# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 00:14:07 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: L-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[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
 NLE  NLE  'L-norleucine             '  L-peptide  21  9  .  2014-12-01  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_NLE
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
 NLE  N    N  NH2    0  -0.788  16.5670  39.4696  18.0132
 NLE  CA   C  CH1    0  -0.206  15.8733  40.5364  17.3029
 NLE  C    C  C      0   0.380  16.7924  41.6430  16.7251
 NLE  O    O  O      0  -0.618  16.3225  42.3126  15.7811
 NLE  OXT  O  OC    -1  -0.605  17.9036  41.7992  17.2712
 NLE  CB   C  CH2    0  -0.411  14.8337  41.1861  18.2227
 NLE  CG   C  CH2    0  -0.396  13.7330  40.2421  18.6888
 NLE  CD   C  CH2    0  -0.417  12.7161  40.9156  19.6026
 NLE  CE   C  CH3    0  -0.659  11.6050  39.9749  20.0501
 NLE  H    H  HNH2   0   0.330  17.1428  38.9610  17.3523
 NLE  HN2  H  HNH2   0   0.320  17.2338  39.9099  18.6384
 NLE  HA   H  HCH1   0   0.196  15.3308  40.0796  16.4672
 NLE  HB2  H  HCH2   0   0.199  15.3476  41.6087  19.0954
 NLE  HB3  H  HCH2   0   0.209  14.3813  42.0317  17.6967
 NLE  HG2  H  HCH2   0   0.197  13.2147  39.8355  17.8126
 NLE  HG3  H  HCH2   0   0.206  14.1754  39.3859  19.2049
 NLE  HD2  H  HCH2   0   0.206  13.2307  41.3187  20.4805
 NLE  HD3  H  HCH2   0   0.206  12.2798  41.7769  19.0870
 NLE  HE1  H  HCH3   0   0.214  12.0060  39.1226  20.6018
 NLE  HE2  H  HCH3   0   0.223  10.8881  40.4784  20.7001
 NLE  HE3  H  HCH3   0   0.213  11.0534  39.5811  19.1943

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
 NLE  N   CA   single  1.458  0.019  1.458
 NLE  N   H    single  0.860  0.020  0.860
 NLE  N   HN2  single  0.890  0.020  1.040
 NLE  CA  C    single  1.525  0.021  1.525
 NLE  CA  CB   single  1.530  0.020  1.530
 NLE  CA  HA   single  0.970  0.020  0.970
 NLE  C   O    deloc   1.231  0.020  1.231
 NLE  C   OXT  deloc   1.248  0.020  1.248
 NLE  CB  CG   single  1.523  0.020  1.523
 NLE  CB  HB2  single  0.970  0.020  1.090
 NLE  CB  HB3  single  0.970  0.020  1.090
 NLE  CG  CD   single  1.524  0.020  1.524
 NLE  CG  HG2  single  0.970  0.020  1.090
 NLE  CG  HG3  single  0.970  0.020  1.090
 NLE  CD  CE   single  1.523  0.020  1.523
 NLE  CD  HD2  single  0.970  0.020  1.090
 NLE  CD  HD3  single  0.970  0.020  1.090
 NLE  CE  HE1  single  0.970  0.020  1.090
 NLE  CE  HE2  single  0.970  0.020  1.090
 NLE  CE  HE3  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
 NLE  HN2  N   H    104.25  3.000
 NLE  HN2  N   CA   107.19  3.000
 NLE  H    N   CA   114.00  3.000
 NLE  HA   CA  CB   109.00  3.000
 NLE  HA   CA  C    109.00  3.000
 NLE  CB   CA  C    110.10  1.900
 NLE  HA   CA  N    110.00  3.000
 NLE  CB   CA  N    110.50  1.700
 NLE  C    CA  N    111.00  2.800
 NLE  OXT  C   O    126.77  3.000
 NLE  OXT  C   CA   117.01  3.000
 NLE  O    C   CA   120.80  1.700
 NLE  HB3  CB  HB2  106.16  3.000
 NLE  HB3  CB  CG   109.11  3.000
 NLE  HB2  CB  CG   109.50  3.000
 NLE  HB3  CB  CA   108.64  3.000
 NLE  HB2  CB  CA   108.84  3.000
 NLE  CG   CB  CA   114.27  3.000
 NLE  HG3  CG  HG2  106.15  3.000
 NLE  HG3  CG  CD   109.46  3.000
 NLE  HG2  CG  CD   109.13  3.000
 NLE  HG3  CG  CB   109.71  3.000
 NLE  HG2  CG  CB   109.09  3.000
 NLE  CD   CG  CB   113.06  3.000
 NLE  HD3  CD  HD2  105.99  3.000
 NLE  HD3  CD  CE   109.49  3.000
 NLE  HD2  CD  CE   109.56  3.000
 NLE  HD3  CD  CG   109.34  3.000
 NLE  HD2  CD  CG   109.27  3.000
 NLE  CE   CD  CG   112.95  3.000
 NLE  HE3  CE  HE2  107.55  3.000
 NLE  HE3  CE  HE1  107.46  3.000
 NLE  HE2  CE  HE1  107.49  3.000
 NLE  HE3  CE  CD   111.17  3.000
 NLE  HE2  CE  CD   111.68  3.000
 NLE  HE1  CE  CD   111.27  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
 NLE  Var_01  CD   CG  CB  CA  179.93  30.0  3
 NLE  Var_02  CE   CD  CG  CB  179.13  30.0  3
 NLE  Var_03  HE1  CE  CD  CG   60.04  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
 NLE  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
 NLE  plan-1  CA   0.020
 NLE  plan-1  C    0.020
 NLE  plan-1  O    0.020
 NLE  plan-1  OXT  0.020

