# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 19:42:55 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: (2S)-2-amino-2-methyloctanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[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
 MKD  MKD  '(2S)-2-amino-2-methyloctanoic acid'  L-peptide  30  12  .  2019-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MKD
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
 MKD  O    O  O      0  -0.607  36.8833  -4.0570  12.2089
 MKD  C    C  C      0   0.421  36.7247  -5.2791  12.0146
 MKD  CA   C  CT     0  -0.033  35.3619  -5.8738  12.4713
 MKD  CB1  C  CH3    0  -0.629  34.2076  -4.9840  12.0101
 MKD  N    N  NH2    0  -0.802  35.1704  -7.1905  11.8704
 MKD  CB   C  CH2    0  -0.402  35.3519  -5.9183  14.0153
 MKD  CG   C  CH2    0  -0.418  36.4455  -6.7592  14.6626
 MKD  CD   C  CH2    0  -0.407  36.2789  -6.8715  16.1735
 MKD  CE   C  CH2    0  -0.403  37.3917  -7.6671  16.8438
 MKD  CF   C  CH2    0  -0.416  37.2186  -7.7972  18.3519
 MKD  CH   C  CH3    0  -0.659  38.3448  -8.5798  19.0127
 MKD  O1   O  OC    -1  -0.603  37.5623  -6.0667  11.5297
 MKD  H1   H  HCH3   0   0.202  33.2489  -5.4215  12.3024
 MKD  H2   H  HCH3   0   0.209  34.2637  -3.9898  12.4495
 MKD  H3   H  HCH3   0   0.212  34.2021  -4.8764  10.9238
 MKD  H4   H  HNH2   0   0.331  36.0216  -7.7281  11.9674
 MKD  H5   H  HNH2   0   0.321  34.4473  -7.6908  12.3754
 MKD  H7   H  HCH2   0   0.202  35.4120  -4.8968  14.4031
 MKD  H8   H  HCH2   0   0.198  34.3749  -6.3051  14.3339
 MKD  H9   H  HCH2   0   0.197  36.4498  -7.7657  14.2319
 MKD  H10  H  HCH2   0   0.209  37.4279  -6.3289  14.4444
 MKD  H11  H  HCH2   0   0.203  36.2373  -5.8674  16.6099
 MKD  H12  H  HCH2   0   0.203  35.3129  -7.3372  16.3987
 MKD  H13  H  HCH2   0   0.203  37.4434  -8.6673  16.3995
 MKD  H14  H  HCH2   0   0.204  38.3557  -7.1924  16.6292
 MKD  H15  H  HCH2   0   0.208  37.1558  -6.7985  18.7948
 MKD  H16  H  HCH2   0   0.208  36.2608  -8.2821  18.5651
 MKD  H17  H  HCH3   0   0.224  38.1981  -8.6639  20.0901
 MKD  H18  H  HCH3   0   0.214  38.4119  -9.5918  18.6087
 MKD  H19  H  HCH3   0   0.214  39.3097  -8.0969  18.8475

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
 MKD  CB1  CA   single  1.529  0.020  1.529
 MKD  O    C    deloc   1.231  0.020  1.231
 MKD  C    CA   single  1.525  0.021  1.525
 MKD  N    CA   single  1.458  0.019  1.458
 MKD  CA   CB   single  1.521  0.033  1.521
 MKD  CB   CG   single  1.524  0.020  1.524
 MKD  CG   CD   single  1.524  0.020  1.524
 MKD  CD   CE   single  1.523  0.020  1.523
 MKD  CE   CF   single  1.524  0.020  1.524
 MKD  CF   CH   single  1.522  0.020  1.522
 MKD  C    O1   deloc   1.248  0.020  1.248
 MKD  CB1  H1   single  0.970  0.020  1.090
 MKD  CB1  H2   single  0.970  0.020  1.090
 MKD  CB1  H3   single  0.970  0.020  1.090
 MKD  N    H4   single  0.890  0.020  1.040
 MKD  N    H5   single  0.890  0.020  1.040
 MKD  CB   H7   single  0.970  0.020  1.090
 MKD  CB   H8   single  0.970  0.020  1.090
 MKD  CG   H9   single  0.970  0.020  1.090
 MKD  CG   H10  single  0.970  0.020  1.090
 MKD  CD   H11  single  0.970  0.020  1.090
 MKD  CD   H12  single  0.970  0.020  1.090
 MKD  CE   H13  single  0.970  0.020  1.090
 MKD  CE   H14  single  0.970  0.020  1.090
 MKD  CF   H15  single  0.970  0.020  1.090
 MKD  CF   H16  single  0.970  0.020  1.090
 MKD  CH   H17  single  0.970  0.020  1.090
 MKD  CH   H18  single  0.970  0.020  1.090
 MKD  CH   H19  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
 MKD  O1   C    CA   117.45  3.000
 MKD  O1   C    O    126.40  3.000
 MKD  CA   C    O    120.80  1.700
 MKD  CB   CA   N    110.40  1.500
 MKD  CB   CA   CB1  108.27  3.000
 MKD  N    CA   CB1  107.56  3.000
 MKD  CB   CA   C    110.50  1.500
 MKD  N    CA   C    111.00  2.800
 MKD  CB1  CA   C    110.51  3.000
 MKD  H3   CB1  H2   108.18  3.000
 MKD  H3   CB1  H1   107.52  3.000
 MKD  H2   CB1  H1   107.62  3.000
 MKD  H3   CB1  CA   111.19  3.000
 MKD  H2   CB1  CA   111.77  3.000
 MKD  H1   CB1  CA   110.38  3.000
 MKD  H5   N    H4   106.87  3.000
 MKD  H5   N    CA   109.48  3.000
 MKD  H4   N    CA   109.24  3.000
 MKD  H8   CB   H7   105.95  3.000
 MKD  H8   CB   CG   108.72  3.000
 MKD  H7   CB   CG   108.98  3.000
 MKD  H8   CB   CA   107.81  3.000
 MKD  H7   CB   CA   109.09  3.000
 MKD  CG   CB   CA   115.84  3.000
 MKD  H10  CG   H9   106.23  3.000
 MKD  H10  CG   CD   108.95  3.000
 MKD  H9   CG   CD   108.83  3.000
 MKD  H10  CG   CB   110.03  3.000
 MKD  H9   CG   CB   110.07  3.000
 MKD  CD   CG   CB   112.54  3.000
 MKD  H12  CD   H11  105.91  3.000
 MKD  H12  CD   CE   109.37  3.000
 MKD  H11  CD   CE   109.34  3.000
 MKD  H12  CD   CG   109.35  3.000
 MKD  H11  CD   CG   109.36  3.000
 MKD  CE   CD   CG   113.25  3.000
 MKD  H14  CE   H13  105.94  3.000
 MKD  H14  CE   CF   109.32  3.000
 MKD  H13  CE   CF   109.20  3.000
 MKD  H14  CE   CD   109.28  3.000
 MKD  H13  CE   CD   109.44  3.000
 MKD  CF   CE   CD   113.39  3.000
 MKD  H16  CF   H15  105.98  3.000
 MKD  H16  CF   CH   109.58  3.000
 MKD  H15  CF   CH   109.63  3.000
 MKD  H16  CF   CE   109.28  3.000
 MKD  H15  CF   CE   109.22  3.000
 MKD  CH   CF   CE   112.92  3.000
 MKD  H19  CH   H18  107.44  3.000
 MKD  H19  CH   H17  107.60  3.000
 MKD  H18  CH   H17  107.60  3.000
 MKD  H19  CH   CF   111.16  3.000
 MKD  H18  CH   CF   111.19  3.000
 MKD  H17  CH   CF   111.65  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
 MKD  Var_01  CD   CG  CB  CA  -173.92  30.0  3
 MKD  Var_02  CE   CD  CG  CB  -177.92  30.0  3
 MKD  Var_03  CF   CE  CD  CG  -179.23  30.0  3
 MKD  Var_04  CH   CF  CE  CD  -179.32  30.0  3
 MKD  Var_05  H17  CH  CF  CE  -179.76  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
 MKD  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
 MKD  plan-1  O   0.020
 MKD  plan-1  C   0.020
 MKD  plan-1  CA  0.020
 MKD  plan-1  O1  0.020

