# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 09:28:53 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: 4-(5-chlorofuran-2-carbonyl)-N-(2-methoxyethyl)piperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCNC(=O)N1CCN(CC1)C(=O)c2oc(Cl)cc2
#
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
 Y2J  Y2J  4-(5-chlorofuran-2-carbonyl)-N-(2-methoxyethyl)piperazine-1-carboxamide  ligand  39  21  .  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_Y2J
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
 Y2J  N1   N   NT    0  -0.512  -17.5089  15.3042  26.0860
 Y2J  C4   C   CH2   0  -0.309  -17.7738  15.0284  24.6870
 Y2J  C5   C   CH2   0  -0.307  -18.1139  13.5592  24.4681
 Y2J  C7   C   CR5   0   0.217  -21.4794  12.4167  25.7282
 Y2J  C8   C   CR15  0  -0.304  -22.5056  11.5318  25.6341
 Y2J  C10  C   CR5   0   0.276  -22.9255  12.9836  27.2355
 Y2J  N    N   NH1   0  -0.676  -15.9274  16.9401  25.5807
 Y2J  C    C   CH3   0  -0.390  -17.1300  20.9245  25.2909
 Y2J  O    O   O2    0  -0.482  -16.3735  19.7615  25.0819
 Y2J  C1   C   CH2   0  -0.142  -15.7201  19.3239  26.2465
 Y2J  C11  C   CH2   0  -0.327  -18.8250  13.3603  26.7476
 Y2J  C12  C   CH2   0  -0.278  -18.5245  14.8231  27.0064
 Y2J  C2   C   CH2   0  -0.332  -15.0265  18.0076  25.9546
 Y2J  C3   C   C     0   0.744  -16.6303  16.2611  26.5289
 Y2J  C9   C   CR15  0  -0.288  -23.4536  11.8941  26.6292
 Y2J  N2   N   NT    0  -0.472  -19.1876  13.1617  25.3555
 Y2J  O1   O   O     0  -0.538  -16.4540  16.4634  27.7259
 Y2J  O2   O   O     0  -0.469  -20.3590  12.1069  23.7299
 Y2J  O3   O   O     0  -0.403  -21.7446  13.3164  26.7114
 Y2J  CL   CL  CL    0  -0.077  -23.4974  13.9608  28.4904
 Y2J  H8   H   HCH2  0   0.242  -18.5949  15.6497  24.3096
 Y2J  H9   H   HCH2  0   0.260  -16.8920  15.2331  24.0823
 Y2J  H11  H   HCH2  0   0.277  -18.4087  13.4120  23.4327
 Y2J  H10  H   HCH2  0   0.250  -17.2313  12.9410  24.6598
 Y2J  H12  H   HCR5  0   0.281  -22.5797  10.7102  24.9404
 Y2J  H7   H   HNH1  0   0.399  -16.2813  16.9884  24.6406
 Y2J  H1   H   HCH3  0   0.231  -17.6155  21.1866  24.3513
 Y2J  H    H   HCH3  0   0.202  -17.9059  20.7779  26.0523
 Y2J  H2   H   HCH3  0   0.201  -16.5087  21.7718  25.6064
 Y2J  H4   H   HCH2  0   0.203  -14.9717  20.0573  26.5806
 Y2J  H3   H   HCH2  0   0.202  -16.4343  19.1959  27.0707
 Y2J  H14  H   HCH2  0   0.280  -19.5954  13.0107  27.4256
 Y2J  H15  H   HCH2  0   0.257  -17.9290  12.7640  26.9494
 Y2J  H17  H   HCH2  0   0.233  -19.4467  15.4083  26.9021
 Y2J  H16  H   HCH2  0   0.268  -18.1701  14.9390  28.0266
 Y2J  H6   H   HCH2  0   0.249  -14.3147  18.1416  25.1382
 Y2J  H5   H   HCH2  0   0.250  -14.4498  17.7095  26.8286
 Y2J  H13  H   HCR5  0   0.289  -24.3917  11.4174  26.8585
 Y2J  C6   C   C     0   0.497  -20.2858  12.5465  24.8699

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
 Y2J  C    O    single    1.403  0.020  1.403
 Y2J  O    C1   single    1.405  0.020  1.405
 Y2J  C1   C2   single    1.516  0.020  1.516
 Y2J  C2   N    single    1.446  0.020  1.446
 Y2J  N    C3   single    1.362  0.020  1.362
 Y2J  O1   C3   double    1.227  0.020  1.227
 Y2J  C3   N1   single    1.373  0.020  1.373
 Y2J  N1   C4   single    1.450  0.020  1.450
 Y2J  C4   C5   single    1.524  0.020  1.524
 Y2J  C5   N2   single    1.449  0.020  1.449
 Y2J  N2   C6   single    1.349  0.020  1.349
 Y2J  O2   C6   double    1.224  0.020  1.224
 Y2J  C6   C7   single    1.476  0.020  1.476
 Y2J  C7   C8   aromatic  1.358  0.020  1.358
 Y2J  C8   C9   aromatic  1.421  0.020  1.421
 Y2J  C9   C10  aromatic  1.354  0.020  1.354
 Y2J  C10  CL   single    1.690  0.020  1.690
 Y2J  O3   C10  aromatic  1.334  0.020  1.334
 Y2J  C7   O3   aromatic  1.359  0.020  1.359
 Y2J  C11  N2   single    1.452  0.020  1.452
 Y2J  C12  C11  single    1.516  0.020  1.516
 Y2J  N1   C12  single    1.453  0.020  1.453
 Y2J  C4   H8   single    0.970  0.020  1.090
 Y2J  C4   H9   single    0.970  0.020  1.090
 Y2J  C5   H11  single    0.970  0.020  1.090
 Y2J  C5   H10  single    0.970  0.020  1.090
 Y2J  C8   H12  single    0.930  0.020  1.080
 Y2J  N    H7   single    0.890  0.020  1.040
 Y2J  C    H1   single    0.970  0.020  1.090
 Y2J  C    H    single    0.970  0.020  1.090
 Y2J  C    H2   single    0.970  0.020  1.090
 Y2J  C1   H4   single    0.970  0.020  1.090
 Y2J  C1   H3   single    0.970  0.020  1.090
 Y2J  C11  H14  single    0.970  0.020  1.090
 Y2J  C11  H15  single    0.970  0.020  1.090
 Y2J  C12  H17  single    0.970  0.020  1.090
 Y2J  C12  H16  single    0.970  0.020  1.090
 Y2J  C2   H6   single    0.970  0.020  1.090
 Y2J  C2   H5   single    0.970  0.020  1.090
 Y2J  C9   H13  single    0.930  0.020  1.080

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
 Y2J  C3   N1   C12  118.29  3.000
 Y2J  C12  N1   C4   114.87  3.000
 Y2J  C3   N1   C4   124.11  3.000
 Y2J  H9   C4   H8   107.99  3.000
 Y2J  H9   C4   C5   106.40  3.000
 Y2J  H8   C4   C5   109.25  3.000
 Y2J  H9   C4   N1   110.62  3.000
 Y2J  H8   C4   N1   111.16  3.000
 Y2J  C5   C4   N1   111.26  3.000
 Y2J  H10  C5   H11  108.01  3.000
 Y2J  H10  C5   N2   109.59  3.000
 Y2J  H11  C5   N2   110.21  3.000
 Y2J  H10  C5   C4   109.84  3.000
 Y2J  H11  C5   C4   109.15  3.000
 Y2J  N2   C5   C4   110.00  3.000
 Y2J  O3   C7   C8   109.52  3.000
 Y2J  O3   C7   C6   121.35  3.000
 Y2J  C8   C7   C6   128.90  3.000
 Y2J  H12  C8   C9   126.80  3.000
 Y2J  H12  C8   C7   126.38  3.000
 Y2J  C9   C8   C7   106.82  3.000
 Y2J  CL   C10  O3   116.55  3.000
 Y2J  O3   C10  C9   111.72  3.000
 Y2J  CL   C10  C9   131.73  3.000
 Y2J  H7   N    C3   119.55  3.000
 Y2J  H7   N    C2   115.19  3.000
 Y2J  C3   N    C2   120.64  3.000
 Y2J  H2   C    H    107.71  3.000
 Y2J  H2   C    H1   108.33  3.000
 Y2J  H    C    H1   108.39  3.000
 Y2J  H2   C    O    112.20  3.000
 Y2J  H    C    O    111.96  3.000
 Y2J  H1   C    O    108.13  3.000
 Y2J  C1   O    C    112.66  3.000
 Y2J  H3   C1   H4   107.00  3.000
 Y2J  H3   C1   C2   109.93  3.000
 Y2J  H4   C1   C2   109.04  3.000
 Y2J  H3   C1   O    110.84  3.000
 Y2J  H4   C1   O    111.13  3.000
 Y2J  C2   C1   O    108.87  3.000
 Y2J  H15  C11  H14  106.90  3.000
 Y2J  H15  C11  N2   107.85  3.000
 Y2J  H14  C11  N2   112.21  3.000
 Y2J  H15  C11  C12  109.38  3.000
 Y2J  H14  C11  C12  110.20  3.000
 Y2J  N2   C11  C12  110.19  3.000
 Y2J  H16  C12  H17  107.85  3.000
 Y2J  H16  C12  C11  109.15  3.000
 Y2J  H17  C12  C11  109.39  3.000
 Y2J  H16  C12  N1   109.37  3.000
 Y2J  H17  C12  N1   110.53  3.000
 Y2J  C11  C12  N1   110.49  3.000
 Y2J  H5   C2   H6   106.77  3.000
 Y2J  H5   C2   C1   108.99  3.000
 Y2J  H6   C2   C1   109.62  3.000
 Y2J  H5   C2   N    109.60  3.000
 Y2J  H6   C2   N    107.67  3.000
 Y2J  C1   C2   N    113.94  3.000
 Y2J  O1   C3   N    121.54  3.000
 Y2J  O1   C3   N1   121.46  3.000
 Y2J  N    C3   N1   116.96  3.000
 Y2J  H13  C9   C10  126.91  3.000
 Y2J  H13  C9   C8   128.11  3.000
 Y2J  C10  C9   C8   104.97  3.000
 Y2J  C11  N2   C6   127.63  3.000
 Y2J  C11  N2   C5   111.39  3.000
 Y2J  C6   N2   C5   120.53  3.000
 Y2J  C10  O3   C7   106.96  3.000
 Y2J  O2   C6   N2   123.20  3.000
 Y2J  O2   C6   C7   117.50  3.000
 Y2J  N2   C6   C7   119.29  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
 Y2J  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 Y2J  CONST_02  C9   C10  O3   C7      0.00   0.0  0
 Y2J  CONST_03  C10  O3   C7   C8      0.00   0.0  0
 Y2J  CONST_04  O3   C10  C9   C8      0.00   0.0  0
 Y2J  CONST_05  O3   C7   C8   C9      0.00   0.0  0
 Y2J  CONST_06  C9   C8   C7   C6    180.00   0.0  0
 Y2J  CONST_07  C10  O3   C7   C6    180.00   0.0  0
 Y2J  CONST_08  CL   C10  O3   C7    180.00   0.0  0
 Y2J  CONST_09  CL   C10  C9   C8    180.00   0.0  0
 Y2J  CONST_10  C7   C6   N2   C5    180.00   0.0  0
 Y2J  CONST_12  H13  C9   C8   C7    180.00   0.0  0
 Y2J  CONST_13  H12  C8   C9   C10   180.00   0.0  0
 Y2J  CONST_14  O1   C3   N1   C4    180.00   0.0  0
 Y2J  CONST_15  O2   C6   N2   C5      0.00   0.0  0
 Y2J  CONST_18  N    C3   N1   C4      0.00   0.0  0
 Y2J  CONST_20  C2   N    C3   N1    180.00   0.0  0
 Y2J  CONST_22  O1   C3   N    C2      0.00   0.0  0
 Y2J  Var_01    N2   C5   C4   N1     52.97  30.0  1
 Y2J  Var_02    N2   C11  C12  N1    -54.67  30.0  1
 Y2J  Var_03    C11  C12  N1   C4     51.28  30.0  1
 Y2J  Var_04    C11  N2   C5   C4    -59.05  30.0  1
 Y2J  Var_05    C12  N1   C4   C5    -50.58  30.0  1
 Y2J  Var_06    C12  C11  N2   C5     60.29  30.0  1
 Y2J  Var_07    N2   C6   C7   C8   -158.10  30.0  2
 Y2J  Var_08    O    C1   C2   N     -62.05  30.0  1
 Y2J  Var_09    C2   C1   O    C     175.36  30.0  3
 Y2J  Var_10    C3   N    C2   C1    -79.45  30.0  3
 Y2J  Var_11    H1   C    O    C1   -179.02  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
 Y2J  plan-1  C7   0.020
 Y2J  plan-1  C8   0.020
 Y2J  plan-1  C10  0.020
 Y2J  plan-1  C9   0.020
 Y2J  plan-1  O3   0.020
 Y2J  plan-1  CL   0.020
 Y2J  plan-1  H12  0.020
 Y2J  plan-1  H13  0.020
 Y2J  plan-1  C6   0.020
 Y2J  plan-2  N1   0.020
 Y2J  plan-2  C4   0.020
 Y2J  plan-2  N    0.020
 Y2J  plan-2  C12  0.020
 Y2J  plan-2  C2   0.020
 Y2J  plan-2  C3   0.020
 Y2J  plan-2  O1   0.020
 Y2J  plan-2  H7   0.020
 Y2J  plan-3  C5   0.020
 Y2J  plan-3  C7   0.020
 Y2J  plan-3  C11  0.020
 Y2J  plan-3  N2   0.020
 Y2J  plan-3  O2   0.020
 Y2J  plan-3  C6   0.020

