# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 02:08:12 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  25  12  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.364  -0.5395   0.7918  -2.1394
 HMI  OH    O  OH1   0  -0.539  -0.9524   0.6267  -3.4238
 HMI  C1    C  C     0   0.549  -0.0743  -0.2534  -1.4417
 HMI  O1    O  O     0  -0.463  -0.0861  -1.4049  -1.8355
 HMI  CA    C  CH1   0  -0.543   0.4295   0.1166  -0.0518
 HMI  CB    C  CH2   0  -0.393  -0.5821  -0.3453   0.9978
 HMI  CG    C  CH1   0  -0.243  -0.2991   0.1289   2.4256
 HMI  CD1   C  CH3   0  -0.663  -0.3234   1.6498   2.5455
 HMI  CD2   C  CH3   0  -0.653  -1.3180  -0.4957   3.3740
 HMI  C     C  C     0   0.573   1.7851  -0.5418   0.0997
 HMI  O     O  O     0  -0.424   2.0240  -1.4940   0.7942
 HMI  OXT   O  OH1   0  -0.590   2.6889   0.0570  -0.6655
 HMI  HN    H  HNH1  0   0.422  -0.4064   1.7492  -1.8469
 HMI  HOH   H  HOH1  0   0.481  -1.9132   0.5291  -3.3893
 HMI  HA    H  HCH1  0   0.304   0.5702   1.1994   0.0177
 HMI  HB1   H  HCH2  0   0.245  -0.6431  -1.4355   0.9761
 HMI  HB2   H  HCH2  0   0.241  -1.5696   0.0248   0.7029
 HMI  HG    H  HCH1  0   0.228   0.6926  -0.2240   2.7235
 HMI  HD11  H  HCH3  0   0.233  -0.1497   1.9578   3.5778
 HMI  HD12  H  HCH3  0   0.228   0.4437   2.1320   1.9374
 HMI  HD13  H  HCH3  0   0.217  -1.2927   2.0520   2.2395
 HMI  HD21  H  HCH3  0   0.215  -2.3324  -0.1758   3.1239
 HMI  HD22  H  HCH3  0   0.227  -1.2921  -1.5857   3.3251
 HMI  HD23  H  HCH3  0   0.229  -1.1247  -0.2042   4.4073
 HMI  HXT   H  HOH1  0   0.484   3.5444  -0.3927  -0.5906

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  1.359  0.020  1.359
 HMI  N    C1    single  1.340  0.020  1.340
 HMI  N    HN    single  0.860  0.020  1.020
 HMI  OH   HOH   single  0.850  0.020  0.980
 HMI  C1   O1    double  1.217  0.020  1.217
 HMI  C1   CA    single  1.524  0.020  1.524
 HMI  CA   CB    single  1.529  0.020  1.529
 HMI  CA   C     single  1.515  0.020  1.515
 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     double  1.203  0.020  1.203
 HMI  C    OXT   single  1.327  0.020  1.327
 HMI  OXT  HXT   single  0.850  0.020  0.980

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    122.89  3.000
 HMI  HN    N    OH    115.39  3.000
 HMI  C1    N    OH    120.18  3.000
 HMI  HOH   OH   N     106.30  3.000
 HMI  CA    C1   O1    121.87  3.000
 HMI  CA    C1   N     113.59  3.000
 HMI  O1    C1   N     124.48  3.000
 HMI  HA    CA   C     107.98  3.000
 HMI  HA    CA   CB    109.90  3.000
 HMI  C     CA   CB    113.09  3.000
 HMI  HA    CA   C1    109.92  3.000
 HMI  C     CA   C1    106.35  3.000
 HMI  CB    CA   C1    109.51  3.000
 HMI  HB2   CB   HB1   106.36  3.000
 HMI  HB2   CB   CG    108.25  3.000
 HMI  HB1   CB   CG    109.76  3.000
 HMI  HB2   CB   CA    108.04  3.000
 HMI  HB1   CB   CA    108.96  3.000
 HMI  CG    CB   CA    115.10  3.000
 HMI  HG    CG   CD2   107.69  3.000
 HMI  HG    CG   CD1   108.34  3.000
 HMI  CD2   CG   CD1   110.40  3.000
 HMI  HG    CG   CB    108.76  3.000
 HMI  CD2   CG   CB    109.24  3.000
 HMI  CD1   CG   CB    112.28  3.000
 HMI  HD13  CD1  HD12  107.74  3.000
 HMI  HD13  CD1  HD11  107.59  3.000
 HMI  HD12  CD1  HD11  106.89  3.000
 HMI  HD13  CD1  CG    111.03  3.000
 HMI  HD12  CD1  CG    112.67  3.000
 HMI  HD11  CD1  CG    110.68  3.000
 HMI  HD23  CD2  HD22  107.77  3.000
 HMI  HD23  CD2  HD21  107.64  3.000
 HMI  HD22  CD2  HD21  107.71  3.000
 HMI  HD23  CD2  CG    111.17  3.000
 HMI  HD22  CD2  CG    111.42  3.000
 HMI  HD21  CD2  CG    110.97  3.000
 HMI  OXT   C    O     123.72  3.000
 HMI  OXT   C    CA    110.84  3.000
 HMI  O     C    CA    125.43  3.000
 HMI  HXT   OXT  C     110.31  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  CONST_01  O1    C1   N   OH    0.00   0.0  0
 HMI  CONST_02  CA    C1   N   OH  180.00   0.0  0
 HMI  CONST_03  HN    N    C1  O1  180.00   0.0  0
 HMI  CONST_04  HXT   OXT  C   CA  180.00   0.0  0
 HMI  Var_01    CD1   CG   CB  CA   61.68  30.0  3
 HMI  Var_02    HD11  CD1  CG  CB  178.24  30.0  3
 HMI  Var_03    HD21  CD2  CG  CB  -62.12  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
 HMI  plan-2  HXT  0.020

