# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 05:28:49 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: (3R,4S,5S)-5-amino-3,7-dimethyloctan-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](C)[C@H](O)[C@@H](N)CC(C)C
#
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
 27W  27W  (3R,4S,5S)-5-amino-3,7-dimethyloctan-4-ol  ligand  35  12  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_27W
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
 27W  N3   N  NH2   0  -0.793   0.4648  -0.0786  -1.7546
 27W  C11  C  CH1   0  -0.141   0.4452  -0.0504  -0.2978
 27W  C12  C  CH2   0  -0.387   1.7810   0.4828   0.2187
 27W  C13  C  CH1   0  -0.227   2.9904  -0.4045  -0.0822
 27W  C15  C  CH3   0  -0.653   4.2839   0.3607   0.1822
 27W  C14  C  CH3   0  -0.659   2.9669  -1.6921   0.7357
 27W  C16  C  CH1   0   0.081  -0.7295   0.7311   0.3231
 27W  O6   O  OH1   0  -0.670  -0.5928   2.1230   0.0877
 27W  C17  C  CH1   0  -0.274  -2.1236   0.2361  -0.0997
 27W  C23  C  CH3   0  -0.661  -3.2081   1.0443   0.6103
 27W  C18  C  CH2   0  -0.427  -2.2950  -1.2666   0.1552
 27W  C44  C  CH3   0  -0.666  -3.6551  -1.8209  -0.2512
 27W  H33  H  HNH2  0   0.348  -0.4052  -0.4440  -2.1225
 27W  H34  H  HCH1  0   0.227   0.3451  -1.0857   0.0413
 27W  H35  H  HCH2  0   0.214   1.9506   1.4781  -0.2049
 27W  H36  H  HCH2  0   0.208   1.7120   0.6269   1.3034
 27W  H37  H  HCH1  0   0.215   2.9583  -0.6685  -1.1438
 27W  H38  H  HCH3  0   0.221   5.1612  -0.2585  -0.0155
 27W  H39  H  HCH3  0   0.221   4.3575   1.2498  -0.4467
 27W  H40  H  HCH3  0   0.209   4.3394   0.6864   1.2242
 27W  H41  H  HCH3  0   0.225   2.0727  -2.2893   0.5503
 27W  H42  H  HCH3  0   0.223   3.8284  -2.3217   0.5059
 27W  H43  H  HCH3  0   0.210   2.9980  -1.4698   1.8060
 27W  H44  H  HCH1  0   0.206  -0.6515   0.6148   1.4120
 27W  H45  H  HOH1  0   0.433  -0.7659   2.2892  -0.8450
 27W  H46  H  HCH1  0   0.201  -2.2310   0.4058  -1.1815
 27W  H47  H  HCH3  0   0.231  -3.0930   2.1130   0.4379
 27W  H48  H  HCH3  0   0.231  -4.2041   0.7687   0.2661
 27W  H49  H  HCH3  0   0.212  -3.1729   0.8744   1.6898
 27W  H50  H  HCH2  0   0.226  -1.5323  -1.8246  -0.3927
 27W  H51  H  HCH2  0   0.214  -2.1147  -1.4719   1.2163
 27W  H52  H  HCH3  0   0.223  -4.4689  -1.4120   0.3474
 27W  H53  H  HCH3  0   0.217  -3.8707  -1.6004  -1.2986
 27W  H54  H  HCH3  0   0.230  -3.6793  -2.9047  -0.1326
 27W  H2   H  HNH2  0   0.331   0.5655   0.8583  -2.1271

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
 27W  C17  C16  single  1.539  0.020  1.539
 27W  C17  C18  single  1.534  0.020  1.534
 27W  C17  C23  single  1.528  0.020  1.528
 27W  C16  O6   single  1.418  0.020  1.418
 27W  C16  C11  single  1.542  0.020  1.542
 27W  C18  C44  single  1.524  0.020  1.524
 27W  C13  C12  single  1.530  0.020  1.530
 27W  C13  C14  single  1.526  0.020  1.526
 27W  C13  C15  single  1.526  0.020  1.526
 27W  C12  C11  single  1.528  0.020  1.528
 27W  C11  N3   single  1.457  0.020  1.457
 27W  N3   H33  single  0.890  0.020  1.040
 27W  C11  H34  single  0.970  0.020  1.090
 27W  C12  H35  single  0.970  0.020  1.090
 27W  C12  H36  single  0.970  0.020  1.090
 27W  C13  H37  single  0.970  0.020  1.090
 27W  C15  H38  single  0.970  0.020  1.090
 27W  C15  H39  single  0.970  0.020  1.090
 27W  C15  H40  single  0.970  0.020  1.090
 27W  C14  H41  single  0.970  0.020  1.090
 27W  C14  H42  single  0.970  0.020  1.090
 27W  C14  H43  single  0.970  0.020  1.090
 27W  C16  H44  single  0.970  0.020  1.090
 27W  O6   H45  single  0.850  0.020  0.980
 27W  C17  H46  single  0.970  0.020  1.090
 27W  C23  H47  single  0.970  0.020  1.090
 27W  C23  H48  single  0.970  0.020  1.090
 27W  C23  H49  single  0.970  0.020  1.090
 27W  C18  H50  single  0.970  0.020  1.090
 27W  C18  H51  single  0.970  0.020  1.090
 27W  C44  H52  single  0.970  0.020  1.090
 27W  C44  H53  single  0.970  0.020  1.090
 27W  C44  H54  single  0.970  0.020  1.090
 27W  N3   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
 27W  H2   N3   H33  106.58  3.000
 27W  H2   N3   C11  110.55  3.000
 27W  H33  N3   C11  111.01  3.000
 27W  H34  C11  C16  106.57  3.000
 27W  H34  C11  C12  107.79  3.000
 27W  C16  C11  C12  110.68  3.000
 27W  H34  C11  N3   107.03  3.000
 27W  C12  C11  N3   109.44  3.000
 27W  C16  C11  N3   115.01  3.000
 27W  H36  C12  H35  105.84  3.000
 27W  H36  C12  C13  108.70  3.000
 27W  H35  C12  C13  109.19  3.000
 27W  H36  C12  C11  108.98  3.000
 27W  H35  C12  C11  108.77  3.000
 27W  C13  C12  C11  114.98  3.000
 27W  H37  C13  C14  108.42  3.000
 27W  H37  C13  C15  108.29  3.000
 27W  C14  C13  C15  110.08  3.000
 27W  H37  C13  C12  107.91  3.000
 27W  C15  C13  C12  110.20  3.000
 27W  C14  C13  C12  111.83  3.000
 27W  H40  C15  H39  107.64  3.000
 27W  H40  C15  H38  107.51  3.000
 27W  H39  C15  H38  107.66  3.000
 27W  H40  C15  C13  110.96  3.000
 27W  H39  C15  C13  111.45  3.000
 27W  H38  C15  C13  111.43  3.000
 27W  H43  C14  H42  107.51  3.000
 27W  H43  C14  H41  107.51  3.000
 27W  H42  C14  H41  107.17  3.000
 27W  H43  C14  C13  110.65  3.000
 27W  H42  C14  C13  111.21  3.000
 27W  H41  C14  C13  112.55  3.000
 27W  H44  C16  C17  107.63  3.000
 27W  H44  C16  O6   105.18  3.000
 27W  C17  C16  O6   110.95  3.000
 27W  H44  C16  C11  106.95  3.000
 27W  O6   C16  C11  110.93  3.000
 27W  C17  C16  C11  114.62  3.000
 27W  H45  O6   C16  108.23  3.000
 27W  H46  C17  C18  107.68  3.000
 27W  H46  C17  C23  107.82  3.000
 27W  C18  C17  C23  111.21  3.000
 27W  H46  C17  C16  108.00  3.000
 27W  C23  C17  C16  110.20  3.000
 27W  C18  C17  C16  111.76  3.000
 27W  H49  C23  H48  107.59  3.000
 27W  H49  C23  H47  107.79  3.000
 27W  H48  C23  H47  107.15  3.000
 27W  H49  C23  C17  110.72  3.000
 27W  H48  C23  C17  111.62  3.000
 27W  H47  C23  C17  111.76  3.000
 27W  H51  C18  H50  105.97  3.000
 27W  H51  C18  C44  109.69  3.000
 27W  H50  C18  C44  107.67  3.000
 27W  H51  C18  C17  109.04  3.000
 27W  H50  C18  C17  109.82  3.000
 27W  C44  C18  C17  114.32  3.000
 27W  H54  C44  H53  107.49  3.000
 27W  H54  C44  H52  107.26  3.000
 27W  H53  C44  H52  107.68  3.000
 27W  H54  C44  C18  110.62  3.000
 27W  H53  C44  C18  111.01  3.000
 27W  H52  C44  C18  112.55  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
 27W  Var_01  C14  C13  C12  C11  -70.29  30.0  1
 27W  Var_02  H41  C14  C13  C12   59.15  30.0  3
 27W  Var_03  H38  C15  C13  C12  179.36  30.0  3
 27W  Var_04  H52  C44  C18  C17  -65.37  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
 27W  chir_01  C11  C16  C12  N3   positiv
 27W  chir_02  C16  O6   C11  C17  positiv
 27W  chir_03  C17  C16  C18  C23  negativ

