# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 20:52:59 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 4-({[(thiophen-2-yl)methyl]amino}methyl)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(CNCc2sccc2)cc1
#
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
 JKG  JKG  4-({[(thiophen-2-yl)methyl]amino}methyl)phenol  ligand  28  15  .  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_JKG
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
 JKG  C10   C  CR16  0  -0.279  -2.1051  -0.7215   0.0527
 JKG  C13   C  CR16  0  -0.324  -4.3887   0.8420  -0.0549
 JKG  C01   C  CR15  0  -0.186   4.9023   0.1082  -0.7611
 JKG  C02   C  CR15  0  -0.240   4.0460   1.0499  -0.1231
 JKG  C03   C  CR5   0  -0.171   2.8048   0.5509   0.1339
 JKG  S04   S  S2    0   0.204   2.6682  -1.0771  -0.4158
 JKG  C05   C  CR15  0  -0.476   4.2897  -1.0867  -0.9804
 JKG  C06   C  CH2   0  -0.302   1.6530   1.1960   0.8306
 JKG  N07   N  NH1   0  -0.596   0.3990   0.7208   0.2876
 JKG  C08   C  CH2   0  -0.304  -0.7582   1.1826   1.0270
 JKG  C09   C  CR6   0   0.053  -2.0351   0.6014   0.4804
 JKG  C11   C  CR16  0  -0.369  -3.2905  -1.2637  -0.4212
 JKG  C12   C  CR6   0   0.337  -4.4432  -0.4836  -0.4760
 JKG  C14   C  CR16  0  -0.298  -3.1940   1.3688   0.4115
 JKG  O15   O  OH1   0  -0.635  -5.6240  -0.9564  -0.9278
 JKG  H101  H  HCR6  0   0.252  -1.2163  -1.3393   0.0804
 JKG  H131  H  HCR6  0   0.260  -5.2768   1.4601  -0.1003
 JKG  H021  H  HCR5  0   0.257   4.3398   2.0580   0.1360
 JKG  H051  H  HCR5  0   0.289   4.6969  -1.9635  -1.4596
 JKG  H062  H  HCH2  0   0.250   1.6751   0.9335   1.8938
 JKG  H061  H  HCH2  0   0.225   1.7775   2.2879   0.7851
 JKG  H071  H  HNH1  0   0.349   0.3162   1.0071  -0.6810
 JKG  H081  H  HCH2  0   0.239  -0.6282   0.8704   2.0693
 JKG  H082  H  HCH2  0   0.214  -0.8450   2.2795   1.0522
 JKG  H111  H  HCR6  0   0.267  -3.3156  -2.2973  -0.7490
 JKG  H141  H  HCR6  0   0.249  -3.1667   2.4058   0.7262
 JKG  H151  H  HOH1  0   0.473  -5.5332  -1.8760  -1.2006
 JKG  H011  H  HCR5  0   0.262   5.9223   0.3187  -1.0499

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
 JKG  S04  C05   aromatic  1.717  0.020  1.717
 JKG  S04  C03   aromatic  1.724  0.020  1.724
 JKG  C13  C14   aromatic  1.386  0.020  1.386
 JKG  C13  C12   aromatic  1.392  0.020  1.392
 JKG  C14  C09   aromatic  1.392  0.020  1.392
 JKG  C05  C01   aromatic  1.361  0.020  1.361
 JKG  O15  C12   single    1.350  0.020  1.350
 JKG  N07  C06   single    1.447  0.020  1.447
 JKG  N07  C08   single    1.449  0.020  1.449
 JKG  C12  C11   aromatic  1.393  0.020  1.393
 JKG  C03  C06   single    1.493  0.020  1.493
 JKG  C03  C02   aromatic  1.362  0.020  1.362
 JKG  C09  C08   single    1.506  0.020  1.506
 JKG  C09  C10   aromatic  1.392  0.020  1.392
 JKG  C01  C02   aromatic  1.424  0.020  1.424
 JKG  C11  C10   aromatic  1.387  0.020  1.387
 JKG  C10  H101  single    0.930  0.020  1.080
 JKG  C13  H131  single    0.930  0.020  1.080
 JKG  C01  H011  single    0.930  0.020  1.080
 JKG  C02  H021  single    0.930  0.020  1.080
 JKG  C05  H051  single    0.930  0.020  1.080
 JKG  C06  H062  single    0.970  0.020  1.090
 JKG  C06  H061  single    0.970  0.020  1.090
 JKG  N07  H071  single    0.890  0.020  1.040
 JKG  C08  H081  single    0.970  0.020  1.090
 JKG  C08  H082  single    0.970  0.020  1.090
 JKG  C11  H111  single    0.930  0.020  1.080
 JKG  C14  H141  single    0.930  0.020  1.080
 JKG  O15  H151  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
 JKG  H101  C10  C11   119.16  3.000
 JKG  H101  C10  C09   119.54  3.000
 JKG  C11   C10  C09   121.29  3.000
 JKG  H131  C13  C14   120.26  3.000
 JKG  H131  C13  C12   119.91  3.000
 JKG  C14   C13  C12   119.83  3.000
 JKG  H011  C01  C05   123.57  3.000
 JKG  H011  C01  C02   123.96  3.000
 JKG  C05   C01  C02   112.47  3.000
 JKG  H021  C02  C03   122.94  3.000
 JKG  H021  C02  C01   124.09  3.000
 JKG  C03   C02  C01   112.97  3.000
 JKG  C06   C03  S04   119.73  3.000
 JKG  C06   C03  C02   129.26  3.000
 JKG  S04   C03  C02   110.98  3.000
 JKG  C05   S04  C03    92.02  3.000
 JKG  H051  C05  S04   120.46  3.000
 JKG  H051  C05  C01   127.97  3.000
 JKG  S04   C05  C01   111.55  3.000
 JKG  H061  C06  H062  106.01  3.000
 JKG  H061  C06  N07   114.12  3.000
 JKG  H062  C06  N07   107.65  3.000
 JKG  H061  C06  C03   108.81  3.000
 JKG  H062  C06  C03   109.51  3.000
 JKG  N07   C06  C03   110.59  3.000
 JKG  H071  N07  C08   109.42  3.000
 JKG  H071  N07  C06   109.68  3.000
 JKG  C08   N07  C06   113.33  3.000
 JKG  H082  C08  H081  105.76  3.000
 JKG  H082  C08  C09   109.03  3.000
 JKG  H081  C08  C09   109.63  3.000
 JKG  H082  C08  N07   113.10  3.000
 JKG  H081  C08  N07   107.45  3.000
 JKG  C09   C08  N07   111.66  3.000
 JKG  C14   C09  C08   120.75  3.000
 JKG  C08   C09  C10   121.40  3.000
 JKG  C14   C09  C10   117.84  3.000
 JKG  H111  C11  C12   120.17  3.000
 JKG  H111  C11  C10   119.71  3.000
 JKG  C12   C11  C10   120.12  3.000
 JKG  O15   C12  C11   122.74  3.000
 JKG  C11   C12  C13   119.28  3.000
 JKG  O15   C12  C13   117.98  3.000
 JKG  H141  C14  C09   119.49  3.000
 JKG  H141  C14  C13   118.87  3.000
 JKG  C09   C14  C13   121.65  3.000
 JKG  H151  O15  C12   110.29  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
 JKG  CONST_01  C13   C14  C09  C10     0.00   0.0  0
 JKG  CONST_02  C13   C12  C11  C10     0.00   0.0  0
 JKG  CONST_03  C03   S04  C05  C01     0.00   0.0  0
 JKG  CONST_04  S04   C03  C02  C01     0.00   0.0  0
 JKG  CONST_05  C05   S04  C03  C02     0.00   0.0  0
 JKG  CONST_06  S04   C05  C01  C02     0.00   0.0  0
 JKG  CONST_07  C05   C01  C02  C03     0.00   0.0  0
 JKG  CONST_08  C12   C13  C14  C09     0.00   0.0  0
 JKG  CONST_09  C12   C11  C10  C09     0.00   0.0  0
 JKG  CONST_10  C14   C13  C12  C11     0.00   0.0  0
 JKG  CONST_11  C14   C09  C10  C11     0.00   0.0  0
 JKG  CONST_12  O15   C12  C11  C10   180.00   0.0  0
 JKG  CONST_13  C08   C09  C14  C13   180.00   0.0  0
 JKG  CONST_14  C06   C03  C02  C01   180.00   0.0  0
 JKG  CONST_15  C06   C03  S04  C05   180.00   0.0  0
 JKG  CONST_16  C11   C10  C09  C08   180.00   0.0  0
 JKG  CONST_17  O15   C12  C13  C14   180.00   0.0  0
 JKG  CONST_18  H141  C14  C09  C10   180.00   0.0  0
 JKG  CONST_19  H111  C11  C12  C13   180.00   0.0  0
 JKG  CONST_20  H051  C05  C01  C02   180.00   0.0  0
 JKG  CONST_21  H011  C01  C02  C03   180.00   0.0  0
 JKG  CONST_22  H021  C02  C03  S04   180.00   0.0  0
 JKG  CONST_23  H131  C13  C14  C09   180.00   0.0  0
 JKG  CONST_24  H101  C10  C11  C12   180.00   0.0  0
 JKG  Var_01    N07   C08  C09  C10    39.54  30.0  2
 JKG  Var_02    N07   C06  C03  C02   148.30  30.0  2
 JKG  Var_03    C08   N07  C06  C03   172.89  30.0  1
 JKG  Var_04    C09   C08  N07  C06  -176.63  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
 JKG  plan-1  C01   0.020
 JKG  plan-1  C02   0.020
 JKG  plan-1  C03   0.020
 JKG  plan-1  S04   0.020
 JKG  plan-1  C05   0.020
 JKG  plan-1  C06   0.020
 JKG  plan-1  H021  0.020
 JKG  plan-1  H051  0.020
 JKG  plan-1  H011  0.020
 JKG  plan-2  C10   0.020
 JKG  plan-2  C13   0.020
 JKG  plan-2  C08   0.020
 JKG  plan-2  C09   0.020
 JKG  plan-2  C11   0.020
 JKG  plan-2  C12   0.020
 JKG  plan-2  C14   0.020
 JKG  plan-2  O15   0.020
 JKG  plan-2  H101  0.020
 JKG  plan-2  H131  0.020
 JKG  plan-2  H111  0.020
 JKG  plan-2  H141  0.020

