# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 00:37:18 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: 5-[(3S,4R)-3-{[(2H-1,3-benzodioxol-5-yl)oxy]methyl}piperidin-4-yl]-2-fluoro-N-[(1H-pyrazol-5-yl)methyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(cc1C(=O)NCc2[nH]ncc2)[C@@H]3CCNC[C@H]3COc4ccc5OCOc5c4
#
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
 T0E  T0E  5-[(3S,4R)-3-{[(2H-1,3-benzodioxol-5-yl)oxy]methyl}piperidin-4-yl]-2-fluoro-N-[(1H-pyrazol-5-yl)methyl]benzamide  ligand  58  33  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_T0E
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
 T0E  O    O  O     0  -0.468   4.7010   0.4783  -1.8063
 T0E  C6   C  C     0   0.535   3.5974   0.5695  -1.2949
 T0E  N    N  NH1   0  -0.631   3.1993   1.6510  -0.6035
 T0E  C7   C  CH2   0  -0.371   4.0993   2.7385  -0.3127
 T0E  C8   C  CR5   0   0.411   5.1282   2.3534   0.7022
 T0E  N2   N  NR15  0  -0.483   6.3685   2.8704   0.7163
 T0E  N1   N  N     0  -0.277   7.1185   2.4213   1.7187
 T0E  C10  C  CR15  0  -0.078   6.3347   1.5833   2.3719
 T0E  C9   C  CR15  0  -0.509   5.0635   1.4978   1.7802
 T0E  C5   C  CR6   0  -0.225   2.5915  -0.5330  -1.3628
 T0E  C    C  CR6   0   0.526   2.3450  -1.2129  -2.5447
 T0E  F    F  F     0  -0.299   2.9537  -0.8214  -3.6712
 T0E  C4   C  CR16  0  -0.345   1.9169  -0.9535  -0.2172
 T0E  C3   C  CR6   0   0.178   1.0287  -2.0211  -0.2344
 T0E  C2   C  CR16  0  -0.293   0.8116  -2.6721  -1.4476
 T0E  C1   C  CR16  0  -0.392   1.4590  -2.2701  -2.6048
 T0E  C11  C  CH1   0  -0.330   0.3403  -2.4682   1.0308
 T0E  C15  C  CH1   0  -0.288  -1.1949  -2.4386   0.9274
 T0E  C14  C  CH2   0  -0.290  -1.8055  -2.9432   2.2418
 T0E  N3   N  NH1   0  -0.576  -1.3356  -4.2505   2.6594
 T0E  C13  C  CH2   0  -0.319   0.1133  -4.3106   2.7335
 T0E  C12  C  CH2   0  -0.419   0.8129  -3.8621   1.4547
 T0E  C16  C  CH2   0  -0.154  -1.6641  -1.0349   0.5889
 T0E  O1   O  O2    0  -0.482  -3.0745  -1.0452   0.4675
 T0E  C17  C  CR6   0   0.385  -3.7091   0.1041   0.1547
 T0E  C23  C  CR16  0  -0.442  -5.1100  -0.0001   0.0570
 T0E  C22  C  CR56  0   0.317  -5.7950   1.1386  -0.2720
 T0E  O3   O  O     0  -0.485  -7.1324   1.3016  -0.4077
 T0E  C21  C  CH2   0   0.067  -7.3091   2.5952  -0.9747
 T0E  O2   O  O     0  -0.490  -6.0948   3.3010  -0.7794
 T0E  C20  C  CR56  0   0.276  -5.1597   2.3506  -0.5017
 T0E  C19  C  CR16  0  -0.331  -3.8002   2.4663  -0.4073
 T0E  C18  C  CR16  0  -0.399  -3.0679   1.3160  -0.0713
 T0E  H1   H  HNH1  0   0.416   2.2580   1.7015  -0.2507
 T0E  H2   H  HCH2  0   0.272   4.5825   3.0892  -1.2272
 T0E  H3   H  HCH2  0   0.291   3.4966   3.5663   0.0607
 T0E  H4   H  HNR5  0   0.417   6.7575   3.5325   0.0632
 T0E  H5   H  HCR5  0   0.257   6.7012   1.0638   3.2445
 T0E  H6   H  HCR5  0   0.259   4.2246   0.8972   2.0908
 T0E  H7   H  HCR6  0   0.269   2.1079  -0.4469   0.7224
 T0E  H8   H  HCR6  0   0.266   0.1241  -3.5070  -1.5036
 T0E  H9   H  HCR6  0   0.284   1.2783  -2.7714  -3.5466
 T0E  H10  H  HCH1  0   0.242   0.6256  -1.7676   1.8272
 T0E  H11  H  HCH1  0   0.235  -1.5064  -3.1140   0.1199
 T0E  H12  H  HCH2  0   0.213  -1.5707  -2.2221   3.0352
 T0E  H13  H  HCH2  0   0.244  -2.8926  -2.9777   2.1619
 T0E  H14  H  HNH1  0   0.341  -1.6612  -4.9451   1.9967
 T0E  H16  H  HCH2  0   0.218   0.4408  -3.6767   3.5651
 T0E  H17  H  HCH2  0   0.239   0.4099  -5.3309   2.9843
 T0E  H18  H  HCH2  0   0.223   0.6102  -4.5823   0.6543
 T0E  H19  H  HCH2  0   0.237   1.8956  -3.8535   1.6045
 T0E  H20  H  HCH2  0   0.217  -1.3515  -0.3376   1.3780
 T0E  H21  H  HCH2  0   0.234  -1.2072  -0.6981  -0.3482
 T0E  H22  H  HCR6  0   0.278  -5.6104  -0.9427   0.2375
 T0E  H23  H  HCH2  0   0.230  -7.5215   2.5010  -2.0459
 T0E  H24  H  HCR6  0   0.275  -3.2933   3.4059  -0.5804
 T0E  H25  H  HCR6  0   0.278  -1.9932   1.4023   0.0009
 T0E  H15  H  HCH2  0   0.246  -8.1234   3.1106  -0.4671

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
 T0E  N3   C13  single    1.452  0.020  1.452
 T0E  N3   C14  single    1.451  0.020  1.451
 T0E  C13  C12  single    1.525  0.020  1.525
 T0E  C14  C15  single    1.535  0.020  1.535
 T0E  C12  C11  single    1.532  0.020  1.532
 T0E  C15  C16  single    1.518  0.020  1.518
 T0E  C15  C11  single    1.539  0.020  1.539
 T0E  C18  C19  aromatic  1.404  0.020  1.404
 T0E  C18  C17  aromatic  1.390  0.020  1.390
 T0E  C19  C20  aromatic  1.368  0.020  1.368
 T0E  O1   C16  single    1.416  0.020  1.416
 T0E  O1   C17  single    1.350  0.020  1.350
 T0E  C11  C3   single    1.508  0.020  1.508
 T0E  C17  C23  aromatic  1.408  0.020  1.408
 T0E  C20  O2   single    1.362  0.020  1.362
 T0E  C20  C22  aromatic  1.388  0.020  1.388
 T0E  O2   C21  single    1.418  0.020  1.418
 T0E  C23  C22  aromatic  1.369  0.020  1.369
 T0E  C22  O3   single    1.354  0.020  1.354
 T0E  C21  O3   single    1.423  0.020  1.423
 T0E  C3   C4   aromatic  1.389  0.020  1.389
 T0E  C3   C2   aromatic  1.394  0.020  1.394
 T0E  C4   C5   aromatic  1.394  0.020  1.394
 T0E  C2   C1   aromatic  1.386  0.020  1.386
 T0E  C5   C6   single    1.494  0.020  1.494
 T0E  C5   C    aromatic  1.386  0.020  1.386
 T0E  C1   C    aromatic  1.381  0.020  1.381
 T0E  N    C7   single    1.441  0.020  1.441
 T0E  N    C6   single    1.344  0.020  1.344
 T0E  C7   C8   single    1.496  0.020  1.496
 T0E  C6   O    double    1.220  0.020  1.220
 T0E  C    F    single    1.339  0.020  1.339
 T0E  N2   C8   aromatic  1.344  0.020  1.344
 T0E  N2   N1   aromatic  1.330  0.020  1.330
 T0E  C8   C9   aromatic  1.378  0.020  1.378
 T0E  N1   C10  aromatic  1.320  0.020  1.320
 T0E  C9   C10  aromatic  1.405  0.020  1.405
 T0E  N    H1   single    0.860  0.020  1.020
 T0E  C7   H2   single    0.970  0.020  1.090
 T0E  C7   H3   single    0.970  0.020  1.090
 T0E  N2   H4   single    0.860  0.020  1.020
 T0E  C10  H5   single    0.930  0.020  1.080
 T0E  C9   H6   single    0.930  0.020  1.080
 T0E  C4   H7   single    0.930  0.020  1.080
 T0E  C2   H8   single    0.930  0.020  1.080
 T0E  C1   H9   single    0.930  0.020  1.080
 T0E  C11  H10  single    0.970  0.020  1.090
 T0E  C15  H11  single    0.970  0.020  1.090
 T0E  C14  H12  single    0.970  0.020  1.090
 T0E  C14  H13  single    0.970  0.020  1.090
 T0E  N3   H14  single    0.890  0.020  1.040
 T0E  C13  H16  single    0.970  0.020  1.090
 T0E  C13  H17  single    0.970  0.020  1.090
 T0E  C12  H18  single    0.970  0.020  1.090
 T0E  C12  H19  single    0.970  0.020  1.090
 T0E  C16  H20  single    0.970  0.020  1.090
 T0E  C16  H21  single    0.970  0.020  1.090
 T0E  C23  H22  single    0.930  0.020  1.080
 T0E  C21  H23  single    0.970  0.020  1.090
 T0E  C19  H24  single    0.930  0.020  1.080
 T0E  C18  H25  single    0.930  0.020  1.080
 T0E  C21  H15  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
 T0E  C5   C6   N    114.69  3.000
 T0E  N    C6   O    122.95  3.000
 T0E  C5   C6   O    122.34  3.000
 T0E  H1   N    C7   118.39  3.000
 T0E  H1   N    C6   119.85  3.000
 T0E  C7   N    C6   121.73  3.000
 T0E  H3   C7   H2   106.72  3.000
 T0E  H3   C7   C8   110.09  3.000
 T0E  H2   C7   C8   110.27  3.000
 T0E  H3   C7   N    107.27  3.000
 T0E  H2   C7   N    110.47  3.000
 T0E  C8   C7   N    111.85  3.000
 T0E  C9   C8   N2   105.91  3.000
 T0E  C9   C8   C7   131.19  3.000
 T0E  N2   C8   C7   122.89  3.000
 T0E  H4   N2   N1   119.50  3.000
 T0E  H4   N2   C8   127.02  3.000
 T0E  N1   N2   C8   113.48  3.000
 T0E  C10  N1   N2   104.62  3.000
 T0E  H5   C10  C9   128.20  3.000
 T0E  H5   C10  N1   120.24  3.000
 T0E  C9   C10  N1   111.56  3.000
 T0E  H6   C9   C10  128.10  3.000
 T0E  H6   C9   C8   127.47  3.000
 T0E  C10  C9   C8   104.43  3.000
 T0E  C4   C5   C    117.82  3.000
 T0E  C    C5   C6   121.37  3.000
 T0E  C4   C5   C6   120.73  3.000
 T0E  C1   C    F    118.62  3.000
 T0E  F    C    C5   119.56  3.000
 T0E  C1   C    C5   121.81  3.000
 T0E  H7   C4   C3   118.84  3.000
 T0E  H7   C4   C5   119.06  3.000
 T0E  C3   C4   C5   122.08  3.000
 T0E  C11  C3   C2   121.37  3.000
 T0E  C2   C3   C4   117.99  3.000
 T0E  C11  C3   C4   120.63  3.000
 T0E  H8   C2   C1   118.49  3.000
 T0E  H8   C2   C3   120.26  3.000
 T0E  C1   C2   C3   121.24  3.000
 T0E  H9   C1   C2   120.96  3.000
 T0E  H9   C1   C    119.99  3.000
 T0E  C2   C1   C    119.05  3.000
 T0E  H10  C11  C12  107.44  3.000
 T0E  H10  C11  C15  107.19  3.000
 T0E  C12  C11  C15  110.11  3.000
 T0E  H10  C11  C3   107.50  3.000
 T0E  C15  C11  C3   113.16  3.000
 T0E  C12  C11  C3   111.17  3.000
 T0E  H11  C15  C16  108.49  3.000
 T0E  H11  C15  C14  108.35  3.000
 T0E  C16  C15  C14  111.84  3.000
 T0E  H11  C15  C11  108.70  3.000
 T0E  C16  C15  C11  109.94  3.000
 T0E  C14  C15  C11  109.45  3.000
 T0E  H13  C14  H12  106.68  3.000
 T0E  H13  C14  N3   108.39  3.000
 T0E  H12  C14  N3   108.34  3.000
 T0E  H13  C14  C15  110.14  3.000
 T0E  H12  C14  C15  108.55  3.000
 T0E  N3   C14  C15  114.45  3.000
 T0E  H14  N3   C13  108.99  3.000
 T0E  H14  N3   C14  108.98  3.000
 T0E  C13  N3   C14  112.04  3.000
 T0E  H17  C13  H16  106.57  3.000
 T0E  H17  C13  C12  110.06  3.000
 T0E  H16  C13  C12  109.22  3.000
 T0E  H17  C13  N3   108.75  3.000
 T0E  H16  C13  N3   108.24  3.000
 T0E  C12  C13  N3   113.75  3.000
 T0E  H19  C12  H18  106.77  3.000
 T0E  H19  C12  C13  109.98  3.000
 T0E  H18  C12  C13  109.53  3.000
 T0E  H19  C12  C11  109.66  3.000
 T0E  H18  C12  C11  109.81  3.000
 T0E  C13  C12  C11  110.99  3.000
 T0E  H21  C16  H20  107.50  3.000
 T0E  H21  C16  O1   110.15  3.000
 T0E  H20  C16  O1   110.47  3.000
 T0E  H21  C16  C15  110.24  3.000
 T0E  H20  C16  C15  109.80  3.000
 T0E  O1   C16  C15  108.68  3.000
 T0E  C17  O1   C16  118.83  3.000
 T0E  C18  C17  C23  120.82  3.000
 T0E  C23  C17  O1   114.89  3.000
 T0E  C18  C17  O1   124.29  3.000
 T0E  H22  C23  C22  122.21  3.000
 T0E  H22  C23  C17  120.86  3.000
 T0E  C22  C23  C17  116.93  3.000
 T0E  C20  C22  O3   109.30  3.000
 T0E  O3   C22  C23  128.20  3.000
 T0E  C20  C22  C23  122.49  3.000
 T0E  C21  O3   C22  105.78  3.000
 T0E  H15  C21  H23  110.56  3.000
 T0E  H15  C21  O2   109.91  3.000
 T0E  H23  C21  O2   110.08  3.000
 T0E  H15  C21  O3   109.71  3.000
 T0E  H23  C21  O3   109.59  3.000
 T0E  O2   C21  O3   106.93  3.000
 T0E  C20  O2   C21  105.59  3.000
 T0E  C19  C20  O2   129.61  3.000
 T0E  O2   C20  C22  109.20  3.000
 T0E  C19  C20  C22  121.17  3.000
 T0E  H24  C19  C18  120.36  3.000
 T0E  H24  C19  C20  121.89  3.000
 T0E  C18  C19  C20  117.75  3.000
 T0E  H25  C18  C19  117.98  3.000
 T0E  H25  C18  C17  121.18  3.000
 T0E  C19  C18  C17  120.84  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
 T0E  CONST_01  C10  N1   N2   C8     0.00   0.0  0
 T0E  CONST_02  N1   C10  C9   C8     0.00   0.0  0
 T0E  CONST_03  C10  C9   C8   N2     0.00   0.0  0
 T0E  CONST_04  C9   C10  N1   N2     0.00   0.0  0
 T0E  CONST_05  C9   C8   N2   N1     0.00   0.0  0
 T0E  CONST_06  C2   C3   C4   C5     0.00   0.0  0
 T0E  CONST_07  C2   C1   C    C5     0.00   0.0  0
 T0E  CONST_08  C3   C4   C5   C      0.00   0.0  0
 T0E  CONST_09  C3   C2   C1   C      0.00   0.0  0
 T0E  CONST_10  C1   C2   C3   C4     0.00   0.0  0
 T0E  CONST_11  C1   C    C5   C4     0.00   0.0  0
 T0E  CONST_12  C20  C19  C18  C17    0.00   0.0  0
 T0E  CONST_13  C20  C22  C23  C17    0.00   0.0  0
 T0E  CONST_14  C19  C18  C17  C23    0.00   0.0  0
 T0E  CONST_15  C19  C20  C22  C23    0.00   0.0  0
 T0E  CONST_16  C18  C19  C20  C22    0.00   0.0  0
 T0E  CONST_17  C18  C17  C23  C22    0.00   0.0  0
 T0E  CONST_18  C11  C3   C4   C5   180.00   0.0  0
 T0E  CONST_19  C11  C3   C2   C1   180.00   0.0  0
 T0E  CONST_20  C3   C4   C5   C6   180.00   0.0  0
 T0E  CONST_21  C1   C    C5   C6   180.00   0.0  0
 T0E  CONST_22  N1   N2   C8   C7   180.00   0.0  0
 T0E  CONST_23  C10  C9   C8   C7   180.00   0.0  0
 T0E  CONST_24  C4   C5   C    F    180.00   0.0  0
 T0E  CONST_25  C2   C1   C    F    180.00   0.0  0
 T0E  CONST_26  C19  C18  C17  O1   180.00   0.0  0
 T0E  CONST_27  C22  C23  C17  O1   180.00   0.0  0
 T0E  CONST_28  H5   C10  C9   C8   180.00   0.0  0
 T0E  CONST_29  H6   C9   C8   N2   180.00   0.0  0
 T0E  CONST_30  H4   N2   N1   C10  180.00   0.0  0
 T0E  CONST_31  H9   C1   C    C5   180.00   0.0  0
 T0E  CONST_32  H7   C4   C5   C    180.00   0.0  0
 T0E  CONST_33  H8   C2   C1   C    180.00   0.0  0
 T0E  CONST_34  H24  C19  C18  C17  180.00   0.0  0
 T0E  CONST_35  H25  C18  C17  C23  180.00   0.0  0
 T0E  CONST_36  H22  C23  C22  O3     0.00   0.0  0
 T0E  CONST_37  C5   C6   N    C7   180.00   0.0  0
 T0E  CONST_38  H1   N    C6   C5     0.00   0.0  0
 T0E  CONST_39  C7   N    C6   O      0.00   0.0  0
 T0E  Var_01    N3   C13  C12  C11   53.87  30.0  1
 T0E  Var_02    C13  N3   C14  C15   54.08  30.0  1
 T0E  Var_03    C12  C13  N3   C14  -53.14  30.0  1
 T0E  Var_04    O2   C21  O3   C22  -17.33  30.0  1
 T0E  Var_05    C19  C20  O2   C21  170.32  30.0  1
 T0E  Var_06    C20  C22  O3   C21   10.59  30.0  1
 T0E  Var_07    C4   C5   C6   O    132.03  30.0  1
 T0E  Var_08    N2   C8   C7   N    148.80  30.0  2
 T0E  Var_09    C18  C17  O1   C16    0.53  30.0  2
 T0E  Var_10    C8   C7   N    C6   -70.95  30.0  3
 T0E  Var_11    H20  C16  O1   C17   60.13  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
 T0E  chir_01  C11  C12  C15  C3   positiv
 T0E  chir_02  C15  C11  C16  C14  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
 T0E  plan-1  C7   0.020
 T0E  plan-1  C8   0.020
 T0E  plan-1  N2   0.020
 T0E  plan-1  N1   0.020
 T0E  plan-1  C10  0.020
 T0E  plan-1  C9   0.020
 T0E  plan-1  H4   0.020
 T0E  plan-1  H5   0.020
 T0E  plan-1  H6   0.020
 T0E  plan-2  C6   0.020
 T0E  plan-2  C5   0.020
 T0E  plan-2  C    0.020
 T0E  plan-2  F    0.020
 T0E  plan-2  C4   0.020
 T0E  plan-2  C3   0.020
 T0E  plan-2  C2   0.020
 T0E  plan-2  C1   0.020
 T0E  plan-2  C11  0.020
 T0E  plan-2  H7   0.020
 T0E  plan-2  H8   0.020
 T0E  plan-2  H9   0.020
 T0E  plan-3  O1   0.020
 T0E  plan-3  C17  0.020
 T0E  plan-3  C23  0.020
 T0E  plan-3  C22  0.020
 T0E  plan-3  O3   0.020
 T0E  plan-3  O2   0.020
 T0E  plan-3  C20  0.020
 T0E  plan-3  C19  0.020
 T0E  plan-3  C18  0.020
 T0E  plan-3  H22  0.020
 T0E  plan-3  H24  0.020
 T0E  plan-3  H25  0.020
 T0E  plan-4  O    0.020
 T0E  plan-4  C6   0.020
 T0E  plan-4  N    0.020
 T0E  plan-4  C7   0.020
 T0E  plan-4  C5   0.020
 T0E  plan-4  H1   0.020

