# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 09:18:40 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 3-[(4-methylpiperidin-1-yl)methyl]-1H-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1CCN(CC1)Cc2c[nH]c3ccccc23
#
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
 LDV  LDV  3-[(4-methylpiperidin-1-yl)methyl]-1H-indole  ligand  37  17  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LDV
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
 LDV  N1   N  NT    0  -0.403  -1.3281   0.1246   0.6841
 LDV  C4   C  CH2   0  -0.279  -2.5307   0.5839   1.3532
 LDV  C5   C  CH2   0  -0.276  -1.6458  -0.6574  -0.4956
 LDV  C6   C  CH2   0  -0.426  -2.4494   0.1689  -1.4886
 LDV  C7   C  CH2   0  -0.343  -0.4507  -0.5741   1.6040
 LDV  C8   C  CR5   0  -0.013   0.8728  -0.9070   1.0007
 LDV  C10  C  CR56  0   0.348   2.8889  -0.7663  -0.0742
 LDV  C13  C  CR16  0  -0.271   2.6722   1.8634  -0.8671
 LDV  C15  C  CR16  0  -0.308   3.9388  -0.2088  -0.8036
 LDV  C1   C  CH3   0  -0.664  -4.7944  -0.3524  -0.6728
 LDV  C11  C  CR56  0   0.030   1.7341  -0.0265   0.2674
 LDV  C12  C  CR16  0  -0.364   1.6324   1.3068  -0.1477
 LDV  C14  C  CR16  0  -0.284   3.8148   1.1119  -1.1906
 LDV  C2   C  CH1   0  -0.250  -3.7335   0.7272  -0.8714
 LDV  C3   C  CH2   0  -0.428  -3.3738   1.4487   0.4292
 LDV  C9   C  CR15  0  -0.088   1.5208  -2.1072   1.0618
 LDV  N2   N  NR15  0  -0.688   2.7293  -2.0250   0.4265
 LDV  H2   H  HCH2  0   0.183  -3.1298  -0.2625   1.7348
 LDV  H3   H  HCH2  0   0.229  -2.2377   1.1660   2.2312
 LDV  H4   H  HCH2  0   0.240  -0.7155  -0.9826  -0.9648
 LDV  H5   H  HCH2  0   0.182  -2.1941  -1.5795  -0.2294
 LDV  H6   H  HCH2  0   0.221  -1.8231   0.9992  -1.8289
 LDV  H7   H  HCH2  0   0.221  -2.6788  -0.4392  -2.3678
 LDV  H8   H  HCH2  0   0.232  -0.3067   0.0818   2.4699
 LDV  H9   H  HCH2  0   0.197  -0.9100  -1.4990   1.9970
 LDV  H10  H  HCR6  0   0.242   2.6066   2.8928  -1.1957
 LDV  H11  H  HCR6  0   0.256   4.8164  -0.7878  -1.0625
 LDV  H12  H  HCH3  0   0.219  -4.4526  -1.1687  -0.0340
 LDV  H13  H  HCH3  0   0.224  -5.6955   0.0613  -0.2162
 LDV  H14  H  HCH3  0   0.224  -5.0821  -0.7906  -1.6304
 LDV  H15  H  HCR6  0   0.238   0.7413   1.8771   0.0805
 LDV  H16  H  HCR6  0   0.247   4.6116   1.5750  -1.7585
 LDV  H17  H  HCH1  0   0.225  -4.1518   1.4674  -1.5613
 LDV  H18  H  HCH2  0   0.223  -4.2775   1.7703   0.9538
 LDV  H19  H  HCH2  0   0.221  -2.8064   2.3528   0.1898
 LDV  H20  H  HCR5  0   0.279   1.2047  -3.0313   1.5209
 LDV  H21  H  HNR5  0   0.406   3.3842  -2.7825   0.3326

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
 LDV  C1   C2   single    1.527  0.020  1.527
 LDV  C6   C2   single    1.530  0.020  1.530
 LDV  C6   C5   single    1.521  0.020  1.521
 LDV  C2   C3   single    1.530  0.020  1.530
 LDV  C5   N1   single    1.451  0.020  1.451
 LDV  C3   C4   single    1.521  0.020  1.521
 LDV  C9   N2   aromatic  1.368  0.020  1.368
 LDV  C9   C8   aromatic  1.365  0.020  1.365
 LDV  N2   C10  aromatic  1.364  0.020  1.364
 LDV  N1   C4   single    1.451  0.020  1.451
 LDV  N1   C7   single    1.451  0.020  1.451
 LDV  C8   C7   single    1.492  0.020  1.492
 LDV  C8   C11  aromatic  1.433  0.020  1.433
 LDV  C10  C11  aromatic  1.413  0.020  1.413
 LDV  C10  C15  aromatic  1.395  0.020  1.395
 LDV  C11  C12  aromatic  1.400  0.020  1.400
 LDV  C15  C14  aromatic  1.382  0.020  1.382
 LDV  C14  C13  aromatic  1.405  0.020  1.405
 LDV  C12  C13  aromatic  1.381  0.020  1.381
 LDV  C4   H2   single    0.970  0.020  1.090
 LDV  C4   H3   single    0.970  0.020  1.090
 LDV  C5   H4   single    0.970  0.020  1.090
 LDV  C5   H5   single    0.970  0.020  1.090
 LDV  C6   H6   single    0.970  0.020  1.090
 LDV  C6   H7   single    0.970  0.020  1.090
 LDV  C7   H8   single    0.970  0.020  1.090
 LDV  C7   H9   single    0.970  0.020  1.090
 LDV  C13  H10  single    0.930  0.020  1.080
 LDV  C15  H11  single    0.930  0.020  1.080
 LDV  C1   H12  single    0.970  0.020  1.090
 LDV  C1   H13  single    0.970  0.020  1.090
 LDV  C1   H14  single    0.970  0.020  1.090
 LDV  C12  H15  single    0.930  0.020  1.080
 LDV  C14  H16  single    0.930  0.020  1.080
 LDV  C2   H17  single    0.970  0.020  1.090
 LDV  C3   H18  single    0.970  0.020  1.090
 LDV  C3   H19  single    0.970  0.020  1.090
 LDV  C9   H20  single    0.930  0.020  1.080
 LDV  N2   H21  single    0.860  0.020  1.020

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
 LDV  C7   N1   C5   112.86  3.000
 LDV  C7   N1   C4   111.19  3.000
 LDV  C5   N1   C4   111.36  3.000
 LDV  H3   C4   H2   106.00  3.000
 LDV  H3   C4   C3   109.49  3.000
 LDV  H2   C4   C3   110.17  3.000
 LDV  H3   C4   N1   108.47  3.000
 LDV  H2   C4   N1   111.48  3.000
 LDV  C3   C4   N1   111.07  3.000
 LDV  H5   C5   H4   106.12  3.000
 LDV  H5   C5   C6   110.38  3.000
 LDV  H4   C5   C6   109.36  3.000
 LDV  H5   C5   N1   111.25  3.000
 LDV  H4   C5   N1   108.88  3.000
 LDV  C6   C5   N1   110.72  3.000
 LDV  H7   C6   H6   106.98  3.000
 LDV  H7   C6   C2   110.56  3.000
 LDV  H6   C6   C2   109.20  3.000
 LDV  H7   C6   C5   109.49  3.000
 LDV  H6   C6   C5   108.22  3.000
 LDV  C2   C6   C5   112.22  3.000
 LDV  H9   C7   H8   105.93  3.000
 LDV  H9   C7   C8   109.02  3.000
 LDV  H8   C7   C8   109.67  3.000
 LDV  H9   C7   N1   112.17  3.000
 LDV  H8   C7   N1   106.99  3.000
 LDV  C8   C7   N1   112.81  3.000
 LDV  C9   C8   C11  106.13  3.000
 LDV  C11  C8   C7   127.06  3.000
 LDV  C9   C8   C7   126.80  3.000
 LDV  N2   C10  C11  107.38  3.000
 LDV  C11  C10  C15  122.16  3.000
 LDV  N2   C10  C15  130.47  3.000
 LDV  H10  C13  C14  119.20  3.000
 LDV  H10  C13  C12  119.71  3.000
 LDV  C14  C13  C12  121.09  3.000
 LDV  H11  C15  C14  121.12  3.000
 LDV  H11  C15  C10  121.43  3.000
 LDV  C14  C15  C10  117.45  3.000
 LDV  H14  C1   H13  107.55  3.000
 LDV  H14  C1   H12  107.20  3.000
 LDV  H13  C1   H12  107.29  3.000
 LDV  H14  C1   C2   110.67  3.000
 LDV  H13  C1   C2   111.10  3.000
 LDV  H12  C1   C2   112.80  3.000
 LDV  C12  C11  C10  119.09  3.000
 LDV  C12  C11  C8   133.87  3.000
 LDV  C10  C11  C8   107.04  3.000
 LDV  H15  C12  C11  119.94  3.000
 LDV  H15  C12  C13  121.14  3.000
 LDV  C11  C12  C13  118.91  3.000
 LDV  H16  C14  C15  119.33  3.000
 LDV  H16  C14  C13  119.37  3.000
 LDV  C15  C14  C13  121.30  3.000
 LDV  H17  C2   C3   107.86  3.000
 LDV  H17  C2   C1   107.13  3.000
 LDV  C3   C2   C1   112.72  3.000
 LDV  H17  C2   C6   108.25  3.000
 LDV  C3   C2   C6   108.52  3.000
 LDV  C1   C2   C6   112.18  3.000
 LDV  H19  C3   H18  106.89  3.000
 LDV  H19  C3   C2   109.00  3.000
 LDV  H18  C3   C2   110.63  3.000
 LDV  H19  C3   C4   108.38  3.000
 LDV  H18  C3   C4   109.52  3.000
 LDV  C2   C3   C4   112.25  3.000
 LDV  H20  C9   N2   120.52  3.000
 LDV  H20  C9   C8   129.25  3.000
 LDV  N2   C9   C8   110.23  3.000
 LDV  H21  N2   C9   124.99  3.000
 LDV  H21  N2   C10  125.77  3.000
 LDV  C9   N2   C10  109.23  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
 LDV  CONST_01  C10  N2   C9   C8      0.00   0.0  0
 LDV  CONST_02  N2   C10  C11  C8      0.00   0.0  0
 LDV  CONST_03  C15  C10  C11  C8    180.00   0.0  0
 LDV  CONST_04  C13  C12  C11  C8    180.00   0.0  0
 LDV  CONST_05  C9   C8   C11  C10     0.00   0.0  0
 LDV  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 LDV  CONST_07  C13  C14  C15  C10     0.00   0.0  0
 LDV  CONST_08  C9   N2   C10  C15   180.00   0.0  0
 LDV  CONST_09  C12  C11  C10  C15     0.00   0.0  0
 LDV  CONST_10  C12  C13  C14  C15     0.00   0.0  0
 LDV  CONST_11  N2   C9   C8   C11     0.00   0.0  0
 LDV  CONST_12  C9   N2   C10  C11     0.00   0.0  0
 LDV  CONST_13  C14  C15  C10  C11     0.00   0.0  0
 LDV  CONST_14  C14  C13  C12  C11     0.00   0.0  0
 LDV  CONST_15  C9   C8   C11  C12   180.00   0.0  0
 LDV  CONST_16  N2   C10  C11  C12   180.00   0.0  0
 LDV  CONST_17  N2   C10  C15  C14   180.00   0.0  0
 LDV  CONST_18  N2   C9   C8   C7    180.00   0.0  0
 LDV  CONST_19  C10  C11  C8   C7    180.00   0.0  0
 LDV  CONST_20  C12  C11  C8   C7      0.00   0.0  0
 LDV  CONST_21  H21  N2   C9   C8    180.00   0.0  0
 LDV  CONST_22  H15  C12  C11  C8      0.00   0.0  0
 LDV  CONST_23  H20  C9   N2   C10   180.00   0.0  0
 LDV  CONST_24  H16  C14  C15  C10   180.00   0.0  0
 LDV  CONST_25  H11  C15  C14  C13   180.00   0.0  0
 LDV  CONST_26  H10  C13  C14  C15   180.00   0.0  0
 LDV  Var_01    C2   C6   C5   N1    -56.75  30.0  1
 LDV  Var_02    C2   C3   C4   N1     56.04  30.0  1
 LDV  Var_03    C6   C5   N1   C4     59.84  30.0  1
 LDV  Var_04    C3   C4   N1   C5    -59.59  30.0  1
 LDV  Var_05    C9   C8   C7   N1   -133.35  30.0  1
 LDV  Var_06    C8   C7   N1   C4   -172.54  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
 LDV  chir_01  C2  C1  C6  C3  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
 LDV  plan-1  C7   0.020
 LDV  plan-1  C8   0.020
 LDV  plan-1  C10  0.020
 LDV  plan-1  C13  0.020
 LDV  plan-1  C15  0.020
 LDV  plan-1  C11  0.020
 LDV  plan-1  C12  0.020
 LDV  plan-1  C14  0.020
 LDV  plan-1  C9   0.020
 LDV  plan-1  N2   0.020
 LDV  plan-1  H10  0.020
 LDV  plan-1  H11  0.020
 LDV  plan-1  H15  0.020
 LDV  plan-1  H16  0.020
 LDV  plan-1  H20  0.020
 LDV  plan-1  H21  0.020

