# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 14:02:12 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: 4-(5-chlorofuran-2-carbonyl)-N-(cyclopropylmethyl)piperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1oc(cc1)C(=O)N2CCN(CC2)C(=O)NCC3CC3
#
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
 XZV  XZV  4-(5-chlorofuran-2-carbonyl)-N-(cyclopropylmethyl)piperazine-1-carboxamide  ligand  39  21  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XZV
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
 XZV  N1   N   NT    0  -0.512  -17.3416  15.0405  26.0489
 XZV  C4   C   CH2   0  -0.488  -14.3976  20.0940  25.5400
 XZV  C5   C   CH2   0  -0.278  -18.4843  14.7351  26.8924
 XZV  C6   C   CH2   0  -0.328  -18.8574  13.2702  26.7683
 XZV  C8   C   CR5   0   0.218  -21.4599  12.3913  25.5685
 XZV  C10  C   CR15  0  -0.288  -23.5340  12.0549  26.3210
 XZV  C13  C   CH2   0  -0.308  -17.4731  14.6143  24.6685
 XZV  N    N   NH1   0  -0.678  -15.5890  16.4919  25.5466
 XZV  C    C   C     0   0.745  -16.4589  16.0036  26.4722
 XZV  O    O   O     0  -0.539  -16.4226  16.3682  27.6430
 XZV  C1   C   CH2   0  -0.304  -14.6507  17.5393  25.8930
 XZV  C11  C   CR5   0   0.276  -22.9950  13.1615  26.8849
 XZV  C12  C   CH2   0  -0.309  -17.8978  13.1543  24.5794
 XZV  C2   C   CH1   0  -0.247  -15.2534  18.9201  25.8998
 XZV  C3   C   CH2   0  -0.486  -15.4705  19.6313  24.6000
 XZV  C9   C   CR15  0  -0.305  -22.5267  11.5597  25.4492
 XZV  N2   N   NT    0  -0.470  -19.0878  12.9320  25.3745
 XZV  O1   O   O     0  -0.471  -20.1891  11.8576  23.7139
 XZV  O2   O   O     0  -0.403  -21.7547  13.3845  26.4474
 XZV  CL   CL  CL    0  -0.077  -23.6109  14.2689  28.0028
 XZV  H6   H   HCH2  0   0.249  -14.5476  21.0224  26.0756
 XZV  H8   H   HCH2  0   0.268  -18.2378  14.9551  27.9271
 XZV  H9   H   HCH2  0   0.233  -19.3472  15.3511  26.6112
 XZV  H11  H   HCH2  0   0.258  -18.0303  12.6514  27.1309
 XZV  H10  H   HCH2  0   0.281  -19.7151  13.0469  27.3921
 XZV  H13  H   HCR5  0   0.289  -24.5161  11.6507  26.4995
 XZV  H17  H   HCH2  0   0.260  -16.5178  14.6880  24.1519
 XZV  H16  H   HCH2  0   0.242  -18.1979  15.2367  24.1298
 XZV  H    H   HNH1  0   0.398  -15.8200  16.4338  24.5693
 XZV  H1   H   HCH2  0   0.248  -14.2111  17.3103  26.8632
 XZV  H2   H   HCH2  0   0.242  -13.8367  17.4979  25.1655
 XZV  H14  H   HCH2  0   0.251  -17.0910  12.5124  24.9462
 XZV  H15  H   HCH2  0   0.278  -18.0846  12.8983  23.5404
 XZV  H3   H   HCH1  0   0.253  -15.9996  19.0871  26.6692
 XZV  H5   H   HCH2  0   0.242  -15.1652  19.1295  23.6891
 XZV  H4   H   HCH2  0   0.248  -16.3563  20.2440  24.4924
 XZV  H12  H   HCR5  0   0.281  -22.5894  10.6876  24.8191
 XZV  C7   C   C     0   0.497  -20.1853  12.3738  24.8241
 XZV  H7   H   HCH2  0   0.242  -13.3667  19.9050  25.2644

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
 XZV  O    C    double    1.227  0.020  1.227
 XZV  N    C    single    1.361  0.020  1.361
 XZV  C1   N    single    1.448  0.020  1.448
 XZV  C2   C1   single    1.507  0.020  1.507
 XZV  C2   C3   single    1.498  0.020  1.498
 XZV  C3   C4   single    1.500  0.020  1.500
 XZV  C4   C2   single    1.497  0.020  1.497
 XZV  C    N1   single    1.373  0.020  1.373
 XZV  N1   C5   single    1.453  0.020  1.453
 XZV  C5   C6   single    1.517  0.020  1.517
 XZV  C6   N2   single    1.453  0.020  1.453
 XZV  N2   C7   single    1.349  0.020  1.349
 XZV  O1   C7   double    1.224  0.020  1.224
 XZV  C7   C8   single    1.476  0.020  1.476
 XZV  C8   C9   aromatic  1.358  0.020  1.358
 XZV  C9   C10  aromatic  1.421  0.020  1.421
 XZV  C10  C11  aromatic  1.354  0.020  1.354
 XZV  C11  CL   single    1.690  0.020  1.690
 XZV  O2   C11  aromatic  1.334  0.020  1.334
 XZV  C8   O2   aromatic  1.359  0.020  1.359
 XZV  C12  N2   single    1.448  0.020  1.448
 XZV  C13  C12  single    1.523  0.020  1.523
 XZV  N1   C13  single    1.451  0.020  1.451
 XZV  C4   H7   single    0.970  0.020  1.090
 XZV  C4   H6   single    0.970  0.020  1.090
 XZV  C5   H8   single    0.970  0.020  1.090
 XZV  C5   H9   single    0.970  0.020  1.090
 XZV  C6   H11  single    0.970  0.020  1.090
 XZV  C6   H10  single    0.970  0.020  1.090
 XZV  C10  H13  single    0.930  0.020  1.080
 XZV  C13  H17  single    0.970  0.020  1.090
 XZV  C13  H16  single    0.970  0.020  1.090
 XZV  N    H    single    0.860  0.020  1.020
 XZV  C1   H1   single    0.970  0.020  1.090
 XZV  C1   H2   single    0.970  0.020  1.090
 XZV  C12  H14  single    0.970  0.020  1.090
 XZV  C12  H15  single    0.970  0.020  1.090
 XZV  C2   H3   single    0.970  0.020  1.090
 XZV  C3   H5   single    0.970  0.020  1.090
 XZV  C3   H4   single    0.970  0.020  1.090
 XZV  C9   H12  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
 XZV  C    N1   C13  123.89  3.000
 XZV  C13  N1   C5   114.80  3.000
 XZV  C    N1   C5   118.30  3.000
 XZV  H6   C4   H7   114.04  3.000
 XZV  H6   C4   C3   118.41  3.000
 XZV  H7   C4   C3   117.86  3.000
 XZV  H6   C4   C2   118.34  3.000
 XZV  H7   C4   C2   117.92  3.000
 XZV  C3   C4   C2    59.97  3.000
 XZV  H9   C5   H8   108.00  3.000
 XZV  H9   C5   C6   109.14  3.000
 XZV  H8   C5   C6   109.23  3.000
 XZV  H9   C5   N1   110.60  3.000
 XZV  H8   C5   N1   109.39  3.000
 XZV  C6   C5   N1   110.43  3.000
 XZV  H10  C6   H11  106.90  3.000
 XZV  H10  C6   N2   112.26  3.000
 XZV  H11  C6   N2   107.82  3.000
 XZV  H10  C6   C5   110.28  3.000
 XZV  H11  C6   C5   109.45  3.000
 XZV  N2   C6   C5   110.02  3.000
 XZV  O2   C8   C9   109.52  3.000
 XZV  O2   C8   C7   121.48  3.000
 XZV  C9   C8   C7   128.81  3.000
 XZV  H13  C10  C9   128.11  3.000
 XZV  H13  C10  C11  126.93  3.000
 XZV  C9   C10  C11  104.96  3.000
 XZV  H16  C13  H17  107.96  3.000
 XZV  H16  C13  C12  109.33  3.000
 XZV  H17  C13  C12  106.37  3.000
 XZV  H16  C13  N1   111.14  3.000
 XZV  H17  C13  N1   110.62  3.000
 XZV  C12  C13  N1   111.26  3.000
 XZV  H    N    C1   115.01  3.000
 XZV  H    N    C    119.56  3.000
 XZV  C1   N    C    120.73  3.000
 XZV  O    C    N    121.57  3.000
 XZV  N    C    N1   116.93  3.000
 XZV  O    C    N1   121.44  3.000
 XZV  H2   C1   H1   106.52  3.000
 XZV  H2   C1   C2   109.62  3.000
 XZV  H1   C1   C2   110.49  3.000
 XZV  H2   C1   N    107.22  3.000
 XZV  H1   C1   N    108.80  3.000
 XZV  C2   C1   N    113.87  3.000
 XZV  CL   C11  O2   116.50  3.000
 XZV  O2   C11  C10  111.73  3.000
 XZV  CL   C11  C10  131.77  3.000
 XZV  H15  C12  H14  108.01  3.000
 XZV  H15  C12  N2   110.35  3.000
 XZV  H14  C12  N2   109.37  3.000
 XZV  H15  C12  C13  109.26  3.000
 XZV  H14  C12  C13  109.69  3.000
 XZV  N2   C12  C13  110.12  3.000
 XZV  H3   C2   C3   116.28  3.000
 XZV  H3   C2   C1   114.81  3.000
 XZV  C3   C2   C1   119.30  3.000
 XZV  H3   C2   C4   116.30  3.000
 XZV  C3   C2   C4    60.11  3.000
 XZV  C1   C2   C4   119.27  3.000
 XZV  H4   C3   H5   114.15  3.000
 XZV  H4   C3   C2   118.28  3.000
 XZV  H5   C3   C2   117.95  3.000
 XZV  H4   C3   C4   118.24  3.000
 XZV  H5   C3   C4   117.91  3.000
 XZV  C2   C3   C4    59.92  3.000
 XZV  H12  C9   C10  126.82  3.000
 XZV  H12  C9   C8   126.35  3.000
 XZV  C10  C9   C8   106.83  3.000
 XZV  C12  N2   C7   120.53  3.000
 XZV  C12  N2   C6   111.15  3.000
 XZV  C7   N2   C6   128.10  3.000
 XZV  C11  O2   C8   106.96  3.000
 XZV  O1   C7   N2   123.17  3.000
 XZV  O1   C7   C8   117.36  3.000
 XZV  N2   C7   C8   119.47  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
 XZV  CONST_01  C11  C10  C9   C8      0.00   0.0  0
 XZV  CONST_02  C10  C11  O2   C8      0.00   0.0  0
 XZV  CONST_03  O2   C8   C9   C10     0.00   0.0  0
 XZV  CONST_04  C9   C8   O2   C11     0.00   0.0  0
 XZV  CONST_05  O2   C11  C10  C9      0.00   0.0  0
 XZV  CONST_06  C10  C9   C8   C7    180.00   0.0  0
 XZV  CONST_07  C11  O2   C8   C7    180.00   0.0  0
 XZV  CONST_08  CL   C11  O2   C8    180.00   0.0  0
 XZV  CONST_09  CL   C11  C10  C9    180.00   0.0  0
 XZV  CONST_11  C12  N2   C7   C8    180.00   0.0  0
 XZV  CONST_12  H13  C10  C9   C8    180.00   0.0  0
 XZV  CONST_13  H12  C9   C10  C11   180.00   0.0  0
 XZV  CONST_16  O    C    N1   C13   180.00   0.0  0
 XZV  CONST_17  O1   C7   N2   C12     0.00   0.0  0
 XZV  CONST_18  N    C    N1   C5    180.00   0.0  0
 XZV  CONST_19  N    C    N1   C13     0.00   0.0  0
 XZV  CONST_20  C1   N    C    N1    180.00   0.0  0
 XZV  CONST_22  C1   N    C    O       0.00   0.0  0
 XZV  Var_01    N2   C6   C5   N1    -55.17  30.0  1
 XZV  Var_02    N2   C12  C13  N1     52.92  30.0  1
 XZV  Var_03    C12  C13  N1   C5    -50.43  30.0  1
 XZV  Var_04    C12  N2   C6   C5     60.70  30.0  1
 XZV  Var_05    C13  N1   C5   C6     51.44  30.0  1
 XZV  Var_06    C13  C12  N2   C6    -59.26  30.0  1
 XZV  Var_07    C1   C2   C3   C4   -108.92  30.0  1
 XZV  Var_08    N2   C7   C8   C9   -156.12  30.0  2
 XZV  Var_09    H7   C4   C3   C2    107.83  30.0  1
 XZV  Var_10    N    C1   C2   C4   -148.81  30.0  3
 XZV  Var_11    C2   C1   N    C     -79.98  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 XZV  chir_01  C2  C1  C3  C4  both

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
 XZV  plan-1  C8   0.020
 XZV  plan-1  C10  0.020
 XZV  plan-1  C11  0.020
 XZV  plan-1  C9   0.020
 XZV  plan-1  O2   0.020
 XZV  plan-1  CL   0.020
 XZV  plan-1  H13  0.020
 XZV  plan-1  H12  0.020
 XZV  plan-1  C7   0.020
 XZV  plan-2  N1   0.020
 XZV  plan-2  C5   0.020
 XZV  plan-2  C13  0.020
 XZV  plan-2  N    0.020
 XZV  plan-2  C    0.020
 XZV  plan-2  O    0.020
 XZV  plan-2  C1   0.020
 XZV  plan-2  H    0.020
 XZV  plan-3  C6   0.020
 XZV  plan-3  C8   0.020
 XZV  plan-3  C12  0.020
 XZV  plan-3  N2   0.020
 XZV  plan-3  O1   0.020
 XZV  plan-3  C7   0.020

