# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 06:46:43 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 3-methyl-N-(naphthalen-1-ylmethyl)-4-(piperidin-4-yloxy)-1-benzofuran-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(oc2cccc(OC3CCNCC3)c12)C(=O)NCc4cccc5ccccc45
#
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
 7I1  7I1  3-methyl-N-(naphthalen-1-ylmethyl)-4-(piperidin-4-yloxy)-1-benzofuran-2-carboxamide  ligand  57  31  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7I1
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
 7I1  O2    O  O     0  -0.491   1.3323  -2.5349   0.2307
 7I1  C14   C  C     0   0.494   1.3189  -1.5036  -0.4321
 7I1  N1    N  NH1   0  -0.638   2.3821  -1.0494  -1.1186
 7I1  C15   C  CH2   0  -0.389   3.6530  -1.7404  -1.1858
 7I1  C16   C  CR6   0   0.081   4.8022  -0.7925  -0.9670
 7I1  C25   C  CR66  0   0.098   5.0752  -0.2475   0.3219
 7I1  C24   C  CR16  0  -0.331   4.3258  -0.5883   1.4744
 7I1  C23   C  CR16  0  -0.249   4.6216  -0.0415   2.6945
 7I1  C22   C  CR16  0  -0.259   5.6813   0.8766   2.8314
 7I1  C21   C  CR16  0  -0.310   6.4293   1.2210   1.7395
 7I1  C20   C  CR66  0   0.112   6.1496   0.6718   0.4662
 7I1  C19   C  CR16  0  -0.326   6.9276   1.0204  -0.6637
 7I1  C18   C  CR16  0  -0.247   6.6545   0.4778  -1.8863
 7I1  C17   C  CR16  0  -0.321   5.5849  -0.4291  -2.0319
 7I1  C2    C  CR5   0   0.178   0.1071  -0.6694  -0.5176
 7I1  O     O  O     0  -0.480   0.2151   0.5060  -1.2115
 7I1  C3    C  CR56  0   0.389  -0.9897   1.0985  -1.1822
 7I1  C13   C  CR56  0  -0.069  -1.8854   0.3086  -0.4669
 7I1  C1    C  CR5   0   0.052  -1.1515  -0.8526  -0.0353
 7I1  C     C  CH3   0  -0.753  -1.7001  -1.9898   0.7548
 7I1  C7    C  CR6   0   0.326  -3.2136   0.7456  -0.3113
 7I1  C6    C  CR16  0  -0.401  -3.5670   1.9552  -0.8956
 7I1  C5    C  CR16  0  -0.258  -2.6259   2.7139  -1.6058
 7I1  C4    C  CR16  0  -0.367  -1.3145   2.3118  -1.7702
 7I1  O1    O  O2    0  -0.475  -4.0189  -0.0459   0.4065
 7I1  C8    C  CH1   0   0.035  -5.4034   0.2664   0.5547
 7I1  C12   C  CH2   0  -0.459  -5.9150  -0.5075   1.7568
 7I1  C11   C  CH2   0  -0.329  -7.4167  -0.2653   1.9269
 7I1  N     N  NH1   0  -0.572  -8.2035  -0.5603   0.7419
 7I1  C10   C  CH2   0  -0.324  -7.6939   0.1343  -0.4274
 7I1  C9    C  CH2   0  -0.481  -6.2038  -0.1003  -0.6876
 7I1  H1    H  HNH1  0   0.407   2.2919  -0.2163  -1.6784
 7I1  H151  H  HCH2  0   0.270   3.6501  -2.5410  -0.4471
 7I1  H152  H  HCH2  0   0.276   3.7614  -2.2173  -2.1632
 7I1  H17   H  HCR6  0   0.257   5.3771  -0.8444  -3.0109
 7I1  H24   H  HCR6  0   0.248   3.5136  -1.2988   1.4056
 7I1  H23   H  HCR6  0   0.260   4.0366  -0.3170   3.5624
 7I1  H22   H  HCR6  0   0.259   5.9019   1.3030   3.8012
 7I1  H21   H  HCR6  0   0.257   7.2504   1.9213   1.8360
 7I1  H19   H  HCR6  0   0.257   7.7438   1.7221  -0.5426
 7I1  H18   H  HCR6  0   0.259   7.2523   0.7410  -2.7490
 7I1  H4    H  HCR6  0   0.269  -0.5945   2.8995  -2.3218
 7I1  HC1   H  HCH3  0   0.249  -2.0478  -1.6475   1.7298
 7I1  HC2   H  HCH3  0   0.247  -2.5610  -2.4247   0.2476
 7I1  HC3   H  HCH3  0   0.258  -0.9589  -2.7661   0.9075
 7I1  H6    H  HCR6  0   0.279  -4.5731   2.3414  -0.8149
 7I1  H5    H  HCR6  0   0.267  -2.9494   3.6499  -2.0413
 7I1  H8    H  HCH1  0   0.226  -5.5160   1.3387   0.7638
 7I1  H121  H  HCH2  0   0.229  -5.7291  -1.5766   1.6107
 7I1  H122  H  HCH2  0   0.241  -5.3834  -0.2013   2.6614
 7I1  H91C  H  HCH2  0   0.245  -5.8840   0.4799  -1.5570
 7I1  H92C  H  HCH2  0   0.232  -6.0329  -1.1557  -0.9235
 7I1  H111  H  HCH2  0   0.245  -7.7945  -0.8590   2.7607
 7I1  H112  H  HCH2  0   0.222  -7.5833   0.7841   2.1935
 7I1  H     H  HNH1  0   0.341  -8.1776  -1.5586   0.5685
 7I1  H101  H  HCH2  0   0.244  -8.2737  -0.1686  -1.3008
 7I1  H102  H  HCH2  0   0.223  -7.8714   1.2069  -0.2925

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
 7I1  O2   C14   double    1.226  0.020  1.226
 7I1  C14  N1    single    1.345  0.020  1.345
 7I1  C14  C2    single    1.474  0.020  1.474
 7I1  N1   C15   single    1.448  0.020  1.448
 7I1  C15  C16   single    1.506  0.020  1.506
 7I1  C16  C25   aromatic  1.426  0.020  1.426
 7I1  C16  C17   aromatic  1.371  0.020  1.371
 7I1  C25  C24   aromatic  1.416  0.020  1.416
 7I1  C25  C20   aromatic  1.421  0.020  1.421
 7I1  C24  C23   aromatic  1.369  0.020  1.369
 7I1  C23  C22   aromatic  1.409  0.020  1.409
 7I1  C22  C21   aromatic  1.368  0.020  1.368
 7I1  C21  C20   aromatic  1.415  0.020  1.415
 7I1  C20  C19   aromatic  1.415  0.020  1.415
 7I1  C19  C18   aromatic  1.365  0.020  1.365
 7I1  C18  C17   aromatic  1.410  0.020  1.410
 7I1  C2   O     aromatic  1.369  0.020  1.369
 7I1  C2   C1    aromatic  1.360  0.020  1.360
 7I1  O    C3    aromatic  1.343  0.020  1.343
 7I1  C3   C13   aromatic  1.392  0.020  1.392
 7I1  C3   C4    aromatic  1.387  0.020  1.387
 7I1  C13  C1    aromatic  1.440  0.020  1.440
 7I1  C13  C7    aromatic  1.407  0.020  1.407
 7I1  C1   C     single    1.489  0.020  1.489
 7I1  C7   C6    aromatic  1.389  0.020  1.389
 7I1  C7   O1    single    1.338  0.020  1.338
 7I1  C6   C5    aromatic  1.402  0.020  1.402
 7I1  C5   C4    aromatic  1.381  0.020  1.381
 7I1  O1   C8    single    1.427  0.020  1.427
 7I1  C8   C12   single    1.519  0.020  1.519
 7I1  C8   C9    single    1.523  0.020  1.523
 7I1  C12  C11   single    1.531  0.020  1.531
 7I1  C11  N     single    1.453  0.020  1.453
 7I1  N    C10   single    1.452  0.020  1.452
 7I1  C10  C9    single    1.531  0.020  1.531
 7I1  N1   H1    single    0.860  0.020  1.020
 7I1  C15  H151  single    0.970  0.020  1.090
 7I1  C15  H152  single    0.970  0.020  1.090
 7I1  C17  H17   single    0.930  0.020  1.080
 7I1  C24  H24   single    0.930  0.020  1.080
 7I1  C23  H23   single    0.930  0.020  1.080
 7I1  C22  H22   single    0.930  0.020  1.080
 7I1  C21  H21   single    0.930  0.020  1.080
 7I1  C19  H19   single    0.930  0.020  1.080
 7I1  C18  H18   single    0.930  0.020  1.080
 7I1  C4   H4    single    0.930  0.020  1.080
 7I1  C    HC1   single    0.970  0.020  1.090
 7I1  C    HC2   single    0.970  0.020  1.090
 7I1  C    HC3   single    0.970  0.020  1.090
 7I1  C6   H6    single    0.930  0.020  1.080
 7I1  C5   H5    single    0.930  0.020  1.080
 7I1  C8   H8    single    0.970  0.020  1.090
 7I1  C12  H121  single    0.970  0.020  1.090
 7I1  C12  H122  single    0.970  0.020  1.090
 7I1  C9   H91C  single    0.970  0.020  1.090
 7I1  C9   H92C  single    0.970  0.020  1.090
 7I1  C11  H111  single    0.970  0.020  1.090
 7I1  C11  H112  single    0.970  0.020  1.090
 7I1  N    H     single    0.860  0.020  1.020
 7I1  C10  H101  single    0.970  0.020  1.090
 7I1  C10  H102  single    0.970  0.020  1.090

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
 7I1  C2    C14  N1    115.43  3.000
 7I1  C2    C14  O2    121.10  3.000
 7I1  N1    C14  O2    123.47  3.000
 7I1  H1    N1   C15   116.56  3.000
 7I1  H1    N1   C14   119.48  3.000
 7I1  C15   N1   C14   123.81  3.000
 7I1  H152  C15  H151  106.62  3.000
 7I1  H152  C15  C16   109.20  3.000
 7I1  H151  C15  C16   111.48  3.000
 7I1  H152  C15  N1    109.68  3.000
 7I1  H151  C15  N1    108.48  3.000
 7I1  C16   C15  N1    111.27  3.000
 7I1  C17   C16  C25   119.45  3.000
 7I1  C17   C16  C15   119.33  3.000
 7I1  C25   C16  C15   121.21  3.000
 7I1  C20   C25  C24   118.22  3.000
 7I1  C20   C25  C16   118.93  3.000
 7I1  C24   C25  C16   122.85  3.000
 7I1  H24   C24  C23   118.77  3.000
 7I1  H24   C24  C25   120.25  3.000
 7I1  C23   C24  C25   120.98  3.000
 7I1  H23   C23  C22   119.64  3.000
 7I1  H23   C23  C24   119.75  3.000
 7I1  C22   C23  C24   120.61  3.000
 7I1  H22   C22  C21   120.32  3.000
 7I1  H22   C22  C23   119.81  3.000
 7I1  C21   C22  C23   119.87  3.000
 7I1  H21   C21  C20   118.75  3.000
 7I1  H21   C21  C22   120.41  3.000
 7I1  C20   C21  C22   120.85  3.000
 7I1  C19   C20  C21   120.95  3.000
 7I1  C19   C20  C25   119.58  3.000
 7I1  C21   C20  C25   119.47  3.000
 7I1  H19   C19  C18   120.55  3.000
 7I1  H19   C19  C20   118.98  3.000
 7I1  C18   C19  C20   120.47  3.000
 7I1  H18   C18  C17   119.55  3.000
 7I1  H18   C18  C19   120.45  3.000
 7I1  C17   C18  C19   120.00  3.000
 7I1  H17   C17  C18   119.04  3.000
 7I1  H17   C17  C16   119.40  3.000
 7I1  C18   C17  C16   121.57  3.000
 7I1  C1    C2   O     111.61  3.000
 7I1  C1    C2   C14   131.61  3.000
 7I1  O     C2   C14   116.78  3.000
 7I1  C3    O    C2    107.27  3.000
 7I1  C4    C3   C13   124.30  3.000
 7I1  C4    C3   O     125.93  3.000
 7I1  C13   C3   O     109.76  3.000
 7I1  C7    C13  C1    134.31  3.000
 7I1  C7    C13  C3    119.21  3.000
 7I1  C1    C13  C3    106.48  3.000
 7I1  C     C1   C13   125.95  3.000
 7I1  C     C1   C2    129.18  3.000
 7I1  C13   C1   C2    104.87  3.000
 7I1  HC3   C    HC2   108.66  3.000
 7I1  HC3   C    HC1   108.47  3.000
 7I1  HC2   C    HC1   106.84  3.000
 7I1  HC3   C    C1    111.69  3.000
 7I1  HC2   C    C1    110.41  3.000
 7I1  HC1   C    C1    110.62  3.000
 7I1  O1    C7   C6    126.00  3.000
 7I1  O1    C7   C13   116.35  3.000
 7I1  C6    C7   C13   117.65  3.000
 7I1  H6    C6   C5    117.99  3.000
 7I1  H6    C6   C7    121.11  3.000
 7I1  C5    C6   C7    120.90  3.000
 7I1  H5    C5   C4    119.20  3.000
 7I1  H5    C5   C6    118.12  3.000
 7I1  C4    C5   C6    122.68  3.000
 7I1  H4    C4   C5    122.33  3.000
 7I1  H4    C4   C3    122.42  3.000
 7I1  C5    C4   C3    115.25  3.000
 7I1  C8    O1   C7    120.67  3.000
 7I1  H8    C8   C9    109.67  3.000
 7I1  H8    C8   C12   108.20  3.000
 7I1  C9    C8   C12   110.25  3.000
 7I1  H8    C8   O1    109.45  3.000
 7I1  C9    C8   O1    111.87  3.000
 7I1  C12   C8   O1    107.31  3.000
 7I1  H122  C12  H121  107.55  3.000
 7I1  H122  C12  C11   109.93  3.000
 7I1  H121  C12  C11   109.63  3.000
 7I1  H122  C12  C8    110.39  3.000
 7I1  H121  C12  C8    109.56  3.000
 7I1  C11   C12  C8    109.75  3.000
 7I1  H112  C11  H111  106.42  3.000
 7I1  H112  C11  N     108.11  3.000
 7I1  H111  C11  N     108.99  3.000
 7I1  H112  C11  C12   109.13  3.000
 7I1  H111  C11  C12   109.78  3.000
 7I1  N     C11  C12   114.12  3.000
 7I1  H     N    C10   108.93  3.000
 7I1  H     N    C11   109.01  3.000
 7I1  C10   N    C11   111.69  3.000
 7I1  H102  C10  H101  106.51  3.000
 7I1  H102  C10  C9    109.19  3.000
 7I1  H101  C10  C9    109.79  3.000
 7I1  H102  C10  N     108.20  3.000
 7I1  H101  C10  N     108.98  3.000
 7I1  C9    C10  N     113.90  3.000
 7I1  H92C  C9   H91C  107.13  3.000
 7I1  H92C  C9   C10   109.65  3.000
 7I1  H91C  C9   C10   109.79  3.000
 7I1  H92C  C9   C8    109.02  3.000
 7I1  H91C  C9   C8    111.56  3.000
 7I1  C10   C9   C8    109.64  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
 7I1  CONST_01  C23  C24  C25  C16   180.00   0.0  0
 7I1  CONST_02  C21  C20  C25  C16   180.00   0.0  0
 7I1  CONST_03  C19  C20  C25  C16     0.00   0.0  0
 7I1  CONST_04  C19  C18  C17  C16     0.00   0.0  0
 7I1  CONST_05  C18  C17  C16  C25     0.00   0.0  0
 7I1  CONST_06  C22  C23  C24  C25     0.00   0.0  0
 7I1  CONST_07  C22  C21  C20  C25     0.00   0.0  0
 7I1  CONST_08  C18  C19  C20  C25     0.00   0.0  0
 7I1  CONST_09  C17  C16  C25  C24   180.00   0.0  0
 7I1  CONST_10  C21  C20  C25  C24     0.00   0.0  0
 7I1  CONST_11  C19  C20  C25  C24   180.00   0.0  0
 7I1  CONST_12  C21  C22  C23  C24     0.00   0.0  0
 7I1  CONST_13  C20  C25  C24  C23     0.00   0.0  0
 7I1  CONST_14  C20  C21  C22  C23     0.00   0.0  0
 7I1  CONST_15  C19  C20  C21  C22   180.00   0.0  0
 7I1  CONST_16  C18  C19  C20  C21   180.00   0.0  0
 7I1  CONST_17  C17  C16  C25  C20     0.00   0.0  0
 7I1  CONST_18  C17  C18  C19  C20     0.00   0.0  0
 7I1  CONST_19  C13  C3   O    C2      0.00   0.0  0
 7I1  CONST_20  C4   C3   O    C2    180.00   0.0  0
 7I1  CONST_21  C3   C13  C1   C2      0.00   0.0  0
 7I1  CONST_22  C7   C13  C1   C2    180.00   0.0  0
 7I1  CONST_23  C13  C1   C2   O       0.00   0.0  0
 7I1  CONST_24  C1   C13  C3   O       0.00   0.0  0
 7I1  CONST_25  C7   C13  C3   O     180.00   0.0  0
 7I1  CONST_26  C5   C4   C3   O     180.00   0.0  0
 7I1  CONST_27  C1   C2   O    C3      0.00   0.0  0
 7I1  CONST_28  C6   C7   C13  C3      0.00   0.0  0
 7I1  CONST_29  C6   C5   C4   C3      0.00   0.0  0
 7I1  CONST_30  C5   C4   C3   C13     0.00   0.0  0
 7I1  CONST_31  C5   C6   C7   C13     0.00   0.0  0
 7I1  CONST_32  C4   C3   C13  C1    180.00   0.0  0
 7I1  CONST_33  C6   C7   C13  C1    180.00   0.0  0
 7I1  CONST_34  C4   C3   C13  C7      0.00   0.0  0
 7I1  CONST_35  C4   C5   C6   C7      0.00   0.0  0
 7I1  CONST_36  C3   O    C2   C14   180.00   0.0  0
 7I1  CONST_37  C13  C1   C2   C14   180.00   0.0  0
 7I1  CONST_38  C24  C25  C16  C15     0.00   0.0  0
 7I1  CONST_39  C20  C25  C16  C15   180.00   0.0  0
 7I1  CONST_40  C18  C17  C16  C15   180.00   0.0  0
 7I1  CONST_41  C    C1   C2   O     180.00   0.0  0
 7I1  CONST_42  C    C1   C13  C3    180.00   0.0  0
 7I1  CONST_43  O1   C7   C13  C3    180.00   0.0  0
 7I1  CONST_44  O1   C7   C13  C1      0.00   0.0  0
 7I1  CONST_45  C7   C13  C1   C       0.00   0.0  0
 7I1  CONST_46  O1   C7   C6   C5    180.00   0.0  0
 7I1  CONST_47  H24  C24  C25  C16     0.00   0.0  0
 7I1  CONST_48  H18  C18  C17  C16   180.00   0.0  0
 7I1  CONST_49  H17  C17  C16  C25   180.00   0.0  0
 7I1  CONST_50  H23  C23  C24  C25   180.00   0.0  0
 7I1  CONST_51  H21  C21  C20  C25   180.00   0.0  0
 7I1  CONST_52  H19  C19  C20  C25   180.00   0.0  0
 7I1  CONST_53  H22  C22  C23  C24   180.00   0.0  0
 7I1  CONST_54  H4   C4   C3   O       0.00   0.0  0
 7I1  CONST_55  H5   C5   C4   C3    180.00   0.0  0
 7I1  CONST_56  H6   C6   C7   C13   180.00   0.0  0
 7I1  CONST_57  C2   C14  N1   C15   180.00   0.0  0
 7I1  CONST_58  H1   N1   C14  C2      0.00   0.0  0
 7I1  CONST_59  C15  N1   C14  O2      0.00   0.0  0
 7I1  Var_01    N    C11  C12  C8     54.58  30.0  1
 7I1  Var_02    N    C10  C9   C8    -55.04  30.0  1
 7I1  Var_03    C10  N    C11  C12   -53.12  30.0  1
 7I1  Var_04    C9   C10  N    C11    53.35  30.0  1
 7I1  Var_05    O    C2   C14  O2    175.96  30.0  2
 7I1  Var_06    C25  C16  C15  N1     72.15  30.0  2
 7I1  Var_07    HC1  C    C1   C2    118.61  30.0  2
 7I1  Var_08    C16  C15  N1   C14  -134.23  30.0  3

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
 7I1  chir_01  C8  O1  C12  C9  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
 7I1  plan-1  C14  0.020
 7I1  plan-1  C2   0.020
 7I1  plan-1  O    0.020
 7I1  plan-1  C3   0.020
 7I1  plan-1  C13  0.020
 7I1  plan-1  C1   0.020
 7I1  plan-1  C    0.020
 7I1  plan-1  C7   0.020
 7I1  plan-1  C6   0.020
 7I1  plan-1  C5   0.020
 7I1  plan-1  C4   0.020
 7I1  plan-1  O1   0.020
 7I1  plan-1  H4   0.020
 7I1  plan-1  H6   0.020
 7I1  plan-1  H5   0.020
 7I1  plan-2  C15  0.020
 7I1  plan-2  C16  0.020
 7I1  plan-2  C25  0.020
 7I1  plan-2  C24  0.020
 7I1  plan-2  C23  0.020
 7I1  plan-2  C22  0.020
 7I1  plan-2  C21  0.020
 7I1  plan-2  C20  0.020
 7I1  plan-2  C19  0.020
 7I1  plan-2  C18  0.020
 7I1  plan-2  C17  0.020
 7I1  plan-2  H17  0.020
 7I1  plan-2  H24  0.020
 7I1  plan-2  H23  0.020
 7I1  plan-2  H22  0.020
 7I1  plan-2  H21  0.020
 7I1  plan-2  H19  0.020
 7I1  plan-2  H18  0.020
 7I1  plan-3  O2   0.020
 7I1  plan-3  C14  0.020
 7I1  plan-3  N1   0.020
 7I1  plan-3  C15  0.020
 7I1  plan-3  C2   0.020
 7I1  plan-3  H1   0.020

