# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 19:54:56 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: (3S)-1-(1,3-benzodioxol-5-ylmethyl)-3-[4-(1H-imidazol-1-yl)phenoxy]piperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1C[C@@H](CN(C1)Cc2ccc3OCOc3c2)Oc4ccc(cc4)n5ccnc5
#
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
 342  342  (3S)-1-(1,3-benzodioxol-5-ylmethyl)-3-[4-(1H-imidazol-1-yl)phenoxy]piperidine  ligand  51  28  .  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_342
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
 342  C36   C  CR16   0  -0.372  -1.0081  -3.0420  -3.6153
 342  C35   C  CR56   0   0.315  -1.0423  -2.7099  -4.9447
 342  O39   O  O      0  -0.489  -0.0558  -2.8251  -5.8695
 342  C38   C  CH2    0   0.070  -0.5367  -2.1900  -7.0462
 342  O37   O  O      0  -0.488  -1.9306  -1.9801  -6.8672
 342  C34   C  CR56   0   0.283  -2.1790  -2.1958  -5.5502
 342  C33   C  CR16   0  -0.332  -3.3353  -1.9848  -4.8438
 342  C32   C  CR16   0  -0.330  -3.3119  -2.3157  -3.4816
 342  C31   C  CR6    0   0.063  -2.1826  -2.8405  -2.8713
 342  C27   C  CH2    0  -0.313  -2.2147  -3.2501  -1.4195
 342  N23   N  NT    -1  -0.410  -0.9694  -2.9731  -0.7435
 342  C22   C  CH2    0  -0.281  -0.7926  -3.7521   0.4609
 342  C24   C  CH2    0  -0.277  -0.7621  -1.5587  -0.5015
 342  C25   C  CH2    0  -0.432   0.6470  -1.2988   0.0079
 342  C26   C  CH2    0  -0.480   0.9333  -2.1280   1.2540
 342  C21   C  CH1    0  -0.021   0.6137  -3.5978   1.0139
 342  O17   O  O2     0  -0.474   1.4919  -4.1647   0.0433
 342  C14   C  CR6    0   0.399   2.7584  -4.4673   0.3650
 342  C15   C  CR16   0  -0.351   3.5764  -4.8701  -0.6947
 342  C16   C  CR16   0  -0.275   4.8924  -5.2247  -0.4757
 342  C13   C  CR16   0  -0.372   3.2939  -4.4294   1.6517
 342  C12   C  CR16   0  -0.282   4.6122  -4.8072   1.8689
 342  C11   C  CR6    0   0.320   5.4189  -5.1974   0.8119
 342  N3    N  NR5    0  -0.516   6.7640  -5.5645   1.0374
 342  C4    C  CR15   0  -0.119   7.4268  -6.6298   0.4839
 342  C5    C  CR15   0  -0.216   8.6924  -6.5734   0.9879
 342  NFE   N  N      0  -0.448   8.8212  -5.5035   1.8291
 342  C2    C  CR15   0   0.084   7.6524  -4.9219   1.8357
 342  H36   H  HCR6   0   0.263  -0.1177  -3.4325  -3.1398
 342  H381  H  HCH2   0   0.243  -0.3681  -2.8349  -7.9088
 342  H382  H  HCH2   0   0.231  -0.0300  -1.2282  -7.1832
 342  H33   H  HCR6   0   0.269  -4.2234  -1.5783  -5.3082
 342  H32   H  HCR6   0   0.249  -4.2042  -2.1504  -2.8900
 342  H271  H  HCH2   0   0.212  -3.0820  -2.7805  -0.9260
 342  H272  H  HCH2   0   0.249  -2.3904  -4.3297  -1.3688
 342  H221  H  HCH2   0   0.247  -0.9816  -4.8056   0.2401
 342  H222  H  HCH2   0   0.202  -1.4984  -3.4661   1.2606
 342  H241  H  HCH2   0   0.189  -1.4930  -1.1688   0.2308
 342  H242  H  HCH2   0   0.240  -0.9270  -1.0099  -1.4309
 342  H251  H  HCH2   0   0.234   0.7622  -0.2368   0.2331
 342  H252  H  HCH2   0   0.227   1.3669  -1.5358  -0.7790
 342  H261  H  HCH2   0   0.251   1.9672  -1.9962   1.5813
 342  H262  H  HCH2   0   0.236   0.3049  -1.7833   2.0810
 342  H21   H  HCH1   0   0.253   0.6700  -4.1661   1.9491
 342  H15   H  HCR6   0   0.268   3.1716  -4.8923  -1.6986
 342  H16   H  HCR6   0   0.278   5.5128  -5.5111  -1.3154
 342  H13   H  HCR6   0   0.286   2.7021  -4.1294   2.5053
 342  H12   H  HCR6   0   0.279   4.9990  -4.8036   2.8799
 342  H4    H  HCR5   0   0.296   6.9438  -7.3241  -0.1829
 342  H5    H  HCR5   0   0.256   9.5110  -7.2479   0.7907
 342  H2    H  HCR5   0   0.286   7.3912  -4.0252   2.3775

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
 342  C36  C31   aromatic  1.405  0.020  1.405
 342  C36  C35   aromatic  1.371  0.020  1.371
 342  C36  H36   single    0.930  0.020  1.080
 342  C35  O39   single    1.357  0.020  1.357
 342  C35  C34   aromatic  1.387  0.020  1.387
 342  O39  C38   single    1.421  0.020  1.421
 342  C38  O37   single    1.421  0.020  1.421
 342  C38  H381  single    0.970  0.020  1.090
 342  C38  H382  single    0.970  0.020  1.090
 342  O37  C34   single    1.357  0.020  1.357
 342  C34  C33   aromatic  1.371  0.020  1.371
 342  C33  C32   aromatic  1.402  0.020  1.402
 342  C33  H33   single    0.930  0.020  1.080
 342  C32  C31   aromatic  1.387  0.020  1.387
 342  C32  H32   single    0.930  0.020  1.080
 342  C31  C27   single    1.509  0.020  1.509
 342  C27  N23   single    1.444  0.020  1.444
 342  C27  H271  single    0.970  0.020  1.090
 342  C27  H272  single    0.970  0.020  1.090
 342  N23  C24   single    1.450  0.020  1.450
 342  N23  C22   single    1.445  0.020  1.445
 342  C22  C21   single    1.519  0.020  1.519
 342  C22  H221  single    0.970  0.020  1.090
 342  C22  H222  single    0.970  0.020  1.090
 342  C24  C25   single    1.521  0.020  1.521
 342  C24  H241  single    0.970  0.020  1.090
 342  C24  H242  single    0.970  0.020  1.090
 342  C25  C26   single    1.524  0.020  1.524
 342  C25  H251  single    0.970  0.020  1.090
 342  C25  H252  single    0.970  0.020  1.090
 342  C26  C21   single    1.523  0.020  1.523
 342  C26  H261  single    0.970  0.020  1.090
 342  C26  H262  single    0.970  0.020  1.090
 342  C21  O17   single    1.426  0.020  1.426
 342  C21  H21   single    0.970  0.020  1.090
 342  O17  C14   single    1.341  0.020  1.341
 342  C14  C15   aromatic  1.398  0.020  1.398
 342  C14  C13   aromatic  1.394  0.020  1.394
 342  C15  C16   aromatic  1.380  0.020  1.380
 342  C15  H15   single    0.930  0.020  1.080
 342  C16  C11   aromatic  1.391  0.020  1.391
 342  C16  H16   single    0.930  0.020  1.080
 342  C13  C12   aromatic  1.388  0.020  1.388
 342  C13  H13   single    0.930  0.020  1.080
 342  C12  C11   aromatic  1.386  0.020  1.386
 342  C12  H12   single    0.930  0.020  1.080
 342  C11  N3    single    1.412  0.020  1.412
 342  N3   C4    aromatic  1.371  0.020  1.371
 342  N3   C2    aromatic  1.356  0.020  1.356
 342  C4   C5    aromatic  1.363  0.020  1.363
 342  C4   H4    single    0.930  0.020  1.080
 342  C5   NFE   aromatic  1.367  0.020  1.367
 342  C5   H5    single    0.930  0.020  1.080
 342  NFE  C2    aromatic  1.306  0.020  1.306
 342  C2   H2    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
 342  H36   C36  C31   120.46  3.000
 342  H36   C36  C35   122.28  3.000
 342  C31   C36  C35   117.25  3.000
 342  C34   C35  O39   109.26  3.000
 342  C34   C35  C36   122.26  3.000
 342  O39   C35  C36   128.47  3.000
 342  C38   O39  C35   106.28  3.000
 342  H382  C38  H381  110.41  3.000
 342  H382  C38  O37   109.86  3.000
 342  H381  C38  O37   109.80  3.000
 342  H382  C38  O39   109.84  3.000
 342  H381  C38  O39   109.78  3.000
 342  O37   C38  O39   107.08  3.000
 342  C34   O37  C38   106.16  3.000
 342  C33   C34  O37   129.03  3.000
 342  C33   C34  C35   121.55  3.000
 342  O37   C34  C35   109.42  3.000
 342  H33   C33  C32   121.31  3.000
 342  H33   C33  C34   121.94  3.000
 342  C32   C33  C34   116.75  3.000
 342  H32   C32  C31   119.22  3.000
 342  H32   C32  C33   118.74  3.000
 342  C31   C32  C33   122.04  3.000
 342  C27   C31  C32   120.59  3.000
 342  C27   C31  C36   119.23  3.000
 342  C32   C31  C36   120.13  3.000
 342  H272  C27  H271  105.84  3.000
 342  H272  C27  N23   107.81  3.000
 342  H271  C27  N23   112.78  3.000
 342  H272  C27  C31   108.40  3.000
 342  H271  C27  C31   109.37  3.000
 342  N23   C27  C31   112.34  3.000
 342  C24   N23  C22   111.67  3.000
 342  C22   N23  C27   113.10  3.000
 342  C24   N23  C27   112.87  3.000
 342  H222  C22  H221  106.58  3.000
 342  H222  C22  C21   107.56  3.000
 342  H221  C22  C21   109.37  3.000
 342  H222  C22  N23   112.69  3.000
 342  H221  C22  N23   109.28  3.000
 342  C21   C22  N23   111.22  3.000
 342  H242  C24  H241  106.66  3.000
 342  H242  C24  C25   109.82  3.000
 342  H241  C24  C25   109.29  3.000
 342  H242  C24  N23   109.07  3.000
 342  H241  C24  N23   111.11  3.000
 342  C25   C24  N23   110.80  3.000
 342  H252  C25  H251  106.86  3.000
 342  H252  C25  C26   110.31  3.000
 342  H251  C25  C26   109.92  3.000
 342  H252  C25  C24   109.41  3.000
 342  H251  C25  C24   109.46  3.000
 342  C26   C25  C24   110.79  3.000
 342  H262  C26  H261  106.21  3.000
 342  H262  C26  C21   107.61  3.000
 342  H261  C26  C21   111.24  3.000
 342  H262  C26  C25   109.80  3.000
 342  H261  C26  C25   110.92  3.000
 342  C21   C26  C25   110.90  3.000
 342  H21   C21  O17   110.05  3.000
 342  H21   C21  C26   110.80  3.000
 342  O17   C21  C26   111.20  3.000
 342  H21   C21  C22   107.80  3.000
 342  O17   C21  C22   106.37  3.000
 342  C26   C21  C22   110.47  3.000
 342  C14   O17  C21   120.52  3.000
 342  C13   C14  C15   118.86  3.000
 342  C13   C14  O17   125.30  3.000
 342  C15   C14  O17   115.83  3.000
 342  H15   C15  C16   119.89  3.000
 342  H15   C15  C14   119.34  3.000
 342  C16   C15  C14   120.77  3.000
 342  H16   C16  C11   120.41  3.000
 342  H16   C16  C15   119.42  3.000
 342  C11   C16  C15   120.17  3.000
 342  H13   C13  C12   118.15  3.000
 342  H13   C13  C14   121.73  3.000
 342  C12   C13  C14   120.11  3.000
 342  H12   C12  C11   120.35  3.000
 342  H12   C12  C13   118.98  3.000
 342  C11   C12  C13   120.67  3.000
 342  N3    C11  C12   120.39  3.000
 342  N3    C11  C16   120.20  3.000
 342  C12   C11  C16   119.41  3.000
 342  C2    N3   C4    106.80  3.000
 342  C2    N3   C11   126.49  3.000
 342  C4    N3   C11   126.71  3.000
 342  H4    C4   C5    132.21  3.000
 342  H4    C4   N3    122.27  3.000
 342  C5    C4   N3    105.50  3.000
 342  H5    C5   NFE   122.02  3.000
 342  H5    C5   C4    127.65  3.000
 342  NFE   C5   C4    110.33  3.000
 342  C2    NFE  C5    105.51  3.000
 342  H2    C2   NFE   126.09  3.000
 342  H2    C2   N3    122.03  3.000
 342  NFE   C2   N3    111.86  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
 342  CONST_01  C33  C32  C31  C36     0.00   0.0  0
 342  CONST_02  C33  C34  C35  C36     0.00   0.0  0
 342  CONST_03  C32  C31  C36  C35     0.00   0.0  0
 342  CONST_04  C32  C33  C34  C35     0.00   0.0  0
 342  CONST_05  C31  C36  C35  C34     0.00   0.0  0
 342  CONST_06  C31  C32  C33  C34     0.00   0.0  0
 342  CONST_07  C11  C16  C15  C14     0.00   0.0  0
 342  CONST_08  C11  C12  C13  C14     0.00   0.0  0
 342  CONST_09  C12  C13  C14  C15     0.00   0.0  0
 342  CONST_10  C12  C11  C16  C15     0.00   0.0  0
 342  CONST_11  N3   C11  C16  C15   180.00   0.0  0
 342  CONST_12  C13  C14  C15  C16     0.00   0.0  0
 342  CONST_13  C13  C12  C11  C16     0.00   0.0  0
 342  CONST_16  N3   C11  C12  C13   180.00   0.0  0
 342  CONST_19  C5   C4   N3   C11   180.00   0.0  0
 342  CONST_20  NFE  C2   N3   C11   180.00   0.0  0
 342  CONST_21  NFE  C5   C4   N3      0.00   0.0  0
 342  CONST_22  C5   NFE  C2   N3      0.00   0.0  0
 342  CONST_23  NFE  C2   N3   C4      0.00   0.0  0
 342  CONST_24  C2   NFE  C5   C4      0.00   0.0  0
 342  CONST_25  C2   N3   C4   C5      0.00   0.0  0
 342  CONST_26  C27  C31  C36  C35   180.00   0.0  0
 342  CONST_27  C27  C31  C32  C33   180.00   0.0  0
 342  CONST_28  C16  C15  C14  O17   180.00   0.0  0
 342  CONST_29  C12  C13  C14  O17   180.00   0.0  0
 342  CONST_30  H32  C32  C31  C36   180.00   0.0  0
 342  CONST_31  H33  C33  C34  C35   180.00   0.0  0
 342  CONST_32  H36  C36  C35  O39     0.00   0.0  0
 342  CONST_33  H16  C16  C15  C14   180.00   0.0  0
 342  CONST_34  H12  C12  C13  C14   180.00   0.0  0
 342  CONST_35  H13  C13  C14  C15   180.00   0.0  0
 342  CONST_36  H15  C15  C14  C13   180.00   0.0  0
 342  CONST_37  H4   C4   N3   C11     0.00   0.0  0
 342  CONST_38  H2   C2   N3   C11     0.00   0.0  0
 342  CONST_39  H5   C5   C4   N3    180.00   0.0  0
 342  Var_01    O37  C38  O39  C35   -13.07  30.0  1
 342  Var_02    C34  C35  O39  C38     8.12  30.0  1
 342  Var_03    C33  C34  O37  C38   172.34  30.0  1
 342  Var_04    C26  C25  C24  N23   -55.62  30.0  1
 342  Var_05    C21  C26  C25  C24    51.91  30.0  1
 342  Var_06    N23  C27  C31  C36    38.54  30.0  2
 342  Var_07    C15  C14  O17  C21  -172.80  30.0  2

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
 342  chir_01  N23  C27  C24  C22  negativ
 342  chir_02  C21  O17  C26  C22  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
 342  plan-1  C11  0.020
 342  plan-1  N3   0.020
 342  plan-1  C4   0.020
 342  plan-1  C5   0.020
 342  plan-1  NFE  0.020
 342  plan-1  C2   0.020
 342  plan-1  H4   0.020
 342  plan-1  H5   0.020
 342  plan-1  H2   0.020
 342  plan-2  C36  0.020
 342  plan-2  C35  0.020
 342  plan-2  O39  0.020
 342  plan-2  O37  0.020
 342  plan-2  C34  0.020
 342  plan-2  C33  0.020
 342  plan-2  C32  0.020
 342  plan-2  C31  0.020
 342  plan-2  C27  0.020
 342  plan-2  H36  0.020
 342  plan-2  H33  0.020
 342  plan-2  H32  0.020
 342  plan-3  O17  0.020
 342  plan-3  C14  0.020
 342  plan-3  C15  0.020
 342  plan-3  C16  0.020
 342  plan-3  C13  0.020
 342  plan-3  C12  0.020
 342  plan-3  C11  0.020
 342  plan-3  N3   0.020
 342  plan-3  H15  0.020
 342  plan-3  H16  0.020
 342  plan-3  H13  0.020
 342  plan-3  H12  0.020

