# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 13:20:16 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: N~5~-[(1E)-pentanimidoyl]-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC(=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
 LN6  LN6  N~5~-[(1E)-pentanimidoyl]-L-ornithine  ligand  35  15  .  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_LN6
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
 LN6  C     C  C      0   0.384   5.0573  -0.0948   0.1176
 LN6  N     N  NH2    0  -0.786   3.6481   1.9684  -0.3343
 LN6  CA    C  CH1    0  -0.215   3.7310   0.6775   0.3326
 LN6  CB    C  CH2    0  -0.415   2.5530  -0.2058  -0.0874
 LN6  CD    C  CH2    0  -0.214   0.0523  -0.5324  -0.1587
 LN6  NE    N  NH1    0  -0.644  -1.2210   0.0494   0.1890
 LN6  CG    C  CH2    0  -0.461   1.1939   0.3771   0.2677
 LN6  CZ    C  C      0   0.420  -2.4075  -0.5260  -0.1115
 LN6  OA1   O  O      0  -0.608   5.8372   0.3256  -0.7600
 LN6  OA2   O  OC    -1  -0.624   5.2313  -1.0958   0.8449
 LN6  CH1   C  CH2    0  -0.533  -3.6051   0.2699   0.3666
 LN6  NH2   N  N      0  -0.693  -2.4365  -1.6507  -0.7242
 LN6  CI1   C  CH2    0  -0.417  -6.1030   0.6470   0.3778
 LN6  CK1   C  CH3    0  -0.662  -7.4618   0.1703  -0.1149
 LN6  CT1   C  CH2    0  -0.443  -4.9552  -0.2117  -0.1403
 LN6  HN    H  HNH2   0   0.334   4.3488   2.5840   0.0606
 LN6  HNA   H  HNH2   0   0.322   3.9450   1.8394  -1.2954
 LN6  HA    H  HCH1   0   0.208   3.6335   0.8592   1.4102
 LN6  HB    H  HCH2   0   0.206   2.6063  -0.3795  -1.1695
 LN6  HBA   H  HCH2   0   0.218   2.6666  -1.1836   0.3861
 LN6  HD    H  HCH2   0   0.209   0.1614  -1.5132   0.3181
 LN6  HDA   H  HCH2   0   0.210   0.1014  -0.7118  -1.2385
 LN6  HNE   H  HNH1   0   0.387  -1.2229   0.9428   0.6507
 LN6  HG    H  HCH2   0   0.215   1.1402   0.5377   1.3504
 LN6  HGA   H  HCH2   0   0.225   1.0794   1.3584  -0.1994
 LN6  HH1   H  HCH2   0   0.258  -3.5990   0.2569   1.4614
 LN6  HH1A  H  HCH2   0   0.248  -3.4621   1.3172   0.0833
 LN6  HNH2  H  H      0   0.329  -3.3925  -1.9526  -0.8649
 LN6  HI1   H  HCH2   0   0.216  -5.9449   1.6862   0.0739
 LN6  HI1A  H  HCH2   0   0.215  -6.0890   0.6457   1.4719
 LN6  HK1   H  HCH3   0   0.228  -8.2663   0.8020   0.2635
 LN6  HK1A  H  HCH3   0   0.217  -7.5160   0.1842  -1.2053
 LN6  HK1B  H  HCH3   0   0.218  -7.6627  -0.8514   0.2116
 LN6  HT1   H  HCH2   0   0.225  -4.9665  -0.2079  -1.2349
 LN6  HT1A  H  HCH2   0   0.221  -5.1240  -1.2486   0.1684

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
 LN6  OA1  C     deloc   1.247  0.020  1.247
 LN6  C    CA    single  1.550  0.020  1.550
 LN6  C    OA2   deloc   1.249  0.020  1.249
 LN6  CA   N     single  1.455  0.020  1.455
 LN6  N    HN    single  0.890  0.020  1.040
 LN6  N    HNA   single  0.890  0.020  1.040
 LN6  CB   CA    single  1.531  0.020  1.531
 LN6  CA   HA    single  0.970  0.020  1.090
 LN6  CG   CB    single  1.521  0.020  1.521
 LN6  CB   HB    single  0.970  0.020  1.090
 LN6  CB   HBA   single  0.970  0.020  1.090
 LN6  NE   CD    single  1.442  0.020  1.442
 LN6  CD   CG    single  1.521  0.020  1.521
 LN6  CD   HD    single  0.970  0.020  1.090
 LN6  CD   HDA   single  0.970  0.020  1.090
 LN6  CZ   NE    single  1.352  0.020  1.352
 LN6  NE   HNE   single  0.860  0.020  1.020
 LN6  CG   HG    single  0.970  0.020  1.090
 LN6  CG   HGA   single  0.970  0.020  1.090
 LN6  NH2  CZ    double  1.281  0.020  1.281
 LN6  CH1  CZ    single  1.515  0.020  1.515
 LN6  CT1  CH1   single  1.520  0.020  1.520
 LN6  CH1  HH1   single  0.970  0.020  1.090
 LN6  CH1  HH1A  single  0.970  0.020  1.090
 LN6  NH2  HNH2  single  0.890  0.020  1.040
 LN6  CK1  CI1   single  1.522  0.020  1.522
 LN6  CI1  CT1   single  1.524  0.020  1.524
 LN6  CI1  HI1   single  0.970  0.020  1.090
 LN6  CI1  HI1A  single  0.970  0.020  1.090
 LN6  CK1  HK1   single  0.970  0.020  1.090
 LN6  CK1  HK1A  single  0.970  0.020  1.090
 LN6  CK1  HK1B  single  0.970  0.020  1.090
 LN6  CT1  HT1   single  0.970  0.020  1.090
 LN6  CT1  HT1A  single  0.970  0.020  1.090

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
 LN6  OA2   C    OA1   126.34  3.000
 LN6  OA2   C    CA    115.96  3.000
 LN6  OA1   C    CA    117.70  3.000
 LN6  HNA   N    HN    104.14  3.000
 LN6  HNA   N    CA    107.74  3.000
 LN6  HN    N    CA    108.73  3.000
 LN6  HA    CA   CB    107.26  3.000
 LN6  HA    CA   N     107.34  3.000
 LN6  CB    CA   N     110.01  3.000
 LN6  HA    CA   C     107.14  3.000
 LN6  CB    CA   C     109.44  3.000
 LN6  N     CA   C     115.29  3.000
 LN6  HBA   CB   HB    106.30  3.000
 LN6  HBA   CB   CG    109.56  3.000
 LN6  HB    CB   CG    109.53  3.000
 LN6  HBA   CB   CA    108.51  3.000
 LN6  HB    CB   CA    108.94  3.000
 LN6  CG    CB   CA    113.73  3.000
 LN6  HDA   CD   HD    106.13  3.000
 LN6  HDA   CD   CG    109.92  3.000
 LN6  HD    CD   CG    109.79  3.000
 LN6  HDA   CD   NE    110.07  3.000
 LN6  HD    CD   NE    110.12  3.000
 LN6  CG    CD   NE    110.72  3.000
 LN6  HNE   NE   CZ    118.58  3.000
 LN6  HNE   NE   CD    118.07  3.000
 LN6  CZ    NE   CD    123.31  3.000
 LN6  HGA   CG   HG    106.60  3.000
 LN6  HGA   CG   CD    109.79  3.000
 LN6  HG    CG   CD    109.14  3.000
 LN6  HGA   CG   CB    109.75  3.000
 LN6  HG    CG   CB    109.31  3.000
 LN6  CD    CG   CB    112.10  3.000
 LN6  NH2   CZ   CH1   126.45  3.000
 LN6  CH1   CZ   NE    113.56  3.000
 LN6  NH2   CZ   NE    119.98  3.000
 LN6  HH1A  CH1  HH1   105.64  3.000
 LN6  HH1A  CH1  CT1   109.44  3.000
 LN6  HH1   CH1  CT1   109.55  3.000
 LN6  HH1A  CH1  CZ    108.53  3.000
 LN6  HH1   CH1  CZ    107.75  3.000
 LN6  CT1   CH1  CZ    115.48  3.000
 LN6  HNH2  NH2  CZ    110.47  3.000
 LN6  HI1A  CI1  HI1   106.08  3.000
 LN6  HI1A  CI1  CT1   109.24  3.000
 LN6  HI1   CI1  CT1   109.38  3.000
 LN6  HI1A  CI1  CK1   109.56  3.000
 LN6  HI1   CI1  CK1   109.67  3.000
 LN6  CT1   CI1  CK1   112.69  3.000
 LN6  HK1B  CK1  HK1A  107.56  3.000
 LN6  HK1B  CK1  HK1   107.62  3.000
 LN6  HK1A  CK1  HK1   107.61  3.000
 LN6  HK1B  CK1  CI1   111.15  3.000
 LN6  HK1A  CK1  CI1   111.32  3.000
 LN6  HK1   CK1  CI1   111.39  3.000
 LN6  HT1A  CT1  HT1   106.48  3.000
 LN6  HT1A  CT1  CI1   108.75  3.000
 LN6  HT1   CT1  CI1   109.27  3.000
 LN6  HT1A  CT1  CH1   110.06  3.000
 LN6  HT1   CT1  CH1   109.97  3.000
 LN6  CI1   CT1  CH1   112.14  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
 LN6  CONST_01  NH2   CZ   NE   CD      0.00   0.0  0
 LN6  CONST_02  CH1   CZ   NE   CD    180.00   0.0  0
 LN6  CONST_03  HNH2  NH2  CZ   NE    180.00   0.0  0
 LN6  CONST_04  HNE   NE   CZ   CH1     0.00   0.0  0
 LN6  Var_01    CD    CG   CB   CA   -179.69  30.0  1
 LN6  Var_02    NE    CD   CG   CB   -179.87  30.0  1
 LN6  Var_03    CT1   CH1  CZ   NE    170.40  30.0  2
 LN6  Var_04    CZ    NE   CD   CG    177.84  30.0  2
 LN6  Var_05    CI1   CT1  CH1  CZ   -179.59  30.0  1
 LN6  Var_06    CK1   CI1  CT1  CH1  -179.63  30.0  1
 LN6  Var_07    HK1   CK1  CI1  CT1  -179.69  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
 LN6  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
 LN6  plan-1  CD    0.020
 LN6  plan-1  NE    0.020
 LN6  plan-1  CZ    0.020
 LN6  plan-1  CH1   0.020
 LN6  plan-1  NH2   0.020
 LN6  plan-1  HNE   0.020
 LN6  plan-1  HNH2  0.020
 LN6  plan-2  C     0.020
 LN6  plan-2  CA    0.020
 LN6  plan-2  OA1   0.020
 LN6  plan-2  OA2   0.020

