# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 09:56:44 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (2S)-2-methyl-2,3-dihydrothieno[2,3-f][1,4]oxazepin-5-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CN=C(N)c2sccc2O1
#
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
 329  329  (2S)-2-methyl-2,3-dihydrothieno[2,3-f][1,4]oxazepin-5-amine  ligand  22  12  .  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_329
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
 329  C1    C  CR15  0  -0.245   1.0956   2.1212   0.3422
 329  C2    C  CR5   0   0.404   0.1579   1.0624   0.1541
 329  O1    O  O2    0  -0.461  -1.1295   1.3851   0.0553
 329  C3    C  CH1   0   0.003  -2.1247   0.3667  -0.0795
 329  C4    C  CH3   0  -0.692  -3.4100   1.0861  -0.4305
 329  N1    N  N     0  -0.423  -0.9450  -1.7676  -0.6297
 329  C5    C  C     0   0.406   0.1807  -1.5109  -0.0853
 329  N2    N  NH2   0  -0.832   1.0017  -2.5505   0.2922
 329  C6    C  CR5   0  -0.376   0.7535  -0.1812   0.1184
 329  S1    S  S2    0   0.220   2.4757  -0.0256   0.3062
 329  C7    C  CR15  0  -0.444   2.3713   1.6723   0.4406
 329  C8    C  CH2   0  -0.361  -1.7367  -0.6785  -1.1329
 329  H1    H  HCR5  0   0.280   0.8095   3.1618   0.4008
 329  H3    H  HCH1  0   0.244  -2.2349  -0.1365   0.8880
 329  H4    H  HCH3  0   0.235  -3.3567   1.5304  -1.4260
 329  H4A   H  HCH3  0   0.240  -4.2405   0.3817  -0.4200
 329  H4B   H  HCH3  0   0.246  -3.6330   1.8738   0.2889
 329  HN2   H  HNH2  0   0.381   0.5632  -3.4558   0.2119
 329  HN2A  H  HNH2  0   0.386   1.4869  -2.4464   1.1708
 329  H7    H  HCR5  0   0.305   3.2631   2.2633   0.5827
 329  H8    H  HCH2  0   0.246  -2.6613  -1.0987  -1.5334
 329  H8A   H  HCH2  0   0.237  -1.2523  -0.1613  -1.9731

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
 329  C1  C2    aromatic  1.427  0.020  1.427
 329  C1  C7    aromatic  1.356  0.020  1.356
 329  C2  O1    single    1.331  0.020  1.331
 329  C2  C6    aromatic  1.379  0.020  1.379
 329  O1  C3    single    1.430  0.020  1.430
 329  C3  C4    single    1.514  0.020  1.514
 329  C3  C8    single    1.534  0.020  1.534
 329  N1  C5    double    1.277  0.020  1.277
 329  N1  C8    single    1.437  0.020  1.437
 329  C5  N2    single    1.377  0.020  1.377
 329  C5  C6    single    1.462  0.020  1.462
 329  C6  S1    aromatic  1.739  0.020  1.739
 329  S1  C7    aromatic  1.706  0.020  1.706
 329  C1  H1    single    0.930  0.020  1.080
 329  C3  H3    single    0.970  0.020  1.090
 329  C4  H4    single    0.970  0.020  1.090
 329  C4  H4A   single    0.970  0.020  1.090
 329  C4  H4B   single    0.970  0.020  1.090
 329  N2  HN2   single    0.890  0.020  1.040
 329  N2  HN2A  single    0.890  0.020  1.040
 329  C7  H7    single    0.930  0.020  1.080
 329  C8  H8    single    0.970  0.020  1.090
 329  C8  H8A   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
 329  H1    C1  C7   124.32  3.000
 329  H1    C1  C2   123.20  3.000
 329  C7    C1  C2   112.47  3.000
 329  C6    C2  O1   129.38  3.000
 329  C6    C2  C1   112.87  3.000
 329  O1    C2  C1   117.75  3.000
 329  C3    O1  C2   120.49  3.000
 329  H3    C3  C8   108.59  3.000
 329  H3    C3  C4   109.72  3.000
 329  C8    C3  C4   112.29  3.000
 329  H3    C3  O1   108.28  3.000
 329  C8    C3  O1   111.96  3.000
 329  C4    C3  O1   105.91  3.000
 329  H4B   C4  H4A  107.76  3.000
 329  H4B   C4  H4   108.53  3.000
 329  H4A   C4  H4   108.02  3.000
 329  H4B   C4  C3   111.35  3.000
 329  H4A   C4  C3   109.74  3.000
 329  H4    C4  C3   111.31  3.000
 329  C8    N1  C5   118.86  3.000
 329  C6    C5  N2   114.50  3.000
 329  C6    C5  N1   126.00  3.000
 329  N2    C5  N1   119.39  3.000
 329  HN2A  N2  HN2  111.77  3.000
 329  HN2A  N2  C5   116.58  3.000
 329  HN2   N2  C5   113.34  3.000
 329  S1    C6  C5   118.97  3.000
 329  S1    C6  C2   110.13  3.000
 329  C5    C6  C2   130.87  3.000
 329  C7    S1  C6    92.12  3.000
 329  H7    C7  S1   120.31  3.000
 329  H7    C7  C1   127.28  3.000
 329  S1    C7  C1   112.41  3.000
 329  H8A   C8  H8   105.90  3.000
 329  H8A   C8  N1   112.42  3.000
 329  H8    C8  N1   107.65  3.000
 329  H8A   C8  C3   108.41  3.000
 329  H8    C8  C3   107.46  3.000
 329  N1    C8  C3   114.53  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
 329  CONST_01  S1   C6  C2  C1     0.00   0.0  0
 329  CONST_02  C6   S1  C7  C1     0.00   0.0  0
 329  CONST_03  S1   C7  C1  C2     0.00   0.0  0
 329  CONST_04  C7   S1  C6  C2     0.00   0.0  0
 329  CONST_05  C7   C1  C2  C6     0.00   0.0  0
 329  CONST_06  C8   N1  C5  C6     0.00   0.0  0
 329  CONST_07  C8   N1  C5  N2   180.00   0.0  0
 329  CONST_08  H7   C7  C1  C2   180.00   0.0  0
 329  CONST_09  H1   C1  C2  O1     0.00   0.0  0
 329  CONST_10  HN2  N2  C5  N1     0.00   0.0  0
 329  Var_01    N1   C5  C6  C2    20.47  30.0  1
 329  Var_02    C6   C2  O1  C3     1.66  30.0  1
 329  Var_03    H8   C8  N1  C5  -178.69  30.0  1

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
 329  chir_01  C3  O1  C4  C8  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
 329  plan-1  N1    0.020
 329  plan-1  C5    0.020
 329  plan-1  N2    0.020
 329  plan-1  C6    0.020
 329  plan-1  C8    0.020
 329  plan-1  HN2   0.020
 329  plan-1  HN2A  0.020
 329  plan-2  C1    0.020
 329  plan-2  C2    0.020
 329  plan-2  O1    0.020
 329  plan-2  C5    0.020
 329  plan-2  C6    0.020
 329  plan-2  S1    0.020
 329  plan-2  C7    0.020
 329  plan-2  H1    0.020
 329  plan-2  H7    0.020

