# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 03:11:36 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: S-[5-(2-aminoethyl)-2,3-dihydroxyphenyl]-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCc1cc(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
 DYS  DYS  S-[5-(2-aminoethyl)-2,3-dihydroxyphenyl]-L-cysteine  L-peptide  33  18  .  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_DYS
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
 DYS  O     O  O      0  -0.600  -26.1159  46.5345  -53.9516
 DYS  C     C  C      0   0.388  -27.2554  46.2103  -53.5599
 DYS  CA    C  CH1    0  -0.200  -27.4107  46.0054  -52.0330
 DYS  N     N  NH2    0  -0.789  -26.3019  45.3056  -51.3948
 DYS  CB    C  CH2    0  -0.522  -27.5303  47.3643  -51.3460
 DYS  SG    S  S2     0  -0.045  -28.8536  48.3776  -52.1059
 DYS  CXP   C  CR6    0  -0.228  -28.7224  49.8196  -51.0858
 DYS  CXH   C  CR16   0  -0.326  -29.5466  49.9934  -49.9765
 DYS  CXQ   C  CR6    0   0.315  -27.7831  50.7884  -51.4341
 DYS  OXF   O  OH1    0  -0.618  -26.9760  50.6812  -52.5039
 DYS  CXO   C  CR6    0   0.303  -27.6594  51.9310  -50.6320
 DYS  OXE   O  OH1    0  -0.627  -26.7274  52.8346  -51.0011
 DYS  CXG   C  CR16   0  -0.437  -28.4803  52.0830  -49.5256
 DYS  CXN   C  CR6    0   0.121  -29.4374  51.1261  -49.1860
 DYS  CXJ   C  CH2    0  -0.512  -30.2960  51.2917  -47.9639
 DYS  CXI   C  CH2    0  -0.266  -29.7177  50.5600  -46.7551
 DYS  NXA   N  NH2    0  -0.797  -30.5905  50.7097  -45.6009
 DYS  OXT   O  OC    -1  -0.601  -28.2827  46.0685  -54.2505
 DYS  HA    H  HCH1   0   0.219  -28.3277  45.4424  -51.8386
 DYS  HN1   H  HNH2   0   0.341  -26.3360  44.3292  -51.6616
 DYS  HN2   H  HNH2   0   0.329  -25.4456  45.6635  -51.8053
 DYS  HB1   H  HCH2   0   0.258  -26.5874  47.9087  -51.4280
 DYS  HB2   H  HCH2   0   0.273  -27.7645  47.2354  -50.2892
 DYS  HXH   H  HCR6   0   0.252  -30.2768  49.2292  -49.7385
 DYS  HOXF  H  HOH1   0   0.462  -27.2329  49.8859  -52.9992
 DYS  HOXE  H  HOH1   0   0.473  -26.7196  53.5758  -50.3849
 DYS  HXG   H  HCR6   0   0.264  -28.3800  52.9744  -48.9136
 DYS  HXJ1  H  HCH2   0   0.237  -30.4026  52.3539  -47.7248
 DYS  HXJ2  H  HCH2   0   0.237  -31.3011  50.9081  -48.1554
 DYS  HXI1  H  HCH2   0   0.219  -29.6411  49.4955  -46.9918
 DYS  HXI2  H  HCH2   0   0.196  -28.6906  50.9135  -46.5864
 DYS  HXA1  H  HNH2   0   0.346  -30.2189  50.1758  -44.8257
 DYS  HXA2  H  HNH2   0   0.338  -30.5795  51.6755  -45.2962

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
 DYS  OXT  C     deloc     1.246  0.020  1.246
 DYS  O    C     deloc     1.231  0.020  1.231
 DYS  C    CA    single    1.525  0.021  1.525
 DYS  OXF  CXQ   single    1.344  0.020  1.344
 DYS  SG   CB    single    1.832  0.020  1.832
 DYS  SG   CXP   single    1.771  0.020  1.771
 DYS  CA   CB    single    1.530  0.020  1.530
 DYS  CA   N     single    1.458  0.019  1.458
 DYS  CXQ  CXP   aromatic  1.394  0.020  1.394
 DYS  CXQ  CXO   aromatic  1.402  0.020  1.402
 DYS  CXP  CXH   aromatic  1.393  0.020  1.393
 DYS  OXE  CXO   single    1.350  0.020  1.350
 DYS  CXO  CXG   aromatic  1.386  0.020  1.386
 DYS  CXH  CXN   aromatic  1.386  0.020  1.386
 DYS  CXG  CXN   aromatic  1.395  0.020  1.395
 DYS  CXN  CXJ   single    1.503  0.020  1.503
 DYS  CXJ  CXI   single    1.527  0.020  1.527
 DYS  CXI  NXA   single    1.455  0.020  1.455
 DYS  CA   HA    single    0.970  0.020  0.970
 DYS  N    HN1   single    0.890  0.020  1.040
 DYS  N    HN2   single    0.890  0.020  1.040
 DYS  CB   HB1   single    0.970  0.020  1.090
 DYS  CB   HB2   single    0.970  0.020  1.090
 DYS  CXH  HXH   single    0.930  0.020  1.080
 DYS  OXF  HOXF  single    0.850  0.020  0.980
 DYS  OXE  HOXE  single    0.850  0.020  0.980
 DYS  CXG  HXG   single    0.930  0.020  1.080
 DYS  CXJ  HXJ1  single    0.970  0.020  1.090
 DYS  CXJ  HXJ2  single    0.970  0.020  1.090
 DYS  CXI  HXI1  single    0.970  0.020  1.090
 DYS  CXI  HXI2  single    0.970  0.020  1.090
 DYS  NXA  HXA1  single    0.890  0.020  1.040
 DYS  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
 DYS  OXT   C    CA    116.66  3.000
 DYS  CA    C    O     120.80  1.700
 DYS  OXT   C    O     127.49  3.000
 DYS  HA    CA   CB    109.00  3.000
 DYS  HA    CA   N     110.00  3.000
 DYS  CB    CA   N     110.50  1.700
 DYS  HA    CA   C     109.00  3.000
 DYS  N     CA   C     111.00  2.800
 DYS  CB    CA   C     110.10  1.900
 DYS  HN2   N    HN1   105.18  3.000
 DYS  HN2   N    CA    107.18  3.000
 DYS  HN1   N    CA    108.77  3.000
 DYS  HB2   CB   HB1   108.50  3.000
 DYS  HB2   CB   SG    108.20  3.000
 DYS  HB1   CB   SG    108.48  3.000
 DYS  HB2   CB   CA    110.35  3.000
 DYS  HB1   CB   CA    110.01  3.000
 DYS  SG    CB   CA    111.23  3.000
 DYS  CXP   SG   CB     99.08  3.000
 DYS  CXQ   CXP  CXH   120.74  3.000
 DYS  CXH   CXP  SG    121.09  3.000
 DYS  CXQ   CXP  SG    118.16  3.000
 DYS  HXH   CXH  CXN   120.29  3.000
 DYS  HXH   CXH  CXP   119.07  3.000
 DYS  CXN   CXH  CXP   120.65  3.000
 DYS  CXO   CXQ  OXF   117.87  3.000
 DYS  CXO   CXQ  CXP   118.89  3.000
 DYS  OXF   CXQ  CXP   123.24  3.000
 DYS  HOXF  OXF  CXQ   108.19  3.000
 DYS  CXG   CXO  OXE   123.64  3.000
 DYS  CXG   CXO  CXQ   119.60  3.000
 DYS  OXE   CXO  CXQ   116.76  3.000
 DYS  HOXE  OXE  CXO   110.21  3.000
 DYS  HXG   CXG  CXN   119.29  3.000
 DYS  HXG   CXG  CXO   119.02  3.000
 DYS  CXN   CXG  CXO   121.69  3.000
 DYS  CXJ   CXN  CXG   120.95  3.000
 DYS  CXJ   CXN  CXH   120.60  3.000
 DYS  CXG   CXN  CXH   118.41  3.000
 DYS  HXJ2  CXJ  HXJ1  106.82  3.000
 DYS  HXJ2  CXJ  CXI   108.60  3.000
 DYS  HXJ1  CXJ  CXI   109.22  3.000
 DYS  HXJ2  CXJ  CXN   110.14  3.000
 DYS  HXJ1  CXJ  CXN   109.91  3.000
 DYS  CXI   CXJ  CXN   112.01  3.000
 DYS  HXI2  CXI  HXI1  106.32  3.000
 DYS  HXI2  CXI  NXA   113.94  3.000
 DYS  HXI1  CXI  NXA   108.30  3.000
 DYS  HXI2  CXI  CXJ   108.74  3.000
 DYS  HXI1  CXI  CXJ   108.77  3.000
 DYS  NXA   CXI  CXJ   110.59  3.000
 DYS  HXA2  NXA  HXA1  105.59  3.000
 DYS  HXA2  NXA  CXI   109.29  3.000
 DYS  HXA1  NXA  CXI   109.46  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
 DYS  CONST_01  CXG   CXO  CXQ  CXP     0.00   0.0  0
 DYS  CONST_02  CXG   CXN  CXH  CXP     0.00   0.0  0
 DYS  CONST_03  CXO   CXQ  CXP  CXH     0.00   0.0  0
 DYS  CONST_04  CXO   CXG  CXN  CXH     0.00   0.0  0
 DYS  CONST_05  CXN   CXH  CXP  CXQ     0.00   0.0  0
 DYS  CONST_06  CXN   CXG  CXO  CXQ     0.00   0.0  0
 DYS  CONST_07  CXO   CXQ  CXP  SG    180.00   0.0  0
 DYS  CONST_08  CXN   CXH  CXP  SG    180.00   0.0  0
 DYS  CONST_09  OXE   CXO  CXQ  CXP   180.00   0.0  0
 DYS  CONST_10  CXJ   CXN  CXH  CXP   180.00   0.0  0
 DYS  CONST_11  OXF   CXQ  CXP  CXH   180.00   0.0  0
 DYS  CONST_12  CXG   CXO  CXQ  OXF   180.00   0.0  0
 DYS  CONST_13  CXJ   CXN  CXG  CXO   180.00   0.0  0
 DYS  CONST_14  CXN   CXG  CXO  OXE   180.00   0.0  0
 DYS  CONST_15  HXG   CXG  CXN  CXH   180.00   0.0  0
 DYS  CONST_16  HXH   CXH  CXP  CXQ   180.00   0.0  0
 DYS  Var_01    CXQ   CXP  SG   CB     85.18  30.0  2
 DYS  Var_02    CXI   CXJ  CXN  CXH    82.73  30.0  2
 DYS  Var_03    NXA   CXI  CXJ  CXN  -178.43  30.0  3
 DYS  Var_04    HB1   CB   SG   CXP   -59.40  30.0  3
 DYS  Var_05    HXA1  NXA  CXI  CXJ   176.81  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
 DYS  chir_01  CA  C  CB  N  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
 DYS  plan-1  SG   0.020
 DYS  plan-1  CXP  0.020
 DYS  plan-1  CXH  0.020
 DYS  plan-1  CXQ  0.020
 DYS  plan-1  OXF  0.020
 DYS  plan-1  CXO  0.020
 DYS  plan-1  OXE  0.020
 DYS  plan-1  CXG  0.020
 DYS  plan-1  CXN  0.020
 DYS  plan-1  CXJ  0.020
 DYS  plan-1  HXH  0.020
 DYS  plan-1  HXG  0.020
 DYS  plan-2  O    0.020
 DYS  plan-2  C    0.020
 DYS  plan-2  CA   0.020
 DYS  plan-2  OXT  0.020

