# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 14:04:15 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: N-[(2R,3S)-3-amino-2-hydroxy-4-(thiophen-2-yl)butanoyl]-L-norvaline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@H](NC(=O)[C@H](O)[C@@H](N)Cc1sccc1)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
 36D  36D  N-[(2R,3S)-3-amino-2-hydroxy-4-(thiophen-2-yl)butanoyl]-L-norvaline  ligand  40  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_36D
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
 36D  N1   N  NH2   0  -0.777  -1.1760  -0.7313  -1.6443
 36D  C1   C  CH1   0  -0.113  -1.1013  -0.7998  -0.2021
 36D  O1   O  OH1   0  -0.669  -0.2347  -3.0684  -0.0089
 36D  C2   C  CH2   0  -0.509  -2.4588  -1.2263   0.3689
 36D  C3   C  CR5   0  -0.105  -3.5705  -0.3075  -0.0096
 36D  S1   S  S2    0   0.187  -3.6132   1.3228   0.5566
 36D  C4   C  CR15  0  -0.475  -5.0768   1.6521  -0.2785
 36D  C5   C  CR15  0  -0.186  -5.5126   0.5580  -0.9581
 36D  C6   C  CR15  0  -0.249  -4.6472  -0.5620  -0.8040
 36D  C7   C  CH1   0  -0.064   0.0032  -1.7368   0.3423
 36D  C8   C  C     0   0.502   1.3578  -1.3036  -0.2039
 36D  O2   O  O     0  -0.484   1.9481  -1.9940  -1.0234
 36D  N2   N  NH1   0  -0.629   1.8124  -0.1157   0.2135
 36D  C9   C  CH1   0  -0.185   3.0657   0.4234  -0.2424
 36D  C10  C  CH2   0  -0.460   3.1777   1.9043   0.1353
 36D  C11  C  CH2   0  -0.421   2.1048   2.7689  -0.5180
 36D  C12  C  CH3   0  -0.663   2.2799   4.2412  -0.1736
 36D  C13  C  C     0   0.548   4.2270  -0.3651   0.3448
 36D  O3   O  O     0  -0.431   4.1508  -1.0755   1.3120
 36D  O4   O  OH1   0  -0.591   5.3446  -0.1447  -0.3318
 36D  H1   H  HNH2  0   0.350  -0.3224  -0.3621  -2.0435
 36D  H2   H  HNH2  0   0.341  -1.3102  -1.6557  -2.0362
 36D  H4   H  HCH1  0   0.236  -0.8827   0.2078   0.1695
 36D  H5   H  HOH1  0   0.447   0.3902  -3.2935  -0.7126
 36D  H6   H  HCH2  0   0.261  -2.7068  -2.2270   0.0085
 36D  H7   H  HCH2  0   0.261  -2.3782  -1.2973   1.4573
 36D  H8   H  HCR5  0   0.290  -5.5322   2.6286  -0.2208
 36D  H9   H  HCR5  0   0.262  -6.4166   0.5467  -1.5501
 36D  H10  H  HCR5  0   0.255  -4.8158  -1.5242  -1.2685
 36D  H11  H  HCH1  0   0.254   0.0215  -1.6506   1.4372
 36D  H12  H  HNH1  0   0.411   1.3529   0.3382   0.9883
 36D  H13  H  HCH1  0   0.291   3.1160   0.3406  -1.3319
 36D  H14  H  HCH2  0   0.244   3.1326   2.0069   1.2247
 36D  H15  H  HCH2  0   0.260   4.1619   2.2647  -0.1702
 36D  H16  H  HCH2  0   0.227   2.1441   2.6314  -1.6023
 36D  H17  H  HCH2  0   0.222   1.1102   2.4429  -0.2039
 36D  H18  H  HCH3  0   0.233   1.5103   4.8510  -0.6469
 36D  H19  H  HCH3  0   0.222   2.2131   4.4030   0.9035
 36D  H20  H  HCH3  0   0.222   3.2503   4.6144  -0.5053
 36D  H21  H  HOH1  0   0.485   6.0840  -0.6218   0.0741

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
 36D  N1   C1   single    1.446  0.020  1.446
 36D  C1   C2   single    1.533  0.020  1.533
 36D  C1   C7   single    1.547  0.020  1.547
 36D  O1   C7   single    1.398  0.020  1.398
 36D  C2   C3   single    1.491  0.020  1.491
 36D  C3   S1   aromatic  1.726  0.020  1.726
 36D  C3   C6   aromatic  1.362  0.020  1.362
 36D  S1   C4   aromatic  1.717  0.020  1.717
 36D  C4   C5   aromatic  1.360  0.020  1.360
 36D  C5   C6   aromatic  1.424  0.020  1.424
 36D  C7   C8   single    1.523  0.020  1.523
 36D  C8   O2   double    1.223  0.020  1.223
 36D  C8   N2   single    1.339  0.020  1.339
 36D  N2   C9   single    1.439  0.020  1.439
 36D  C9   C10  single    1.532  0.020  1.532
 36D  C9   C13  single    1.522  0.020  1.522
 36D  C10  C11  single    1.525  0.020  1.525
 36D  C11  C12  single    1.522  0.020  1.522
 36D  C13  O3   double    1.203  0.020  1.203
 36D  C13  O4   single    1.325  0.020  1.325
 36D  N1   H1   single    0.890  0.020  1.040
 36D  N1   H2   single    0.890  0.020  1.040
 36D  C1   H4   single    0.970  0.020  1.090
 36D  O1   H5   single    0.850  0.020  0.980
 36D  C2   H6   single    0.970  0.020  1.090
 36D  C2   H7   single    0.970  0.020  1.090
 36D  C4   H8   single    0.930  0.020  1.080
 36D  C5   H9   single    0.930  0.020  1.080
 36D  C6   H10  single    0.930  0.020  1.080
 36D  C7   H11  single    0.970  0.020  1.090
 36D  N2   H12  single    0.860  0.020  1.020
 36D  C9   H13  single    0.970  0.020  1.090
 36D  C10  H14  single    0.970  0.020  1.090
 36D  C10  H15  single    0.970  0.020  1.090
 36D  C11  H16  single    0.970  0.020  1.090
 36D  C11  H17  single    0.970  0.020  1.090
 36D  C12  H18  single    0.970  0.020  1.090
 36D  C12  H19  single    0.970  0.020  1.090
 36D  C12  H20  single    0.970  0.020  1.090
 36D  O4   H21  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
 36D  H2   N1   H1   106.98  3.000
 36D  H2   N1   C1   110.46  3.000
 36D  H1   N1   C1   111.54  3.000
 36D  H4   C1   C7   107.16  3.000
 36D  H4   C1   C2   107.82  3.000
 36D  C7   C1   C2   109.42  3.000
 36D  H4   C1   N1   107.76  3.000
 36D  C7   C1   N1   114.62  3.000
 36D  C2   C1   N1   109.81  3.000
 36D  H5   O1   C7   107.13  3.000
 36D  H7   C2   H6   106.59  3.000
 36D  H7   C2   C3   110.34  3.000
 36D  H6   C2   C3   108.16  3.000
 36D  H7   C2   C1   108.87  3.000
 36D  H6   C2   C1   109.45  3.000
 36D  C3   C2   C1   113.22  3.000
 36D  C6   C3   S1   110.37  3.000
 36D  C6   C3   C2   128.49  3.000
 36D  S1   C3   C2   121.14  3.000
 36D  C4   S1   C3    92.45  3.000
 36D  H8   C4   C5   128.29  3.000
 36D  H8   C4   S1   120.49  3.000
 36D  C5   C4   S1   111.22  3.000
 36D  H9   C5   C6   124.03  3.000
 36D  H9   C5   C4   123.39  3.000
 36D  C6   C5   C4   112.59  3.000
 36D  H10  C6   C5   123.95  3.000
 36D  H10  C6   C3   122.68  3.000
 36D  C5   C6   C3   113.37  3.000
 36D  H11  C7   C8   108.68  3.000
 36D  H11  C7   O1   109.16  3.000
 36D  C8   C7   O1   109.40  3.000
 36D  H11  C7   C1   108.37  3.000
 36D  C8   C7   C1   109.66  3.000
 36D  O1   C7   C1   111.53  3.000
 36D  N2   C8   O2   123.08  3.000
 36D  N2   C8   C7   116.26  3.000
 36D  O2   C8   C7   120.58  3.000
 36D  H12  N2   C9   118.14  3.000
 36D  H12  N2   C8   118.96  3.000
 36D  C9   N2   C8   121.98  3.000
 36D  H13  C9   C13  108.06  3.000
 36D  H13  C9   C10  108.38  3.000
 36D  C13  C9   C10  110.48  3.000
 36D  H13  C9   N2   109.11  3.000
 36D  C13  C9   N2   110.39  3.000
 36D  C10  C9   N2   110.35  3.000
 36D  H15  C10  H14  106.53  3.000
 36D  H15  C10  C11  109.10  3.000
 36D  H14  C10  C11  110.13  3.000
 36D  H15  C10  C9   108.41  3.000
 36D  H14  C10  C9   109.44  3.000
 36D  C11  C10  C9   113.01  3.000
 36D  H17  C11  H16  106.27  3.000
 36D  H17  C11  C12  109.16  3.000
 36D  H16  C11  C12  109.99  3.000
 36D  H17  C11  C10  110.37  3.000
 36D  H16  C11  C10  109.16  3.000
 36D  C12  C11  C10  111.75  3.000
 36D  H20  C12  H19  107.69  3.000
 36D  H20  C12  H18  107.73  3.000
 36D  H19  C12  H18  107.60  3.000
 36D  H20  C12  C11  111.37  3.000
 36D  H19  C12  C11  111.08  3.000
 36D  H18  C12  C11  111.20  3.000
 36D  O4   C13  O3   124.23  3.000
 36D  O4   C13  C9   111.13  3.000
 36D  O3   C13  C9   124.62  3.000
 36D  H21  O4   C13  110.35  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
 36D  CONST_01  C5   C4   S1   C3      0.00   0.0  0
 36D  CONST_02  C4   C5   C6   C3      0.00   0.0  0
 36D  CONST_03  C5   C6   C3   S1      0.00   0.0  0
 36D  CONST_04  C6   C5   C4   S1      0.00   0.0  0
 36D  CONST_05  C6   C3   S1   C4      0.00   0.0  0
 36D  CONST_06  C4   S1   C3   C2    180.00   0.0  0
 36D  CONST_07  C5   C6   C3   C2    180.00   0.0  0
 36D  CONST_08  H8   C4   S1   C3    180.00   0.0  0
 36D  CONST_09  H9   C5   C6   C3    180.00   0.0  0
 36D  CONST_10  H10  C6   C3   S1    180.00   0.0  0
 36D  CONST_11  C9   N2   C8   C7    180.00   0.0  0
 36D  CONST_12  C9   N2   C8   O2      0.00   0.0  0
 36D  CONST_13  H12  N2   C8   C7      0.00   0.0  0
 36D  CONST_14  H21  O4   C13  C9    180.00   0.0  0
 36D  Var_01    S1   C3   C2   C1    -65.80  30.0  2
 36D  Var_02    C12  C11  C10  C9   -177.45  30.0  3
 36D  Var_03    H18  C12  C11  C10   179.86  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
 36D  chir_01  C1  N1  C2   C7   negativ
 36D  chir_02  C7  O1  C1   C8   positiv
 36D  chir_03  C9  N2  C10  C13  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
 36D  plan-1  C2   0.020
 36D  plan-1  C3   0.020
 36D  plan-1  S1   0.020
 36D  plan-1  C4   0.020
 36D  plan-1  C5   0.020
 36D  plan-1  C6   0.020
 36D  plan-1  H8   0.020
 36D  plan-1  H9   0.020
 36D  plan-1  H10  0.020
 36D  plan-2  C7   0.020
 36D  plan-2  C8   0.020
 36D  plan-2  O2   0.020
 36D  plan-2  N2   0.020
 36D  plan-2  C9   0.020
 36D  plan-2  H12  0.020
 36D  plan-3  C9   0.020
 36D  plan-3  C13  0.020
 36D  plan-3  O3   0.020
 36D  plan-3  O4   0.020
 36D  plan-3  H21  0.020

