# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 10:05:06 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  22  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   0.519  -0.1824   0.1574  -1.7726
 DMV  C2    C  CH1   0  -0.080   0.5183   0.5631  -0.4848
 DMV  C3    C  CT    0   0.193  -0.1133  -0.1552   0.7472
 DMV  C32   C  CH3   0  -0.699   0.2210  -1.6420   0.7491
 DMV  C4    C  CH2   0  -0.449   0.4063   0.5381   2.0139
 DMV  C5    C  CH3   0  -0.671  -0.1479  -0.0134   3.3203
 DMV  O11   O  OH1   0  -0.580  -1.2108   0.9323  -2.0695
 DMV  O12   O  O     0  -0.445   0.1821  -0.7664  -2.4583
 DMV  O21   O  OH1   0  -0.652   1.8957   0.3482  -0.5944
 DMV  O31   O  OH1   0  -0.668  -1.5212  -0.0660   0.6556
 DMV  H2    H  HCH1  0   0.271   0.3834   1.6413  -0.3476
 DMV  H323  H  HCH3  0   0.233   1.2872  -1.8083   0.8999
 DMV  H322  H  HCH3  0   0.253  -0.3001  -2.1435   1.5639
 DMV  H321  H  HCH3  0   0.245  -0.0748  -2.1338  -0.1780
 DMV  H42   H  HCH2  0   0.229   0.1668   1.6056   1.9441
 DMV  H41   H  HCH2  0   0.234   1.4968   0.4782   2.0251
 DMV  H53   H  HCH3  0   0.234   0.2252   0.5724   4.1607
 DMV  H52   H  HCH3  0   0.222  -1.2369   0.0305   3.3487
 DMV  H51   H  HCH3  0   0.226   0.1511  -1.0478   3.4901
 DMV  H1O   H  HOH1  0   0.483  -1.6348   0.6258  -2.8861
 DMV  H21   H  HOH1  0   0.452   2.0494  -0.5533  -0.8997
 DMV  H31   H  HOH1  0   0.447  -1.7887   0.8530   0.7684

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  1.521  0.020  1.521
 DMV  C1   O11   single  1.321  0.020  1.321
 DMV  C1   O12   double  1.207  0.020  1.207
 DMV  C2   C3    single  1.560  0.020  1.560
 DMV  C2   O21   single  1.398  0.020  1.398
 DMV  C2   H2    single  0.970  0.020  1.090
 DMV  C3   C32   single  1.524  0.020  1.524
 DMV  C3   C4    single  1.535  0.020  1.535
 DMV  C3   O31   single  1.414  0.020  1.414
 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  1.522  0.020  1.522
 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  O11  H1O   single  0.850  0.020  0.980
 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   123.80  3.000
 DMV  O12   C1   C2    123.09  3.000
 DMV  O11   C1   C2    113.10  3.000
 DMV  H2    C2   O21   106.40  3.000
 DMV  H2    C2   C3    107.73  3.000
 DMV  O21   C2   C3    112.95  3.000
 DMV  H2    C2   C1    108.17  3.000
 DMV  O21   C2   C1    110.27  3.000
 DMV  C3    C2   C1    111.06  3.000
 DMV  O31   C3   C4    111.23  3.000
 DMV  O31   C3   C32   106.27  3.000
 DMV  C4    C3   C32   111.44  3.000
 DMV  O31   C3   C2    108.85  3.000
 DMV  C4    C3   C2    107.87  3.000
 DMV  C32   C3   C2    111.19  3.000
 DMV  H321  C32  H322  107.37  3.000
 DMV  H321  C32  H323  108.32  3.000
 DMV  H322  C32  H323  107.11  3.000
 DMV  H321  C32  C3    112.30  3.000
 DMV  H322  C32  C3    110.19  3.000
 DMV  H323  C32  C3    111.33  3.000
 DMV  H41   C4   H42   105.79  3.000
 DMV  H41   C4   C5    109.56  3.000
 DMV  H42   C4   C5    109.14  3.000
 DMV  H41   C4   C3    108.76  3.000
 DMV  H42   C4   C3    108.26  3.000
 DMV  C5    C4   C3    114.92  3.000
 DMV  H51   C5   H52   107.94  3.000
 DMV  H51   C5   H53   107.21  3.000
 DMV  H52   C5   H53   107.46  3.000
 DMV  H51   C5   C4    112.18  3.000
 DMV  H52   C5   C4    111.80  3.000
 DMV  H53   C5   C4    110.02  3.000
 DMV  H1O   O11  C1    110.12  3.000
 DMV  H21   O21  C2    109.00  3.000
 DMV  H31   O31  C3    109.21  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  CONST_01  H1O  O11  C1  C2   180.00   0.0  0
 DMV  Var_01    H53  C5   C4  C3  -176.61  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
 DMV  plan-1  H1O  0.020

