# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 16:14:02 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: N-(cyclopropylmethyl)-4-(5-methylfuran-2-carbonyl)piperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1oc(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
 Y2M  Y2M  N-(cyclopropylmethyl)-4-(5-methylfuran-2-carbonyl)piperazine-1-carboxamide  ligand  42  21  .  2022-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_Y2M
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
 Y2M  N1   N  NR6   0  -0.496  -17.0810  14.7259  26.8665
 Y2M  C4   C  CR5   0   0.201  -21.1467  13.2374  25.3958
 Y2M  C5   C  C     0   0.487  -19.8502  13.2886  24.6960
 Y2M  C6   C  C     0  -0.253  -17.4563  13.5916  24.7352
 Y2M  C7   C  C     0  -0.392  -16.4320  14.0051  25.7951
 Y2M  C8   C  C     0   0.740  -16.9616  16.0582  27.1317
 Y2M  C10  C  CH1   0  -0.286  -15.1575  18.8042  25.4315
 Y2M  C13  C  C     0  -0.244  -18.0131  13.9293  27.6455
 Y2M  N    N  NR6   0  -0.464  -18.7040  13.2526  25.4066
 Y2M  O    O  O     0  -0.480  -19.8541  13.3892  23.4742
 Y2M  C1   C  CR5   0   0.366  -22.5939  13.6219  26.9911
 Y2M  C11  C  CH2   0  -0.484  -15.6512  19.1165  24.0492
 Y2M  C12  C  CH2   0  -0.490  -15.3126  20.2268  24.9974
 Y2M  C14  C  C     0  -0.376  -18.5314  12.7886  26.7700
 Y2M  C2   C  CR15  0  -0.376  -23.2913  13.0742  25.9605
 Y2M  C3   C  CR15  0  -0.299  -22.3536  12.8341  24.9207
 Y2M  N2   N  NH1   0  -0.691  -16.2347  16.8049  26.2526
 Y2M  O1   O  O     0  -0.542  -17.4613  16.5544  28.1368
 Y2M  O2   O  O     0  -0.428  -21.2934  13.7218  26.6527
 Y2M  H6   H  H     0   0.244  -17.0693  12.7510  24.1512
 Y2M  H5   H  H     0   0.254  -17.6393  14.4166  24.0466
 Y2M  H7   H  H     0   0.270  -15.9340  13.1256  26.2122
 Y2M  H8   H  H     0   0.279  -15.6395  14.5919  25.3382
 Y2M  H12  H  HCH1  0   0.260  -14.1407  18.4325  25.5069
 Y2M  H18  H  H     0   0.233  -17.5450  13.5151  28.5444
 Y2M  H17  H  H     0   0.248  -18.8467  14.5529  27.9632
 Y2M  H2   H  HCH3  0   0.260  -22.7832  15.1670  28.4574
 Y2M  H1   H  HCH3  0   0.261  -24.0648  13.9555  28.4669
 Y2M  H    H  HCH3  0   0.259  -22.4755  13.5662  29.1255
 Y2M  H14  H  HCH2  0   0.250  -14.9885  18.9342  23.2134
 Y2M  H13  H  HCH2  0   0.246  -16.6984  18.9378  23.8357
 Y2M  H16  H  HCH2  0   0.252  -14.4153  20.8029  24.8140
 Y2M  H15  H  HCH2  0   0.245  -16.1292  20.8011  25.4183
 Y2M  H20  H  H     0   0.268  -17.8242  11.9544  26.7579
 Y2M  H19  H  H     0   0.290  -19.4517  12.3867  27.1799
 Y2M  H3   H  HCR5  0   0.265  -24.3505  12.8746  25.9469
 Y2M  H4   H  HCR5  0   0.267  -22.5480  12.4118  23.9482
 Y2M  H10  H  HCH2  0   0.217  -17.0808  18.7422  26.3559
 Y2M  H11  H  HCH2  0   0.240  -15.7425  18.4331  27.4520
 Y2M  H9   H  HNH1  0   0.397  -16.1595  16.4967  25.2964
 Y2M  C    C  CH3   0  -0.753  -22.9959  14.1040  28.3312
 Y2M  C9   C  CH2   0  -0.244  -16.1114  18.2365  26.4439

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
 Y2M  C    C1   single    1.480  0.020  1.480
 Y2M  C1   C2   aromatic  1.359  0.020  1.359
 Y2M  C2   C3   aromatic  1.421  0.020  1.421
 Y2M  C3   C4   aromatic  1.358  0.020  1.358
 Y2M  C4   C5   single    1.474  0.020  1.474
 Y2M  O    C5   double    1.226  0.020  1.226
 Y2M  C5   N    single    1.349  0.020  1.349
 Y2M  N    C6   single    1.457  0.020  1.457
 Y2M  C6   C7   single    1.531  0.020  1.531
 Y2M  C7   N1   single    1.445  0.020  1.445
 Y2M  N1   C8   single    1.364  0.020  1.364
 Y2M  C8   O1   double    1.227  0.020  1.227
 Y2M  N2   C8   single    1.363  0.020  1.363
 Y2M  C9   N2   single    1.450  0.020  1.450
 Y2M  C10  C9   single    1.502  0.020  1.502
 Y2M  C10  C11  single    1.501  0.020  1.501
 Y2M  C11  C12  single    1.499  0.020  1.499
 Y2M  C12  C10  single    1.495  0.020  1.495
 Y2M  C13  N1   single    1.453  0.020  1.453
 Y2M  C14  C13  single    1.529  0.020  1.529
 Y2M  N    C14  single    1.450  0.020  1.450
 Y2M  O2   C4   aromatic  1.355  0.020  1.355
 Y2M  C1   O2   aromatic  1.348  0.020  1.348
 Y2M  C6   H6   single    0.970  0.020  1.090
 Y2M  C6   H5   single    0.970  0.020  1.090
 Y2M  C7   H7   single    0.970  0.020  1.090
 Y2M  C7   H8   single    0.970  0.020  1.090
 Y2M  C10  H12  single    0.970  0.020  1.090
 Y2M  C13  H18  single    0.970  0.020  1.090
 Y2M  C13  H17  single    0.970  0.020  1.090
 Y2M  C    H2   single    0.970  0.020  1.090
 Y2M  C    H1   single    0.970  0.020  1.090
 Y2M  C    H    single    0.970  0.020  1.090
 Y2M  C11  H14  single    0.970  0.020  1.090
 Y2M  C11  H13  single    0.970  0.020  1.090
 Y2M  C12  H16  single    0.970  0.020  1.090
 Y2M  C12  H15  single    0.970  0.020  1.090
 Y2M  C14  H20  single    0.970  0.020  1.090
 Y2M  C14  H19  single    0.970  0.020  1.090
 Y2M  C2   H3   single    0.930  0.020  1.080
 Y2M  C3   H4   single    0.930  0.020  1.080
 Y2M  C9   H10  single    0.970  0.020  1.090
 Y2M  C9   H11  single    0.970  0.020  1.090
 Y2M  N2   H9   single    0.890  0.020  1.040

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
 Y2M  C13  N1   C8   119.18  3.000
 Y2M  C13  N1   C7   114.34  3.000
 Y2M  C8   N1   C7   126.31  3.000
 Y2M  O2   C4   C3   109.54  3.000
 Y2M  O2   C4   C5   121.54  3.000
 Y2M  C3   C4   C5   128.74  3.000
 Y2M  O    C5   N    121.99  3.000
 Y2M  N    C5   C4   119.75  3.000
 Y2M  O    C5   C4   118.24  3.000
 Y2M  H5   C6   H6   107.68  3.000
 Y2M  H5   C6   N    108.87  3.000
 Y2M  H6   C6   N    111.72  3.000
 Y2M  H5   C6   C7   110.19  3.000
 Y2M  H6   C6   C7   109.90  3.000
 Y2M  N    C6   C7   108.47  3.000
 Y2M  H8   C7   H7   105.22  3.000
 Y2M  H8   C7   C6   110.04  3.000
 Y2M  H7   C7   C6   110.58  3.000
 Y2M  H8   C7   N1   111.71  3.000
 Y2M  H7   C7   N1   108.84  3.000
 Y2M  C6   C7   N1   110.34  3.000
 Y2M  O1   C8   N2   121.58  3.000
 Y2M  N2   C8   N1   117.15  3.000
 Y2M  O1   C8   N1   121.24  3.000
 Y2M  H12  C10  C9   114.75  3.000
 Y2M  H12  C10  C12  116.30  3.000
 Y2M  C9   C10  C12  119.29  3.000
 Y2M  H12  C10  C11  116.33  3.000
 Y2M  C12  C10  C11   60.03  3.000
 Y2M  C9   C10  C11  119.37  3.000
 Y2M  H17  C13  H18  107.73  3.000
 Y2M  H17  C13  C14  109.58  3.000
 Y2M  H18  C13  C14  109.45  3.000
 Y2M  H17  C13  N1   109.50  3.000
 Y2M  H18  C13  N1   111.92  3.000
 Y2M  C14  C13  N1   108.64  3.000
 Y2M  C14  N    C6   113.93  3.000
 Y2M  C14  N    C5   127.21  3.000
 Y2M  C6   N    C5   118.60  3.000
 Y2M  O2   C1   C2   109.55  3.000
 Y2M  O2   C1   C    117.74  3.000
 Y2M  C2   C1   C    132.72  3.000
 Y2M  H13  C11  H14  114.32  3.000
 Y2M  H13  C11  C12  117.72  3.000
 Y2M  H14  C11  C12  118.36  3.000
 Y2M  H13  C11  C10  117.72  3.000
 Y2M  H14  C11  C10  118.35  3.000
 Y2M  C12  C11  C10   59.81  3.000
 Y2M  H15  C12  H16  114.12  3.000
 Y2M  H15  C12  C11  117.92  3.000
 Y2M  H16  C12  C11  118.33  3.000
 Y2M  H15  C12  C10  118.01  3.000
 Y2M  H16  C12  C10  118.02  3.000
 Y2M  C11  C12  C10   60.16  3.000
 Y2M  H19  C14  H20  105.67  3.000
 Y2M  H19  C14  N    111.89  3.000
 Y2M  H20  C14  N    108.09  3.000
 Y2M  H19  C14  C13  110.35  3.000
 Y2M  H20  C14  C13  110.87  3.000
 Y2M  N    C14  C13  109.88  3.000
 Y2M  H3   C2   C3   127.45  3.000
 Y2M  H3   C2   C1   126.03  3.000
 Y2M  C3   C2   C1   106.52  3.000
 Y2M  H4   C3   C2   127.41  3.000
 Y2M  H4   C3   C4   126.31  3.000
 Y2M  C2   C3   C4   106.28  3.000
 Y2M  H9   N2   C9   114.89  3.000
 Y2M  H9   N2   C8   118.97  3.000
 Y2M  C9   N2   C8   120.08  3.000
 Y2M  C1   O2   C4   108.11  3.000
 Y2M  H    C    H1   108.09  3.000
 Y2M  H    C    H2   107.64  3.000
 Y2M  H1   C    H2   108.07  3.000
 Y2M  H    C    C1   111.65  3.000
 Y2M  H1   C    C1   109.60  3.000
 Y2M  H2   C    C1   111.66  3.000
 Y2M  H11  C9   H10  106.85  3.000
 Y2M  H11  C9   N2   109.18  3.000
 Y2M  H10  C9   N2   111.69  3.000
 Y2M  H11  C9   C10  109.87  3.000
 Y2M  H10  C9   C10  109.44  3.000
 Y2M  N2   C9   C10  109.77  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
 Y2M  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 Y2M  CONST_02  C2   C1   O2   C4      0.00   0.0  0
 Y2M  CONST_03  C3   C4   O2   C1      0.00   0.0  0
 Y2M  CONST_04  O2   C4   C3   C2      0.00   0.0  0
 Y2M  CONST_05  O2   C1   C2   C3      0.00   0.0  0
 Y2M  CONST_06  C    C1   O2   C4    180.00   0.0  0
 Y2M  CONST_07  C2   C3   C4   C5    180.00   0.0  0
 Y2M  CONST_08  C1   O2   C4   C5    180.00   0.0  0
 Y2M  CONST_09  C3   C2   C1   C     180.00   0.0  0
 Y2M  CONST_10  C6   N    C5   C4    180.00   0.0  0
 Y2M  CONST_12  H3   C2   C3   C4    180.00   0.0  0
 Y2M  CONST_13  H4   C3   C2   C1    180.00   0.0  0
 Y2M  CONST_14  O    C5   N    C6      0.00   0.0  0
 Y2M  CONST_15  O1   C8   N1   C7    180.00   0.0  0
 Y2M  CONST_16  O1   C8   N1   C13     0.00   0.0  0
 Y2M  CONST_18  N2   C8   N1   C7      0.00   0.0  0
 Y2M  CONST_19  N2   C8   N1   C13   180.00   0.0  0
 Y2M  CONST_20  C9   N2   C8   N1    180.00   0.0  0
 Y2M  CONST_22  O1   C8   N2   C9      0.00   0.0  0
 Y2M  Var_01    N    C6   C7   N1    -35.92  30.0  1
 Y2M  Var_02    N    C14  C13  N1    -36.99  30.0  1
 Y2M  Var_03    C13  C14  N    C6     66.84  30.0  1
 Y2M  Var_04    C13  N1   C7   C6     65.86  30.0  1
 Y2M  Var_05    C14  N    C6   C7    -26.98  30.0  1
 Y2M  Var_06    C14  C13  N1   C7    -25.94  30.0  1
 Y2M  Var_07    C3   C4   C5   N    -156.43  30.0  3
 Y2M  Var_08    C9   C10  C12  C11  -109.01  30.0  1
 Y2M  Var_09    H16  C12  C11  C10   107.82  30.0  1
 Y2M  Var_10    N2   C9   C10  C11    82.30  30.0  3
 Y2M  Var_11    H2   C    C1   C2   -118.86  30.0  2
 Y2M  Var_12    C10  C9   N2   C8    174.40  30.0  2

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
 Y2M  chir_01  C10  C9  C11  C12  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
 Y2M  plan-1  C4   0.020
 Y2M  plan-1  C5   0.020
 Y2M  plan-1  C1   0.020
 Y2M  plan-1  C2   0.020
 Y2M  plan-1  C3   0.020
 Y2M  plan-1  O2   0.020
 Y2M  plan-1  H3   0.020
 Y2M  plan-1  H4   0.020
 Y2M  plan-1  C    0.020
 Y2M  plan-2  N1   0.020
 Y2M  plan-2  C7   0.020
 Y2M  plan-2  C8   0.020
 Y2M  plan-2  C13  0.020
 Y2M  plan-2  N2   0.020
 Y2M  plan-2  O1   0.020
 Y2M  plan-2  H9   0.020
 Y2M  plan-2  C9   0.020
 Y2M  plan-3  C4   0.020
 Y2M  plan-3  C5   0.020
 Y2M  plan-3  C6   0.020
 Y2M  plan-3  N    0.020
 Y2M  plan-3  O    0.020
 Y2M  plan-3  C14  0.020

