# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 22:21:09 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: (4R)-2-methylpentane-2,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)CC(C)(C)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
 MRD  MRD  (4R)-2-methylpentane-2,4-diol  ligand  22  8  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MRD
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
 MRD  C1    C  CH3   0  -0.667  -0.7007  -0.8120  -2.2399
 MRD  C2    C  CT    0   0.182  -0.0689  -0.0421  -1.0835
 MRD  O2    O  OH1   0  -0.678   1.3415  -0.2999  -1.0459
 MRD  CM    C  CH3   0  -0.663  -0.2092   1.4557  -1.3215
 MRD  C3    C  CH2   0  -0.458  -0.7255  -0.4776   0.2368
 MRD  C4    C  CH1   0   0.048  -0.2197   0.2112   1.5033
 MRD  O4    O  OH1   0  -0.699   1.1570  -0.0295   1.7317
 MRD  C5    C  CH3   0  -0.673  -0.9879  -0.2670   2.7223
 MRD  H1C1  H  HCH3  0   0.236  -0.2422  -0.5342  -3.1904
 MRD  H1C2  H  HCH3  0   0.230  -0.5862  -1.8909  -2.1080
 MRD  H1C3  H  HCH3  0   0.231  -1.7689  -0.6026  -2.3082
 MRD  H2    H  HOH1  0   0.451   1.4754  -1.2548  -1.0657
 MRD  HMC1  H  HCH3  0   0.228  -1.2588   1.7491  -1.2960
 MRD  HMC2  H  HCH3  0   0.236   0.3189   2.0446  -0.5704
 MRD  HMC3  H  HCH3  0   0.236   0.1908   1.7277  -2.2993
 MRD  H3C1  H  HCH2  0   0.227  -0.6073  -1.5631   0.3478
 MRD  H3C2  H  HCH2  0   0.228  -1.8017  -0.2985   0.1574
 MRD  H4    H  HCH1  0   0.189  -0.4005   1.2920   1.4005
 MRD  HA    H  HOH1  0   0.440   1.5920  -0.0027   0.8683
 MRD  H5C1  H  HCH3  0   0.233  -0.6199   0.2106   3.6316
 MRD  H5C2  H  HCH3  0   0.224  -2.0464  -0.0247   2.6252
 MRD  H5C3  H  HCH3  0   0.219  -0.8993  -1.3487   2.8443

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
 MRD  C1  C2    single  1.526  0.020  1.526
 MRD  C1  H1C1  single  0.970  0.020  1.090
 MRD  C1  H1C2  single  0.970  0.020  1.090
 MRD  C1  H1C3  single  0.970  0.020  1.090
 MRD  C2  O2    single  1.434  0.020  1.434
 MRD  C2  CM    single  1.523  0.020  1.523
 MRD  C2  C3    single  1.537  0.020  1.537
 MRD  O2  H2    single  0.850  0.020  0.980
 MRD  CM  HMC1  single  0.970  0.020  1.090
 MRD  CM  HMC2  single  0.970  0.020  1.090
 MRD  CM  HMC3  single  0.970  0.020  1.090
 MRD  C3  C4    single  1.528  0.020  1.528
 MRD  C3  H3C1  single  0.970  0.020  1.090
 MRD  C3  H3C2  single  0.970  0.020  1.090
 MRD  C4  O4    single  1.416  0.020  1.416
 MRD  C4  C5    single  1.518  0.020  1.518
 MRD  C4  H4    single  0.970  0.020  1.090
 MRD  O4  HA    single  0.850  0.020  0.980
 MRD  C5  H5C1  single  0.970  0.020  1.090
 MRD  C5  H5C2  single  0.970  0.020  1.090
 MRD  C5  H5C3  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
 MRD  H1C3  C1  H1C2  107.44  3.000
 MRD  H1C3  C1  H1C1  107.94  3.000
 MRD  H1C2  C1  H1C1  108.21  3.000
 MRD  H1C3  C1  C2    110.85  3.000
 MRD  H1C2  C1  C2    111.30  3.000
 MRD  H1C1  C1  C2    110.96  3.000
 MRD  C3    C2  CM    111.93  3.000
 MRD  C3    C2  O2    110.28  3.000
 MRD  CM    C2  O2    105.75  3.000
 MRD  C3    C2  C1    109.33  3.000
 MRD  CM    C2  C1    109.85  3.000
 MRD  O2    C2  C1    109.65  3.000
 MRD  H2    O2  C2    108.30  3.000
 MRD  HMC3  CM  HMC2  107.76  3.000
 MRD  HMC3  CM  HMC1  107.87  3.000
 MRD  HMC2  CM  HMC1  107.74  3.000
 MRD  HMC3  CM  C2    110.58  3.000
 MRD  HMC2  CM  C2    112.26  3.000
 MRD  HMC1  CM  C2    110.47  3.000
 MRD  H3C2  C3  H3C1  105.98  3.000
 MRD  H3C2  C3  C4    108.18  3.000
 MRD  H3C1  C3  C4    109.05  3.000
 MRD  H3C2  C3  C2    108.15  3.000
 MRD  H3C1  C3  C2    108.72  3.000
 MRD  C4    C3  C2    116.28  3.000
 MRD  H4    C4  C5    107.53  3.000
 MRD  H4    C4  O4    109.98  3.000
 MRD  C5    C4  O4    107.99  3.000
 MRD  H4    C4  C3    108.11  3.000
 MRD  C5    C4  C3    110.86  3.000
 MRD  O4    C4  C3    112.27  3.000
 MRD  HA    O4  C4    106.77  3.000
 MRD  H5C3  C5  H5C2  107.99  3.000
 MRD  H5C3  C5  H5C1  108.24  3.000
 MRD  H5C2  C5  H5C1  107.72  3.000
 MRD  H5C3  C5  C4    111.14  3.000
 MRD  H5C2  C5  C4    110.47  3.000
 MRD  H5C1  C5  C4    111.14  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
 MRD  Var_01  C4    C3  C2  C1  -179.30  30.0  3
 MRD  Var_02  HMC1  CM  C2  C1    65.61  30.0  3
 MRD  Var_03  H1C1  C1  C2  O2   -58.09  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
 MRD  chir_01  C4  C3  O4  C5  positiv

