# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 21:37:29 2021
#   Inital geometry file: a 77 line input string
#   Ligand name: (1R,2S,3R,4R)-3-amino-4-cyclohexylcyclopentane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1[C@H](O)[C@H](O)C[C@@H]1C2CCCCC2
#
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
 D8A  D8A  (1R,2S,3R,4R)-3-amino-4-cyclohexylcyclopentane-1,2-diol  ligand  35  14  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D8A
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
 D8A  C4   C  CH2   0  -0.417  -11.4516  1.4602  -0.6989
 D8A  C5   C  CH2   0  -0.430  -12.9359  1.7197  -0.9325
 D8A  C6   C  CH1   0  -0.235   -9.5872  1.2421   0.9751
 D8A  C7   C  CH2   0  -0.464   -8.5840  2.1591   0.2345
 D8A  C8   C  CH1   0   0.009   -7.3882  2.3564   1.1736
 D8A  C9   C  CH1   0   0.047   -7.5788  1.2543   2.2145
 D8A  C10  C  CH1   0  -0.094   -9.0885  1.2215   2.4212
 D8A  O1   O  OH1   0  -0.676   -7.4709  3.6424   1.7539
 D8A  O    O  OH1   0  -0.681   -6.8044  1.5085   3.3611
 D8A  N    N  NH2   0  -0.813   -9.5292  0.0411   3.1450
 D8A  C3   C  CH1   0  -0.230  -11.0680  1.5751   0.7773
 D8A  C2   C  CH2   0  -0.429  -11.4981  2.9322   1.3358
 D8A  C1   C  CH2   0  -0.425  -12.9865  3.1876   1.1045
 D8A  C    C  CH2   0  -0.429  -13.3549  3.0735  -0.3702
 D8A  H1   H  HCH2  0   0.222  -11.1796  0.4688  -1.0746
 D8A  H2   H  HCH2  0   0.214  -10.8665  2.1806  -1.2820
 D8A  H3   H  HCH2  0   0.224  -13.1629  1.6639  -2.0002
 D8A  H4   H  HCH2  0   0.206  -13.5222  0.9298  -0.4491
 D8A  H5   H  HCH1  0   0.223   -9.4465  0.2209   0.5979
 D8A  H6   H  HCH2  0   0.244   -8.2715  1.7076  -0.7069
 D8A  H7   H  HCH2  0   0.237   -9.0098  3.1321  -0.0160
 D8A  H8   H  HCH1  0   0.214   -6.4321  2.2390   0.6471
 D8A  H9   H  HCH1  0   0.199   -7.2908  0.2997   1.7483
 D8A  H10  H  HCH1  0   0.203   -9.3803  2.1592   2.9178
 D8A  H11  H  HOH1  0   0.443   -6.7995  3.7033   2.4413
 D8A  H12  H  HOH1  0   0.454   -6.7510  0.7043   3.8849
 D8A  H13  H  HNH2  0   0.341   -9.2819  0.1300   4.1235
 D8A  H14  H  HNH2  0   0.345  -10.5415  0.0015   3.1387
 D8A  H16  H  HCH1  0   0.205  -11.6464  0.8102   1.3163
 D8A  H17  H  HCH2  0   0.227  -11.2814  2.9896   2.4056
 D8A  H18  H  HCH2  0   0.208  -10.9231  3.7350   0.8607
 D8A  H19  H  HCH2  0   0.224  -13.2583  4.1732   1.4907
 D8A  H20  H  HCH2  0   0.207  -13.5713  2.4598   1.6780
 D8A  H21  H  HCH2  0   0.206  -12.8534  3.8701  -0.9315
 D8A  H22  H  HCH2  0   0.224  -14.4285  3.2272  -0.5062

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
 D8A  C5   C4   single  1.525  0.020  1.525
 D8A  C5   C    single  1.525  0.020  1.525
 D8A  C4   C3   single  1.530  0.020  1.530
 D8A  C    C1   single  1.524  0.020  1.524
 D8A  C7   C6   single  1.548  0.020  1.548
 D8A  C7   C8   single  1.533  0.020  1.533
 D8A  C3   C6   single  1.531  0.020  1.531
 D8A  C3   C2   single  1.529  0.020  1.529
 D8A  C6   C10  single  1.530  0.020  1.530
 D8A  C1   C2   single  1.528  0.020  1.528
 D8A  C8   O1   single  1.413  0.020  1.413
 D8A  C8   C9   single  1.528  0.020  1.528
 D8A  C9   C10  single  1.524  0.020  1.524
 D8A  C9   O    single  1.407  0.020  1.407
 D8A  C10  N    single  1.453  0.020  1.453
 D8A  C4   H1   single  0.970  0.020  1.090
 D8A  C4   H2   single  0.970  0.020  1.090
 D8A  C5   H3   single  0.970  0.020  1.090
 D8A  C5   H4   single  0.970  0.020  1.090
 D8A  C6   H5   single  0.970  0.020  1.090
 D8A  C7   H6   single  0.970  0.020  1.090
 D8A  C7   H7   single  0.970  0.020  1.090
 D8A  C8   H8   single  0.970  0.020  1.090
 D8A  C9   H9   single  0.970  0.020  1.090
 D8A  C10  H10  single  0.970  0.020  1.090
 D8A  O1   H11  single  0.850  0.020  0.980
 D8A  O    H12  single  0.850  0.020  0.980
 D8A  N    H13  single  0.890  0.020  1.040
 D8A  N    H14  single  0.890  0.020  1.040
 D8A  C3   H16  single  0.970  0.020  1.090
 D8A  C2   H17  single  0.970  0.020  1.090
 D8A  C2   H18  single  0.970  0.020  1.090
 D8A  C1   H19  single  0.970  0.020  1.090
 D8A  C1   H20  single  0.970  0.020  1.090
 D8A  C    H21  single  0.970  0.020  1.090
 D8A  C    H22  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
 D8A  H2   C4   H1   106.27  3.000
 D8A  H2   C4   C3   109.28  3.000
 D8A  H1   C4   C3   109.69  3.000
 D8A  H2   C4   C5   109.05  3.000
 D8A  H1   C4   C5   110.09  3.000
 D8A  C3   C4   C5   112.28  3.000
 D8A  H4   C5   H3   106.44  3.000
 D8A  H4   C5   C    109.28  3.000
 D8A  H3   C5   C    110.39  3.000
 D8A  H4   C5   C4   109.30  3.000
 D8A  H3   C5   C4   110.07  3.000
 D8A  C    C5   C4   111.23  3.000
 D8A  H5   C6   C3   106.39  3.000
 D8A  H5   C6   C10  105.69  3.000
 D8A  C3   C6   C10  116.14  3.000
 D8A  H5   C6   C7   107.68  3.000
 D8A  C10  C6   C7   104.41  3.000
 D8A  C3   C6   C7   115.87  3.000
 D8A  H7   C7   H6   106.44  3.000
 D8A  H7   C7   C8   109.28  3.000
 D8A  H6   C7   C8   111.02  3.000
 D8A  H7   C7   C6   112.66  3.000
 D8A  H6   C7   C6   110.71  3.000
 D8A  C8   C7   C6   106.78  3.000
 D8A  H8   C8   O1   110.19  3.000
 D8A  H8   C8   C9   110.99  3.000
 D8A  O1   C8   C9   111.67  3.000
 D8A  H8   C8   C7   111.83  3.000
 D8A  C9   C8   C7   103.13  3.000
 D8A  O1   C8   C7   108.84  3.000
 D8A  H9   C9   O    110.97  3.000
 D8A  H9   C9   C10  107.34  3.000
 D8A  O    C9   C10  116.01  3.000
 D8A  H9   C9   C8   107.72  3.000
 D8A  O    C9   C8   110.87  3.000
 D8A  C10  C9   C8   103.38  3.000
 D8A  H10  C10  N    112.77  3.000
 D8A  H10  C10  C9   107.79  3.000
 D8A  N    C10  C9   112.67  3.000
 D8A  H10  C10  C6   109.19  3.000
 D8A  N    C10  C6   112.51  3.000
 D8A  C9   C10  C6   101.21  3.000
 D8A  H11  O1   C8   108.06  3.000
 D8A  H12  O    C9   108.87  3.000
 D8A  H14  N    H13  104.67  3.000
 D8A  H14  N    C10  109.37  3.000
 D8A  H13  N    C10  109.62  3.000
 D8A  H16  C3   C2   106.87  3.000
 D8A  H16  C3   C6   107.10  3.000
 D8A  C2   C3   C6   114.71  3.000
 D8A  H16  C3   C4   106.79  3.000
 D8A  C2   C3   C4   110.40  3.000
 D8A  C6   C3   C4   110.55  3.000
 D8A  H18  C2   H17  106.37  3.000
 D8A  H18  C2   C1   108.85  3.000
 D8A  H17  C2   C1   109.42  3.000
 D8A  H18  C2   C3   110.14  3.000
 D8A  H17  C2   C3   110.39  3.000
 D8A  C1   C2   C3   111.54  3.000
 D8A  H20  C1   H19  106.34  3.000
 D8A  H20  C1   C    109.13  3.000
 D8A  H19  C1   C    110.44  3.000
 D8A  H20  C1   C2   109.25  3.000
 D8A  H19  C1   C2   109.85  3.000
 D8A  C    C1   C2   111.68  3.000
 D8A  H22  C    H21  106.47  3.000
 D8A  H22  C    C1   110.32  3.000
 D8A  H21  C    C1   109.30  3.000
 D8A  H22  C    C5   110.42  3.000
 D8A  H21  C    C5   109.32  3.000
 D8A  C1   C    C5   110.90  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
 D8A  Var_01  C1  C   C5  C4  -54.96  30.0  1
 D8A  Var_02  C2  C1  C   C5   55.46  30.0  1
 D8A  Var_03  C   C5  C4  C3   55.30  30.0  1
 D8A  Var_04  C   C1  C2  C3  -55.68  30.0  1

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
 D8A  chir_01  C6   C7  C3   C10  positiv
 D8A  chir_02  C8   O1  C9   C7   negativ
 D8A  chir_03  C9   O   C10  C8   negativ
 D8A  chir_04  C10  N   C9   C6   negativ
 D8A  chir_05  C3   C4  C6   C2   negativ

