# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 12:33:27 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: D-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: 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
 ORD  ORD  'D-ornithine              '  D-peptide  20  9  .  2016-04-26  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_ORD
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
 ORD  N    N  NH2    0  -0.815  21.2724  24.1418  15.9316
 ORD  CA   C  CH1    0  -0.168  22.3414  23.1452  15.8514
 ORD  CB   C  CH2    0  -0.414  23.0333  23.2378  14.4936
 ORD  CG   C  CH2    0  -0.436  23.7702  24.5501  14.2510
 ORD  CD   C  CH2    0  -0.267  24.5143  24.5589  12.9240
 ORD  NE   N  NH2    0  -0.797  25.2062  25.8235  12.7157
 ORD  C    C  C      0   0.388  21.7546  21.7253  16.0566
 ORD  H    H  HNH2   0   0.335  20.8051  24.0627  16.8271
 ORD  H2   H  HNH2   0   0.336  21.6788  25.0694  15.9325
 ORD  HA   H  HCH1   0   0.164  23.1078  23.3018  16.6263
 ORD  HB2  H  HCH2   0   0.205  23.7527  22.4156  14.4112
 ORD  HB3  H  HCH2   0   0.202  22.2881  23.0787  13.7087
 ORD  HG2  H  HCH2   0   0.210  23.0763  25.3958  14.2600
 ORD  HG3  H  HCH2   0   0.206  24.4843  24.7224  15.0652
 ORD  HD2  H  HCH2   0   0.184  25.1800  23.6838  12.8858
 ORD  HD3  H  HCH2   0   0.208  23.7932  24.4271  12.1122
 ORD  HE1  H  HNH2   0   0.334  25.9509  25.9102  13.3969
 ORD  HE2  H  HNH2   0   0.342  25.6656  25.8132  11.8139
 ORD  O    O  O      0  -0.609  20.8989  21.3451  15.2324
 ORD  OXT  O  OC    -1  -0.610  22.1959  21.0740  17.0261

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
 ORD  N   CA   single  1.458  0.019  1.458
 ORD  CA  CB   single  1.521  0.033  1.521
 ORD  CA  C    single  1.525  0.021  1.525
 ORD  CB  CG   single  1.524  0.020  1.524
 ORD  CG  CD   single  1.521  0.020  1.521
 ORD  CD  NE   single  1.456  0.020  1.456
 ORD  C   O    deloc   1.231  0.020  1.231
 ORD  C   OXT  deloc   1.249  0.020  1.249
 ORD  N   H    single  0.860  0.020  0.860
 ORD  N   H2   single  0.890  0.020  1.040
 ORD  CA  HA   single  0.970  0.020  0.970
 ORD  CB  HB2  single  0.970  0.020  1.090
 ORD  CB  HB3  single  0.970  0.020  1.090
 ORD  CG  HG2  single  0.970  0.020  1.090
 ORD  CG  HG3  single  0.970  0.020  1.090
 ORD  CD  HD2  single  0.970  0.020  1.090
 ORD  CD  HD3  single  0.970  0.020  1.090
 ORD  NE  HE1  single  0.890  0.020  1.040
 ORD  NE  HE2  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
 ORD  H2   N   H    104.83  3.000
 ORD  H2   N   CA   109.31  3.000
 ORD  H    N   CA   114.00  3.000
 ORD  HA   CA  C    110.00  3.000
 ORD  HA   CA  CB   109.00  3.000
 ORD  C    CA  CB   110.50  1.500
 ORD  HA   CA  N    110.00  3.000
 ORD  C    CA  N    111.00  2.800
 ORD  CB   CA  N    110.40  1.500
 ORD  HB3  CB  HB2  106.51  3.000
 ORD  HB3  CB  CG   109.90  3.000
 ORD  HB2  CB  CG   108.46  3.000
 ORD  HB3  CB  CA   108.70  3.000
 ORD  HB2  CB  CA   108.59  3.000
 ORD  CG   CB  CA   114.38  3.000
 ORD  HG3  CG  HG2  106.59  3.000
 ORD  HG3  CG  CD   109.16  3.000
 ORD  HG2  CG  CD   108.24  3.000
 ORD  HG3  CG  CB   109.38  3.000
 ORD  HG2  CG  CB   110.95  3.000
 ORD  CD   CG  CB   112.34  3.000
 ORD  HD3  CD  HD2  106.10  3.000
 ORD  HD3  CD  NE   108.15  3.000
 ORD  HD2  CD  NE   113.47  3.000
 ORD  HD3  CD  CG   108.92  3.000
 ORD  HD2  CD  CG   108.76  3.000
 ORD  NE   CD  CG   111.23  3.000
 ORD  HE2  NE  HE1  105.44  3.000
 ORD  HE2  NE  CD   109.53  3.000
 ORD  HE1  NE  CD   109.11  3.000
 ORD  OXT  C   O    126.63  3.000
 ORD  OXT  C   CA   120.80  1.700
 ORD  O    C   CA   120.80  1.700

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
 ORD  Var_01  CD   CG  CB  CA  176.39  30.0  3
 ORD  Var_02  NE   CD  CG  CB  179.86  30.0  3
 ORD  Var_03  HE1  NE  CD  CG   66.94  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
 ORD  chir_01  CA  N  CB  C  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
 ORD  plan-1  CA   0.020
 ORD  plan-1  C    0.020
 ORD  plan-1  O    0.020
 ORD  plan-1  OXT  0.020

