# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 21:10:36 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: N-[(1R)-1-(naphthalen-1-yl)ethyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(C)=O)c1cccc2ccccc12
#
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
 T4M  T4M  N-[(1R)-1-(naphthalen-1-yl)ethyl]acetamide  ligand  31  16  .  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_T4M
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
 T4M  C4   C  CR6   0   0.118  -0.0779  -0.3525   0.3035
 T4M  C5   C  CR16  0  -0.334  -0.2020  -1.7110   0.1693
 T4M  C6   C  CR16  0  -0.242   0.8872  -2.5201  -0.2106
 T4M  C7   C  CR16  0  -0.332   2.1071  -1.9599  -0.4594
 T4M  C8   C  CR66  0   0.109   2.2862  -0.5631  -0.3318
 T4M  C10  C  CR16  0  -0.261   3.7259   1.3800  -0.4570
 T4M  C13  C  CR66  0   0.098   1.1894   0.2550   0.0586
 T4M  N    N  NH1   0  -0.633  -2.5304  -0.1061   0.4222
 T4M  C    C  CH3   0  -0.670  -1.2042   0.7188   2.2688
 T4M  O    O  O     0  -0.498  -2.4576   0.4580  -1.7562
 T4M  C1   C  CH1   0  -0.141  -1.2571   0.4885   0.7606
 T4M  C11  C  CR16  0  -0.248   2.6464   2.1957  -0.0648
 T4M  C12  C  CR16  0  -0.342   1.4166   1.6492   0.1856
 T4M  C3   C  CH3   0  -0.777  -4.3530  -0.7945  -1.0059
 T4M  C9   C  CR16  0  -0.310   3.5448   0.0312  -0.5861
 T4M  H7   H  HCR6  0   0.245  -1.1573  -2.1862   0.3526
 T4M  H8   H  HCR6  0   0.256   0.7463  -3.5889  -0.3046
 T4M  H9   H  HCR6  0   0.253   2.9495  -2.5742  -0.7543
 T4M  H11  H  HCR6  0   0.258   4.6932   1.8230  -0.6550
 T4M  H4   H  HNH1  0   0.401  -3.0229  -0.6125   1.1400
 T4M  H1   H  HCH3  0   0.236  -1.3109  -0.2221   2.8116
 T4M  H2   H  HCH3  0   0.247  -0.2510   1.1580   2.5582
 T4M  H    H  HCH3  0   0.248  -1.9989   1.3945   2.5860
 T4M  H3   H  HCH1  0   0.254  -1.2146   1.4580   0.2604
 T4M  H12  H  HCR6  0   0.259   2.7907   3.2632   0.0391
 T4M  H13  H  HCR6  0   0.248   0.6131   2.3080   0.4860
 T4M  H14  H  HCH3  0   0.248  -4.7367  -1.2458  -0.0931
 T4M  H6   H  HCH3  0   0.266  -5.0922  -0.0849  -1.3775
 T4M  H5   H  HCH3  0   0.266  -4.2457  -1.5749  -1.7589
 T4M  H10  H  HCR6  0   0.255   4.3692  -0.6048  -0.8859
 T4M  C2   C  C     0   0.522  -3.0313  -0.0917  -0.8265

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
 T4M  C1   C    single    1.527  0.020  1.527
 T4M  N    C1   single    1.445  0.020  1.445
 T4M  C2   N    single    1.346  0.020  1.346
 T4M  C2   O    double    1.223  0.020  1.223
 T4M  C3   C2   single    1.508  0.020  1.508
 T4M  C1   C4   single    1.519  0.020  1.519
 T4M  C4   C5   aromatic  1.371  0.020  1.371
 T4M  C6   C5   aromatic  1.409  0.020  1.409
 T4M  C7   C6   aromatic  1.365  0.020  1.365
 T4M  C8   C7   aromatic  1.414  0.020  1.414
 T4M  C9   C8   aromatic  1.415  0.020  1.415
 T4M  C10  C9   aromatic  1.367  0.020  1.367
 T4M  C11  C10  aromatic  1.409  0.020  1.409
 T4M  C12  C11  aromatic  1.369  0.020  1.369
 T4M  C13  C12  aromatic  1.418  0.020  1.418
 T4M  C4   C13  aromatic  1.427  0.020  1.427
 T4M  C13  C8   aromatic  1.423  0.020  1.423
 T4M  C5   H7   single    0.930  0.020  1.080
 T4M  C6   H8   single    0.930  0.020  1.080
 T4M  C7   H9   single    0.930  0.020  1.080
 T4M  C10  H11  single    0.930  0.020  1.080
 T4M  N    H4   single    0.860  0.020  1.020
 T4M  C    H1   single    0.970  0.020  1.090
 T4M  C    H2   single    0.970  0.020  1.090
 T4M  C    H    single    0.970  0.020  1.090
 T4M  C1   H3   single    0.970  0.020  1.090
 T4M  C11  H12  single    0.930  0.020  1.080
 T4M  C12  H13  single    0.930  0.020  1.080
 T4M  C3   H14  single    0.970  0.020  1.090
 T4M  C3   H6   single    0.970  0.020  1.090
 T4M  C3   H5   single    0.970  0.020  1.090
 T4M  C9   H10  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
 T4M  C1   C4   C13  120.37  3.000
 T4M  C13  C4   C5   119.06  3.000
 T4M  C1   C4   C5   120.53  3.000
 T4M  H7   C5   C6   118.41  3.000
 T4M  H7   C5   C4   119.89  3.000
 T4M  C6   C5   C4   121.70  3.000
 T4M  H8   C6   C7   120.38  3.000
 T4M  H8   C6   C5   119.33  3.000
 T4M  C7   C6   C5   120.29  3.000
 T4M  H9   C7   C8   119.09  3.000
 T4M  H9   C7   C6   120.78  3.000
 T4M  C8   C7   C6   120.13  3.000
 T4M  C9   C8   C13  119.57  3.000
 T4M  C13  C8   C7   119.68  3.000
 T4M  C9   C8   C7   120.75  3.000
 T4M  H11  C10  C9   120.33  3.000
 T4M  H11  C10  C11  119.93  3.000
 T4M  C9   C10  C11  119.74  3.000
 T4M  C12  C13  C8   117.79  3.000
 T4M  C8   C13  C4   119.14  3.000
 T4M  C12  C13  C4   123.06  3.000
 T4M  H4   N    C2   118.99  3.000
 T4M  H4   N    C1   118.09  3.000
 T4M  C2   N    C1   122.74  3.000
 T4M  H    C    H2   108.11  3.000
 T4M  H    C    H1   108.56  3.000
 T4M  H2   C    H1   107.53  3.000
 T4M  H    C    C1   110.84  3.000
 T4M  H2   C    C1   110.72  3.000
 T4M  H1   C    C1   110.97  3.000
 T4M  H3   C1   C    108.50  3.000
 T4M  H3   C1   N    107.00  3.000
 T4M  C    C1   N    108.90  3.000
 T4M  H3   C1   C4   108.88  3.000
 T4M  N    C1   C4   112.69  3.000
 T4M  C    C1   C4   110.73  3.000
 T4M  H12  C11  C12  119.74  3.000
 T4M  H12  C11  C10  119.72  3.000
 T4M  C12  C11  C10  120.55  3.000
 T4M  H13  C12  C11  118.36  3.000
 T4M  H13  C12  C13  120.30  3.000
 T4M  C11  C12  C13  121.33  3.000
 T4M  H5   C3   H6   107.30  3.000
 T4M  H5   C3   H14  108.50  3.000
 T4M  H6   C3   H14  108.47  3.000
 T4M  H5   C3   C2   109.25  3.000
 T4M  H6   C3   C2   109.37  3.000
 T4M  H14  C3   C2   113.75  3.000
 T4M  H10  C9   C10  120.30  3.000
 T4M  H10  C9   C8   118.69  3.000
 T4M  C10  C9   C8   121.02  3.000
 T4M  C3   C2   O    122.03  3.000
 T4M  C3   C2   N    115.58  3.000
 T4M  O    C2   N    122.39  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
 T4M  CONST_01  C7   C6   C5   C4     0.00   0.0  0
 T4M  CONST_02  C11  C12  C13  C4   180.00   0.0  0
 T4M  CONST_03  C7   C8   C13  C4     0.00   0.0  0
 T4M  CONST_04  C9   C8   C13  C4   180.00   0.0  0
 T4M  CONST_05  C12  C13  C4   C5   180.00   0.0  0
 T4M  CONST_06  C8   C13  C4   C5     0.00   0.0  0
 T4M  CONST_07  C8   C7   C6   C5     0.00   0.0  0
 T4M  CONST_08  C13  C4   C5   C6     0.00   0.0  0
 T4M  CONST_09  C9   C8   C7   C6   180.00   0.0  0
 T4M  CONST_10  C13  C8   C7   C6     0.00   0.0  0
 T4M  CONST_11  C10  C9   C8   C7   180.00   0.0  0
 T4M  CONST_12  C12  C13  C8   C7   180.00   0.0  0
 T4M  CONST_13  C11  C10  C9   C8     0.00   0.0  0
 T4M  CONST_14  C11  C12  C13  C8     0.00   0.0  0
 T4M  CONST_15  C13  C8   C9   C10    0.00   0.0  0
 T4M  CONST_16  C13  C12  C11  C10    0.00   0.0  0
 T4M  CONST_17  C9   C10  C11  C12    0.00   0.0  0
 T4M  CONST_18  C9   C8   C13  C12    0.00   0.0  0
 T4M  CONST_19  C1   C4   C5   C6   180.00   0.0  0
 T4M  CONST_20  C1   C4   C13  C8   180.00   0.0  0
 T4M  CONST_21  C12  C13  C4   C1     0.00   0.0  0
 T4M  CONST_22  H8   C6   C5   C4   180.00   0.0  0
 T4M  CONST_23  H13  C12  C13  C4     0.00   0.0  0
 T4M  CONST_24  H9   C7   C6   C5   180.00   0.0  0
 T4M  CONST_25  H7   C5   C6   C7   180.00   0.0  0
 T4M  CONST_26  H10  C9   C8   C7     0.00   0.0  0
 T4M  CONST_27  H11  C10  C9   C8   180.00   0.0  0
 T4M  CONST_28  H12  C11  C12  C13  180.00   0.0  0
 T4M  CONST_29  C1   N    C2   O      0.00   0.0  0
 T4M  CONST_30  C3   C2   N    C1   180.00   0.0  0
 T4M  CONST_31  H4   N    C2   O    180.00   0.0  0
 T4M  Var_01    H14  C3   C2   N     -0.88  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
 T4M  chir_01  C1  C  N  C4  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
 T4M  plan-1  C4   0.020
 T4M  plan-1  C5   0.020
 T4M  plan-1  C6   0.020
 T4M  plan-1  C7   0.020
 T4M  plan-1  C8   0.020
 T4M  plan-1  C10  0.020
 T4M  plan-1  C13  0.020
 T4M  plan-1  C1   0.020
 T4M  plan-1  C11  0.020
 T4M  plan-1  C12  0.020
 T4M  plan-1  C9   0.020
 T4M  plan-1  H7   0.020
 T4M  plan-1  H8   0.020
 T4M  plan-1  H9   0.020
 T4M  plan-1  H11  0.020
 T4M  plan-1  H12  0.020
 T4M  plan-1  H13  0.020
 T4M  plan-1  H10  0.020
 T4M  plan-2  N    0.020
 T4M  plan-2  O    0.020
 T4M  plan-2  C1   0.020
 T4M  plan-2  C3   0.020
 T4M  plan-2  H4   0.020
 T4M  plan-2  C2   0.020

