# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 21:38:31 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 1,3-dideoxy-4-C-methyl-D-erythro-pentitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)C[C@](C)(O)CO
#
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
 MQD  MQD  1,3-dideoxy-4-C-methyl-D-erythro-pentitol  ligand  23  9  .  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_MQD
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
 MQD  C1    C  CH3   0  -0.672  -0.1080  -1.5613  -0.8503
 MQD  C2    C  CT    0   0.158  -0.0090  -0.0501  -0.6888
 MQD  O2    O  OH1   0  -0.677   1.3877   0.2514  -0.6539
 MQD  CM    C  CH2   0  -0.142  -0.6757   0.6666  -1.8632
 MQD  C3    C  CH2   0  -0.471  -0.6991   0.4353   0.5966
 MQD  C4    C  CH1   0   0.050  -0.2084  -0.1882   1.9022
 MQD  O4    O  OH1   0  -0.696   1.1589   0.0842   2.1481
 MQD  C5    C  CH3   0  -0.674  -1.0074   0.3368   3.0815
 MQD  O6    O  OH1   0  -0.668  -0.0611   0.3007  -3.0730
 MQD  H1C1  H  HCH3  0   0.226  -1.1499  -1.8805  -0.8116
 MQD  H1C2  H  HCH3  0   0.244   0.3080  -1.8828  -1.8041
 MQD  H1C3  H  HCH3  0   0.236   0.4291  -2.0865  -0.0599
 MQD  H2    H  HOH1  0   0.451   1.4994   1.2090  -0.6839
 MQD  HMC1  H  HCH2  0   0.204  -1.7437   0.4139  -1.8536
 MQD  HMC2  H  HCH2  0   0.200  -0.6107   1.7527  -1.6949
 MQD  H3C1  H  HCH2  0   0.231  -1.7714   0.2380   0.5089
 MQD  H3C2  H  HCH2  0   0.231  -0.5971   1.5261   0.6649
 MQD  H4    H  HCH1  0   0.192  -0.3726  -1.2747   1.8481
 MQD  HA    H  HOH1  0   0.441   1.6209   0.0031   1.3031
 MQD  H5C1  H  HCH3  0   0.234  -0.6564  -0.0982   4.0184
 MQD  H5C2  H  HCH3  0   0.220  -0.9289   1.4233   3.1589
 MQD  H5C3  H  HCH3  0   0.225  -2.0618   0.0820   2.9722
 MQD  H6    H  HOH1  0   0.456  -0.6002   0.6376  -3.7935

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
 MQD  C1  C2    single  1.523  0.020  1.523
 MQD  C1  H1C1  single  0.970  0.020  1.090
 MQD  C1  H1C2  single  0.970  0.020  1.090
 MQD  C1  H1C3  single  0.970  0.020  1.090
 MQD  C2  O2    single  1.429  0.020  1.429
 MQD  C2  CM    single  1.529  0.020  1.529
 MQD  C2  C3    single  1.538  0.020  1.538
 MQD  O2  H2    single  0.850  0.020  0.980
 MQD  CM  O6    single  1.405  0.020  1.405
 MQD  CM  HMC1  single  0.970  0.020  1.090
 MQD  CM  HMC2  single  0.970  0.020  1.090
 MQD  C3  C4    single  1.528  0.020  1.528
 MQD  C3  H3C1  single  0.970  0.020  1.090
 MQD  C3  H3C2  single  0.970  0.020  1.090
 MQD  C4  O4    single  1.416  0.020  1.416
 MQD  C4  C5    single  1.518  0.020  1.518
 MQD  C4  H4    single  0.970  0.020  1.090
 MQD  O4  HA    single  0.850  0.020  0.980
 MQD  C5  H5C1  single  0.970  0.020  1.090
 MQD  C5  H5C2  single  0.970  0.020  1.090
 MQD  C5  H5C3  single  0.970  0.020  1.090
 MQD  O6  H6    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
 MQD  H1C3  C1  H1C2  107.73  3.000
 MQD  H1C3  C1  H1C1  107.70  3.000
 MQD  H1C2  C1  H1C1  108.04  3.000
 MQD  H1C3  C1  C2    111.65  3.000
 MQD  H1C2  C1  C2    111.16  3.000
 MQD  H1C1  C1  C2    110.41  3.000
 MQD  C3    C2  CM    107.37  3.000
 MQD  C3    C2  O2    110.59  3.000
 MQD  CM    C2  O2    110.24  3.000
 MQD  C3    C2  C1    111.88  3.000
 MQD  CM    C2  C1    110.81  3.000
 MQD  O2    C2  C1    105.99  3.000
 MQD  H2    O2  C2    108.78  3.000
 MQD  HMC2  CM  HMC1  106.45  3.000
 MQD  HMC2  CM  O6    111.26  3.000
 MQD  HMC1  CM  O6    111.91  3.000
 MQD  HMC2  CM  C2    108.62  3.000
 MQD  HMC1  CM  C2    108.04  3.000
 MQD  O6    CM  C2    110.40  3.000
 MQD  H3C2  C3  H3C1  105.98  3.000
 MQD  H3C2  C3  C4    108.82  3.000
 MQD  H3C1  C3  C4    108.04  3.000
 MQD  H3C2  C3  C2    108.91  3.000
 MQD  H3C1  C3  C2    108.42  3.000
 MQD  C4    C3  C2    116.19  3.000
 MQD  H4    C4  C5    107.52  3.000
 MQD  H4    C4  O4    110.04  3.000
 MQD  C5    C4  O4    107.87  3.000
 MQD  H4    C4  C3    108.25  3.000
 MQD  C5    C4  C3    110.71  3.000
 MQD  O4    C4  C3    112.34  3.000
 MQD  HA    O4  C4    107.08  3.000
 MQD  H5C3  C5  H5C2  108.01  3.000
 MQD  H5C3  C5  H5C1  107.71  3.000
 MQD  H5C2  C5  H5C1  108.22  3.000
 MQD  H5C3  C5  C4    110.51  3.000
 MQD  H5C2  C5  C4    111.18  3.000
 MQD  H5C1  C5  C4    111.09  3.000
 MQD  H6    O6  CM    107.99  3.000

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
 MQD  chir_01  C2  O2  CM  C3  positiv
 MQD  chir_02  C4  O4  C5  C3  negativ

