# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 17:35:58 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N-ethyl-4-{[4-(1H-indol-3-yl)-5-iodopyrimidin-2-yl]amino}piperidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)N1CCC(CC1)Nc2ncc(I)c(n2)c3c[nH]c4ccccc34
#
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
 3WH  3WH  N-ethyl-4-{[4-(1H-indol-3-yl)-5-iodopyrimidin-2-yl]amino}piperidine-1-carboxamide  ligand  51  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3WH
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
 3WH  C11  C  CH2   0  -0.325   5.2508   0.3228  -2.1649
 3WH  C10  C  CH2   0  -0.451   3.8696  -0.3255  -2.1600
 3WH  C13  C  CR6   0   0.607   0.4724   0.4055  -0.8893
 3WH  C01  C  CH3   0  -0.693   7.7083  -1.3557   3.1234
 3WH  C02  C  CH2   0  -0.257   7.7445  -1.4607   1.6100
 3WH  N03  N  NH1   0  -0.675   6.8179  -0.5150   1.0196
 3WH  O05  O  O     0  -0.545   6.9144  -1.4910  -1.0116
 3WH  N06  N  NT    0  -0.483   5.7715   0.4662  -0.8155
 3WH  C07  C  CH2   0  -0.354   4.9031   1.2992   0.0021
 3WH  C08  C  CH2   0  -0.429   3.5104   0.6896   0.1137
 3WH  C09  C  CH1   0  -0.055   2.9121   0.4703  -1.2780
 3WH  N12  N  NH1   0  -0.670   1.6277  -0.1934  -1.2287
 3WH  N14  N  N     0  -0.487  -0.5921  -0.3882  -0.7528
 3WH  C15  C  CR6   0   0.271  -1.7622   0.1422  -0.4142
 3WH  C16  C  CR6   0  -0.371  -1.8447   1.5291  -0.1920
 3WH  I17  I  I     0   0.066  -3.5254   2.5463   0.5407
 3WH  C18  C  CR16  0   0.002  -0.6883   2.2682  -0.3878
 3WH  N19  N  N     0  -0.458   0.4661   1.7346  -0.7389
 3WH  C20  C  CR5   0  -0.068  -2.8557  -0.8087  -0.2826
 3WH  C21  C  CR15  0  -0.046  -4.1820  -0.6313  -0.6036
 3WH  N22  N  NR15  0  -0.677  -4.8647  -1.7782  -0.3912
 3WH  C23  C  CR56  0   0.351  -4.0172  -2.7444   0.0787
 3WH  C24  C  CR56  0   0.065  -2.7279  -2.1791   0.1455
 3WH  C25  C  CR16  0  -0.367  -1.6701  -2.9732   0.6043
 3WH  C26  C  CR16  0  -0.262  -1.9277  -4.2788   0.9750
 3WH  C27  C  CR16  0  -0.282  -3.2214  -4.8188   0.8992
 3WH  C28  C  CR16  0  -0.300  -4.2842  -4.0595   0.4516
 3WH  H1   H  HCH2  0   0.264   5.9446  -0.2499  -2.7732
 3WH  H2   H  HCH2  0   0.243   5.1853   1.3219  -2.6053
 3WH  H3   H  HCH2  0   0.250   3.4824  -0.3790  -3.1801
 3WH  H4   H  HCH2  0   0.232   3.9571  -1.3527  -1.7904
 3WH  H5   H  HCH3  0   0.229   7.9904  -0.3579   3.4637
 3WH  H6   H  HCH3  0   0.231   6.7148  -1.5801   3.5127
 3WH  H7   H  HCH3  0   0.240   8.4109  -2.0630   3.5623
 3WH  H8   H  HCH2  0   0.220   8.7661  -1.2926   1.2522
 3WH  H9   H  HCH2  0   0.235   7.4646  -2.4683   1.3046
 3WH  H10  H  HNH1  0   0.390   6.7284   0.3604   1.5076
 3WH  H11  H  HCH2  0   0.259   5.3226   1.4820   0.9885
 3WH  H12  H  HCH2  0   0.252   4.8393   2.2818  -0.4739
 3WH  H13  H  HCH2  0   0.228   3.5679  -0.2646   0.6471
 3WH  H14  H  HCH2  0   0.247   2.8649   1.3506   0.6958
 3WH  H15  H  HCH1  0   0.243   2.7604   1.4504  -1.7398
 3WH  H16  H  HNH1  0   0.389   1.6154  -1.2016  -1.2294
 3WH  H17  H  HCR6  0   0.279  -0.6921   3.3434  -0.2427
 3WH  H18  H  HCR5  0   0.298  -4.6885   0.2249  -1.0164
 3WH  H19  H  HNR5  0   0.419  -5.8491  -1.8970  -0.5674
 3WH  H20  H  HCR6  0   0.247  -0.6658  -2.5767   0.6566
 3WH  H21  H  HCR6  0   0.249  -1.1152  -4.9017   1.3268
 3WH  H22  H  HCR6  0   0.253  -3.3892  -5.8461   1.1954
 3WH  H23  H  HCR6  0   0.264  -5.2852  -4.4676   0.3936
 3WH  C04  C  C     0   0.734   6.5202  -0.5673  -0.3056

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
 3WH  I17  C16  single    2.097  0.020  2.097
 3WH  C21  N22  aromatic  1.352  0.020  1.352
 3WH  C21  C20  aromatic  1.376  0.020  1.376
 3WH  N22  C23  aromatic  1.369  0.020  1.369
 3WH  C16  C18  aromatic  1.386  0.020  1.386
 3WH  C16  C15  aromatic  1.407  0.020  1.407
 3WH  C18  N19  aromatic  1.319  0.020  1.319
 3WH  C20  C15  single    1.455  0.020  1.455
 3WH  C20  C24  aromatic  1.441  0.020  1.441
 3WH  C15  N14  aromatic  1.329  0.020  1.329
 3WH  C23  C24  aromatic  1.409  0.020  1.409
 3WH  C23  C28  aromatic  1.393  0.020  1.393
 3WH  N19  C13  aromatic  1.338  0.020  1.338
 3WH  N14  C13  aromatic  1.335  0.020  1.335
 3WH  C24  C25  aromatic  1.400  0.020  1.400
 3WH  C28  C27  aromatic  1.381  0.020  1.381
 3WH  C13  N12  single    1.345  0.020  1.345
 3WH  C10  C11  single    1.526  0.020  1.526
 3WH  C10  C09  single    1.526  0.020  1.526
 3WH  C01  C02  single    1.517  0.020  1.517
 3WH  N12  C09  single    1.447  0.020  1.447
 3WH  C02  N03  single    1.450  0.020  1.450
 3WH  C25  C26  aromatic  1.381  0.020  1.381
 3WH  C27  C26  aromatic  1.404  0.020  1.404
 3WH  N03  C04  single    1.359  0.020  1.359
 3WH  C11  N06  single    1.453  0.020  1.453
 3WH  C09  C08  single    1.531  0.020  1.531
 3WH  C04  N06  single    1.374  0.020  1.374
 3WH  C04  O05  double    1.228  0.020  1.228
 3WH  N06  C07  single    1.455  0.020  1.455
 3WH  C08  C07  single    1.524  0.020  1.524
 3WH  C11  H1   single    0.970  0.020  1.090
 3WH  C11  H2   single    0.970  0.020  1.090
 3WH  C10  H3   single    0.970  0.020  1.090
 3WH  C10  H4   single    0.970  0.020  1.090
 3WH  C01  H5   single    0.970  0.020  1.090
 3WH  C01  H6   single    0.970  0.020  1.090
 3WH  C01  H7   single    0.970  0.020  1.090
 3WH  C02  H8   single    0.970  0.020  1.090
 3WH  C02  H9   single    0.970  0.020  1.090
 3WH  N03  H10  single    0.890  0.020  1.040
 3WH  C07  H11  single    0.970  0.020  1.090
 3WH  C07  H12  single    0.970  0.020  1.090
 3WH  C08  H13  single    0.970  0.020  1.090
 3WH  C08  H14  single    0.970  0.020  1.090
 3WH  C09  H15  single    0.970  0.020  1.090
 3WH  N12  H16  single    0.860  0.020  1.020
 3WH  C18  H17  single    0.930  0.020  1.080
 3WH  C21  H18  single    0.930  0.020  1.080
 3WH  N22  H19  single    0.860  0.020  1.020
 3WH  C25  H20  single    0.930  0.020  1.080
 3WH  C26  H21  single    0.930  0.020  1.080
 3WH  C27  H22  single    0.930  0.020  1.080
 3WH  C28  H23  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
 3WH  H2   C11  H1   107.12  3.000
 3WH  H2   C11  N06  107.77  3.000
 3WH  H1   C11  N06  110.07  3.000
 3WH  H2   C11  C10  109.58  3.000
 3WH  H1   C11  C10  110.85  3.000
 3WH  N06  C11  C10  111.30  3.000
 3WH  H4   C10  H3   107.31  3.000
 3WH  H4   C10  C09  110.14  3.000
 3WH  H3   C10  C09  110.05  3.000
 3WH  H4   C10  C11  109.11  3.000
 3WH  H3   C10  C11  109.80  3.000
 3WH  C09  C10  C11  110.38  3.000
 3WH  N19  C13  N14  125.14  3.000
 3WH  N14  C13  N12  116.49  3.000
 3WH  N19  C13  N12  118.36  3.000
 3WH  H7   C01  H6   108.08  3.000
 3WH  H7   C01  H5   107.53  3.000
 3WH  H6   C01  H5   108.20  3.000
 3WH  H7   C01  C02  109.97  3.000
 3WH  H6   C01  C02  111.32  3.000
 3WH  H5   C01  C02  111.59  3.000
 3WH  H9   C02  H8   106.86  3.000
 3WH  H9   C02  N03  108.96  3.000
 3WH  H8   C02  N03  111.28  3.000
 3WH  H9   C02  C01  109.72  3.000
 3WH  H8   C02  C01  109.72  3.000
 3WH  N03  C02  C01  110.23  3.000
 3WH  H10  N03  C04  119.13  3.000
 3WH  H10  N03  C02  115.27  3.000
 3WH  C04  N03  C02  120.79  3.000
 3WH  C07  N06  C04  123.18  3.000
 3WH  C07  N06  C11  111.37  3.000
 3WH  C04  N06  C11  117.74  3.000
 3WH  H12  C07  H11  105.45  3.000
 3WH  H12  C07  C08  109.74  3.000
 3WH  H11  C07  C08  110.69  3.000
 3WH  H12  C07  N06  107.74  3.000
 3WH  H11  C07  N06  112.08  3.000
 3WH  C08  C07  N06  110.95  3.000
 3WH  H14  C08  H13  107.39  3.000
 3WH  H14  C08  C09  109.90  3.000
 3WH  H13  C08  C09  109.79  3.000
 3WH  H14  C08  C07  109.70  3.000
 3WH  H13  C08  C07  109.65  3.000
 3WH  C09  C08  C07  110.36  3.000
 3WH  H15  C09  N12  107.60  3.000
 3WH  H15  C09  C08  108.03  3.000
 3WH  N12  C09  C08  112.44  3.000
 3WH  H15  C09  C10  108.08  3.000
 3WH  C08  C09  C10  110.79  3.000
 3WH  N12  C09  C10  109.73  3.000
 3WH  H16  N12  C09  118.00  3.000
 3WH  H16  N12  C13  115.79  3.000
 3WH  C09  N12  C13  124.54  3.000
 3WH  C15  N14  C13  119.41  3.000
 3WH  C20  C15  C16  125.86  3.000
 3WH  C20  C15  N14  115.09  3.000
 3WH  C16  C15  N14  119.04  3.000
 3WH  C18  C16  I17  117.35  3.000
 3WH  C18  C16  C15  117.02  3.000
 3WH  I17  C16  C15  125.48  3.000
 3WH  H17  C18  N19  116.07  3.000
 3WH  H17  C18  C16  120.44  3.000
 3WH  N19  C18  C16  123.49  3.000
 3WH  C18  N19  C13  115.85  3.000
 3WH  C24  C20  C21  106.10  3.000
 3WH  C24  C20  C15  125.56  3.000
 3WH  C21  C20  C15  128.24  3.000
 3WH  H18  C21  N22  119.82  3.000
 3WH  H18  C21  C20  130.18  3.000
 3WH  N22  C21  C20  109.93  3.000
 3WH  H19  N22  C23  125.60  3.000
 3WH  H19  N22  C21  124.51  3.000
 3WH  C23  N22  C21  109.89  3.000
 3WH  C28  C23  C24  122.78  3.000
 3WH  C28  C23  N22  129.78  3.000
 3WH  C24  C23  N22  107.44  3.000
 3WH  C25  C24  C23  118.63  3.000
 3WH  C25  C24  C20  134.71  3.000
 3WH  C23  C24  C20  106.63  3.000
 3WH  H20  C25  C26  120.46  3.000
 3WH  H20  C25  C24  120.65  3.000
 3WH  C26  C25  C24  118.89  3.000
 3WH  H21  C26  C27  119.19  3.000
 3WH  H21  C26  C25  119.41  3.000
 3WH  C27  C26  C25  121.39  3.000
 3WH  H22  C27  C28  119.43  3.000
 3WH  H22  C27  C26  119.56  3.000
 3WH  C28  C27  C26  121.01  3.000
 3WH  H23  C28  C27  121.45  3.000
 3WH  H23  C28  C23  121.26  3.000
 3WH  C27  C28  C23  117.29  3.000
 3WH  N06  C04  O05  121.83  3.000
 3WH  O05  C04  N03  121.29  3.000
 3WH  N06  C04  N03  116.88  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
 3WH  CONST_01  C16  C18  N19  C13     0.00   0.0  0
 3WH  CONST_02  C16  C15  N14  C13     0.00   0.0  0
 3WH  CONST_03  C20  C15  N14  C13   180.00   0.0  0
 3WH  CONST_04  C18  C16  C15  N14     0.00   0.0  0
 3WH  CONST_07  C18  N19  C13  N14     0.00   0.0  0
 3WH  CONST_08  N19  C18  C16  C15     0.00   0.0  0
 3WH  CONST_09  N22  C21  C20  C15   180.00   0.0  0
 3WH  CONST_10  C23  C24  C20  C15   180.00   0.0  0
 3WH  CONST_11  C25  C24  C20  C15     0.00   0.0  0
 3WH  CONST_12  N19  C13  N14  C15     0.00   0.0  0
 3WH  CONST_15  C20  C15  C16  C18   180.00   0.0  0
 3WH  CONST_16  C23  N22  C21  C20     0.00   0.0  0
 3WH  CONST_17  N22  C23  C24  C20     0.00   0.0  0
 3WH  CONST_18  C28  C23  C24  C20   180.00   0.0  0
 3WH  CONST_19  C26  C25  C24  C20   180.00   0.0  0
 3WH  CONST_20  C24  C23  N22  C21     0.00   0.0  0
 3WH  CONST_21  C28  C23  N22  C21   180.00   0.0  0
 3WH  CONST_22  C23  C24  C20  C21     0.00   0.0  0
 3WH  CONST_23  C25  C24  C20  C21   180.00   0.0  0
 3WH  CONST_24  C24  C20  C21  N22     0.00   0.0  0
 3WH  CONST_25  C25  C24  C23  N22   180.00   0.0  0
 3WH  CONST_26  C27  C28  C23  N22   180.00   0.0  0
 3WH  CONST_27  C26  C25  C24  C23     0.00   0.0  0
 3WH  CONST_28  C26  C27  C28  C23     0.00   0.0  0
 3WH  CONST_29  C27  C28  C23  C24     0.00   0.0  0
 3WH  CONST_30  C27  C26  C25  C24     0.00   0.0  0
 3WH  CONST_31  C28  C23  C24  C25     0.00   0.0  0
 3WH  CONST_32  C28  C27  C26  C25     0.00   0.0  0
 3WH  CONST_33  C18  N19  C13  N12   180.00   0.0  0
 3WH  CONST_34  C15  N14  C13  N12   180.00   0.0  0
 3WH  CONST_35  I17  C16  C15  N14   180.00   0.0  0
 3WH  CONST_36  N19  C18  C16  I17   180.00   0.0  0
 3WH  CONST_37  C20  C15  C16  I17     0.00   0.0  0
 3WH  CONST_38  N19  C13  N12  C09     0.00   0.0  0
 3WH  CONST_39  N14  C13  N12  C09   180.00   0.0  0
 3WH  CONST_40  H17  C18  N19  C13   180.00   0.0  0
 3WH  CONST_41  H18  C21  C20  C15     0.00   0.0  0
 3WH  CONST_42  H19  N22  C21  C20   180.00   0.0  0
 3WH  CONST_43  H20  C25  C24  C20     0.00   0.0  0
 3WH  CONST_44  H23  C28  C23  N22     0.00   0.0  0
 3WH  CONST_45  H22  C27  C28  C23   180.00   0.0  0
 3WH  CONST_46  H21  C26  C25  C24   180.00   0.0  0
 3WH  CONST_47  O05  C04  N06  C11     0.00   0.0  0
 3WH  CONST_49  N03  C04  N06  C11   180.00   0.0  0
 3WH  CONST_51  H16  N12  C13  N14     0.00   0.0  0
 3WH  CONST_52  N06  C04  N03  C02   180.00   0.0  0
 3WH  CONST_54  O05  C04  N03  C02     0.00   0.0  0
 3WH  Var_01    C08  C07  N06  C11    60.44  30.0  1
 3WH  Var_02    C07  N06  C11  C10   -60.20  30.0  1
 3WH  Var_03    C09  C10  C11  N06    55.89  30.0  1
 3WH  Var_04    C09  C08  C07  N06   -56.44  30.0  1
 3WH  Var_05    C04  N03  C02  C01  -169.59  30.0  3
 3WH  Var_06    H5   C01  C02  N03   -60.36  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
 3WH  chir_01  C09  C10  N12  C08  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
 3WH  plan-1  C13  0.020
 3WH  plan-1  N12  0.020
 3WH  plan-1  N14  0.020
 3WH  plan-1  C15  0.020
 3WH  plan-1  C16  0.020
 3WH  plan-1  I17  0.020
 3WH  plan-1  C18  0.020
 3WH  plan-1  N19  0.020
 3WH  plan-1  C20  0.020
 3WH  plan-1  H17  0.020
 3WH  plan-2  C15  0.020
 3WH  plan-2  C20  0.020
 3WH  plan-2  C21  0.020
 3WH  plan-2  N22  0.020
 3WH  plan-2  C23  0.020
 3WH  plan-2  C24  0.020
 3WH  plan-2  C25  0.020
 3WH  plan-2  C26  0.020
 3WH  plan-2  C27  0.020
 3WH  plan-2  C28  0.020
 3WH  plan-2  H18  0.020
 3WH  plan-2  H19  0.020
 3WH  plan-2  H20  0.020
 3WH  plan-2  H21  0.020
 3WH  plan-2  H22  0.020
 3WH  plan-2  H23  0.020
 3WH  plan-3  C11  0.020
 3WH  plan-3  C02  0.020
 3WH  plan-3  N03  0.020
 3WH  plan-3  O05  0.020
 3WH  plan-3  N06  0.020
 3WH  plan-3  C07  0.020
 3WH  plan-3  H10  0.020
 3WH  plan-3  C04  0.020
 3WH  plan-4  C13  0.020
 3WH  plan-4  C09  0.020
 3WH  plan-4  N12  0.020
 3WH  plan-4  H16  0.020

