# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 10:32:34 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: N~5~-dodecanoyl-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCC(=O)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
 O12  O12  N~5~-dodecanoyl-L-ornithine  L-peptide  55  22  .  2012-08-28  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_O12
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
 O12  N     N  NH2    0  -0.788  20.2226  32.7934  -17.1833
 O12  CA    C  CH1    0  -0.212  19.8877  34.1366  -17.6354
 O12  CB    C  CH2    0  -0.414  20.0088  35.1273  -16.4730
 O12  CG    C  CH2    0  -0.463  19.0743  34.8206  -15.3111
 O12  CD    C  CH2    0  -0.234  19.2325  35.8151  -14.1723
 O12  NE    N  NH1    0  -0.642  18.3152  35.5038  -13.0950
 O12  C1    C  C      0   0.549  18.1522  36.2822  -12.0147
 O12  O1    O  O      0  -0.503  18.7998  37.3074  -11.8407
 O12  C2    C  CH2    0  -0.578  17.0778  35.8306  -11.0454
 O12  C3    C  CH2    0  -0.419  17.4317  36.0813   -9.5855
 O12  C4    C  CH2    0  -0.411  18.5912  35.2313   -9.0815
 O12  C5    C  CH2    0  -0.416  18.8753  35.4460   -7.5999
 O12  C6    C  CH2    0  -0.420  20.0165  34.5781   -7.0823
 O12  C7    C  CH2    0  -0.417  20.3694  34.8070   -5.6152
 O12  C8    C  CH2    0  -0.421  19.2579  34.4446   -4.6350
 O12  C9    C  CH2    0  -0.417  19.7086  34.5406   -3.1810
 O12  C10   C  CH2    0  -0.413  18.6510  34.1211   -2.1641
 O12  C11   C  CH2    0  -0.422  17.4474  35.0539   -2.0812
 O12  C12   C  CH3    0  -0.657  16.4461  34.6209   -1.0190
 O12  C     C  C      0   0.383  20.7213  34.6529  -18.8395
 O12  O     O  O      0  -0.616  20.2753  35.6659  -19.4180
 O12  OXT   O  OC    -1  -0.601  21.7699  34.0359  -19.1138
 O12  HN    H  HNH2   0   0.332  19.9499  32.1318  -17.9005
 O12  HNA   H  HNH2   0   0.321  21.2343  32.7267  -17.1550
 O12  HA    H  HCH1   0   0.203  18.8360  34.1270  -17.9453
 O12  HB    H  HCH2   0   0.206  21.0460  35.1377  -16.1160
 O12  HBA   H  HCH2   0   0.218  19.8024  36.1330  -16.8470
 O12  HG    H  HCH2   0   0.218  18.0384  34.8392  -15.6663
 O12  HGA   H  HCH2   0   0.227  19.2630  33.8089  -14.9442
 O12  HD    H  HCH2   0   0.223  20.2637  35.7977  -13.8055
 O12  HDA   H  HCH2   0   0.224  19.0447  36.8299  -14.5342
 O12  HNE   H  HNH1   0   0.397  17.7689  34.6610  -13.1703
 O12  H2    H  HCH2   0   0.270  16.1694  36.3865  -11.3004
 O12  H2A   H  HCH2   0   0.243  16.8388  34.7750  -11.1984
 O12  H3    H  HCH2   0   0.218  17.6583  37.1403   -9.4398
 O12  H3A   H  HCH2   0   0.225  16.5459  35.8739   -8.9789
 O12  H4    H  HCH2   0   0.207  18.3671  34.1734   -9.2577
 O12  H4A   H  HCH2   0   0.213  19.4957  35.4517   -9.6576
 O12  H5    H  HCH2   0   0.206  19.1140  36.5009   -7.4237
 O12  H5A   H  HCH2   0   0.213  17.9614  35.2439   -7.0330
 O12  H6    H  HCH2   0   0.205  19.7640  33.5224   -7.2320
 O12  H6A   H  HCH2   0   0.214  20.9055  34.7650   -7.6932
 O12  H7    H  HCH2   0   0.213  21.2584  34.2165   -5.3706
 O12  H7A   H  HCH2   0   0.205  20.6550  35.8546   -5.4682
 O12  H8    H  HCH2   0   0.218  18.3929  35.0921   -4.8005
 O12  H8A   H  HCH2   0   0.203  18.9158  33.4231   -4.8385
 O12  H9    H  HCH2   0   0.213  20.5945  33.9115   -3.0491
 O12  H9A   H  HCH2   0   0.205  20.0331  35.5651   -2.9660
 O12  H10   H  HCH2   0   0.204  18.3071  33.1069   -2.3970
 O12  H10A  H  HCH2   0   0.213  19.1142  34.0615   -1.1738
 O12  H11   H  HCH2   0   0.208  17.7961  36.0690   -1.8662
 O12  H11A  H  HCH2   0   0.215  16.9437  35.1061   -3.0500
 O12  H12   H  HCH3   0   0.214  16.9081  34.5882   -0.0303
 O12  H12A  H  HCH3   0   0.224  15.5973  35.3034   -0.9641
 O12  H12B  H  HCH3   0   0.215  16.0542  33.6242   -1.2303

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
 O12  CA   N     single  1.458  0.019  1.458
 O12  N    HN    single  0.890  0.020  1.040
 O12  N    HNA   single  0.890  0.020  1.040
 O12  C    CA    single  1.525  0.021  1.525
 O12  CA   CB    single  1.521  0.033  1.521
 O12  CA   HA    single  0.970  0.020  0.970
 O12  CB   CG    single  1.522  0.020  1.522
 O12  CB   HB    single  0.970  0.020  1.090
 O12  CB   HBA   single  0.970  0.020  1.090
 O12  CG   CD    single  1.520  0.020  1.520
 O12  CG   HG    single  0.970  0.020  1.090
 O12  CG   HGA   single  0.970  0.020  1.090
 O12  CD   NE    single  1.449  0.020  1.449
 O12  CD   HD    single  0.970  0.020  1.090
 O12  CD   HDA   single  0.970  0.020  1.090
 O12  NE   C1    single  1.341  0.020  1.341
 O12  NE   HNE   single  0.860  0.020  1.020
 O12  C1   O1    double  1.225  0.020  1.225
 O12  C1   C2    single  1.516  0.020  1.516
 O12  C2   C3    single  1.523  0.020  1.523
 O12  C2   H2    single  0.970  0.020  1.090
 O12  C2   H2A   single  0.970  0.020  1.090
 O12  C3   C4    single  1.523  0.020  1.523
 O12  C3   H3    single  0.970  0.020  1.090
 O12  C3   H3A   single  0.970  0.020  1.090
 O12  C4   C5    single  1.524  0.020  1.524
 O12  C4   H4    single  0.970  0.020  1.090
 O12  C4   H4A   single  0.970  0.020  1.090
 O12  C5   C6    single  1.524  0.020  1.524
 O12  C5   H5    single  0.970  0.020  1.090
 O12  C5   H5A   single  0.970  0.020  1.090
 O12  C6   C7    single  1.526  0.020  1.526
 O12  C6   H6    single  0.970  0.020  1.090
 O12  C6   H6A   single  0.970  0.020  1.090
 O12  C7   C8    single  1.526  0.020  1.526
 O12  C7   H7    single  0.970  0.020  1.090
 O12  C7   H7A   single  0.970  0.020  1.090
 O12  C8   C9    single  1.525  0.020  1.525
 O12  C8   H8    single  0.970  0.020  1.090
 O12  C8   H8A   single  0.970  0.020  1.090
 O12  C9   C10   single  1.526  0.020  1.526
 O12  C9   H9    single  0.970  0.020  1.090
 O12  C9   H9A   single  0.970  0.020  1.090
 O12  C10  C11   single  1.525  0.020  1.525
 O12  C10  H10   single  0.970  0.020  1.090
 O12  C10  H10A  single  0.970  0.020  1.090
 O12  C11  C12   single  1.523  0.020  1.523
 O12  C11  H11   single  0.970  0.020  1.090
 O12  C11  H11A  single  0.970  0.020  1.090
 O12  C12  H12   single  0.970  0.020  1.090
 O12  C12  H12A  single  0.970  0.020  1.090
 O12  C12  H12B  single  0.970  0.020  1.090
 O12  O    C     deloc   1.231  0.020  1.231
 O12  C    OXT   deloc   1.247  0.020  1.247

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
 O12  HNA   N    HN    104.21  3.000
 O12  HNA   N    CA    107.38  3.000
 O12  HN    N    CA    108.70  3.000
 O12  HA    CA   C     110.00  3.000
 O12  HA    CA   CB    109.00  3.000
 O12  C     CA   CB    110.50  1.500
 O12  HA    CA   N     110.00  3.000
 O12  CB    CA   N     110.40  1.500
 O12  C     CA   N     111.00  2.800
 O12  HBA   CB   HB    106.33  3.000
 O12  HBA   CB   CG    109.32  3.000
 O12  HB    CB   CG    109.50  3.000
 O12  HBA   CB   CA    108.70  3.000
 O12  HB    CB   CA    109.13  3.000
 O12  CG    CB   CA    113.60  3.000
 O12  HGA   CG   HG    106.74  3.000
 O12  HGA   CG   CD    109.65  3.000
 O12  HG    CG   CD    109.28  3.000
 O12  HGA   CG   CB    109.69  3.000
 O12  HG    CG   CB    109.24  3.000
 O12  CD    CG   CB    112.09  3.000
 O12  HDA   CD   HD    106.70  3.000
 O12  HDA   CD   NE    109.68  3.000
 O12  HD    CD   NE    110.11  3.000
 O12  HDA   CD   CG    109.96  3.000
 O12  HD    CD   CG    109.79  3.000
 O12  NE    CD   CG    110.52  3.000
 O12  HNE   NE   C1    118.68  3.000
 O12  HNE   NE   CD    117.88  3.000
 O12  C1    NE   CD    123.44  3.000
 O12  C2    C1   O1    122.22  3.000
 O12  C2    C1   NE    115.35  3.000
 O12  O1    C1   NE    122.39  3.000
 O12  H2A   C2   H2    106.04  3.000
 O12  H2A   C2   C3    110.12  3.000
 O12  H2    C2   C3    109.42  3.000
 O12  H2A   C2   C1    110.68  3.000
 O12  H2    C2   C1    106.73  3.000
 O12  C3    C2   C1    113.53  3.000
 O12  H3A   C3   H3    106.13  3.000
 O12  H3A   C3   C4    109.10  3.000
 O12  H3    C3   C4    109.80  3.000
 O12  H3A   C3   C2    108.20  3.000
 O12  H3    C3   C2    109.61  3.000
 O12  C4    C3   C2    113.71  3.000
 O12  H4A   C4   H4    106.18  3.000
 O12  H4A   C4   C5    109.22  3.000
 O12  H4    C4   C5    109.30  3.000
 O12  H4A   C4   C3    110.02  3.000
 O12  H4    C4   C3    109.26  3.000
 O12  C5    C4   C3    112.64  3.000
 O12  H5A   C5   H5    106.04  3.000
 O12  H5A   C5   C6    110.13  3.000
 O12  H5    C5   C6    109.29  3.000
 O12  H5A   C5   C4    108.78  3.000
 O12  H5    C5   C4    109.43  3.000
 O12  C6    C5   C4    112.93  3.000
 O12  H6A   C6   H6    105.98  3.000
 O12  H6A   C6   C7    108.85  3.000
 O12  H6    C6   C7    109.22  3.000
 O12  H6A   C6   C5    108.74  3.000
 O12  H6    C6   C5    109.25  3.000
 O12  C7    C6   C5    114.47  3.000
 O12  H7A   C7   H7    105.91  3.000
 O12  H7A   C7   C8    109.32  3.000
 O12  H7    C7   C8    108.66  3.000
 O12  H7A   C7   C6    109.43  3.000
 O12  H7    C7   C6    108.76  3.000
 O12  C8    C7   C6    114.43  3.000
 O12  H8A   C8   H8    106.07  3.000
 O12  H8A   C8   C9    109.14  3.000
 O12  H8    C8   C9    109.93  3.000
 O12  H8A   C8   C7    109.23  3.000
 O12  H8    C8   C7    109.79  3.000
 O12  C9    C8   C7    112.47  3.000
 O12  H9A   C9   H9    105.90  3.000
 O12  H9A   C9   C10   109.36  3.000
 O12  H9    C9   C10   108.83  3.000
 O12  H9A   C9   C8    109.47  3.000
 O12  H9    C9   C8    108.53  3.000
 O12  C10   C9   C8    114.41  3.000
 O12  H10A  C10  H10   105.94  3.000
 O12  H10A  C10  C11   108.55  3.000
 O12  H10   C10  C11   109.26  3.000
 O12  H10A  C10  C9    108.94  3.000
 O12  H10   C10  C9    109.28  3.000
 O12  C11   C10  C9    114.52  3.000
 O12  H11A  C11  H11   106.05  3.000
 O12  H11A  C11  C12   109.20  3.000
 O12  H11   C11  C12   109.64  3.000
 O12  H11A  C11  C10   110.16  3.000
 O12  H11   C11  C10   109.05  3.000
 O12  C12   C11  C10   112.52  3.000
 O12  H12B  C12  H12A  107.56  3.000
 O12  H12B  C12  H12   107.45  3.000
 O12  H12A  C12  H12   107.61  3.000
 O12  H12B  C12  C11   111.14  3.000
 O12  H12A  C12  C11   111.65  3.000
 O12  H12   C12  C11   111.22  3.000
 O12  OXT   C    O     126.84  3.000
 O12  OXT   C    CA    120.80  1.700
 O12  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
 O12  CONST_01  O1   C1   NE   CD      0.00   0.0  0
 O12  CONST_02  C2   C1   NE   CD    180.00   0.0  0
 O12  CONST_03  HNE  NE   C1   O1    180.00   0.0  0
 O12  Var_01    CD   CG   CB   CA    179.42  30.0  3
 O12  Var_02    NE   CD   CG   CB    179.15  30.0  3
 O12  Var_03    C1   NE   CD   CG   -173.89  30.0  3
 O12  Var_04    C3   C2   C1   NE    143.76  30.0  3
 O12  Var_05    C4   C3   C2   C1    -67.43  30.0  3
 O12  Var_06    C5   C4   C3   C2   -176.88  30.0  3
 O12  Var_07    C6   C5   C4   C3    178.86  30.0  3
 O12  Var_08    C7   C6   C5   C4    177.59  30.0  3
 O12  Var_09    C8   C7   C6   C5     64.00  30.0  3
 O12  Var_10    C9   C8   C7   C6    173.56  30.0  3
 O12  Var_11    C10  C9   C8   C7   -177.14  30.0  3
 O12  Var_12    C11  C10  C9   C8    -67.70  30.0  3
 O12  Var_13    C12  C11  C10  C9   -177.93  30.0  3
 O12  Var_14    H12  C12  C11  C10    59.14  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
 O12  chir_01  CA  N  C  CB  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
 O12  plan-1  CD   0.020
 O12  plan-1  NE   0.020
 O12  plan-1  C1   0.020
 O12  plan-1  O1   0.020
 O12  plan-1  C2   0.020
 O12  plan-1  HNE  0.020
 O12  plan-2  CA   0.020
 O12  plan-2  C    0.020
 O12  plan-2  O    0.020
 O12  plan-2  OXT  0.020

