# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 08:29:58 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: 4-(furan-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)c2occc2
#
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
 Y1P  Y1P  4-(furan-2-carbonyl)-N-(2-methoxyethyl)piperazine-1-carboxamide  ligand  39  20  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_Y1P
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
 Y1P  N1   N  NT    0  -0.512  -17.6078  15.4000  26.1692
 Y1P  C4   C  CH2   0  -0.281  -18.6244  14.9384  27.0976
 Y1P  C5   C  CH2   0  -0.322  -18.9316  13.4724  26.8641
 Y1P  C7   C  CR5   0   0.211  -21.5593  12.4214  25.8792
 Y1P  C8   C  CR15  0  -0.314  -22.5343  11.4766  25.8130
 Y1P  C10  C  CR15  0   0.016  -23.0285  12.9504  27.3939
 Y1P  N    N  NH1   0  -0.677  -15.9736  16.9773  25.6474
 Y1P  C    C  CH3   0  -0.390  -16.9813  21.0194  25.3701
 Y1P  O    O  O2    0  -0.482  -16.2742  19.8276  25.1504
 Y1P  C1   C  CH2   0  -0.142  -15.6415  19.3497  26.3105
 Y1P  C11  C  CH2   0  -0.304  -18.2325  13.6400  24.5771
 Y1P  C12  C  CH2   0  -0.310  -17.8852  15.1103  24.7760
 Y1P  C2   C  CH2   0  -0.331  -15.0184  18.0000  26.0119
 Y1P  C3   C  C     0   0.744  -16.6941  16.3269  26.6025
 Y1P  C9   C  CR15  0  -0.335  -23.4885  11.8165  26.8104
 Y1P  N2   N  NT    0  -0.472  -19.2998  13.2524  25.4766
 Y1P  O1   O  O     0  -0.539  -16.5031  16.5282  27.7977
 Y1P  O2   O  O     0  -0.473  -20.4383  12.1310  23.8741
 Y1P  O3   O  O     0  -0.405  -21.8639  13.3245  26.8385
 Y1P  H8   H  HCH2  0   0.268  -18.2697  15.0711  28.1157
 Y1P  H9   H  HCH2  0   0.233  -19.5442  15.5251  26.9822
 Y1P  H11  H  HCH2  0   0.253  -18.0373  12.8766  27.0763
 Y1P  H10  H  HCH2  0   0.280  -19.7039  13.1408  27.5489
 Y1P  H12  H  HCR5  0   0.271  -22.5655  10.6360  25.1391
 Y1P  H14  H  HCR5  0   0.286  -23.4117  13.5787  28.1819
 Y1P  H7   H  HNH1  0   0.399  -16.3287  17.0352  24.7083
 Y1P  H    H  HCH3  0   0.230  -17.4505  21.3125  24.4314
 Y1P  H1   H  HCH3  0   0.202  -17.7664  20.8972  26.1264
 Y1P  H2   H  HCH3  0   0.201  -16.3261  21.8357  25.6977
 Y1P  H4   H  HCH2  0   0.202  -14.8549  20.0412  26.6460
 Y1P  H3   H  HCH2  0   0.201  -16.3584  19.2541  27.1368
 Y1P  H15  H  HCH2  0   0.248  -17.3487  13.0221  24.7672
 Y1P  H16  H  HCH2  0   0.275  -18.5364  13.4824  23.5459
 Y1P  H18  H  HCH2  0   0.260  -17.0094  15.3055  24.1601
 Y1P  H17  H  HCH2  0   0.242  -18.7078  15.7306  24.4004
 Y1P  H6   H  HCH2  0   0.249  -14.3074  18.0979  25.1897
 Y1P  H5   H  HCH2  0   0.249  -14.4506  17.6732  26.8814
 Y1P  H13  H  HCR5  0   0.271  -24.3962  11.2909  27.0576
 Y1P  C6   C  C     0   0.498  -20.3786  12.5874  25.0089

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
 Y1P  C    O    single    1.403  0.020  1.403
 Y1P  O    C1   single    1.405  0.020  1.405
 Y1P  C1   C2   single    1.516  0.020  1.516
 Y1P  C2   N    single    1.446  0.020  1.446
 Y1P  N    C3   single    1.362  0.020  1.362
 Y1P  O1   C3   double    1.227  0.020  1.227
 Y1P  C3   N1   single    1.372  0.020  1.372
 Y1P  N1   C4   single    1.452  0.020  1.452
 Y1P  C4   C5   single    1.516  0.020  1.516
 Y1P  C5   N2   single    1.452  0.020  1.452
 Y1P  N2   C6   single    1.351  0.020  1.351
 Y1P  C6   O2   double    1.225  0.020  1.225
 Y1P  C7   C6   single    1.476  0.020  1.476
 Y1P  C7   C8   aromatic  1.359  0.020  1.359
 Y1P  C8   C9   aromatic  1.422  0.020  1.422
 Y1P  C9   C10  aromatic  1.356  0.020  1.356
 Y1P  C10  O3   aromatic  1.343  0.020  1.343
 Y1P  O3   C7   aromatic  1.352  0.020  1.352
 Y1P  C11  N2   single    1.449  0.020  1.449
 Y1P  C12  C11  single    1.524  0.020  1.524
 Y1P  N1   C12  single    1.450  0.020  1.450
 Y1P  C4   H8   single    0.970  0.020  1.090
 Y1P  C4   H9   single    0.970  0.020  1.090
 Y1P  C5   H11  single    0.970  0.020  1.090
 Y1P  C5   H10  single    0.970  0.020  1.090
 Y1P  C8   H12  single    0.930  0.020  1.080
 Y1P  C10  H14  single    0.930  0.020  1.080
 Y1P  N    H7   single    0.890  0.020  1.040
 Y1P  C    H    single    0.970  0.020  1.090
 Y1P  C    H1   single    0.970  0.020  1.090
 Y1P  C    H2   single    0.970  0.020  1.090
 Y1P  C1   H4   single    0.970  0.020  1.090
 Y1P  C1   H3   single    0.970  0.020  1.090
 Y1P  C11  H15  single    0.970  0.020  1.090
 Y1P  C11  H16  single    0.970  0.020  1.090
 Y1P  C12  H18  single    0.970  0.020  1.090
 Y1P  C12  H17  single    0.970  0.020  1.090
 Y1P  C2   H6   single    0.970  0.020  1.090
 Y1P  C2   H5   single    0.970  0.020  1.090
 Y1P  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
 Y1P  C3   N1   C12  124.47  3.000
 Y1P  C12  N1   C4   114.64  3.000
 Y1P  C3   N1   C4   118.63  3.000
 Y1P  H9   C4   H8   107.88  3.000
 Y1P  H9   C4   C5   109.33  3.000
 Y1P  H8   C4   C5   109.19  3.000
 Y1P  H9   C4   N1   110.47  3.000
 Y1P  H8   C4   N1   109.38  3.000
 Y1P  C5   C4   N1   110.54  3.000
 Y1P  H10  C5   H11  107.03  3.000
 Y1P  H10  C5   N2   112.13  3.000
 Y1P  H11  C5   N2   108.04  3.000
 Y1P  H10  C5   C4   110.05  3.000
 Y1P  H11  C5   C4   109.31  3.000
 Y1P  N2   C5   C4   110.18  3.000
 Y1P  O3   C7   C8   109.70  3.000
 Y1P  O3   C7   C6   121.55  3.000
 Y1P  C8   C7   C6   128.55  3.000
 Y1P  H12  C8   C9   127.28  3.000
 Y1P  H12  C8   C7   126.39  3.000
 Y1P  C9   C8   C7   106.33  3.000
 Y1P  H14  C10  O3   116.61  3.000
 Y1P  H14  C10  C9   132.95  3.000
 Y1P  O3   C10  C9   110.44  3.000
 Y1P  H7   N    C3   119.71  3.000
 Y1P  H7   N    C2   115.34  3.000
 Y1P  C3   N    C2   120.70  3.000
 Y1P  H2   C    H1   107.73  3.000
 Y1P  H2   C    H    108.32  3.000
 Y1P  H1   C    H    108.40  3.000
 Y1P  H2   C    O    112.20  3.000
 Y1P  H1   C    O    111.97  3.000
 Y1P  H    C    O    108.10  3.000
 Y1P  C1   O    C    112.74  3.000
 Y1P  H3   C1   H4   106.98  3.000
 Y1P  H3   C1   C2   109.81  3.000
 Y1P  H4   C1   C2   109.02  3.000
 Y1P  H3   C1   O    110.91  3.000
 Y1P  H4   C1   O    111.11  3.000
 Y1P  C2   C1   O    108.98  3.000
 Y1P  H16  C11  H15  107.97  3.000
 Y1P  H16  C11  N2   110.14  3.000
 Y1P  H15  C11  N2   109.63  3.000
 Y1P  H16  C11  C12  109.12  3.000
 Y1P  H15  C11  C12  109.75  3.000
 Y1P  N2   C11  C12  110.19  3.000
 Y1P  H17  C12  H18  107.96  3.000
 Y1P  H17  C12  C11  109.28  3.000
 Y1P  H18  C12  C11  106.42  3.000
 Y1P  H17  C12  N1   111.08  3.000
 Y1P  H18  C12  N1   110.73  3.000
 Y1P  C11  C12  N1   111.21  3.000
 Y1P  H5   C2   H6   106.79  3.000
 Y1P  H5   C2   C1   108.92  3.000
 Y1P  H6   C2   C1   109.65  3.000
 Y1P  H5   C2   N    109.48  3.000
 Y1P  H6   C2   N    107.69  3.000
 Y1P  C1   C2   N    114.06  3.000
 Y1P  O1   C3   N    121.50  3.000
 Y1P  O1   C3   N1   121.48  3.000
 Y1P  N    C3   N1   116.98  3.000
 Y1P  H13  C9   C10  126.52  3.000
 Y1P  H13  C9   C8   127.57  3.000
 Y1P  C10  C9   C8   105.92  3.000
 Y1P  C11  N2   C6   120.34  3.000
 Y1P  C11  N2   C5   111.47  3.000
 Y1P  C6   N2   C5   127.43  3.000
 Y1P  C10  O3   C7   107.61  3.000
 Y1P  O2   C6   N2   122.91  3.000
 Y1P  O2   C6   C7   117.74  3.000
 Y1P  N2   C6   C7   119.34  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
 Y1P  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 Y1P  CONST_02  C9   C10  O3   C7      0.00   0.0  0
 Y1P  CONST_03  C10  O3   C7   C8      0.00   0.0  0
 Y1P  CONST_04  O3   C10  C9   C8      0.00   0.0  0
 Y1P  CONST_05  O3   C7   C8   C9      0.00   0.0  0
 Y1P  CONST_06  C9   C8   C7   C6    180.00   0.0  0
 Y1P  CONST_07  C10  O3   C7   C6    180.00   0.0  0
 Y1P  CONST_09  C11  N2   C6   C7    180.00   0.0  0
 Y1P  CONST_10  H13  C9   C8   C7    180.00   0.0  0
 Y1P  CONST_11  H14  C10  O3   C7    180.00   0.0  0
 Y1P  CONST_12  H12  C8   C9   C10   180.00   0.0  0
 Y1P  CONST_15  O2   C6   N2   C11     0.00   0.0  0
 Y1P  CONST_16  O1   C3   N1   C12   180.00   0.0  0
 Y1P  CONST_18  C12  N1   C3   N       0.00   0.0  0
 Y1P  CONST_19  C2   N    C3   N1    180.00   0.0  0
 Y1P  CONST_21  O1   C3   N    C2      0.00   0.0  0
 Y1P  Var_01    N2   C5   C4   N1    -54.83  30.0  1
 Y1P  Var_02    N2   C11  C12  N1     52.95  30.0  1
 Y1P  Var_03    C11  C12  N1   C4    -50.96  30.0  1
 Y1P  Var_04    C11  N2   C5   C4     59.85  30.0  1
 Y1P  Var_05    C12  N1   C4   C5     51.81  30.0  1
 Y1P  Var_06    C12  C11  N2   C5    -58.61  30.0  1
 Y1P  Var_07    N2   C6   C7   C8   -156.78  30.0  2
 Y1P  Var_08    O    C1   C2   N     -62.58  30.0  2
 Y1P  Var_09    C2   C1   O    C     174.64  30.0  3
 Y1P  Var_10    C3   N    C2   C1    -79.84  30.0  3
 Y1P  Var_11    H    C    O    C1   -179.21  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
 Y1P  plan-1  C7   0.020
 Y1P  plan-1  C8   0.020
 Y1P  plan-1  C10  0.020
 Y1P  plan-1  C9   0.020
 Y1P  plan-1  O3   0.020
 Y1P  plan-1  H12  0.020
 Y1P  plan-1  H14  0.020
 Y1P  plan-1  H13  0.020
 Y1P  plan-1  C6   0.020
 Y1P  plan-2  N1   0.020
 Y1P  plan-2  C4   0.020
 Y1P  plan-2  N    0.020
 Y1P  plan-2  C12  0.020
 Y1P  plan-2  C2   0.020
 Y1P  plan-2  C3   0.020
 Y1P  plan-2  O1   0.020
 Y1P  plan-2  H7   0.020
 Y1P  plan-3  C5   0.020
 Y1P  plan-3  C7   0.020
 Y1P  plan-3  C11  0.020
 Y1P  plan-3  N2   0.020
 Y1P  plan-3  O2   0.020
 Y1P  plan-3  C6   0.020

