# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 09:19:07 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (3S)-N-methyl-3-(naphthalen-1-yloxy)-3-(thiophen-2-yl)propan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCC[C@H](Oc1cccc2ccccc12)c3sccc3
#
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
 29E  29E  (3S)-N-methyl-3-(naphthalen-1-yloxy)-3-(thiophen-2-yl)propan-1-amine  ligand  40  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_29E
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
 29E  C    C  CH3   0  -0.518   2.5829   5.1509  -0.2622
 29E  N    N  NH1   0  -0.595   2.8809   3.7960   0.1545
 29E  C1   C  CH2   0  -0.261   1.9674   2.8268  -0.4194
 29E  C2   C  CH2   0  -0.450   2.3434   1.4181   0.0190
 29E  C3   C  CH1   0  -0.035   1.4700   0.3340  -0.5997
 29E  C14  C  CR5   0  -0.169   1.9314  -1.0388  -0.2206
 29E  S    S  S2    0   0.219   1.5448  -1.6830   1.3288
 29E  C17  C  CR15  0  -0.469   2.4354  -3.1155   1.0197
 29E  C16  C  CR15  0  -0.179   3.0041  -3.0957  -0.2163
 29E  C15  C  CR15  0  -0.238   2.7112  -1.9000  -0.9299
 29E  O    O  O2    0  -0.482   0.1490   0.5592  -0.1319
 29E  C4   C  CR6   0   0.377  -0.8939  -0.1000  -0.6725
 29E  C13  C  CR66  0  -0.030  -2.1388   0.1147  -0.0088
 29E  C12  C  CR16  0  -0.286  -2.2490   0.9413   1.1339
 29E  C11  C  CR16  0  -0.257  -3.4593   1.1213   1.7492
 29E  C10  C  CR16  0  -0.252  -4.6143   0.4857   1.2529
 29E  C9   C  CR16  0  -0.317  -4.5336  -0.3189   0.1492
 29E  C8   C  CR66  0   0.124  -3.2998  -0.5274  -0.5108
 29E  C7   C  CR16  0  -0.345  -3.2019  -1.3619  -1.6504
 29E  C6   C  CR16  0  -0.248  -1.9932  -1.5440  -2.2578
 29E  C5   C  CR16  0  -0.376  -0.8264  -0.9155  -1.7741
 29E  H1   H  HCH3  0   0.221   2.7567   5.2557  -1.3350
 29E  H2   H  HCH3  0   0.192   1.5481   5.4658  -0.0666
 29E  H3   H  HCH3  0   0.231   3.2469   5.8500   0.2463
 29E  H4   H  HNH1  0   0.342   2.8145   3.7444   1.1639
 29E  H6   H  HCH2  0   0.202   0.9179   3.0362  -0.1651
 29E  H7   H  HCH2  0   0.218   2.0405   2.8939  -1.5103
 29E  H8   H  HCH2  0   0.249   3.3762   1.2167  -0.2728
 29E  H9   H  HCH2  0   0.234   2.3016   1.3353   1.1101
 29E  H10  H  HCH1  0   0.257   1.5154   0.4306  -1.6925
 29E  H11  H  HCR5  0   0.295   2.4791  -3.8986   1.7606
 29E  H12  H  HCR5  0   0.267   3.6017  -3.9044  -0.6117
 29E  H13  H  HCR5  0   0.264   3.0626  -1.6887  -1.9309
 29E  H14  H  HCR6  0   0.255  -1.3724   1.4363   1.5280
 29E  H15  H  HCR6  0   0.258  -3.5295   1.7550   2.6236
 29E  H16  H  HCR6  0   0.258  -5.5649   0.6351   1.7482
 29E  H17  H  HCR6  0   0.255  -5.4188  -0.8121  -0.2342
 29E  H18  H  HCR6  0   0.251  -4.0904  -1.8531  -2.0268
 29E  H19  H  HCR6  0   0.259  -1.9127  -2.1832  -3.1273
 29E  H20  H  HCR6  0   0.278   0.1076  -1.1011  -2.2848

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
 29E  C7   C6   aromatic  1.365  0.020  1.365
 29E  C7   C8   aromatic  1.416  0.020  1.416
 29E  C6   C5   aromatic  1.411  0.020  1.411
 29E  S    C17  aromatic  1.715  0.020  1.715
 29E  S    C14  aromatic  1.722  0.020  1.722
 29E  C9   C8   aromatic  1.415  0.020  1.415
 29E  C9   C10  aromatic  1.368  0.020  1.368
 29E  C17  C16  aromatic  1.361  0.020  1.361
 29E  C8   C13  aromatic  1.419  0.020  1.419
 29E  C5   C4   aromatic  1.372  0.020  1.372
 29E  C10  C11  aromatic  1.409  0.020  1.409
 29E  C13  C4   aromatic  1.427  0.020  1.427
 29E  C13  C12  aromatic  1.415  0.020  1.415
 29E  C4   O    single    1.347  0.020  1.347
 29E  C16  C15  aromatic  1.423  0.020  1.423
 29E  C14  C3   single    1.497  0.020  1.497
 29E  C14  C15  aromatic  1.361  0.020  1.361
 29E  C11  C12  aromatic  1.370  0.020  1.370
 29E  C3   O    single    1.419  0.020  1.419
 29E  C3   C2   single    1.523  0.020  1.523
 29E  C2   C1   single    1.523  0.020  1.523
 29E  C1   N    single    1.450  0.020  1.450
 29E  C    N    single    1.449  0.020  1.449
 29E  C    H1   single    0.970  0.020  1.090
 29E  C    H2   single    0.970  0.020  1.090
 29E  C    H3   single    0.970  0.020  1.090
 29E  N    H4   single    0.890  0.020  1.040
 29E  C1   H6   single    0.970  0.020  1.090
 29E  C1   H7   single    0.970  0.020  1.090
 29E  C2   H8   single    0.970  0.020  1.090
 29E  C2   H9   single    0.970  0.020  1.090
 29E  C3   H10  single    0.970  0.020  1.090
 29E  C17  H11  single    0.930  0.020  1.080
 29E  C16  H12  single    0.930  0.020  1.080
 29E  C15  H13  single    0.930  0.020  1.080
 29E  C12  H14  single    0.930  0.020  1.080
 29E  C11  H15  single    0.930  0.020  1.080
 29E  C10  H16  single    0.930  0.020  1.080
 29E  C9   H17  single    0.930  0.020  1.080
 29E  C7   H18  single    0.930  0.020  1.080
 29E  C6   H19  single    0.930  0.020  1.080
 29E  C5   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
 29E  H3   C    H2   107.87  3.000
 29E  H3   C    H1   107.45  3.000
 29E  H2   C    H1   107.29  3.000
 29E  H3   C    N    109.90  3.000
 29E  H2   C    N    114.23  3.000
 29E  H1   C    N    109.85  3.000
 29E  H4   N    C1   108.60  3.000
 29E  H4   N    C    108.72  3.000
 29E  C1   N    C    112.44  3.000
 29E  H7   C1   H6   106.40  3.000
 29E  H7   C1   C2   109.09  3.000
 29E  H6   C1   C2   110.19  3.000
 29E  H7   C1   N    108.13  3.000
 29E  H6   C1   N    112.48  3.000
 29E  C2   C1   N    110.41  3.000
 29E  H9   C2   H8   106.77  3.000
 29E  H9   C2   C3   109.21  3.000
 29E  H8   C2   C3   107.61  3.000
 29E  H9   C2   C1   110.33  3.000
 29E  H8   C2   C1   109.10  3.000
 29E  C3   C2   C1   113.57  3.000
 29E  H10  C3   O    110.64  3.000
 29E  H10  C3   C14  108.66  3.000
 29E  O    C3   C14  110.42  3.000
 29E  H10  C3   C2   108.53  3.000
 29E  O    C3   C2   106.67  3.000
 29E  C14  C3   C2   111.90  3.000
 29E  C15  C14  S    111.15  3.000
 29E  C15  C14  C3   128.67  3.000
 29E  S    C14  C3   120.11  3.000
 29E  C17  S    C14   91.93  3.000
 29E  H11  C17  C16  128.13  3.000
 29E  H11  C17  S    120.23  3.000
 29E  C16  C17  S    111.63  3.000
 29E  H12  C16  C15  124.00  3.000
 29E  H12  C16  C17  123.55  3.000
 29E  C15  C16  C17  112.44  3.000
 29E  H13  C15  C16  124.15  3.000
 29E  H13  C15  C14  123.00  3.000
 29E  C16  C15  C14  112.85  3.000
 29E  C4   O    C3   120.71  3.000
 29E  C5   C4   C13  120.38  3.000
 29E  C13  C4   O    114.52  3.000
 29E  C5   C4   O    125.10  3.000
 29E  C8   C13  C12  119.12  3.000
 29E  C12  C13  C4   122.11  3.000
 29E  C8   C13  C4   118.77  3.000
 29E  H14  C12  C11  119.50  3.000
 29E  H14  C12  C13  119.93  3.000
 29E  C11  C12  C13  120.57  3.000
 29E  H15  C11  C10  119.72  3.000
 29E  H15  C11  C12  119.82  3.000
 29E  C10  C11  C12  120.46  3.000
 29E  H16  C10  C9   120.14  3.000
 29E  H16  C10  C11  119.78  3.000
 29E  C9   C10  C11  120.08  3.000
 29E  H17  C9   C8   118.71  3.000
 29E  H17  C9   C10  120.33  3.000
 29E  C8   C9   C10  120.96  3.000
 29E  C7   C8   C9   121.51  3.000
 29E  C9   C8   C13  118.81  3.000
 29E  C7   C8   C13  119.67  3.000
 29E  H18  C7   C6   120.76  3.000
 29E  H18  C7   C8   119.37  3.000
 29E  C6   C7   C8   119.87  3.000
 29E  H19  C6   C5   118.50  3.000
 29E  H19  C6   C7   120.14  3.000
 29E  C5   C6   C7   121.36  3.000
 29E  H20  C5   C6   118.45  3.000
 29E  H20  C5   C4   121.60  3.000
 29E  C6   C5   C4   119.95  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
 29E  CONST_01  C16  C17  S    C14     0.00   0.0  0
 29E  CONST_02  C17  C16  C15  C14     0.00   0.0  0
 29E  CONST_03  C15  C16  C17  S       0.00   0.0  0
 29E  CONST_04  C16  C15  C14  S       0.00   0.0  0
 29E  CONST_05  C15  C14  S    C17     0.00   0.0  0
 29E  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 29E  CONST_07  C7   C8   C13  C4      0.00   0.0  0
 29E  CONST_08  C9   C8   C13  C4    180.00   0.0  0
 29E  CONST_09  C11  C12  C13  C4    180.00   0.0  0
 29E  CONST_10  C6   C7   C8   C13     0.00   0.0  0
 29E  CONST_11  C10  C9   C8   C13     0.00   0.0  0
 29E  CONST_12  C6   C5   C4   C13     0.00   0.0  0
 29E  CONST_13  C10  C11  C12  C13     0.00   0.0  0
 29E  CONST_14  C7   C8   C13  C12   180.00   0.0  0
 29E  CONST_15  C9   C8   C13  C12     0.00   0.0  0
 29E  CONST_16  C5   C4   C13  C12   180.00   0.0  0
 29E  CONST_17  C9   C10  C11  C12     0.00   0.0  0
 29E  CONST_18  C8   C9   C10  C11     0.00   0.0  0
 29E  CONST_19  C8   C13  C12  C11     0.00   0.0  0
 29E  CONST_20  C7   C8   C9   C10   180.00   0.0  0
 29E  CONST_21  C6   C7   C8   C9    180.00   0.0  0
 29E  CONST_22  C5   C6   C7   C8      0.00   0.0  0
 29E  CONST_23  C5   C4   C13  C8      0.00   0.0  0
 29E  CONST_24  C17  S    C14  C3    180.00   0.0  0
 29E  CONST_25  C16  C15  C14  C3    180.00   0.0  0
 29E  CONST_26  C6   C5   C4   O     180.00   0.0  0
 29E  CONST_27  C8   C13  C4   O     180.00   0.0  0
 29E  CONST_28  C12  C13  C4   O       0.00   0.0  0
 29E  CONST_29  H11  C17  S    C14   180.00   0.0  0
 29E  CONST_30  H12  C16  C15  C14   180.00   0.0  0
 29E  CONST_31  H13  C15  C14  S     180.00   0.0  0
 29E  CONST_32  H19  C6   C5   C4    180.00   0.0  0
 29E  CONST_33  H14  C12  C13  C4      0.00   0.0  0
 29E  CONST_34  H18  C7   C8   C13   180.00   0.0  0
 29E  CONST_35  H17  C9   C8   C13   180.00   0.0  0
 29E  CONST_36  H20  C5   C4   C13   180.00   0.0  0
 29E  CONST_37  H15  C11  C12  C13   180.00   0.0  0
 29E  CONST_38  H16  C10  C11  C12   180.00   0.0  0
 29E  Var_01    C5   C4   O    C3     -7.01  30.0  2
 29E  Var_02    C2   C1   N    C     178.55  30.0  2
 29E  Var_03    C3   C2   C1   N    -177.13  30.0  1
 29E  Var_04    H1   C    N    C1    -65.96  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
 29E  chir_01  C3  C14  O  C2  negativ

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
 29E  plan-1  C3   0.020
 29E  plan-1  C14  0.020
 29E  plan-1  S    0.020
 29E  plan-1  C17  0.020
 29E  plan-1  C16  0.020
 29E  plan-1  C15  0.020
 29E  plan-1  H11  0.020
 29E  plan-1  H12  0.020
 29E  plan-1  H13  0.020
 29E  plan-2  O    0.020
 29E  plan-2  C4   0.020
 29E  plan-2  C13  0.020
 29E  plan-2  C12  0.020
 29E  plan-2  C11  0.020
 29E  plan-2  C10  0.020
 29E  plan-2  C9   0.020
 29E  plan-2  C8   0.020
 29E  plan-2  C7   0.020
 29E  plan-2  C6   0.020
 29E  plan-2  C5   0.020
 29E  plan-2  H14  0.020
 29E  plan-2  H15  0.020
 29E  plan-2  H16  0.020
 29E  plan-2  H17  0.020
 29E  plan-2  H18  0.020
 29E  plan-2  H19  0.020
 29E  plan-2  H20  0.020

