# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 10:28:19 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (2R,3R,4S)-4-amino-2,6-dimethylheptane-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)[C@H](O)[C@H](C)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
 04D  04D  (2R,3R,4S)-4-amino-2,6-dimethylheptane-1,3-diol  ligand  33  12  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_04D
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
 04D  N5    N  NH2   0  -0.789   0.3231   0.6455   1.6063
 04D  O6    O  OH1   0  -0.667  -0.6766  -1.3362  -1.3450
 04D  O7    O  OH1   0  -0.675  -3.6985   1.4271   0.1162
 04D  C20   C  CH1   0  -0.153   0.4568   0.0988   0.2634
 04D  C21   C  CH1   0   0.056  -0.7106  -0.8671  -0.0096
 04D  C24   C  CH3   0  -0.648   4.3023  -0.5552   0.0047
 04D  C25   C  CH3   0  -0.658   3.0481   1.4266  -0.8690
 04D  C26   C  CH2   0  -0.388   1.8004  -0.5970   0.0064
 04D  C27   C  CH2   0  -0.147  -2.4284   0.9832  -0.3151
 04D  C28   C  CH3   0  -0.653  -3.1684  -1.3906   0.1351
 04D  C29   C  CH1   0  -0.264  -2.0975  -0.3298   0.3803
 04D  HN5   H  HNH2  0   0.336   0.5065  -0.0832   2.2880
 04D  HO6   H  HOH1  0   0.439  -0.6799  -0.5791  -1.9392
 04D  HO7   H  HOH1  0   0.451  -3.8986   2.2462  -0.3450
 04D  H20   H  HCH1  0   0.220   0.3623   0.9422  -0.4321
 04D  H21   H  HCH1  0   0.215  -0.5428  -1.7610   0.6061
 04D  H23   H  HCH1  0   0.204   3.0478   0.7272   1.1534
 04D  H24   H  HCH3  0   0.224   5.2024   0.0502   0.1274
 04D  H24A  H  HCH3  0   0.223   4.3361  -1.3560   0.7457
 04D  H24B  H  HCH3  0   0.211   4.3491  -1.0178  -0.9846
 04D  H25   H  HCH3  0   0.213   3.0284   1.0316  -1.8880
 04D  H25A  H  HCH3  0   0.226   2.1921   2.0935  -0.7579
 04D  H25B  H  HCH3  0   0.227   3.9475   2.0365  -0.7690
 04D  H26   H  HCH2  0   0.210   1.8820  -1.4376   0.7073
 04D  H26A  H  HCH2  0   0.210   1.8047  -1.0328  -0.9973
 04D  H27   H  HCH2  0   0.175  -2.4176   0.8429  -1.4062
 04D  H27A  H  HCH2  0   0.207  -1.6594   1.7282  -0.0786
 04D  H28   H  HCH3  0   0.219  -2.8856  -2.3379   0.5991
 04D  H28A  H  HCH3  0   0.228  -4.1259  -1.0941   0.5604
 04D  H28B  H  HCH3  0   0.213  -3.3189  -1.5773  -0.9289
 04D  H29   H  HCH1  0   0.226  -2.0549  -0.1280   1.4539
 04D  H2    H  HNH2  0   0.351   1.0280   1.3537   1.7663
 04D  C23   C  CH1   0  -0.243   3.0397   0.2896   0.1483

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
 04D  C20  N5    single  1.456  0.020  1.456
 04D  N5   HN5   single  0.890  0.020  1.040
 04D  C21  O6    single  1.416  0.020  1.416
 04D  O6   HO6   single  0.850  0.020  0.980
 04D  O7   C27   single  1.413  0.020  1.413
 04D  O7   HO7   single  0.850  0.020  0.980
 04D  C21  C20   single  1.540  0.020  1.540
 04D  C26  C20   single  1.535  0.020  1.535
 04D  C20  H20   single  0.970  0.020  1.090
 04D  C29  C21   single  1.538  0.020  1.538
 04D  C21  H21   single  0.970  0.020  1.090
 04D  C26  C23   single  1.530  0.020  1.530
 04D  C23  C25   single  1.526  0.020  1.526
 04D  C23  C24   single  1.526  0.020  1.526
 04D  C23  H23   single  0.970  0.020  1.090
 04D  C24  H24   single  0.970  0.020  1.090
 04D  C24  H24A  single  0.970  0.020  1.090
 04D  C24  H24B  single  0.970  0.020  1.090
 04D  C25  H25   single  0.970  0.020  1.090
 04D  C25  H25A  single  0.970  0.020  1.090
 04D  C25  H25B  single  0.970  0.020  1.090
 04D  C26  H26   single  0.970  0.020  1.090
 04D  C26  H26A  single  0.970  0.020  1.090
 04D  C29  C27   single  1.522  0.020  1.522
 04D  C27  H27   single  0.970  0.020  1.090
 04D  C27  H27A  single  0.970  0.020  1.090
 04D  C29  C28   single  1.527  0.020  1.527
 04D  C28  H28   single  0.970  0.020  1.090
 04D  C28  H28A  single  0.970  0.020  1.090
 04D  C28  H28B  single  0.970  0.020  1.090
 04D  C29  H29   single  0.970  0.020  1.090
 04D  N5   H2    single  0.890  0.020  1.040

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
 04D  H2    N5   HN5   105.70  3.000
 04D  H2    N5   C20   110.16  3.000
 04D  HN5   N5   C20   109.48  3.000
 04D  HO6   O6   C21   108.75  3.000
 04D  HO7   O7   C27   107.97  3.000
 04D  H20   C20  C26   108.53  3.000
 04D  H20   C20  C21   107.73  3.000
 04D  C26   C20  C21   110.47  3.000
 04D  H20   C20  N5    106.74  3.000
 04D  C26   C20  N5    113.90  3.000
 04D  C21   C20  N5    109.23  3.000
 04D  H21   C21  C29   106.27  3.000
 04D  H21   C21  C20   107.18  3.000
 04D  C29   C21  C20   114.82  3.000
 04D  H21   C21  O6    104.80  3.000
 04D  C29   C21  O6    112.12  3.000
 04D  C20   C21  O6    110.91  3.000
 04D  H24B  C24  H24A  107.61  3.000
 04D  H24B  C24  H24   107.53  3.000
 04D  H24A  C24  H24   107.76  3.000
 04D  H24B  C24  C23   110.79  3.000
 04D  H24A  C24  C23   111.59  3.000
 04D  H24   C24  C23   111.39  3.000
 04D  H25B  C25  H25A  107.20  3.000
 04D  H25B  C25  H25   107.59  3.000
 04D  H25A  C25  H25   107.56  3.000
 04D  H25B  C25  C23   111.10  3.000
 04D  H25A  C25  C23   112.55  3.000
 04D  H25   C25  C23   110.62  3.000
 04D  H26A  C26  H26   106.29  3.000
 04D  H26A  C26  C23   108.21  3.000
 04D  H26   C26  C23   108.93  3.000
 04D  H26A  C26  C20   109.73  3.000
 04D  H26   C26  C20   107.78  3.000
 04D  C23   C26  C20   115.51  3.000
 04D  H27A  C27  H27   107.07  3.000
 04D  H27A  C27  C29   109.58  3.000
 04D  H27   C27  C29   109.94  3.000
 04D  H27A  C27  O7    110.56  3.000
 04D  H27   C27  O7    110.58  3.000
 04D  C29   C27  O7    109.09  3.000
 04D  H28B  C28  H28A  107.84  3.000
 04D  H28B  C28  H28   107.56  3.000
 04D  H28A  C28  H28   107.34  3.000
 04D  H28B  C28  C29   111.85  3.000
 04D  H28A  C28  C29   111.39  3.000
 04D  H28   C28  C29   110.65  3.000
 04D  H29   C29  C28   108.25  3.000
 04D  H29   C29  C27   107.33  3.000
 04D  C28   C29  C27   111.93  3.000
 04D  H29   C29  C21   106.16  3.000
 04D  C28   C29  C21   110.43  3.000
 04D  C27   C29  C21   112.43  3.000
 04D  H23   C23  C26   108.79  3.000
 04D  H23   C23  C25   108.29  3.000
 04D  C26   C23  C25   111.99  3.000
 04D  H23   C23  C24   107.53  3.000
 04D  C25   C23  C24   110.20  3.000
 04D  C26   C23  C24   109.91  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
 04D  Var_01  C25  C23  C26  C20  -62.78  30.0  3
 04D  Var_02  H25  C25  C23  C24   63.31  30.0  3
 04D  Var_03  H24  C24  C23  C25   57.56  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
 04D  chir_01  C20  N5   C21  C26  positiv
 04D  chir_02  C21  O6   C20  C29  negativ
 04D  chir_03  C29  C21  C27  C28  negativ

