# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 05:11:43 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: N-[(2R,3S)-3-amino-2-hydroxy-4-(thiophen-2-yl)butyl]-L-norvaline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@H](NC[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
 TVA  TVA  N-[(2R,3S)-3-amino-2-hydroxy-4-(thiophen-2-yl)butyl]-L-norvaline  peptide  40  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TVA
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
 TVA  C19  C  CH2    0  -0.497   2.6138   0.5269  -0.7790
 TVA  C20  C  CR5    0  -0.148   3.9435   0.0301  -0.3204
 TVA  C21  C  CR15   0  -0.243   4.7817  -0.8541  -0.9333
 TVA  C22  C  CR15   0  -0.185   5.9473  -1.1500  -0.1714
 TVA  N4   N  NH2    0  -0.783   1.4604  -1.6124  -0.1583
 TVA  C23  C  CH1    0  -0.125   1.4462  -0.1656  -0.0447
 TVA  S2   S  S2     0   0.192   4.5840   0.4957   1.2144
 TVA  C24  C  CR15   0  -0.472   5.9744  -0.4914   1.0181
 TVA  C25  C  CH1    0   0.019   0.0910   0.3616  -0.5376
 TVA  O6   O  OH1    0  -0.665   0.0614   1.7768  -0.5754
 TVA  C26  C  CH2    0  -0.265  -1.0674  -0.1860   0.2862
 TVA  N5   N  NH1    0  -0.608  -2.3400   0.2403  -0.2562
 TVA  C27  C  CH1    0  -0.160  -3.4683  -0.0754   0.5983
 TVA  C28  C  CH2    0  -0.426  -4.7387   0.5931   0.0630
 TVA  C29  C  CH2    0  -0.433  -4.7228   2.1189   0.0797
 TVA  C30  C  CH3    0  -0.658  -6.0556   2.7091  -0.3627
 TVA  C31  C  C      0   0.396  -3.7367  -1.5936   0.7212
 TVA  O7   O  O      0  -0.601  -3.3065  -2.3468  -0.1711
 TVA  O8   O  OC    -1  -0.625  -4.4151  -1.9321   1.7147
 TVA  H28  H  HCH2   0   0.254   2.5498   1.6083  -0.6480
 TVA  H29  H  HCH2   0   0.247   2.5248   0.3338  -1.8524
 TVA  H30  H  HCR5   0   0.257   4.5705  -1.2786  -1.9054
 TVA  H31  H  HCR5   0   0.263   6.7284  -1.8218  -0.4981
 TVA  H32  H  HNH2   0   0.338   1.4306  -1.8778  -1.1372
 TVA  H33  H  HCH1   0   0.221   1.5319   0.0753   1.0234
 TVA  H34  H  HCR5   0   0.291   6.7332  -0.5264   1.7841
 TVA  H35  H  HCH1   0   0.217  -0.0427   0.0453  -1.5793
 TVA  H36  H  HOH1   0   0.443   0.1339   2.1031   0.3288
 TVA  H37  H  HCH2   0   0.230  -1.0183  -1.2732   0.2824
 TVA  H38  H  HCH2   0   0.170  -0.9256   0.1293   1.3382
 TVA  H39  H  HNH1   0   0.330  -2.3011   1.2454  -0.3711
 TVA  H41  H  HCH1   0   0.168  -3.3065   0.3000   1.6259
 TVA  H42  H  HCH2   0   0.208  -4.9229   0.2399  -0.9581
 TVA  H43  H  HCH2   0   0.216  -5.5820   0.2509   0.6688
 TVA  H44  H  HCH2   0   0.213  -4.4829   2.4664   1.0895
 TVA  H45  H  HCH2   0   0.211  -3.9351   2.5070  -0.5727
 TVA  H46  H  HCH3   0   0.226  -6.0435   3.7991  -0.3293
 TVA  H47  H  HCH3   0   0.217  -6.2963   2.4128  -1.3853
 TVA  H48  H  HCH3   0   0.216  -6.8693   2.3662   0.2794
 TVA  H2   H  HNH2   0   0.354   2.3363  -1.9761   0.1976

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
 TVA  C19  C23  single    1.543  0.020  1.543
 TVA  C19  C20  single    1.492  0.020  1.492
 TVA  C20  C21  aromatic  1.364  0.020  1.364
 TVA  C20  S2   aromatic  1.727  0.020  1.727
 TVA  C21  C22  aromatic  1.424  0.020  1.424
 TVA  C22  C24  aromatic  1.360  0.020  1.360
 TVA  N4   C23  single    1.451  0.020  1.451
 TVA  C23  C25  single    1.535  0.020  1.535
 TVA  S2   C24  aromatic  1.716  0.020  1.716
 TVA  C25  C26  single    1.523  0.020  1.523
 TVA  C25  O6   single    1.416  0.020  1.416
 TVA  C26  N5   single    1.448  0.020  1.448
 TVA  N5   C27  single    1.450  0.020  1.450
 TVA  C27  C28  single    1.532  0.020  1.532
 TVA  C27  C31  single    1.547  0.020  1.547
 TVA  C28  C29  single    1.526  0.020  1.526
 TVA  C29  C30  single    1.523  0.020  1.523
 TVA  C31  O7   deloc     1.244  0.020  1.244
 TVA  C31  O8   deloc     1.250  0.020  1.250
 TVA  C19  H28  single    0.970  0.020  1.090
 TVA  C19  H29  single    0.970  0.020  1.090
 TVA  C21  H30  single    0.930  0.020  1.080
 TVA  C22  H31  single    0.930  0.020  1.080
 TVA  N4   H32  single    0.890  0.020  1.040
 TVA  C23  H33  single    0.970  0.020  1.090
 TVA  C24  H34  single    0.930  0.020  1.080
 TVA  C25  H35  single    0.970  0.020  1.090
 TVA  O6   H36  single    0.850  0.020  0.980
 TVA  C26  H37  single    0.970  0.020  1.090
 TVA  C26  H38  single    0.970  0.020  1.090
 TVA  N5   H39  single    0.890  0.020  1.040
 TVA  C27  H41  single    0.970  0.020  1.090
 TVA  C28  H42  single    0.970  0.020  1.090
 TVA  C28  H43  single    0.970  0.020  1.090
 TVA  C29  H44  single    0.970  0.020  1.090
 TVA  C29  H45  single    0.970  0.020  1.090
 TVA  C30  H46  single    0.970  0.020  1.090
 TVA  C30  H47  single    0.970  0.020  1.090
 TVA  C30  H48  single    0.970  0.020  1.090
 TVA  N4   H2   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
 TVA  H29  C19  H28  106.73  3.000
 TVA  H29  C19  C23  109.02  3.000
 TVA  H28  C19  C23  110.07  3.000
 TVA  H29  C19  C20  108.38  3.000
 TVA  H28  C19  C20  110.21  3.000
 TVA  C23  C19  C20  112.25  3.000
 TVA  S2   C20  C21  110.25  3.000
 TVA  S2   C20  C19  120.93  3.000
 TVA  C21  C20  C19  128.73  3.000
 TVA  H30  C21  C22  124.00  3.000
 TVA  H30  C21  C20  122.57  3.000
 TVA  C22  C21  C20  113.42  3.000
 TVA  H31  C22  C24  123.43  3.000
 TVA  H31  C22  C21  124.00  3.000
 TVA  C24  C22  C21  112.56  3.000
 TVA  H2   N4   H32  105.69  3.000
 TVA  H2   N4   C23  109.81  3.000
 TVA  H32  N4   C23  109.63  3.000
 TVA  H33  C23  C25  107.80  3.000
 TVA  H33  C23  N4   107.10  3.000
 TVA  C25  C23  N4   109.02  3.000
 TVA  H33  C23  C19  107.77  3.000
 TVA  C25  C23  C19  111.16  3.000
 TVA  N4   C23  C19  113.74  3.000
 TVA  C24  S2   C20   92.51  3.000
 TVA  H34  C24  S2   120.48  3.000
 TVA  H34  C24  C22  128.27  3.000
 TVA  S2   C24  C22  111.25  3.000
 TVA  H35  C25  C26  108.50  3.000
 TVA  H35  C25  O6   105.08  3.000
 TVA  C26  C25  O6   110.97  3.000
 TVA  H35  C25  C23  108.27  3.000
 TVA  O6   C25  C23  111.73  3.000
 TVA  C26  C25  C23  111.97  3.000
 TVA  H36  O6   C25  108.16  3.000
 TVA  H38  C26  H37  106.38  3.000
 TVA  H38  C26  N5   112.63  3.000
 TVA  H37  C26  N5   109.42  3.000
 TVA  H38  C26  C25  108.30  3.000
 TVA  H37  C26  C25  108.84  3.000
 TVA  N5   C26  C25  111.10  3.000
 TVA  H39  N5   C27  108.23  3.000
 TVA  H39  N5   C26  107.52  3.000
 TVA  C27  N5   C26  113.52  3.000
 TVA  H41  C27  C31  106.54  3.000
 TVA  H41  C27  C28  107.33  3.000
 TVA  C31  C27  C28  108.19  3.000
 TVA  H41  C27  N5   111.09  3.000
 TVA  C31  C27  N5   113.30  3.000
 TVA  C28  C27  N5   110.14  3.000
 TVA  H43  C28  H42  106.60  3.000
 TVA  H43  C28  C29  108.35  3.000
 TVA  H42  C28  C29  109.52  3.000
 TVA  H43  C28  C27  108.03  3.000
 TVA  H42  C28  C27  108.93  3.000
 TVA  C29  C28  C27  115.07  3.000
 TVA  H45  C29  H44  106.24  3.000
 TVA  H45  C29  C30  108.62  3.000
 TVA  H44  C29  C30  109.67  3.000
 TVA  H45  C29  C28  110.84  3.000
 TVA  H44  C29  C28  109.26  3.000
 TVA  C30  C29  C28  112.03  3.000
 TVA  H48  C30  H47  107.54  3.000
 TVA  H48  C30  H46  107.71  3.000
 TVA  H47  C30  H46  107.60  3.000
 TVA  H48  C30  C29  111.08  3.000
 TVA  H47  C30  C29  111.09  3.000
 TVA  H46  C30  C29  111.63  3.000
 TVA  O8   C31  O7   126.42  3.000
 TVA  O8   C31  C27  115.04  3.000
 TVA  O7   C31  C27  118.50  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
 TVA  CONST_01  C24  C22  C21  C20     0.00   0.0  0
 TVA  CONST_02  C22  C24  S2   C20     0.00   0.0  0
 TVA  CONST_03  C24  S2   C20  C21     0.00   0.0  0
 TVA  CONST_04  S2   C24  C22  C21     0.00   0.0  0
 TVA  CONST_05  S2   C20  C21  C22     0.00   0.0  0
 TVA  CONST_06  C22  C21  C20  C19   180.00   0.0  0
 TVA  CONST_07  C24  S2   C20  C19   180.00   0.0  0
 TVA  CONST_08  H31  C22  C21  C20   180.00   0.0  0
 TVA  CONST_09  H34  C24  S2   C20   180.00   0.0  0
 TVA  CONST_10  H30  C21  C20  S2    180.00   0.0  0
 TVA  Var_01    C23  C19  C20  C21   102.07  30.0  1
 TVA  Var_02    C27  N5   C26  C25  -171.01  30.0  3
 TVA  Var_03    C30  C29  C28  C27  -175.51  30.0  3
 TVA  Var_04    H46  C30  C29  C28   178.87  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
 TVA  chir_01  C23  C19  N4   C25  positiv
 TVA  chir_02  C25  O6   C23  C26  negativ
 TVA  chir_03  C27  N5   C28  C31  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
 TVA  plan-1  C19  0.020
 TVA  plan-1  C20  0.020
 TVA  plan-1  C21  0.020
 TVA  plan-1  C22  0.020
 TVA  plan-1  S2   0.020
 TVA  plan-1  C24  0.020
 TVA  plan-1  H30  0.020
 TVA  plan-1  H31  0.020
 TVA  plan-1  H34  0.020
 TVA  plan-2  C27  0.020
 TVA  plan-2  C31  0.020
 TVA  plan-2  O7   0.020
 TVA  plan-2  O8   0.020

