# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 01:01:43 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: N~5~-[(1E)-2-sulfanylethanimidoyl]-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(=N)CS)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
 VUR  VUR  N~5~-[(1E)-2-sulfanylethanimidoyl]-L-ornithine  ligand  28  13  .  2022-07-22  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VUR
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
 VUR  C     C  C     0   0.520  -4.4896  -0.3306  -0.0870
 VUR  N     N  NH2   0  -0.776  -3.3173   1.8563  -0.0519
 VUR  C1    C  C     0   0.419   2.9407  -0.1292   0.0693
 VUR  C2    C  CH2   0  -0.669   4.0595   0.8765  -0.1510
 VUR  S3    S  S2    0  -0.226   5.7141   0.1692  -0.3179
 VUR  CA    C  CH1   0  -0.205  -3.2547   0.4759  -0.4663
 VUR  CB    C  CH2   0  -0.436  -2.0122  -0.2095   0.1196
 VUR  CD    C  CH2   0  -0.231   0.4980  -0.2661   0.2475
 VUR  NE    N  NH1   0  -0.633   1.7139   0.4199  -0.1234
 VUR  CG    C  CH2   0  -0.452  -0.7143   0.4378  -0.3412
 VUR  NH    N  N     0  -0.662   3.0775  -1.3504   0.4057
 VUR  OA1   O  OH1   0  -0.594  -4.5828  -1.4609  -0.7791
 VUR  OA2   O  O     0  -0.441  -5.2903  -0.0027   0.7530
 VUR  HN    H  HNH2  0   0.355  -4.0993   2.3236  -0.4923
 VUR  HNA   H  HNH2  0   0.343  -3.4773   1.9150   0.9465
 VUR  H2    H  HCH2  0   0.299   3.8412   1.5063  -1.0134
 VUR  H2A   H  HCH2  0   0.313   4.1096   1.5394   0.7158
 VUR  HS3   H  HSH1  0   0.236   5.5523  -0.3643  -1.5341
 VUR  HA    H  HCH1  0   0.266  -3.1701   0.4490  -1.5574
 VUR  HB    H  HCH2  0   0.233  -2.0727  -0.1808   1.2131
 VUR  HBA   H  HCH2  0   0.244  -2.0107  -1.2653  -0.1610
 VUR  HD    H  HCH2  0   0.230   0.5549  -1.2919  -0.1193
 VUR  HDA   H  HCH2  0   0.214   0.3979  -0.3315   1.3389
 VUR  HNE   H  HNH1  0   0.387   1.6608   1.4256  -0.1644
 VUR  HG    H  HCH2  0   0.228  -0.6563   0.4104  -1.4334
 VUR  HGA   H  HCH2  0   0.233  -0.7102   1.4918  -0.0527
 VUR  HNH   H  H     0   0.325   4.0647  -1.5820   0.4570
 VUR  HOA1  H  HOH1  0   0.480  -5.3562  -1.9666  -0.4875

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
 VUR  OA2  C     double  1.206  0.020  1.206
 VUR  CA   C     single  1.523  0.020  1.523
 VUR  C    OA1   single  1.329  0.020  1.329
 VUR  N    CA    single  1.443  0.020  1.443
 VUR  N    HN    single  0.890  0.020  1.040
 VUR  N    HNA   single  0.890  0.020  1.040
 VUR  NH   C1    double  1.274  0.020  1.274
 VUR  C1   NE    single  1.358  0.020  1.358
 VUR  C1   C2    single  1.520  0.020  1.520
 VUR  C2   S3    single  1.807  0.020  1.807
 VUR  C2   H2    single  0.970  0.020  1.090
 VUR  C2   H2A   single  0.970  0.020  1.090
 VUR  S3   HS3   single  1.200  0.020  1.300
 VUR  CA   CB    single  1.535  0.020  1.535
 VUR  CA   HA    single  0.970  0.020  1.090
 VUR  CG   CB    single  1.522  0.020  1.522
 VUR  CB   HB    single  0.970  0.020  1.090
 VUR  CB   HBA   single  0.970  0.020  1.090
 VUR  CD   CG    single  1.520  0.020  1.520
 VUR  CD   NE    single  1.444  0.020  1.444
 VUR  CD   HD    single  0.970  0.020  1.090
 VUR  CD   HDA   single  0.970  0.020  1.090
 VUR  NE   HNE   single  0.890  0.020  1.040
 VUR  CG   HG    single  0.970  0.020  1.090
 VUR  CG   HGA   single  0.970  0.020  1.090
 VUR  NH   HNH   single  0.890  0.020  1.040
 VUR  OA1  HOA1  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
 VUR  OA2   C    OA1  123.20  3.000
 VUR  OA1   C    CA   112.19  3.000
 VUR  OA2   C    CA   124.61  3.000
 VUR  HNA   N    HN   106.27  3.000
 VUR  HNA   N    CA   110.21  3.000
 VUR  HN    N    CA   110.52  3.000
 VUR  NH    C1   NE   121.47  3.000
 VUR  NE    C1   C2   112.14  3.000
 VUR  NH    C1   C2   126.39  3.000
 VUR  H2A   C2   H2   106.64  3.000
 VUR  H2A   C2   S3   105.60  3.000
 VUR  H2    C2   S3   109.66  3.000
 VUR  H2A   C2   C1   108.67  3.000
 VUR  H2    C2   C1   110.45  3.000
 VUR  S3    C2   C1   115.36  3.000
 VUR  HS3   S3   C2    97.43  3.000
 VUR  HA    CA   CB   107.88  3.000
 VUR  HA    CA   N    108.25  3.000
 VUR  CB    CA   N    110.66  3.000
 VUR  HA    CA   C    107.33  3.000
 VUR  CB    CA   C    108.95  3.000
 VUR  N     CA   C    113.57  3.000
 VUR  HBA   CB   HB   106.37  3.000
 VUR  HBA   CB   CG   109.39  3.000
 VUR  HB    CB   CG   109.76  3.000
 VUR  HBA   CB   CA   109.55  3.000
 VUR  HB    CB   CA   108.94  3.000
 VUR  CG    CB   CA   112.63  3.000
 VUR  HDA   CD   HD   106.43  3.000
 VUR  HDA   CD   CG   109.86  3.000
 VUR  HD    CD   CG   110.29  3.000
 VUR  HDA   CD   NE   111.11  3.000
 VUR  HD    CD   NE   108.45  3.000
 VUR  CG    CD   NE   110.61  3.000
 VUR  HNE   NE   CD   116.10  3.000
 VUR  HNE   NE   C1   117.19  3.000
 VUR  CD    NE   C1   122.14  3.000
 VUR  HGA   CG   HG   106.71  3.000
 VUR  HGA   CG   CD   109.95  3.000
 VUR  HG    CG   CD   109.43  3.000
 VUR  HGA   CG   CB   109.49  3.000
 VUR  HG    CG   CB   109.69  3.000
 VUR  CD    CG   CB   111.46  3.000
 VUR  HNH   NH   C1   109.66  3.000
 VUR  HOA1  OA1  C    110.08  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
 VUR  CONST_01  CD    NE   C1  C2   180.00   0.0  0
 VUR  CONST_02  NH    C1   NE  CD     0.00   0.0  0
 VUR  CONST_03  HNH   NH   C1  C2     0.00   0.0  0
 VUR  CONST_04  HNE   NE   C1  C2     0.00   0.0  0
 VUR  CONST_05  HOA1  OA1  C   CA   180.00   0.0  0
 VUR  Var_01    CG    CD   NE  C1  -168.04  30.0  1
 VUR  Var_02    NH    C1   C2  S3    14.86  30.0  2
 VUR  Var_03    CD    CG   CB  CA  -179.66  30.0  1
 VUR  Var_04    NE    CD   CG  CB  -175.89  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
 VUR  chir_01  CA  C  N  CB  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
 VUR  plan-1  C1    0.020
 VUR  plan-1  C2    0.020
 VUR  plan-1  CD    0.020
 VUR  plan-1  NE    0.020
 VUR  plan-1  NH    0.020
 VUR  plan-1  HNE   0.020
 VUR  plan-1  HNH   0.020
 VUR  plan-2  C     0.020
 VUR  plan-2  CA    0.020
 VUR  plan-2  OA1   0.020
 VUR  plan-2  OA2   0.020
 VUR  plan-2  HOA1  0.020

