# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:58:37 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: 2-methyl-L-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[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
 MK8  MK8  '2-methyl-L-norleucine    '  L-peptide  24  10  .  2017-07-05  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MK8
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
 MK8  C     C  C      0   0.428   8.7724  -1.3965   -8.0564
 MK8  N     N  NH2    0  -0.801   8.3668  -1.6859   -5.6873
 MK8  O     O  O      0  -0.600   8.1330  -1.9916   -8.9487
 MK8  CA    C  CT     0  -0.022   7.9628  -0.8523   -6.8331
 MK8  CB    C  CH2    0  -0.404   8.3723   0.5848   -6.4719
 MK8  CD    C  CH2    0  -0.422   8.2504   1.6740   -8.8210
 MK8  CE    C  CH3    0  -0.657   7.7449   2.8871   -9.5910
 MK8  CG    C  CH2    0  -0.423   7.8407   1.7129   -7.3536
 MK8  CB1   C  CH3    0  -0.652   6.4537  -0.9334   -7.0610
 MK8  OXT   O  OC    -1  -0.604  10.0068  -1.2252   -8.0273
 MK8  HN    H  HNH2   0   0.325   7.8171  -1.4103   -4.8794
 MK8  HNA   H  HNH2   0   0.328   8.1040  -2.6497   -5.8654
 MK8  HB    H  HCH2   0   0.199   8.0192   0.7803   -5.4518
 MK8  HBA   H  HCH2   0   0.210   9.4626   0.6320   -6.4295
 MK8  HD    H  HCH2   0   0.204   9.3400   1.6170   -8.8955
 MK8  HDA   H  HCH2   0   0.213   7.8659   0.7661   -9.2909
 MK8  HE    H  HCH3   0   0.222   8.0312   2.8445  -10.6427
 MK8  HEA   H  HCH3   0   0.212   6.6555   2.9526   -9.5498
 MK8  HEB   H  HCH3   0   0.212   8.1441   3.8151   -9.1772
 MK8  HG    H  HCH2   0   0.210   8.1840   2.6604   -6.9235
 MK8  HGA   H  HCH2   0   0.205   6.7481   1.7487   -7.2925
 MK8  HB1   H  HCH3   0   0.197   5.9196  -0.5248   -6.1976
 MK8  HB1A  H  HCH3   0   0.209   6.1228  -0.3819   -7.9418
 MK8  HB1B  H  HCH3   0   0.212   6.1323  -1.9680   -7.1861

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
 MK8  C    CA    single  1.525  0.021  1.525
 MK8  C    OXT   deloc   1.247  0.020  1.247
 MK8  N    HN    single  0.890  0.020  1.040
 MK8  N    HNA   single  0.890  0.020  1.040
 MK8  O    C     deloc   1.231  0.020  1.231
 MK8  CA   N     single  1.458  0.019  1.458
 MK8  CA   CB    single  1.530  0.020  1.530
 MK8  CB   HB    single  0.970  0.020  1.090
 MK8  CB   HBA   single  0.970  0.020  1.090
 MK8  CD   CG    single  1.524  0.020  1.524
 MK8  CD   HD    single  0.970  0.020  1.090
 MK8  CD   HDA   single  0.970  0.020  1.090
 MK8  CE   CD    single  1.523  0.020  1.523
 MK8  CE   HE    single  0.970  0.020  1.090
 MK8  CE   HEA   single  0.970  0.020  1.090
 MK8  CE   HEB   single  0.970  0.020  1.090
 MK8  CG   CB    single  1.527  0.020  1.527
 MK8  CG   HG    single  0.970  0.020  1.090
 MK8  CG   HGA   single  0.970  0.020  1.090
 MK8  CB1  CA    single  1.528  0.020  1.528
 MK8  CB1  HB1   single  0.970  0.020  1.090
 MK8  CB1  HB1A  single  0.970  0.020  1.090
 MK8  CB1  HB1B  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
 MK8  OXT   C    CA    116.51  3.000
 MK8  OXT   C    O     126.10  3.000
 MK8  CA    C    O     120.80  1.700
 MK8  HNA   N    HN    104.91  3.000
 MK8  HNA   N    CA    109.26  3.000
 MK8  HN    N    CA    108.47  3.000
 MK8  CB1   CA   CB    110.34  3.000
 MK8  CB1   CA   N     110.89  3.000
 MK8  CB    CA   N     110.50  1.700
 MK8  CB1   CA   C     112.08  3.000
 MK8  CB    CA   C     110.10  1.900
 MK8  N     CA   C     111.00  2.800
 MK8  HBA   CB   HB    106.11  3.000
 MK8  HBA   CB   CG    109.75  3.000
 MK8  HB    CB   CG    107.05  3.000
 MK8  CG    CB   CA    117.52  3.000
 MK8  HBA   CB   CA    108.38  3.000
 MK8  HB    CB   CA    107.42  3.000
 MK8  HDA   CD   HD    106.15  3.000
 MK8  HDA   CD   CG    109.93  3.000
 MK8  HD    CD   CG    109.55  3.000
 MK8  HDA   CD   CE    109.13  3.000
 MK8  HD    CD   CE    109.74  3.000
 MK8  CG    CD   CE    112.16  3.000
 MK8  HEB   CE   HEA   107.42  3.000
 MK8  HEB   CE   HE    107.61  3.000
 MK8  HEA   CE   HE    107.49  3.000
 MK8  HEB   CE   CD    111.35  3.000
 MK8  HEA   CE   CD    111.09  3.000
 MK8  HE    CE   CD    111.67  3.000
 MK8  HGA   CG   HG    105.22  3.000
 MK8  HGA   CG   CD    108.84  3.000
 MK8  HG    CG   CD    108.41  3.000
 MK8  HGA   CG   CB    109.83  3.000
 MK8  HG    CG   CB    107.64  3.000
 MK8  CD    CG   CB    116.33  3.000
 MK8  HB1B  CB1  HB1A  107.32  3.000
 MK8  HB1B  CB1  HB1   107.51  3.000
 MK8  HB1A  CB1  HB1   107.48  3.000
 MK8  HB1B  CB1  CA    111.01  3.000
 MK8  HB1A  CB1  CA    113.15  3.000
 MK8  HB1   CB1  CA    110.15  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
 MK8  Var_01  CD  CG  CB  CA   -61.16  30.0  1
 MK8  Var_02  CE  CD  CG  CB  -176.30  30.0  1
 MK8  Var_03  HE  CE  CD  CG  -179.25  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
 MK8  chir_01  CA  N  CB  CB1  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
 MK8  plan-1  C    0.020
 MK8  plan-1  O    0.020
 MK8  plan-1  CA   0.020
 MK8  plan-1  OXT  0.020

