# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 10:30:01 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: N-(2-methoxyethyl)-4-(5-methylfuran-2-carbonyl)piperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCNC(=O)N1CCN(CC1)C(=O)c2oc(C)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
 Y2G  Y2G  N-(2-methoxyethyl)-4-(5-methylfuran-2-carbonyl)piperazine-1-carboxamide  ligand  42  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 PERFECT
;

data_comp_Y2G
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
 Y2G  N1   N  NT    0  -0.512  -17.3845  15.3831  26.2769
 Y2G  C4   C  CH2   0  -0.277  -18.3893  14.8737  27.1957
 Y2G  C5   C  CH2   0  -0.326  -18.6806  13.4144  26.9109
 Y2G  C7   C  CR5   0   0.197  -21.3472  12.5258  25.8755
 Y2G  C8   C  CR15  0  -0.296  -22.3954  11.6684  25.7663
 Y2G  C10  C  CR5   0   0.369  -22.7888  13.1188  27.4116
 Y2G  C13  C  CH2   0  -0.311  -17.6423  15.1185  24.8736
 Y2G  N    N  NH1   0  -0.675  -15.9131  17.1152  25.7668
 Y2G  C    C  CH3   0  -0.390  -17.4217  20.9978  25.5222
 Y2G  O    O  O2    0  -0.482  -16.6177  19.8694  25.3028
 Y2G  C1   C  CH2   0  -0.142  -15.8777  19.5054  26.4403
 Y2G  C11  C  CH3   0  -0.753  -23.2657  13.9730  28.5222
 Y2G  C12  C  CH2   0  -0.308  -17.9712  13.6496  24.6381
 Y2G  C2   C  CH2   0  -0.332  -15.0903  18.2470  26.1310
 Y2G  C3   C  C     0   0.743  -16.5633  16.3914  26.7186
 Y2G  C9   C  CR15  0  -0.378  -23.3264  12.0468  26.7704
 Y2G  N2   N  NT    0  -0.471  -19.0441  13.2369  25.5174
 Y2G  O1   O  O     0  -0.537  -16.3906  16.6001  27.9149
 Y2G  O2   O  O     0  -0.476  -20.2187  12.2131  23.8762
 Y2G  O3   O  O     0  -0.428  -21.5903  13.4116  26.8718
 Y2G  H8   H  HCH2  0   0.266  -18.0267  14.9719  28.2151
 Y2G  H9   H  HCH2  0   0.231  -19.3174  15.4528  27.1112
 Y2G  H11  H  HCH2  0   0.254  -17.7803  12.8206  27.1017
 Y2G  H10  H  HCH2  0   0.279  -19.4492  13.0494  27.5827
 Y2G  H12  H  HCR5  0   0.268  -22.4898  10.8610  25.0583
 Y2G  H20  H  HCH2  0   0.259  -16.7568  15.3363  24.2781
 Y2G  H19  H  HCH2  0   0.241  -18.4657  15.7377  24.4965
 Y2G  H7   H  HNH1  0   0.400  -16.2791  17.1390  24.8304
 Y2G  H    H  HCH3  0   0.231  -17.9665  21.2100  24.6027
 Y2G  H1   H  HCH3  0   0.202  -18.1499  20.8334  26.3260
 Y2G  H2   H  HCH3  0   0.201  -16.8296  21.8831  25.7843
 Y2G  H4   H  HCH2  0   0.203  -15.1777  20.3023  26.7305
 Y2G  H3   H  HCH2  0   0.201  -16.5413  19.3331  27.2983
 Y2G  H16  H  HCH3  0   0.259  -22.5849  13.9435  29.3746
 Y2G  H15  H  HCH3  0   0.260  -23.3624  15.0154  28.2138
 Y2G  H14  H  HCH3  0   0.261  -24.2415  13.6285  28.8569
 Y2G  H17  H  HCH2  0   0.247  -17.0842  13.0359  24.8255
 Y2G  H18  H  HCH2  0   0.275  -18.2609  13.5111  23.6000
 Y2G  H6   H  HCH2  0   0.249  -14.4051  18.4362  25.3028
 Y2G  H5   H  HCH2  0   0.250  -14.4763  17.9924  26.9937
 Y2G  H13  H  HCR5  0   0.265  -24.2765  11.5872  26.9898
 Y2G  C6   C  C     0   0.484  -20.1517  12.6401  25.0226

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
 Y2G  C    O    single    1.403  0.020  1.403
 Y2G  O    C1   single    1.405  0.020  1.405
 Y2G  C1   C2   single    1.516  0.020  1.516
 Y2G  C2   N    single    1.446  0.020  1.446
 Y2G  N    C3   single    1.361  0.020  1.361
 Y2G  O1   C3   double    1.227  0.020  1.227
 Y2G  C3   N1   single    1.373  0.020  1.373
 Y2G  N1   C4   single    1.454  0.020  1.454
 Y2G  C4   C5   single    1.515  0.020  1.515
 Y2G  C5   N2   single    1.451  0.020  1.451
 Y2G  N2   C6   single    1.352  0.020  1.352
 Y2G  C6   O2   double    1.225  0.020  1.225
 Y2G  C7   C6   single    1.473  0.020  1.473
 Y2G  C7   C8   aromatic  1.359  0.020  1.359
 Y2G  C8   C9   aromatic  1.421  0.020  1.421
 Y2G  C9   C10  aromatic  1.360  0.020  1.360
 Y2G  C11  C10  single    1.480  0.020  1.480
 Y2G  C10  O3   aromatic  1.347  0.020  1.347
 Y2G  O3   C7   aromatic  1.355  0.020  1.355
 Y2G  C12  N2   single    1.447  0.020  1.447
 Y2G  C13  C12  single    1.524  0.020  1.524
 Y2G  N1   C13  single    1.451  0.020  1.451
 Y2G  C4   H8   single    0.970  0.020  1.090
 Y2G  C4   H9   single    0.970  0.020  1.090
 Y2G  C5   H11  single    0.970  0.020  1.090
 Y2G  C5   H10  single    0.970  0.020  1.090
 Y2G  C8   H12  single    0.930  0.020  1.080
 Y2G  C13  H20  single    0.970  0.020  1.090
 Y2G  C13  H19  single    0.970  0.020  1.090
 Y2G  N    H7   single    0.890  0.020  1.040
 Y2G  C    H    single    0.970  0.020  1.090
 Y2G  C    H1   single    0.970  0.020  1.090
 Y2G  C    H2   single    0.970  0.020  1.090
 Y2G  C1   H4   single    0.970  0.020  1.090
 Y2G  C1   H3   single    0.970  0.020  1.090
 Y2G  C11  H16  single    0.970  0.020  1.090
 Y2G  C11  H15  single    0.970  0.020  1.090
 Y2G  C11  H14  single    0.970  0.020  1.090
 Y2G  C12  H17  single    0.970  0.020  1.090
 Y2G  C12  H18  single    0.970  0.020  1.090
 Y2G  C2   H6   single    0.970  0.020  1.090
 Y2G  C2   H5   single    0.970  0.020  1.090
 Y2G  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
 Y2G  C3   N1   C13  123.44  3.000
 Y2G  C13  N1   C4   115.12  3.000
 Y2G  C3   N1   C4   117.86  3.000
 Y2G  H9   C4   H8   107.87  3.000
 Y2G  H9   C4   C5   109.34  3.000
 Y2G  H8   C4   C5   109.12  3.000
 Y2G  H9   C4   N1   110.55  3.000
 Y2G  H8   C4   N1   109.31  3.000
 Y2G  C5   C4   N1   110.58  3.000
 Y2G  H10  C5   H11  107.00  3.000
 Y2G  H10  C5   N2   112.11  3.000
 Y2G  H11  C5   N2   107.87  3.000
 Y2G  H10  C5   C4   110.13  3.000
 Y2G  H11  C5   C4   109.35  3.000
 Y2G  N2   C5   C4   110.27  3.000
 Y2G  O3   C7   C8   109.46  3.000
 Y2G  O3   C7   C6   121.37  3.000
 Y2G  C8   C7   C6   128.95  3.000
 Y2G  H12  C8   C9   127.32  3.000
 Y2G  H12  C8   C7   126.37  3.000
 Y2G  C9   C8   C7   106.30  3.000
 Y2G  O3   C10  C9   109.52  3.000
 Y2G  O3   C10  C11  117.52  3.000
 Y2G  C9   C10  C11  132.96  3.000
 Y2G  H19  C13  H20  108.02  3.000
 Y2G  H19  C13  C12  109.21  3.000
 Y2G  H20  C13  C12  106.48  3.000
 Y2G  H19  C13  N1   111.28  3.000
 Y2G  H20  C13  N1   110.36  3.000
 Y2G  C12  C13  N1   111.32  3.000
 Y2G  H7   N    C3   119.33  3.000
 Y2G  H7   N    C2   115.04  3.000
 Y2G  C3   N    C2   120.79  3.000
 Y2G  H2   C    H1   107.71  3.000
 Y2G  H2   C    H    108.33  3.000
 Y2G  H1   C    H    108.40  3.000
 Y2G  H2   C    O    112.17  3.000
 Y2G  H1   C    O    111.99  3.000
 Y2G  H    C    O    108.13  3.000
 Y2G  C1   O    C    112.56  3.000
 Y2G  H3   C1   H4   106.98  3.000
 Y2G  H3   C1   C2   110.06  3.000
 Y2G  H4   C1   C2   108.94  3.000
 Y2G  H3   C1   O    110.79  3.000
 Y2G  H4   C1   O    111.17  3.000
 Y2G  C2   C1   O    108.87  3.000
 Y2G  H14  C11  H15  108.06  3.000
 Y2G  H14  C11  H16  108.10  3.000
 Y2G  H15  C11  H16  107.57  3.000
 Y2G  H14  C11  C10  109.71  3.000
 Y2G  H15  C11  C10  111.58  3.000
 Y2G  H16  C11  C10  111.68  3.000
 Y2G  H18  C12  H17  107.95  3.000
 Y2G  H18  C12  N2   110.26  3.000
 Y2G  H17  C12  N2   109.68  3.000
 Y2G  H18  C12  C13  109.16  3.000
 Y2G  H17  C12  C13  109.82  3.000
 Y2G  N2   C12  C13  109.94  3.000
 Y2G  H5   C2   H6   106.72  3.000
 Y2G  H5   C2   C1   108.98  3.000
 Y2G  H6   C2   C1   109.69  3.000
 Y2G  H5   C2   N    109.72  3.000
 Y2G  H6   C2   N    107.56  3.000
 Y2G  C1   C2   N    113.92  3.000
 Y2G  O1   C3   N    121.62  3.000
 Y2G  O1   C3   N1   121.52  3.000
 Y2G  N    C3   N1   116.82  3.000
 Y2G  H13  C9   C10  126.05  3.000
 Y2G  H13  C9   C8   127.44  3.000
 Y2G  C10  C9   C8   106.51  3.000
 Y2G  C12  N2   C6   120.73  3.000
 Y2G  C12  N2   C5   111.28  3.000
 Y2G  C6   N2   C5   127.63  3.000
 Y2G  C10  O3   C7   108.19  3.000
 Y2G  O2   C6   N2   122.75  3.000
 Y2G  O2   C6   C7   118.06  3.000
 Y2G  N2   C6   C7   119.17  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
 Y2G  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 Y2G  CONST_02  C9   C10  O3   C7      0.00   0.0  0
 Y2G  CONST_03  C10  O3   C7   C8      0.00   0.0  0
 Y2G  CONST_04  O3   C10  C9   C8      0.00   0.0  0
 Y2G  CONST_05  O3   C7   C8   C9      0.00   0.0  0
 Y2G  CONST_06  C9   C8   C7   C6    180.00   0.0  0
 Y2G  CONST_07  C10  O3   C7   C6    180.00   0.0  0
 Y2G  CONST_08  C11  C10  O3   C7    180.00   0.0  0
 Y2G  CONST_09  C11  C10  C9   C8    180.00   0.0  0
 Y2G  CONST_11  C12  N2   C6   C7    180.00   0.0  0
 Y2G  CONST_12  H13  C9   C8   C7    180.00   0.0  0
 Y2G  CONST_13  H12  C8   C9   C10   180.00   0.0  0
 Y2G  CONST_16  O1   C3   N1   C13   180.00   0.0  0
 Y2G  CONST_17  O2   C6   N2   C12     0.00   0.0  0
 Y2G  CONST_19  N    C3   N1   C13     0.00   0.0  0
 Y2G  CONST_20  C2   N    C3   N1    180.00   0.0  0
 Y2G  CONST_22  O1   C3   N    C2      0.00   0.0  0
 Y2G  Var_01    N2   C5   C4   N1    -54.27  30.0  1
 Y2G  Var_02    N2   C12  C13  N1     52.93  30.0  1
 Y2G  Var_03    C12  C13  N1   C4    -49.87  30.0  1
 Y2G  Var_04    C12  N2   C5   C4     60.63  30.0  1
 Y2G  Var_05    C13  N1   C4   C5     50.35  30.0  1
 Y2G  Var_06    C13  C12  N2   C5    -59.53  30.0  1
 Y2G  Var_07    N2   C6   C7   C8   -158.94  30.0  2
 Y2G  Var_08    H16  C11  C10  C9    120.17  30.0  2
 Y2G  Var_09    O    C1   C2   N     -60.04  30.0  1
 Y2G  Var_10    C2   C1   O    C     177.51  30.0  3
 Y2G  Var_11    C3   N    C2   C1    -78.47  30.0  3
 Y2G  Var_12    H    C    O    C1   -179.52  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
 Y2G  plan-1  C7   0.020
 Y2G  plan-1  C8   0.020
 Y2G  plan-1  C10  0.020
 Y2G  plan-1  C11  0.020
 Y2G  plan-1  C9   0.020
 Y2G  plan-1  O3   0.020
 Y2G  plan-1  H12  0.020
 Y2G  plan-1  H13  0.020
 Y2G  plan-1  C6   0.020
 Y2G  plan-2  N1   0.020
 Y2G  plan-2  C4   0.020
 Y2G  plan-2  C13  0.020
 Y2G  plan-2  N    0.020
 Y2G  plan-2  C2   0.020
 Y2G  plan-2  C3   0.020
 Y2G  plan-2  O1   0.020
 Y2G  plan-2  H7   0.020
 Y2G  plan-3  C5   0.020
 Y2G  plan-3  C7   0.020
 Y2G  plan-3  C12  0.020
 Y2G  plan-3  N2   0.020
 Y2G  plan-3  O2   0.020
 Y2G  plan-3  C6   0.020

