# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 19:37:43 2021
#   Inital geometry file: a 139 line input string
#   Ligand name: 2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]-5-{[(prop-2-en-1-yl)carbamoyl]amino}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)c1cc(NC(=O)NCC=C)ccc1C)c2cccc3ccccc23
#
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
 Y94  Y94  2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]-5-{[(prop-2-en-1-yl)carbamoyl]amino}benzamide  ligand  54  29  .  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_Y94
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
 Y94  O26  O  O     0  -0.519  51.2429  37.5146  -0.4281
 Y94  C24  C  C     0   0.731  52.1252  36.7100  -0.1681
 Y94  N25  N  NH1   0  -0.672  53.4438  36.9950  -0.2860
 Y94  C27  C  CH2   0  -0.352  53.9208  38.3299  -0.5751
 Y94  C28  C  C1    0  -0.168  54.0709  39.1703   0.6588
 Y94  C29  C  C2    0  -0.527  55.2122  39.7279   1.0432
 Y94  N01  N  NH1   0  -0.788  51.8765  35.4262   0.2594
 Y94  C19  C  CR6   0   0.376  50.6343  34.7941   0.3106
 Y94  C13  C  CR16  0  -0.373  50.6098  33.4052   0.1801
 Y94  C21  C  CR16  0  -0.289  49.4266  35.4545   0.5258
 Y94  C17  C  CR16  0  -0.295  48.2445  34.7298   0.5724
 Y94  C10  C  CR6   0   0.077  48.1971  33.3496   0.4118
 Y94  C16  C  CH3   0  -0.731  46.8816  32.6272   0.4688
 Y94  C3   C  CR6   0  -0.066  49.4187  32.6932   0.2269
 Y94  C1   C  C     0   0.489  49.4662  31.2135   0.0026
 Y94  O7   O  O     0  -0.472  48.7887  30.6666  -0.8540
 Y94  N2   N  NH1   0  -0.633  50.3080  30.5444   0.8098
 Y94  C6   C  CH1   0  -0.150  50.5252  29.1177   0.7030
 Y94  C01  C  CH3   0  -0.666  51.0237  28.5934   2.0479
 Y94  C5   C  CR6   0   0.117  51.4933  28.7554  -0.4090
 Y94  C8   C  CR66  0   0.099  51.4346  27.4671  -1.0203
 Y94  C14  C  CR16  0  -0.342  50.4743  26.4859  -0.6654
 Y94  C20  C  CR16  0  -0.248  50.4475  25.2631  -1.2806
 Y94  C22  C  CR16  0  -0.261  51.3809  24.9459  -2.2865
 Y94  C18  C  CR16  0  -0.309  52.3240  25.8660  -2.6516
 Y94  C11  C  CR66  0   0.110  52.3769  27.1381  -2.0342
 Y94  C12  C  CR16  0  -0.331  53.3556  28.0858  -2.4134
 Y94  C9   C  CR16  0  -0.242  53.3946  29.3105  -1.8117
 Y94  C4   C  CR16  0  -0.343  52.4607  29.6398  -0.8095
 Y94  H1   H  HNH1  0   0.399  54.1273  36.3269   0.0320
 Y94  H2   H  HCH2  0   0.262  54.8780  38.2432  -1.0906
 Y94  H3   H  HCH2  0   0.258  53.2278  38.8037  -1.2714
 Y94  H4   H  H     0   0.249  53.1724  39.3124   1.2524
 Y94  H5   H  H     0   0.242  55.2762  40.3323   1.9387
 Y94  H6   H  H     0   0.237  56.1264  39.6033   0.4740
 Y94  H7   H  HNH1  0   0.407  52.6711  34.8088   0.3373
 Y94  H8   H  HCR6  0   0.278  51.5438  32.8776   0.0181
 Y94  H9   H  HCR6  0   0.272  49.3936  36.5224   0.6669
 Y94  H10  H  HCR6  0   0.253  47.3207  35.2677   0.7500
 Y94  H11  H  HCH3  0   0.241  46.9157  31.7671   1.1384
 Y94  H12  H  HCH3  0   0.244  46.0985  33.2940   0.8272
 Y94  H13  H  HCH3  0   0.250  46.5816  32.2582  -0.5117
 Y94  H14  H  HNH1  0   0.409  50.8291  31.0576   1.5039
 Y94  H15  H  HCH1  0   0.258  49.5550  28.6679   0.4854
 Y94  H16  H  HCH3  0   0.249  50.2860  28.7730   2.8303
 Y94  H17  H  HCH3  0   0.248  51.2128  27.5222   1.9991
 Y94  H18  H  HCH3  0   0.237  51.9559  29.0858   2.3300
 Y94  H19  H  HCR6  0   0.250  49.7443  26.6880   0.1068
 Y94  H20  H  HCR6  0   0.260  49.7034  24.5329  -0.9902
 Y94  H21  H  HCR6  0   0.259  51.3492  23.9759  -2.7652
 Y94  H22  H  HCR6  0   0.256  53.0494  25.6337  -3.4224
 Y94  H23  H  HCR6  0   0.255  54.0742  27.8264  -3.1808
 Y94  H24  H  HCR6  0   0.256  54.1411  30.0389  -2.1001
 Y94  H25  H  HCR6  0   0.254  52.5220  30.6193  -0.3530

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
 Y94  C22  C18  aromatic  1.367  0.020  1.367
 Y94  C22  C20  aromatic  1.409  0.020  1.409
 Y94  C18  C11  aromatic  1.415  0.020  1.415
 Y94  C20  C14  aromatic  1.369  0.020  1.369
 Y94  C11  C12  aromatic  1.414  0.020  1.414
 Y94  C11  C8   aromatic  1.423  0.020  1.423
 Y94  C14  C8   aromatic  1.418  0.020  1.418
 Y94  C12  C9   aromatic  1.365  0.020  1.365
 Y94  C27  N25  single    1.447  0.020  1.447
 Y94  C27  C28  single    1.500  0.020  1.500
 Y94  N25  C24  single    1.354  0.020  1.354
 Y94  C8   C5   aromatic  1.427  0.020  1.427
 Y94  O7   C1   double    1.221  0.020  1.221
 Y94  C24  O26  double    1.222  0.020  1.222
 Y94  C24  N01  single    1.376  0.020  1.376
 Y94  N01  C19  single    1.395  0.020  1.395
 Y94  C9   C4   aromatic  1.409  0.020  1.409
 Y94  C28  C29  double    1.327  0.020  1.327
 Y94  C13  C19  aromatic  1.395  0.020  1.395
 Y94  C13  C3   aromatic  1.389  0.020  1.389
 Y94  C19  C21  aromatic  1.393  0.020  1.393
 Y94  C5   C4   aromatic  1.371  0.020  1.371
 Y94  C5   C6   single    1.518  0.020  1.518
 Y94  C1   C3   single    1.497  0.020  1.497
 Y94  C1   N2   single    1.345  0.020  1.345
 Y94  C3   C10  aromatic  1.399  0.020  1.399
 Y94  C21  C17  aromatic  1.387  0.020  1.387
 Y94  C10  C17  aromatic  1.390  0.020  1.390
 Y94  C10  C16  single    1.502  0.020  1.502
 Y94  C6   N2   single    1.447  0.020  1.447
 Y94  C6   C01  single    1.527  0.020  1.527
 Y94  N25  H1   single    0.860  0.020  1.020
 Y94  C27  H2   single    0.970  0.020  1.090
 Y94  C27  H3   single    0.970  0.020  1.090
 Y94  C28  H4   single    0.930  0.020  1.080
 Y94  C29  H5   single    0.930  0.020  1.080
 Y94  C29  H6   single    0.930  0.020  1.080
 Y94  N01  H7   single    0.860  0.020  1.020
 Y94  C13  H8   single    0.930  0.020  1.080
 Y94  C21  H9   single    0.930  0.020  1.080
 Y94  C17  H10  single    0.930  0.020  1.080
 Y94  C16  H11  single    0.970  0.020  1.090
 Y94  C16  H12  single    0.970  0.020  1.090
 Y94  C16  H13  single    0.970  0.020  1.090
 Y94  N2   H14  single    0.860  0.020  1.020
 Y94  C6   H15  single    0.970  0.020  1.090
 Y94  C01  H16  single    0.970  0.020  1.090
 Y94  C01  H17  single    0.970  0.020  1.090
 Y94  C01  H18  single    0.970  0.020  1.090
 Y94  C14  H19  single    0.930  0.020  1.080
 Y94  C20  H20  single    0.930  0.020  1.080
 Y94  C22  H21  single    0.930  0.020  1.080
 Y94  C18  H22  single    0.930  0.020  1.080
 Y94  C12  H23  single    0.930  0.020  1.080
 Y94  C9   H24  single    0.930  0.020  1.080
 Y94  C4   H25  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
 Y94  N01  C24  N25  113.55  3.000
 Y94  N01  C24  O26  123.37  3.000
 Y94  N25  C24  O26  123.09  3.000
 Y94  H1   N25  C27  116.83  3.000
 Y94  H1   N25  C24  119.58  3.000
 Y94  C27  N25  C24  122.18  3.000
 Y94  H3   C27  H2   106.88  3.000
 Y94  H3   C27  C28  110.20  3.000
 Y94  H2   C27  C28  110.21  3.000
 Y94  H3   C27  N25  108.60  3.000
 Y94  H2   C27  N25  108.09  3.000
 Y94  C28  C27  N25  112.67  3.000
 Y94  H4   C28  C29  119.87  3.000
 Y94  H4   C28  C27  116.10  3.000
 Y94  C29  C28  C27  124.03  3.000
 Y94  H6   C29  H5   116.67  3.000
 Y94  H6   C29  C28  121.65  3.000
 Y94  H5   C29  C28  121.68  3.000
 Y94  H7   N01  C19  114.91  3.000
 Y94  H7   N01  C24  116.91  3.000
 Y94  C19  N01  C24  126.53  3.000
 Y94  C21  C19  C13  118.11  3.000
 Y94  C21  C19  N01  124.26  3.000
 Y94  C13  C19  N01  117.60  3.000
 Y94  H8   C13  C3   119.62  3.000
 Y94  H8   C13  C19  118.88  3.000
 Y94  C3   C13  C19  121.49  3.000
 Y94  H9   C21  C17  119.15  3.000
 Y94  H9   C21  C19  121.10  3.000
 Y94  C17  C21  C19  119.75  3.000
 Y94  H10  C17  C10  118.86  3.000
 Y94  H10  C17  C21  118.21  3.000
 Y94  C10  C17  C21  122.94  3.000
 Y94  C3   C10  C16  122.97  3.000
 Y94  C16  C10  C17  120.20  3.000
 Y94  C3   C10  C17  116.83  3.000
 Y94  H13  C16  H12  107.79  3.000
 Y94  H13  C16  H11  107.09  3.000
 Y94  H12  C16  H11  107.66  3.000
 Y94  H13  C16  C10  111.71  3.000
 Y94  H12  C16  C10  110.35  3.000
 Y94  H11  C16  C10  112.04  3.000
 Y94  C1   C3   C10  120.74  3.000
 Y94  C10  C3   C13  120.86  3.000
 Y94  C1   C3   C13  118.32  3.000
 Y94  N2   C1   O7   123.06  3.000
 Y94  N2   C1   C3   114.94  3.000
 Y94  O7   C1   C3   122.00  3.000
 Y94  H14  N2   C6   118.36  3.000
 Y94  H14  N2   C1   118.92  3.000
 Y94  C6   N2   C1   122.70  3.000
 Y94  H15  C6   C5   108.81  3.000
 Y94  H15  C6   C01  108.93  3.000
 Y94  C5   C6   C01  110.79  3.000
 Y94  H15  C6   N2   106.72  3.000
 Y94  C01  C6   N2   108.82  3.000
 Y94  C5   C6   N2   112.65  3.000
 Y94  H18  C01  H17  107.89  3.000
 Y94  H18  C01  H16  108.55  3.000
 Y94  H17  C01  H16  108.16  3.000
 Y94  H18  C01  C6   110.58  3.000
 Y94  H17  C01  C6   110.79  3.000
 Y94  H16  C01  C6   110.76  3.000
 Y94  C4   C5   C8   119.10  3.000
 Y94  C4   C5   C6   120.67  3.000
 Y94  C8   C5   C6   120.19  3.000
 Y94  C11  C8   C14  117.83  3.000
 Y94  C14  C8   C5   123.04  3.000
 Y94  C11  C8   C5   119.13  3.000
 Y94  H19  C14  C20  118.32  3.000
 Y94  H19  C14  C8   120.42  3.000
 Y94  C20  C14  C8   121.25  3.000
 Y94  H20  C20  C22  119.69  3.000
 Y94  H20  C20  C14  119.70  3.000
 Y94  C22  C20  C14  120.60  3.000
 Y94  H21  C22  C18  120.36  3.000
 Y94  H21  C22  C20  119.89  3.000
 Y94  C18  C22  C20  119.75  3.000
 Y94  H22  C18  C11  118.56  3.000
 Y94  H22  C18  C22  120.49  3.000
 Y94  C11  C18  C22  120.95  3.000
 Y94  C12  C11  C18  120.75  3.000
 Y94  C12  C11  C8   119.64  3.000
 Y94  C18  C11  C8   119.61  3.000
 Y94  H23  C12  C9   120.55  3.000
 Y94  H23  C12  C11  119.26  3.000
 Y94  C9   C12  C11  120.19  3.000
 Y94  H24  C9   C4   119.31  3.000
 Y94  H24  C9   C12  120.40  3.000
 Y94  C4   C9   C12  120.28  3.000
 Y94  H25  C4   C9   118.29  3.000
 Y94  H25  C4   C5   120.04  3.000
 Y94  C9   C4   C5   121.66  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
 Y94  CONST_01  C10  C3   C13  C19     0.00   0.0  0
 Y94  CONST_02  C10  C17  C21  C19     0.00   0.0  0
 Y94  CONST_03  C17  C21  C19  C13     0.00   0.0  0
 Y94  CONST_04  C17  C10  C3   C13     0.00   0.0  0
 Y94  CONST_05  C3   C13  C19  C21     0.00   0.0  0
 Y94  CONST_06  C3   C10  C17  C21     0.00   0.0  0
 Y94  CONST_07  C18  C11  C8   C5    180.00   0.0  0
 Y94  CONST_08  C12  C11  C8   C5      0.00   0.0  0
 Y94  CONST_09  C20  C14  C8   C5    180.00   0.0  0
 Y94  CONST_10  C12  C9   C4   C5      0.00   0.0  0
 Y94  CONST_11  C22  C18  C11  C8      0.00   0.0  0
 Y94  CONST_12  C9   C12  C11  C8      0.00   0.0  0
 Y94  CONST_13  C22  C20  C14  C8      0.00   0.0  0
 Y94  CONST_14  C9   C4   C5   C8      0.00   0.0  0
 Y94  CONST_15  C18  C22  C20  C14     0.00   0.0  0
 Y94  CONST_16  C18  C11  C8   C14     0.00   0.0  0
 Y94  CONST_17  C12  C11  C8   C14   180.00   0.0  0
 Y94  CONST_18  C4   C5   C8   C14   180.00   0.0  0
 Y94  CONST_19  C11  C18  C22  C20     0.00   0.0  0
 Y94  CONST_20  C11  C8   C14  C20     0.00   0.0  0
 Y94  CONST_21  C12  C11  C18  C22   180.00   0.0  0
 Y94  CONST_22  C9   C12  C11  C18   180.00   0.0  0
 Y94  CONST_23  C4   C9   C12  C11     0.00   0.0  0
 Y94  CONST_24  C4   C5   C8   C11     0.00   0.0  0
 Y94  CONST_25  C3   C13  C19  N01   180.00   0.0  0
 Y94  CONST_26  C17  C21  C19  N01   180.00   0.0  0
 Y94  CONST_27  C1   C3   C13  C19   180.00   0.0  0
 Y94  CONST_28  C16  C10  C3   C13   180.00   0.0  0
 Y94  CONST_29  C16  C10  C17  C21   180.00   0.0  0
 Y94  CONST_30  C1   C3   C10  C17   180.00   0.0  0
 Y94  CONST_31  C11  C8   C5   C6    180.00   0.0  0
 Y94  CONST_32  C14  C8   C5   C6      0.00   0.0  0
 Y94  CONST_33  C9   C4   C5   C6    180.00   0.0  0
 Y94  CONST_34  H10  C17  C21  C19   180.00   0.0  0
 Y94  CONST_35  H9   C21  C19  C13   180.00   0.0  0
 Y94  CONST_36  H8   C13  C19  C21   180.00   0.0  0
 Y94  CONST_37  H19  C14  C8   C5      0.00   0.0  0
 Y94  CONST_38  H24  C9   C4   C5    180.00   0.0  0
 Y94  CONST_39  H22  C18  C11  C8    180.00   0.0  0
 Y94  CONST_40  H23  C12  C11  C8    180.00   0.0  0
 Y94  CONST_41  H20  C20  C14  C8    180.00   0.0  0
 Y94  CONST_42  H25  C4   C5   C8    180.00   0.0  0
 Y94  CONST_43  H21  C22  C20  C14   180.00   0.0  0
 Y94  CONST_46  H7   N01  C19  C13     0.00   0.0  0
 Y94  CONST_47  C19  N01  C24  O26     0.00   0.0  0
 Y94  CONST_48  C6   N2   C1   C3    180.00   0.0  0
 Y94  CONST_49  C19  N01  C24  N25   180.00   0.0  0
 Y94  CONST_50  H14  N2   C1   C3      0.00   0.0  0
 Y94  CONST_51  C27  N25  C24  O26     0.00   0.0  0
 Y94  CONST_52  C6   N2   C1   O7      0.00   0.0  0
 Y94  CONST_53  N01  C24  N25  C27   180.00   0.0  0
 Y94  CONST_54  H1   N25  C24  O26   180.00   0.0  0
 Y94  Var_01    O7   C1   C3   C13  -125.20  30.0  2
 Y94  Var_02    H11  C16  C10  C17  -130.68  30.0  2
 Y94  Var_03    C28  C27  N25  C24    85.48  30.0  2
 Y94  Var_04    C29  C28  C27  N25   121.33  30.0  3
 Y94  Var_05    H5   C29  C28  C27   179.66   0.0  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
 Y94  chir_01  C6  C5  N2  C01  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
 Y94  plan-1  N01  0.020
 Y94  plan-1  C19  0.020
 Y94  plan-1  C13  0.020
 Y94  plan-1  C21  0.020
 Y94  plan-1  C17  0.020
 Y94  plan-1  C10  0.020
 Y94  plan-1  C16  0.020
 Y94  plan-1  C3   0.020
 Y94  plan-1  C1   0.020
 Y94  plan-1  H8   0.020
 Y94  plan-1  H9   0.020
 Y94  plan-1  H10  0.020
 Y94  plan-2  C27  0.020
 Y94  plan-2  C28  0.020
 Y94  plan-2  C29  0.020
 Y94  plan-2  H4   0.020
 Y94  plan-2  H5   0.020
 Y94  plan-2  H6   0.020
 Y94  plan-3  C6   0.020
 Y94  plan-3  C5   0.020
 Y94  plan-3  C8   0.020
 Y94  plan-3  C14  0.020
 Y94  plan-3  C20  0.020
 Y94  plan-3  C22  0.020
 Y94  plan-3  C18  0.020
 Y94  plan-3  C11  0.020
 Y94  plan-3  C12  0.020
 Y94  plan-3  C9   0.020
 Y94  plan-3  C4   0.020
 Y94  plan-3  H19  0.020
 Y94  plan-3  H20  0.020
 Y94  plan-3  H21  0.020
 Y94  plan-3  H22  0.020
 Y94  plan-3  H23  0.020
 Y94  plan-3  H24  0.020
 Y94  plan-3  H25  0.020
 Y94  plan-4  O26  0.020
 Y94  plan-4  C24  0.020
 Y94  plan-4  N25  0.020
 Y94  plan-4  C27  0.020
 Y94  plan-4  N01  0.020
 Y94  plan-4  C19  0.020
 Y94  plan-4  H1   0.020
 Y94  plan-4  H7   0.020
 Y94  plan-5  C3   0.020
 Y94  plan-5  C1   0.020
 Y94  plan-5  O7   0.020
 Y94  plan-5  N2   0.020
 Y94  plan-5  C6   0.020
 Y94  plan-5  H14  0.020

