# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:14:49 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: (2S)-1-[(1-methylethyl)amino]-3-(naphthalen-1-yloxy)propan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)NC[C@H](O)COc1cccc2ccccc12
#
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
 SNP  SNP  (2S)-1-[(1-methylethyl)amino]-3-(naphthalen-1-yloxy)propan-2-ol  ligand  40  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SNP
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
 SNP  C1    C  CR6   0   0.370   0.7396   0.0555  -1.6077
 SNP  C2    C  CR16  0  -0.408   2.1034  -0.0907  -1.6836
 SNP  C3    C  CR16  0  -0.245   2.7318  -0.2108  -2.9411
 SNP  C4    C  CR16  0  -0.345   2.0115  -0.1846  -4.0998
 SNP  C5    C  CR16  0  -0.317  -0.1750   0.0014  -5.2320
 SNP  C6    C  CR16  0  -0.251  -1.5342   0.1483  -5.1741
 SNP  C7    C  CR16  0  -0.257  -2.1792   0.2659  -3.9276
 SNP  C8    C  CR16  0  -0.287  -1.4545   0.2373  -2.7654
 SNP  C9    C  CR66  0  -0.022  -0.0484   0.0895  -2.7984
 SNP  C10   C  CR66  0   0.126   0.6042  -0.0319  -4.0521
 SNP  O1    O  O2    0  -0.462   0.0482   0.1759  -0.4631
 SNP  C11   C  CH2   0  -0.186   0.7369   0.0788   0.7673
 SNP  C12   C  CH1   0  -0.031  -0.2851   0.1173   1.8897
 SNP  O2    O  OH1   0  -0.657  -1.2204  -0.9338   1.7872
 SNP  C13   C  CH2   0  -0.278   0.4257   0.1188   3.2383
 SNP  N1    N  NH1   0  -0.595  -0.5250   0.2768   4.3169
 SNP  C14   C  CH1   0  -0.086   0.0616   0.3658   5.6482
 SNP  C15   C  CH3   0  -0.656  -1.0150   0.7985   6.6342
 SNP  C16   C  CH3   0  -0.668   0.7371  -0.9206   6.1247
 SNP  H2    H  HCR6  0   0.281   2.7194  -0.1149  -0.7954
 SNP  H3    H  HCR6  0   0.259   3.8077  -0.3233  -2.9723
 SNP  H4    H  HCR6  0   0.250   2.5028  -0.2797  -5.0601
 SNP  H5    H  HCR6  0   0.254   0.3252  -0.0934  -6.1884
 SNP  H6    H  HCR6  0   0.258  -2.1185   0.1739  -6.0847
 SNP  H7    H  HCR6  0   0.258  -3.2548   0.3774  -3.8888
 SNP  H8    H  HCR6  0   0.255  -1.9660   0.3273  -1.8169
 SNP  H112  H  HCH2  0   0.232   1.4428   0.9089   0.8813
 SNP  H111  H  HCH2  0   0.225   1.3131  -0.8544   0.8117
 SNP  H12   H  HCH1  0   0.235  -0.8675   1.0402   1.8082
 SNP  H2O1  H  HOH1  0   0.445  -0.7489  -1.7716   1.8616
 SNP  H132  H  HCH2  0   0.228   1.1219   0.9624   3.2688
 SNP  H131  H  HCH2  0   0.195   1.0443  -0.7917   3.3114
 SNP  H1    H  HNH1  0   0.332  -1.1861  -0.4918   4.2974
 SNP  H14   H  HCH1  0   0.216   0.8207   1.1551   5.6046
 SNP  H153  H  HCH3  0   0.223  -0.6009   0.9238   7.6354
 SNP  H152  H  HCH3  0   0.227  -1.4676   1.7436   6.3326
 SNP  H151  H  HCH3  0   0.215  -1.8088   0.0497   6.6982
 SNP  H163  H  HCH3  0   0.213   0.0122  -1.7372   6.1761
 SNP  H162  H  HCH3  0   0.229   1.5473  -1.2331   5.4645
 SNP  H161  H  HCH3  0   0.224   1.1625  -0.7926   7.1215

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
 SNP  C1   C2    aromatic  1.374  0.020  1.374
 SNP  C1   C9    aromatic  1.428  0.020  1.428
 SNP  C1   O1    single    1.343  0.020  1.343
 SNP  C2   C3    aromatic  1.411  0.020  1.411
 SNP  C2   H2    single    0.930  0.020  1.080
 SNP  C3   C4    aromatic  1.365  0.020  1.365
 SNP  C3   H3    single    0.930  0.020  1.080
 SNP  C4   C10   aromatic  1.416  0.020  1.416
 SNP  C4   H4    single    0.930  0.020  1.080
 SNP  C5   C6    aromatic  1.368  0.020  1.368
 SNP  C5   C10   aromatic  1.414  0.020  1.414
 SNP  C5   H5    single    0.930  0.020  1.080
 SNP  C6   C7    aromatic  1.408  0.020  1.408
 SNP  C6   H6    single    0.930  0.020  1.080
 SNP  C7   C8    aromatic  1.370  0.020  1.370
 SNP  C7   H7    single    0.930  0.020  1.080
 SNP  C8   C9    aromatic  1.414  0.020  1.414
 SNP  C8   H8    single    0.930  0.020  1.080
 SNP  C9   C10   aromatic  1.419  0.020  1.419
 SNP  O1   C11   single    1.413  0.020  1.413
 SNP  C11  C12   single    1.518  0.020  1.518
 SNP  C11  H112  single    0.970  0.020  1.090
 SNP  C11  H111  single    0.970  0.020  1.090
 SNP  C12  O2    single    1.411  0.020  1.411
 SNP  C12  C13   single    1.524  0.020  1.524
 SNP  C12  H12   single    0.970  0.020  1.090
 SNP  O2   H2O1  single    0.850  0.020  0.980
 SNP  C13  N1    single    1.446  0.020  1.446
 SNP  C13  H132  single    0.970  0.020  1.090
 SNP  C13  H131  single    0.970  0.020  1.090
 SNP  N1   C14   single    1.458  0.020  1.458
 SNP  N1   H1    single    0.890  0.020  1.040
 SNP  C14  C15   single    1.523  0.020  1.523
 SNP  C14  C16   single    1.529  0.020  1.529
 SNP  C14  H14   single    0.970  0.020  1.090
 SNP  C15  H153  single    0.970  0.020  1.090
 SNP  C15  H152  single    0.970  0.020  1.090
 SNP  C15  H151  single    0.970  0.020  1.090
 SNP  C16  H163  single    0.970  0.020  1.090
 SNP  C16  H162  single    0.970  0.020  1.090
 SNP  C16  H161  single    0.970  0.020  1.090

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
 SNP  O1    C1   C9    115.11  3.000
 SNP  O1    C1   C2    124.61  3.000
 SNP  C9    C1   C2    120.28  3.000
 SNP  H2    C2   C3    118.46  3.000
 SNP  H2    C2   C1    121.51  3.000
 SNP  C3    C2   C1    120.03  3.000
 SNP  H3    C3   C4    120.15  3.000
 SNP  H3    C3   C2    118.52  3.000
 SNP  C4    C3   C2    121.34  3.000
 SNP  H4    C4   C10   119.35  3.000
 SNP  H4    C4   C3    120.78  3.000
 SNP  C10   C4   C3    119.86  3.000
 SNP  H5    C5   C10   118.69  3.000
 SNP  H5    C5   C6    120.35  3.000
 SNP  C10   C5   C6    120.96  3.000
 SNP  H6    C6   C7    119.70  3.000
 SNP  H6    C6   C5    120.21  3.000
 SNP  C7    C6   C5    120.09  3.000
 SNP  H7    C7   C8    119.84  3.000
 SNP  H7    C7   C6    119.70  3.000
 SNP  C8    C7   C6    120.45  3.000
 SNP  H8    C8   C9    119.96  3.000
 SNP  H8    C8   C7    119.48  3.000
 SNP  C9    C8   C7    120.56  3.000
 SNP  C10   C9   C8    119.14  3.000
 SNP  C10   C9   C1    118.74  3.000
 SNP  C8    C9   C1    122.12  3.000
 SNP  C9    C10  C5    118.80  3.000
 SNP  C9    C10  C4    119.74  3.000
 SNP  C5    C10  C4    121.45  3.000
 SNP  C11   O1   C1    119.01  3.000
 SNP  H111  C11  H112  107.56  3.000
 SNP  H111  C11  C12   110.18  3.000
 SNP  H112  C11  C12   109.72  3.000
 SNP  H111  C11  O1    110.45  3.000
 SNP  H112  C11  O1    110.64  3.000
 SNP  C12   C11  O1    108.29  3.000
 SNP  H12   C12  C13   108.25  3.000
 SNP  H12   C12  O2    105.67  3.000
 SNP  C13   C12  O2    111.97  3.000
 SNP  H12   C12  C11   108.94  3.000
 SNP  C13   C12  C11   109.89  3.000
 SNP  O2    C12  C11   111.94  3.000
 SNP  H2O1  O2   C12   108.51  3.000
 SNP  H131  C13  H132  106.12  3.000
 SNP  H131  C13  N1    114.16  3.000
 SNP  H132  C13  N1    108.25  3.000
 SNP  H131  C13  C12   108.62  3.000
 SNP  H132  C13  C12   108.79  3.000
 SNP  N1    C13  C12   110.69  3.000
 SNP  H1    N1   C14   109.04  3.000
 SNP  H1    N1   C13   109.35  3.000
 SNP  C14   N1   C13   115.04  3.000
 SNP  H14   C14  C16   108.20  3.000
 SNP  H14   C14  C15   108.11  3.000
 SNP  C16   C14  C15   110.47  3.000
 SNP  H14   C14  N1    106.64  3.000
 SNP  C16   C14  N1    114.27  3.000
 SNP  C15   C14  N1    108.92  3.000
 SNP  H151  C15  H152  107.97  3.000
 SNP  H151  C15  H153  107.50  3.000
 SNP  H152  C15  H153  108.17  3.000
 SNP  H151  C15  C14   110.90  3.000
 SNP  H152  C15  C14   111.14  3.000
 SNP  H153  C15  C14   111.01  3.000
 SNP  H161  C16  H162  107.27  3.000
 SNP  H161  C16  H163  107.64  3.000
 SNP  H162  C16  H163  107.87  3.000
 SNP  H161  C16  C14   110.99  3.000
 SNP  H162  C16  C14   112.37  3.000
 SNP  H163  C16  C14   110.50  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
 SNP  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 SNP  CONST_02  C7    C8   C9   C1    180.00   0.0  0
 SNP  CONST_03  C4    C10  C9   C1      0.00   0.0  0
 SNP  CONST_04  C5    C10  C9   C1    180.00   0.0  0
 SNP  CONST_05  C8    C9   C1   C2    180.00   0.0  0
 SNP  CONST_06  C10   C9   C1   C2      0.00   0.0  0
 SNP  CONST_07  C10   C4   C3   C2      0.00   0.0  0
 SNP  CONST_08  C9    C1   C2   C3      0.00   0.0  0
 SNP  CONST_09  C5    C10  C4   C3    180.00   0.0  0
 SNP  CONST_10  C9    C10  C4   C3      0.00   0.0  0
 SNP  CONST_11  C6    C5   C10  C4    180.00   0.0  0
 SNP  CONST_12  C8    C9   C10  C4    180.00   0.0  0
 SNP  CONST_13  C8    C7   C6   C5      0.00   0.0  0
 SNP  CONST_14  C8    C9   C10  C5      0.00   0.0  0
 SNP  CONST_15  C9    C10  C5   C6      0.00   0.0  0
 SNP  CONST_16  C9    C8   C7   C6      0.00   0.0  0
 SNP  CONST_17  C10   C5   C6   C7      0.00   0.0  0
 SNP  CONST_18  C10   C9   C8   C7      0.00   0.0  0
 SNP  CONST_19  O1    C1   C2   C3    180.00   0.0  0
 SNP  CONST_20  O1    C1   C9   C8      0.00   0.0  0
 SNP  CONST_21  O1    C1   C9   C10   180.00   0.0  0
 SNP  CONST_22  H3    C3   C2   C1    180.00   0.0  0
 SNP  CONST_23  H8    C8   C9   C1      0.00   0.0  0
 SNP  CONST_24  H4    C4   C3   C2    180.00   0.0  0
 SNP  CONST_25  H2    C2   C3   C4    180.00   0.0  0
 SNP  CONST_26  H5    C5   C10  C4      0.00   0.0  0
 SNP  CONST_27  H7    C7   C6   C5    180.00   0.0  0
 SNP  CONST_28  H6    C6   C7   C8    180.00   0.0  0
 SNP  Var_01    C12   C11  O1   C1   -174.73  30.0  3
 SNP  Var_02    C14   N1   C13  C12  -176.74  30.0  3
 SNP  Var_03    C15   C14  N1   C13   169.03  30.0  3
 SNP  Var_04    H153  C15  C14  N1   -177.20  30.0  3
 SNP  Var_05    H163  C16  C14  N1    -61.04  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
 SNP  chir_01  C12  C11  O2  C13  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
 SNP  plan-1  C1   0.020
 SNP  plan-1  C2   0.020
 SNP  plan-1  C3   0.020
 SNP  plan-1  C4   0.020
 SNP  plan-1  C5   0.020
 SNP  plan-1  C6   0.020
 SNP  plan-1  C7   0.020
 SNP  plan-1  C8   0.020
 SNP  plan-1  C9   0.020
 SNP  plan-1  C10  0.020
 SNP  plan-1  O1   0.020
 SNP  plan-1  H2   0.020
 SNP  plan-1  H3   0.020
 SNP  plan-1  H4   0.020
 SNP  plan-1  H5   0.020
 SNP  plan-1  H6   0.020
 SNP  plan-1  H7   0.020
 SNP  plan-1  H8   0.020

