# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 10:20:46 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 4-(dimethylamino)butyl imidothiocarbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCCCSC(N)=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
 4DI  4DI  '4-(dimethylamino)butyl imidothiocarbamate'  ligand  28  11  .  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_4DI
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
 4DI  C1    C  C     0   0.280  -3.7253   0.3666   0.0309
 4DI  S     S  S2    0  -0.009  -2.3823  -0.7754  -0.1657
 4DI  C2    C  CH2   0  -0.538  -0.9380   0.2904   0.0852
 4DI  C3    C  CH2   0  -0.430   0.3225  -0.5513  -0.0523
 4DI  C4    C  CH2   0  -0.439   1.5770   0.2975   0.1232
 4DI  C5    C  CH2   0  -0.250   2.8388  -0.5413  -0.0249
 4DI  N1    N  NT    0  -0.408   4.0643   0.1867   0.2496
 4DI  C6    C  CH3   0  -0.518   5.1866  -0.7210   0.3537
 4DI  C7    C  CH3   0  -0.526   4.3339   1.2144  -0.7335
 4DI  N2    N  NH2   0  -0.807  -4.9324  -0.2449  -0.1449
 4DI  N3    N  N     0  -0.645  -3.4953   1.5966   0.2499
 4DI  H21   H  HCH2  0   0.269  -0.9979   0.7460   1.0735
 4DI  H22   H  HCH2  0   0.269  -0.9586   1.0893  -0.6558
 4DI  H31   H  HCH2  0   0.234   0.3413  -1.0320  -1.0350
 4DI  H32   H  HCH2  0   0.234   0.3141  -1.3551   0.6897
 4DI  H41   H  HCH2  0   0.223   1.5740   0.7689   1.1106
 4DI  H42   H  HCH2  0   0.227   1.5601   1.1067  -0.6119
 4DI  H51   H  HCH2  0   0.183   2.8565  -0.9977  -1.0316
 4DI  H52   H  HCH2  0   0.224   2.7838  -1.3719   0.6857
 4DI  H61   H  HCH3  0   0.230   6.0904  -0.1704   0.6191
 4DI  H62   H  HCH3  0   0.231   5.0033  -1.4575   1.1374
 4DI  H63   H  HCH3  0   0.188   5.3930  -1.2693  -0.5795
 4DI  H71   H  HCH3  0   0.235   3.5498   1.9709  -0.7397
 4DI  H72   H  HCH3  0   0.233   5.2693   1.7200  -0.4900
 4DI  H73   H  HCH3  0   0.189   4.4261   0.8177  -1.7577
 4DI  HN21  H  HNH2  0   0.396  -5.7482   0.2616   0.1623
 4DI  HN22  H  HNH2  0   0.397  -5.0000  -1.2401  -0.0031
 4DI  HN3   H  H     0   0.330  -4.3619   2.1192   0.3475

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
 4DI  C1  S     single  1.774  0.020  1.774
 4DI  C1  N2    single  1.364  0.020  1.364
 4DI  C1  N3    double  1.270  0.020  1.270
 4DI  S   C2    single  1.812  0.020  1.812
 4DI  C2  C3    single  1.522  0.020  1.522
 4DI  C2  H21   single  0.970  0.020  1.090
 4DI  C2  H22   single  0.970  0.020  1.090
 4DI  C3  C4    single  1.525  0.020  1.525
 4DI  C3  H31   single  0.970  0.020  1.090
 4DI  C3  H32   single  0.970  0.020  1.090
 4DI  C4  C5    single  1.522  0.020  1.522
 4DI  C4  H41   single  0.970  0.020  1.090
 4DI  C4  H42   single  0.970  0.020  1.090
 4DI  C5  N1    single  1.452  0.020  1.452
 4DI  C5  H51   single  0.970  0.020  1.090
 4DI  C5  H52   single  0.970  0.020  1.090
 4DI  N1  C6    single  1.447  0.020  1.447
 4DI  N1  C7    single  1.448  0.020  1.448
 4DI  C6  H61   single  0.970  0.020  1.090
 4DI  C6  H62   single  0.970  0.020  1.090
 4DI  C6  H63   single  0.970  0.020  1.090
 4DI  C7  H71   single  0.970  0.020  1.090
 4DI  C7  H72   single  0.970  0.020  1.090
 4DI  C7  H73   single  0.970  0.020  1.090
 4DI  N2  HN21  single  0.890  0.020  1.040
 4DI  N2  HN22  single  0.890  0.020  1.040
 4DI  N3  HN3   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
 4DI  N3    C1  N2    128.05  3.000
 4DI  N3    C1  S     120.36  3.000
 4DI  N2    C1  S     111.53  3.000
 4DI  C2    S   C1    102.09  3.000
 4DI  H22   C2  H21   108.01  3.000
 4DI  H22   C2  C3    111.08  3.000
 4DI  H21   C2  C3    111.02  3.000
 4DI  H22   C2  S     108.78  3.000
 4DI  H21   C2  S     109.12  3.000
 4DI  C3    C2  S     108.80  3.000
 4DI  H32   C3  H31   106.65  3.000
 4DI  H32   C3  C4    109.71  3.000
 4DI  H31   C3  C4    109.50  3.000
 4DI  H32   C3  C2    109.80  3.000
 4DI  H31   C3  C2    109.78  3.000
 4DI  C4    C3  C2    111.29  3.000
 4DI  H42   C4  H41   106.73  3.000
 4DI  H42   C4  C5    110.81  3.000
 4DI  H41   C4  C5    109.12  3.000
 4DI  H42   C4  C3    108.77  3.000
 4DI  H41   C4  C3    109.96  3.000
 4DI  C5    C4  C3    111.34  3.000
 4DI  H52   C5  H51   106.19  3.000
 4DI  H52   C5  N1    107.47  3.000
 4DI  H51   C5  N1    111.45  3.000
 4DI  H52   C5  C4    108.27  3.000
 4DI  H51   C5  C4    109.23  3.000
 4DI  N1    C5  C4    113.89  3.000
 4DI  C7    N1  C6    110.47  3.000
 4DI  C7    N1  C5    112.64  3.000
 4DI  C6    N1  C5    110.71  3.000
 4DI  H63   C6  H62   107.69  3.000
 4DI  H63   C6  H61   107.58  3.000
 4DI  H62   C6  H61   107.76  3.000
 4DI  H63   C6  N1    113.36  3.000
 4DI  H62   C6  N1    110.17  3.000
 4DI  H61   C6  N1    110.08  3.000
 4DI  H73   C7  H72   107.61  3.000
 4DI  H73   C7  H71   107.75  3.000
 4DI  H72   C7  H71   107.26  3.000
 4DI  H73   C7  N1    113.02  3.000
 4DI  H72   C7  N1    109.70  3.000
 4DI  H71   C7  N1    111.26  3.000
 4DI  HN22  N2  HN21  113.52  3.000
 4DI  HN22  N2  C1    118.94  3.000
 4DI  HN21  N2  C1    116.84  3.000
 4DI  HN3   N3  C1    111.09  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
 4DI  CONST_01  HN21  N2  C1  S    180.00   0.0  0
 4DI  CONST_03  HN3   N3  C1  S    180.00   0.0  0
 4DI  Var_01    C3    C2  S   C1   179.98  30.0  3
 4DI  Var_02    C4    C3  C2  S    178.94  30.0  3
 4DI  Var_03    N2    C1  S   C2   179.01  30.0  2
 4DI  Var_04    C5    C4  C3  C2  -179.56  30.0  3
 4DI  Var_05    N1    C5  C4  C3  -174.80  30.0  3
 4DI  Var_06    C6    N1  C5  C4   168.52  30.0  3
 4DI  Var_07    H61   C6  N1  C5  -176.61  30.0  3
 4DI  Var_08    H71   C7  N1  C5    62.29  30.0  3

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
 4DI  plan-1  C1    0.020
 4DI  plan-1  S     0.020
 4DI  plan-1  N2    0.020
 4DI  plan-1  N3    0.020
 4DI  plan-1  HN21  0.020
 4DI  plan-1  HN22  0.020
 4DI  plan-1  HN3   0.020

