# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 10:59:00 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: (3R,4S,5S)-3-methoxy-5-methyl-4-(methylamino)heptanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)[C@H](NC)[C@@H](CC(O)=O)OC
#
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
 3WT  3WT  '(3R,4S,5S)-3-methoxy-5-methyl-4-(methylamino)heptanoic acid'  peptide  34  14  .  2022-09-22  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_3WT
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
 3WT  N3   N  NH1    0  -0.590   0.3513   1.6743   0.2214
 3WT  C20  C  CH1    0   0.077  -0.5690  -0.5555   0.7095
 3WT  C21  C  CH1    0  -0.239   1.9064  -0.2977   0.0379
 3WT  C19  C  CH1    0  -0.060   0.4655   0.2576  -0.0997
 3WT  C26  C  CH2    0  -0.592  -1.8222   0.2259   1.0872
 3WT  C27  C  C      0   0.425  -2.5783   0.9492  -0.0355
 3WT  O5   O  O2     0  -0.485  -0.8885  -1.7133  -0.0423
 3WT  O6   O  O      0  -0.609  -2.4276   0.5570  -1.2085
 3WT  C23  C  CH2    0  -0.418   2.8716   0.5055  -0.8438
 3WT  C24  C  CH3    0  -0.670   4.3464   0.1857  -0.6278
 3WT  C22  C  CH3    0  -0.653   2.0237  -1.7903  -0.2634
 3WT  C25  C  CH3    0  -0.531   0.9432   2.1173   1.4646
 3WT  C28  C  CH3    0  -0.401  -1.3007  -2.8041   0.7307
 3WT  H23  H  HCH1   0   0.181  -0.0902  -0.8725   1.6530
 3WT  H24  H  HCH1   0   0.202   2.2209  -0.1575   1.0817
 3WT  H29  H  HCH1   0   0.217   0.1663   0.1705  -1.1482
 3WT  H30  H  HCH2   0   0.224  -2.5247  -0.4683   1.5686
 3WT  H31  H  HCH2   0   0.217  -1.5801   0.9490   1.8678
 3WT  H40  H  HCH2   0   0.209   2.6098   0.3472  -1.8964
 3WT  H41  H  HCH2   0   0.212   2.7348   1.5737  -0.6567
 3WT  H42  H  HCH3   0   0.214   4.6211   0.2948   0.4239
 3WT  H43  H  HCH3   0   0.219   4.6044  -0.8287  -0.9310
 3WT  H44  H  HCH3   0   0.227   4.9786   0.8638  -1.2024
 3WT  H45  H  HCH3   0   0.231   1.4785  -2.4032   0.4519
 3WT  H46  H  HCH3   0   0.207   1.6503  -2.0281  -1.2611
 3WT  H47  H  HCH3   0   0.218   3.0653  -2.1108  -0.2165
 3WT  H49  H  HCH3   0   0.229   0.7299   3.1778   1.6046
 3WT  H50  H  HCH3   0   0.220   0.4993   1.5879   2.3094
 3WT  H51  H  HCH3   0   0.196   2.0314   1.9909   1.5416
 3WT  H52  H  HCH3   0   0.192  -0.5347  -3.1143   1.4544
 3WT  H53  H  HCH3   0   0.201  -2.2239  -2.6112   1.2904
 3WT  H54  H  HCH3   0   0.225  -1.4880  -3.6418   0.0577
 3WT  H1   H  HNH1   0   0.345   0.7032   2.2311  -0.5432
 3WT  OXT  O  OC    -1  -0.643  -3.3453   1.8666   0.3343

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
 3WT  O6   C27  deloc   1.246  0.020  1.246
 3WT  C27  C26  single  1.535  0.020  1.535
 3WT  C26  C20  single  1.524  0.020  1.524
 3WT  C20  O5   single  1.417  0.020  1.417
 3WT  C20  C19  single  1.545  0.020  1.545
 3WT  C28  O5   single  1.399  0.020  1.399
 3WT  C22  C21  single  1.527  0.020  1.527
 3WT  C19  C21  single  1.550  0.020  1.550
 3WT  C19  N3   single  1.457  0.020  1.457
 3WT  C21  C23  single  1.534  0.020  1.534
 3WT  C23  C24  single  1.524  0.020  1.524
 3WT  N3   C25  single  1.446  0.020  1.446
 3WT  C20  H23  single  0.970  0.020  1.090
 3WT  C21  H24  single  0.970  0.020  1.090
 3WT  C19  H29  single  0.970  0.020  1.090
 3WT  C26  H30  single  0.970  0.020  1.090
 3WT  C26  H31  single  0.970  0.020  1.090
 3WT  C23  H40  single  0.970  0.020  1.090
 3WT  C23  H41  single  0.970  0.020  1.090
 3WT  C24  H42  single  0.970  0.020  1.090
 3WT  C24  H43  single  0.970  0.020  1.090
 3WT  C24  H44  single  0.970  0.020  1.090
 3WT  C22  H45  single  0.970  0.020  1.090
 3WT  C22  H46  single  0.970  0.020  1.090
 3WT  C22  H47  single  0.970  0.020  1.090
 3WT  C25  H49  single  0.970  0.020  1.090
 3WT  C25  H50  single  0.970  0.020  1.090
 3WT  C25  H51  single  0.970  0.020  1.090
 3WT  C28  H52  single  0.970  0.020  1.090
 3WT  C28  H53  single  0.970  0.020  1.090
 3WT  C28  H54  single  0.970  0.020  1.090
 3WT  N3   H1   single  0.890  0.020  1.040
 3WT  C27  OXT  deloc   1.252  0.020  1.252

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
 3WT  H1   N3   C25  109.84  3.000
 3WT  H1   N3   C19  110.01  3.000
 3WT  C25  N3   C19  117.07  3.000
 3WT  H23  C20  O5   108.44  3.000
 3WT  H23  C20  C26  106.96  3.000
 3WT  O5   C20  C26  111.40  3.000
 3WT  H23  C20  C19  107.96  3.000
 3WT  O5   C20  C19  107.65  3.000
 3WT  C26  C20  C19  114.24  3.000
 3WT  H24  C21  C22  106.86  3.000
 3WT  H24  C21  C23  107.39  3.000
 3WT  C22  C21  C23  110.48  3.000
 3WT  H24  C21  C19  107.73  3.000
 3WT  C23  C21  C19  110.25  3.000
 3WT  C22  C21  C19  113.82  3.000
 3WT  H29  C19  C21  108.11  3.000
 3WT  H29  C19  C20  106.08  3.000
 3WT  C21  C19  C20  112.80  3.000
 3WT  H29  C19  N3   105.50  3.000
 3WT  C21  C19  N3   113.67  3.000
 3WT  C20  C19  N3   110.11  3.000
 3WT  H31  C26  H30  104.31  3.000
 3WT  H31  C26  C27  108.68  3.000
 3WT  H30  C26  C27  107.66  3.000
 3WT  H31  C26  C20  109.54  3.000
 3WT  H30  C26  C20  108.08  3.000
 3WT  C27  C26  C20  117.73  3.000
 3WT  OXT  C27  O6   125.66  3.000
 3WT  OXT  C27  C26  115.54  3.000
 3WT  O6   C27  C26  118.74  3.000
 3WT  C28  O5   C20  114.23  3.000
 3WT  H41  C23  H40  106.00  3.000
 3WT  H41  C23  C24  107.57  3.000
 3WT  H40  C23  C24  109.68  3.000
 3WT  H41  C23  C21  109.54  3.000
 3WT  H40  C23  C21  109.02  3.000
 3WT  C24  C23  C21  114.67  3.000
 3WT  H44  C24  H43  107.15  3.000
 3WT  H44  C24  H42  107.41  3.000
 3WT  H43  C24  H42  107.53  3.000
 3WT  H44  C24  C23  110.84  3.000
 3WT  H43  C24  C23  112.64  3.000
 3WT  H42  C24  C23  111.02  3.000
 3WT  H47  C22  H46  107.58  3.000
 3WT  H47  C22  H45  106.53  3.000
 3WT  H46  C22  H45  107.86  3.000
 3WT  H47  C22  C21  110.61  3.000
 3WT  H46  C22  C21  111.53  3.000
 3WT  H45  C22  C21  112.47  3.000
 3WT  H51  C25  H50  107.04  3.000
 3WT  H51  C25  H49  107.26  3.000
 3WT  H50  C25  H49  107.02  3.000
 3WT  H51  C25  N3   115.50  3.000
 3WT  H50  C25  N3   110.51  3.000
 3WT  H49  C25  N3   109.15  3.000
 3WT  H54  C28  H53  107.78  3.000
 3WT  H54  C28  H52  108.02  3.000
 3WT  H53  C28  H52  107.49  3.000
 3WT  H54  C28  O5   107.97  3.000
 3WT  H53  C28  O5   113.13  3.000
 3WT  H52  C28  O5   112.25  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
 3WT  Var_01  O6   C27  C26  C20    22.36  30.0  2
 3WT  Var_02  H52  C28  O5   C20   -59.25  30.0  3
 3WT  Var_03  H42  C24  C23  C21   -54.51  30.0  3
 3WT  Var_04  H49  C25  N3   C19  -176.51  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
 3WT  chir_01  C20  C26  O5   C19  negativ
 3WT  chir_02  C21  C23  C19  C22  negativ
 3WT  chir_03  C19  N3   C20  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
 3WT  plan-1  C26  0.020
 3WT  plan-1  C27  0.020
 3WT  plan-1  O6   0.020
 3WT  plan-1  OXT  0.020

