# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 04:44:41 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: 6-{4-[3-chloro-4-(hydroxymethyl)phenyl]piperazine-1-carbonyl}pyrimidine-2,4(3H,5H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1ccc(cc1Cl)N2CCN(CC2)C(=O)C3=NC(=O)NC(=O)C3
#
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
 5ZT  5ZT  "6-{4-[3-chloro-4-(hydroxymethyl)phenyl]piperazine-1-carbonyl}pyrimidine-2,4(3H,5H)-dione"  ligand  42  25  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5ZT
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
 5ZT  C2    C   C     0   0.556  14.0758  -0.4251  18.0440
 5ZT  C6    C   CH2   0  -0.306  10.7482  -1.3531  18.6476
 5ZT  C5    C   CH2   0  -0.318  12.1833  -1.6858  19.0221
 5ZT  N7    N   NT    0  -0.523  10.2735  -0.2156  19.4077
 5ZT  C8    C   CH2   0  -0.304  11.1267   0.9518  19.2291
 5ZT  C1    C   C     0   0.133  14.5330  -1.6660  17.3186
 5ZT  C10   C   CR6   0   0.351   8.8966   0.0141  19.4450
 5ZT  C11   C   CR16  0  -0.300   8.3649   0.9844  20.3030
 5ZT  C12   C   CR16  0  -0.304   7.0036   1.2140  20.3675
 5ZT  C13   C   CR6   0   0.079   6.0939   0.4876  19.6017
 5ZT  C14   C   CR6   0  -0.086   6.6369  -0.4785  18.7671
 5ZT  C15   C   CR16  0  -0.292   7.9986  -0.7177  18.6655
 5ZT  C17   C   C     0   0.617  15.7047  -3.6524  17.3462
 5ZT  C20   C   C     0   0.582  14.8916  -2.8786  15.1555
 5ZT  C22   C   CH2   0  -0.665  14.3366  -1.6691  15.8451
 5ZT  C23   C   CH2   0  -0.178   4.6094   0.7198  19.6713
 5ZT  C9    C   CH2   0  -0.323  12.5581   0.6322  19.6150
 5ZT  N16   N   N     0  -0.413  15.1423  -2.5484  17.9990
 5ZT  N19   N   NH1   0  -0.697  15.5423  -3.7602  15.9783
 5ZT  N4    N   NT    0  -0.446  13.0320  -0.5195  18.8689
 5ZT  O18   O   O     0  -0.404  16.3081  -4.4884  17.9672
 5ZT  O21   O   O     0  -0.413  14.7875  -3.0701  13.9688
 5ZT  O24   O   OH1   0  -0.661   4.3397   1.7774  20.5523
 5ZT  O3    O   O     0  -0.467  14.7280   0.5836  17.8253
 5ZT  CL25  CL  CL    0  -0.131   5.5760  -1.4347  17.7741
 5ZT  H1    H   HCH2  0   0.228  10.6871  -1.1816  17.5620
 5ZT  H2    H   HCH2  0   0.268  10.1415  -2.2294  18.8784
 5ZT  H3    H   HCH2  0   0.263  12.2277  -2.0208  20.0615
 5ZT  H4    H   HCH2  0   0.285  12.5251  -2.5078  18.3975
 5ZT  H5    H   HCH2  0   0.233  11.0981   1.3012  18.1869
 5ZT  H6    H   HCH2  0   0.269  10.7854   1.7725  19.8561
 5ZT  H7    H   HCR6  0   0.264   9.0174   1.5567  20.9487
 5ZT  H8    H   HCR6  0   0.261   6.6400   1.9716  21.0472
 5ZT  H9    H   HCR6  0   0.287   8.3419  -1.4658  17.9656
 5ZT  H10   H   HCH2  0   0.348  14.7971  -0.7730  15.4169
 5ZT  H11   H   HCH2  0   0.345  13.2681  -1.5815  15.6199
 5ZT  H12   H   HCH2  0   0.216   4.2336   0.9312  18.6610
 5ZT  H13   H   HCH2  0   0.218   4.1171  -0.2089  19.9914
 5ZT  H14   H   HCH2  0   0.262  12.6164   0.4035  20.6828
 5ZT  H15   H   HCH2  0   0.278  13.1960   1.4891  19.4161
 5ZT  H16   H   HNH1  0   0.428  15.9458  -4.5825  15.5429
 5ZT  H17   H   HOH1  0   0.462   3.3866   1.8947  20.5948

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
 5ZT  O21   C20  double    1.207  0.020  1.207
 5ZT  C20   C22  single    1.499  0.020  1.499
 5ZT  C20   N19  single    1.370  0.020  1.370
 5ZT  C22   C1   single    1.487  0.020  1.487
 5ZT  N19   C17  single    1.382  0.020  1.382
 5ZT  C1    N16  double    1.270  0.020  1.270
 5ZT  C1    C2   single    1.508  0.020  1.508
 5ZT  C17   N16  single    1.401  0.020  1.401
 5ZT  C17   O18  double    1.204  0.020  1.204
 5ZT  CL25  C14  single    1.740  0.020  1.740
 5ZT  O3    C2   double    1.221  0.020  1.221
 5ZT  C2    N4   single    1.334  0.020  1.334
 5ZT  C6    C5   single    1.520  0.020  1.520
 5ZT  C6    N7   single    1.448  0.020  1.448
 5ZT  C15   C14  aromatic  1.386  0.020  1.386
 5ZT  C15   C10  aromatic  1.396  0.020  1.396
 5ZT  C14   C13  aromatic  1.387  0.020  1.387
 5ZT  N4    C5   single    1.450  0.020  1.450
 5ZT  N4    C9   single    1.452  0.020  1.452
 5ZT  C8    N7   single    1.457  0.020  1.457
 5ZT  C8    C9   single    1.517  0.020  1.517
 5ZT  N7    C10  single    1.396  0.020  1.396
 5ZT  C10   C11  aromatic  1.400  0.020  1.400
 5ZT  C13   C23  single    1.504  0.020  1.504
 5ZT  C13   C12  aromatic  1.393  0.020  1.393
 5ZT  C23   O24  single    1.403  0.020  1.403
 5ZT  C11   C12  aromatic  1.382  0.020  1.382
 5ZT  C6    H1   single    0.970  0.020  1.090
 5ZT  C6    H2   single    0.970  0.020  1.090
 5ZT  C5    H3   single    0.970  0.020  1.090
 5ZT  C5    H4   single    0.970  0.020  1.090
 5ZT  C8    H5   single    0.970  0.020  1.090
 5ZT  C8    H6   single    0.970  0.020  1.090
 5ZT  C11   H7   single    0.930  0.020  1.080
 5ZT  C12   H8   single    0.930  0.020  1.080
 5ZT  C15   H9   single    0.930  0.020  1.080
 5ZT  C22   H10  single    0.970  0.020  1.090
 5ZT  C22   H11  single    0.970  0.020  1.090
 5ZT  C23   H12  single    0.970  0.020  1.090
 5ZT  C23   H13  single    0.970  0.020  1.090
 5ZT  C9    H14  single    0.970  0.020  1.090
 5ZT  C9    H15  single    0.970  0.020  1.090
 5ZT  N19   H16  single    0.860  0.020  1.020
 5ZT  O24   H17  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
 5ZT  O3    C2   N4   125.97  3.000
 5ZT  N4    C2   C1   118.45  3.000
 5ZT  O3    C2   C1   115.57  3.000
 5ZT  H2    C6   H1   107.64  3.000
 5ZT  H2    C6   N7   109.74  3.000
 5ZT  H1    C6   N7   112.15  3.000
 5ZT  H2    C6   C5   107.29  3.000
 5ZT  H1    C6   C5   109.24  3.000
 5ZT  N7    C6   C5   110.62  3.000
 5ZT  H4    C5   H3   107.56  3.000
 5ZT  H4    C5   N4   111.30  3.000
 5ZT  H3    C5   N4   108.85  3.000
 5ZT  H4    C5   C6   108.70  3.000
 5ZT  H3    C5   C6   109.86  3.000
 5ZT  N4    C5   C6   110.51  3.000
 5ZT  C10   N7   C8   116.67  3.000
 5ZT  C10   N7   C6   117.80  3.000
 5ZT  C8    N7   C6   111.90  3.000
 5ZT  H6    C8   H5   107.37  3.000
 5ZT  H6    C8   C9   107.97  3.000
 5ZT  H5    C8   C9   109.43  3.000
 5ZT  H6    C8   N7   110.49  3.000
 5ZT  H5    C8   N7   110.83  3.000
 5ZT  C9    C8   N7   110.65  3.000
 5ZT  N16   C1   C22  126.37  3.000
 5ZT  N16   C1   C2   117.35  3.000
 5ZT  C22   C1   C2   116.00  3.000
 5ZT  C15   C10  C11  117.46  3.000
 5ZT  C11   C10  N7   120.32  3.000
 5ZT  C15   C10  N7   122.21  3.000
 5ZT  H7    C11  C12  118.58  3.000
 5ZT  H7    C11  C10  120.22  3.000
 5ZT  C12   C11  C10  121.18  3.000
 5ZT  H8    C12  C13  119.44  3.000
 5ZT  H8    C12  C11  118.50  3.000
 5ZT  C13   C12  C11  122.06  3.000
 5ZT  C23   C13  C14  121.44  3.000
 5ZT  C23   C13  C12  122.57  3.000
 5ZT  C14   C13  C12  115.99  3.000
 5ZT  CL25  C14  C15  117.54  3.000
 5ZT  C15   C14  C13  123.28  3.000
 5ZT  CL25  C14  C13  119.18  3.000
 5ZT  H9    C15  C14  118.63  3.000
 5ZT  H9    C15  C10  121.34  3.000
 5ZT  C14   C15  C10  120.02  3.000
 5ZT  O18   C17  N19  121.03  3.000
 5ZT  O18   C17  N16  120.55  3.000
 5ZT  N19   C17  N16  118.41  3.000
 5ZT  O21   C20  N19  121.97  3.000
 5ZT  N19   C20  C22  114.76  3.000
 5ZT  O21   C20  C22  123.27  3.000
 5ZT  H11   C22  H10  105.33  3.000
 5ZT  H11   C22  C20  109.33  3.000
 5ZT  H10   C22  C20  108.96  3.000
 5ZT  H11   C22  C1   109.42  3.000
 5ZT  H10   C22  C1   109.30  3.000
 5ZT  C20   C22  C1   114.13  3.000
 5ZT  H13   C23  H12  106.10  3.000
 5ZT  H13   C23  O24  111.61  3.000
 5ZT  H12   C23  O24  111.52  3.000
 5ZT  H13   C23  C13  108.98  3.000
 5ZT  H12   C23  C13  108.95  3.000
 5ZT  O24   C23  C13  109.59  3.000
 5ZT  H15   C9   H14  108.20  3.000
 5ZT  H15   C9   N4   109.87  3.000
 5ZT  H14   C9   N4   108.57  3.000
 5ZT  H15   C9   C8   109.96  3.000
 5ZT  H14   C9   C8   110.06  3.000
 5ZT  N4    C9   C8   110.15  3.000
 5ZT  C17   N16  C1   119.38  3.000
 5ZT  H16   N19  C20  116.93  3.000
 5ZT  H16   N19  C17  116.20  3.000
 5ZT  C20   N19  C17  126.87  3.000
 5ZT  C9    N4   C5   113.11  3.000
 5ZT  C9    N4   C2   121.14  3.000
 5ZT  C5    N4   C2   125.46  3.000
 5ZT  H17   O24  C23  108.09  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
 5ZT  CONST_01  C13   C14  C15  C10     0.00   0.0  0
 5ZT  CONST_02  C13   C12  C11  C10     0.00   0.0  0
 5ZT  CONST_03  C14   C15  C10  C11     0.00   0.0  0
 5ZT  CONST_04  C14   C13  C12  C11     0.00   0.0  0
 5ZT  CONST_05  C15   C14  C13  C12     0.00   0.0  0
 5ZT  CONST_06  C15   C10  C11  C12     0.00   0.0  0
 5ZT  CONST_07  C14   C15  C10  N7    180.00   0.0  0
 5ZT  CONST_08  C12   C11  C10  N7    180.00   0.0  0
 5ZT  CONST_09  N19   C17  N16  C1      0.00   0.0  0
 5ZT  CONST_10  N16   C17  N19  C20     0.00   0.0  0
 5ZT  CONST_11  CL25  C14  C15  C10   180.00   0.0  0
 5ZT  CONST_12  C23   C13  C12  C11   180.00   0.0  0
 5ZT  CONST_13  CL25  C14  C13  C12   180.00   0.0  0
 5ZT  CONST_14  C23   C13  C14  C15   180.00   0.0  0
 5ZT  CONST_15  C1    C2   N4   C5      0.00   0.0  0
 5ZT  CONST_16  C9    N4   C2   C1    180.00   0.0  0
 5ZT  CONST_17  O18   C17  N16  C1    180.00   0.0  0
 5ZT  CONST_18  O18   C17  N19  C20   180.00   0.0  0
 5ZT  CONST_19  H9    C15  C10  N7      0.00   0.0  0
 5ZT  CONST_20  H7    C11  C10  N7      0.00   0.0  0
 5ZT  CONST_21  H8    C12  C11  C10   180.00   0.0  0
 5ZT  CONST_22  H9    C15  C10  C11   180.00   0.0  0
 5ZT  CONST_23  H9    C15  C14  C13   180.00   0.0  0
 5ZT  CONST_24  H7    C11  C12  C13   180.00   0.0  0
 5ZT  CONST_25  H8    C12  C13  C14   180.00   0.0  0
 5ZT  CONST_26  H7    C11  C10  C15   180.00   0.0  0
 5ZT  CONST_27  H16   N19  C17  N16   180.00   0.0  0
 5ZT  CONST_28  O3    C2   N4   C5    180.00   0.0  0
 5ZT  CONST_29  O3    C2   N4   C9      0.00   0.0  0
 5ZT  CONST_30  H16   N19  C17  O18     0.00   0.0  0
 5ZT  Var_01    C9    N4   C5   C6     55.11  30.0  1
 5ZT  Var_02    C9    C8   N7   C6    -56.99  30.0  1
 5ZT  Var_03    C15   C10  N7   C6     -7.18  30.0  2
 5ZT  Var_04    C11   C10  N7   C6    171.43  30.0  2
 5ZT  Var_05    C8    N7   C6   C5     56.55  30.0  1
 5ZT  Var_06    C10   N7   C6   C5   -164.07  30.0  1
 5ZT  Var_07    C8    C9   N4   C5    -55.33  30.0  1
 5ZT  Var_08    N4    C5   C6   N7    -54.61  30.0  1
 5ZT  Var_09    N4    C9   C8   N7     55.07  30.0  1
 5ZT  Var_10    C15   C10  N7   C8    130.28  30.0  2
 5ZT  Var_11    C11   C10  N7   C8    -51.10  30.0  2
 5ZT  Var_12    N19   C20  C22  C1     -2.75  30.0  1
 5ZT  Var_13    C9    C8   N7   C10   163.14  30.0  1
 5ZT  Var_14    C22   C20  N19  C17     1.37  30.0  1
 5ZT  Var_15    C22   C1   N16  C17     0.10  30.0  1
 5ZT  Var_16    N16   C1   C22  C20     2.23  30.0  1
 5ZT  Var_17    C20   C22  C1   C2    175.94  30.0  1
 5ZT  Var_18    C17   N16  C1   C2   -173.54  30.0  1
 5ZT  Var_19    C6    C5   N4   C2   -118.82  30.0  1
 5ZT  Var_20    C8    C9   N4   C2    118.89  30.0  1
 5ZT  Var_21    O21   C20  C22  C1    177.65  30.0  1
 5ZT  Var_22    O21   C20  N19  C17  -179.02  30.0  1
 5ZT  Var_23    N4    C2   C1   C22   112.36  30.0  2
 5ZT  Var_24    N4    C2   C1   N16   -73.34  30.0  2
 5ZT  Var_25    H5    C8   N7   C6     64.59  30.0  1
 5ZT  Var_26    H6    C8   N7   C6   -176.52  30.0  1
 5ZT  Var_27    H14   C9   N4   C5     65.24  30.0  1
 5ZT  Var_28    H15   C9   N4   C5   -176.61  30.0  1
 5ZT  Var_29    H3    C5   C6   N7     65.52  30.0  1
 5ZT  Var_30    H4    C5   C6   N7   -177.03  30.0  1
 5ZT  Var_31    H14   C9   C8   N7    -64.61  30.0  1
 5ZT  Var_32    H15   C9   C8   N7    176.30  30.0  1
 5ZT  Var_33    H1    C6   N7   C8    -65.68  30.0  1
 5ZT  Var_34    H2    C6   N7   C8    174.74  30.0  1
 5ZT  Var_35    H1    C6   N7   C10    73.70  30.0  1
 5ZT  Var_36    H2    C6   N7   C10   -45.89  30.0  1
 5ZT  Var_37    H5    C8   N7   C10   -75.28  30.0  1
 5ZT  Var_38    H6    C8   N7   C10    43.61  30.0  1
 5ZT  Var_39    H16   N19  C20  C22  -178.91  30.0  1
 5ZT  Var_40    H3    C5   N4   C9    -65.63  30.0  1
 5ZT  Var_41    H4    C5   N4   C9    175.99  30.0  1
 5ZT  Var_42    H10   C22  C1   N16  -120.05  30.0  1
 5ZT  Var_43    H11   C22  C1   N16   125.08  30.0  1
 5ZT  Var_44    H10   C22  C20  N19   119.72  30.0  1
 5ZT  Var_45    H11   C22  C20  N19  -125.65  30.0  1
 5ZT  Var_46    H1    C6   C5   N4     69.31  30.0  1
 5ZT  Var_47    H2    C6   C5   N4   -174.28  30.0  1
 5ZT  Var_48    H5    C8   C9   N4    -67.33  30.0  1
 5ZT  Var_49    H6    C8   C9   N4    176.11  30.0  1
 5ZT  Var_50    O24   C23  C13  C12     2.43  30.0  2
 5ZT  Var_51    O24   C23  C13  C14  -177.96  30.0  2
 5ZT  Var_52    O3    C2   C1   C22   -68.70  30.0  2
 5ZT  Var_53    O3    C2   C1   N16   105.60  30.0  2
 5ZT  Var_54    H10   C22  C1   C2     53.66  30.0  1
 5ZT  Var_55    H11   C22  C1   C2    -61.21  30.0  1
 5ZT  Var_56    H3    C5   N4   C2    120.44  30.0  1
 5ZT  Var_57    H4    C5   N4   C2      2.07  30.0  1
 5ZT  Var_58    H14   C9   N4   C2   -120.53  30.0  1
 5ZT  Var_59    H15   C9   N4   C2     -2.39  30.0  1
 5ZT  Var_60    H12   C23  C13  C12   124.69  30.0  2
 5ZT  Var_61    H13   C23  C13  C12  -119.96  30.0  2
 5ZT  Var_62    H12   C23  C13  C14   -55.70  30.0  2
 5ZT  Var_63    H13   C23  C13  C14    59.65  30.0  2
 5ZT  Var_64    H10   C22  C20  O21   -59.89  30.0  1
 5ZT  Var_65    H11   C22  C20  O21    54.75  30.0  1
 5ZT  Var_66    H16   N19  C20  O21     0.70  30.0  1

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
 5ZT  plan-1  N7    0.020
 5ZT  plan-1  C10   0.020
 5ZT  plan-1  C11   0.020
 5ZT  plan-1  C12   0.020
 5ZT  plan-1  C13   0.020
 5ZT  plan-1  C14   0.020
 5ZT  plan-1  C15   0.020
 5ZT  plan-1  C23   0.020
 5ZT  plan-1  CL25  0.020
 5ZT  plan-1  H7    0.020
 5ZT  plan-1  H8    0.020
 5ZT  plan-1  H9    0.020
 5ZT  plan-2  C2    0.020
 5ZT  plan-2  C5    0.020
 5ZT  plan-2  C1    0.020
 5ZT  plan-2  C9    0.020
 5ZT  plan-2  N4    0.020
 5ZT  plan-2  O3    0.020
 5ZT  plan-3  C20   0.020
 5ZT  plan-3  C22   0.020
 5ZT  plan-3  N19   0.020
 5ZT  plan-3  O21   0.020
 5ZT  plan-4  C1    0.020
 5ZT  plan-4  C17   0.020
 5ZT  plan-4  C20   0.020
 5ZT  plan-4  N16   0.020
 5ZT  plan-4  N19   0.020
 5ZT  plan-4  O18   0.020
 5ZT  plan-4  H16   0.020

