# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 00:32:52 2022
#   Inital geometry file: a 107 line input string
#   Ligand name: 4-({methyl[(1R)-1-(naphthalen-1-yl)ethyl]amino}methyl)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N(C)Cc1ccc(O)cc1)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
 JW9  JW9  "4-({methyl[(1R)-1-(naphthalen-1-yl)ethyl]amino}methyl)phenol"
  ligand  43  22  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JW9
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
 JW9  O1   O  OH1   0  -0.632  2.2562  53.8693  58.6894
 JW9  C34  C  CR6   0   0.338  2.8602  54.5788  59.6655
 JW9  C33  C  CR16  0  -0.322  2.8118  55.9672  59.5880
 JW9  C32  C  CR16  0  -0.301  3.4196  56.7351  60.5707
 JW9  C35  C  CR16  0  -0.367  3.5244  53.9795  60.7348
 JW9  C36  C  CR16  0  -0.280  4.1218  54.7634  61.7089
 JW9  C31  C  CR6   0   0.077  4.0786  56.1539  61.6488
 JW9  C22  C  CH2   0  -0.339  4.6957  56.9954  62.7332
 JW9  N1   N  NT    0  -0.412  6.0942  56.6726  62.9799
 JW9  C23  C  CH3   0  -0.533  6.9085  57.0716  61.8491
 JW9  C20  C  CH1   0  -0.105  6.5325  57.2576  64.2448
 JW9  C21  C  CH3   0  -0.681  8.0461  57.1747  64.4477
 JW9  C5   C  CR6   0   0.062  5.8657  56.5572  65.4166
 JW9  C4   C  CR16  0  -0.308  5.6859  55.1969  65.3712
 JW9  C3   C  CR16  0  -0.238  5.1322  54.4844  66.4508
 JW9  C2   C  CR16  0  -0.335  4.7589  55.1413  67.5886
 JW9  C1   C  CR66  0   0.109  4.9322  56.5401  67.6898
 JW9  C6   C  CR66  0   0.091  5.4945  57.2637  66.5993
 JW9  C14  C  CR16  0  -0.308  4.5557  57.2296  68.8672
 JW9  C13  C  CR16  0  -0.262  4.7282  58.5808  68.9784
 JW9  C12  C  CR16  0  -0.246  5.2898  59.3027  67.9071
 JW9  C11  C  CR16  0  -0.350  5.6614  58.6641  66.7550
 JW9  H1   H  HOH1  0   0.471  2.3598  52.9241  58.8477
 JW9  H2   H  HCR6  0   0.256  2.3043  56.4428  58.7577
 JW9  H3   H  HCR6  0   0.247  3.3771  57.8154  60.4916
 JW9  H4   H  HCR6  0   0.265  3.5738  52.8984  60.8085
 JW9  H5   H  HCR6  0   0.254  4.6308  54.2777  62.5323
 JW9  H6   H  HCH2  0   0.217  4.5686  58.0623  62.4834
 JW9  H7   H  HCH2  0   0.255  4.1407  56.8343  63.6608
 JW9  H9   H  HCH3  0   0.243  7.9250  56.6944  61.9424
 JW9  H10  H  HCH3  0   0.244  6.4925  56.6460  60.9363
 JW9  H11  H  HCH3  0   0.193  6.9581  58.1633  61.7134
 JW9  H12  H  HCH1  0   0.214  6.2627  58.3254  64.2563
 JW9  H13  H  HCH3  0   0.247  8.2978  57.5124  65.4528
 JW9  H14  H  HCH3  0   0.231  8.3969  56.1470  64.3414
 JW9  H15  H  HCH3  0   0.240  8.5945  57.8047  63.7482
 JW9  H16  H  HCR6  0   0.251  5.9703  54.6619  64.4747
 JW9  H17  H  HCR6  0   0.251  5.0044  53.4125  66.3710
 JW9  H18  H  HCR6  0   0.251  4.3299  54.6028  68.4252
 JW9  H19  H  HCR6  0   0.253  4.1264  56.6630  69.6851
 JW9  H20  H  HCR6  0   0.255  4.4367  59.0972  69.8837
 JW9  H21  H  HCR6  0   0.256  5.4291  60.3724  67.9961
 JW9  H22  H  HCR6  0   0.249  6.0925  59.2523  65.9571

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
 JW9  O1   C34  single    1.349  0.020  1.349
 JW9  C33  C34  aromatic  1.391  0.020  1.391
 JW9  C33  C32  aromatic  1.387  0.020  1.387
 JW9  C34  C35  aromatic  1.394  0.020  1.394
 JW9  C32  C31  aromatic  1.391  0.020  1.391
 JW9  C35  C36  aromatic  1.386  0.020  1.386
 JW9  C31  C36  aromatic  1.392  0.020  1.392
 JW9  C31  C22  single    1.505  0.020  1.505
 JW9  C23  N1   single    1.449  0.020  1.449
 JW9  N1   C22  single    1.456  0.020  1.456
 JW9  N1   C20  single    1.461  0.020  1.461
 JW9  C20  C21  single    1.529  0.020  1.529
 JW9  C20  C5   single    1.519  0.020  1.519
 JW9  C5   C4   aromatic  1.373  0.020  1.373
 JW9  C5   C6   aromatic  1.427  0.020  1.427
 JW9  C4   C3   aromatic  1.407  0.020  1.407
 JW9  C11  C6   aromatic  1.419  0.020  1.419
 JW9  C11  C12  aromatic  1.369  0.020  1.369
 JW9  C6   C1   aromatic  1.424  0.020  1.424
 JW9  C3   C2   aromatic  1.366  0.020  1.366
 JW9  C12  C13  aromatic  1.409  0.020  1.409
 JW9  C1   C2   aromatic  1.413  0.020  1.413
 JW9  C1   C14  aromatic  1.415  0.020  1.415
 JW9  C13  C14  aromatic  1.367  0.020  1.367
 JW9  O1   H1   single    0.850  0.020  0.980
 JW9  C33  H2   single    0.930  0.020  1.080
 JW9  C32  H3   single    0.930  0.020  1.080
 JW9  C35  H4   single    0.930  0.020  1.080
 JW9  C36  H5   single    0.930  0.020  1.080
 JW9  C22  H6   single    0.970  0.020  1.090
 JW9  C22  H7   single    0.970  0.020  1.090
 JW9  C23  H9   single    0.970  0.020  1.090
 JW9  C23  H10  single    0.970  0.020  1.090
 JW9  C23  H11  single    0.970  0.020  1.090
 JW9  C20  H12  single    0.970  0.020  1.090
 JW9  C21  H13  single    0.970  0.020  1.090
 JW9  C21  H14  single    0.970  0.020  1.090
 JW9  C21  H15  single    0.970  0.020  1.090
 JW9  C4   H16  single    0.930  0.020  1.080
 JW9  C3   H17  single    0.930  0.020  1.080
 JW9  C2   H18  single    0.930  0.020  1.080
 JW9  C14  H19  single    0.930  0.020  1.080
 JW9  C13  H20  single    0.930  0.020  1.080
 JW9  C12  H21  single    0.930  0.020  1.080
 JW9  C11  H22  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
 JW9  H1   O1   C34  110.40  3.000
 JW9  C35  C34  C33  119.22  3.000
 JW9  C35  C34  O1   122.83  3.000
 JW9  C33  C34  O1   117.95  3.000
 JW9  H2   C33  C32  120.35  3.000
 JW9  H2   C33  C34  119.81  3.000
 JW9  C32  C33  C34  119.84  3.000
 JW9  H3   C32  C31  119.45  3.000
 JW9  H3   C32  C33  118.86  3.000
 JW9  C31  C32  C33  121.69  3.000
 JW9  H4   C35  C36  119.77  3.000
 JW9  H4   C35  C34  120.14  3.000
 JW9  C36  C35  C34  120.09  3.000
 JW9  H5   C36  C31  119.69  3.000
 JW9  H5   C36  C35  118.90  3.000
 JW9  C31  C36  C35  121.41  3.000
 JW9  C22  C31  C36  120.97  3.000
 JW9  C22  C31  C32  121.28  3.000
 JW9  C36  C31  C32  117.74  3.000
 JW9  H7   C22  H6   106.04  3.000
 JW9  H7   C22  N1   108.13  3.000
 JW9  H6   C22  N1   111.31  3.000
 JW9  H7   C22  C31  108.72  3.000
 JW9  H6   C22  C31  109.29  3.000
 JW9  N1   C22  C31  113.07  3.000
 JW9  C20  N1   C23  113.37  3.000
 JW9  C20  N1   C22  110.24  3.000
 JW9  C23  N1   C22  110.26  3.000
 JW9  H11  C23  H10  107.53  3.000
 JW9  H11  C23  H9   108.18  3.000
 JW9  H10  C23  H9   107.04  3.000
 JW9  H11  C23  N1   113.23  3.000
 JW9  H10  C23  N1   109.36  3.000
 JW9  H9   C23  N1   111.25  3.000
 JW9  H12  C20  C5   109.35  3.000
 JW9  H12  C20  C21  107.08  3.000
 JW9  C5   C20  C21  107.88  3.000
 JW9  H12  C20  N1   108.89  3.000
 JW9  C5   C20  N1   110.58  3.000
 JW9  C21  C20  N1   112.96  3.000
 JW9  H15  C21  H14  108.68  3.000
 JW9  H15  C21  H13  107.26  3.000
 JW9  H14  C21  H13  107.90  3.000
 JW9  H15  C21  C20  112.43  3.000
 JW9  H14  C21  C20  110.88  3.000
 JW9  H13  C21  C20  109.52  3.000
 JW9  C6   C5   C4   118.95  3.000
 JW9  C6   C5   C20  121.68  3.000
 JW9  C4   C5   C20  119.26  3.000
 JW9  H16  C4   C3   119.26  3.000
 JW9  H16  C4   C5   118.88  3.000
 JW9  C3   C4   C5   121.86  3.000
 JW9  H17  C3   C2   120.36  3.000
 JW9  H17  C3   C4   119.43  3.000
 JW9  C2   C3   C4   120.21  3.000
 JW9  H18  C2   C1   119.03  3.000
 JW9  H18  C2   C3   120.82  3.000
 JW9  C1   C2   C3   120.14  3.000
 JW9  C14  C1   C6   119.63  3.000
 JW9  C14  C1   C2   120.60  3.000
 JW9  C6   C1   C2   119.77  3.000
 JW9  C11  C6   C1   117.63  3.000
 JW9  C1   C6   C5   119.06  3.000
 JW9  C11  C6   C5   123.31  3.000
 JW9  H19  C14  C13  120.36  3.000
 JW9  H19  C14  C1   118.59  3.000
 JW9  C13  C14  C1   121.05  3.000
 JW9  H20  C13  C12  119.93  3.000
 JW9  H20  C13  C14  120.39  3.000
 JW9  C12  C13  C14  119.68  3.000
 JW9  H21  C12  C11  119.69  3.000
 JW9  H21  C12  C13  119.69  3.000
 JW9  C11  C12  C13  120.61  3.000
 JW9  H22  C11  C12  118.40  3.000
 JW9  H22  C11  C6   120.20  3.000
 JW9  C12  C11  C6   121.40  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
 JW9  CONST_01  C31  C32  C33  C34     0.00   0.0  0
 JW9  CONST_02  C31  C36  C35  C34     0.00   0.0  0
 JW9  CONST_03  C36  C35  C34  C33     0.00   0.0  0
 JW9  CONST_04  C36  C31  C32  C33     0.00   0.0  0
 JW9  CONST_05  C35  C34  C33  C32     0.00   0.0  0
 JW9  CONST_06  C35  C36  C31  C32     0.00   0.0  0
 JW9  CONST_07  C2   C3   C4   C5      0.00   0.0  0
 JW9  CONST_08  C12  C11  C6   C5    180.00   0.0  0
 JW9  CONST_09  C2   C1   C6   C5      0.00   0.0  0
 JW9  CONST_10  C14  C1   C6   C5    180.00   0.0  0
 JW9  CONST_11  C11  C6   C5   C4    180.00   0.0  0
 JW9  CONST_12  C1   C6   C5   C4      0.00   0.0  0
 JW9  CONST_13  C1   C2   C3   C4      0.00   0.0  0
 JW9  CONST_14  C6   C5   C4   C3      0.00   0.0  0
 JW9  CONST_15  C6   C1   C2   C3      0.00   0.0  0
 JW9  CONST_16  C14  C1   C2   C3    180.00   0.0  0
 JW9  CONST_17  C11  C6   C1   C2    180.00   0.0  0
 JW9  CONST_18  C13  C14  C1   C2    180.00   0.0  0
 JW9  CONST_19  C12  C11  C6   C1      0.00   0.0  0
 JW9  CONST_20  C12  C13  C14  C1      0.00   0.0  0
 JW9  CONST_21  C13  C12  C11  C6      0.00   0.0  0
 JW9  CONST_22  C13  C14  C1   C6      0.00   0.0  0
 JW9  CONST_23  C11  C6   C1   C14     0.00   0.0  0
 JW9  CONST_24  C11  C12  C13  C14     0.00   0.0  0
 JW9  CONST_25  C32  C33  C34  O1    180.00   0.0  0
 JW9  CONST_26  C36  C35  C34  O1    180.00   0.0  0
 JW9  CONST_27  C22  C31  C32  C33   180.00   0.0  0
 JW9  CONST_28  C22  C31  C36  C35   180.00   0.0  0
 JW9  CONST_29  C3   C4   C5   C20   180.00   0.0  0
 JW9  CONST_30  C11  C6   C5   C20     0.00   0.0  0
 JW9  CONST_31  C1   C6   C5   C20   180.00   0.0  0
 JW9  CONST_32  H3   C32  C33  C34   180.00   0.0  0
 JW9  CONST_33  H5   C36  C35  C34   180.00   0.0  0
 JW9  CONST_34  H4   C35  C34  C33   180.00   0.0  0
 JW9  CONST_35  H5   C36  C31  C32   180.00   0.0  0
 JW9  CONST_36  H2   C33  C34  C35   180.00   0.0  0
 JW9  CONST_37  H3   C32  C31  C36   180.00   0.0  0
 JW9  CONST_38  H2   C33  C32  C31   180.00   0.0  0
 JW9  CONST_39  H4   C35  C36  C31   180.00   0.0  0
 JW9  CONST_40  H17  C3   C4   C5    180.00   0.0  0
 JW9  CONST_41  H22  C11  C6   C5      0.00   0.0  0
 JW9  CONST_42  H18  C2   C3   C4    180.00   0.0  0
 JW9  CONST_43  H16  C4   C3   C2    180.00   0.0  0
 JW9  CONST_44  H19  C14  C1   C2      0.00   0.0  0
 JW9  CONST_45  H22  C11  C6   C1    180.00   0.0  0
 JW9  CONST_46  H17  C3   C2   C1    180.00   0.0  0
 JW9  CONST_47  H20  C13  C14  C1    180.00   0.0  0
 JW9  CONST_48  H16  C4   C5   C6    180.00   0.0  0
 JW9  CONST_49  H21  C12  C11  C6    180.00   0.0  0
 JW9  CONST_50  H18  C2   C1   C6    180.00   0.0  0
 JW9  CONST_51  H19  C14  C1   C6    180.00   0.0  0
 JW9  CONST_52  H18  C2   C1   C14     0.00   0.0  0
 JW9  CONST_53  H21  C12  C13  C14   180.00   0.0  0
 JW9  CONST_54  H22  C11  C12  C13   180.00   0.0  0
 JW9  CONST_55  H19  C14  C13  C12   180.00   0.0  0
 JW9  CONST_56  H20  C13  C12  C11   180.00   0.0  0
 JW9  Var_01    N1   C22  C31  C32  -127.21  30.0  2
 JW9  Var_02    N1   C22  C31  C36    54.33  30.0  2
 JW9  Var_03    H6   C22  C31  C32    -2.63  30.0  2
 JW9  Var_04    H7   C22  C31  C32   112.69  30.0  2
 JW9  Var_05    H6   C22  C31  C36   178.91  30.0  2
 JW9  Var_06    H7   C22  C31  C36   -65.77  30.0  2
 JW9  Var_07    C23  N1   C22  C31    68.70  30.0  1
 JW9  Var_08    C20  N1   C22  C31  -165.37  30.0  1
 JW9  Var_09    H9   C23  N1   C22  -170.70  30.0  3
 JW9  Var_10    H10  C23  N1   C22   -52.67  30.0  3
 JW9  Var_11    H11  C23  N1   C22    67.21  30.0  3
 JW9  Var_12    H6   C22  N1   C23   -54.78  30.0  3
 JW9  Var_13    H7   C22  N1   C23  -170.87  30.0  3
 JW9  Var_14    H9   C23  N1   C20    65.16  30.0  3
 JW9  Var_15    H10  C23  N1   C20  -176.81  30.0  3
 JW9  Var_16    H11  C23  N1   C20   -56.93  30.0  3
 JW9  Var_17    H6   C22  N1   C20    71.15  30.0  3
 JW9  Var_18    H7   C22  N1   C20   -44.94  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
 JW9  chir_01  C20  N1  C21  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
 JW9  plan-1  O1   0.020
 JW9  plan-1  C34  0.020
 JW9  plan-1  C33  0.020
 JW9  plan-1  C32  0.020
 JW9  plan-1  C35  0.020
 JW9  plan-1  C36  0.020
 JW9  plan-1  C31  0.020
 JW9  plan-1  C22  0.020
 JW9  plan-1  H2   0.020
 JW9  plan-1  H3   0.020
 JW9  plan-1  H4   0.020
 JW9  plan-1  H5   0.020
 JW9  plan-2  C20  0.020
 JW9  plan-2  C5   0.020
 JW9  plan-2  C4   0.020
 JW9  plan-2  C3   0.020
 JW9  plan-2  C2   0.020
 JW9  plan-2  C1   0.020
 JW9  plan-2  C6   0.020
 JW9  plan-2  C14  0.020
 JW9  plan-2  C13  0.020
 JW9  plan-2  C12  0.020
 JW9  plan-2  C11  0.020
 JW9  plan-2  H16  0.020
 JW9  plan-2  H17  0.020
 JW9  plan-2  H18  0.020
 JW9  plan-2  H19  0.020
 JW9  plan-2  H20  0.020
 JW9  plan-2  H21  0.020
 JW9  plan-2  H22  0.020

