# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 10:23:20 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (3~{R},4~{S})-4-azanyl-2-methyl-5-phenyl-pentane-2,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(O)[C@H](O)[C@@H](N)Cc1ccccc1
#
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
 6VA  6VA  (3~{R},4~{S})-4-azanyl-2-methyl-5-phenyl-pentane-2,3-diol  ligand  34  15  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6VA
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
 6VA  N3   N  NH2   0  -0.781  -0.3183  -0.6816   1.2993
 6VA  C14  C  CH2   0  -0.510   0.6369  -0.5201  -1.0184
 6VA  C15  C  CR6   0   0.126   2.0328  -0.2126  -0.5606
 6VA  C16  C  CR16  0  -0.305   2.5752   1.0579  -0.7558
 6VA  C17  C  CR16  0  -0.240   3.8416   1.3761  -0.2866
 6VA  C18  C  CR16  0  -0.274   4.5934   0.4247   0.3928
 6VA  C19  C  CR16  0  -0.241   4.0680  -0.8441   0.5928
 6VA  C20  C  CR16  0  -0.325   2.7991  -1.1576   0.1193
 6VA  C22  C  CT    0   0.186  -2.9842   0.4113   0.2377
 6VA  C24  C  CH3   0  -0.686  -2.6124   1.7425   0.8811
 6VA  C13  C  CH1   0  -0.112  -0.4167  -0.0373   0.0038
 6VA  C23  C  CH3   0  -0.693  -4.1969   0.6040  -0.6745
 6VA  C21  C  CH1   0   0.064  -1.8208  -0.1749  -0.5997
 6VA  O5   O  OH1   0  -0.682  -2.1074  -1.5148  -0.9379
 6VA  H1   H  HNH2  0   0.330  -0.4851  -1.6763   1.2011
 6VA  H2   H  HNH2  0   0.346   0.6279  -0.5962   1.6508
 6VA  H4   H  HCH2  0   0.235   0.4532  -0.0355  -1.9820
 6VA  H5   H  HCH2  0   0.241   0.5192  -1.5950  -1.1753
 6VA  H6   H  HCR6  0   0.245   1.9983   1.8074  -1.2862
 6VA  H7   H  HCR6  0   0.252   4.2431   2.3680  -0.4522
 6VA  H8   H  HCR6  0   0.252   5.5813   0.6705   0.7602
 6VA  H9   H  HCR6  0   0.253   4.6452  -1.5943   1.1185
 6VA  H10  H  HCR6  0   0.248   2.4039  -2.1553   0.2737
 6VA  H11  H  HCH3  0   0.244  -1.8238   1.6149   1.6214
 6VA  H12  H  HCH3  0   0.222  -2.2707   2.4595   0.1321
 6VA  H13  H  HCH3  0   0.231  -3.4809   2.1799   1.3773
 6VA  H14  H  HCH1  0   0.237  -0.2422   1.0332   0.1555
 6VA  H15  H  HCH3  0   0.233  -5.0593   0.9538  -0.1008
 6VA  H16  H  HCH3  0   0.233  -3.9941   1.3528  -1.4407
 6VA  H17  H  HCH3  0   0.237  -4.4780  -0.3236  -1.1748
 6VA  H18  H  HCH1  0   0.223  -1.7980   0.3931  -1.5372
 6VA  H19  H  HOH1  0   0.451  -4.2190  -0.4775   1.4664
 6VA  H20  H  HOH1  0   0.440  -2.5514  -1.9011  -0.1718
 6VA  O6   O  OH1   0  -0.678  -3.2878  -0.5570   1.2366

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
 6VA  C17  C18  aromatic  1.390  0.020  1.390
 6VA  C17  C16  aromatic  1.387  0.020  1.387
 6VA  C18  C19  aromatic  1.388  0.020  1.388
 6VA  C16  C15  aromatic  1.395  0.020  1.395
 6VA  C19  C20  aromatic  1.390  0.020  1.390
 6VA  C15  C20  aromatic  1.394  0.020  1.394
 6VA  C15  C14  single    1.501  0.020  1.501
 6VA  C14  C13  single    1.545  0.020  1.545
 6VA  C13  N3   single    1.450  0.020  1.450
 6VA  C13  C21  single    1.534  0.020  1.534
 6VA  O5   C21  single    1.411  0.020  1.411
 6VA  C21  C22  single    1.549  0.020  1.549
 6VA  C22  O6   single    1.424  0.020  1.424
 6VA  C22  C24  single    1.525  0.020  1.525
 6VA  C22  C23  single    1.530  0.020  1.530
 6VA  N3   H1   single    0.890  0.020  1.040
 6VA  N3   H2   single    0.890  0.020  1.040
 6VA  C14  H4   single    0.970  0.020  1.090
 6VA  C14  H5   single    0.970  0.020  1.090
 6VA  C16  H6   single    0.930  0.020  1.080
 6VA  C17  H7   single    0.930  0.020  1.080
 6VA  C18  H8   single    0.930  0.020  1.080
 6VA  C19  H9   single    0.930  0.020  1.080
 6VA  C20  H10  single    0.930  0.020  1.080
 6VA  C24  H11  single    0.970  0.020  1.090
 6VA  C24  H12  single    0.970  0.020  1.090
 6VA  C24  H13  single    0.970  0.020  1.090
 6VA  C13  H14  single    0.970  0.020  1.090
 6VA  C23  H15  single    0.970  0.020  1.090
 6VA  C23  H16  single    0.970  0.020  1.090
 6VA  C23  H17  single    0.970  0.020  1.090
 6VA  C21  H18  single    0.970  0.020  1.090
 6VA  O6   H19  single    0.850  0.020  0.980
 6VA  O5   H20  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
 6VA  H2   N3   H1   105.67  3.000
 6VA  H2   N3   C13  109.63  3.000
 6VA  H1   N3   C13  109.78  3.000
 6VA  H5   C14  H4   106.93  3.000
 6VA  H5   C14  C13  109.20  3.000
 6VA  H4   C14  C13  109.25  3.000
 6VA  H5   C14  C15  110.21  3.000
 6VA  H4   C14  C15  109.51  3.000
 6VA  C13  C14  C15  111.61  3.000
 6VA  C20  C15  C16  118.16  3.000
 6VA  C20  C15  C14  121.42  3.000
 6VA  C16  C15  C14  120.36  3.000
 6VA  H6   C16  C17  119.50  3.000
 6VA  H6   C16  C15  119.41  3.000
 6VA  C17  C16  C15  121.09  3.000
 6VA  H7   C17  C18  120.08  3.000
 6VA  H7   C17  C16  119.79  3.000
 6VA  C18  C17  C16  120.13  3.000
 6VA  H8   C18  C19  120.28  3.000
 6VA  H8   C18  C17  120.28  3.000
 6VA  C19  C18  C17  119.44  3.000
 6VA  H9   C19  C20  119.72  3.000
 6VA  H9   C19  C18  120.11  3.000
 6VA  C20  C19  C18  120.18  3.000
 6VA  H10  C20  C19  119.46  3.000
 6VA  H10  C20  C15  119.54  3.000
 6VA  C19  C20  C15  121.00  3.000
 6VA  O6   C22  C21  106.38  3.000
 6VA  O6   C22  C23  109.57  3.000
 6VA  C21  C22  C23  108.71  3.000
 6VA  C23  C22  C24  109.57  3.000
 6VA  O6   C22  C24  110.47  3.000
 6VA  C21  C22  C24  112.06  3.000
 6VA  H13  C24  H12  107.32  3.000
 6VA  H13  C24  H11  108.30  3.000
 6VA  H12  C24  H11  108.46  3.000
 6VA  H13  C24  C22  110.35  3.000
 6VA  H12  C24  C22  111.12  3.000
 6VA  H11  C24  C22  111.17  3.000
 6VA  H14  C13  C21  106.74  3.000
 6VA  H14  C13  C14  106.76  3.000
 6VA  C21  C13  C14  109.61  3.000
 6VA  H14  C13  N3   107.44  3.000
 6VA  C21  C13  N3   111.94  3.000
 6VA  C14  C13  N3   113.94  3.000
 6VA  H17  C23  H16  108.04  3.000
 6VA  H17  C23  H15  108.03  3.000
 6VA  H16  C23  H15  107.21  3.000
 6VA  H17  C23  C22  111.75  3.000
 6VA  H16  C23  C22  110.99  3.000
 6VA  H15  C23  C22  110.65  3.000
 6VA  H18  C21  O5   106.93  3.000
 6VA  H18  C21  C13  105.71  3.000
 6VA  O5   C21  C13  111.42  3.000
 6VA  H18  C21  C22  106.37  3.000
 6VA  O5   C21  C22  109.66  3.000
 6VA  C13  C21  C22  116.15  3.000
 6VA  H20  O5   C21  106.43  3.000
 6VA  H19  O6   C22  108.52  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
 6VA  CONST_01  C18  C17  C16  C15    0.00   0.0  0
 6VA  CONST_02  C18  C19  C20  C15    0.00   0.0  0
 6VA  CONST_03  C19  C18  C17  C16    0.00   0.0  0
 6VA  CONST_04  C19  C20  C15  C16    0.00   0.0  0
 6VA  CONST_05  C20  C19  C18  C17    0.00   0.0  0
 6VA  CONST_06  C20  C15  C16  C17    0.00   0.0  0
 6VA  CONST_07  C17  C16  C15  C14  180.00   0.0  0
 6VA  CONST_08  C19  C20  C15  C14  180.00   0.0  0
 6VA  CONST_09  H7   C17  C16  C15  180.00   0.0  0
 6VA  CONST_10  H9   C19  C20  C15  180.00   0.0  0
 6VA  CONST_11  H8   C18  C17  C16  180.00   0.0  0
 6VA  CONST_12  H10  C20  C15  C16  180.00   0.0  0
 6VA  CONST_13  H6   C16  C17  C18  180.00   0.0  0
 6VA  Var_01    C13  C14  C15  C16  -81.90  30.0  2
 6VA  Var_02    H15  C23  C22  C24  -61.06  30.0  3
 6VA  Var_03    H11  C24  C22  C23  173.60  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
 6VA  chir_01  C13  C14  N3   C21  positiv
 6VA  chir_02  C21  O5   C13  C22  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
 6VA  plan-1  C14  0.020
 6VA  plan-1  C15  0.020
 6VA  plan-1  C16  0.020
 6VA  plan-1  C17  0.020
 6VA  plan-1  C18  0.020
 6VA  plan-1  C19  0.020
 6VA  plan-1  C20  0.020
 6VA  plan-1  H6   0.020
 6VA  plan-1  H7   0.020
 6VA  plan-1  H8   0.020
 6VA  plan-1  H9   0.020
 6VA  plan-1  H10  0.020

