# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 19:44:07 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: (4S)-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
 MPD  MPD  (4S)-2-methylpentane-2,4-diol  ligand  22  8  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MPD
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
 MPD  C1   C  CH3   0  -0.653  -2.5669  -3.3055   8.5397
 MPD  C2   C  CT    0   0.207  -2.9214  -4.0790   9.8049
 MPD  O2   O  OH1   0  -0.696  -2.5097  -5.4207   9.5854
 MPD  CM   C  CH3   0  -0.675  -4.4346  -4.0245  10.0264
 MPD  C3   C  CH2   0  -0.447  -2.1576  -3.4630  10.9905
 MPD  C4   C  CH1   0   0.034  -2.4722  -4.0328  12.3678
 MPD  O4   O  OH1   0  -0.680  -2.2574  -5.4404  12.3218
 MPD  C5   C  CH3   0  -0.674  -1.6159  -3.3868  13.4458
 MPD  H11  H  HCH3  0   0.220  -2.9005  -2.2703   8.6143
 MPD  H12  H  HCH3  0   0.225  -1.4885  -3.3003   8.3697
 MPD  H13  H  HCH3  0   0.227  -3.0473  -3.7484   7.6651
 MPD  HO2  H  HOH1  0   0.439  -2.4951  -5.8456  10.4543
 MPD  HM1  H  HCH3  0   0.228  -4.7470  -4.6441  10.8689
 MPD  HM2  H  HCH3  0   0.216  -4.7730  -3.0050  10.2204
 MPD  HM3  H  HCH3  0   0.228  -4.9598  -4.3856   9.1402
 MPD  H31  H  HCH2  0   0.226  -1.0819  -3.5558  10.7990
 MPD  H32  H  HCH2  0   0.228  -2.3693  -2.3910  11.0276
 MPD  H4   H  HCH1  0   0.210  -3.5253  -3.8291  12.6001
 MPD  HO4  H  HOH1  0   0.457  -2.6221  -5.8374  13.1192
 MPD  H51  H  HCH3  0   0.232  -1.8537  -3.7908  14.4317
 MPD  H52  H  HCH3  0   0.223  -0.5541  -3.5533  13.2554
 MPD  H53  H  HCH3  0   0.225  -1.7886  -2.3105  13.4817

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
 MPD  C1  C2   single  1.525  0.020  1.525
 MPD  C1  H11  single  0.970  0.020  1.090
 MPD  C1  H12  single  0.970  0.020  1.090
 MPD  C1  H13  single  0.970  0.020  1.090
 MPD  C2  O2   single  1.421  0.020  1.421
 MPD  C2  CM   single  1.530  0.020  1.530
 MPD  C2  C3   single  1.539  0.020  1.539
 MPD  O2  HO2  single  0.850  0.020  0.980
 MPD  CM  HM1  single  0.970  0.020  1.090
 MPD  CM  HM2  single  0.970  0.020  1.090
 MPD  CM  HM3  single  0.970  0.020  1.090
 MPD  C3  C4   single  1.523  0.020  1.523
 MPD  C3  H31  single  0.970  0.020  1.090
 MPD  C3  H32  single  0.970  0.020  1.090
 MPD  C4  O4   single  1.425  0.020  1.425
 MPD  C4  C5   single  1.521  0.020  1.521
 MPD  C4  H4   single  0.970  0.020  1.090
 MPD  O4  HO4  single  0.850  0.020  0.980
 MPD  C5  H51  single  0.970  0.020  1.090
 MPD  C5  H52  single  0.970  0.020  1.090
 MPD  C5  H53  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
 MPD  H13  C1  H12  108.17  3.000
 MPD  H13  C1  H11  107.78  3.000
 MPD  H12  C1  H11  107.96  3.000
 MPD  H13  C1  C2   110.90  3.000
 MPD  H12  C1  C2   111.18  3.000
 MPD  H11  C1  C2   110.72  3.000
 MPD  C3   C2  CM   111.41  3.000
 MPD  C3   C2  O2   110.69  3.000
 MPD  CM   C2  O2   110.04  3.000
 MPD  C3   C2  C1   108.71  3.000
 MPD  CM   C2  C1   109.39  3.000
 MPD  O2   C2  C1   106.47  3.000
 MPD  HO2  O2  C2   106.29  3.000
 MPD  HM3  CM  HM2  107.70  3.000
 MPD  HM3  CM  HM1  107.53  3.000
 MPD  HM2  CM  HM1  107.71  3.000
 MPD  HM3  CM  C2   110.27  3.000
 MPD  HM2  CM  C2   111.44  3.000
 MPD  HM1  CM  C2   112.00  3.000
 MPD  H32  C3  H31  106.19  3.000
 MPD  H32  C3  C4   107.23  3.000
 MPD  H31  C3  C4   109.20  3.000
 MPD  H32  C3  C2   108.81  3.000
 MPD  H31  C3  C2   108.57  3.000
 MPD  C4   C3  C2   116.38  3.000
 MPD  H4   C4  C5   108.15  3.000
 MPD  H4   C4  O4   109.56  3.000
 MPD  C5   C4  O4   110.96  3.000
 MPD  H4   C4  C3   108.67  3.000
 MPD  C5   C4  C3   111.45  3.000
 MPD  O4   C4  C3   108.01  3.000
 MPD  HO4  O4  C4   108.89  3.000
 MPD  H53  C5  H52  108.08  3.000
 MPD  H53  C5  H51  107.52  3.000
 MPD  H52  C5  H51  108.24  3.000
 MPD  H53  C5  C4   110.69  3.000
 MPD  H52  C5  C4   111.06  3.000
 MPD  H51  C5  C4   111.12  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
 MPD  Var_01  C4   C3  C2  C1  175.15  30.0  3
 MPD  Var_02  HM1  CM  C2  C1  174.58  30.0  3
 MPD  Var_03  H11  C1  C2  O2  177.16  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
 MPD  chir_01  C4  C3  O4  C5  negativ

