# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:13:48 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: N~5~-[(Z)-imino(methylsulfanyl)methyl]-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSC(=N)NCCC[C@H](N)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
 SMZ  SMZ  N~5~-[(Z)-imino(methylsulfanyl)methyl]-L-ornithine  ligand  27  13  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SMZ
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
 SMZ  C8    C  CH3    0  -0.804   5.7320   0.3832  -0.0661
 SMZ  S1    S  S2     0  -0.013   4.3146  -0.6946   0.2045
 SMZ  C2    C  CH1    0  -0.212  -3.2114  -0.5393   0.3170
 SMZ  C4    C  CH2    0  -0.449  -0.6610  -0.4140   0.1503
 SMZ  C5    C  CH2    0  -0.229   0.5183   0.4893  -0.1720
 SMZ  C1    C  C      0   0.384  -4.4916   0.3020   0.0861
 SMZ  N2    N  NH2    0  -0.786  -3.1931  -1.8377  -0.3393
 SMZ  C3    C  CH2    0  -0.420  -1.9902   0.2843  -0.1025
 SMZ  N6    N  NH1    0  -0.632   1.7686  -0.2127   0.0349
 SMZ  C7    C  C      0   0.284   2.9556   0.3696  -0.2673
 SMZ  N8    N  N      0  -0.656   3.0271   1.4996  -0.8443
 SMZ  H8    H  HCH3   0   0.276   5.8498   0.6390  -1.1174
 SMZ  H8A   H  HCH3   0   0.281   5.6670   1.2868   0.5372
 SMZ  H8B   H  HCH3   0   0.297   6.6070  -0.1823   0.2475
 SMZ  H2    H  HCH1   0   0.208  -3.1254  -0.7182   1.3956
 SMZ  H4    H  HCH2   0   0.227  -0.6015  -1.3251  -0.4475
 SMZ  H4A   H  HCH2   0   0.214  -0.6078  -0.7227   1.2006
 SMZ  H5    H  HCH2   0   0.226   0.4680   0.8142  -1.2134
 SMZ  H5A   H  HCH2   0   0.214   0.4751   1.3975   0.4415
 SMZ  HN2   H  HNH2   0   0.334  -3.9470  -2.4001   0.0373
 SMZ  HN2A  H  HNH2   0   0.322  -3.4488  -1.6997  -1.3110
 SMZ  H3    H  HCH2   0   0.208  -2.0716   0.5315  -1.1684
 SMZ  H3A   H  HCH2   0   0.219  -2.0151   1.2338   0.4366
 SMZ  HN6   H  HNH1   0   0.390   1.7671  -0.9178   0.7550
 SMZ  HN8   H  H      0   0.350   3.9737   1.7734  -1.0720
 SMZ  O1    O  O      0  -0.608  -5.2706  -0.0665  -0.8153
 SMZ  O2    O  OC    -1  -0.625  -4.6274   1.3049   0.8184

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
 SMZ  S1  C8    single  1.801  0.020  1.801
 SMZ  C8  H8    single  0.970  0.020  1.090
 SMZ  C8  H8A   single  0.970  0.020  1.090
 SMZ  C8  H8B   single  0.970  0.020  1.090
 SMZ  C7  S1    single  1.789  0.020  1.789
 SMZ  C3  C2    single  1.532  0.020  1.532
 SMZ  C1  C2    single  1.549  0.020  1.549
 SMZ  C2  N2    single  1.455  0.020  1.455
 SMZ  C2  H2    single  0.970  0.020  1.090
 SMZ  C1  O2    deloc   1.249  0.020  1.249
 SMZ  C5  C4    single  1.520  0.020  1.520
 SMZ  C4  C3    single  1.523  0.020  1.523
 SMZ  C4  H4    single  0.970  0.020  1.090
 SMZ  C4  H4A   single  0.970  0.020  1.090
 SMZ  N6  C5    single  1.449  0.020  1.449
 SMZ  C5  H5    single  0.970  0.020  1.090
 SMZ  C5  H5A   single  0.970  0.020  1.090
 SMZ  O1  C1    deloc   1.247  0.020  1.247
 SMZ  N2  HN2   single  0.890  0.020  1.040
 SMZ  N2  HN2A  single  0.890  0.020  1.040
 SMZ  C3  H3    single  0.970  0.020  1.090
 SMZ  C3  H3A   single  0.970  0.020  1.090
 SMZ  C7  N6    single  1.356  0.020  1.356
 SMZ  N6  HN6   single  0.890  0.020  1.040
 SMZ  N8  C7    double  1.271  0.020  1.271
 SMZ  N8  HN8   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
 SMZ  H8B   C8  H8A  108.65  3.000
 SMZ  H8B   C8  H8   108.27  3.000
 SMZ  H8A   C8  H8   110.29  3.000
 SMZ  H8B   C8  S1   106.17  3.000
 SMZ  H8A   C8  S1   111.50  3.000
 SMZ  H8    C8  S1   111.77  3.000
 SMZ  C7    S1  C8   101.66  3.000
 SMZ  H2    C2  C3   107.13  3.000
 SMZ  H2    C2  N2   107.28  3.000
 SMZ  C3    C2  N2   110.26  3.000
 SMZ  H2    C2  C1   107.45  3.000
 SMZ  N2    C2  C1   115.33  3.000
 SMZ  C3    C2  C1   109.03  3.000
 SMZ  H4A   C4  H4   106.69  3.000
 SMZ  H4A   C4  C3   109.31  3.000
 SMZ  H4    C4  C3   109.85  3.000
 SMZ  H4A   C4  C5   109.45  3.000
 SMZ  H4    C4  C5   109.73  3.000
 SMZ  C3    C4  C5   111.69  3.000
 SMZ  H5A   C5  H5   106.57  3.000
 SMZ  H5A   C5  N6   110.82  3.000
 SMZ  H5    C5  N6   108.67  3.000
 SMZ  H5A   C5  C4   110.06  3.000
 SMZ  H5    C5  C4   110.07  3.000
 SMZ  N6    C5  C4   110.57  3.000
 SMZ  O1    C1  O2   126.37  3.000
 SMZ  O1    C1  C2   117.61  3.000
 SMZ  O2    C1  C2   116.01  3.000
 SMZ  HN2A  N2  HN2  104.13  3.000
 SMZ  HN2A  N2  C2   107.92  3.000
 SMZ  HN2   N2  C2   108.56  3.000
 SMZ  H3A   C3  H3   106.38  3.000
 SMZ  H3A   C3  C4   109.67  3.000
 SMZ  H3    C3  C4   109.23  3.000
 SMZ  H3A   C3  C2   108.31  3.000
 SMZ  H3    C3  C2   109.16  3.000
 SMZ  C4    C3  C2   113.83  3.000
 SMZ  HN6   N6  C7   117.44  3.000
 SMZ  HN6   N6  C5   116.09  3.000
 SMZ  C7    N6  C5   121.03  3.000
 SMZ  N8    C7  N6   122.15  3.000
 SMZ  N8    C7  S1   127.29  3.000
 SMZ  N6    C7  S1   110.53  3.000
 SMZ  HN8   N8  C7   113.31  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
 SMZ  CONST_01  C5   N6  C7  S1   180.00   0.0  0
 SMZ  CONST_02  N8   C7  N6  C5     0.00   0.0  0
 SMZ  CONST_04  HN8  N8  C7  S1     0.00   0.0  0
 SMZ  Var_01    N6   C7  S1  C8  -172.02  30.0  1
 SMZ  Var_02    C5   C4  C3  C2  -175.15  30.0  1
 SMZ  Var_03    C7   N6  C5  C4   175.98  30.0  1
 SMZ  Var_04    N6   C5  C4  C3  -178.12  30.0  2
 SMZ  Var_05    H8   C8  S1  C7   -64.80  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
 SMZ  chir_01  C2  C3  C1  N2  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
 SMZ  plan-1  S1   0.020
 SMZ  plan-1  C5   0.020
 SMZ  plan-1  N6   0.020
 SMZ  plan-1  C7   0.020
 SMZ  plan-1  N8   0.020
 SMZ  plan-1  HN6  0.020
 SMZ  plan-1  HN8  0.020
 SMZ  plan-2  C2   0.020
 SMZ  plan-2  C1   0.020
 SMZ  plan-2  O1   0.020
 SMZ  plan-2  O2   0.020

