# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 13:23:30 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: S-[(S)-hydroxy(5-methoxypyridin-3-yl)methyl]-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cncc(c1)[C@@H](O)SC[C@H](N)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
 JJL  JJL  S-[(S)-hydroxy(5-methoxypyridin-3-yl)methyl]-L-cysteine  L-peptide  30  17  .  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_JJL
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
 JJL  C     C  C      0   0.399  3.0189  35.0369  17.8562
 JJL  N     N  NH2    0  -0.818  2.8153  36.2295  15.6376
 JJL  O     O  O      0  -0.602  3.7149  34.2983  18.5778
 JJL  N1    N  N      0  -0.379  7.6761  40.9636  14.1128
 JJL  C2    C  CR16   0  -0.117  6.7373  40.2494  14.7220
 JJL  C3    C  CR6    0   0.023  6.0678  39.2018  14.1064
 JJL  C4    C  CR16   0  -0.313  6.3895  38.8894  12.7905
 JJL  C5    C  CR6    0   0.320  7.3703  39.6366  12.1499
 JJL  C6    C  CR16   0  -0.152  7.9876  40.6679  12.8638
 JJL  C7    C  CH1    0  -0.136  5.0414  38.4033  14.8619
 JJL  O7    O  OH1    0  -0.671  4.0669  37.9365  14.0138
 JJL  CA    C  CH1    0  -0.178  3.7250  35.5799  16.5775
 JJL  CB    C  CH2    0  -0.576  4.8329  36.5351  17.0131
 JJL  SG    S  S2     0  -0.058  5.9884  37.0603  15.7094
 JJL  O15   O  O2     0  -0.463  7.7802  39.4531  10.8851
 JJL  C16   C  CH3    0  -0.439  7.1772  38.4207  10.1292
 JJL  OXT   O  OC    -1  -0.589  1.8469  35.4077  18.0534
 JJL  HN    H  HNH2   0   0.368  2.2970  35.5213  15.1306
 JJL  HNA   H  HNH2   0   0.357  2.1124  36.7196  16.1837
 JJL  H2    H  HCR6   0   0.255  6.5043  40.5187  15.7474
 JJL  H4    H  HCR6   0   0.289  5.8735  38.0803  12.2918
 JJL  H6    H  HCR6   0   0.262  8.7571  41.2659  12.3851
 JJL  H7    H  HCH1   0   0.244  4.6395  39.0195  15.6801
 JJL  HO7   H  HOH1   0   0.474  3.5153  37.2848  14.5489
 JJL  HA    H  HCH1   0   0.236  4.1954  34.7378  16.0636
 JJL  HB    H  HCH2   0   0.263  4.4122  37.4293  17.4834
 JJL  HBA   H  HCH2   0   0.280  5.4543  36.0443  17.7621
 JJL  H16   H  HCH3   0   0.261  7.6409  38.4469   9.1465
 JJL  H16A  H  HCH3   0   0.231  7.3481  37.4372  10.5747
 JJL  H16B  H  HCH3   0   0.231  6.1010  38.5744  10.0147

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
 JJL  C    O     deloc     1.231  0.020  1.231
 JJL  C    OXT   deloc     1.245  0.020  1.245
 JJL  N    CA    single    1.458  0.019  1.458
 JJL  N    HN    single    0.890  0.020  1.040
 JJL  N    HNA   single    0.890  0.020  1.040
 JJL  N1   C2    aromatic  1.328  0.020  1.328
 JJL  C2   H2    single    0.930  0.020  1.080
 JJL  C3   C2    aromatic  1.387  0.020  1.387
 JJL  C3   C7    single    1.504  0.020  1.504
 JJL  C4   C3    aromatic  1.390  0.020  1.390
 JJL  C4   H4    single    0.930  0.020  1.080
 JJL  C5   C4    aromatic  1.389  0.020  1.389
 JJL  C5   C6    aromatic  1.398  0.020  1.398
 JJL  C6   N1    aromatic  1.321  0.020  1.321
 JJL  C6   H6    single    0.930  0.020  1.080
 JJL  C7   SG    single    1.849  0.020  1.849
 JJL  C7   H7    single    0.970  0.020  1.090
 JJL  O7   C7    single    1.374  0.020  1.374
 JJL  O7   HO7   single    0.850  0.020  0.980
 JJL  CA   C     single    1.525  0.021  1.525
 JJL  CA   CB    single    1.530  0.020  1.530
 JJL  CA   HA    single    0.970  0.020  0.970
 JJL  CB   HB    single    0.970  0.020  1.090
 JJL  CB   HBA   single    0.970  0.020  1.090
 JJL  SG   CB    single    1.820  0.020  1.820
 JJL  O15  C5    single    1.342  0.020  1.342
 JJL  C16  O15   single    1.415  0.020  1.415
 JJL  C16  H16   single    0.970  0.020  1.090
 JJL  C16  H16A  single    0.970  0.020  1.090
 JJL  C16  H16B  single    0.970  0.020  1.090

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
 JJL  OXT   C    CA    116.92  3.000
 JJL  CA    C    O     120.80  1.700
 JJL  OXT   C    O     127.66  3.000
 JJL  HNA   N    HN    104.61  3.000
 JJL  HNA   N    CA    107.43  3.000
 JJL  HN    N    CA    109.25  3.000
 JJL  C6    N1   C2    118.70  3.000
 JJL  H2    C2   C3    120.19  3.000
 JJL  C3    C2   N1    122.95  3.000
 JJL  H2    C2   N1    116.86  3.000
 JJL  C7    C3   C4    120.94  3.000
 JJL  C4    C3   C2    118.56  3.000
 JJL  C7    C3   C2    120.49  3.000
 JJL  H4    C4   C5    121.77  3.000
 JJL  C5    C4   C3    118.62  3.000
 JJL  H4    C4   C3    119.62  3.000
 JJL  O15   C5   C6    116.56  3.000
 JJL  O15   C5   C4    125.21  3.000
 JJL  C6    C5   C4    118.23  3.000
 JJL  H6    C6   C5    119.61  3.000
 JJL  H6    C6   N1    117.44  3.000
 JJL  C5    C6   N1    122.95  3.000
 JJL  H7    C7   SG    104.66  3.000
 JJL  H7    C7   O7    112.98  3.000
 JJL  SG    C7   O7    113.54  3.000
 JJL  O7    C7   C3    110.76  3.000
 JJL  H7    C7   C3    109.00  3.000
 JJL  SG    C7   C3    105.44  3.000
 JJL  HO7   O7   C7    106.28  3.000
 JJL  HA    CA   CB    109.00  3.000
 JJL  HA    CA   N     110.00  3.000
 JJL  CB    CA   N     110.50  1.700
 JJL  HA    CA   C     109.00  3.000
 JJL  CB    CA   C     110.10  1.900
 JJL  N     CA   C     111.00  2.800
 JJL  HBA   CB   HB    106.96  3.000
 JJL  HBA   CB   SG    105.09  3.000
 JJL  HB    CB   SG    108.43  3.000
 JJL  SG    CB   CA    115.92  3.000
 JJL  HBA   CB   CA    109.16  3.000
 JJL  HB    CB   CA    110.79  3.000
 JJL  CB    SG   C7    102.29  3.000
 JJL  C16   O15  C5    118.24  3.000
 JJL  H16B  C16  H16A  108.85  3.000
 JJL  H16B  C16  H16   108.78  3.000
 JJL  H16A  C16  H16   108.87  3.000
 JJL  H16B  C16  O15   111.90  3.000
 JJL  H16A  C16  O15   111.85  3.000
 JJL  H16   C16  O15   106.48  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
 JJL  CONST_01  C4   C3   C2   N1    0.00   0.0  0
 JJL  CONST_02  C4   C5   C6   N1    0.00   0.0  0
 JJL  CONST_03  C5   C6   N1   C2    0.00   0.0  0
 JJL  CONST_04  C5   C4   C3   C2    0.00   0.0  0
 JJL  CONST_05  C6   N1   C2   C3    0.00   0.0  0
 JJL  CONST_06  C6   C5   C4   C3    0.00   0.0  0
 JJL  CONST_07  C7   C3   C2   N1  180.00   0.0  0
 JJL  CONST_08  O15  C5   C6   N1  180.00   0.0  0
 JJL  CONST_09  O15  C5   C4   C3  180.00   0.0  0
 JJL  CONST_10  C7   C3   C4   C5  180.00   0.0  0
 JJL  CONST_11  H6   C6   N1   C2  180.00   0.0  0
 JJL  CONST_12  H4   C4   C3   C2  180.00   0.0  0
 JJL  CONST_13  H2   C2   C3   C4  180.00   0.0  0
 JJL  Var_01    H16  C16  O15  C5  179.62  30.0  3
 JJL  Var_02    CA   CB   SG   C7   80.76  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
 JJL  chir_01  C7  C3  SG  O7  positiv
 JJL  chir_02  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
 JJL  plan-1  N1   0.020
 JJL  plan-1  C2   0.020
 JJL  plan-1  C3   0.020
 JJL  plan-1  C4   0.020
 JJL  plan-1  C5   0.020
 JJL  plan-1  C6   0.020
 JJL  plan-1  C7   0.020
 JJL  plan-1  O15  0.020
 JJL  plan-1  H2   0.020
 JJL  plan-1  H4   0.020
 JJL  plan-1  H6   0.020
 JJL  plan-2  C    0.020
 JJL  plan-2  O    0.020
 JJL  plan-2  CA   0.020
 JJL  plan-2  OXT  0.020

