# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 05:53:01 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: S-{5-[(1R)-2-amino-1-hydroxyethyl]-2,3-dihydroxyphenyl}-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H](O)c1cc(O)c(O)c(SC[C@H](N)C(O)=O)c1
#
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
 NYS  NYS  S-{5-[(1R)-2-amino-1-hydroxyethyl]-2,3-dihydroxyphenyl}-L-cysteine  L-peptide  34  19  .  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_NYS
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
 NYS  N     N  NH2    0  -0.788  23.0836   0.1258  -3.5817
 NYS  CA    C  CH1    0  -0.205  21.9021  -0.6659  -3.8964
 NYS  CB    C  CH2    0  -0.527  20.6953   0.0712  -3.3122
 NYS  C     C  C      0   0.391  21.6690  -0.9409  -5.4031
 NYS  O     O  O      0  -0.596  22.1273  -0.1052  -6.2064
 NYS  SG    S  S2     0  -0.011  19.1407  -0.8632  -3.5491
 NYS  CXP   C  C      0  -0.230  18.1175  -0.0287  -2.3684
 NYS  CXH   C  C1     0  -0.320  17.8326  -0.6420  -1.1482
 NYS  CXQ   C  C      0   0.327  17.5717   1.2175  -2.6591
 NYS  OXF   O  OH1    0  -0.615  17.8536   1.8144  -3.8326
 NYS  CXO   C  C      0   0.285  16.7454   1.8362  -1.7092
 NYS  OXE   O  OH1    0  -0.646  16.2621   3.0513  -2.0588
 NYS  CXG   C  C1     0  -0.428  16.4653   1.2120  -0.5067
 NYS  CXN   C  C      0   0.098  17.0091  -0.0377  -0.2124
 NYS  CXJ   C  CH1    0  -0.035  16.6689  -0.7474   1.0702
 NYS  OXG   O  OH1    0  -0.665  16.5928   0.2091   2.1034
 NYS  CXI   C  CH2    0  -0.305  15.3578  -1.5328   0.9068
 NYS  NXA   N  NH2    0  -0.793  14.9263  -2.3076   2.0549
 NYS  OXT   O  OC    -1  -0.602  21.0017  -1.9604  -5.6725
 NYS  HN1   H  HNH2   0   0.339  23.9048  -0.4507  -3.7212
 NYS  HN2   H  HNH2   0   0.327  23.1566   0.8537  -4.2845
 NYS  HA    H  HCH1   0   0.218  21.9892  -1.6241  -3.3759
 NYS  HB1   H  HCH2   0   0.252  20.5975   1.0568  -3.7723
 NYS  HB2   H  HCH2   0   0.265  20.8396   0.2070  -2.2403
 NYS  HXH   H  H      0   0.251  18.2768  -1.6072  -0.9359
 NYS  HOXF  H  HOH1   0   0.472  17.4057   2.6673  -3.8895
 NYS  HOXE  H  HOH1   0   0.481  15.6872   3.4056  -1.3711
 NYS  HXG   H  H      0   0.269  15.8221   1.7134   0.2082
 NYS  HXJ   H  HCH1   0   0.211  17.4655  -1.4787   1.2794
 NYS  HOXG  H  HOH1   0   0.445  16.3914  -0.2470   2.9268
 NYS  HXI1  H  HCH2   0   0.226  14.5574  -0.8369   0.6385
 NYS  HXI2  H  HCH2   0   0.223  15.4797  -2.2087   0.0564
 NYS  HXA1  H  HNH2   0   0.344  15.6713  -2.9120   2.3789
 NYS  HXA2  H  HNH2   0   0.343  14.6720  -1.7095   2.8301

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
 NYS  OXT  C     deloc     1.248  0.020  1.248
 NYS  O    C     deloc     1.231  0.020  1.231
 NYS  C    CA    single    1.525  0.021  1.525
 NYS  OXF  CXQ   single    1.346  0.020  1.346
 NYS  SG   CB    single    1.829  0.020  1.829
 NYS  SG   CXP   single    1.771  0.020  1.771
 NYS  CA   CB    single    1.530  0.020  1.530
 NYS  CA   N     single    1.458  0.019  1.458
 NYS  CXQ  CXP   aromatic  1.391  0.020  1.391
 NYS  CXQ  CXO   aromatic  1.403  0.020  1.403
 NYS  CXP  CXH   aromatic  1.395  0.020  1.395
 NYS  OXE  CXO   single    1.354  0.020  1.354
 NYS  CXO  CXG   aromatic  1.383  0.020  1.383
 NYS  CXH  CXN   aromatic  1.385  0.020  1.385
 NYS  CXG  CXN   aromatic  1.394  0.020  1.394
 NYS  CXN  CXJ   single    1.505  0.020  1.505
 NYS  CXJ  CXI   single    1.537  0.020  1.537
 NYS  CXJ  OXG   single    1.410  0.020  1.410
 NYS  CXI  NXA   single    1.451  0.020  1.451
 NYS  N    HN1   single    0.890  0.020  1.040
 NYS  N    HN2   single    0.890  0.020  1.040
 NYS  CA   HA    single    0.970  0.020  0.970
 NYS  CB   HB1   single    0.970  0.020  1.090
 NYS  CB   HB2   single    0.970  0.020  1.090
 NYS  CXH  HXH   single    0.930  0.020  1.080
 NYS  OXF  HOXF  single    0.850  0.020  0.980
 NYS  OXE  HOXE  single    0.850  0.020  0.980
 NYS  CXG  HXG   single    0.930  0.020  1.080
 NYS  CXJ  HXJ   single    0.970  0.020  1.090
 NYS  OXG  HOXG  single    0.850  0.020  0.980
 NYS  CXI  HXI1  single    0.970  0.020  1.090
 NYS  CXI  HXI2  single    0.970  0.020  1.090
 NYS  NXA  HXA1  single    0.890  0.020  1.040
 NYS  NXA  HXA2  single    0.890  0.020  1.040

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
 NYS  HN2   N    HN1   104.75  3.000
 NYS  HN2   N    CA    107.38  3.000
 NYS  HN1   N    CA    108.57  3.000
 NYS  HA    CA   C     109.00  3.000
 NYS  HA    CA   CB    109.00  3.000
 NYS  C     CA   CB    110.10  1.900
 NYS  HA    CA   N     110.00  3.000
 NYS  CB    CA   N     110.50  1.700
 NYS  C     CA   N     111.00  2.800
 NYS  HB2   CB   HB1   108.29  3.000
 NYS  HB2   CB   SG    107.66  3.000
 NYS  HB1   CB   SG    109.29  3.000
 NYS  HB2   CB   CA    109.34  3.000
 NYS  HB1   CB   CA    110.15  3.000
 NYS  SG    CB   CA    112.01  3.000
 NYS  OXT   C    O     127.25  3.000
 NYS  O     C    CA    120.80  1.700
 NYS  OXT   C    CA    115.81  3.000
 NYS  CXP   SG   CB     99.44  3.000
 NYS  CXQ   CXP  CXH   119.77  3.000
 NYS  CXH   CXP  SG    119.59  3.000
 NYS  CXQ   CXP  SG    120.62  3.000
 NYS  HXH   CXH  CXN   120.00  3.000
 NYS  HXH   CXH  CXP   118.64  3.000
 NYS  CXN   CXH  CXP   121.36  3.000
 NYS  CXO   CXQ  OXF   121.20  3.000
 NYS  CXO   CXQ  CXP   118.99  3.000
 NYS  OXF   CXQ  CXP   119.81  3.000
 NYS  HOXF  OXF  CXQ   110.25  3.000
 NYS  CXG   CXO  OXE   123.86  3.000
 NYS  CXG   CXO  CXQ   120.58  3.000
 NYS  OXE   CXO  CXQ   115.55  3.000
 NYS  HOXE  OXE  CXO   111.01  3.000
 NYS  HXG   CXG  CXN   120.43  3.000
 NYS  HXG   CXG  CXO   118.98  3.000
 NYS  CXN   CXG  CXO   120.59  3.000
 NYS  CXJ   CXN  CXG   120.96  3.000
 NYS  CXJ   CXN  CXH   120.29  3.000
 NYS  CXG   CXN  CXH   118.70  3.000
 NYS  HXJ   CXJ  CXI   107.34  3.000
 NYS  HXJ   CXJ  OXG   110.50  3.000
 NYS  CXI   CXJ  OXG   112.24  3.000
 NYS  HXJ   CXJ  CXN   108.15  3.000
 NYS  OXG   CXJ  CXN   108.47  3.000
 NYS  CXI   CXJ  CXN   110.07  3.000
 NYS  HOXG  OXG  CXJ   108.46  3.000
 NYS  HXI2  CXI  HXI1  106.51  3.000
 NYS  HXI2  CXI  NXA   108.58  3.000
 NYS  HXI1  CXI  NXA   108.44  3.000
 NYS  HXI2  CXI  CXJ   107.67  3.000
 NYS  HXI1  CXI  CXJ   108.97  3.000
 NYS  NXA   CXI  CXJ   116.26  3.000
 NYS  HXA2  NXA  HXA1  107.02  3.000
 NYS  HXA2  NXA  CXI   111.43  3.000
 NYS  HXA1  NXA  CXI   110.68  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
 NYS  CONST_01  CXG   CXO  CXQ  CXP    0.00   0.0  0
 NYS  CONST_02  CXG   CXN  CXH  CXP    0.00   0.0  0
 NYS  CONST_03  CXO   CXQ  CXP  CXH    0.00   0.0  0
 NYS  CONST_04  CXO   CXG  CXN  CXH    0.00   0.0  0
 NYS  CONST_05  CXN   CXH  CXP  CXQ    0.00   0.0  0
 NYS  CONST_06  CXN   CXG  CXO  CXQ    0.00   0.0  0
 NYS  CONST_07  CXO   CXQ  CXP  SG   180.00   0.0  0
 NYS  CONST_08  CXN   CXH  CXP  SG   180.00   0.0  0
 NYS  CONST_09  OXE   CXO  CXQ  CXP  180.00   0.0  0
 NYS  CONST_10  CXJ   CXN  CXH  CXP  180.00   0.0  0
 NYS  CONST_11  OXF   CXQ  CXP  CXH  180.00   0.0  0
 NYS  CONST_12  CXG   CXO  CXQ  OXF  180.00   0.0  0
 NYS  CONST_13  CXJ   CXN  CXG  CXO  180.00   0.0  0
 NYS  CONST_14  CXN   CXG  CXO  OXE  180.00   0.0  0
 NYS  CONST_15  HXG   CXG  CXN  CXH  180.00   0.0  0
 NYS  CONST_16  HXH   CXH  CXP  CXQ  180.00   0.0  0
 NYS  Var_01    CXQ   CXP  SG   CB    77.72  30.0  2
 NYS  Var_02    HB1   CB   SG   CXP  -74.41  30.0  3
 NYS  Var_03    HXA1  NXA  CXI  CXJ  -52.32  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
 NYS  chir_01  CA   C    CB   N    positiv
 NYS  chir_02  CXJ  OXG  CXN  CXI  positiv

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
 NYS  plan-1  SG   0.020
 NYS  plan-1  CXP  0.020
 NYS  plan-1  CXH  0.020
 NYS  plan-1  CXQ  0.020
 NYS  plan-1  OXF  0.020
 NYS  plan-1  CXO  0.020
 NYS  plan-1  OXE  0.020
 NYS  plan-1  CXG  0.020
 NYS  plan-1  CXN  0.020
 NYS  plan-1  CXJ  0.020
 NYS  plan-1  HXH  0.020
 NYS  plan-1  HXG  0.020
 NYS  plan-2  CA   0.020
 NYS  plan-2  C    0.020
 NYS  plan-2  O    0.020
 NYS  plan-2  OXT  0.020

