# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 00:13:42 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: [(2~{S},4~{S})-1-[(5,7-dimethyl-1~{H}-indol-4-yl)methyl]-4-methoxy-piperidin-2-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1CCN(Cc2c(C)cc(C)c3[nH]ccc23)[C@H](CO)C1
#
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
 JGN  JGN  '[(2~{S},4~{S})-1-[(5,7-dimethyl-1~{H}-indol-4-yl)methyl]-4-methoxy-piperidin-2-yl]methanol'  ligand  48  22  .  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_JGN
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
 JGN  C1   C  CR56  0   0.048  -2.0986  -0.6211   0.8823
 JGN  C2   C  CR56  0   0.306  -3.3693  -0.7992   0.2983
 JGN  C11  C  CH3   0  -0.738  -5.2330  -0.1554  -1.2803
 JGN  C12  C  CH3   0  -0.718  -0.9640   2.4907  -0.9731
 JGN  C14  C  CH2   0  -0.270   1.1624  -0.7042  -0.5139
 JGN  C15  C  CH2   0  -0.470   2.1991  -0.7297  -1.6223
 JGN  C16  C  CH1   0   0.033   3.5959  -0.4549  -1.0793
 JGN  C17  C  CH2   0  -0.446   3.5535   0.8287  -0.2697
 JGN  C18  C  CH1   0  -0.059   2.4643   0.8156   0.8044
 JGN  C19  C  CH2   0  -0.200   2.5319   2.0946   1.6260
 JGN  N3   N  NR15  0  -0.687  -3.9327  -1.9118   0.8594
 JGN  C4   C  CR15  0  -0.034  -3.0696  -2.4429   1.7730
 JGN  C5   C  CR15  0  -0.447  -1.9319  -1.6896   1.8223
 JGN  C6   C  CR6   0   0.062  -3.8783   0.0599  -0.6774
 JGN  C7   C  CR6   0  -0.023  -1.2868   0.4579   0.4895
 JGN  C8   C  CR6   0   0.045  -1.7768   1.3266  -0.4780
 JGN  C9   C  CR16  0  -0.392  -3.0533   1.1098  -1.0364
 JGN  C10  C  CH2   0  -0.364   0.0619   0.6623   1.1273
 JGN  N13  N  NT    0  -0.403   1.1651   0.5696   0.1863
 JGN  O21  O  O2    0  -0.493   4.0645  -1.4815  -0.2247
 JGN  H1   H  HCH3  0   0.243  -6.0220  -0.1018  -0.5267
 JGN  H2   H  HCH3  0   0.250  -5.4489   0.5948  -2.0396
 JGN  H3   H  HCH3  0   0.242  -5.3101  -1.1376  -1.7523
 JGN  H4   H  HCH3  0   0.239  -0.2180   2.1724  -1.7023
 JGN  H5   H  HCH3  0   0.224  -1.6034   3.2341  -1.4499
 JGN  H6   H  HCH3  0   0.238  -0.4083   2.9797  -0.1739
 JGN  H7   H  HCH2  0   0.241   0.1759  -0.8612  -0.9513
 JGN  H8   H  HCH2  0   0.182   1.3312  -1.5472   0.1800
 JGN  H9   H  HCH2  0   0.236   2.1505  -1.6826  -2.1552
 JGN  H10  H  HCH2  0   0.230   1.9618   0.0471  -2.3547
 JGN  H11  H  HCH1  0   0.213   4.2990  -0.3372  -1.9185
 JGN  H12  H  HCH2  0   0.227   4.5260   1.0031   0.1991
 JGN  H13  H  HCH2  0   0.234   3.3717   1.6606  -0.9532
 JGN  H14  H  HCH1  0   0.191   2.6983   0.0109   1.5277
 JGN  H15  H  HCH2  0   0.212   1.8763   2.0221   2.5026
 JGN  H16  H  HCH2  0   0.208   3.5553   2.1581   2.0216
 JGN  H17  H  HCH3  0   0.204   3.4910  -3.1969  -1.2759
 JGN  H18  H  HCH3  0   0.200   5.0734  -2.5304  -1.7092
 JGN  H19  H  HCH3  0   0.232   4.8461  -3.3454  -0.1526
 JGN  H20  H  HNR5  0   0.408  -4.8431  -2.2830   0.6468
 JGN  H21  H  HCR5  0   0.276  -3.3342  -3.3297   2.3263
 JGN  H22  H  HCR5  0   0.240  -1.0833  -1.8806   2.4592
 JGN  H23  H  HCR6  0   0.227  -3.4101   1.8081  -1.7867
 JGN  H24  H  HCH2  0   0.252   0.0685   1.6579   1.5760
 JGN  H25  H  HCH2  0   0.209   0.1807  -0.0507   1.9601
 JGN  H27  H  HOH1  0   0.452   2.3180   3.9992   1.3794
 JGN  O20  O  OH1   0  -0.660   2.2120   3.2147   0.8343
 JGN  C22  C  CH3   0  -0.400   4.3732  -2.6841  -0.8786

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
 JGN  C22  O21  single    1.403  0.020  1.403
 JGN  C16  C15  single    1.524  0.020  1.524
 JGN  C16  O21  single    1.415  0.020  1.415
 JGN  C16  C17  single    1.518  0.020  1.518
 JGN  C15  C14  single    1.518  0.020  1.518
 JGN  C17  C18  single    1.530  0.020  1.530
 JGN  C14  N13  single    1.454  0.020  1.454
 JGN  C18  N13  single    1.460  0.020  1.460
 JGN  C18  C19  single    1.522  0.020  1.522
 JGN  N13  C10  single    1.453  0.020  1.453
 JGN  O20  C19  single    1.408  0.020  1.408
 JGN  C4   C5   aromatic  1.365  0.020  1.365
 JGN  C4   N3   aromatic  1.364  0.020  1.364
 JGN  C5   C1   aromatic  1.433  0.020  1.433
 JGN  N3   C2   aromatic  1.368  0.020  1.368
 JGN  C10  C7   single    1.506  0.020  1.506
 JGN  C1   C2   aromatic  1.410  0.020  1.410
 JGN  C1   C7   aromatic  1.406  0.020  1.406
 JGN  C2   C6   aromatic  1.396  0.020  1.396
 JGN  C7   C8   aromatic  1.390  0.020  1.390
 JGN  C6   C11  single    1.498  0.020  1.498
 JGN  C6   C9   aromatic  1.383  0.020  1.383
 JGN  C8   C9   aromatic  1.410  0.020  1.410
 JGN  C8   C12  single    1.504  0.020  1.504
 JGN  C11  H1   single    0.970  0.020  1.090
 JGN  C11  H2   single    0.970  0.020  1.090
 JGN  C11  H3   single    0.970  0.020  1.090
 JGN  C12  H4   single    0.970  0.020  1.090
 JGN  C12  H5   single    0.970  0.020  1.090
 JGN  C12  H6   single    0.970  0.020  1.090
 JGN  C14  H7   single    0.970  0.020  1.090
 JGN  C14  H8   single    0.970  0.020  1.090
 JGN  C15  H9   single    0.970  0.020  1.090
 JGN  C15  H10  single    0.970  0.020  1.090
 JGN  C16  H11  single    0.970  0.020  1.090
 JGN  C17  H12  single    0.970  0.020  1.090
 JGN  C17  H13  single    0.970  0.020  1.090
 JGN  C18  H14  single    0.970  0.020  1.090
 JGN  C19  H15  single    0.970  0.020  1.090
 JGN  C19  H16  single    0.970  0.020  1.090
 JGN  C22  H17  single    0.970  0.020  1.090
 JGN  C22  H18  single    0.970  0.020  1.090
 JGN  C22  H19  single    0.970  0.020  1.090
 JGN  N3   H20  single    0.860  0.020  1.020
 JGN  C4   H21  single    0.930  0.020  1.080
 JGN  C5   H22  single    0.930  0.020  1.080
 JGN  C9   H23  single    0.930  0.020  1.080
 JGN  C10  H24  single    0.970  0.020  1.090
 JGN  C10  H25  single    0.970  0.020  1.090
 JGN  O20  H27  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
 JGN  C7   C1   C5   133.50  3.000
 JGN  C7   C1   C2   120.11  3.000
 JGN  C5   C1   C2   106.40  3.000
 JGN  C6   C2   N3   129.58  3.000
 JGN  C6   C2   C1   122.71  3.000
 JGN  N3   C2   C1   107.71  3.000
 JGN  H3   C11  H2   107.70  3.000
 JGN  H3   C11  H1   106.94  3.000
 JGN  H2   C11  H1   107.70  3.000
 JGN  H3   C11  C6   111.52  3.000
 JGN  H2   C11  C6   111.15  3.000
 JGN  H1   C11  C6   111.62  3.000
 JGN  H6   C12  H5   108.29  3.000
 JGN  H6   C12  H4   105.82  3.000
 JGN  H5   C12  H4   107.92  3.000
 JGN  H6   C12  C8   112.44  3.000
 JGN  H5   C12  C8   110.79  3.000
 JGN  H4   C12  C8   111.34  3.000
 JGN  H8   C14  H7   106.27  3.000
 JGN  H8   C14  N13  111.46  3.000
 JGN  H7   C14  N13  108.73  3.000
 JGN  H8   C14  C15  109.97  3.000
 JGN  H7   C14  C15  108.82  3.000
 JGN  N13  C14  C15  111.42  3.000
 JGN  H10  C15  H9   106.44  3.000
 JGN  H10  C15  C16  108.03  3.000
 JGN  H9   C15  C16  111.82  3.000
 JGN  H10  C15  C14  109.20  3.000
 JGN  H9   C15  C14  109.90  3.000
 JGN  C16  C15  C14  111.28  3.000
 JGN  H11  C16  O21  109.05  3.000
 JGN  H11  C16  C17  109.50  3.000
 JGN  O21  C16  C17  107.48  3.000
 JGN  H11  C16  C15  109.46  3.000
 JGN  C17  C16  C15  108.47  3.000
 JGN  O21  C16  C15  112.82  3.000
 JGN  H13  C17  H12  107.15  3.000
 JGN  H13  C17  C18  109.12  3.000
 JGN  H12  C17  C18  109.48  3.000
 JGN  H13  C17  C16  108.36  3.000
 JGN  H12  C17  C16  109.79  3.000
 JGN  C18  C17  C16  112.77  3.000
 JGN  H14  C18  N13  110.02  3.000
 JGN  H14  C18  C19  104.41  3.000
 JGN  N13  C18  C19  114.20  3.000
 JGN  H14  C18  C17  108.33  3.000
 JGN  C19  C18  C17  109.89  3.000
 JGN  N13  C18  C17  109.75  3.000
 JGN  H16  C19  H15  105.83  3.000
 JGN  H16  C19  O20  111.59  3.000
 JGN  H15  C19  O20  111.47  3.000
 JGN  H16  C19  C18  106.52  3.000
 JGN  H15  C19  C18  110.44  3.000
 JGN  O20  C19  C18  110.78  3.000
 JGN  H20  N3   C4   124.78  3.000
 JGN  H20  N3   C2   125.91  3.000
 JGN  C4   N3   C2   109.31  3.000
 JGN  H21  C4   C5   129.78  3.000
 JGN  H21  C4   N3   120.56  3.000
 JGN  C5   C4   N3   109.66  3.000
 JGN  H22  C5   C4   125.41  3.000
 JGN  H22  C5   C1   127.68  3.000
 JGN  C4   C5   C1   106.91  3.000
 JGN  C9   C6   C11  122.96  3.000
 JGN  C9   C6   C2   115.55  3.000
 JGN  C11  C6   C2   121.49  3.000
 JGN  C10  C7   C8   121.73  3.000
 JGN  C8   C7   C1   118.07  3.000
 JGN  C10  C7   C1   120.19  3.000
 JGN  C9   C8   C7   119.93  3.000
 JGN  C9   C8   C12  118.55  3.000
 JGN  C7   C8   C12  121.51  3.000
 JGN  H23  C9   C8   118.19  3.000
 JGN  H23  C9   C6   118.16  3.000
 JGN  C8   C9   C6   123.64  3.000
 JGN  H25  C10  H24  106.17  3.000
 JGN  H25  C10  N13  111.48  3.000
 JGN  H24  C10  N13  108.64  3.000
 JGN  H25  C10  C7   109.18  3.000
 JGN  H24  C10  C7   107.64  3.000
 JGN  N13  C10  C7   113.40  3.000
 JGN  C10  N13  C18  113.01  3.000
 JGN  C10  N13  C14  111.50  3.000
 JGN  C18  N13  C14  110.69  3.000
 JGN  C22  O21  C16  114.39  3.000
 JGN  H27  O20  C19  107.77  3.000
 JGN  H19  C22  H18  108.20  3.000
 JGN  H19  C22  H17  107.88  3.000
 JGN  H18  C22  H17  107.76  3.000
 JGN  H19  C22  O21  107.76  3.000
 JGN  H18  C22  O21  111.91  3.000
 JGN  H17  C22  O21  113.15  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
 JGN  CONST_01  N3   C4   C5   C1     0.00   0.0  0
 JGN  CONST_02  C4   N3   C2   C1     0.00   0.0  0
 JGN  CONST_03  C9   C6   C2   C1     0.00   0.0  0
 JGN  CONST_04  C9   C8   C7   C1     0.00   0.0  0
 JGN  CONST_05  C5   C4   N3   C2     0.00   0.0  0
 JGN  CONST_06  C4   C5   C1   C2     0.00   0.0  0
 JGN  CONST_07  C8   C7   C1   C2     0.00   0.0  0
 JGN  CONST_08  C8   C9   C6   C2     0.00   0.0  0
 JGN  CONST_09  C5   C1   C2   N3     0.00   0.0  0
 JGN  CONST_10  C7   C1   C2   N3   180.00   0.0  0
 JGN  CONST_11  C9   C6   C2   N3   180.00   0.0  0
 JGN  CONST_12  C7   C1   C5   C4   180.00   0.0  0
 JGN  CONST_13  C6   C2   N3   C4   180.00   0.0  0
 JGN  CONST_14  C6   C2   C1   C5   180.00   0.0  0
 JGN  CONST_15  C8   C7   C1   C5   180.00   0.0  0
 JGN  CONST_16  C7   C1   C2   C6     0.00   0.0  0
 JGN  CONST_17  C7   C8   C9   C6     0.00   0.0  0
 JGN  CONST_18  C11  C6   C2   C1   180.00   0.0  0
 JGN  CONST_19  C12  C8   C7   C1   180.00   0.0  0
 JGN  CONST_20  C10  C7   C1   C2   180.00   0.0  0
 JGN  CONST_21  N3   C2   C6   C11    0.00   0.0  0
 JGN  CONST_22  C8   C9   C6   C11  180.00   0.0  0
 JGN  CONST_23  C6   C9   C8   C12  180.00   0.0  0
 JGN  CONST_24  C10  C7   C1   C5     0.00   0.0  0
 JGN  CONST_25  C10  C7   C8   C9   180.00   0.0  0
 JGN  CONST_26  H21  C4   C5   C1   180.00   0.0  0
 JGN  CONST_27  H20  N3   C2   C1   180.00   0.0  0
 JGN  CONST_28  H22  C5   C1   C2   180.00   0.0  0
 JGN  CONST_29  H23  C9   C6   C2   180.00   0.0  0
 JGN  Var_01    C18  N13  C14  C15  -60.80  30.0  1
 JGN  Var_02    N13  C14  C15  C16   57.67  30.0  1
 JGN  Var_03    N13  C10  C7   C1   117.85  30.0  2
 JGN  Var_04    C7   C10  N13  C14  -56.60  30.0  3
 JGN  Var_05    H1   C11  C6   C2    61.28  30.0  2
 JGN  Var_06    H4   C12  C8   C7    79.23  30.0  2
 JGN  Var_07    H17  C22  O21  C16  -68.38  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
 JGN  chir_01  C16  C15  O21  C17  positiv
 JGN  chir_02  C18  N13  C19  C17  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
 JGN  plan-1  C1   0.020
 JGN  plan-1  C2   0.020
 JGN  plan-1  C11  0.020
 JGN  plan-1  C12  0.020
 JGN  plan-1  N3   0.020
 JGN  plan-1  C4   0.020
 JGN  plan-1  C5   0.020
 JGN  plan-1  C6   0.020
 JGN  plan-1  C7   0.020
 JGN  plan-1  C8   0.020
 JGN  plan-1  C9   0.020
 JGN  plan-1  C10  0.020
 JGN  plan-1  H20  0.020
 JGN  plan-1  H21  0.020
 JGN  plan-1  H22  0.020
 JGN  plan-1  H23  0.020

