# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 21:55:51 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: N-cyclohexyl-N'-methylthiourea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=S)NC1CCCCC1
#
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
 JLV  JLV  N-cyclohexyl-N'-methylthiourea  ligand  27  11  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JLV
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
 JLV  C10   C  CH2   0  -0.439  -2.6499  -1.2529   0.6412
 JLV  C01   C  CH3   0  -0.493   4.1530   0.3813   0.2975
 JLV  N02   N  NH1   0  -0.612   2.7909   0.8424   0.4001
 JLV  C03   C  C     0   0.427   1.7254   0.1685  -0.0499
 JLV  S04   S  S1    0  -0.462   1.8942  -1.3314  -0.8074
 JLV  N05   N  NH1   0  -0.627   0.5394   0.7676   0.1261
 JLV  C06   C  CH1   0  -0.039  -0.7562   0.1919  -0.1808
 JLV  C07   C  CH2   0  -0.444  -1.7450   1.3108  -0.4948
 JLV  C08   C  CH2   0  -0.436  -3.1305   0.7499  -0.8005
 JLV  C09   C  CH2   0  -0.431  -3.6395  -0.1341   0.3333
 JLV  C11   C  CH2   0  -0.421  -1.2651  -0.6951   0.9548
 JLV  H102  H  HCH2  0   0.231  -3.0058  -1.8567   1.4789
 JLV  H101  H  HCH2  0   0.213  -2.5830  -1.9256  -0.2204
 JLV  H012  H  HCH3  0   0.249   4.7946   1.1465   0.7264
 JLV  H013  H  HCH3  0   0.235   4.3079  -0.5506   0.8420
 JLV  H011  H  HCH3  0   0.237   4.4468   0.2206  -0.7394
 JLV  H021  H  HNH1  0   0.401   2.6425   1.7270   0.8602
 JLV  H051  H  HNH1  0   0.391   0.5250   1.6360   0.6436
 JLV  H061  H  HCH1  0   0.234  -0.6309  -0.4271  -1.0731
 JLV  H072  H  HCH2  0   0.217  -1.8121   1.9902   0.3632
 JLV  H071  H  HCH2  0   0.240  -1.3776   1.8988  -1.3392
 JLV  H082  H  HCH2  0   0.233  -3.8270   1.5706  -0.9857
 JLV  H081  H  HCH2  0   0.215  -3.0886   0.1651  -1.7260
 JLV  H092  H  HCH2  0   0.229  -4.6162  -0.5509   0.0760
 JLV  H091  H  HCH2  0   0.211  -3.7866   0.4766   1.2309
 JLV  H112  H  HCH2  0   0.210  -1.3029  -0.1055   1.8779
 JLV  H111  H  HCH2  0   0.232  -0.5512  -1.5053   1.1195

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
 JLV  C11  C10   single  1.525  0.020  1.525
 JLV  C11  C06   single  1.528  0.020  1.528
 JLV  C10  C09   single  1.525  0.020  1.525
 JLV  C01  N02   single  1.442  0.020  1.442
 JLV  S04  C03   double  1.689  0.020  1.689
 JLV  N02  C03   single  1.339  0.020  1.339
 JLV  C03  N05   single  1.340  0.020  1.340
 JLV  N05  C06   single  1.451  0.020  1.451
 JLV  C09  C08   single  1.525  0.020  1.525
 JLV  C06  C07   single  1.526  0.020  1.526
 JLV  C07  C08   single  1.526  0.020  1.526
 JLV  C10  H102  single  0.970  0.020  1.090
 JLV  C10  H101  single  0.970  0.020  1.090
 JLV  C01  H012  single  0.970  0.020  1.090
 JLV  C01  H013  single  0.970  0.020  1.090
 JLV  C01  H011  single  0.970  0.020  1.090
 JLV  N02  H021  single  0.860  0.020  1.020
 JLV  N05  H051  single  0.860  0.020  1.020
 JLV  C06  H061  single  0.970  0.020  1.090
 JLV  C07  H072  single  0.970  0.020  1.090
 JLV  C07  H071  single  0.970  0.020  1.090
 JLV  C08  H082  single  0.970  0.020  1.090
 JLV  C08  H081  single  0.970  0.020  1.090
 JLV  C09  H092  single  0.970  0.020  1.090
 JLV  C09  H091  single  0.970  0.020  1.090
 JLV  C11  H112  single  0.970  0.020  1.090
 JLV  C11  H111  single  0.970  0.020  1.090

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
 JLV  H101  C10  H102  106.48  3.000
 JLV  H101  C10  C11   109.32  3.000
 JLV  H102  C10  C11   109.89  3.000
 JLV  H101  C10  C09   109.35  3.000
 JLV  H102  C10  C09   110.42  3.000
 JLV  C11   C10  C09   111.24  3.000
 JLV  H011  C01  H013  108.12  3.000
 JLV  H011  C01  H012  108.67  3.000
 JLV  H013  C01  H012  108.71  3.000
 JLV  H011  C01  N02   111.70  3.000
 JLV  H013  C01  N02   111.84  3.000
 JLV  H012  C01  N02   107.73  3.000
 JLV  H021  N02  C03   118.56  3.000
 JLV  H021  N02  C01   116.88  3.000
 JLV  C03   N02  C01   124.55  3.000
 JLV  N05   C03  S04   122.98  3.000
 JLV  N05   C03  N02   115.79  3.000
 JLV  S04   C03  N02   121.22  3.000
 JLV  H051  N05  C06   115.88  3.000
 JLV  H051  N05  C03   117.63  3.000
 JLV  C06   N05  C03   125.81  3.000
 JLV  H061  C06  C11   108.42  3.000
 JLV  H061  C06  C07   108.76  3.000
 JLV  C11   C06  C07   111.27  3.000
 JLV  H061  C06  N05   107.16  3.000
 JLV  C07   C06  N05   109.35  3.000
 JLV  C11   C06  N05   111.75  3.000
 JLV  H071  C07  H072  106.98  3.000
 JLV  H071  C07  C08   110.39  3.000
 JLV  H072  C07  C08   109.21  3.000
 JLV  H071  C07  C06   109.62  3.000
 JLV  H072  C07  C06   109.45  3.000
 JLV  C08   C07  C06   111.10  3.000
 JLV  H081  C08  H082  106.39  3.000
 JLV  H081  C08  C09   109.36  3.000
 JLV  H082  C08  C09   110.42  3.000
 JLV  H081  C08  C07   109.31  3.000
 JLV  H082  C08  C07   109.68  3.000
 JLV  C09   C08  C07   111.54  3.000
 JLV  H091  C09  H092  106.59  3.000
 JLV  H091  C09  C08   109.31  3.000
 JLV  H092  C09  C08   110.14  3.000
 JLV  H091  C09  C10   109.31  3.000
 JLV  H092  C09  C10   110.35  3.000
 JLV  C08   C09  C10   111.02  3.000
 JLV  H111  C11  H112  107.13  3.000
 JLV  H111  C11  C06   108.96  3.000
 JLV  H112  C11  C06   108.97  3.000
 JLV  H111  C11  C10   110.67  3.000
 JLV  H112  C11  C10   109.79  3.000
 JLV  C06   C11  C10   111.21  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
 JLV  CONST_01  C06   N05  C03  N02  180.00   0.0  0
 JLV  CONST_02  C06   N05  C03  S04    0.00   0.0  0
 JLV  CONST_03  S04   C03  N02  C01    0.00   0.0  0
 JLV  CONST_04  N05   C03  N02  C01  180.00   0.0  0
 JLV  CONST_05  H051  N05  C03  N02    0.00   0.0  0
 JLV  CONST_06  H021  N02  C03  S04  180.00   0.0  0
 JLV  Var_01    C07   C08  C09  C10  -55.50  30.0  1
 JLV  Var_02    C09   C10  C11  C06  -55.61  30.0  1
 JLV  Var_03    C09   C08  C07  C06   55.30  30.0  1
 JLV  Var_04    C11   C10  C09  C08   55.56  30.0  1
 JLV  Var_05    H012  C01  N02  C03  178.71  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
 JLV  chir_01  C06  C11  N05  C07  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
 JLV  plan-1  C01   0.020
 JLV  plan-1  N02   0.020
 JLV  plan-1  C03   0.020
 JLV  plan-1  S04   0.020
 JLV  plan-1  N05   0.020
 JLV  plan-1  C06   0.020
 JLV  plan-1  H021  0.020
 JLV  plan-1  H051  0.020

