# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 23:18:37 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 4,5-dideoxy-3-C-methyl-D-erythro-pentonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@](C)(O)[C@@H](O)C(O)=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
 DMV  DMV  '4,5-dideoxy-3-C-methyl-D-erythro-pentonic acid'  ligand  21  10  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DMV
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
 DMV  C1    C  C      0   0.420  -0.1110   0.1963  -1.7127
 DMV  C2    C  CH1    0  -0.104   0.5572   0.6176  -0.3865
 DMV  C3    C  CT     0   0.208  -0.1238  -0.0538   0.8326
 DMV  C32   C  CH3    0  -0.687  -0.0280  -1.5776   0.7312
 DMV  C4    C  CH2    0  -0.416   0.5383   0.4576   2.1162
 DMV  C5    C  CH3    0  -0.676  -0.0848  -0.0503   3.4108
 DMV  O11   O  OC    -1  -0.598  -1.3546   0.3192  -1.7948
 DMV  O12   O  O      0  -0.583   0.6554  -0.2377  -2.5921
 DMV  O21   O  OH1    0  -0.691   1.9268   0.3279  -0.4443
 DMV  O31   O  OH1    0  -0.720  -1.4786   0.3572   0.8658
 DMV  H2    H  HCH1   0   0.213   0.4067   1.7046  -0.2709
 DMV  H323  H  HCH3   0   0.217   1.0088  -1.9145   0.7115
 DMV  H322  H  HCH3   0   0.232  -0.5149  -2.0569   1.5810
 DMV  H321  H  HCH3   0   0.226  -0.5187  -1.9521  -0.1695
 DMV  H42   H  HCH2   0   0.212   0.4931   1.5522   2.1064
 DMV  H41   H  HCH2   0   0.220   1.5984   0.1965   2.0982
 DMV  H53   H  HCH3   0   0.226   0.3939   0.4201   4.2706
 DMV  H52   H  HCH3   0   0.222  -1.1496   0.1762   3.4634
 DMV  H51   H  HCH3   0   0.218   0.0329  -1.1281   3.5296
 DMV  H21   H  HOH1   0   0.430   2.0334  -0.0537  -1.3337
 DMV  H31   H  HOH1   0   0.431  -1.7637   0.3720  -0.0708

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
 DMV  C1   C2    single  1.544  0.020  1.544
 DMV  C1   O11   deloc   1.252  0.020  1.252
 DMV  C1   O12   deloc   1.245  0.020  1.245
 DMV  C2   C3    single  1.549  0.020  1.549
 DMV  C2   O21   single  1.401  0.020  1.401
 DMV  C2   H2    single  0.970  0.020  1.090
 DMV  C3   C32   single  1.530  0.020  1.530
 DMV  C3   C4    single  1.532  0.020  1.532
 DMV  C3   O31   single  1.416  0.020  1.416
 DMV  C32  H323  single  0.970  0.020  1.090
 DMV  C32  H322  single  0.970  0.020  1.090
 DMV  C32  H321  single  0.970  0.020  1.090
 DMV  C4   C5    single  1.524  0.020  1.524
 DMV  C4   H42   single  0.970  0.020  1.090
 DMV  C4   H41   single  0.970  0.020  1.090
 DMV  C5   H53   single  0.970  0.020  1.090
 DMV  C5   H52   single  0.970  0.020  1.090
 DMV  C5   H51   single  0.970  0.020  1.090
 DMV  O21  H21   single  0.850  0.020  0.980
 DMV  O31  H31   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
 DMV  O12   C1   O11   126.82  3.000
 DMV  O12   C1   C2    115.83  3.000
 DMV  O11   C1   C2    117.35  3.000
 DMV  H2    C2   O21   109.96  3.000
 DMV  H2    C2   C3    106.52  3.000
 DMV  O21   C2   C3    111.87  3.000
 DMV  H2    C2   C1    107.45  3.000
 DMV  O21   C2   C1    109.35  3.000
 DMV  C3    C2   C1    111.56  3.000
 DMV  O31   C3   C4    107.27  3.000
 DMV  O31   C3   C32   110.52  3.000
 DMV  C4    C3   C32   111.15  3.000
 DMV  O31   C3   C2    108.26  3.000
 DMV  C4    C3   C2    108.94  3.000
 DMV  C32   C3   C2    110.60  3.000
 DMV  H321  C32  H322  106.94  3.000
 DMV  H321  C32  H323  107.85  3.000
 DMV  H322  C32  H323  107.62  3.000
 DMV  H321  C32  C3    111.59  3.000
 DMV  H322  C32  C3    110.98  3.000
 DMV  H323  C32  C3    111.63  3.000
 DMV  H41   C4   H42   106.19  3.000
 DMV  H41   C4   C5    109.34  3.000
 DMV  H42   C4   C5    108.89  3.000
 DMV  H41   C4   C3    109.02  3.000
 DMV  H42   C4   C3    107.95  3.000
 DMV  C5    C4   C3    115.07  3.000
 DMV  H51   C5   H52   107.79  3.000
 DMV  H51   C5   H53   107.04  3.000
 DMV  H52   C5   H53   107.52  3.000
 DMV  H51   C5   C4    112.19  3.000
 DMV  H52   C5   C4    111.79  3.000
 DMV  H53   C5   C4    110.27  3.000
 DMV  H21   O21  C2    103.05  3.000
 DMV  H31   O31  C3    105.10  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
 DMV  Var_01  H53  C5  C4  C3  -175.61  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
 DMV  chir_01  C2  C1  C3   O21  negativ
 DMV  chir_02  C3  C4  C32  C2   positiv

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
 DMV  plan-1  C1   0.020
 DMV  plan-1  C2   0.020
 DMV  plan-1  O11  0.020
 DMV  plan-1  O12  0.020

