# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 04:16:08 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: N-[(1R)-1-(naphthalen-1-yl)ethyl]-3-[3-(trifluoromethyl)phenyl]propan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NCCCc1cccc(c1)C(F)(F)F)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
 YP4  YP4  N-[(1R)-1-(naphthalen-1-yl)ethyl]-3-[3-(trifluoromethyl)phenyl]propan-1-amine  ligand  48  26  .  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_YP4
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
 YP4  C1   C  CH3   0  -0.650  211.7494  208.8861  229.4459
 YP4  C4   C  CH2   0  -0.428  210.2370  204.7461  228.9607
 YP4  C5   C  CH2   0  -0.509  210.1883  203.2183  228.9940
 YP4  C6   C  CR6   0   0.157  208.9234  202.7166  229.6286
 YP4  N    N  NH1   0  -0.577  211.6268  206.7075  228.3766
 YP4  CA   C  CH1   0  -0.206  211.7388  207.3772  229.6660
 YP4  CB   C  CR6   0   0.122  212.9438  206.9259  230.4857
 YP4  CG   C  CR66  0   0.089  212.8226  206.2228  231.7222
 YP4  CD1  C  CR66  0   0.108  214.0044  205.7931  232.3945
 YP4  CD2  C  CR16  0  -0.351  211.5770  205.9137  232.3300
 YP4  CE1  C  CR16  0  -0.305  213.8988  205.0797  233.6130
 YP4  CE2  C  CR16  0  -0.244  211.5061  205.2156  233.5047
 YP4  CZ   C  CR16  0  -0.263  212.6799  204.7902  234.1577
 YP4  C7   C  CR16  0  -0.344  208.8716  202.4717  230.9969
 YP4  C8   C  CR6   0  -0.173  207.6907  202.0533  231.6002
 YP4  C9   C  CR16  0  -0.299  206.5413  201.8735  230.8406
 YP4  C10  C  CR16  0  -0.222  206.5861  202.1190  229.4760
 YP4  C11  C  CR16  0  -0.300  207.7654  202.5348  228.8769
 YP4  C12  C  CT    0   1.049  207.6867  201.7258  233.0603
 YP4  C14  C  CR16  0  -0.337  214.2008  207.1656  229.9847
 YP4  C15  C  CR16  0  -0.239  215.3657  206.7499  230.6532
 YP4  C16  C  CR16  0  -0.336  215.2708  206.0744  231.8372
 YP4  F1   F  F     0  -0.306  206.4672  201.8139  233.6028
 YP4  F2   F  F     0  -0.316  208.1152  200.4717  233.2812
 YP4  F3   F  F     0  -0.309  208.4876  202.5319  233.7695
 YP4  H1   H  HCH3  0   0.233  211.7917  209.4192  230.3955
 YP4  H2   H  HCH3  0   0.224  212.6063  209.2022  228.8480
 YP4  H3   H  HCH3  0   0.234  210.8442  209.1946  228.9224
 YP4  H4   H  HCH2  0   0.230  211.7014  204.8899  227.4060
 YP4  H5   H  HCH2  0   0.193  212.3826  204.8138  229.0201
 YP4  H6   H  HCH2  0   0.228  210.0611  205.1188  229.9727
 YP4  H7   H  HCH2  0   0.228  209.4221  205.1321  228.3422
 YP4  H8   H  HCH2  0   0.245  210.2761  202.8291  227.9762
 YP4  H9   H  HCH2  0   0.243  211.0513  202.8416  229.5495
 YP4  H10  H  HNH1  0   0.346  212.4027  206.9883  227.7889
 YP4  H12  H  HCH1  0   0.243  210.8264  207.1557  230.2183
 YP4  H13  H  HCR6  0   0.250  210.6523  206.2320  231.8707
 YP4  H14  H  HCR6  0   0.253  214.8091  204.7619  234.1075
 YP4  H15  H  HCR6  0   0.255  210.5393  204.9898  233.9360
 YP4  H16  H  HCR6  0   0.255  212.6120  204.2403  235.0873
 YP4  H17  H  HCR6  0   0.262  209.7710  202.6121  231.5855
 YP4  H18  H  HCR6  0   0.269  205.6155  201.5444  231.2927
 YP4  H19  H  HCR6  0   0.264  205.6949  201.9810  228.8782
 YP4  H20  H  HCR6  0   0.256  207.7888  202.7188  227.8091
 YP4  H21  H  HCR6  0   0.251  214.3112  207.6901  229.0422
 YP4  H22  H  HCR6  0   0.253  216.3346  206.9653  230.2215
 YP4  H23  H  HCR6  0   0.252  216.1607  205.7442  232.3595
 YP4  C3   C  CH2   0  -0.274  211.5681  205.2573  228.4268

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
 YP4  C3   N    single    1.452  0.020  1.452
 YP4  C3   C4   single    1.523  0.020  1.523
 YP4  N    CA   single    1.457  0.020  1.457
 YP4  C5   C4   single    1.529  0.020  1.529
 YP4  C5   C6   single    1.501  0.020  1.501
 YP4  C11  C6   aromatic  1.393  0.020  1.393
 YP4  C11  C10  aromatic  1.387  0.020  1.387
 YP4  C1   CA   single    1.525  0.020  1.525
 YP4  CA   CB   single    1.526  0.020  1.526
 YP4  C6   C7   aromatic  1.391  0.020  1.391
 YP4  C10  C9   aromatic  1.387  0.020  1.387
 YP4  C14  CB   aromatic  1.374  0.020  1.374
 YP4  C14  C15  aromatic  1.406  0.020  1.406
 YP4  CB   CG   aromatic  1.427  0.020  1.427
 YP4  C7   C8   aromatic  1.391  0.020  1.391
 YP4  C15  C16  aromatic  1.366  0.020  1.366
 YP4  C9   C8   aromatic  1.389  0.020  1.389
 YP4  C8   C12  single    1.496  0.020  1.496
 YP4  CG   CD2  aromatic  1.420  0.020  1.420
 YP4  CG   CD1  aromatic  1.426  0.020  1.426
 YP4  CD2  CE2  aromatic  1.368  0.020  1.368
 YP4  C16  CD1  aromatic  1.412  0.020  1.412
 YP4  CD1  CE1  aromatic  1.416  0.020  1.416
 YP4  F2   C12  single    1.344  0.020  1.344
 YP4  C12  F3   single    1.339  0.020  1.339
 YP4  C12  F1   single    1.338  0.020  1.338
 YP4  CE2  CZ   aromatic  1.409  0.020  1.409
 YP4  CE1  CZ   aromatic  1.366  0.020  1.366
 YP4  C1   H1   single    0.970  0.020  1.090
 YP4  C1   H2   single    0.970  0.020  1.090
 YP4  C1   H3   single    0.970  0.020  1.090
 YP4  C3   H4   single    0.970  0.020  1.090
 YP4  C3   H5   single    0.970  0.020  1.090
 YP4  C4   H6   single    0.970  0.020  1.090
 YP4  C4   H7   single    0.970  0.020  1.090
 YP4  C5   H8   single    0.970  0.020  1.090
 YP4  C5   H9   single    0.970  0.020  1.090
 YP4  N    H10  single    0.890  0.020  1.040
 YP4  CA   H12  single    0.970  0.020  1.090
 YP4  CD2  H13  single    0.930  0.020  1.080
 YP4  CE1  H14  single    0.930  0.020  1.080
 YP4  CE2  H15  single    0.930  0.020  1.080
 YP4  CZ   H16  single    0.930  0.020  1.080
 YP4  C7   H17  single    0.930  0.020  1.080
 YP4  C9   H18  single    0.930  0.020  1.080
 YP4  C10  H19  single    0.930  0.020  1.080
 YP4  C11  H20  single    0.930  0.020  1.080
 YP4  C14  H21  single    0.930  0.020  1.080
 YP4  C15  H22  single    0.930  0.020  1.080
 YP4  C16  H23  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
 YP4  H3   C1   H2   107.86  3.000
 YP4  H3   C1   H1   108.19  3.000
 YP4  H2   C1   H1   107.76  3.000
 YP4  H3   C1   CA   110.10  3.000
 YP4  H2   C1   CA   111.78  3.000
 YP4  H1   C1   CA   111.01  3.000
 YP4  H7   C4   H6   106.47  3.000
 YP4  H7   C4   C5   109.95  3.000
 YP4  H6   C4   C5   108.39  3.000
 YP4  H7   C4   C3   109.55  3.000
 YP4  H6   C4   C3   110.55  3.000
 YP4  C5   C4   C3   111.78  3.000
 YP4  H9   C5   H8   106.68  3.000
 YP4  H9   C5   C6   109.58  3.000
 YP4  H8   C5   C6   110.01  3.000
 YP4  H9   C5   C4   109.28  3.000
 YP4  H8   C5   C4   109.45  3.000
 YP4  C6   C5   C4   111.71  3.000
 YP4  C11  C6   C7   118.49  3.000
 YP4  C7   C6   C5   120.40  3.000
 YP4  C11  C6   C5   121.07  3.000
 YP4  H10  N    CA   109.09  3.000
 YP4  H10  N    C3   109.13  3.000
 YP4  CA   N    C3   115.56  3.000
 YP4  H12  CA   CB   109.20  3.000
 YP4  H12  CA   N    106.91  3.000
 YP4  CB   CA   N    113.59  3.000
 YP4  H12  CA   C1   106.27  3.000
 YP4  CB   CA   C1   111.40  3.000
 YP4  N    CA   C1   109.12  3.000
 YP4  C14  CB   CG   118.64  3.000
 YP4  CG   CB   CA   122.96  3.000
 YP4  C14  CB   CA   118.35  3.000
 YP4  CD2  CG   CD1  117.36  3.000
 YP4  CD1  CG   CB   119.11  3.000
 YP4  CD2  CG   CB   123.54  3.000
 YP4  C16  CD1  CE1  120.46  3.000
 YP4  CE1  CD1  CG   119.72  3.000
 YP4  C16  CD1  CG   119.82  3.000
 YP4  H13  CD2  CE2  118.10  3.000
 YP4  H13  CD2  CG   120.30  3.000
 YP4  CE2  CD2  CG   121.60  3.000
 YP4  H14  CE1  CZ   120.36  3.000
 YP4  H14  CE1  CD1  118.55  3.000
 YP4  CZ   CE1  CD1  121.09  3.000
 YP4  H15  CE2  CZ   119.76  3.000
 YP4  H15  CE2  CD2  119.65  3.000
 YP4  CZ   CE2  CD2  120.58  3.000
 YP4  H16  CZ   CE2  119.95  3.000
 YP4  H16  CZ   CE1  120.41  3.000
 YP4  CE2  CZ   CE1  119.64  3.000
 YP4  H17  C7   C8   120.53  3.000
 YP4  H17  C7   C6   118.71  3.000
 YP4  C8   C7   C6   120.76  3.000
 YP4  C12  C8   C9   120.20  3.000
 YP4  C12  C8   C7   119.44  3.000
 YP4  C9   C8   C7   120.28  3.000
 YP4  H18  C9   C10  119.52  3.000
 YP4  H18  C9   C8   121.26  3.000
 YP4  C10  C9   C8   119.22  3.000
 YP4  H19  C10  C11  120.00  3.000
 YP4  H19  C10  C9   119.62  3.000
 YP4  C11  C10  C9   120.37  3.000
 YP4  H20  C11  C10  119.67  3.000
 YP4  H20  C11  C6   119.45  3.000
 YP4  C10  C11  C6   120.88  3.000
 YP4  F3   C12  F2   106.50  3.000
 YP4  F3   C12  F1   106.91  3.000
 YP4  F2   C12  F1   106.59  3.000
 YP4  F1   C12  C8   112.57  3.000
 YP4  F3   C12  C8   112.54  3.000
 YP4  F2   C12  C8   111.33  3.000
 YP4  H21  C14  C15  118.17  3.000
 YP4  H21  C14  CB   119.63  3.000
 YP4  C15  C14  CB   122.20  3.000
 YP4  H22  C15  C16  120.41  3.000
 YP4  H22  C15  C14  119.55  3.000
 YP4  C16  C15  C14  120.04  3.000
 YP4  H23  C16  C15  120.76  3.000
 YP4  H23  C16  CD1  119.06  3.000
 YP4  C15  C16  CD1  120.18  3.000
 YP4  H5   C3   H4   106.12  3.000
 YP4  H5   C3   N    113.02  3.000
 YP4  H4   C3   N    107.36  3.000
 YP4  H5   C3   C4   108.82  3.000
 YP4  H4   C3   C4   108.74  3.000
 YP4  N    C3   C4   112.50  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
 YP4  CONST_01  C9   C10  C11  C6     0.00   0.0  0
 YP4  CONST_02  C9   C8   C7   C6     0.00   0.0  0
 YP4  CONST_03  C16  C15  C14  CB     0.00   0.0  0
 YP4  CONST_04  CE2  CD2  CG   CB   180.00   0.0  0
 YP4  CONST_05  C16  CD1  CG   CB     0.00   0.0  0
 YP4  CONST_06  CE1  CD1  CG   CB   180.00   0.0  0
 YP4  CONST_07  C15  C14  CB   CG     0.00   0.0  0
 YP4  CONST_08  CZ   CE2  CD2  CG     0.00   0.0  0
 YP4  CONST_09  C15  C16  CD1  CG     0.00   0.0  0
 YP4  CONST_10  CZ   CE1  CD1  CG     0.00   0.0  0
 YP4  CONST_11  C14  CB   CG   CD1    0.00   0.0  0
 YP4  CONST_12  CE2  CD2  CG   CD1    0.00   0.0  0
 YP4  CONST_13  C14  C15  C16  CD1    0.00   0.0  0
 YP4  CONST_14  CE2  CZ   CE1  CD1    0.00   0.0  0
 YP4  CONST_15  C14  CB   CG   CD2  180.00   0.0  0
 YP4  CONST_16  C16  CD1  CG   CD2  180.00   0.0  0
 YP4  CONST_17  CE1  CD1  CG   CD2    0.00   0.0  0
 YP4  CONST_18  CE1  CZ   CE2  CD2    0.00   0.0  0
 YP4  CONST_19  C15  C16  CD1  CE1  180.00   0.0  0
 YP4  CONST_20  C16  CD1  CE1  CZ   180.00   0.0  0
 YP4  CONST_21  C10  C11  C6   C7     0.00   0.0  0
 YP4  CONST_22  C10  C9   C8   C7     0.00   0.0  0
 YP4  CONST_23  C11  C6   C7   C8     0.00   0.0  0
 YP4  CONST_24  C11  C10  C9   C8     0.00   0.0  0
 YP4  CONST_25  C10  C11  C6   C5   180.00   0.0  0
 YP4  CONST_26  C8   C7   C6   C5   180.00   0.0  0
 YP4  CONST_27  C12  C8   C7   C6   180.00   0.0  0
 YP4  CONST_28  C15  C14  CB   CA   180.00   0.0  0
 YP4  CONST_29  CD2  CG   CB   CA     0.00   0.0  0
 YP4  CONST_30  CD1  CG   CB   CA   180.00   0.0  0
 YP4  CONST_31  C12  C8   C9   C10  180.00   0.0  0
 YP4  CONST_32  H19  C10  C11  C6   180.00   0.0  0
 YP4  CONST_33  H22  C15  C14  CB   180.00   0.0  0
 YP4  CONST_34  H13  CD2  CG   CB     0.00   0.0  0
 YP4  CONST_35  H21  C14  CB   CG   180.00   0.0  0
 YP4  CONST_36  H15  CE2  CD2  CG   180.00   0.0  0
 YP4  CONST_37  H23  C16  CD1  CG   180.00   0.0  0
 YP4  CONST_38  H14  CE1  CD1  CG   180.00   0.0  0
 YP4  CONST_39  H16  CZ   CE1  CD1  180.00   0.0  0
 YP4  CONST_40  H20  C11  C6   C7   180.00   0.0  0
 YP4  CONST_41  H18  C9   C8   C7   180.00   0.0  0
 YP4  CONST_42  H17  C7   C8   C9   180.00   0.0  0
 YP4  Var_01    C11  C6   C5   C4    86.71  30.0  2
 YP4  Var_02    F2   C12  C8   C7   -83.10  30.0  2
 YP4  Var_03    C6   C5   C4   C3   175.14  30.0  2
 YP4  Var_04    CA   N    C3   C4    72.26  30.0  3
 YP4  Var_05    N    C3   C4   C5   179.46  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
 YP4  chir_01  CA  N  C1  CB  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
 YP4  plan-1  C5   0.020
 YP4  plan-1  C6   0.020
 YP4  plan-1  C7   0.020
 YP4  plan-1  C8   0.020
 YP4  plan-1  C9   0.020
 YP4  plan-1  C10  0.020
 YP4  plan-1  C11  0.020
 YP4  plan-1  C12  0.020
 YP4  plan-1  H17  0.020
 YP4  plan-1  H18  0.020
 YP4  plan-1  H19  0.020
 YP4  plan-1  H20  0.020
 YP4  plan-2  CA   0.020
 YP4  plan-2  CB   0.020
 YP4  plan-2  CG   0.020
 YP4  plan-2  CD1  0.020
 YP4  plan-2  CD2  0.020
 YP4  plan-2  CE1  0.020
 YP4  plan-2  CE2  0.020
 YP4  plan-2  CZ   0.020
 YP4  plan-2  C14  0.020
 YP4  plan-2  C15  0.020
 YP4  plan-2  C16  0.020
 YP4  plan-2  H13  0.020
 YP4  plan-2  H14  0.020
 YP4  plan-2  H15  0.020
 YP4  plan-2  H16  0.020
 YP4  plan-2  H21  0.020
 YP4  plan-2  H22  0.020
 YP4  plan-2  H23  0.020

