# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 00:18:43 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: (2R)-2-(hydroxycarbamoyl)-4-methylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@@H](C(O)=O)C(=O)NO
#
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
 HMI  HMI  '(2R)-2-(hydroxycarbamoyl)-4-methylpentanoic acid'  ligand  24  12  .  2021-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HMI
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
 HMI  N     N  NH1    0  -0.385  -0.1318   0.6271  -2.4017
 HMI  OH    O  OH1    0  -0.558  -0.3959   0.2277  -3.6883
 HMI  C1    C  C      0   0.525  -0.5701  -0.1690  -1.3897
 HMI  O1    O  O      0  -0.469  -1.4145  -1.0321  -1.5391
 HMI  CA    C  CH1    0  -0.546   0.0809   0.1667  -0.0603
 HMI  CB    C  CH2    0  -0.371  -0.7237  -0.3813   1.1078
 HMI  CG    C  CH1    0  -0.234  -0.2631   0.0982   2.4863
 HMI  CD1   C  CH3    0  -0.663  -0.3338   1.6156   2.6332
 HMI  CD2   C  CH3    0  -0.653  -1.1041  -0.5768   3.5663
 HMI  C     C  C      0   0.443   1.5595  -0.3361  -0.1309
 HMI  O     O  O      0  -0.573   1.8459  -1.3663   0.4956
 HMI  OXT   O  OC    -1  -0.603   2.3199   0.3465  -0.8496
 HMI  HN    H  HNH1   0   0.397   0.7946   1.0280  -2.2897
 HMI  HOH   H  HOH1   0   0.473  -1.0721   0.8344  -4.0113
 HMI  HA    H  HCH1   0   0.266   0.1268   1.2585   0.0039
 HMI  HB1   H  HCH2   0   0.216  -0.6939  -1.4724   1.0856
 HMI  HB2   H  HCH2   0   0.206  -1.7758  -0.0999   0.9875
 HMI  HG    H  HCH1   0   0.215   0.7762  -0.2118   2.6289
 HMI  HD11  H  HCH3   0   0.224  -0.0732   1.9201   3.6485
 HMI  HD12  H  HCH3   0   0.226   0.3523   2.1315   1.9600
 HMI  HD13  H  HCH3   0   0.210  -1.3422   1.9845   2.4266
 HMI  HD21  H  HCH3   0   0.209  -2.1597  -0.3115   3.4633
 HMI  HD22  H  HCH3   0   0.221  -1.0315  -1.6645   3.5049
 HMI  HD23  H  HCH3   0   0.222  -0.7856  -0.2777   4.5664

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
 HMI  N    OH    single  1.373  0.020  1.373
 HMI  N    C1    single  1.360  0.020  1.360
 HMI  N    HN    single  0.890  0.020  1.040
 HMI  OH   HOH   single  0.850  0.020  0.980
 HMI  C1   O1    double  1.217  0.020  1.217
 HMI  C1   CA    single  1.518  0.020  1.518
 HMI  CA   CB    single  1.521  0.020  1.521
 HMI  CA   C     single  1.563  0.020  1.563
 HMI  CA   HA    single  0.970  0.020  1.090
 HMI  CB   CG    single  1.531  0.020  1.531
 HMI  CB   HB1   single  0.970  0.020  1.090
 HMI  CB   HB2   single  0.970  0.020  1.090
 HMI  CG   CD1   single  1.526  0.020  1.526
 HMI  CG   CD2   single  1.526  0.020  1.526
 HMI  CG   HG    single  0.970  0.020  1.090
 HMI  CD1  HD11  single  0.970  0.020  1.090
 HMI  CD1  HD12  single  0.970  0.020  1.090
 HMI  CD1  HD13  single  0.970  0.020  1.090
 HMI  CD2  HD21  single  0.970  0.020  1.090
 HMI  CD2  HD22  single  0.970  0.020  1.090
 HMI  CD2  HD23  single  0.970  0.020  1.090
 HMI  C    O     deloc   1.239  0.020  1.239
 HMI  C    OXT   deloc   1.249  0.020  1.249

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
 HMI  HN    N    C1    116.29  3.000
 HMI  HN    N    OH    113.19  3.000
 HMI  C1    N    OH    117.72  3.000
 HMI  HOH   OH   N     105.42  3.000
 HMI  CA    C1   O1    124.20  3.000
 HMI  CA    C1   N     112.58  3.000
 HMI  O1    C1   N     123.19  3.000
 HMI  HA    CA   C     106.48  3.000
 HMI  HA    CA   CB    109.67  3.000
 HMI  C     CA   CB    114.79  3.000
 HMI  HA    CA   C1    106.85  3.000
 HMI  C     CA   C1    107.16  3.000
 HMI  CB    CA   C1    111.48  3.000
 HMI  HB2   CB   HB1   106.30  3.000
 HMI  HB2   CB   CG    107.90  3.000
 HMI  HB1   CB   CG    108.86  3.000
 HMI  HB2   CB   CA    109.34  3.000
 HMI  HB1   CB   CA    109.28  3.000
 HMI  CG    CB   CA    114.82  3.000
 HMI  HG    CG   CD2   107.82  3.000
 HMI  HG    CG   CD1   108.25  3.000
 HMI  CD2   CG   CD1   110.25  3.000
 HMI  HG    CG   CB    108.33  3.000
 HMI  CD2   CG   CB    109.45  3.000
 HMI  CD1   CG   CB    112.60  3.000
 HMI  HD13  CD1  HD12  107.69  3.000
 HMI  HD13  CD1  HD11  107.56  3.000
 HMI  HD12  CD1  HD11  106.98  3.000
 HMI  HD13  CD1  CG    111.10  3.000
 HMI  HD12  CD1  CG    112.44  3.000
 HMI  HD11  CD1  CG    110.84  3.000
 HMI  HD23  CD2  HD22  107.76  3.000
 HMI  HD23  CD2  HD21  107.56  3.000
 HMI  HD22  CD2  HD21  107.50  3.000
 HMI  HD23  CD2  CG    111.49  3.000
 HMI  HD22  CD2  CG    111.36  3.000
 HMI  HD21  CD2  CG    110.98  3.000
 HMI  OXT   C    O     127.19  3.000
 HMI  OXT   C    CA    115.21  3.000
 HMI  O     C    CA    117.58  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
 HMI  Var_01  CD1   CG   CB  CA   59.82  30.0  3
 HMI  Var_02  HD11  CD1  CG  CB  175.64  30.0  3
 HMI  Var_03  HD21  CD2  CG  CB  -61.61  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
 HMI  chir_01  CA  C1  CB  C  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
 HMI  plan-1  N    0.020
 HMI  plan-1  OH   0.020
 HMI  plan-1  C1   0.020
 HMI  plan-1  O1   0.020
 HMI  plan-1  CA   0.020
 HMI  plan-1  HN   0.020
 HMI  plan-2  CA   0.020
 HMI  plan-2  C    0.020
 HMI  plan-2  O    0.020
 HMI  plan-2  OXT  0.020

