# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 11:07:00 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: 3-hydroxypentanedinitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(CC#N)CC#N
#
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
 4SD  4SD  3-hydroxypentanedinitrile  ligand  14  8  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4SD
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
 4SD  C1  C  CH1   0   0.026  -0.0035   0.0740   0.1192
 4SD  C2  C  CH2   0  -0.572   1.2363   0.8919  -0.2641
 4SD  C5  C  CSP   0   0.130  -2.4644   0.1359   0.0849
 4SD  C4  C  CH2   0  -0.572  -1.2584   0.8730  -0.2531
 4SD  C3  C  CSP   0   0.131   2.4550   0.1727   0.0655
 4SD  N2  N  NS    0  -0.267  -3.4168  -0.4482   0.3580
 4SD  O1  O  OH1   0  -0.641   0.0039  -1.1990  -0.4536
 4SD  N1  N  NS    0  -0.267   3.4177  -0.3977   0.3314
 4SD  H1  H  HCH1  0   0.287   0.0021  -0.0765   1.2004
 4SD  H2  H  HCH2  0   0.319   1.2446   1.1127  -1.3350
 4SD  H3  H  HCH2  0   0.325   1.2450   1.8466   0.2645
 4SD  H4  H  HCH2  0   0.325  -1.2773   1.8267   0.2770
 4SD  H5  H  HCH2  0   0.319  -1.2793   1.0955  -1.3234
 4SD  H6  H  HOH1  0   0.457  -0.0002  -1.1188  -1.4147

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
 4SD  C2  C3  single  1.453  0.020  1.453
 4SD  C2  C1  single  1.534  0.020  1.534
 4SD  O1  C1  single  1.396  0.020  1.396
 4SD  C3  N1  triple  1.150  0.020  1.150
 4SD  C1  C4  single  1.534  0.020  1.534
 4SD  C4  C5  single  1.453  0.020  1.453
 4SD  C5  N2  triple  1.150  0.020  1.150
 4SD  C1  H1  single  0.970  0.020  1.090
 4SD  C2  H2  single  0.970  0.020  1.090
 4SD  C2  H3  single  0.970  0.020  1.090
 4SD  C4  H4  single  0.970  0.020  1.090
 4SD  C4  H5  single  0.970  0.020  1.090
 4SD  O1  H6  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
 4SD  H1  C1  O1  106.29  3.000
 4SD  H1  C1  C4  108.45  3.000
 4SD  O1  C1  C4  112.32  3.000
 4SD  H1  C1  C2  108.48  3.000
 4SD  C4  C1  C2  108.84  3.000
 4SD  O1  C1  C2  112.30  3.000
 4SD  H3  C2  H2  107.32  3.000
 4SD  H3  C2  C3  108.45  3.000
 4SD  H2  C2  C3  108.41  3.000
 4SD  H3  C2  C1  110.60  3.000
 4SD  H2  C2  C1  111.01  3.000
 4SD  C3  C2  C1  110.94  3.000
 4SD  N2  C5  C4  180.00  3.000
 4SD  H5  C4  H4  107.29  3.000
 4SD  H5  C4  C5  108.36  3.000
 4SD  H4  C4  C5  108.42  3.000
 4SD  H5  C4  C1  111.05  3.000
 4SD  H4  C4  C1  110.58  3.000
 4SD  C5  C4  C1  111.00  3.000
 4SD  N1  C3  C2  180.00  3.000
 4SD  H6  O1  C1  109.45  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
 4SD  Var_01  C5  C4  C1  C2   179.71  30.0  3
 4SD  Var_02  C3  C2  C1  C4  -179.80  30.0  2

