# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 15:44:36 2021
#   Inital geometry file: a 65 line input string
#   Ligand name: (2~{R})-2-azanyl-3-[[(2~{R})-2-azanyl-3-oxidanylidene-propyl]disulfanyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSSC[C@H](N)C(N)=O)C=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
 MV5  MV5  (2~{R})-2-azanyl-3-[[(2~{R})-2-azanyl-3-oxidanylidene-propyl]disulfanyl]propanamide  ligand  26  13  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MV5
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
 MV5  C8   C  C1    0   0.180  -3.5201  1.4178  -11.9299
 MV5  C10  C  CH1   0  -0.208  -2.2164  2.1869  -11.9404
 MV5  O9   O  O     0  -0.366  -3.7178  0.4094  -12.5574
 MV5  C16  C  CH2   0  -0.579  -2.5075  3.6184  -12.3785
 MV5  C19  C  CH2   0  -0.563  -1.4196  6.5591  -10.1107
 MV5  N22  N  NH2   0  -0.761  -3.5886  5.4880   -9.6884
 MV5  N12  N  NH2   0  -0.773  -1.1567  1.6268  -12.7382
 MV5  S17  S  S2    0  -0.036  -0.9377  4.5547  -12.3346
 MV5  S18  S  S2    0  -0.037  -1.5779  6.4592  -11.9188
 MV5  C20  C  CH1   0  -0.203  -2.1932  5.4966   -9.3337
 MV5  C68  C  C     0   0.501  -1.9332  5.7583   -7.8421
 MV5  N69  N  NH2   0  -0.794  -0.8236  5.1913   -7.3516
 MV5  O70  O  O     0  -0.483  -2.6820  6.4609   -7.1804
 MV5  H1   H  H     0   0.189  -4.3049  1.8530  -11.2841
 MV5  H2   H  HCH1  0   0.278  -1.8868  2.2234  -10.8936
 MV5  H3   H  HCH2  0   0.305  -3.2206  4.1088  -11.7155
 MV5  H4   H  HCH2  0   0.286  -2.9036  3.6391  -13.3958
 MV5  H5   H  HCH2  0   0.288  -0.3620  6.5282   -9.8492
 MV5  H6   H  HCH2  0   0.290  -1.7885  7.5599   -9.8661
 MV5  H8   H  HNH2  0   0.349  -4.0226  6.3659   -9.4282
 MV5  H10  H  HNH2  0   0.362  -0.8821  0.7214  -12.3802
 MV5  H11  H  HNH2  0   0.351  -1.4716  1.4773  -13.6894
 MV5  H13  H  HCH1  0   0.256  -1.7703  4.5201   -9.5941
 MV5  H14  H  HNH2  0   0.404  -0.5452  5.3450   -6.3956
 MV5  H15  H  HNH2  0   0.406  -0.2386  4.5938   -7.9100
 MV5  H7   H  HNH2  0   0.357  -4.0714  4.7670   -9.1672

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
 MV5  C16  S17  single  1.828  0.020  1.828
 MV5  C16  C10  single  1.525  0.020  1.525
 MV5  N12  C10  single  1.440  0.020  1.440
 MV5  O9   C8   double  1.204  0.020  1.204
 MV5  S17  S18  single  2.052  0.020  2.052
 MV5  C8   C10  single  1.514  0.020  1.514
 MV5  S18  C19  single  1.818  0.020  1.818
 MV5  C19  C20  single  1.527  0.020  1.527
 MV5  N22  C20  single  1.440  0.020  1.440
 MV5  C20  C68  single  1.536  0.020  1.536
 MV5  C68  N69  single  1.339  0.020  1.339
 MV5  C68  O70  double  1.222  0.020  1.222
 MV5  C8   H1   single  0.930  0.020  1.080
 MV5  C10  H2   single  0.970  0.020  1.090
 MV5  C16  H3   single  0.970  0.020  1.090
 MV5  C16  H4   single  0.970  0.020  1.090
 MV5  C19  H5   single  0.970  0.020  1.090
 MV5  C19  H6   single  0.970  0.020  1.090
 MV5  N22  H7   single  0.890  0.020  1.040
 MV5  N22  H8   single  0.890  0.020  1.040
 MV5  N12  H10  single  0.890  0.020  1.040
 MV5  N12  H11  single  0.890  0.020  1.040
 MV5  C20  H13  single  0.970  0.020  1.090
 MV5  N69  H14  single  0.860  0.020  1.020
 MV5  N69  H15  single  0.860  0.020  1.020

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
 MV5  H1   C8   O9   121.17  3.000
 MV5  H1   C8   C10  114.54  3.000
 MV5  O9   C8   C10  124.28  3.000
 MV5  H2   C10  N12  108.68  3.000
 MV5  H2   C10  C16  107.46  3.000
 MV5  N12  C10  C16  110.27  3.000
 MV5  H2   C10  C8   105.59  3.000
 MV5  N12  C10  C8   116.11  3.000
 MV5  C16  C10  C8   108.33  3.000
 MV5  H4   C16  H3   108.71  3.000
 MV5  H4   C16  S17  108.92  3.000
 MV5  H3   C16  S17  108.46  3.000
 MV5  H4   C16  C10  110.78  3.000
 MV5  H3   C16  C10  111.86  3.000
 MV5  S17  C16  C10  108.05  3.000
 MV5  H6   C19  H5   107.43  3.000
 MV5  H6   C19  C20  110.60  3.000
 MV5  H5   C19  C20  110.48  3.000
 MV5  H6   C19  S18  104.08  3.000
 MV5  H5   C19  S18  108.76  3.000
 MV5  C20  C19  S18  115.07  3.000
 MV5  H8   N22  H7   106.29  3.000
 MV5  H8   N22  C20  110.28  3.000
 MV5  H7   N22  C20  109.86  3.000
 MV5  H11  N12  H10  106.54  3.000
 MV5  H11  N12  C10  110.42  3.000
 MV5  H10  N12  C10  110.60  3.000
 MV5  S18  S17  C16  102.26  3.000
 MV5  S17  S18  C19  103.03  3.000
 MV5  H13  C20  C68  108.50  3.000
 MV5  H13  C20  N22  108.07  3.000
 MV5  C68  C20  N22  113.84  3.000
 MV5  H13  C20  C19  107.68  3.000
 MV5  C68  C20  C19  106.84  3.000
 MV5  N22  C20  C19  111.71  3.000
 MV5  O70  C68  N69  123.57  3.000
 MV5  O70  C68  C20  121.34  3.000
 MV5  N69  C68  C20  115.07  3.000
 MV5  H15  N69  H14  117.18  3.000
 MV5  H15  N69  C68  122.02  3.000
 MV5  H14  N69  C68  120.79  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
 MV5  CONST_01  H14  N69  C68  C20  180.00   0.0  0
 MV5  CONST_02  H15  N69  C68  C20    0.00   0.0  0
 MV5  Var_01    C20  C19  S18  S17  -57.03  30.0  3
 MV5  Var_02    H3   C16  S17  S18  -28.82  30.0  1

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
 MV5  chir_01  C10  C16  N12  C8   positiv
 MV5  chir_02  C20  N22  C19  C68  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
 MV5  plan-1  C20  0.020
 MV5  plan-1  C68  0.020
 MV5  plan-1  N69  0.020
 MV5  plan-1  O70  0.020
 MV5  plan-1  H14  0.020
 MV5  plan-1  H15  0.020
 MV5  plan-2  C8   0.020
 MV5  plan-2  C10  0.020
 MV5  plan-2  O9   0.020
 MV5  plan-2  H1   0.020

