# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 14:44:58 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 5-cyano-N-[5-(hydroxymethyl)-2-(4-methylpiperidin-1-yl)phenyl]furan-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1CCN(CC1)c2ccc(CO)cc2NC(=O)c3oc(cc3)C#N
#
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
 5CN  5CN  5-cyano-N-[5-(hydroxymethyl)-2-(4-methylpiperidin-1-yl)phenyl]furan-2-carboxamide  ligand  46  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5CN
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
 5CN  C1    C  CR6   0   0.237  -1.9295   3.6671  -1.0719
 5CN  C2    C  CR16  0  -0.293  -1.7096   4.0806  -2.3803
 5CN  C3    C  CR16  0  -0.307  -1.4000   5.4003  -2.6814
 5CN  C7    C  CH2   0  -0.412  -4.5310   1.7785  -1.4515
 5CN  C8    C  CH2   0  -0.341  -3.6205   2.1106  -0.2772
 5CN  C9    C  CH2   0  -0.333  -1.6992   1.2438  -1.4722
 5CN  C10   C  CH2   0  -0.432  -2.5793   0.7942  -2.6388
 5CN  C11   C  CH1   0  -0.234  -4.0229   0.5514  -2.2043
 5CN  C12   C  CH3   0  -0.653  -4.9129   0.2009  -3.3873
 5CN  C14   C  C     0   0.486  -2.1217   4.7979   2.4008
 5CN  C15   C  CR5   0   0.244  -2.1661   3.9610   3.6166
 5CN  C16   C  CR15  0  -0.297  -2.3661   4.3258   4.9124
 5CN  C19   C  CSP   0  -0.004  -1.9374   0.7439   4.9359
 5CN  C4    C  CR6   0   0.023  -1.3069   6.3474  -1.6720
 5CN  C5    C  CR16  0  -0.362  -1.4869   5.9472  -0.3515
 5CN  C6    C  CR6   0   0.346  -1.7817   4.6248  -0.0451
 5CN  N1    N  NT    0  -0.518  -2.2339   2.3479  -0.6865
 5CN  O1    O  OH1   0  -0.655  -0.3285   8.0172  -3.1678
 5CN  N2    N  NH1   0  -0.747  -1.8716   4.1288   1.2588
 5CN  O2    O  O     0  -0.452  -2.3115   5.9979   2.4994
 5CN  C17   C  CR15  0  -0.279  -2.3130   3.1326   5.6705
 5CN  C18   C  CR5   0   0.358  -2.0847   2.1368   4.7711
 5CN  O3    O  O     0  -0.420  -1.9949   2.6313   3.5224
 5CN  N3    N  NS    0  -0.221  -1.8166  -0.3914   5.0903
 5CN  H2    H  HCR6  0   0.261  -1.7874   3.3683  -3.1894
 5CN  H3    H  HCR6  0   0.251  -1.2459   5.6828  -3.7146
 5CN  H71   H  HCH2  0   0.234  -5.5450   1.6065  -1.0795
 5CN  H72   H  HCH2  0   0.215  -4.5851   2.6359  -2.1336
 5CN  H81   H  HCH2  0   0.255  -3.9942   2.9839   0.2585
 5CN  H82   H  HCH2  0   0.233  -3.6266   1.2753   0.4315
 5CN  H91   H  HCH2  0   0.241  -1.5762   0.3961  -0.7885
 5CN  H92   H  HCH2  0   0.251  -0.6997   1.5112  -1.8183
 5CN  H101  H  HCH2  0   0.218  -2.5738   1.5391  -3.4409
 5CN  H102  H  HCH2  0   0.235  -2.1520  -0.1185  -3.0635
 5CN  H11   H  HCH1  0   0.214  -4.0306  -0.2952  -1.5041
 5CN  H121  H  HCH3  0   0.214  -4.9369   1.0160  -4.1142
 5CN  H122  H  HCH3  0   0.225  -4.5554  -0.6923  -3.9033
 5CN  H123  H  HCH3  0   0.225  -5.9393   0.0109  -3.0684
 5CN  H131  H  HCH2  0   0.240  -1.9787   8.3333  -2.0733
 5CN  H132  H  HCH2  0   0.217  -0.5167   8.2518  -1.1103
 5CN  H16   H  HCR5  0   0.294  -2.5337   5.3237   5.2812
 5CN  H5    H  HCR6  0   0.268  -1.3644   6.6732   0.4388
 5CN  HO1   H  HOH1  0   0.450   0.5435   7.6186  -3.0837
 5CN  HN2   H  HNH1  0   0.420  -1.7689   3.1199   1.2921
 5CN  H17   H  HCR5  0   0.302  -2.4249   3.0182   6.7359
 5CN  C13   C  CH2   0  -0.196  -1.0294   7.8011  -1.9696

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
 5CN  C1   N1    single    1.408  0.020  1.408
 5CN  C1   C2    aromatic  1.390  0.020  1.390
 5CN  C1   C6    aromatic  1.412  0.020  1.412
 5CN  C2   C3    aromatic  1.389  0.020  1.389
 5CN  C2   H2    single    0.930  0.020  1.080
 5CN  C3   C4    aromatic  1.387  0.020  1.387
 5CN  C3   H3    single    0.930  0.020  1.080
 5CN  C7   C11   single    1.527  0.020  1.527
 5CN  C7   C8    single    1.523  0.020  1.523
 5CN  C7   H71   single    0.970  0.020  1.090
 5CN  C7   H72   single    0.970  0.020  1.090
 5CN  C8   N1    single    1.465  0.020  1.465
 5CN  C8   H81   single    0.970  0.020  1.090
 5CN  C8   H82   single    0.970  0.020  1.090
 5CN  C9   C10   single    1.529  0.020  1.529
 5CN  C9   N1    single    1.457  0.020  1.457
 5CN  C9   H91   single    0.970  0.020  1.090
 5CN  C9   H92   single    0.970  0.020  1.090
 5CN  C10  C11   single    1.527  0.020  1.527
 5CN  C10  H101  single    0.970  0.020  1.090
 5CN  C10  H102  single    0.970  0.020  1.090
 5CN  C11  C12   single    1.521  0.020  1.521
 5CN  C11  H11   single    0.970  0.020  1.090
 5CN  C12  H121  single    0.970  0.020  1.090
 5CN  C12  H122  single    0.970  0.020  1.090
 5CN  C12  H123  single    0.970  0.020  1.090
 5CN  C13  C4    single    1.510  0.020  1.510
 5CN  C13  O1    single    1.405  0.020  1.405
 5CN  C13  H131  single    0.970  0.020  1.090
 5CN  C13  H132  single    0.970  0.020  1.090
 5CN  C14  C15   single    1.477  0.020  1.477
 5CN  C14  N2    single    1.347  0.020  1.347
 5CN  C14  O2    double    1.219  0.020  1.219
 5CN  C15  O3    aromatic  1.344  0.020  1.344
 5CN  C15  C16   aromatic  1.361  0.020  1.361
 5CN  C16  C17   aromatic  1.415  0.020  1.415
 5CN  C16  H16   single    0.930  0.020  1.080
 5CN  C19  N3    triple    1.152  0.020  1.152
 5CN  C19  C18   single    1.410  0.020  1.410
 5CN  C4   C5    aromatic  1.392  0.020  1.392
 5CN  C5   C6    aromatic  1.389  0.020  1.389
 5CN  C5   H5    single    0.930  0.020  1.080
 5CN  C6   N2    single    1.398  0.020  1.398
 5CN  O1   HO1   single    0.850  0.020  0.980
 5CN  N2   HN2   single    0.860  0.020  1.020
 5CN  C17  C18   aromatic  1.361  0.020  1.361
 5CN  C17  H17   single    0.930  0.020  1.080
 5CN  C18  O3    aromatic  1.346  0.020  1.346

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
 5CN  N1    C1   C6    117.33  3.000
 5CN  C6    C1   C2    117.80  3.000
 5CN  N1    C1   C2    124.81  3.000
 5CN  H2    C2   C3    118.69  3.000
 5CN  H2    C2   C1    119.82  3.000
 5CN  C3    C2   C1    121.48  3.000
 5CN  H3    C3   C4    120.46  3.000
 5CN  H3    C3   C2    119.14  3.000
 5CN  C4    C3   C2    120.40  3.000
 5CN  H72   C7   H71   106.78  3.000
 5CN  H72   C7   C11   109.76  3.000
 5CN  H71   C7   C11   110.48  3.000
 5CN  H72   C7   C8    109.79  3.000
 5CN  H71   C7   C8    109.05  3.000
 5CN  C11   C7   C8    110.89  3.000
 5CN  H82   C8   H81   106.92  3.000
 5CN  H82   C8   N1    108.03  3.000
 5CN  H81   C8   N1    109.39  3.000
 5CN  H82   C8   C7    109.23  3.000
 5CN  H81   C8   C7    110.40  3.000
 5CN  N1    C8   C7    112.69  3.000
 5CN  H92   C9   H91   106.54  3.000
 5CN  H92   C9   N1    108.76  3.000
 5CN  H91   C9   N1    106.91  3.000
 5CN  H92   C9   C10   110.94  3.000
 5CN  H91   C9   C10   108.25  3.000
 5CN  N1    C9   C10   115.03  3.000
 5CN  H102  C10  H101  106.34  3.000
 5CN  H102  C10  C11   110.31  3.000
 5CN  H101  C10  C11   108.75  3.000
 5CN  H102  C10  C9    108.47  3.000
 5CN  H101  C10  C9    110.86  3.000
 5CN  C11   C10  C9    111.95  3.000
 5CN  H11   C11  C12   108.30  3.000
 5CN  H11   C11  C10   108.09  3.000
 5CN  C12   C11  C10   111.62  3.000
 5CN  H11   C11  C7    107.63  3.000
 5CN  C12   C11  C7    111.96  3.000
 5CN  C10   C11  C7    109.09  3.000
 5CN  H123  C12  H122  107.68  3.000
 5CN  H123  C12  H121  107.68  3.000
 5CN  H122  C12  H121  107.65  3.000
 5CN  H123  C12  C11   111.28  3.000
 5CN  H122  C12  C11   111.37  3.000
 5CN  H121  C12  C11   111.00  3.000
 5CN  O2    C14  N2    125.91  3.000
 5CN  O2    C14  C15   119.13  3.000
 5CN  N2    C14  C15   114.97  3.000
 5CN  O3    C15  C16   110.53  3.000
 5CN  C16   C15  C14   129.52  3.000
 5CN  O3    C15  C14   119.95  3.000
 5CN  H16   C16  C17   127.15  3.000
 5CN  H16   C16  C15   126.68  3.000
 5CN  C17   C16  C15   106.17  3.000
 5CN  N3    C19  C18   180.00  3.000
 5CN  C5    C4   C13   119.20  3.000
 5CN  C5    C4   C3    119.04  3.000
 5CN  C13   C4   C3    121.75  3.000
 5CN  H5    C5   C6    120.17  3.000
 5CN  H5    C5   C4    119.10  3.000
 5CN  C6    C5   C4    120.70  3.000
 5CN  N2    C6   C5    123.86  3.000
 5CN  N2    C6   C1    115.53  3.000
 5CN  C5    C6   C1    120.50  3.000
 5CN  C9    N1   C8    112.04  3.000
 5CN  C9    N1   C1    118.89  3.000
 5CN  C8    N1   C1    115.65  3.000
 5CN  HO1   O1   C13   108.29  3.000
 5CN  HN2   N2   C6    112.14  3.000
 5CN  HN2   N2   C14   119.00  3.000
 5CN  C6    N2   C14   128.79  3.000
 5CN  H17   C17  C18   126.38  3.000
 5CN  H17   C17  C16   127.99  3.000
 5CN  C18   C17  C16   105.62  3.000
 5CN  O3    C18  C17   110.82  3.000
 5CN  O3    C18  C19   117.66  3.000
 5CN  C17   C18  C19   131.52  3.000
 5CN  C18   O3   C15   106.86  3.000
 5CN  H132  C13  H131  106.26  3.000
 5CN  H132  C13  O1    111.81  3.000
 5CN  H131  C13  O1    106.10  3.000
 5CN  H132  C13  C4    109.09  3.000
 5CN  H131  C13  C4    109.14  3.000
 5CN  O1    C13  C4    114.08  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
 5CN  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 5CN  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 5CN  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 5CN  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 5CN  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 5CN  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 5CN  CONST_07  C17  C18  O3   C15     0.00   0.0  0
 5CN  CONST_08  C18  C17  C16  C15     0.00   0.0  0
 5CN  CONST_09  C18  O3   C15  C16     0.00   0.0  0
 5CN  CONST_10  O3   C18  C17  C16     0.00   0.0  0
 5CN  CONST_11  O3   C15  C16  C17     0.00   0.0  0
 5CN  CONST_12  N1   C1   C2   C3    180.00   0.0  0
 5CN  CONST_13  N1   C1   C6   C5    180.00   0.0  0
 5CN  CONST_14  N2   C6   C1   C2    180.00   0.0  0
 5CN  CONST_15  C13  C4   C3   C2    180.00   0.0  0
 5CN  CONST_16  C6   C5   C4   C13   180.00   0.0  0
 5CN  CONST_17  C18  O3   C15  C14   180.00   0.0  0
 5CN  CONST_18  C17  C16  C15  C14   180.00   0.0  0
 5CN  CONST_19  C19  C18  O3   C15   180.00   0.0  0
 5CN  CONST_20  C19  C18  C17  C16   180.00   0.0  0
 5CN  CONST_21  N2   C6   C5   C4    180.00   0.0  0
 5CN  CONST_22  N2   C6   C1   N1      0.00   0.0  0
 5CN  CONST_23  H3   C3   C2   C1    180.00   0.0  0
 5CN  CONST_24  H5   C5   C6   C1    180.00   0.0  0
 5CN  CONST_25  H17  C17  C16  C15   180.00   0.0  0
 5CN  CONST_26  H2   C2   C3   C4    180.00   0.0  0
 5CN  CONST_27  H16  C16  C17  C18   180.00   0.0  0
 5CN  CONST_28  C6   N2   C14  C15   180.00   0.0  0
 5CN  CONST_32  O2   C14  N2   C6      0.00   0.0  0
 5CN  Var_01    C7   C8   N1   C1     86.93  30.0  1
 5CN  Var_02    C10  C9   N1   C1    -89.04  30.0  1
 5CN  Var_03    C8   N1   C1   C2   -106.79  30.0  2
 5CN  Var_04    N1   C8   C7   C11    57.74  30.0  1
 5CN  Var_05    N1   C9   C10  C11   -50.18  30.0  1
 5CN  Var_06    O1   C13  C4   C3    -26.15  30.0  2
 5CN  Var_07    N2   C14  C15  C16   178.54  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
 5CN  chir_01  C11  C7  C10  C12  positiv

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
 5CN  plan-1  C14  0.020
 5CN  plan-1  C15  0.020
 5CN  plan-1  C16  0.020
 5CN  plan-1  C19  0.020
 5CN  plan-1  C17  0.020
 5CN  plan-1  C18  0.020
 5CN  plan-1  O3   0.020
 5CN  plan-1  N3   0.020
 5CN  plan-1  H16  0.020
 5CN  plan-1  H17  0.020
 5CN  plan-2  C1   0.020
 5CN  plan-2  C2   0.020
 5CN  plan-2  C3   0.020
 5CN  plan-2  C4   0.020
 5CN  plan-2  C5   0.020
 5CN  plan-2  C6   0.020
 5CN  plan-2  N1   0.020
 5CN  plan-2  N2   0.020
 5CN  plan-2  H2   0.020
 5CN  plan-2  H3   0.020
 5CN  plan-2  H5   0.020
 5CN  plan-2  C13  0.020
 5CN  plan-3  C14  0.020
 5CN  plan-3  C15  0.020
 5CN  plan-3  C6   0.020
 5CN  plan-3  N2   0.020
 5CN  plan-3  O2   0.020
 5CN  plan-3  HN2  0.020

