# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 08:15:26 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (2R,4S)-2-[(1R)-2-hydroxy-1-{[(2-hydroxynaphthalen-1-yl)carbonyl]amino}ethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)S[C@@H](N[C@H]1C(O)=O)[C@@H](CO)NC(=O)c2c(O)ccc3ccccc23
#
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
 NXU  NXU  '(2R,4S)-2-[(1R)-2-hydroxy-1-{[(2-hydroxynaphthalen-1-yl)carbonyl]amino}ethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid'  ligand  48  27  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NXU
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
 NXU  O2   O  O      0  -0.468   1.0016  -0.7005   1.7876
 NXU  C11  C  C      0   0.439   1.1568  -0.6769   0.5753
 NXU  N1   N  NH1    0  -0.597   0.4338  -1.4216  -0.2852
 NXU  C12  C  CH1    0  -0.155  -0.8763  -1.9554   0.0405
 NXU  C13  C  CH1    0  -0.162  -1.9158  -0.9186  -0.3871
 NXU  S1   S  S2     0  -0.022  -3.6289  -1.3847   0.0942
 NXU  C15  C  CT     0  -0.202  -4.0332   0.2989   0.7296
 NXU  C19  C  CH3    0  -0.626  -4.0527   0.2638   2.2569
 NXU  C20  C  CH3    0  -0.634  -5.4033   0.7199   0.2151
 NXU  C16  C  CH1    0  -0.186  -2.8549   1.1906   0.2322
 NXU  C21  C  C      0   0.433  -3.1209   1.8733  -1.1278
 NXU  O5   O  OC    -1  -0.609  -3.6824   2.9829  -1.0578
 NXU  O4   O  O      0  -0.580  -2.7730   1.2740  -2.1609
 NXU  N2   N  NH1    0  -0.638  -1.6474   0.3656   0.2290
 NXU  C14  C  CH2    0  -0.157  -1.0771  -3.3119  -0.6067
 NXU  O3   O  OH1    0  -0.669  -0.9930  -3.1632  -2.0041
 NXU  C1   C  CR6    0  -0.227   2.1545   0.2205  -0.0809
 NXU  C2   C  CR6    0   0.345   1.7013   1.3022  -0.8165
 NXU  C3   C  CR16   0  -0.343   2.6473   2.1963  -1.3862
 NXU  O1   O  OH1    0  -0.655   0.4245   1.6081  -1.0478
 NXU  C9   C  CR66   0   0.145   3.5481   0.0169   0.1254
 NXU  C8   C  CR16   0  -0.335   4.0586  -1.0769   0.8665
 NXU  C7   C  CR16   0  -0.248   5.4088  -1.2517   1.0230
 NXU  C6   C  CR16   0  -0.271   6.3260  -0.3489   0.4526
 NXU  C5   C  CR16   0  -0.307   5.8625   0.7146  -0.2740
 NXU  C10  C  CR66   0   0.072   4.4771   0.9176  -0.4553
 NXU  C4   C  CR16   0  -0.298   3.9829   2.0076  -1.2123
 NXU  H1   H  HNH1   0   0.404   0.6507  -1.3371  -1.2677
 NXU  H2   H  HCH1   0   0.273  -0.9305  -2.0983   1.1217
 NXU  H3   H  HCH1   0   0.287  -1.9000  -0.7898  -1.4658
 NXU  H4   H  HCH3   0   0.228  -3.0835  -0.0083   2.6777
 NXU  H5   H  HCH3   0   0.232  -4.3254   1.2456   2.6524
 NXU  H6   H  HCH3   0   0.240  -4.7836  -0.4580   2.6230
 NXU  H7   H  HCH3   0   0.233  -6.1778   0.0728   0.6294
 NXU  H8   H  HCH3   0   0.235  -5.6243   1.7417   0.5241
 NXU  H9   H  HCH3   0   0.238  -5.4665   0.6671  -0.8704
 NXU  H10  H  HCH1   0   0.260  -2.7036   1.9788   0.9735
 NXU  H12  H  HNH1   0   0.369  -1.3826   0.2131   1.1983
 NXU  H14  H  HCH2   0   0.227  -0.3072  -3.9903  -0.2211
 NXU  H15  H  HCH2   0   0.213  -2.0479  -3.7160  -0.2930
 NXU  H16  H  HOH1   0   0.464  -1.0204  -4.0365  -2.4049
 NXU  H17  H  HCR6   0   0.267   2.2800   3.0397  -1.9575
 NXU  H18  H  HOH1   0   0.507  -0.2761   1.0906  -0.5497
 NXU  H19  H  HCR6   0   0.250   3.3832  -1.7895   1.3207
 NXU  H20  H  HCR6   0   0.258   5.7744  -2.0971   1.5915
 NXU  H21  H  HCR6   0   0.255   7.3887  -0.5007   0.5873
 NXU  H22  H  HCR6   0   0.255   6.5551   1.4161  -0.7240
 NXU  H23  H  HCR6   0   0.260   4.6865   2.7016  -1.6560

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
 NXU  O1   C2   single    1.333  0.020  1.333
 NXU  O3   C14  single    1.408  0.020  1.408
 NXU  C14  C12  single    1.516  0.020  1.516
 NXU  C2   C3   aromatic  1.421  0.020  1.421
 NXU  C2   C1   aromatic  1.384  0.020  1.384
 NXU  C12  N1   single    1.452  0.020  1.452
 NXU  C12  C13  single    1.529  0.020  1.529
 NXU  C3   C4   aromatic  1.360  0.020  1.360
 NXU  N1   C11  single    1.348  0.020  1.348
 NXU  C11  O2   double    1.222  0.020  1.222
 NXU  C11  C1   single    1.494  0.020  1.494
 NXU  N2   C13  single    1.449  0.020  1.449
 NXU  N2   C16  single    1.462  0.020  1.462
 NXU  C1   C9   aromatic  1.423  0.020  1.423
 NXU  C13  S1   single    1.839  0.020  1.839
 NXU  C4   C10  aromatic  1.416  0.020  1.416
 NXU  O4   C21  deloc     1.244  0.020  1.244
 NXU  C21  C16  single    1.545  0.020  1.545
 NXU  C21  O5   deloc     1.246  0.020  1.246
 NXU  C16  C15  single    1.559  0.020  1.559
 NXU  C9   C10  aromatic  1.418  0.020  1.418
 NXU  C9   C8   aromatic  1.416  0.020  1.416
 NXU  C10  C5   aromatic  1.412  0.020  1.412
 NXU  S1   C15  single    1.844  0.020  1.844
 NXU  C15  C20  single    1.523  0.020  1.523
 NXU  C15  C19  single    1.528  0.020  1.528
 NXU  C8   C7   aromatic  1.370  0.020  1.370
 NXU  C5   C6   aromatic  1.369  0.020  1.369
 NXU  C7   C6   aromatic  1.408  0.020  1.408
 NXU  N1   H1   single    0.890  0.020  1.040
 NXU  C12  H2   single    0.970  0.020  1.090
 NXU  C13  H3   single    0.970  0.020  1.090
 NXU  C19  H4   single    0.970  0.020  1.090
 NXU  C19  H5   single    0.970  0.020  1.090
 NXU  C19  H6   single    0.970  0.020  1.090
 NXU  C20  H7   single    0.970  0.020  1.090
 NXU  C20  H8   single    0.970  0.020  1.090
 NXU  C20  H9   single    0.970  0.020  1.090
 NXU  C16  H10  single    0.970  0.020  1.090
 NXU  N2   H12  single    0.890  0.020  1.040
 NXU  C14  H14  single    0.970  0.020  1.090
 NXU  C14  H15  single    0.970  0.020  1.090
 NXU  O3   H16  single    0.850  0.020  0.980
 NXU  C3   H17  single    0.930  0.020  1.080
 NXU  O1   H18  single    0.850  0.020  0.980
 NXU  C8   H19  single    0.930  0.020  1.080
 NXU  C7   H20  single    0.930  0.020  1.080
 NXU  C6   H21  single    0.930  0.020  1.080
 NXU  C5   H22  single    0.930  0.020  1.080
 NXU  C4   H23  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
 NXU  C1   C11  N1   114.19  3.000
 NXU  C1   C11  O2   122.14  3.000
 NXU  N1   C11  O2   123.65  3.000
 NXU  H1   N1   C12  116.29  3.000
 NXU  H1   N1   C11  117.36  3.000
 NXU  C12  N1   C11  122.95  3.000
 NXU  H2   C12  C14  107.39  3.000
 NXU  H2   C12  C13  109.38  3.000
 NXU  C14  C12  C13  113.40  3.000
 NXU  H2   C12  N1   108.36  3.000
 NXU  C13  C12  N1   107.54  3.000
 NXU  C14  C12  N1   110.65  3.000
 NXU  H3   C13  N2   108.32  3.000
 NXU  H3   C13  S1   107.66  3.000
 NXU  N2   C13  S1   106.60  3.000
 NXU  H3   C13  C12  110.37  3.000
 NXU  S1   C13  C12  112.84  3.000
 NXU  N2   C13  C12  110.85  3.000
 NXU  C15  S1   C13   93.61  3.000
 NXU  C16  C15  C20  114.46  3.000
 NXU  C20  C15  C19  109.43  3.000
 NXU  C16  C15  C19  109.98  3.000
 NXU  C19  C15  S1   109.04  3.000
 NXU  C20  C15  S1   109.46  3.000
 NXU  C16  C15  S1   104.27  3.000
 NXU  H6   C19  H5   107.81  3.000
 NXU  H6   C19  H4   107.51  3.000
 NXU  H5   C19  H4   107.82  3.000
 NXU  H6   C19  C15  111.06  3.000
 NXU  H5   C19  C15  110.13  3.000
 NXU  H4   C19  C15  112.33  3.000
 NXU  H9   C20  H8   108.44  3.000
 NXU  H9   C20  H7   107.98  3.000
 NXU  H8   C20  H7   107.73  3.000
 NXU  H9   C20  C15  112.07  3.000
 NXU  H8   C20  C15  110.22  3.000
 NXU  H7   C20  C15  110.27  3.000
 NXU  H10  C16  N2   107.10  3.000
 NXU  H10  C16  C21  107.60  3.000
 NXU  N2   C16  C21  112.93  3.000
 NXU  H10  C16  C15  107.50  3.000
 NXU  C21  C16  C15  113.80  3.000
 NXU  N2   C16  C15  107.58  3.000
 NXU  O4   C21  O5   127.01  3.000
 NXU  O5   C21  C16  114.95  3.000
 NXU  O4   C21  C16  118.04  3.000
 NXU  H12  N2   C16  107.32  3.000
 NXU  H12  N2   C13  108.71  3.000
 NXU  C16  N2   C13  110.35  3.000
 NXU  H15  C14  H14  107.03  3.000
 NXU  H15  C14  O3   112.05  3.000
 NXU  H14  C14  O3   111.87  3.000
 NXU  H15  C14  C12  108.94  3.000
 NXU  H14  C14  C12  108.09  3.000
 NXU  O3   C14  C12  108.74  3.000
 NXU  H16  O3   C14  108.44  3.000
 NXU  C9   C1   C2   120.62  3.000
 NXU  C9   C1   C11  120.28  3.000
 NXU  C2   C1   C11  118.96  3.000
 NXU  O1   C2   C3   115.07  3.000
 NXU  C3   C2   C1   119.12  3.000
 NXU  O1   C2   C1   125.80  3.000
 NXU  H17  C3   C4   120.57  3.000
 NXU  H17  C3   C2   118.41  3.000
 NXU  C4   C3   C2   121.02  3.000
 NXU  H18  O1   C2   117.66  3.000
 NXU  C10  C9   C8   117.94  3.000
 NXU  C8   C9   C1   122.63  3.000
 NXU  C10  C9   C1   119.41  3.000
 NXU  H19  C8   C7   118.89  3.000
 NXU  H19  C8   C9   120.22  3.000
 NXU  C7   C8   C9   120.89  3.000
 NXU  H20  C7   C6   119.58  3.000
 NXU  H20  C7   C8   119.50  3.000
 NXU  C6   C7   C8   120.92  3.000
 NXU  H21  C6   C5   120.51  3.000
 NXU  H21  C6   C7   119.97  3.000
 NXU  C5   C6   C7   119.52  3.000
 NXU  H22  C5   C10  118.73  3.000
 NXU  H22  C5   C6   120.46  3.000
 NXU  C10  C5   C6   120.81  3.000
 NXU  C4   C10  C5   121.45  3.000
 NXU  C5   C10  C9   119.92  3.000
 NXU  C4   C10  C9   118.63  3.000
 NXU  H23  C4   C10  119.04  3.000
 NXU  H23  C4   C3   119.77  3.000
 NXU  C10  C4   C3   121.19  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
 NXU  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 NXU  CONST_02  C4   C10  C9   C1      0.00   0.0  0
 NXU  CONST_03  C5   C10  C9   C1    180.00   0.0  0
 NXU  CONST_04  C7   C8   C9   C1    180.00   0.0  0
 NXU  CONST_05  C10  C4   C3   C2      0.00   0.0  0
 NXU  CONST_06  C10  C9   C1   C2      0.00   0.0  0
 NXU  CONST_07  C8   C9   C1   C2    180.00   0.0  0
 NXU  CONST_08  C9   C1   C2   C3      0.00   0.0  0
 NXU  CONST_09  C9   C10  C4   C3      0.00   0.0  0
 NXU  CONST_10  C5   C10  C4   C3    180.00   0.0  0
 NXU  CONST_11  C6   C5   C10  C9      0.00   0.0  0
 NXU  CONST_12  C6   C7   C8   C9      0.00   0.0  0
 NXU  CONST_13  C4   C10  C9   C8    180.00   0.0  0
 NXU  CONST_14  C5   C10  C9   C8      0.00   0.0  0
 NXU  CONST_15  C5   C6   C7   C8      0.00   0.0  0
 NXU  CONST_16  C10  C9   C8   C7      0.00   0.0  0
 NXU  CONST_17  C10  C5   C6   C7      0.00   0.0  0
 NXU  CONST_18  C4   C10  C5   C6    180.00   0.0  0
 NXU  CONST_19  C3   C2   C1   C11   180.00   0.0  0
 NXU  CONST_20  C10  C9   C1   C11   180.00   0.0  0
 NXU  CONST_21  C8   C9   C1   C11     0.00   0.0  0
 NXU  CONST_22  C4   C3   C2   O1    180.00   0.0  0
 NXU  CONST_23  C9   C1   C2   O1    180.00   0.0  0
 NXU  CONST_24  H17  C3   C2   C1    180.00   0.0  0
 NXU  CONST_25  H19  C8   C9   C1      0.00   0.0  0
 NXU  CONST_26  H23  C4   C3   C2    180.00   0.0  0
 NXU  CONST_27  H22  C5   C10  C9    180.00   0.0  0
 NXU  CONST_28  H20  C7   C8   C9    180.00   0.0  0
 NXU  CONST_29  H21  C6   C7   C8    180.00   0.0  0
 NXU  CONST_31  H1   N1   C11  C1      0.00   0.0  0
 NXU  Var_01    C16  C15  S1   C13    11.52  30.0  1
 NXU  Var_02    C2   C1   C11  O2   -109.14  30.0  2
 NXU  Var_03    H7   C20  C15  S1     65.24  30.0  3
 NXU  Var_04    H4   C19  C15  S1     61.78  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
 NXU  chir_01  C12  C14  N1   C13  negativ
 NXU  chir_02  C13  S1   N2   C12  negativ
 NXU  chir_03  C16  N2   C15  C21  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
 NXU  plan-1  C11  0.020
 NXU  plan-1  C1   0.020
 NXU  plan-1  C2   0.020
 NXU  plan-1  C3   0.020
 NXU  plan-1  O1   0.020
 NXU  plan-1  C9   0.020
 NXU  plan-1  C8   0.020
 NXU  plan-1  C7   0.020
 NXU  plan-1  C6   0.020
 NXU  plan-1  C5   0.020
 NXU  plan-1  C10  0.020
 NXU  plan-1  C4   0.020
 NXU  plan-1  H17  0.020
 NXU  plan-1  H19  0.020
 NXU  plan-1  H20  0.020
 NXU  plan-1  H21  0.020
 NXU  plan-1  H22  0.020
 NXU  plan-1  H23  0.020
 NXU  plan-2  O2   0.020
 NXU  plan-2  C11  0.020
 NXU  plan-2  N1   0.020
 NXU  plan-2  C12  0.020
 NXU  plan-2  C1   0.020
 NXU  plan-2  H1   0.020
 NXU  plan-3  C16  0.020
 NXU  plan-3  C21  0.020
 NXU  plan-3  O5   0.020
 NXU  plan-3  O4   0.020

