# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:33:40 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: (4S)-2,4-dimethyl-L-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)C[C@](C)(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
 5GM  5GM  (4S)-2,4-dimethyl-L-norleucine  L-peptide  27  11  .  2017-07-04  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5GM
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
 5GM  N    N  NH2    0  -0.801  66.4018  18.3233  60.8829
 5GM  CA   C  CT     0  -0.029  66.1567  17.5828  59.6313
 5GM  CB   C  CH2    0  -0.377  66.9450  16.2706  59.7633
 5GM  CC   C  CH1    0  -0.231  67.1554  15.4083  58.5140
 5GM  CD2  C  CH3    0  -0.658  68.0329  14.2145  58.8900
 5GM  CD   C  CH2    0  -0.412  65.8533  14.9598  57.8480
 5GM  CE   C  CH3    0  -0.665  66.0576  14.1535  56.5706
 5GM  CB2  C  CH3    0  -0.653  66.6416  18.3858  58.4238
 5GM  C    C  C      0   0.428  64.6124  17.3372  59.5948
 5GM  O    O  O      0  -0.601  63.9495  17.9979  58.7687
 5GM  HAX  H  HNH2   0   0.326  67.3879  18.5613  60.9264
 5GM  HBA  H  HCH2   0   0.194  67.9444  16.5268  60.1383
 5GM  HE6  H  HCH2   0   0.206  66.4754  15.6671  60.5446
 5GM  HBD  H  HCH1   0   0.202  67.7113  16.0028  57.7781
 5GM  HE8  H  HCH3   0   0.226  68.3162  13.6163  58.0236
 5GM  HE9  H  HCH3   0   0.220  68.9563  14.5436  59.3707
 5GM  HBE  H  HCH3   0   0.208  67.5160  13.5554  59.5927
 5GM  HE7  H  HCH2   0   0.200  65.2639  14.3768  58.5631
 5GM  HBB  H  HCH2   0   0.221  65.2503  15.8375  57.6046
 5GM  HBC  H  HCH3   0   0.224  65.1065  13.9658  56.0705
 5GM  HBF  H  HCH3   0   0.209  66.4064  17.9113  57.4704
 5GM  HFA  H  HCH3   0   0.212  66.1923  19.3791  58.4120
 5GM  HFB  H  HCH3   0   0.197  67.7272  18.5152  58.4678
 5GM  H2   H  HNH2   0   0.328  65.9199  19.2154  60.8399
 5GM  H1   H  HCH3   0   0.211  66.6973  14.6894  55.8657
 5GM  OXT  O  OC    -1  -0.603  64.1553  16.5303  60.4274
 5GM  H3   H  HCH3   0   0.217  66.5191  13.1839  56.7595

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
 5GM  N    CA   single  1.458  0.019  1.458
 5GM  CA   C    single  1.525  0.021  1.525
 5GM  CA   CB   single  1.540  0.027  1.540
 5GM  CA   CB2  single  1.529  0.020  1.529
 5GM  CB   CC   single  1.532  0.020  1.532
 5GM  CC   CD2  single  1.529  0.020  1.529
 5GM  CC   CD   single  1.530  0.020  1.530
 5GM  CD   CE   single  1.524  0.020  1.524
 5GM  C    O    deloc   1.231  0.020  1.231
 5GM  N    HAX  single  0.890  0.020  1.040
 5GM  CB   HBA  single  0.970  0.020  1.090
 5GM  CB   HE6  single  0.970  0.020  1.090
 5GM  CC   HBD  single  0.970  0.020  1.090
 5GM  CD2  HE8  single  0.970  0.020  1.090
 5GM  CD2  HE9  single  0.970  0.020  1.090
 5GM  CD2  HBE  single  0.970  0.020  1.090
 5GM  CD   HE7  single  0.970  0.020  1.090
 5GM  CD   HBB  single  0.970  0.020  1.090
 5GM  CE   HBC  single  0.970  0.020  1.090
 5GM  CB2  HBF  single  0.970  0.020  1.090
 5GM  CB2  HFA  single  0.970  0.020  1.090
 5GM  CB2  HFB  single  0.970  0.020  1.090
 5GM  N    H2   single  0.890  0.020  1.040
 5GM  CE   H1   single  0.970  0.020  1.090
 5GM  C    OXT  deloc   1.246  0.020  1.246
 5GM  CE   H3   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
 5GM  H2   N    HAX  104.89  3.000
 5GM  H2   N    CA   109.06  3.000
 5GM  HAX  N    CA   108.39  3.000
 5GM  C    CA   CB2  112.16  3.000
 5GM  CB2  CA   CB   110.71  3.000
 5GM  C    CA   CB   111.60  2.000
 5GM  CB2  CA   N    110.72  3.000
 5GM  CB   CA   N    111.50  1.700
 5GM  C    CA   N    111.00  2.800
 5GM  HE6  CB   HBA  106.00  3.000
 5GM  HE6  CB   CC   109.33  3.000
 5GM  HBA  CB   CC   106.55  3.000
 5GM  HE6  CB   CA   108.21  3.000
 5GM  HBA  CB   CA   107.28  3.000
 5GM  CC   CB   CA   118.75  3.000
 5GM  HBD  CC   CD   107.34  3.000
 5GM  HBD  CC   CD2  107.30  3.000
 5GM  CD   CC   CD2  111.52  3.000
 5GM  HBD  CC   CB   108.14  3.000
 5GM  CD   CC   CB   113.77  3.000
 5GM  CD2  CC   CB   108.53  3.000
 5GM  HBE  CD2  HE9  107.37  3.000
 5GM  HBE  CD2  HE8  107.63  3.000
 5GM  HE9  CD2  HE8  107.18  3.000
 5GM  HBE  CD2  CC   110.95  3.000
 5GM  HE9  CD2  CC   111.00  3.000
 5GM  HE8  CD2  CC   112.47  3.000
 5GM  HBB  CD   HE7  106.03  3.000
 5GM  HBB  CD   CE   108.20  3.000
 5GM  HE7  CD   CE   109.75  3.000
 5GM  HBB  CD   CC   109.35  3.000
 5GM  HE7  CD   CC   109.26  3.000
 5GM  CE   CD   CC   113.95  3.000
 5GM  H3   CE   H1   107.47  3.000
 5GM  H3   CE   HBC  107.19  3.000
 5GM  H1   CE   HBC  107.41  3.000
 5GM  H3   CE   CD   112.45  3.000
 5GM  H1   CE   CD   111.08  3.000
 5GM  HBC  CE   CD   111.00  3.000
 5GM  HFB  CB2  HFA  107.56  3.000
 5GM  HFB  CB2  HBF  107.49  3.000
 5GM  HFA  CB2  HBF  107.34  3.000
 5GM  HFB  CB2  CA   110.18  3.000
 5GM  HFA  CB2  CA   110.87  3.000
 5GM  HBF  CB2  CA   113.17  3.000
 5GM  OXT  C    O    126.16  3.000
 5GM  OXT  C    CA   116.62  3.000
 5GM  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
 5GM  Var_01  HBC  CE  CD  CC  -172.93  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
 5GM  chir_01  CA  C   CB   CB2  negativ
 5GM  chir_02  CC  CD  CD2  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
 5GM  plan-1  CA   0.020
 5GM  plan-1  C    0.020
 5GM  plan-1  O    0.020
 5GM  plan-1  OXT  0.020

