# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 22:40:18 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: 2-(3-azanylpropylamino)ethanethiol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCNCCS
#
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
 UGH  UGH  "WR-1065"
  ligand  22  8  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UGH
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
 UGH  N1   N  NH1   0  -0.590  -18.9210  -21.9894   -7.8061
 UGH  C4   C  CH2   0  -0.563  -20.8543  -23.2616   -7.0569
 UGH  C3   C  CH2   0  -0.243  -19.3993  -23.3198   -7.4953
 UGH  C2   C  CH2   0  -0.270  -17.5589  -21.9862   -8.3107
 UGH  C1   C  CH2   0  -0.457  -17.0503  -20.5761   -8.5666
 UGH  SG   S  S2    0  -0.262  -21.4122  -24.9473   -6.6397
 UGH  C    C  CH2   0  -0.265  -17.8348  -19.8192   -9.6280
 UGH  N    N  NH2   0  -0.799  -17.2497  -18.5038   -9.8583
 UGH  H1   H  HNH1  0   0.339  -18.9549  -21.4239   -6.9647
 UGH  H3   H  HCH2  0   0.263  -20.9621  -22.6190   -6.1822
 UGH  H4   H  HCH2  0   0.266  -21.4701  -22.8583   -7.8600
 UGH  H5   H  HCH2  0   0.229  -19.3192  -23.9350   -8.3960
 UGH  H6   H  HCH2  0   0.200  -18.7976  -23.8209   -6.7205
 UGH  H7   H  HCH2  0   0.215  -17.5410  -22.5563   -9.2455
 UGH  H8   H  HCH2  0   0.199  -16.8618  -22.4977   -7.6284
 UGH  H9   H  HCH2  0   0.225  -16.0025  -20.6344   -8.8724
 UGH  H10  H  HCH2  0   0.215  -17.0630  -20.0111   -7.6267
 UGH  H11  H  HSH1  0   0.224  -22.6903  -24.6511   -6.3818
 UGH  H12  H  HCH2  0   0.192  -18.8931  -19.7835   -9.3417
 UGH  H13  H  HCH2  0   0.206  -17.7898  -20.3811  -10.5657
 UGH  H14  H  HNH2  0   0.342  -17.7736  -18.0266  -10.5810
 UGH  H15  H  HNH2  0   0.335  -17.3676  -17.9390   -9.0255

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
 UGH  C   N    single  1.458  0.020  1.458
 UGH  C   C1   single  1.521  0.020  1.521
 UGH  C1  C2   single  1.521  0.020  1.521
 UGH  C2  N1   single  1.453  0.020  1.453
 UGH  N1  C3   single  1.448  0.020  1.448
 UGH  C3  C4   single  1.521  0.020  1.521
 UGH  C4  SG   single  1.824  0.020  1.824
 UGH  N1  H1   single  0.890  0.020  1.040
 UGH  C4  H3   single  0.970  0.020  1.090
 UGH  C4  H4   single  0.970  0.020  1.090
 UGH  C3  H5   single  0.970  0.020  1.090
 UGH  C3  H6   single  0.970  0.020  1.090
 UGH  C2  H7   single  0.970  0.020  1.090
 UGH  C2  H8   single  0.970  0.020  1.090
 UGH  C1  H9   single  0.970  0.020  1.090
 UGH  C1  H10  single  0.970  0.020  1.090
 UGH  SG  H11  single  1.200  0.020  1.300
 UGH  C   H12  single  0.970  0.020  1.090
 UGH  C   H13  single  0.970  0.020  1.090
 UGH  N   H14  single  0.890  0.020  1.040
 UGH  N   H15  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
 UGH  H1   N1  C2   108.56  3.000
 UGH  H1   N1  C3   108.86  3.000
 UGH  C2   N1  C3   112.73  3.000
 UGH  H4   C4  H3   108.49  3.000
 UGH  H4   C4  SG   109.75  3.000
 UGH  H3   C4  SG   109.32  3.000
 UGH  H4   C4  C3   110.03  3.000
 UGH  H3   C4  C3   110.38  3.000
 UGH  SG   C4  C3   108.86  3.000
 UGH  H6   C3  H5   106.46  3.000
 UGH  H6   C3  C4   109.71  3.000
 UGH  H5   C3  C4   109.21  3.000
 UGH  H6   C3  N1   112.87  3.000
 UGH  H5   C3  N1   108.42  3.000
 UGH  C4   C3  N1   110.05  3.000
 UGH  H8   C2  H7   106.07  3.000
 UGH  H8   C2  C1   108.86  3.000
 UGH  H7   C2  C1   109.49  3.000
 UGH  H8   C2  N1   112.16  3.000
 UGH  H7   C2  N1   108.10  3.000
 UGH  C1   C2  N1   111.97  3.000
 UGH  H10  C1  H9   106.16  3.000
 UGH  H10  C1  C    109.61  3.000
 UGH  H9   C1  C    109.01  3.000
 UGH  H10  C1  C2   109.24  3.000
 UGH  H9   C1  C2   108.55  3.000
 UGH  C    C1  C2   113.97  3.000
 UGH  H11  SG  C4    97.57  3.000
 UGH  H13  C   H12  106.27  3.000
 UGH  H13  C   N    108.15  3.000
 UGH  H12  C   N    113.52  3.000
 UGH  H13  C   C1   108.74  3.000
 UGH  H12  C   C1   109.36  3.000
 UGH  N    C   C1   110.61  3.000
 UGH  H15  N   H14  105.30  3.000
 UGH  H15  N   C    109.05  3.000
 UGH  H14  N   C    109.29  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
 UGH  Var_01  C    C1  C2  N1   -62.44  30.0  1
 UGH  Var_02  SG   C4  C3  N1  -178.80  30.0  3
 UGH  Var_03  C2   N1  C3  C4  -176.46  30.0  1
 UGH  Var_04  C1   C2  N1  C3  -177.19  30.0  1
 UGH  Var_05  N    C   C1  C2  -177.38  30.0  1
 UGH  Var_06  H9   C1  C2  N1   175.88  30.0  1
 UGH  Var_07  H10  C1  C2  N1    60.53  30.0  1
 UGH  Var_08  H3   C4  C3  N1   -58.81  30.0  3
 UGH  Var_09  H4   C4  C3  N1    60.90  30.0  3
 UGH  Var_10  H1   N1  C3  C4    63.02  30.0  1
 UGH  Var_11  H7   C2  N1  C3    62.13  30.0  1
 UGH  Var_12  H8   C2  N1  C3   -54.46  30.0  1
 UGH  Var_13  H12  C   C1  C2    56.88  30.0  1
 UGH  Var_14  H13  C   C1  C2   -58.76  30.0  1
 UGH  Var_15  H5   C3  N1  C2   -57.07  30.0  3
 UGH  Var_16  H6   C3  N1  C2    60.61  30.0  3
 UGH  Var_17  H14  N   C   C1   178.76  30.0  3
 UGH  Var_18  H15  N   C   C1   -66.62  30.0  3
 UGH  Var_19  H1   N1  C2  C1   -56.50  30.0  3
 UGH  Var_20  H5   C3  C4  SG    62.30  30.0  1
 UGH  Var_21  H6   C3  C4  SG   -54.03  30.0  1
 UGH  Var_22  H7   C2  C1  C     57.43  30.0  3
 UGH  Var_23  H8   C2  C1  C    172.97  30.0  3
 UGH  Var_24  H9   C1  C   N    -55.96  30.0  3
 UGH  Var_25  H10  C1  C   N     59.84  30.0  3

