# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 09:56:47 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: N~5~-[(1Z)-2-oxoethanimidoyl]-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(=N)C=O)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
 WT2  WT2  N~5~-[(1Z)-2-oxoethanimidoyl]-L-ornithine  ligand  26  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_WT2
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
 WT2  CH    C  C1    0   0.115  -4.6238   0.5567   0.4202
 WT2  CZ    C  C     0   0.336  -3.4806  -0.2770  -0.1107
 WT2  NH    N  N     0  -0.646  -3.6478  -1.3738  -0.7419
 WT2  NE    N  NH1   0  -0.648  -2.2726   0.2495   0.1535
 WT2  CD    C  CH2   0  -0.227  -1.0415  -0.3702  -0.2731
 WT2  CG    C  CH2   0  -0.469   0.1546   0.3868   0.2795
 WT2  CB    C  CH2   0  -0.432   1.4701  -0.2534  -0.1372
 WT2  CA    C  CH1   0  -0.209   2.6856   0.5509   0.3460
 WT2  C     C  C     0   0.521   3.9532  -0.2568   0.0989
 WT2  OA2   O  O     0  -0.440   4.7582  -0.0194  -0.7666
 WT2  OA1   O  OH1   0  -0.593   4.0700  -1.2740   0.9454
 WT2  N     N  NH2   0  -0.775   2.7044   1.8555  -0.2703
 WT2  OH    O  O     0  -0.347  -5.7706   0.2311   0.2767
 WT2  HA1   H  HOH1  0   0.481   4.8703  -1.7837   0.7488
 WT2  HA    H  HCH1  0   0.267   2.5937   0.6846   1.4289
 WT2  HN1   H  HNH2  0   0.355   3.4573   2.4158   0.1080
 WT2  HN2   H  HNH2  0   0.344   2.8858   1.7687  -1.2628
 WT2  HB1C  H  HCH2  0   0.246   1.5200  -1.2712   0.2555
 WT2  HB2C  H  HCH2  0   0.234   1.5174  -0.3393  -1.2282
 WT2  HG1C  H  HCH2  0   0.242   0.1255   1.4226  -0.0650
 WT2  HG2C  H  HCH2  0   0.234   0.0938   0.4130   1.3717
 WT2  HD1C  H  HCH2  0   0.230  -1.0244  -1.4107   0.0651
 WT2  HD2C  H  HCH2  0   0.228  -0.9952  -0.4010  -1.3677
 WT2  HH1N  H  H     0   0.333  -4.6387  -1.5839  -0.8075
 WT2  HH    H  H     0   0.220  -4.3462   1.4849   0.9479
 WT2  HNE   H  HNH1  0   0.401  -2.2198   1.1404   0.6193

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
 WT2  OA1  C     single  1.328  0.020  1.328
 WT2  C    OA2   double  1.206  0.020  1.206
 WT2  C    CA    single  1.523  0.020  1.523
 WT2  CA   N     single  1.443  0.020  1.443
 WT2  CA   CB    single  1.536  0.020  1.536
 WT2  CB   CG    single  1.521  0.020  1.521
 WT2  CG   CD    single  1.520  0.020  1.520
 WT2  CD   NE    single  1.443  0.020  1.443
 WT2  NE   CZ    single  1.344  0.020  1.344
 WT2  CZ   NH    double  1.276  0.020  1.276
 WT2  CZ   CH    single  1.511  0.020  1.511
 WT2  CH   OH    double  1.201  0.020  1.201
 WT2  OA1  HA1   single  0.850  0.020  0.980
 WT2  CA   HA    single  0.970  0.020  1.090
 WT2  N    HN1   single  0.890  0.020  1.040
 WT2  N    HN2   single  0.890  0.020  1.040
 WT2  CB   HB1C  single  0.970  0.020  1.090
 WT2  CB   HB2C  single  0.970  0.020  1.090
 WT2  CG   HG1C  single  0.970  0.020  1.090
 WT2  CG   HG2C  single  0.970  0.020  1.090
 WT2  CD   HD1C  single  0.970  0.020  1.090
 WT2  CD   HD2C  single  0.970  0.020  1.090
 WT2  NH   HH1N  single  0.890  0.020  1.040
 WT2  CH   HH    single  0.930  0.020  1.080
 WT2  NE   HNE   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
 WT2  HH    CH   OH    121.71  3.000
 WT2  HH    CH   CZ    116.22  3.000
 WT2  OH    CH   CZ    122.07  3.000
 WT2  NE    CZ   NH    123.48  3.000
 WT2  NH    CZ   CH    123.27  3.000
 WT2  NE    CZ   CH    113.25  3.000
 WT2  HH1N  NH   CZ    109.74  3.000
 WT2  HNE   NE   CD    118.17  3.000
 WT2  HNE   NE   CZ    119.00  3.000
 WT2  CD    NE   CZ    122.72  3.000
 WT2  HD2C  CD   HD1C  106.34  3.000
 WT2  HD2C  CD   CG    110.11  3.000
 WT2  HD1C  CD   CG    110.42  3.000
 WT2  HD2C  CD   NE    110.09  3.000
 WT2  HD1C  CD   NE    109.29  3.000
 WT2  CG    CD   NE    110.49  3.000
 WT2  HG2C  CG   HG1C  106.90  3.000
 WT2  HG2C  CG   CB    109.37  3.000
 WT2  HG1C  CG   CB    109.62  3.000
 WT2  HG2C  CG   CD    109.34  3.000
 WT2  HG1C  CG   CD    109.69  3.000
 WT2  CB    CG   CD    111.80  3.000
 WT2  HB2C  CB   HB1C  106.44  3.000
 WT2  HB2C  CB   CA    108.68  3.000
 WT2  HB1C  CB   CA    109.81  3.000
 WT2  HB2C  CB   CG    110.07  3.000
 WT2  HB1C  CB   CG    109.47  3.000
 WT2  CA    CB   CG    112.20  3.000
 WT2  HA    CA   N     108.25  3.000
 WT2  HA    CA   C     107.16  3.000
 WT2  N     CA   C     113.54  3.000
 WT2  HA    CA   CB    107.98  3.000
 WT2  N     CA   CB    110.45  3.000
 WT2  C     CA   CB    109.26  3.000
 WT2  OA1   C    OA2   123.34  3.000
 WT2  OA2   C    CA    124.58  3.000
 WT2  OA1   C    CA    112.08  3.000
 WT2  HA1   OA1  C     110.25  3.000
 WT2  HN2   N    HN1   106.29  3.000
 WT2  HN2   N    CA    110.08  3.000
 WT2  HN1   N    CA    110.53  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
 WT2  CONST_01  CD    NE   CZ  CH   180.00   0.0  0
 WT2  CONST_02  CD    NE   CZ  NH     0.00   0.0  0
 WT2  CONST_03  HNE   NE   CZ  CH     0.00   0.0  0
 WT2  CONST_04  HH1N  NH   CZ  CH     0.00   0.0  0
 WT2  CONST_05  HA1   OA1  C   CA   180.00   0.0  0
 WT2  Var_01    CG    CD   NE  CZ  -174.85  30.0  1
 WT2  Var_02    OH    CH   CZ  NH    -0.02  30.0  2
 WT2  Var_03    CB    CG   CD  NE   179.22  30.0  1
 WT2  Var_04    CA    CB   CG  CD   176.60  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
 WT2  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
 WT2  plan-1  CH    0.020
 WT2  plan-1  CZ    0.020
 WT2  plan-1  NH    0.020
 WT2  plan-1  NE    0.020
 WT2  plan-1  CD    0.020
 WT2  plan-1  HH1N  0.020
 WT2  plan-1  HNE   0.020
 WT2  plan-2  CA    0.020
 WT2  plan-2  C     0.020
 WT2  plan-2  OA2   0.020
 WT2  plan-2  OA1   0.020
 WT2  plan-2  HA1   0.020
 WT2  plan-3  CH    0.020
 WT2  plan-3  CZ    0.020
 WT2  plan-3  OH    0.020
 WT2  plan-3  HH    0.020

