# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 04:06:48 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: 2-chloro-4-[4-(2,6-dioxo-1,2,5,6-tetrahydropyrimidine-4-carbonyl)piperazin-1-yl]benzaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(ccc1C=O)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
 5ZN  5ZN  "2-chloro-4-[4-(2,6-dioxo-1,2,5,6-tetrahydropyrimidine-4-carbonyl)piperazin-1-yl]benzaldehyde"  ligand  40  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 PERFECT
;

data_comp_5ZN
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
 5ZN  C8    C   CH2   0  -0.306  107.0818  -1.0800  110.2382
 5ZN  C9    C   CH2   0  -0.327  108.4267  -1.5382  110.7707
 5ZN  C1    C   C     0   0.129  110.4135  -3.8261  108.4773
 5ZN  C10   C   CR6   0   0.413  104.7843  -1.9388  110.3631
 5ZN  C11   C   CR16  0  -0.318  104.3094  -0.9323  111.2317
 5ZN  C12   C   CR16  0  -0.265  102.9638  -0.7398  111.4093
 5ZN  C13   C   CR6   0  -0.070  102.4786  -2.4869  109.8742
 5ZN  C14   C   CR16  0  -0.304  103.8269  -2.7037  109.6742
 5ZN  C16   C   C     0   0.617  111.4848  -5.8687  108.4651
 5ZN  C19   C   C     0   0.582  110.7433  -4.9952  106.2868
 5ZN  C21   C   CH2   0  -0.666  110.2599  -3.7681  107.0001
 5ZN  C22   C   CR6   0   0.018  101.9985  -1.5088  110.7459
 5ZN  C23   C   C1    0   0.114  100.5782  -1.2723  111.0004
 5ZN  C5    C   CH2   0  -0.322  107.9557  -3.7806  110.0083
 5ZN  C6    C   CH2   0  -0.305  106.5992  -3.3300  109.4835
 5ZN  N15   N   N     0  -0.411  110.9604  -4.7598  109.1418
 5ZN  N18   N   NH1   0  -0.696  111.3371  -5.9306  107.0929
 5ZN  N4    N   NT    0  -0.445  108.8984  -2.6797  110.0089
 5ZN  N7    N   NT    0  -0.527  106.1254  -2.1771  110.2228
 5ZN  O17   O   O     0  -0.404  112.0390  -6.7493  109.0699
 5ZN  O20   O   O     0  -0.412  110.6347  -5.1549  105.0959
 5ZN  O24   O   O     0  -0.390  100.1619  -0.4315  111.7690
 5ZN  O3    O   O     0  -0.463  110.6932  -1.6108  109.1038
 5ZN  CL25  CL  CL    0  -0.115  101.3826  -3.4757  108.9623
 5ZN  H1    H   HCH2  0   0.251  107.2076  -0.6841  109.2223
 5ZN  H2    H   HCH2  0   0.278  106.7283  -0.2632  110.8603
 5ZN  H3    H   HCH2  0   0.269  108.3342  -1.8346  111.8188
 5ZN  H4    H   HCH2  0   0.282  109.1458  -0.7259  110.7082
 5ZN  H5    H   HCR6  0   0.277  104.9952  -0.3240  111.8031
 5ZN  H6    H   HCR6  0   0.271  102.6319   0.0248  112.0999
 5ZN  H7    H   HCR6  0   0.296  104.1243  -3.4524  108.9552
 5ZN  H8    H   HCH2  0   0.349  110.8041  -2.8987  106.6161
 5ZN  H9    H   HCH2  0   0.344  109.2098  -3.5894  106.7464
 5ZN  H10   H   H     0   0.191   99.8770  -1.9165  110.4484
 5ZN  H11   H   HCH2  0   0.269  107.8514  -4.1530  111.0302
 5ZN  H12   H   HCH2  0   0.290  108.3076  -4.6065  109.3943
 5ZN  H13   H   HCH2  0   0.246  106.6708  -3.1173  108.4085
 5ZN  H14   H   HCH2  0   0.276  105.9162  -4.1671  109.6163
 5ZN  H15   H   HNH1  0   0.428  111.6979  -6.7639  106.6413
 5ZN  C2    C   C     0   0.557  109.9852  -2.5953  109.2375

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
 5ZN  O20   C19  double    1.206  0.020  1.206
 5ZN  C19   C21  single    1.499  0.020  1.499
 5ZN  C19   N18  single    1.370  0.020  1.370
 5ZN  C21   C1   single    1.486  0.020  1.486
 5ZN  N18   C16  single    1.381  0.020  1.381
 5ZN  C1    N15  double    1.270  0.020  1.270
 5ZN  C1    C2   single    1.509  0.020  1.509
 5ZN  C16   N15  single    1.401  0.020  1.401
 5ZN  C16   O17  double    1.203  0.020  1.203
 5ZN  CL25  C13  single    1.735  0.020  1.735
 5ZN  O3    C2   double    1.220  0.020  1.220
 5ZN  C2    N4   single    1.335  0.020  1.335
 5ZN  C6    C5   single    1.523  0.020  1.523
 5ZN  C6    N7   single    1.449  0.020  1.449
 5ZN  C14   C13  aromatic  1.380  0.020  1.380
 5ZN  C14   C10  aromatic  1.406  0.020  1.406
 5ZN  C13   C22  aromatic  1.395  0.020  1.395
 5ZN  N4    C5   single    1.449  0.020  1.449
 5ZN  N4    C9   single    1.451  0.020  1.451
 5ZN  N7    C8   single    1.455  0.020  1.455
 5ZN  N7    C10  single    1.369  0.020  1.369
 5ZN  C8    C9   single    1.517  0.020  1.517
 5ZN  C10   C11  aromatic  1.412  0.020  1.412
 5ZN  C22   C23  single    1.462  0.020  1.462
 5ZN  C22   C12  aromatic  1.401  0.020  1.401
 5ZN  C23   O24  double    1.213  0.020  1.213
 5ZN  C11   C12  aromatic  1.371  0.020  1.371
 5ZN  C8    H1   single    0.970  0.020  1.090
 5ZN  C8    H2   single    0.970  0.020  1.090
 5ZN  C9    H3   single    0.970  0.020  1.090
 5ZN  C9    H4   single    0.970  0.020  1.090
 5ZN  C11   H5   single    0.930  0.020  1.080
 5ZN  C12   H6   single    0.930  0.020  1.080
 5ZN  C14   H7   single    0.930  0.020  1.080
 5ZN  C21   H8   single    0.970  0.020  1.090
 5ZN  C21   H9   single    0.970  0.020  1.090
 5ZN  C23   H10  single    0.930  0.020  1.080
 5ZN  C5    H11  single    0.970  0.020  1.090
 5ZN  C5    H12  single    0.970  0.020  1.090
 5ZN  C6    H13  single    0.970  0.020  1.090
 5ZN  C6    H14  single    0.970  0.020  1.090
 5ZN  N18   H15  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
 5ZN  H2    C8   H1   107.23  3.000
 5ZN  H2    C8   N7   111.05  3.000
 5ZN  H1    C8   N7   109.72  3.000
 5ZN  H2    C8   C9   108.34  3.000
 5ZN  H1    C8   C9   109.40  3.000
 5ZN  N7    C8   C9   111.01  3.000
 5ZN  H4    C9   H3   108.29  3.000
 5ZN  H4    C9   N4   110.04  3.000
 5ZN  H3    C9   N4   108.51  3.000
 5ZN  H4    C9   C8   109.92  3.000
 5ZN  H3    C9   C8   110.08  3.000
 5ZN  N4    C9   C8   109.96  3.000
 5ZN  N15   C1   C21  126.39  3.000
 5ZN  N15   C1   C2   117.29  3.000
 5ZN  C21   C1   C2   116.08  3.000
 5ZN  N7    C10  C14  121.47  3.000
 5ZN  N7    C10  C11  121.10  3.000
 5ZN  C14   C10  C11  117.41  3.000
 5ZN  H5    C11  C12  118.39  3.000
 5ZN  H5    C11  C10  120.89  3.000
 5ZN  C12   C11  C10  120.67  3.000
 5ZN  H6    C12  C22  118.59  3.000
 5ZN  H6    C12  C11  118.88  3.000
 5ZN  C22   C12  C11  122.53  3.000
 5ZN  CL25  C13  C22  120.69  3.000
 5ZN  C22   C13  C14  122.46  3.000
 5ZN  CL25  C13  C14  116.84  3.000
 5ZN  H7    C14  C13  118.33  3.000
 5ZN  H7    C14  C10  121.06  3.000
 5ZN  C13   C14  C10  120.59  3.000
 5ZN  O17   C16  N18  121.03  3.000
 5ZN  O17   C16  N15  120.59  3.000
 5ZN  N18   C16  N15  118.38  3.000
 5ZN  O20   C19  N18  121.97  3.000
 5ZN  N18   C19  C21  114.74  3.000
 5ZN  O20   C19  C21  123.29  3.000
 5ZN  H9    C21  H8   105.41  3.000
 5ZN  H9    C21  C19  109.42  3.000
 5ZN  H8    C21  C19  108.83  3.000
 5ZN  H9    C21  C1   109.61  3.000
 5ZN  H8    C21  C1   109.15  3.000
 5ZN  C19   C21  C1   114.06  3.000
 5ZN  C23   C22  C13  123.80  3.000
 5ZN  C23   C22  C12  119.87  3.000
 5ZN  C13   C22  C12  116.32  3.000
 5ZN  H10   C23  O24  120.32  3.000
 5ZN  H10   C23  C22  115.90  3.000
 5ZN  O24   C23  C22  123.77  3.000
 5ZN  H12   C5   H11  107.46  3.000
 5ZN  H12   C5   N4   111.51  3.000
 5ZN  H11   C5   N4   108.70  3.000
 5ZN  H12   C5   C6   108.56  3.000
 5ZN  H11   C5   C6   109.76  3.000
 5ZN  N4    C5   C6   110.78  3.000
 5ZN  H14   C6   H13  108.02  3.000
 5ZN  H14   C6   N7   110.15  3.000
 5ZN  H13   C6   N7   111.50  3.000
 5ZN  H14   C6   C5   106.82  3.000
 5ZN  H13   C6   C5   109.67  3.000
 5ZN  N7    C6   C5   110.54  3.000
 5ZN  C16   N15  C1   119.37  3.000
 5ZN  H15   N18  C19  116.94  3.000
 5ZN  H15   N18  C16  116.18  3.000
 5ZN  C19   N18  C16  126.88  3.000
 5ZN  C5    N4   C2   125.25  3.000
 5ZN  C5    N4   C9   112.72  3.000
 5ZN  C2    N4   C9   121.20  3.000
 5ZN  C6    N7   C10  120.72  3.000
 5ZN  C10   N7   C8   120.75  3.000
 5ZN  C6    N7   C8   112.97  3.000
 5ZN  O3    C2   N4   125.92  3.000
 5ZN  N4    C2   C1   118.06  3.000
 5ZN  O3    C2   C1   116.00  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
 5ZN  CONST_01  C22   C13  C14  C10     0.00   0.0  0
 5ZN  CONST_02  C22   C12  C11  C10     0.00   0.0  0
 5ZN  CONST_03  C13   C14  C10  C11     0.00   0.0  0
 5ZN  CONST_04  C13   C22  C12  C11     0.00   0.0  0
 5ZN  CONST_05  C14   C13  C22  C12     0.00   0.0  0
 5ZN  CONST_06  C14   C10  C11  C12     0.00   0.0  0
 5ZN  CONST_07  N7    C10  C11  C12   180.00   0.0  0
 5ZN  CONST_08  N7    C10  C14  C13   180.00   0.0  0
 5ZN  CONST_09  N18   C16  N15  C1      0.00   0.0  0
 5ZN  CONST_10  N15   C16  N18  C19     0.00   0.0  0
 5ZN  CONST_11  CL25  C13  C14  C10   180.00   0.0  0
 5ZN  CONST_12  C23   C22  C12  C11   180.00   0.0  0
 5ZN  CONST_13  CL25  C13  C22  C12   180.00   0.0  0
 5ZN  CONST_14  C23   C22  C13  C14   180.00   0.0  0
 5ZN  CONST_15  C1    C2   N4   C9    180.00   0.0  0
 5ZN  CONST_16  C5    N4   C2   C1      0.00   0.0  0
 5ZN  CONST_17  O17   C16  N15  C1    180.00   0.0  0
 5ZN  CONST_18  O17   C16  N18  C19   180.00   0.0  0
 5ZN  CONST_19  H6    C12  C11  C10   180.00   0.0  0
 5ZN  CONST_20  H7    C14  C10  C11   180.00   0.0  0
 5ZN  CONST_21  H6    C12  C22  C13   180.00   0.0  0
 5ZN  CONST_22  H5    C11  C10  C14   180.00   0.0  0
 5ZN  CONST_23  H7    C14  C13  C22   180.00   0.0  0
 5ZN  CONST_24  H5    C11  C12  C22   180.00   0.0  0
 5ZN  CONST_25  H7    C14  C10  N7      0.00   0.0  0
 5ZN  CONST_26  H5    C11  C10  N7      0.00   0.0  0
 5ZN  CONST_27  H15   N18  C16  N15   180.00   0.0  0
 5ZN  CONST_28  O3    C2   N4   C9      0.00   0.0  0
 5ZN  CONST_29  O3    C2   N4   C5    180.00   0.0  0
 5ZN  CONST_30  H15   N18  C16  O17     0.00   0.0  0
 5ZN  Var_01    C5    C6   N7   C8     54.32  30.0  1
 5ZN  Var_02    C14   C10  N7   C8    144.38  30.0  2
 5ZN  Var_03    C11   C10  N7   C8    -37.10  30.0  2
 5ZN  Var_04    C5    N4   C9   C8    -56.45  30.0  1
 5ZN  Var_05    C6    C5   N4   C9     56.30  30.0  1
 5ZN  Var_06    C6    N7   C8   C9    -55.17  30.0  1
 5ZN  Var_07    C10   N7   C8   C9    150.96  30.0  1
 5ZN  Var_08    N18   C19  C21  C1     -4.56  30.0  1
 5ZN  Var_09    C5    C6   N7   C10  -151.80  30.0  1
 5ZN  Var_10    C6    N7   C10  C11   171.05  30.0  3
 5ZN  Var_11    C6    N7   C10  C14    -7.48  30.0  3
 5ZN  Var_12    C21   C19  N18  C16     2.35  30.0  1
 5ZN  Var_13    C21   C1   N15  C16    -0.12  30.0  1
 5ZN  Var_14    N15   C1   C21  C19     3.82  30.0  1
 5ZN  Var_15    N7    C6   C5   N4    -53.86  30.0  1
 5ZN  Var_16    N7    C8   C9   N4     54.68  30.0  1
 5ZN  Var_17    C2    N4   C9   C8    113.66  30.0  1
 5ZN  Var_18    O20   C19  C21  C1    176.04  30.0  1
 5ZN  Var_19    O20   C19  N18  C16  -178.24  30.0  1
 5ZN  Var_20    C2    C1   N15  C16  -174.22  30.0  1
 5ZN  Var_21    C2    C1   C21  C19   177.97  30.0  1
 5ZN  Var_22    C6    C5   N4   C2   -113.34  30.0  1
 5ZN  Var_23    N4    C2   C1   C21   111.13  30.0  2
 5ZN  Var_24    N4    C2   C1   N15   -74.17  30.0  2
 5ZN  Var_25    H13   C6   N7   C8    -67.95  30.0  1
 5ZN  Var_26    H14   C6   N7   C8    172.13  30.0  1
 5ZN  Var_27    H11   C5   N4   C9    -64.39  30.0  1
 5ZN  Var_28    H12   C5   N4   C9    177.33  30.0  1
 5ZN  Var_29    H13   C6   N7   C10    85.93  30.0  1
 5ZN  Var_30    H14   C6   N7   C10   -33.99  30.0  1
 5ZN  Var_31    H1    C8   N7   C10   -88.00  30.0  1
 5ZN  Var_32    H2    C8   N7   C10    30.36  30.0  1
 5ZN  Var_33    H15   N18  C19  C21  -178.48  30.0  1
 5ZN  Var_34    H3    C9   N4   C5     64.01  30.0  1
 5ZN  Var_35    H4    C9   N4   C5   -177.67  30.0  1
 5ZN  Var_36    H1    C8   N7   C6     65.87  30.0  1
 5ZN  Var_37    H2    C8   N7   C6   -175.76  30.0  1
 5ZN  Var_38    H8    C21  C1   N15  -118.14  30.0  1
 5ZN  Var_39    H9    C21  C1   N15   126.88  30.0  1
 5ZN  Var_40    H8    C21  C19  N18   117.57  30.0  1
 5ZN  Var_41    H9    C21  C19  N18  -127.73  30.0  1
 5ZN  Var_42    H13   C6   C5   N4     69.48  30.0  1
 5ZN  Var_43    H14   C6   C5   N4   -173.70  30.0  1
 5ZN  Var_44    H1    C8   C9   N4    -66.55  30.0  1
 5ZN  Var_45    H2    C8   C9   N4    176.86  30.0  1
 5ZN  Var_46    H11   C5   C6   N7     66.19  30.0  1
 5ZN  Var_47    H12   C5   C6   N7   -176.62  30.0  1
 5ZN  Var_48    H3    C9   C8   N7    -64.83  30.0  1
 5ZN  Var_49    H4    C9   C8   N7    175.97  30.0  1
 5ZN  Var_50    O24   C23  C22  C12     0.00  30.0  2
 5ZN  Var_51    O24   C23  C22  C13   179.19  30.0  2
 5ZN  Var_52    O3    C2   C1   C21   -70.22  30.0  2
 5ZN  Var_53    O3    C2   C1   N15   104.49  30.0  2
 5ZN  Var_54    H10   C23  C22  C12  -179.71  30.0  2
 5ZN  Var_55    H10   C23  C22  C13    -0.52  30.0  2
 5ZN  Var_56    H8    C21  C1   C2     56.02  30.0  1
 5ZN  Var_57    H9    C21  C1   C2    -58.96  30.0  1
 5ZN  Var_58    H11   C5   N4   C2    125.98  30.0  1
 5ZN  Var_59    H12   C5   N4   C2      7.70  30.0  1
 5ZN  Var_60    H3    C9   N4   C2   -125.88  30.0  1
 5ZN  Var_61    H4    C9   N4   C2     -7.56  30.0  1
 5ZN  Var_62    H8    C21  C19  O20   -61.83  30.0  1
 5ZN  Var_63    H9    C21  C19  O20    52.87  30.0  1
 5ZN  Var_64    H15   N18  C19  O20     0.93  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
 5ZN  plan-1  C10   0.020
 5ZN  plan-1  C11   0.020
 5ZN  plan-1  C12   0.020
 5ZN  plan-1  C13   0.020
 5ZN  plan-1  C14   0.020
 5ZN  plan-1  C22   0.020
 5ZN  plan-1  C23   0.020
 5ZN  plan-1  N7    0.020
 5ZN  plan-1  CL25  0.020
 5ZN  plan-1  H5    0.020
 5ZN  plan-1  H6    0.020
 5ZN  plan-1  H7    0.020
 5ZN  plan-2  C22   0.020
 5ZN  plan-2  C23   0.020
 5ZN  plan-2  O24   0.020
 5ZN  plan-2  H10   0.020
 5ZN  plan-3  C9    0.020
 5ZN  plan-3  C1    0.020
 5ZN  plan-3  C5    0.020
 5ZN  plan-3  N4    0.020
 5ZN  plan-3  O3    0.020
 5ZN  plan-3  C2    0.020
 5ZN  plan-4  C19   0.020
 5ZN  plan-4  C21   0.020
 5ZN  plan-4  N18   0.020
 5ZN  plan-4  O20   0.020
 5ZN  plan-5  C1    0.020
 5ZN  plan-5  C16   0.020
 5ZN  plan-5  C19   0.020
 5ZN  plan-5  N15   0.020
 5ZN  plan-5  N18   0.020
 5ZN  plan-5  O17   0.020
 5ZN  plan-5  H15   0.020

