# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 15:49:31 2021
#   Inital geometry file: a 110 line input string
#   Ligand name: 3-amino-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)c1cccc(N)c1C)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
 Y41  Y41  3-amino-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide  ligand  43  23  .  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_Y41
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
 Y41  O7   O  O     0  -0.475  50.9381  31.2839  -1.6167
 Y41  C1   C  C     0   0.480  50.9559  31.4967  -0.4136
 Y41  C3   C  CR6   0  -0.080  50.6607  32.8429   0.1734
 Y41  C10  C  CR16  0  -0.302  49.6157  32.9299   1.0924
 Y41  C17  C  CR16  0  -0.256  49.2586  34.1670   1.6039
 Y41  C21  C  CR16  0  -0.321  49.9431  35.3030   1.2142
 Y41  C19  C  CR6   0   0.272  50.9994  35.2247   0.3008
 Y41  N01  N  NH2   0  -0.858  51.6323  36.3787  -0.1133
 Y41  C13  C  CR6   0   0.031  51.3703  33.9746  -0.2347
 Y41  C23  C  CH3   0  -0.758  52.5294  33.9239  -1.1896
 Y41  N2   N  NH1   0  -0.627  51.2116  30.5355   0.4920
 Y41  C6   C  CH1   0  -0.146  51.5220  29.1741   0.1150
 Y41  C01  C  CH3   0  -0.668  51.3160  28.2669   1.3256
 Y41  C5   C  CR6   0   0.117  52.9317  29.0322  -0.4323
 Y41  C8   C  CR66  0   0.097  53.2615  27.9453  -1.2949
 Y41  C14  C  CR16  0  -0.342  52.3112  26.9843  -1.7242
 Y41  C20  C  CR16  0  -0.249  52.6660  25.9550  -2.5537
 Y41  C22  C  CR16  0  -0.261  53.9944  25.8230  -3.0034
 Y41  C18  C  CR16  0  -0.310  54.9370  26.7326  -2.6119
 Y41  C11  C  CR66  0   0.110  54.6008  27.8071  -1.7546
 Y41  C12  C  CR16  0  -0.333  55.5792  28.7442  -1.3497
 Y41  C9   C  CR16  0  -0.242  55.2405  29.7756  -0.5219
 Y41  C4   C  CR16  0  -0.332  53.9147  29.9146  -0.0663
 Y41  H1   H  HCR6  0   0.253  49.0716  32.0418   1.3874
 Y41  H2   H  HCR6  0   0.254  48.4430  34.2473   2.3107
 Y41  H3   H  HCR6  0   0.258  49.6645  36.2689   1.6196
 Y41  H4   H  HNH2  0   0.381  51.5234  37.1708   0.5000
 Y41  H5   H  HNH2  0   0.383  52.5860  36.2867  -0.4235
 Y41  H6   H  HCH3  0   0.250  52.3058  34.4681  -2.1105
 Y41  H7   H  HCH3  0   0.239  53.4189  34.3864  -0.7543
 Y41  H8   H  HCH3  0   0.260  52.8071  32.9135  -1.4714
 Y41  H9   H  HNH1  0   0.407  51.2775  30.7917   1.4650
 Y41  H10  H  HCH1  0   0.257  50.8100  28.8901  -0.6631
 Y41  H11  H  HCH3  0   0.248  50.2864  28.3211   1.6800
 Y41  H12  H  HCH3  0   0.248  51.5327  27.2295   1.0744
 Y41  H13  H  HCH3  0   0.237  51.9806  28.5553   2.1419
 Y41  H14  H  HCR6  0   0.249  51.2815  27.0542  -1.4006
 Y41  H15  H  HCR6  0   0.259  51.9197  25.2364  -2.8666
 Y41  H16  H  HCR6  0   0.258  54.2628  25.0030  -3.6566
 Y41  H17  H  HCR6  0   0.256  55.9612  26.6417  -2.9536
 Y41  H18  H  HCR6  0   0.254  56.5962  28.6318  -1.7056
 Y41  H19  H  HCR6  0   0.256  55.9868  30.4947  -0.2100
 Y41  H20  H  HCR6  0   0.245  53.6780  30.7456   0.5863

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
 Y41  C22  C18  aromatic  1.367  0.020  1.367
 Y41  C22  C20  aromatic  1.409  0.020  1.409
 Y41  C18  C11  aromatic  1.415  0.020  1.415
 Y41  C20  C14  aromatic  1.369  0.020  1.369
 Y41  C11  C12  aromatic  1.414  0.020  1.414
 Y41  C11  C8   aromatic  1.423  0.020  1.423
 Y41  C14  C8   aromatic  1.418  0.020  1.418
 Y41  C12  C9   aromatic  1.365  0.020  1.365
 Y41  C8   C5   aromatic  1.426  0.020  1.426
 Y41  O7   C1   double    1.222  0.020  1.222
 Y41  C23  C13  single    1.503  0.020  1.503
 Y41  C9   C4   aromatic  1.409  0.020  1.409
 Y41  C1   C3   single    1.498  0.020  1.498
 Y41  C1   N2   single    1.345  0.020  1.345
 Y41  C13  C3   aromatic  1.397  0.020  1.397
 Y41  C13  C19  aromatic  1.410  0.020  1.410
 Y41  N01  C19  single    1.380  0.020  1.380
 Y41  C5   C4   aromatic  1.371  0.020  1.371
 Y41  C5   C6   single    1.519  0.020  1.519
 Y41  C3   C10  aromatic  1.394  0.020  1.394
 Y41  C19  C21  aromatic  1.399  0.020  1.399
 Y41  C10  C17  aromatic  1.385  0.020  1.385
 Y41  C21  C17  aromatic  1.382  0.020  1.382
 Y41  C6   N2   single    1.446  0.020  1.446
 Y41  C6   C01  single    1.527  0.020  1.527
 Y41  C10  H1   single    0.930  0.020  1.080
 Y41  C17  H2   single    0.930  0.020  1.080
 Y41  C21  H3   single    0.930  0.020  1.080
 Y41  N01  H4   single    0.890  0.020  1.040
 Y41  N01  H5   single    0.890  0.020  1.040
 Y41  C23  H6   single    0.970  0.020  1.090
 Y41  C23  H7   single    0.970  0.020  1.090
 Y41  C23  H8   single    0.970  0.020  1.090
 Y41  N2   H9   single    0.860  0.020  1.020
 Y41  C6   H10  single    0.970  0.020  1.090
 Y41  C01  H11  single    0.970  0.020  1.090
 Y41  C01  H12  single    0.970  0.020  1.090
 Y41  C01  H13  single    0.970  0.020  1.090
 Y41  C14  H14  single    0.930  0.020  1.080
 Y41  C20  H15  single    0.930  0.020  1.080
 Y41  C22  H16  single    0.930  0.020  1.080
 Y41  C18  H17  single    0.930  0.020  1.080
 Y41  C12  H18  single    0.930  0.020  1.080
 Y41  C9   H19  single    0.930  0.020  1.080
 Y41  C4   H20  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
 Y41  N2   C1   C3   114.57  3.000
 Y41  N2   C1   O7   122.76  3.000
 Y41  C3   C1   O7   122.65  3.000
 Y41  C13  C3   C10  121.52  3.000
 Y41  C10  C3   C1   117.52  3.000
 Y41  C13  C3   C1   120.91  3.000
 Y41  H1   C10  C17  120.16  3.000
 Y41  H1   C10  C3   120.34  3.000
 Y41  C17  C10  C3   119.49  3.000
 Y41  H2   C17  C21  119.75  3.000
 Y41  H2   C17  C10  120.11  3.000
 Y41  C21  C17  C10  120.14  3.000
 Y41  H3   C21  C19  119.22  3.000
 Y41  H3   C21  C17  119.98  3.000
 Y41  C19  C21  C17  120.80  3.000
 Y41  C13  C19  N01  120.47  3.000
 Y41  N01  C19  C21  119.71  3.000
 Y41  C13  C19  C21  119.76  3.000
 Y41  H5   N01  H4   111.20  3.000
 Y41  H5   N01  C19  116.77  3.000
 Y41  H4   N01  C19  115.16  3.000
 Y41  C23  C13  C19  118.31  3.000
 Y41  C19  C13  C3   118.29  3.000
 Y41  C23  C13  C3   123.38  3.000
 Y41  H8   C23  H7   106.81  3.000
 Y41  H8   C23  H6   107.29  3.000
 Y41  H7   C23  H6   106.94  3.000
 Y41  H8   C23  C13  113.19  3.000
 Y41  H7   C23  C13  111.13  3.000
 Y41  H6   C23  C13  111.16  3.000
 Y41  H9   N2   C6   118.47  3.000
 Y41  H9   N2   C1   118.72  3.000
 Y41  C6   N2   C1   122.54  3.000
 Y41  H10  C6   C5   108.91  3.000
 Y41  H10  C6   C01  108.81  3.000
 Y41  C5   C6   C01  110.82  3.000
 Y41  H10  C6   N2   106.89  3.000
 Y41  C01  C6   N2   108.89  3.000
 Y41  C5   C6   N2   112.39  3.000
 Y41  H13  C01  H12  107.64  3.000
 Y41  H13  C01  H11  108.59  3.000
 Y41  H12  C01  H11  108.07  3.000
 Y41  H13  C01  C6   110.73  3.000
 Y41  H12  C01  C6   110.87  3.000
 Y41  H11  C01  C6   110.83  3.000
 Y41  C4   C5   C8   119.09  3.000
 Y41  C4   C5   C6   120.61  3.000
 Y41  C8   C5   C6   120.25  3.000
 Y41  C11  C8   C14  117.85  3.000
 Y41  C14  C8   C5   122.99  3.000
 Y41  C11  C8   C5   119.16  3.000
 Y41  H14  C14  C20  118.47  3.000
 Y41  H14  C14  C8   120.24  3.000
 Y41  C20  C14  C8   121.29  3.000
 Y41  H15  C20  C22  119.73  3.000
 Y41  H15  C20  C14  119.72  3.000
 Y41  C22  C20  C14  120.55  3.000
 Y41  H16  C22  C18  120.40  3.000
 Y41  H16  C22  C20  119.83  3.000
 Y41  C18  C22  C20  119.77  3.000
 Y41  H17  C18  C11  118.64  3.000
 Y41  H17  C18  C22  120.37  3.000
 Y41  C11  C18  C22  120.99  3.000
 Y41  C12  C11  C18  120.81  3.000
 Y41  C12  C11  C8   119.63  3.000
 Y41  C18  C11  C8   119.55  3.000
 Y41  H18  C12  C9   120.70  3.000
 Y41  H18  C12  C11  119.13  3.000
 Y41  C9   C12  C11  120.17  3.000
 Y41  H19  C9   C4   119.35  3.000
 Y41  H19  C9   C12  120.37  3.000
 Y41  C4   C9   C12  120.28  3.000
 Y41  H20  C4   C9   118.45  3.000
 Y41  H20  C4   C5   119.88  3.000
 Y41  C9   C4   C5   121.67  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
 Y41  CONST_01  C21  C19  C13  C3     0.00   0.0  0
 Y41  CONST_02  C21  C17  C10  C3     0.00   0.0  0
 Y41  CONST_03  C19  C13  C3   C10    0.00   0.0  0
 Y41  CONST_04  C19  C21  C17  C10    0.00   0.0  0
 Y41  CONST_05  C13  C3   C10  C17    0.00   0.0  0
 Y41  CONST_06  C13  C19  C21  C17    0.00   0.0  0
 Y41  CONST_07  C18  C11  C8   C5   180.00   0.0  0
 Y41  CONST_08  C12  C11  C8   C5     0.00   0.0  0
 Y41  CONST_09  C20  C14  C8   C5   180.00   0.0  0
 Y41  CONST_10  C12  C9   C4   C5     0.00   0.0  0
 Y41  CONST_11  C22  C18  C11  C8     0.00   0.0  0
 Y41  CONST_12  C9   C12  C11  C8     0.00   0.0  0
 Y41  CONST_13  C22  C20  C14  C8     0.00   0.0  0
 Y41  CONST_14  C9   C4   C5   C8     0.00   0.0  0
 Y41  CONST_15  C18  C22  C20  C14    0.00   0.0  0
 Y41  CONST_16  C18  C11  C8   C14    0.00   0.0  0
 Y41  CONST_17  C12  C11  C8   C14  180.00   0.0  0
 Y41  CONST_18  C4   C5   C8   C14  180.00   0.0  0
 Y41  CONST_19  C11  C18  C22  C20    0.00   0.0  0
 Y41  CONST_20  C11  C8   C14  C20    0.00   0.0  0
 Y41  CONST_21  C12  C11  C18  C22  180.00   0.0  0
 Y41  CONST_22  C9   C12  C11  C18  180.00   0.0  0
 Y41  CONST_23  C4   C9   C12  C11    0.00   0.0  0
 Y41  CONST_24  C4   C5   C8   C11    0.00   0.0  0
 Y41  CONST_25  C19  C13  C3   C1   180.00   0.0  0
 Y41  CONST_26  C17  C10  C3   C1   180.00   0.0  0
 Y41  CONST_27  N01  C19  C13  C3   180.00   0.0  0
 Y41  CONST_28  C23  C13  C3   C10  180.00   0.0  0
 Y41  CONST_29  N01  C19  C21  C17  180.00   0.0  0
 Y41  CONST_30  C23  C13  C19  C21  180.00   0.0  0
 Y41  CONST_31  C11  C8   C5   C6   180.00   0.0  0
 Y41  CONST_32  C14  C8   C5   C6     0.00   0.0  0
 Y41  CONST_33  C9   C4   C5   C6   180.00   0.0  0
 Y41  CONST_34  H2   C17  C10  C3   180.00   0.0  0
 Y41  CONST_35  H3   C21  C17  C10  180.00   0.0  0
 Y41  CONST_36  H1   C10  C17  C21  180.00   0.0  0
 Y41  CONST_37  H14  C14  C8   C5     0.00   0.0  0
 Y41  CONST_38  H19  C9   C4   C5   180.00   0.0  0
 Y41  CONST_39  H17  C18  C11  C8   180.00   0.0  0
 Y41  CONST_40  H18  C12  C11  C8   180.00   0.0  0
 Y41  CONST_41  H15  C20  C14  C8   180.00   0.0  0
 Y41  CONST_42  H20  C4   C5   C8   180.00   0.0  0
 Y41  CONST_43  H16  C22  C20  C14  180.00   0.0  0
 Y41  CONST_46  C6   N2   C1   C3   180.00   0.0  0
 Y41  CONST_47  H9   N2   C1   C3     0.00   0.0  0
 Y41  CONST_48  C6   N2   C1   O7     0.00   0.0  0
 Y41  Var_01    C13  C3   C1   O7   -54.82  30.0  2
 Y41  Var_02    H6   C23  C13  C3   116.47  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
 Y41  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
 Y41  plan-1  C1   0.020
 Y41  plan-1  C3   0.020
 Y41  plan-1  C10  0.020
 Y41  plan-1  C17  0.020
 Y41  plan-1  C21  0.020
 Y41  plan-1  C19  0.020
 Y41  plan-1  N01  0.020
 Y41  plan-1  C13  0.020
 Y41  plan-1  C23  0.020
 Y41  plan-1  H1   0.020
 Y41  plan-1  H2   0.020
 Y41  plan-1  H3   0.020
 Y41  plan-2  C6   0.020
 Y41  plan-2  C5   0.020
 Y41  plan-2  C8   0.020
 Y41  plan-2  C14  0.020
 Y41  plan-2  C20  0.020
 Y41  plan-2  C22  0.020
 Y41  plan-2  C18  0.020
 Y41  plan-2  C11  0.020
 Y41  plan-2  C12  0.020
 Y41  plan-2  C9   0.020
 Y41  plan-2  C4   0.020
 Y41  plan-2  H14  0.020
 Y41  plan-2  H15  0.020
 Y41  plan-2  H16  0.020
 Y41  plan-2  H17  0.020
 Y41  plan-2  H18  0.020
 Y41  plan-2  H19  0.020
 Y41  plan-2  H20  0.020
 Y41  plan-3  O7   0.020
 Y41  plan-3  C1   0.020
 Y41  plan-3  C3   0.020
 Y41  plan-3  N2   0.020
 Y41  plan-3  C6   0.020
 Y41  plan-3  H9   0.020
 Y41  plan-4  C19  0.020
 Y41  plan-4  N01  0.020
 Y41  plan-4  H4   0.020
 Y41  plan-4  H5   0.020

