# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 20:18:07 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: [3-[(1~{R})-1-(dimethylamino)ethyl]-4-oxidanyl-phenyl] ~{N}-ethyl-~{N}-methyl-carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(C)C(=O)Oc1ccc(O)c(c1)[C@@H](C)N(C)C
#
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
 BY2  BY2  '[3-[(1~{R})-1-(dimethylamino)ethyl]-4-oxidanyl-phenyl] ~{N}-ethyl-~{N}-methyl-carbamate'  ligand  41  19  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BY2
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
 BY2  C10  C  CH3   0  -0.526   3.9180   2.8204   0.0848
 BY2  C11  C  C     0   0.742  -2.5442   0.0456  -0.4404
 BY2  C12  C  CH2   0  -0.316  -4.7833   0.7271  -1.0098
 BY2  C13  C  CH3   0  -0.658  -5.7189  -0.4715  -0.9920
 BY2  C14  C  CH3   0  -0.520  -3.9673   0.9331   1.3417
 BY2  C01  C  CR6   0   0.316   2.0572  -1.7362  -0.0820
 BY2  C02  C  CR16  0  -0.382   0.9485  -2.5544   0.1237
 BY2  C03  C  CR16  0  -0.313  -0.3060  -2.0055   0.3318
 BY2  C04  C  CR6   0   0.366  -0.4451  -0.6295   0.3319
 BY2  C05  C  CR16  0  -0.338   0.6509   0.1892   0.1327
 BY2  C06  C  CR6   0  -0.015   1.9185  -0.3456  -0.0659
 BY2  C07  C  CH1   0  -0.081   3.0967   0.5710  -0.3340
 BY2  C08  C  CH3   0  -0.684   3.1444   0.8588  -1.8345
 BY2  C09  C  CH3   0  -0.524   3.1424   1.4794   1.8800
 BY2  N01  N  NT    0  -0.408   2.9821   1.7838   0.4711
 BY2  N02  N  NT    0  -0.474  -3.6955   0.6143  -0.0501
 BY2  O01  O  O2    0  -0.529  -1.6744  -0.0552   0.5921
 BY2  O02  O  OH1   0  -0.630   3.2863  -2.2512  -0.3038
 BY2  O03  O  O     0  -0.511  -2.2747  -0.3298  -1.5618
 BY2  H1   H  HCH3  0   0.242   3.7175   3.1835  -0.9218
 BY2  H2   H  HCH3  0   0.236   3.8083   3.6692   0.7609
 BY2  H3   H  HCH3  0   0.191   4.9701   2.4970   0.1286
 BY2  H4   H  HCH2  0   0.255  -4.3644   0.8662  -2.0045
 BY2  H5   H  HCH2  0   0.248  -5.3351   1.6379  -0.7747
 BY2  H6   H  HCH3  0   0.230  -5.1914  -1.3860  -1.2634
 BY2  H7   H  HCH3  0   0.229  -6.1670  -0.6146  -0.0077
 BY2  H8   H  HCH3  0   0.234  -6.5288  -0.3252  -1.7069
 BY2  H9   H  HCH3  0   0.251  -3.2671   1.6707   1.7326
 BY2  H10  H  HCH3  0   0.251  -4.9644   1.3617   1.4031
 BY2  H11  H  HCH3  0   0.245  -3.9412   0.0528   1.9842
 BY2  H12  H  HCR6  0   0.273   1.0641  -3.6325   0.1216
 BY2  H13  H  HCR6  0   0.271  -1.1596  -2.6503   0.4971
 BY2  H14  H  HCR6  0   0.260   0.5352   1.2660   0.1511
 BY2  H15  H  HCH1  0   0.213   4.0286   0.0443  -0.0712
 BY2  H16  H  HCH3  0   0.240   4.0595   1.3715  -2.1293
 BY2  H17  H  HCH3  0   0.246   3.1082  -0.0778  -2.3905
 BY2  H18  H  HCH3  0   0.228   2.2904   1.4643  -2.1438
 BY2  H19  H  HCH3  0   0.195   4.1401   1.0774   2.1175
 BY2  H20  H  HCH3  0   0.233   2.9967   2.3821   2.4741
 BY2  H21  H  HCH3  0   0.239   2.4043   0.7475   2.2067
 BY2  H23  H  HOH1  0   0.475   3.2550  -3.2139  -0.2766

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
 BY2  C08  C07  single    1.529  0.020  1.529
 BY2  C09  N01  single    1.450  0.020  1.450
 BY2  C07  N01  single    1.460  0.020  1.460
 BY2  C07  C06  single    1.517  0.020  1.517
 BY2  N01  C10  single    1.449  0.020  1.449
 BY2  O02  C01  single    1.351  0.020  1.351
 BY2  C06  C01  aromatic  1.398  0.020  1.398
 BY2  C06  C05  aromatic  1.390  0.020  1.390
 BY2  C01  C02  aromatic  1.393  0.020  1.393
 BY2  C05  C04  aromatic  1.382  0.020  1.382
 BY2  C02  C03  aromatic  1.385  0.020  1.385
 BY2  C04  C03  aromatic  1.383  0.020  1.383
 BY2  C04  O01  single    1.382  0.020  1.382
 BY2  O03  C11  double    1.213  0.020  1.213
 BY2  O01  C11  single    1.354  0.020  1.354
 BY2  C11  N02  single    1.342  0.020  1.342
 BY2  N02  C12  single    1.455  0.020  1.455
 BY2  N02  C14  single    1.453  0.020  1.453
 BY2  C12  C13  single    1.521  0.020  1.521
 BY2  C10  H1   single    0.970  0.020  1.090
 BY2  C10  H2   single    0.970  0.020  1.090
 BY2  C10  H3   single    0.970  0.020  1.090
 BY2  C12  H4   single    0.970  0.020  1.090
 BY2  C12  H5   single    0.970  0.020  1.090
 BY2  C13  H6   single    0.970  0.020  1.090
 BY2  C13  H7   single    0.970  0.020  1.090
 BY2  C13  H8   single    0.970  0.020  1.090
 BY2  C14  H9   single    0.970  0.020  1.090
 BY2  C14  H10  single    0.970  0.020  1.090
 BY2  C14  H11  single    0.970  0.020  1.090
 BY2  C02  H12  single    0.930  0.020  1.080
 BY2  C03  H13  single    0.930  0.020  1.080
 BY2  C05  H14  single    0.930  0.020  1.080
 BY2  C07  H15  single    0.970  0.020  1.090
 BY2  C08  H16  single    0.970  0.020  1.090
 BY2  C08  H17  single    0.970  0.020  1.090
 BY2  C08  H18  single    0.970  0.020  1.090
 BY2  C09  H19  single    0.970  0.020  1.090
 BY2  C09  H20  single    0.970  0.020  1.090
 BY2  C09  H21  single    0.970  0.020  1.090
 BY2  O02  H23  single    0.850  0.020  0.980

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
 BY2  H3   C10  H2   107.45  3.000
 BY2  H3   C10  H1   108.09  3.000
 BY2  H2   C10  H1   107.17  3.000
 BY2  H3   C10  N01  113.34  3.000
 BY2  H2   C10  N01  109.06  3.000
 BY2  H1   C10  N01  111.48  3.000
 BY2  O03  C11  O01  122.64  3.000
 BY2  O01  C11  N02  111.15  3.000
 BY2  O03  C11  N02  126.21  3.000
 BY2  H5   C12  H4   106.56  3.000
 BY2  H5   C12  N02  107.51  3.000
 BY2  H4   C12  N02  108.97  3.000
 BY2  H5   C12  C13  110.15  3.000
 BY2  H4   C12  C13  110.38  3.000
 BY2  N02  C12  C13  113.03  3.000
 BY2  H8   C13  H7   107.70  3.000
 BY2  H8   C13  H6   107.99  3.000
 BY2  H7   C13  H6   108.26  3.000
 BY2  H8   C13  C12  110.10  3.000
 BY2  H7   C13  C12  111.51  3.000
 BY2  H6   C13  C12  111.14  3.000
 BY2  H11  C14  H10  107.88  3.000
 BY2  H11  C14  H9   108.65  3.000
 BY2  H10  C14  H9   107.59  3.000
 BY2  H11  C14  N02  112.51  3.000
 BY2  H10  C14  N02  108.19  3.000
 BY2  H9   C14  N02  111.83  3.000
 BY2  O02  C01  C06  118.13  3.000
 BY2  C06  C01  C02  120.24  3.000
 BY2  O02  C01  C02  121.63  3.000
 BY2  H12  C02  C03  119.39  3.000
 BY2  H12  C02  C01  119.92  3.000
 BY2  C03  C02  C01  120.68  3.000
 BY2  H13  C03  C04  120.89  3.000
 BY2  H13  C03  C02  120.07  3.000
 BY2  C04  C03  C02  119.04  3.000
 BY2  O01  C04  C05  119.10  3.000
 BY2  O01  C04  C03  120.20  3.000
 BY2  C05  C04  C03  120.63  3.000
 BY2  H14  C05  C06  118.83  3.000
 BY2  H14  C05  C04  120.11  3.000
 BY2  C06  C05  C04  121.05  3.000
 BY2  C07  C06  C05  120.08  3.000
 BY2  C05  C06  C01  118.35  3.000
 BY2  C07  C06  C01  121.48  3.000
 BY2  H15  C07  N01  109.37  3.000
 BY2  H15  C07  C08  107.32  3.000
 BY2  N01  C07  C08  112.78  3.000
 BY2  H15  C07  C06  109.02  3.000
 BY2  N01  C07  C06  110.09  3.000
 BY2  C08  C07  C06  108.15  3.000
 BY2  H18  C08  H17  107.83  3.000
 BY2  H18  C08  H16  108.63  3.000
 BY2  H17  C08  H16  107.11  3.000
 BY2  H18  C08  C07  110.99  3.000
 BY2  H17  C08  C07  109.75  3.000
 BY2  H16  C08  C07  112.35  3.000
 BY2  H21  C09  H20  107.58  3.000
 BY2  H21  C09  H19  107.68  3.000
 BY2  H20  C09  H19  107.80  3.000
 BY2  H21  C09  N01  110.94  3.000
 BY2  H20  C09  N01  109.92  3.000
 BY2  H19  C09  N01  112.72  3.000
 BY2  C09  N01  C07  110.64  3.000
 BY2  C07  N01  C10  113.36  3.000
 BY2  C09  N01  C10  109.74  3.000
 BY2  C14  N02  C12  118.35  3.000
 BY2  C14  N02  C11  122.13  3.000
 BY2  C12  N02  C11  118.84  3.000
 BY2  C04  O01  C11  117.32  3.000
 BY2  H23  O02  C01  110.28  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
 BY2  CONST_01  C04  C05  C06  C01    0.00   0.0  0
 BY2  CONST_02  C04  C03  C02  C01    0.00   0.0  0
 BY2  CONST_03  C05  C06  C01  C02    0.00   0.0  0
 BY2  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 BY2  CONST_05  C06  C01  C02  C03    0.00   0.0  0
 BY2  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 BY2  CONST_07  C07  C06  C01  C02  180.00   0.0  0
 BY2  CONST_08  O01  C04  C03  C02  180.00   0.0  0
 BY2  CONST_09  O02  C01  C02  C03  180.00   0.0  0
 BY2  CONST_10  C07  C06  C05  C04  180.00   0.0  0
 BY2  CONST_11  O02  C01  C06  C05  180.00   0.0  0
 BY2  CONST_12  O01  C04  C05  C06  180.00   0.0  0
 BY2  CONST_13  H14  C05  C06  C01  180.00   0.0  0
 BY2  CONST_14  H13  C03  C02  C01  180.00   0.0  0
 BY2  CONST_15  H12  C02  C03  C04  180.00   0.0  0
 BY2  Var_01    C05  C04  O01  C11   99.80  30.0  2
 BY2  Var_02    O03  C11  O01  C04   -0.89  30.0  3
 BY2  Var_03    C13  C12  N02  C11   90.60  30.0  3
 BY2  Var_04    H19  C09  N01  C10  -62.80  30.0  3
 BY2  Var_05    H9   C14  N02  C11   62.92  30.0  3
 BY2  Var_06    H1   C10  N01  C07   64.81  30.0  3
 BY2  Var_07    H6   C13  C12  N02  -61.95  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
 BY2  chir_01  C07  C08  N01  C06  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
 BY2  plan-1  C01  0.020
 BY2  plan-1  C02  0.020
 BY2  plan-1  C03  0.020
 BY2  plan-1  C04  0.020
 BY2  plan-1  C05  0.020
 BY2  plan-1  C06  0.020
 BY2  plan-1  C07  0.020
 BY2  plan-1  O01  0.020
 BY2  plan-1  O02  0.020
 BY2  plan-1  H12  0.020
 BY2  plan-1  H13  0.020
 BY2  plan-1  H14  0.020
 BY2  plan-2  C11  0.020
 BY2  plan-2  N02  0.020
 BY2  plan-2  O01  0.020
 BY2  plan-2  O03  0.020

