# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 15:34:39 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: 6-[4-(3,4-dichlorophenyl)piperazin-1-yl]carbonyl-1~{H}-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(cc1Cl)N2CCN(CC2)C(=O)C3=CC(=O)NC(=O)N3
#
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
 YD1  YD1  6-[4-(3,4-dichlorophenyl)piperazin-1-yl]carbonyl-1~{H}-pyrimidine-2,4-dione  ligand  38  24  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YD1
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
 YD1  C1    C   CR6   0   0.303  60.2593  -1.8079  105.1571
 YD1  C2    C   C     0   0.511  59.8703  -0.6730  106.0670
 YD1  C5    C   CH2   0  -0.324  57.7231  -1.8156  106.6244
 YD1  C6    C   CH2   0  -0.312  56.3696  -1.4271  106.0569
 YD1  C8    C   CH2   0  -0.303  56.7750   0.8548  106.7455
 YD1  C9    C   CH2   0  -0.319  58.1220   0.4541  107.3193
 YD1  C12   C   CR16  0  -0.205  52.5431   1.2893  107.2862
 YD1  C14   C   CR6   0   0.022  52.3148  -0.4340  105.6529
 YD1  C10   C   CR6   0   0.387  54.4925   0.0178  106.6122
 YD1  C11   C   CR16  0  -0.325  53.8928   1.0241  107.3850
 YD1  C13   C   CR6   0  -0.046  51.7348   0.5613  106.4224
 YD1  C16   C   CR16  0  -0.314  53.6738  -0.6986  105.7343
 YD1  C19   C   CR6   0   0.673  61.9840  -3.4251  104.7059
 YD1  C22   C   CR6   0   0.585  60.1262  -3.0752  103.1067
 YD1  C24   C   CR16  0  -0.494  59.6043  -2.0748  104.0133
 YD1  N18   N   NR16  0  -0.714  61.4111  -2.4536  105.4888
 YD1  N21   N   NR16  0  -0.719  61.2929  -3.6821  103.5489
 YD1  N4    N   NT    0  -0.449  58.6383  -0.6899  106.5893
 YD1  N7    N   NT    0  -0.524  55.8455  -0.2671  106.7495
 YD1  O20   O   O     0  -0.458  63.0046  -4.0002  105.0111
 YD1  O23   O   O     0  -0.446  59.6268  -3.3917  102.0455
 YD1  O3    O   O     0  -0.456  60.6910   0.2136  106.2373
 YD1  CL17  CL  CL    0  -0.110  50.0466   0.8985  106.3309
 YD1  H1    H   HCH2  0   0.269  57.6044  -2.1260  107.6668
 YD1  H2    H   HCH2  0   0.288  58.1179  -2.6646  106.0738
 YD1  H3    H   HCH2  0   0.236  56.4587  -1.2556  104.9739
 YD1  H4    H   HCH2  0   0.271  55.7015  -2.2757  106.2051
 YD1  H5    H   HCH2  0   0.237  56.9153   1.2376  105.7250
 YD1  H6    H   HCH2  0   0.271  56.3874   1.6725  107.3487
 YD1  H7    H   HCH2  0   0.260  58.0185   0.1900  108.3756
 YD1  H8    H   HCH2  0   0.281  58.8132   1.2889  107.2435
 YD1  H9    H   HCR6  0   0.285  52.1054   2.0636  107.9020
 YD1  H10   H   HCR6  0   0.278  54.4749   1.5941  108.0956
 YD1  H11   H   HCR6  0   0.297  54.0803  -1.4640  105.0895
 YD1  H12   H   HCR6  0   0.304  58.6985  -1.5501  103.7478
 YD1  H13   H   HNR6  0   0.436  61.8978  -2.2149  106.3425
 YD1  H14   H   HNR6  0   0.427  61.6927  -4.3938  102.9491
 YD1  CL15  CL  CL    0  -0.100  51.3589  -1.3562  104.5526

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
 YD1  O23   C22   double    1.215  0.020  1.215
 YD1  C22   C24   single    1.447  0.020  1.447
 YD1  C22   N21   single    1.387  0.020  1.387
 YD1  C24   C1    double    1.345  0.020  1.345
 YD1  N21   C19   single    1.372  0.020  1.372
 YD1  CL15  C14   single    1.725  0.020  1.725
 YD1  C1    N18   single    1.361  0.020  1.361
 YD1  C1    C2    single    1.506  0.020  1.506
 YD1  C19   N18   single    1.373  0.020  1.373
 YD1  C19   O20   double    1.211  0.020  1.211
 YD1  C2    O3    double    1.220  0.020  1.220
 YD1  C2    N4    single    1.338  0.020  1.338
 YD1  C14   C16   aromatic  1.387  0.020  1.387
 YD1  C14   C13   aromatic  1.385  0.020  1.385
 YD1  C16   C10   aromatic  1.398  0.020  1.398
 YD1  C6    C5    single    1.518  0.020  1.518
 YD1  C6    N7    single    1.449  0.020  1.449
 YD1  N4    C5    single    1.451  0.020  1.451
 YD1  N4    C9    single    1.452  0.020  1.452
 YD1  C13   CL17  single    1.724  0.020  1.724
 YD1  C13   C12   aromatic  1.389  0.020  1.389
 YD1  C8    N7    single    1.457  0.020  1.457
 YD1  C8    C9    single    1.518  0.020  1.518
 YD1  C10   N7    single    1.389  0.020  1.389
 YD1  C10   C11   aromatic  1.403  0.020  1.403
 YD1  C12   C11   aromatic  1.379  0.020  1.379
 YD1  C5    H1    single    0.970  0.020  1.090
 YD1  C5    H2    single    0.970  0.020  1.090
 YD1  C6    H3    single    0.970  0.020  1.090
 YD1  C6    H4    single    0.970  0.020  1.090
 YD1  C8    H5    single    0.970  0.020  1.090
 YD1  C8    H6    single    0.970  0.020  1.090
 YD1  C9    H7    single    0.970  0.020  1.090
 YD1  C9    H8    single    0.970  0.020  1.090
 YD1  C12   H9    single    0.930  0.020  1.080
 YD1  C11   H10   single    0.930  0.020  1.080
 YD1  C16   H11   single    0.930  0.020  1.080
 YD1  C24   H12   single    0.930  0.020  1.080
 YD1  N18   H13   single    0.860  0.020  1.020
 YD1  N21   H14   single    0.860  0.020  1.020

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
 YD1  N18   C1   C24  121.67  3.000
 YD1  N18   C1   C2   115.39  3.000
 YD1  C24   C1   C2   122.53  3.000
 YD1  O3    C2   N4   125.03  3.000
 YD1  N4    C2   C1   117.65  3.000
 YD1  O3    C2   C1   117.28  3.000
 YD1  H2    C5   H1   107.49  3.000
 YD1  H2    C5   N4   111.40  3.000
 YD1  H1    C5   N4   108.15  3.000
 YD1  H2    C5   C6   109.55  3.000
 YD1  H1    C5   C6   109.39  3.000
 YD1  N4    C5   C6   110.77  3.000
 YD1  H4    C6   H3   107.74  3.000
 YD1  H4    C6   N7   109.66  3.000
 YD1  H3    C6   N7   112.03  3.000
 YD1  H4    C6   C5   107.24  3.000
 YD1  H3    C6   C5   109.61  3.000
 YD1  N7    C6   C5   110.40  3.000
 YD1  H6    C8   H5   107.38  3.000
 YD1  H6    C8   N7   110.49  3.000
 YD1  H5    C8   N7   110.63  3.000
 YD1  H6    C8   C9   107.77  3.000
 YD1  H5    C8   C9   109.25  3.000
 YD1  N7    C8   C9   111.21  3.000
 YD1  H8    C9   H7   108.24  3.000
 YD1  H8    C9   N4   110.13  3.000
 YD1  H7    C9   N4   109.21  3.000
 YD1  H8    C9   C8   109.59  3.000
 YD1  H7    C9   C8   110.17  3.000
 YD1  N4    C9   C8   109.48  3.000
 YD1  H9    C12  C13  119.58  3.000
 YD1  H9    C12  C11  119.53  3.000
 YD1  C13   C12  C11  120.88  3.000
 YD1  CL15  C14  C16  118.59  3.000
 YD1  C16   C14  C13  120.97  3.000
 YD1  CL15  C14  C13  120.43  3.000
 YD1  N7    C10  C16  121.82  3.000
 YD1  N7    C10  C11  120.58  3.000
 YD1  C16   C10  C11  117.58  3.000
 YD1  H10   C11  C10  120.66  3.000
 YD1  H10   C11  C12  118.21  3.000
 YD1  C10   C11  C12  121.11  3.000
 YD1  CL17  C13  C14  121.40  3.000
 YD1  CL17  C13  C12  120.02  3.000
 YD1  C14   C13  C12  118.58  3.000
 YD1  H11   C16  C10  121.18  3.000
 YD1  H11   C16  C14  117.96  3.000
 YD1  C10   C16  C14  120.86  3.000
 YD1  O20   C19  N21  123.25  3.000
 YD1  O20   C19  N18  122.97  3.000
 YD1  N21   C19  N18  113.78  3.000
 YD1  O23   C22  N21  120.67  3.000
 YD1  N21   C22  C24  113.95  3.000
 YD1  O23   C22  C24  125.38  3.000
 YD1  H12   C24  C22  118.97  3.000
 YD1  H12   C24  C1   121.41  3.000
 YD1  C22   C24  C1   119.62  3.000
 YD1  H13   N18  C19  116.59  3.000
 YD1  H13   N18  C1   120.05  3.000
 YD1  C19   N18  C1   123.35  3.000
 YD1  H14   N21  C22  116.77  3.000
 YD1  H14   N21  C19  115.60  3.000
 YD1  C22   N21  C19  127.62  3.000
 YD1  C9    N4   C5   112.01  3.000
 YD1  C9    N4   C2   120.90  3.000
 YD1  C5    N4   C2   126.86  3.000
 YD1  C10   N7   C8   117.58  3.000
 YD1  C10   N7   C6   117.98  3.000
 YD1  C8    N7   C6   112.60  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
 YD1  CONST_01  C16   C14  C13  C12    0.00   0.0  0
 YD1  CONST_02  C16   C10  C11  C12    0.00   0.0  0
 YD1  CONST_03  C11   C10  C16  C14    0.00   0.0  0
 YD1  CONST_04  C11   C12  C13  C14    0.00   0.0  0
 YD1  CONST_05  C13   C14  C16  C10    0.00   0.0  0
 YD1  CONST_06  C13   C12  C11  C10    0.00   0.0  0
 YD1  CONST_07  N7    C10  C11  C12  180.00   0.0  0
 YD1  CONST_08  N7    C10  C16  C14  180.00   0.0  0
 YD1  CONST_09  N21   C19  N18  C1     0.00   0.0  0
 YD1  CONST_10  C24   C22  N21  C19    0.00   0.0  0
 YD1  CONST_11  N18   C19  N21  C22    0.00   0.0  0
 YD1  CONST_12  CL15  C14  C13  C12  180.00   0.0  0
 YD1  CONST_13  CL15  C14  C16  C10  180.00   0.0  0
 YD1  CONST_14  CL17  C13  C12  C11  180.00   0.0  0
 YD1  CONST_15  CL17  C13  C14  C16  180.00   0.0  0
 YD1  CONST_16  C5    N4   C2   C1     0.00   0.0  0
 YD1  CONST_17  C9    N4   C2   C1   180.00   0.0  0
 YD1  CONST_18  O20   C19  N18  C1   180.00   0.0  0
 YD1  CONST_19  O23   C22  N21  C19  180.00   0.0  0
 YD1  CONST_20  O20   C19  N21  C22  180.00   0.0  0
 YD1  CONST_21  H9    C12  C13  C14  180.00   0.0  0
 YD1  CONST_22  H11   C16  C10  C11  180.00   0.0  0
 YD1  CONST_23  H10   C11  C12  C13  180.00   0.0  0
 YD1  CONST_24  H14   N21  C22  C24  180.00   0.0  0
 YD1  CONST_25  H13   N18  C19  N21  180.00   0.0  0
 YD1  CONST_26  O3    C2   N4   C5   180.00   0.0  0
 YD1  CONST_27  O3    C2   N4   C9     0.00   0.0  0
 YD1  Var_01    C8    N7   C6   C5    54.32  30.0  1
 YD1  Var_02    C8    C9   N4   C5   -57.42  30.0  1
 YD1  Var_03    C9    N4   C5   C6    57.67  30.0  1
 YD1  Var_04    C9    C8   N7   C6   -55.24  30.0  1
 YD1  Var_05    C16   C10  N7   C6    -6.30  30.0  2
 YD1  Var_06    N7    C6   C5   N4   -54.82  30.0  1
 YD1  Var_07    N7    C8   C9   N4    55.40  30.0  1
 YD1  Var_08    N4    C2   C1   C24   60.43  30.0  2

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
 YD1  plan-1  C12   0.020
 YD1  plan-1  C14   0.020
 YD1  plan-1  C10   0.020
 YD1  plan-1  C11   0.020
 YD1  plan-1  C13   0.020
 YD1  plan-1  C16   0.020
 YD1  plan-1  N7    0.020
 YD1  plan-1  CL17  0.020
 YD1  plan-1  H9    0.020
 YD1  plan-1  H10   0.020
 YD1  plan-1  H11   0.020
 YD1  plan-1  CL15  0.020
 YD1  plan-2  C1    0.020
 YD1  plan-2  C2    0.020
 YD1  plan-2  C19   0.020
 YD1  plan-2  C22   0.020
 YD1  plan-2  C24   0.020
 YD1  plan-2  N18   0.020
 YD1  plan-2  N21   0.020
 YD1  plan-2  O20   0.020
 YD1  plan-2  O23   0.020
 YD1  plan-2  H12   0.020
 YD1  plan-2  H13   0.020
 YD1  plan-2  H14   0.020
 YD1  plan-3  C1    0.020
 YD1  plan-3  C2    0.020
 YD1  plan-3  C5    0.020
 YD1  plan-3  C9    0.020
 YD1  plan-3  N4    0.020
 YD1  plan-3  O3    0.020

