# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 07:50:31 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)c1cc(N)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
 TTT  TTT  5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide  ligand  43  23  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TTT
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
 TTT  C1    C  C     0   0.496  -1.2510   0.8953  -0.9786
 TTT  C3    C  CR6   0  -0.054  -2.4325   0.5296  -0.1359
 TTT  C8    C  CR66  0   0.105   2.5708   0.0545  -0.0293
 TTT  C9    C  CR16  0  -0.240   3.5851  -2.4244  -0.8677
 TTT  C10   C  CR6   0   0.061  -2.8437   1.3691   0.9052
 TTT  C11   C  CR66  0   0.109   3.6254  -0.5787   0.6827
 TTT  C12   C  CR16  0  -0.327   4.1182  -1.8284   0.2375
 TTT  C13   C  CR16  0  -0.345  -3.1208  -0.6411  -0.4354
 TTT  C14   C  CR16  0  -0.333   2.1102   1.3089   0.4435
 TTT  C16   C  CH3   0  -0.727  -2.1168   2.6304   1.2806
 TTT  C19   C  CR6   0   0.302  -4.2639  -1.0142   0.2768
 TTT  C20   C  CR16  0  -0.248   2.6579   1.8914   1.5552
 TTT  C21   C  CR16  0  -0.309  -4.6737  -0.1832   1.3223
 TTT  C22   C  CR16  0  -0.261   3.6971   1.2546   2.2612
 TTT  O7    O  O     0  -0.494  -1.1432   1.9989  -1.4973
 TTT  C17   C  CR16  0  -0.294  -3.9687   0.9705   1.6222
 TTT  N01   N  NH2   0  -0.863  -4.9898  -2.1323  -0.0771
 TTT  N2    N  NH1   0  -0.612  -0.3276  -0.0719  -1.1063
 TTT  C6    C  CH1   0  -0.185   0.8706   0.0534  -1.9229
 TTT  C01   C  CH3   0  -0.662   0.6235  -0.4823  -3.3280
 TTT  C5    C  CR6   0   0.104   2.0226  -0.5920  -1.1807
 TTT  C18   C  CR16  0  -0.310   4.1706   0.0471   1.8284
 TTT  C4    C  CR16  0  -0.342   2.5345  -1.8012  -1.5725
 TTT  H12   H  HCR6  0   0.256   4.9209  -2.3037   0.7882
 TTT  H13   H  HCR6  0   0.259  -2.7818  -1.2678  -1.2531
 TTT  H14   H  HCR6  0   0.247   1.3239   1.8356  -0.0795
 TTT  H16   H  HCH3  0   0.245  -2.2696   3.4242   0.5495
 TTT  H16A  H  HCH3  0   0.240  -2.4685   2.9973   2.2445
 TTT  H16B  H  HCH3  0   0.231  -1.0397   2.4770   1.3659
 TTT  H20   H  HCR6  0   0.260   2.2906   2.8519   1.8926
 TTT  H21   H  HCR6  0   0.258  -5.5501  -0.4430   1.9048
 TTT  H22   H  HCR6  0   0.259   4.1194   1.7254   3.1393
 TTT  H17   H  HCR6  0   0.248  -4.3095   1.5832   2.4490
 TTT  HN01  H  HNH2  0   0.378  -4.4880  -2.8265  -0.6076
 TTT  HN0A  H  HNH2  0   0.379  -5.5304  -2.5521   0.6620
 TTT  HN2   H  HNH1  0   0.406  -0.4764  -0.9494  -0.6319
 TTT  H6    H  HCH1  0   0.266   1.0810   1.1199  -2.0190
 TTT  H01   H  HCH3  0   0.250  -0.1674   0.0996  -3.8001
 TTT  H01A  H  HCH3  0   0.240   1.5182  -0.3981  -3.9446
 TTT  H01B  H  HCH3  0   0.230   0.3076  -1.5256  -3.3185
 TTT  H18   H  HCR6  0   0.256   4.9726  -0.4496   2.3614
 TTT  H4    H  HCR6  0   0.259   2.1344  -2.3058  -2.4420
 TTT  H9    H  HCR6  0   0.259   3.9604  -3.3800  -1.2093

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
 TTT  C1   C3    single    1.497  0.020  1.497
 TTT  C1   O7    double    1.224  0.020  1.224
 TTT  C1   N2    single    1.343  0.020  1.343
 TTT  C3   C10   aromatic  1.399  0.020  1.399
 TTT  C3   C13   aromatic  1.391  0.020  1.391
 TTT  C8   C11   aromatic  1.421  0.020  1.421
 TTT  C8   C14   aromatic  1.417  0.020  1.417
 TTT  C8   C5    aromatic  1.430  0.020  1.430
 TTT  C9   C12   aromatic  1.364  0.020  1.364
 TTT  C9   C4    aromatic  1.410  0.020  1.410
 TTT  C10  C16   single    1.503  0.020  1.503
 TTT  C10  C17   aromatic  1.392  0.020  1.392
 TTT  C11  C12   aromatic  1.415  0.020  1.415
 TTT  C11  C18   aromatic  1.415  0.020  1.415
 TTT  C13  C19   aromatic  1.398  0.020  1.398
 TTT  C14  C20   aromatic  1.369  0.020  1.369
 TTT  C19  C21   aromatic  1.397  0.020  1.397
 TTT  C19  N01   single    1.379  0.020  1.379
 TTT  C20  C22   aromatic  1.408  0.020  1.408
 TTT  C21  C17   aromatic  1.385  0.020  1.385
 TTT  C22  C18   aromatic  1.367  0.020  1.367
 TTT  N2   C6    single    1.455  0.020  1.455
 TTT  C6   C01   single    1.524  0.020  1.524
 TTT  C6   C5    single    1.515  0.020  1.515
 TTT  C5   C4    aromatic  1.370  0.020  1.370
 TTT  C9   H9    single    0.930  0.020  1.080
 TTT  C12  H12   single    0.930  0.020  1.080
 TTT  C13  H13   single    0.930  0.020  1.080
 TTT  C14  H14   single    0.930  0.020  1.080
 TTT  C16  H16   single    0.970  0.020  1.090
 TTT  C16  H16A  single    0.970  0.020  1.090
 TTT  C16  H16B  single    0.970  0.020  1.090
 TTT  C20  H20   single    0.930  0.020  1.080
 TTT  C21  H21   single    0.930  0.020  1.080
 TTT  C22  H22   single    0.930  0.020  1.080
 TTT  C17  H17   single    0.930  0.020  1.080
 TTT  N01  HN01  single    0.890  0.020  1.040
 TTT  N01  HN0A  single    0.890  0.020  1.040
 TTT  N2   HN2   single    0.860  0.020  1.020
 TTT  C6   H6    single    0.970  0.020  1.090
 TTT  C01  H01   single    0.970  0.020  1.090
 TTT  C01  H01A  single    0.970  0.020  1.090
 TTT  C01  H01B  single    0.970  0.020  1.090
 TTT  C18  H18   single    0.930  0.020  1.080
 TTT  C4   H4    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
 TTT  N2    C1   O7    123.25  3.000
 TTT  N2    C1   C3    114.85  3.000
 TTT  O7    C1   C3    121.89  3.000
 TTT  C13   C3   C10   121.32  3.000
 TTT  C13   C3   C1    118.37  3.000
 TTT  C10   C3   C1    120.29  3.000
 TTT  C5    C8   C14   122.97  3.000
 TTT  C5    C8   C11   119.11  3.000
 TTT  C14   C8   C11   117.92  3.000
 TTT  H9    C9   C4    119.39  3.000
 TTT  H9    C9   C12   120.41  3.000
 TTT  C4    C9   C12   120.20  3.000
 TTT  C17   C10  C16   120.15  3.000
 TTT  C17   C10  C3    116.67  3.000
 TTT  C16   C10  C3    123.17  3.000
 TTT  C18   C11  C12   120.74  3.000
 TTT  C18   C11  C8    119.64  3.000
 TTT  C12   C11  C8    119.62  3.000
 TTT  H12   C12  C11   119.05  3.000
 TTT  H12   C12  C9    120.65  3.000
 TTT  C11   C12  C9    120.30  3.000
 TTT  H13   C13  C19   119.05  3.000
 TTT  H13   C13  C3    119.61  3.000
 TTT  C19   C13  C3    121.32  3.000
 TTT  H14   C14  C20   118.45  3.000
 TTT  H14   C14  C8    120.40  3.000
 TTT  C20   C14  C8    121.15  3.000
 TTT  H16B  C16  H16A  107.26  3.000
 TTT  H16B  C16  H16   107.05  3.000
 TTT  H16A  C16  H16   107.64  3.000
 TTT  H16B  C16  C10   112.26  3.000
 TTT  H16A  C16  C10   110.33  3.000
 TTT  H16   C16  C10   112.07  3.000
 TTT  N01   C19  C21   121.32  3.000
 TTT  N01   C19  C13   121.08  3.000
 TTT  C21   C19  C13   117.55  3.000
 TTT  H20   C20  C22   119.69  3.000
 TTT  H20   C20  C14   119.66  3.000
 TTT  C22   C20  C14   120.65  3.000
 TTT  H21   C21  C17   119.66  3.000
 TTT  H21   C21  C19   119.79  3.000
 TTT  C17   C21  C19   120.55  3.000
 TTT  H22   C22  C18   120.39  3.000
 TTT  H22   C22  C20   119.87  3.000
 TTT  C18   C22  C20   119.74  3.000
 TTT  H17   C17  C21   118.42  3.000
 TTT  H17   C17  C10   119.01  3.000
 TTT  C21   C17  C10   122.57  3.000
 TTT  HN0A  N01  HN01  111.49  3.000
 TTT  HN0A  N01  C19   115.59  3.000
 TTT  HN01  N01  C19   115.56  3.000
 TTT  HN2   N2   C6    117.41  3.000
 TTT  HN2   N2   C1    118.70  3.000
 TTT  C6    N2   C1    123.87  3.000
 TTT  H6    C6   C5    108.24  3.000
 TTT  H6    C6   C01   107.07  3.000
 TTT  C5    C6   C01   115.17  3.000
 TTT  H6    C6   N2    107.00  3.000
 TTT  C5    C6   N2    108.33  3.000
 TTT  C01   C6   N2    110.71  3.000
 TTT  H01B  C01  H01A  108.47  3.000
 TTT  H01B  C01  H01   107.73  3.000
 TTT  H01A  C01  H01   108.03  3.000
 TTT  H01B  C01  C6    112.05  3.000
 TTT  H01A  C01  C6    111.19  3.000
 TTT  H01   C01  C6    109.24  3.000
 TTT  C4    C5   C6    121.33  3.000
 TTT  C4    C5   C8    119.08  3.000
 TTT  C6    C5   C8    119.57  3.000
 TTT  H18   C18  C22   120.36  3.000
 TTT  H18   C18  C11   118.74  3.000
 TTT  C22   C18  C11   120.90  3.000
 TTT  H4    C4   C5    120.21  3.000
 TTT  H4    C4   C9    118.10  3.000
 TTT  C5    C4   C9    121.69  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
 TTT  CONST_01  C21  C17  C10  C3     0.00   0.0  0
 TTT  CONST_02  C21  C19  C13  C3     0.00   0.0  0
 TTT  CONST_03  C9   C12  C11  C8     0.00   0.0  0
 TTT  CONST_04  C22  C18  C11  C8     0.00   0.0  0
 TTT  CONST_05  C22  C20  C14  C8     0.00   0.0  0
 TTT  CONST_06  C9   C4   C5   C8     0.00   0.0  0
 TTT  CONST_07  C18  C11  C12  C9   180.00   0.0  0
 TTT  CONST_08  C19  C13  C3   C10    0.00   0.0  0
 TTT  CONST_09  C19  C21  C17  C10    0.00   0.0  0
 TTT  CONST_10  C20  C14  C8   C11    0.00   0.0  0
 TTT  CONST_11  C4   C5   C8   C11    0.00   0.0  0
 TTT  CONST_12  C4   C9   C12  C11    0.00   0.0  0
 TTT  CONST_13  C20  C22  C18  C11    0.00   0.0  0
 TTT  CONST_14  C5   C4   C9   C12    0.00   0.0  0
 TTT  CONST_15  C14  C8   C11  C12  180.00   0.0  0
 TTT  CONST_16  C5   C8   C11  C12    0.00   0.0  0
 TTT  CONST_17  C22  C18  C11  C12  180.00   0.0  0
 TTT  CONST_18  C17  C10  C3   C13    0.00   0.0  0
 TTT  CONST_19  C17  C21  C19  C13    0.00   0.0  0
 TTT  CONST_20  C18  C11  C8   C14    0.00   0.0  0
 TTT  CONST_21  C4   C5   C8   C14  180.00   0.0  0
 TTT  CONST_22  C18  C22  C20  C14    0.00   0.0  0
 TTT  CONST_23  C5   C8   C14  C20  180.00   0.0  0
 TTT  CONST_24  C18  C11  C8   C5   180.00   0.0  0
 TTT  CONST_25  C17  C10  C3   C1   180.00   0.0  0
 TTT  CONST_26  C19  C13  C3   C1   180.00   0.0  0
 TTT  CONST_27  N01  C19  C13  C3   180.00   0.0  0
 TTT  CONST_28  C6   C5   C4   C9   180.00   0.0  0
 TTT  CONST_29  C6   C5   C8   C11  180.00   0.0  0
 TTT  CONST_30  C16  C10  C3   C13  180.00   0.0  0
 TTT  CONST_31  C6   C5   C8   C14    0.00   0.0  0
 TTT  CONST_32  C21  C17  C10  C16  180.00   0.0  0
 TTT  CONST_33  N01  C19  C21  C17  180.00   0.0  0
 TTT  CONST_34  H17  C17  C10  C3   180.00   0.0  0
 TTT  CONST_35  H12  C12  C11  C8   180.00   0.0  0
 TTT  CONST_36  H18  C18  C11  C8   180.00   0.0  0
 TTT  CONST_37  H20  C20  C14  C8   180.00   0.0  0
 TTT  CONST_38  H4   C4   C5   C8   180.00   0.0  0
 TTT  CONST_39  H13  C13  C3   C10  180.00   0.0  0
 TTT  CONST_40  H21  C21  C17  C10  180.00   0.0  0
 TTT  CONST_41  H14  C14  C8   C11  180.00   0.0  0
 TTT  CONST_42  H9   C9   C12  C11  180.00   0.0  0
 TTT  CONST_43  H22  C22  C18  C11  180.00   0.0  0
 TTT  CONST_46  C6   N2   C1   C3   180.00   0.0  0
 TTT  CONST_47  HN2  N2   C1   C3     0.00   0.0  0
 TTT  CONST_48  C6   N2   C1   O7     0.00   0.0  0
 TTT  Var_01    O7   C1   C3   C10  -50.51  30.0  2
 TTT  Var_02    H16  C16  C10  C3    73.02  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
 TTT  chir_01  C6  N2  C01  C5  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
 TTT  plan-1  C1    0.020
 TTT  plan-1  C3    0.020
 TTT  plan-1  C10   0.020
 TTT  plan-1  C13   0.020
 TTT  plan-1  C16   0.020
 TTT  plan-1  C19   0.020
 TTT  plan-1  C21   0.020
 TTT  plan-1  C17   0.020
 TTT  plan-1  N01   0.020
 TTT  plan-1  H13   0.020
 TTT  plan-1  H21   0.020
 TTT  plan-1  H17   0.020
 TTT  plan-2  C8    0.020
 TTT  plan-2  C9    0.020
 TTT  plan-2  C11   0.020
 TTT  plan-2  C12   0.020
 TTT  plan-2  C14   0.020
 TTT  plan-2  C20   0.020
 TTT  plan-2  C22   0.020
 TTT  plan-2  C6    0.020
 TTT  plan-2  C5    0.020
 TTT  plan-2  C18   0.020
 TTT  plan-2  C4    0.020
 TTT  plan-2  H12   0.020
 TTT  plan-2  H14   0.020
 TTT  plan-2  H20   0.020
 TTT  plan-2  H22   0.020
 TTT  plan-2  H18   0.020
 TTT  plan-2  H4    0.020
 TTT  plan-2  H9    0.020
 TTT  plan-3  C1    0.020
 TTT  plan-3  C3    0.020
 TTT  plan-3  O7    0.020
 TTT  plan-3  N2    0.020
 TTT  plan-3  C6    0.020
 TTT  plan-3  HN2   0.020
 TTT  plan-4  C19   0.020
 TTT  plan-4  N01   0.020
 TTT  plan-4  HN01  0.020
 TTT  plan-4  HN0A  0.020

