# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 10:37:30 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: 5-[(4-chlorophenyl)methyl]-6-[[2-(dimethylamino)ethylamino]methyl]-4-oxidanyl-1~{H}-pyrimidine-2-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCNCC1=C(Cc2ccc(Cl)cc2)C(=NC(=S)N1)O
#
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
 P62  P62  "5-[(4-chlorophenyl)methyl]-6-[[2-(dimethylamino)ethylamino]methyl]-4-oxidanyl-1~{H}-pyrimidine-2-thione"
  ligand  44  23  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P62
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
 P62  N    N   N     0  -0.466  24.4884  13.5065  46.4913
 P62  C    C   C     0   0.364  25.4730  11.5743  44.8063
 P62  O    O   OH1   0  -0.574  26.0541  12.9478  48.0130
 P62  C1   C   C     0  -0.110  26.0585  11.7200  46.0347
 P62  C10  C   CR16  0  -0.328  27.3615   9.9907  48.9205
 P62  C11  C   CH2   0  -0.356  25.9062  10.5651  43.7538
 P62  C12  C   CH2   0  -0.310  25.9674  11.8914  41.6646
 P62  C13  C   CH2   0  -0.303  27.3694  11.6466  41.1005
 P62  C14  C   CH3   0  -0.496  27.5165   9.2580  40.5528
 P62  C15  C   CH3   0  -0.517  26.7304  10.8210  38.9102
 P62  C2   C   C     0   0.519  25.5002  12.7464  46.8355
 P62  C3   C   C     0   0.270  23.9045  13.3282  45.3015
 P62  C4   C   CH2   0  -0.593  27.1739  10.8602  46.5588
 P62  C5   C   CR6   0   0.153  26.7266   9.9572  47.6844
 P62  C6   C   CR16  0  -0.291  25.6730   9.0648  47.5059
 P62  C7   C   CR16  0  -0.193  25.2564   8.2301  48.5309
 P62  C8   C   CR6   0  -0.058  25.9060   8.2888  49.7548
 P62  C9   C   CR16  0  -0.194  26.9596   9.1634  49.9600
 P62  N1   N   NH1   0  -0.633  24.4280  12.3621  44.4893
 P62  N2   N   NH1   0  -0.610  25.4371  10.7792  42.4253
 P62  N3   N   NT    0  -0.393  27.5373  10.6262  40.0889
 P62  S    S   S1    0  -0.422  22.5896  14.2236  44.7732
 P62  CL   CL  CL    0  -0.133  25.3914   7.2521  51.0467
 P62  H1   H   HOH1  0   0.486  25.5913  13.6657  48.4709
 P62  H7   H   HCR6  0   0.260  28.1818  10.6788  49.0837
 P62  H8   H   HCH2  0   0.298  25.5886   9.5765  44.0983
 P62  H19  H   HCH2  0   0.270  26.9980  10.5395  43.7551
 P62  H9   H   HCH2  0   0.209  26.0139  12.8232  42.2487
 P62  H10  H   HCH2  0   0.245  25.2697  12.0940  40.8503
 P62  H12  H   HCH2  0   0.228  28.0614  11.4245  41.9188
 P62  H11  H   HCH2  0   0.226  27.7056  12.6007  40.6780
 P62  H13  H   HCH3  0   0.221  28.1080   9.1654  41.4647
 P62  H14  H   HCH3  0   0.192  26.5146   8.8647  40.7652
 P62  H15  H   HCH3  0   0.215  27.9711   8.6097  39.7987
 P62  H16  H   HCH3  0   0.227  26.8061  11.8552  38.5691
 P62  H18  H   HCH3  0   0.228  27.0914  10.1797  38.1029
 P62  H17  H   HCH3  0   0.191  25.6626  10.5929  39.0507
 P62  H3   H   HCH2  0   0.282  27.5838  10.2507  45.7520
 P62  H2   H   HCH2  0   0.284  27.9987  11.4863  46.9049
 P62  H4   H   HCR6  0   0.265  25.1603   9.0125  46.5526
 P62  H5   H   HCR6  0   0.277  24.4395   7.5387  48.3732
 P62  H6   H   HCR6  0   0.276  27.4608   9.2086  50.9176
 P62  H    H   HNH1  0   0.420  23.9983  12.2393  43.5799
 P62  H20  H   HNH1  0   0.373  24.4690  10.5573  42.2598

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
 P62  C15  N3   single    1.442  0.020  1.442
 P62  N3   C14  single    1.445  0.020  1.445
 P62  N3   C13  single    1.447  0.020  1.447
 P62  C13  C12  single    1.531  0.020  1.531
 P62  C12  N2   single    1.448  0.020  1.448
 P62  N2   C11  single    1.425  0.020  1.425
 P62  C11  C    single    1.521  0.020  1.521
 P62  N1   C    single    1.347  0.020  1.347
 P62  N1   C3   single    1.366  0.020  1.366
 P62  S    C3   double    1.676  0.020  1.676
 P62  C    C1   double    1.369  0.020  1.369
 P62  C3   N    single    1.337  0.020  1.337
 P62  C1   C4   single    1.503  0.020  1.503
 P62  C1   C2   single    1.417  0.020  1.417
 P62  N    C2   double    1.311  0.020  1.311
 P62  C4   C5   single    1.511  0.020  1.511
 P62  C2   O    single    1.317  0.020  1.317
 P62  C6   C5   aromatic  1.392  0.020  1.392
 P62  C6   C7   aromatic  1.386  0.020  1.386
 P62  C5   C10  aromatic  1.390  0.020  1.390
 P62  C7   C8   aromatic  1.387  0.020  1.387
 P62  C10  C9   aromatic  1.388  0.020  1.388
 P62  C8   C9   aromatic  1.385  0.020  1.385
 P62  C8   CL   single    1.735  0.020  1.735
 P62  O    H1   single    0.850  0.020  0.980
 P62  C10  H7   single    0.930  0.020  1.080
 P62  C11  H8   single    0.970  0.020  1.090
 P62  C11  H19  single    0.970  0.020  1.090
 P62  C12  H9   single    0.970  0.020  1.090
 P62  C12  H10  single    0.970  0.020  1.090
 P62  C13  H12  single    0.970  0.020  1.090
 P62  C13  H11  single    0.970  0.020  1.090
 P62  C14  H13  single    0.970  0.020  1.090
 P62  C14  H14  single    0.970  0.020  1.090
 P62  C14  H15  single    0.970  0.020  1.090
 P62  C15  H16  single    0.970  0.020  1.090
 P62  C15  H18  single    0.970  0.020  1.090
 P62  C15  H17  single    0.970  0.020  1.090
 P62  C4   H3   single    0.970  0.020  1.090
 P62  C4   H2   single    0.970  0.020  1.090
 P62  C6   H4   single    0.930  0.020  1.080
 P62  C7   H5   single    0.930  0.020  1.080
 P62  C9   H6   single    0.930  0.020  1.080
 P62  N1   H    single    0.860  0.020  1.020
 P62  N2   H20  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
 P62  C3   N    C2   119.54  3.000
 P62  N1   C    C11  116.50  3.000
 P62  N1   C    C1   118.75  3.000
 P62  C11  C    C1   124.74  3.000
 P62  H1   O    C2   109.57  3.000
 P62  C4   C1   C2   120.66  3.000
 P62  C2   C1   C    114.58  3.000
 P62  C4   C1   C    124.73  3.000
 P62  H7   C10  C9   119.02  3.000
 P62  H7   C10  C5   119.69  3.000
 P62  C9   C10  C5   121.30  3.000
 P62  H19  C11  H8   105.58  3.000
 P62  H19  C11  N2   109.49  3.000
 P62  H8   C11  N2   109.50  3.000
 P62  H19  C11  C    107.42  3.000
 P62  H8   C11  C    107.40  3.000
 P62  N2   C11  C    116.85  3.000
 P62  H10  C12  H9   105.41  3.000
 P62  H10  C12  N2   107.49  3.000
 P62  H9   C12  N2   112.76  3.000
 P62  H10  C12  C13  109.89  3.000
 P62  H9   C12  C13  106.99  3.000
 P62  N2   C12  C13  113.96  3.000
 P62  H11  C13  H12  105.71  3.000
 P62  H11  C13  N3   107.99  3.000
 P62  H12  C13  N3   107.84  3.000
 P62  H11  C13  C12  106.48  3.000
 P62  H12  C13  C12  109.63  3.000
 P62  N3   C13  C12  118.47  3.000
 P62  H15  C14  H14  107.49  3.000
 P62  H15  C14  H13  107.50  3.000
 P62  H14  C14  H13  107.64  3.000
 P62  H15  C14  N3   109.51  3.000
 P62  H14  C14  N3   114.51  3.000
 P62  H13  C14  N3   109.94  3.000
 P62  H17  C15  H18  107.05  3.000
 P62  H17  C15  H16  107.67  3.000
 P62  H18  C15  H16  107.60  3.000
 P62  H17  C15  N3   114.24  3.000
 P62  H18  C15  N3   109.87  3.000
 P62  H16  C15  N3   110.16  3.000
 P62  C1   C2   O    116.79  3.000
 P62  O    C2   N    118.07  3.000
 P62  C1   C2   N    125.15  3.000
 P62  S    C3   N1   119.40  3.000
 P62  S    C3   N    123.48  3.000
 P62  N1   C3   N    117.12  3.000
 P62  H2   C4   H3   105.72  3.000
 P62  H2   C4   C5   109.27  3.000
 P62  H3   C4   C5   109.16  3.000
 P62  H2   C4   C1   110.07  3.000
 P62  H3   C4   C1   109.92  3.000
 P62  C5   C4   C1   112.47  3.000
 P62  C6   C5   C4   120.77  3.000
 P62  C6   C5   C10  118.37  3.000
 P62  C4   C5   C10  120.86  3.000
 P62  H4   C6   C7   118.64  3.000
 P62  H4   C6   C5   120.11  3.000
 P62  C7   C6   C5   121.24  3.000
 P62  H5   C7   C8   120.63  3.000
 P62  H5   C7   C6   120.27  3.000
 P62  C8   C7   C6   119.10  3.000
 P62  CL   C8   C9   119.53  3.000
 P62  CL   C8   C7   119.54  3.000
 P62  C9   C8   C7   120.93  3.000
 P62  H6   C9   C8   120.67  3.000
 P62  H6   C9   C10  120.26  3.000
 P62  C8   C9   C10  119.06  3.000
 P62  H    N1   C3   117.17  3.000
 P62  H    N1   C    118.00  3.000
 P62  C3   N1   C    124.82  3.000
 P62  H20  N2   C12  115.79  3.000
 P62  H20  N2   C11  115.88  3.000
 P62  C12  N2   C11  118.98  3.000
 P62  C15  N3   C14  112.48  3.000
 P62  C14  N3   C13  116.21  3.000
 P62  C15  N3   C13  114.30  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
 P62  CONST_01  C7   C6   C5   C10     0.00   0.0  0
 P62  CONST_02  C7   C8   C9   C10     0.00   0.0  0
 P62  CONST_03  C8   C7   C6   C5      0.00   0.0  0
 P62  CONST_04  C8   C9   C10  C5      0.00   0.0  0
 P62  CONST_05  C9   C10  C5   C6      0.00   0.0  0
 P62  CONST_06  C9   C8   C7   C6      0.00   0.0  0
 P62  CONST_07  C    N1   C3   N       0.00   0.0  0
 P62  CONST_08  N1   C3   N    C2      0.00   0.0  0
 P62  CONST_09  CL   C8   C9   C10   180.00   0.0  0
 P62  CONST_10  C7   C6   C5   C4    180.00   0.0  0
 P62  CONST_11  C9   C10  C5   C4    180.00   0.0  0
 P62  CONST_12  CL   C8   C7   C6    180.00   0.0  0
 P62  CONST_13  S    C3   N1   C     180.00   0.0  0
 P62  CONST_14  S    C3   N    C2    180.00   0.0  0
 P62  CONST_15  H4   C6   C5   C10   180.00   0.0  0
 P62  CONST_16  H5   C7   C6   C5    180.00   0.0  0
 P62  CONST_17  H6   C9   C10  C5    180.00   0.0  0
 P62  CONST_18  H7   C10  C5   C6    180.00   0.0  0
 P62  CONST_19  H6   C9   C8   C7    180.00   0.0  0
 P62  CONST_20  H4   C6   C7   C8    180.00   0.0  0
 P62  CONST_21  H7   C10  C9   C8    180.00   0.0  0
 P62  CONST_22  H5   C7   C8   C9    180.00   0.0  0
 P62  CONST_23  H    N1   C3   N     180.00   0.0  0
 P62  CONST_24  H    N1   C3   S       0.00   0.0  0
 P62  Var_01    C    C1   C2   N       1.37  30.0  1
 P62  Var_02    C3   N1   C    C1      1.00  30.0  1
 P62  Var_03    C3   N    C2   C1      0.32  30.0  1
 P62  Var_04    N1   C    C1   C2     -1.92  30.0  1
 P62  Var_05    C4   C1   C2   N    -176.76  30.0  1
 P62  Var_06    C5   C4   C1   C    -110.08  30.0  3
 P62  Var_07    O    C2   C1   C    -178.26  30.0  1
 P62  Var_08    C3   N    C2   O     179.94  30.0  1
 P62  Var_09    C6   C5   C4   C1     56.77  30.0  2
 P62  Var_10    C10  C5   C4   C1   -123.63  30.0  2
 P62  Var_11    C3   N1   C    C11  -179.60  30.0  1
 P62  Var_12    C2   C1   C    C11   178.74  30.0  1
 P62  Var_13    C5   C4   C1   C2     67.85  30.0  3
 P62  Var_14    N1   C    C1   C4    176.13  30.0  1
 P62  Var_15    H    N1   C    C1   -179.50  30.0  1
 P62  Var_16    C4   C1   C2   O       3.61  30.0  1
 P62  Var_17    N2   C11  C    C1   -163.85  30.0  1
 P62  Var_18    C4   C1   C    C11    -3.21  30.0  1
 P62  Var_19    N2   C11  C    N1     16.80  30.0  1
 P62  Var_20    H3   C4   C1   C      11.76  30.0  3
 P62  Var_21    H2   C4   C1   C     127.82  30.0  3
 P62  Var_22    H8   C11  C    C1     72.74  30.0  1
 P62  Var_23    H19  C11  C    C1    -40.42  30.0  1
 P62  Var_24    H3   C4   C5   C10   114.10  30.0  2
 P62  Var_25    H2   C4   C5   C10    -1.08  30.0  2
 P62  Var_26    H    N1   C    C11    -0.10  30.0  1
 P62  Var_27    H3   C4   C1   C2   -170.30  30.0  3
 P62  Var_28    H2   C4   C1   C2    -54.25  30.0  3
 P62  Var_29    H3   C4   C5   C6    -65.51  30.0  2
 P62  Var_30    H2   C4   C5   C6    179.32  30.0  2
 P62  Var_31    H8   C11  C    N1   -106.61  30.0  1
 P62  Var_32    H19  C11  C    N1    140.23  30.0  1
 P62  Var_33    C12  N2   C11  C      70.49  30.0  1
 P62  Var_34    H20  N2   C11  C     -74.76  30.0  1
 P62  Var_35    C13  C12  N2   C11    77.08  30.0  1
 P62  Var_36    C15  N3   C13  C12    57.62  30.0  2
 P62  Var_37    C14  N3   C13  C12   -76.01  30.0  2
 P62  Var_38    N3   C13  C12  N2     66.10  30.0  1
 P62  Var_39    H9   C12  N2   C11   -45.14  30.0  1
 P62  Var_40    H10  C12  N2   C11  -160.89  30.0  1
 P62  Var_41    H8   C11  N2   C12  -167.19  30.0  3
 P62  Var_42    H19  C11  N2   C12   -51.87  30.0  3
 P62  Var_43    H16  C15  N3   C13    47.00  30.0  3
 P62  Var_44    H18  C15  N3   C13   165.37  30.0  3
 P62  Var_45    H17  C15  N3   C13   -74.32  30.0  3
 P62  Var_46    H13  C14  N3   C13   -43.44  30.0  3
 P62  Var_47    H14  C14  N3   C13    77.87  30.0  3
 P62  Var_48    H15  C14  N3   C13  -161.34  30.0  3
 P62  Var_49    H20  N2   C12  C13  -137.64  30.0  3
 P62  Var_50    H16  C15  N3   C14  -177.65  30.0  3
 P62  Var_51    H18  C15  N3   C14   -59.29  30.0  3
 P62  Var_52    H17  C15  N3   C14    61.03  30.0  3
 P62  Var_53    H12  C13  N3   C14    49.16  30.0  3
 P62  Var_54    H11  C13  N3   C14   162.97  30.0  3
 P62  Var_55    H13  C14  N3   C15  -177.88  30.0  3
 P62  Var_56    H14  C14  N3   C15   -56.58  30.0  3
 P62  Var_57    H15  C14  N3   C15    64.22  30.0  3
 P62  Var_58    H12  C13  N3   C15  -177.21  30.0  3
 P62  Var_59    H11  C13  N3   C15   -63.41  30.0  3
 P62  Var_60    H12  C13  C12  N2    -58.20  30.0  1
 P62  Var_61    H11  C13  C12  N2   -172.12  30.0  1
 P62  Var_62    H9   C12  C13  N3   -168.56  30.0  3
 P62  Var_63    H10  C12  C13  N3    -54.60  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
 P62  plan-1  C10  0.020
 P62  plan-1  C4   0.020
 P62  plan-1  C5   0.020
 P62  plan-1  C6   0.020
 P62  plan-1  C7   0.020
 P62  plan-1  C8   0.020
 P62  plan-1  C9   0.020
 P62  plan-1  CL   0.020
 P62  plan-1  H7   0.020
 P62  plan-1  H4   0.020
 P62  plan-1  H5   0.020
 P62  plan-1  H6   0.020
 P62  plan-2  N    0.020
 P62  plan-2  C    0.020
 P62  plan-2  C2   0.020
 P62  plan-2  C3   0.020
 P62  plan-2  N1   0.020
 P62  plan-2  S    0.020
 P62  plan-2  H    0.020

