# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 03:56:58 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 3-{[(2S)-2-amino-2-carboxyethyl]sulfanyl}-5-hydroxy-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CSc1cc(C[C@H](N)C(O)=O)cc(O)c1O)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
 HKS  HKS  3-{[(2S)-2-amino-2-carboxyethyl]sulfanyl}-5-hydroxy-L-tyrosine  ligand  35  21  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HKS
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
 HKS  C02  C  C      0   0.387  -4.2687  -2.4745   0.0368
 HKS  C04  C  CH1    0  -0.203  -3.2428  -1.3791   0.4377
 HKS  C06  C  CH2    0  -0.537  -2.5799  -0.7900  -0.8126
 HKS  C07  C  CR6    0   0.180  -1.7471   0.4298  -0.5394
 HKS  C08  C  CR16   0  -0.347  -0.3876   0.3301  -0.2718
 HKS  C09  C  CR6    0  -0.202   0.3799   1.4636  -0.0051
 HKS  C11  C  CH2    0  -0.569   2.5757  -0.2646  -0.0254
 HKS  C12  C  CH1    0  -0.225   4.0951  -0.3549  -0.0759
 HKS  C13  C  C      0   0.400   4.5185  -1.8115  -0.4184
 HKS  C17  C  CR6    0   0.274  -0.2298   2.7172   0.0078
 HKS  C19  C  CR6    0   0.284  -1.5953   2.8219  -0.2556
 HKS  C21  C  CR16   0  -0.456  -2.3438   1.6868  -0.5282
 HKS  N05  N  NH2    0  -0.779  -2.2316  -1.7867   1.3977
 HKS  N16  N  NH2    0  -0.781   4.6599   0.2044   1.1386
 HKS  O01  O  OC    -1  -0.620  -5.1224  -2.1404  -0.8115
 HKS  O03  O  O      0  -0.605  -4.1816  -3.5814   0.6027
 HKS  O14  O  OC    -1  -0.615   3.9534  -2.3248  -1.4056
 HKS  O15  O  O      0  -0.600   5.3941  -2.3318   0.2957
 HKS  O18  O  OH1    0  -0.630   0.5384   3.7998   0.2739
 HKS  O20  O  OH1    0  -0.650  -2.1096   4.0754  -0.2351
 HKS  S10  S  S2     0   0.047   2.1058   1.4460   0.3627
 HKS  H1   H  HCH1   0   0.218  -3.8277  -0.5716   0.9004
 HKS  H2   H  HCH2   0   0.232  -1.9615  -1.5619  -1.2841
 HKS  H3   H  HCH2   0   0.244  -3.3658  -0.5443  -1.5267
 HKS  H4   H  HCR6   0   0.244   0.0703  -0.6492  -0.2719
 HKS  H5   H  HCH2   0   0.275   2.1547  -0.5485  -0.9877
 HKS  H6   H  HCH2   0   0.260   2.1744  -0.9365   0.7384
 HKS  H7   H  HCH1   0   0.236   4.4316   0.2732  -0.9106
 HKS  H8   H  HCR6   0   0.259  -3.4046   1.7842  -0.7363
 HKS  H9   H  HNH2   0   0.332  -2.6900  -2.3207   2.1263
 HKS  H10  H  HNH2   0   0.323  -1.6125  -2.4552   0.9523
 HKS  H12  H  HNH2   0   0.330   4.3686  -0.3654   1.9257
 HKS  H13  H  HNH2   0   0.342   5.6661   0.0960   1.1057
 HKS  H17  H  HOH1   0   0.473   0.0088   4.6050   0.2419
 HKS  H18  H  HOH1   0   0.480  -3.0549   4.0577  -0.4199

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
 HKS  O20  C19  single    1.355  0.020  1.355
 HKS  O18  C17  single    1.354  0.020  1.354
 HKS  C19  C17  aromatic  1.395  0.020  1.395
 HKS  C19  C21  aromatic  1.387  0.020  1.387
 HKS  C17  C09  aromatic  1.394  0.020  1.394
 HKS  C21  C07  aromatic  1.392  0.020  1.392
 HKS  C09  C08  aromatic  1.395  0.020  1.395
 HKS  C09  S10  single    1.765  0.020  1.765
 HKS  C07  C08  aromatic  1.389  0.020  1.389
 HKS  C07  C06  single    1.502  0.020  1.502
 HKS  O15  C13  deloc     1.244  0.020  1.244
 HKS  C06  C04  single    1.533  0.020  1.533
 HKS  S10  C11  single    1.816  0.020  1.816
 HKS  O14  C13  deloc     1.248  0.020  1.248
 HKS  C13  C12  single    1.555  0.020  1.555
 HKS  C04  N05  single    1.453  0.020  1.453
 HKS  C04  C02  single    1.553  0.020  1.553
 HKS  O03  C02  deloc     1.246  0.020  1.246
 HKS  C11  C12  single    1.523  0.020  1.523
 HKS  C12  N16  single    1.452  0.020  1.452
 HKS  C02  O01  deloc     1.249  0.020  1.249
 HKS  C04  H1   single    0.970  0.020  1.090
 HKS  C06  H2   single    0.970  0.020  1.090
 HKS  C06  H3   single    0.970  0.020  1.090
 HKS  C08  H4   single    0.930  0.020  1.080
 HKS  C11  H5   single    0.970  0.020  1.090
 HKS  C11  H6   single    0.970  0.020  1.090
 HKS  C12  H7   single    0.970  0.020  1.090
 HKS  C21  H8   single    0.930  0.020  1.080
 HKS  N05  H9   single    0.890  0.020  1.040
 HKS  N05  H10  single    0.890  0.020  1.040
 HKS  N16  H12  single    0.890  0.020  1.040
 HKS  N16  H13  single    0.890  0.020  1.040
 HKS  O18  H17  single    0.850  0.020  0.980
 HKS  O20  H18  single    0.850  0.020  0.980

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
 HKS  O03  C02  O01  126.43  3.000
 HKS  O01  C02  C04  115.97  3.000
 HKS  O03  C02  C04  117.58  3.000
 HKS  H1   C04  N05  107.36  3.000
 HKS  H1   C04  C06  106.93  3.000
 HKS  N05  C04  C06  110.23  3.000
 HKS  H1   C04  C02  105.98  3.000
 HKS  N05  C04  C02  115.62  3.000
 HKS  C06  C04  C02  110.25  3.000
 HKS  H3   C06  H2   106.49  3.000
 HKS  H3   C06  C07  109.63  3.000
 HKS  H2   C06  C07  109.73  3.000
 HKS  H3   C06  C04  108.01  3.000
 HKS  H2   C06  C04  108.92  3.000
 HKS  C07  C06  C04  113.80  3.000
 HKS  C21  C07  C08  118.88  3.000
 HKS  C08  C07  C06  121.29  3.000
 HKS  C21  C07  C06  119.82  3.000
 HKS  H4   C08  C09  120.21  3.000
 HKS  H4   C08  C07  118.65  3.000
 HKS  C09  C08  C07  121.14  3.000
 HKS  S10  C09  C17  115.77  3.000
 HKS  S10  C09  C08  124.75  3.000
 HKS  C17  C09  C08  119.47  3.000
 HKS  H6   C11  H5   108.39  3.000
 HKS  H6   C11  S10  109.55  3.000
 HKS  H5   C11  S10  109.56  3.000
 HKS  H6   C11  C12  110.66  3.000
 HKS  H5   C11  C12  109.95  3.000
 HKS  S10  C11  C12  108.73  3.000
 HKS  H7   C12  N16  107.25  3.000
 HKS  H7   C12  C13  106.56  3.000
 HKS  N16  C12  C13  116.06  3.000
 HKS  H7   C12  C11  107.29  3.000
 HKS  N16  C12  C11  109.73  3.000
 HKS  C13  C12  C11  109.55  3.000
 HKS  O15  C13  O14  126.93  3.000
 HKS  O14  C13  C12  115.86  3.000
 HKS  O15  C13  C12  117.19  3.000
 HKS  O18  C17  C19  122.18  3.000
 HKS  C19  C17  C09  119.60  3.000
 HKS  O18  C17  C09  118.21  3.000
 HKS  O20  C19  C21  123.73  3.000
 HKS  C21  C19  C17  120.28  3.000
 HKS  O20  C19  C17  115.99  3.000
 HKS  H8   C21  C19  119.46  3.000
 HKS  H8   C21  C07  119.91  3.000
 HKS  C19  C21  C07  120.63  3.000
 HKS  H10  N05  H9   104.16  3.000
 HKS  H10  N05  C04  108.65  3.000
 HKS  H9   N05  C04  107.95  3.000
 HKS  H13  N16  H12  104.51  3.000
 HKS  H13  N16  C12  108.55  3.000
 HKS  H12  N16  C12  108.73  3.000
 HKS  H17  O18  C17  110.46  3.000
 HKS  H18  O20  C19  110.64  3.000
 HKS  C11  S10  C09  102.59  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
 HKS  CONST_01  C17  C19  C21  C07     0.00   0.0  0
 HKS  CONST_02  C17  C09  C08  C07     0.00   0.0  0
 HKS  CONST_03  C19  C17  C09  C08     0.00   0.0  0
 HKS  CONST_04  C19  C21  C07  C08     0.00   0.0  0
 HKS  CONST_05  C21  C19  C17  C09     0.00   0.0  0
 HKS  CONST_06  C21  C07  C08  C09     0.00   0.0  0
 HKS  CONST_07  C19  C21  C07  C06   180.00   0.0  0
 HKS  CONST_08  C09  C08  C07  C06   180.00   0.0  0
 HKS  CONST_09  O20  C19  C21  C07   180.00   0.0  0
 HKS  CONST_10  S10  C09  C08  C07   180.00   0.0  0
 HKS  CONST_11  O18  C17  C09  C08   180.00   0.0  0
 HKS  CONST_12  O20  C19  C17  C09   180.00   0.0  0
 HKS  CONST_13  S10  C09  C17  C19   180.00   0.0  0
 HKS  CONST_14  O18  C17  C19  C21   180.00   0.0  0
 HKS  CONST_15  H8   C21  C07  C08   180.00   0.0  0
 HKS  CONST_16  H4   C08  C09  C17   180.00   0.0  0
 HKS  Var_01    C21  C07  C06  C04   -86.71  30.0  2
 HKS  Var_02    C17  C09  S10  C11  -170.76  30.0  1
 HKS  Var_03    C12  C11  S10  C09   166.68  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
 HKS  chir_01  C04  C06  N05  C02  positiv
 HKS  chir_02  C12  C13  C11  N16  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
 HKS  plan-1  C06  0.020
 HKS  plan-1  C07  0.020
 HKS  plan-1  C08  0.020
 HKS  plan-1  C09  0.020
 HKS  plan-1  C17  0.020
 HKS  plan-1  C19  0.020
 HKS  plan-1  C21  0.020
 HKS  plan-1  O18  0.020
 HKS  plan-1  O20  0.020
 HKS  plan-1  S10  0.020
 HKS  plan-1  H4   0.020
 HKS  plan-1  H8   0.020
 HKS  plan-2  C02  0.020
 HKS  plan-2  C04  0.020
 HKS  plan-2  O01  0.020
 HKS  plan-2  O03  0.020
 HKS  plan-3  C12  0.020
 HKS  plan-3  C13  0.020
 HKS  plan-3  O14  0.020
 HKS  plan-3  O15  0.020

