1011  51.3312
 ZZD  HAI   H  HCR6   0   0.252  -1.8089  -21.8393  56.0945
 ZZD  HAE   H  HCR6   0   0.253  -2.9533  -23.9095  55.3585
 ZZD  HAJ   H  HCR6   0   0.253  -2.9304  -24.5205  52.9532
 ZZD  HAM   H  HCR6   0   0.260  -0.9808  -21.6791  49.1222
 ZZD  HAG   H  HCR6   0   0.254  -2.8178  -21.0008  47.6643

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
 ZZD  N    CA    single    1.458  0.019  1.458
 ZZD  CA   CB    single    1.530  0.020  1.530
 ZZD  CA   C     single    1.525  0.021  1.525
 ZZD  CB   SG    single    1.820  0.020  1.820
 ZZD  C    O     deloc     1.231  0.020  1.231
 ZZD  C    OXT   deloc     1.244  0.020  1.244
 ZZD  SG   CAZ   single    1.852  0.020  1.852
 ZZD  CAM  CAG   aromatic  1.390  0.020  1.390
 ZZD  CAM  CAV   aromatic  1.391  0.020  1.391
 ZZD  CAG  CAD   aromatic  1.386  0.020  1.386
 ZZD  CAD  CAH   aromatic  1.389  0.020  1.389
 ZZD  CAH  CAN   aromatic  1.386  0.020  1.386
 ZZD  CAN  CAV   aromatic  1.396  0.020  1.396
 ZZD  CAV  CAZ   single    1.531  0.020  1.531
 ZZD  CAZ  CAX   single    1.525  0.020  1.525
 ZZD  CAZ  CAW   single    1.531  0.020  1.531
 ZZD  CAX  CAQ   aromatic  1.398  0.020  1.398
 ZZD  CAX  CAR   aromatic  1.390  0.020  1.390
 ZZD  CAQ  CAK   aromatic  1.384  0.020  1.384
 ZZD  CAK  CAF   aromatic  1.391  0.020  1.391
 ZZD  CAF  CAL   aromatic  1.384  0.020  1.384
 ZZD  CAL  CAR   aromatic  1.392  0.020  1.392
 ZZD  CAW  CAO   aromatic  1.389  0.020  1.389
 ZZD  CAW  CAP   aromatic  1.398  0.020  1.398
 ZZD  CAO  CAI   aromatic  1.392  0.020  1.392
 ZZD  CAI  CAE   aromatic  1.385  0.020  1.385
 ZZD  CAE  CAJ   aromatic  1.390  0.020  1.390
 ZZD  CAJ  CAP   aromatic  1.385  0.020  1.385
 ZZD  N    HN1   single    0.890  0.020  1.040
 ZZD  N    HN2   single    0.890  0.020  1.040
 ZZD  CA   HA    single    0.970  0.020  0.970
 ZZD  CB   HB1C  single    0.970  0.020  1.090
 ZZD  CB   HB2C  single    0.970  0.020  1.090
 ZZD  CAM  HAM   single    0.930  0.020  1.080
 ZZD  CAG  HAG   single    0.930  0.020  1.080
 ZZD  CAD  HAD   single    0.930  0.020  1.080
 ZZD  CAH  HAH   single    0.930  0.020  1.080
 ZZD  CAN  HAN   single    0.930  0.020  1.080
 ZZD  CAQ  HAQ   single    0.930  0.020  1.080
 ZZD  CAR  HAR   single    0.930  0.020  1.080
 ZZD  CAK  HAK   single    0.930  0.020  1.080
 ZZD  CAF  HAF   single    0.930  0.020  1.080
 ZZD  CAL  HAL   single    0.930  0.020  1.080
 ZZD  CAO  HAO   single    0.930  0.020  1.080
 ZZD  CAP  HAP   single    0.930  0.020  1.080
 ZZD  CAI  HAI   single    0.930  0.020  1.080
 ZZD  CAE  HAE   single    0.930  0.020  1.080
 ZZD  CAJ  HAJ   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
 ZZD  HN2   N    HN1   104.66  3.000
 ZZD  HN2   N    CA    108.35  3.000
 ZZD  HN1   N    CA    108.97  3.000
 ZZD  HA    CA   C     109.00  3.000
 ZZD  HA    CA   CB    109.00  3.000
 ZZD  C     CA   CB    110.10  1.900
 ZZD  HA    CA   N     110.00  3.000
 ZZD  C     CA   N     111.00  2.800
 ZZD  CB    CA   N     110.50  1.700
 ZZD  HB2C  CB   HB1C  107.78  3.000
 ZZD  HB2C  CB   SG    109.65  3.000
 ZZD  HB1C  CB   SG    108.99  3.000
 ZZD  HB2C  CB   CA    110.28  3.000
 ZZD  HB1C  CB   CA    110.88  3.000
 ZZD  SG    CB   CA    109.24  3.000
 ZZD  OXT   C    O     127.44  3.000
 ZZD  OXT   C    CA    117.21  3.000
 ZZD  O     C    CA    120.80  1.700
 ZZD  CAZ   SG   CB    101.71  3.000
 ZZD  HAM   CAM  CAV   120.39  3.000
 ZZD  HAM   CAM  CAG   118.75  3.000
 ZZD  CAV   CAM  CAG   120.85  3.000
 ZZD  HAG   CAG  CAD   120.22  3.000
 ZZD  HAG   CAG  CAM   119.37  3.000
 ZZD  CAD   CAG  CAM   120.42  3.000
 ZZD  HAD   CAD  CAH   120.36  3.000
 ZZD  HAD   CAD  CAG   120.41  3.000
 ZZD  CAH   CAD  CAG   119.22  3.000
 ZZD  HAH   CAH  CAN   119.54  3.000
 ZZD  HAH   CAH  CAD   120.17  3.000
 ZZD  CAN   CAH  CAD   120.29  3.000
 ZZD  HAN   CAN  CAV   120.03  3.000
 ZZD  HAN   CAN  CAH   118.99  3.000
 ZZD  CAV   CAN  CAH   120.98  3.000
 ZZD  CAZ   CAV  CAN   119.15  3.000
 ZZD  CAZ   CAV  CAM   122.50  3.000
 ZZD  CAN   CAV  CAM   118.21  3.000
 ZZD  CAW   CAZ  CAX   112.61  3.000
 ZZD  CAW   CAZ  CAV   106.32  3.000
 ZZD  CAX   CAZ  CAV   113.34  3.000
 ZZD  CAW   CAZ  SG    113.17  3.000
 ZZD  CAX   CAZ  SG    106.23  3.000
 ZZD  CAV   CAZ  SG    105.04  3.000
 ZZD  CAR   CAX  CAQ   117.99  3.000
 ZZD  CAR   CAX  CAZ   122.60  3.000
 ZZD  CAQ   CAX  CAZ   119.26  3.000
 ZZD  HAQ   CAQ  CAK   119.07  3.000
 ZZD  HAQ   CAQ  CAX   119.80  3.000
 ZZD  CAK   CAQ  CAX   121.13  3.000
 ZZD  HAK   CAK  CAF   120.12  3.000
 ZZD  HAK   CAK  CAQ   119.58  3.000
 ZZD  CAF   CAK  CAQ   120.29  3.000
 ZZD  HAF   CAF  CAL   120.48  3.000
 ZZD  HAF   CAF  CAK   120.36  3.000
 ZZD  CAL   CAF  CAK   119.16  3.000
 ZZD  HAL   CAL  CAR   119.34  3.000
 ZZD  HAL   CAL  CAF   120.25  3.000
 ZZD  CAR   CAL  CAF   120.41  3.000
 ZZD  HAR   CAR  CAL   118.47  3.000
 ZZD  HAR   CAR  CAX   120.53  3.000
 ZZD  CAL   CAR  CAX   121.00  3.000
 ZZD  CAP   CAW  CAO   118.09  3.000
 ZZD  CAP   CAW  CAZ   118.15  3.000
 ZZD  CAO   CAW  CAZ   123.74  3.000
 ZZD  HAO   CAO  CAI   119.07  3.000
 ZZD  HAO   CAO  CAW   120.02  3.000
 ZZD  CAI   CAO  CAW   120.90  3.000
 ZZD  HAI   CAI  CAE   120.17  3.000
 ZZD  HAI   CAI  CAO   119.36  3.000
 ZZD  CAE   CAI  CAO   120.47  3.000
 ZZD  HAE   CAE  CAJ   120.35  3.000
 ZZD  HAE   CAE  CAI   120.45  3.000
 ZZD  CAJ   CAE  CAI   119.20  3.000
 ZZD  HAJ   CAJ  CAP   119.64  3.000
 ZZD  HAJ   CAJ  CAE   120.20  3.000
 ZZD  CAP   CAJ  CAE   120.17  3.000
 ZZD  HAP   CAP  CAJ   118.98  3.000
 ZZD  HAP   CAP  CAW   119.84  3.000
 ZZD  CAJ   CAP  CAW   121.18  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
 ZZD  CONST_01  CAH   CAD  CAG  CAM     0.00   0.0  0
 ZZD  CONST_02  CAH   CAN  CAV  CAM     0.00   0.0  0
 ZZD  CONST_03  CAN   CAV  CAM  CAG     0.00   0.0  0
 ZZD  CONST_04  CAN   CAH  CAD  CAG     0.00   0.0  0
 ZZD  CONST_05  CAV   CAM  CAG  CAD     0.00   0.0  0
 ZZD  CONST_06  CAV   CAN  CAH  CAD     0.00   0.0  0
 ZZD  CONST_07  CAF   CAK  CAQ  CAX     0.00   0.0  0
 ZZD  CONST_08  CAF   CAL  CAR  CAX     0.00   0.0  0
 ZZD  CONST_09  CAL   CAR  CAX  CAQ     0.00   0.0  0
 ZZD  CONST_10  CAL   CAF  CAK  CAQ     0.00   0.0  0
 ZZD  CONST_11  CAR   CAX  CAQ  CAK     0.00   0.0  0
 ZZD  CONST_12  CAR   CAL  CAF  CAK     0.00   0.0  0
 ZZD  CONST_13  CAE   CAI  CAO  CAW     0.00   0.0  0
 ZZD  CONST_14  CAE   CAJ  CAP  CAW     0.00   0.0  0
 ZZD  CONST_15  CAJ   CAP  CAW  CAO     0.00   0.0  0
 ZZD  CONST_16  CAJ   CAE  CAI  CAO     0.00   0.0  0
 ZZD  CONST_17  CAP   CAW  CAO  CAI     0.00   0.0  0
 ZZD  CONST_18  CAP   CAJ  CAE  CAI     0.00   0.0  0
 ZZD  CONST_19  CAZ   CAV  CAM  CAG   180.00   0.0  0
 ZZD  CONST_20  CAZ   CAV  CAN  CAH   180.00   0.0  0
 ZZD  CONST_21  CAK   CAQ  CAX  CAZ   180.00   0.0  0
 ZZD  CONST_22  CAL   CAR  CAX  CAZ   180.00   0.0  0
 ZZD  CONST_23  CAI   CAO  CAW  CAZ   180.00   0.0  0
 ZZD  CONST_24  CAJ   CAP  CAW  CAZ   180.00   0.0  0
 ZZD  CONST_25  HAD   CAD  CAG  CAM   180.00   0.0  0
 ZZD  CONST_26  HAN   CAN  CAV  CAM   180.00   0.0  0
 ZZD  CONST_27  HAH   CAH  CAD  CAG   180.00   0.0  0
 ZZD  CONST_28  HAM   CAM  CAG  CAD   180.00   0.0  0
 ZZD  CONST_29  HAG   CAG  CAD  CAH   180.00   0.0  0
 ZZD  CONST_30  HAK   CAK  CAQ  CAX   180.00   0.0  0
 ZZD  CONST_31  HAL   CAL  CAR  CAX   180.00   0.0  0
 ZZD  CONST_32  HAR   CAR  CAX  CAQ   180.00   0.0  0
 ZZD  CONST_33  HAF   CAF  CAK  CAQ   180.00   0.0  0
 ZZD  CONST_34  HAQ   CAQ  CAK  CAF   180.00   0.0  0
 ZZD  CONST_35  HAI   CAI  CAO  CAW   180.00   0.0  0
 ZZD  CONST_36  HAJ   CAJ  CAP  CAW   180.00   0.0  0
 ZZD  CONST_37  HAP   CAP  CAW  CAO   180.00   0.0  0
 ZZD  CONST_38  HAE   CAE  CAI  CAO   180.00   0.0  0
 ZZD  CONST_39  HAO   CAO  CAI  CAE   180.00   0.0  0
 ZZD  Var_01    CAX   CAZ  CAV  CAM    19.13  30.0  2
 ZZD  Var_02    CAQ   CAX  CAZ  CAV    53.25  30.0  2
 ZZD  Var_03    CAO   CAW  CAZ  CAV  -117.86  30.0  2
 ZZD  Var_04    CAV   CAZ  SG   CB   -169.85  30.0  3
 ZZD  Var_05    HB1C  CB   SG   CAZ    81.37  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
 ZZD  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
 ZZD  plan-1  CAM  0.020
 ZZD  plan-1  CAG  0.020
 ZZD  plan-1  CAD  0.020
 ZZD  plan-1  CAH  0.020
 ZZD  plan-1  CAN  0.020
 ZZD  plan-1  CAV  0.020
 ZZD  plan-1  CAZ  0.020
 ZZD  plan-1  HAD  0.020
 ZZD  plan-1  HAH  0.020
 ZZD  plan-1  HAN  0.020
 ZZD  plan-1  HAM  0.020
 ZZD  plan-1  HAG  0.020
 ZZD  plan-2  CAZ  0.020
 ZZD  plan-2  CAX  0.020
 ZZD  plan-2  CAQ  0.020
 ZZD  plan-2  CAK  0.020
 ZZD  plan-2  CAF  0.020
 ZZD  plan-2  CAL  0.020
 ZZD  plan-2  CAR  0.020
 ZZD  plan-2  HAQ  0.020
 ZZD  plan-2  HAR  0.020
 ZZD  plan-2  HAK  0.020
 ZZD  plan-2  HAF  0.020
 ZZD  plan-2  HAL  0.020
 ZZD  plan-3  CAZ  0.020
 ZZD  plan-3  CAW  0.020
 ZZD  plan-3  CAO  0.020
 ZZD  plan-3  CAI  0.020
 ZZD  plan-3  CAE  0.020
 ZZD  plan-3  CAJ  0.020
 ZZD  plan-3  CAP  0.020
 ZZD  plan-3  HAO  0.020
 ZZD  plan-3  HAP  0.020
 ZZD  plan-3  HAI  0.020
 ZZD  plan-3  HAE  0.020
 ZZD  plan-3  HAJ  0.020
 ZZD  plan-4  CA   0.020
 ZZD  plan-4  C    0.020
 ZZD  plan-4  O    0.020
 ZZD  plan-4  OXT  0.020

