# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:42:03 2021
#   Inital geometry file: a 77 line input string
#   Ligand name: (3R,4S)-4-(3-methoxyphenyl)oxan-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)[C@@H]2CCOC[C@@H]2N
#
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
 W34  W34  (3R,4S)-4-(3-methoxyphenyl)oxan-3-amine  ligand  32  15  .  2022-03-29  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W34
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
 W34  C4   C  CH1   0  -0.336   4.2020  27.3934  16.3379
 W34  C5   C  CR6   0   0.173   2.7978  27.8498  16.0318
 W34  C6   C  CR16  0  -0.338   2.3179  29.0175  16.6321
 W34  C7   C  CR16  0  -0.226   1.0224  29.4412  16.3976
 W34  C8   C  CR16  0  -0.403   0.1691  28.7214  15.5673
 W34  C10  C  CH3   0  -0.436  -1.4287  27.1516  13.8760
 W34  N    N  NH2   0  -0.800   3.4458  25.3144  17.4224
 W34  C    C  CH1   0  -0.089   4.2526  26.5089  17.5998
 W34  C3   C  CH2   0  -0.436   4.9164  26.6851  15.1894
 W34  C2   C  CH2   0  -0.180   6.3226  26.2989  15.6191
 W34  O    O  O2    0  -0.480   6.3184  25.4878  16.7738
 W34  C1   C  CH2   0  -0.185   5.7053  26.1286  17.8659
 W34  C11  C  CR16  0  -0.427   1.9484  27.1297  15.2041
 W34  C9   C  CR6   0   0.406   0.6386  27.5565  14.9683
 W34  O1   O  O2    0  -0.474  -0.0944  26.7760  14.1488
 W34  H1   H  HCH1  0   0.242   4.7799  28.2937  16.5819
 W34  H2   H  HCR6  0   0.243   2.9687  29.5937  17.2787
 W34  H3   H  HCR6  0   0.255   0.6604  30.3500  16.8612
 W34  H4   H  HCR6  0   0.276  -0.8370  29.0816  15.4011
 W34  H5   H  HCH3  0   0.258  -1.8317  26.3974  13.2045
 W34  H6   H  HCH3  0   0.227  -2.0399  27.1777  14.7823
 W34  H7   H  HCH3  0   0.227  -1.4878  28.1263  13.3846
 W34  H8   H  HNH2  0   0.346   3.5150  24.7345  18.2498
 W34  H9   H  HNH2  0   0.351   2.4690  25.5706  17.3499
 W34  H11  H  HCH1  0   0.219   3.9294  27.1219  18.4558
 W34  H12  H  HCH2  0   0.238   4.9732  27.3372  14.3146
 W34  H13  H  HCH2  0   0.231   4.3744  25.7859  14.8908
 W34  H14  H  HCH2  0   0.235   6.8246  25.7310  14.8339
 W34  H15  H  HCH2  0   0.193   6.9159  27.2090  15.7969
 W34  H16  H  HCH2  0   0.235   5.7675  25.4430  18.7153
 W34  H17  H  HCH2  0   0.201   6.2570  27.0401  18.1425
 W34  H18  H  HCR6  0   0.253   2.2840  26.2210  14.7195

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
 W34  C10  O1   single    1.413  0.020  1.413
 W34  O1   C9   single    1.348  0.020  1.348
 W34  C9   C11  aromatic  1.398  0.020  1.398
 W34  C9   C8   aromatic  1.391  0.020  1.391
 W34  C3   C2   single    1.520  0.020  1.520
 W34  C3   C4   single    1.527  0.020  1.527
 W34  C11  C5   aromatic  1.387  0.020  1.387
 W34  C8   C7   aromatic  1.391  0.020  1.391
 W34  C2   O    single    1.411  0.020  1.411
 W34  C5   C6   aromatic  1.398  0.020  1.398
 W34  C5   C4   single    1.508  0.020  1.508
 W34  C7   C6   aromatic  1.383  0.020  1.383
 W34  C4   C    single    1.542  0.020  1.542
 W34  O    C1   single    1.407  0.020  1.407
 W34  N    C    single    1.452  0.020  1.452
 W34  C    C1   single    1.525  0.020  1.525
 W34  C4   H1   single    0.970  0.020  1.090
 W34  C6   H2   single    0.930  0.020  1.080
 W34  C7   H3   single    0.930  0.020  1.080
 W34  C8   H4   single    0.930  0.020  1.080
 W34  C10  H5   single    0.970  0.020  1.090
 W34  C10  H6   single    0.970  0.020  1.090
 W34  C10  H7   single    0.970  0.020  1.090
 W34  N    H8   single    0.890  0.020  1.040
 W34  N    H9   single    0.890  0.020  1.040
 W34  C    H11  single    0.970  0.020  1.090
 W34  C3   H12  single    0.970  0.020  1.090
 W34  C3   H13  single    0.970  0.020  1.090
 W34  C2   H14  single    0.970  0.020  1.090
 W34  C2   H15  single    0.970  0.020  1.090
 W34  C1   H16  single    0.970  0.020  1.090
 W34  C1   H17  single    0.970  0.020  1.090
 W34  C11  H18  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
 W34  H1   C4   C3   107.55  3.000
 W34  H1   C4   C    105.75  3.000
 W34  C3   C4   C    109.52  3.000
 W34  H1   C4   C5   106.69  3.000
 W34  C    C4   C5   111.74  3.000
 W34  C3   C4   C5   115.05  3.000
 W34  C11  C5   C6   118.66  3.000
 W34  C6   C5   C4   119.03  3.000
 W34  C11  C5   C4   122.28  3.000
 W34  H2   C6   C7   120.07  3.000
 W34  H2   C6   C5   119.62  3.000
 W34  C7   C6   C5   120.31  3.000
 W34  H3   C7   C8   119.00  3.000
 W34  H3   C7   C6   119.85  3.000
 W34  C8   C7   C6   121.15  3.000
 W34  H4   C8   C9   121.77  3.000
 W34  H4   C8   C7   119.34  3.000
 W34  C9   C8   C7   118.89  3.000
 W34  H7   C10  H6   108.73  3.000
 W34  H7   C10  H5   108.71  3.000
 W34  H6   C10  H5   108.74  3.000
 W34  H7   C10  O1   112.02  3.000
 W34  H6   C10  O1   111.98  3.000
 W34  H5   C10  O1   106.56  3.000
 W34  H9   N    H8   105.62  3.000
 W34  H9   N    C    109.67  3.000
 W34  H8   N    C    109.46  3.000
 W34  H11  C    C1   106.42  3.000
 W34  H11  C    N    112.94  3.000
 W34  C1   C    N    110.21  3.000
 W34  H11  C    C4   107.89  3.000
 W34  C1   C    C4   108.49  3.000
 W34  N    C    C4   110.71  3.000
 W34  H13  C3   H12  107.37  3.000
 W34  H13  C3   C2   109.11  3.000
 W34  H12  C3   C2   109.26  3.000
 W34  H13  C3   C4   110.83  3.000
 W34  H12  C3   C4   110.47  3.000
 W34  C2   C3   C4   109.76  3.000
 W34  H15  C2   H14  107.37  3.000
 W34  H15  C2   O    110.16  3.000
 W34  H14  C2   O    106.92  3.000
 W34  H15  C2   C3   109.52  3.000
 W34  H14  C2   C3   110.75  3.000
 W34  O    C2   C3   112.00  3.000
 W34  C1   O    C2   112.01  3.000
 W34  H17  C1   H16  107.19  3.000
 W34  H17  C1   O    110.72  3.000
 W34  H16  C1   O    107.02  3.000
 W34  H17  C1   C    108.35  3.000
 W34  H16  C1   C    110.25  3.000
 W34  O    C1   C    113.16  3.000
 W34  H18  C11  C9   118.10  3.000
 W34  H18  C11  C5   120.84  3.000
 W34  C9   C11  C5   121.06  3.000
 W34  O1   C9   C11  115.80  3.000
 W34  C11  C9   C8   119.95  3.000
 W34  O1   C9   C8   124.25  3.000
 W34  C9   O1   C10  118.49  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
 W34  CONST_01  C8   C9   C11  C5      0.00   0.0  0
 W34  CONST_02  C8   C7   C6   C5      0.00   0.0  0
 W34  CONST_03  C9   C11  C5   C6      0.00   0.0  0
 W34  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 W34  CONST_05  C11  C9   C8   C7      0.00   0.0  0
 W34  CONST_06  C11  C5   C6   C7      0.00   0.0  0
 W34  CONST_07  C9   C11  C5   C4    180.00   0.0  0
 W34  CONST_08  C7   C6   C5   C4    180.00   0.0  0
 W34  CONST_09  O1   C9   C11  C5    180.00   0.0  0
 W34  CONST_10  O1   C9   C8   C7    180.00   0.0  0
 W34  CONST_11  H18  C11  C5   C4      0.00   0.0  0
 W34  CONST_12  H2   C6   C5   C4      0.00   0.0  0
 W34  CONST_13  H3   C7   C6   C5    180.00   0.0  0
 W34  CONST_14  H4   C8   C7   C6    180.00   0.0  0
 W34  Var_01    O    C2   C3   C4     56.87  30.0  1
 W34  Var_02    H16  C1   O    C2   -178.70  30.0  1
 W34  Var_03    C11  C9   O1   C10   179.73  30.0  2
 W34  Var_04    H5   C10  O1   C9    179.98  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
 W34  chir_01  C4  C3  C5  C   negativ
 W34  chir_02  C   N   C4  C1  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
 W34  plan-1  C4   0.020
 W34  plan-1  C5   0.020
 W34  plan-1  C6   0.020
 W34  plan-1  C7   0.020
 W34  plan-1  C8   0.020
 W34  plan-1  C11  0.020
 W34  plan-1  C9   0.020
 W34  plan-1  O1   0.020
 W34  plan-1  H2   0.020
 W34  plan-1  H3   0.020
 W34  plan-1  H4   0.020
 W34  plan-1  H18  0.020

