# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 11:23:53 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 4-{[5-chloro-4-(1H-indol-3-yl)pyrimidin-2-yl]amino}-N-ethylpiperidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)N1CCC(CC1)Nc2ncc(Cl)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
 J07  J07  4-{[5-chloro-4-(1H-indol-3-yl)pyrimidin-2-yl]amino}-N-ethylpiperidine-1-carboxamide  ligand  51  28  .  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_J07
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
 J07  C01   C   CH3   0  -0.694  -6.8518   2.2065   2.7054
 J07  C02   C   CH2   0  -0.256  -6.8245   2.0335   1.1981
 J07  N03   N   NH1   0  -0.677  -5.9511   0.9334   0.8384
 J07  C04   C   C     0   0.734  -5.6266   0.6980  -0.4605
 J07  O05   O   O     0  -0.547  -5.9233   1.4980  -1.3434
 J07  N06   N   NT    0  -0.484  -4.9681  -0.4751  -0.7373
 J07  C07   C   CH2   0  -0.325  -4.3890  -0.6367  -2.0602
 J07  C08   C   CH2   0  -0.449  -2.9303  -0.1914  -2.0902
 J07  C09   C   CH1   0  -0.056  -2.1188  -0.9288  -1.0287
 J07  C10   C   CH2   0  -0.429  -2.7894  -0.8076   0.3421
 J07  C11   C   CH2   0  -0.352  -4.2452  -1.2504   0.2581
 J07  N12   N   NH1   0  -0.672  -0.7604  -0.4335  -1.0259
 J07  C13   C   CR6   0   0.598   0.2970  -1.1033  -0.5291
 J07  N14   N   N     0  -0.504   1.4484  -0.4317  -0.4675
 J07  C15   C   CR6   0   0.325   2.5379  -1.0381  -0.0083
 J07  C16   C   CR6   0  -0.219   2.4348  -2.3763   0.4098
 J07  C17   C   CR16  0   0.019   1.2000  -2.9875   0.3035
 J07  N18   N   N     0  -0.463   0.1260  -2.3773  -0.1619
 J07  CL1   CL  CL    0  -0.134   3.7386  -3.2762   1.1014
 J07  C20   C   CR5   0  -0.062   3.7428  -0.2290   0.0360
 J07  C21   C   CR56  0   0.064   3.7889   1.2140   0.0691
 J07  C22   C   CR16  0  -0.368   2.8314   2.2344   0.1308
 J07  C23   C   CR16  0  -0.260   3.2557   3.5482   0.1846
 J07  C24   C   CR16  0  -0.282   4.6196   3.8785   0.1756
 J07  C25   C   CR16  0  -0.298   5.5871   2.8952   0.1174
 J07  C26   C   CR56  0   0.351   5.1517   1.5735   0.0669
 J07  N27   N   NR15  0  -0.676   5.8818   0.4169   0.0141
 J07  C28   C   CR15  0  -0.043   5.0556  -0.6498   0.0005
 J07  H011  H   HCH3  0   0.241  -7.5175   3.0252   2.9758
 J07  H012  H   HCH3  0   0.229  -7.2163   1.3071   3.2051
 J07  H013  H   HCH3  0   0.232  -5.8596   2.4335   3.0964
 J07  H021  H   HCH2  0   0.221  -7.8416   1.8696   0.8266
 J07  H022  H   HCH2  0   0.234  -6.4598   2.9468   0.7289
 J07  HN03  H   HNH1  0   0.390  -5.9255   0.1738   1.4971
 J07  H071  H   HCH2  0   0.242  -4.4554  -1.6955  -2.3283
 J07  H072  H   HCH2  0   0.265  -4.9732  -0.0864  -2.7914
 J07  H081  H   HCH2  0   0.249  -2.5113  -0.3826  -3.0807
 J07  H082  H   HCH2  0   0.231  -2.8776   0.8892  -1.9175
 J07  H09   H   HCH1  0   0.243  -2.0862  -1.9883  -1.2984
 J07  H101  H   HCH2  0   0.247  -2.2591  -1.4206   1.0738
 J07  H102  H   HCH2  0   0.228  -2.7399   0.2303   0.6855
 J07  H111  H   HCH2  0   0.258  -4.7187  -1.2090   1.2360
 J07  H112  H   HCH2  0   0.252  -4.2954  -2.3013  -0.0419
 J07  HN12  H   HNH1  0   0.388  -0.6175   0.5508  -1.1910
 J07  H17   H   HCR6  0   0.283   1.0793  -4.0185   0.6200
 J07  H22   H   HCR6  0   0.251   1.7771   1.9999   0.1263
 J07  H23   H   HCR6  0   0.249   2.5211   4.3415   0.2307
 J07  H24   H   HCR6  0   0.253   4.9167   4.9185   0.2146
 J07  H25   H   HCR6  0   0.264   6.6418   3.1388   0.1140
 J07  HN27  H   HNR5  0   0.419   6.8865   0.3585  -0.0196
 J07  H28   H   HCR5  0   0.291   5.4667  -1.6420  -0.0671

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
 J07  O05  C04   double    1.228  0.020  1.228
 J07  C02  N03   single    1.450  0.020  1.450
 J07  C02  C01   single    1.517  0.020  1.517
 J07  C04  N03   single    1.359  0.020  1.359
 J07  C04  N06   single    1.373  0.020  1.373
 J07  C07  N06   single    1.453  0.020  1.453
 J07  C07  C08   single    1.525  0.020  1.525
 J07  N06  C11   single    1.454  0.020  1.454
 J07  C08  C09   single    1.526  0.020  1.526
 J07  C11  C10   single    1.524  0.020  1.524
 J07  C24  C23   aromatic  1.403  0.020  1.403
 J07  C24  C25   aromatic  1.381  0.020  1.381
 J07  C23  C22   aromatic  1.382  0.020  1.382
 J07  C25  C26   aromatic  1.392  0.020  1.392
 J07  C09  C10   single    1.531  0.020  1.531
 J07  C09  N12   single    1.446  0.020  1.446
 J07  C22  C21   aromatic  1.401  0.020  1.401
 J07  C26  C21   aromatic  1.409  0.020  1.409
 J07  C26  N27   aromatic  1.369  0.020  1.369
 J07  C21  C20   aromatic  1.444  0.020  1.444
 J07  N12  C13   single    1.347  0.020  1.347
 J07  N27  C28   aromatic  1.349  0.020  1.349
 J07  N14  C13   aromatic  1.334  0.020  1.334
 J07  N14  C15   aromatic  1.329  0.020  1.329
 J07  C20  C28   aromatic  1.379  0.020  1.379
 J07  C20  C15   single    1.452  0.020  1.452
 J07  C13  N18   aromatic  1.337  0.020  1.337
 J07  C15  C16   aromatic  1.406  0.020  1.406
 J07  N18  C17   aromatic  1.320  0.020  1.320
 J07  C16  C17   aromatic  1.382  0.020  1.382
 J07  C16  CL1   single    1.729  0.020  1.729
 J07  C01  H011  single    0.970  0.020  1.090
 J07  C01  H012  single    0.970  0.020  1.090
 J07  C01  H013  single    0.970  0.020  1.090
 J07  C02  H021  single    0.970  0.020  1.090
 J07  C02  H022  single    0.970  0.020  1.090
 J07  N03  HN03  single    0.890  0.020  1.040
 J07  C07  H071  single    0.970  0.020  1.090
 J07  C07  H072  single    0.970  0.020  1.090
 J07  C08  H081  single    0.970  0.020  1.090
 J07  C08  H082  single    0.970  0.020  1.090
 J07  C09  H09   single    0.970  0.020  1.090
 J07  C10  H101  single    0.970  0.020  1.090
 J07  C10  H102  single    0.970  0.020  1.090
 J07  C11  H111  single    0.970  0.020  1.090
 J07  C11  H112  single    0.970  0.020  1.090
 J07  N12  HN12  single    0.860  0.020  1.020
 J07  C17  H17   single    0.930  0.020  1.080
 J07  C22  H22   single    0.930  0.020  1.080
 J07  C23  H23   single    0.930  0.020  1.080
 J07  C24  H24   single    0.930  0.020  1.080
 J07  C25  H25   single    0.930  0.020  1.080
 J07  N27  HN27  single    0.860  0.020  1.020
 J07  C28  H28   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
 J07  H013  C01  H012  108.14  3.000
 J07  H013  C01  H011  108.09  3.000
 J07  H012  C01  H011  107.55  3.000
 J07  H013  C01  C02   111.32  3.000
 J07  H012  C01  C02   111.52  3.000
 J07  H011  C01  C02   110.08  3.000
 J07  H022  C02  H021  106.87  3.000
 J07  H022  C02  N03   109.12  3.000
 J07  H021  C02  N03   111.21  3.000
 J07  H022  C02  C01   109.77  3.000
 J07  H021  C02  C01   109.71  3.000
 J07  N03   C02  C01   110.10  3.000
 J07  HN03  N03  C04   119.27  3.000
 J07  HN03  N03  C02   115.21  3.000
 J07  C04   N03  C02   120.81  3.000
 J07  N06   C04  O05   121.83  3.000
 J07  N06   C04  N03   117.06  3.000
 J07  O05   C04  N03   121.10  3.000
 J07  C11   N06  C07   111.45  3.000
 J07  C11   N06  C04   123.76  3.000
 J07  C07   N06  C04   118.01  3.000
 J07  H072  C07  H071  107.03  3.000
 J07  H072  C07  C08   110.69  3.000
 J07  H071  C07  C08   109.62  3.000
 J07  H072  C07  N06   110.01  3.000
 J07  H071  C07  N06   107.85  3.000
 J07  C08   C07  N06   111.50  3.000
 J07  H082  C08  H081  107.29  3.000
 J07  H082  C08  C09   109.96  3.000
 J07  H081  C08  C09   110.01  3.000
 J07  H082  C08  C07   109.32  3.000
 J07  H081  C08  C07   109.48  3.000
 J07  C09   C08  C07   110.71  3.000
 J07  H09   C09  N12   107.72  3.000
 J07  H09   C09  C10   108.09  3.000
 J07  N12   C09  C10   112.50  3.000
 J07  H09   C09  C08   108.20  3.000
 J07  N12   C09  C08   109.59  3.000
 J07  C10   C09  C08   110.59  3.000
 J07  H102  C10  H101  107.46  3.000
 J07  H102  C10  C11   109.64  3.000
 J07  H101  C10  C11   109.74  3.000
 J07  H102  C10  C09   109.65  3.000
 J07  H101  C10  C09   110.05  3.000
 J07  C11   C10  C09   110.25  3.000
 J07  H112  C11  H111  105.26  3.000
 J07  H112  C11  C10   109.76  3.000
 J07  H111  C11  C10   110.82  3.000
 J07  H112  C11  N06   107.56  3.000
 J07  H111  C11  N06   112.26  3.000
 J07  C10   C11  N06   110.96  3.000
 J07  HN12  N12  C13   115.77  3.000
 J07  HN12  N12  C09   117.86  3.000
 J07  C13   N12  C09   124.61  3.000
 J07  N18   C13  N14   125.26  3.000
 J07  N18   C13  N12   118.35  3.000
 J07  N14   C13  N12   116.37  3.000
 J07  C15   N14  C13   119.59  3.000
 J07  C20   C15  C16   125.61  3.000
 J07  C16   C15  N14   118.49  3.000
 J07  C20   C15  N14   115.89  3.000
 J07  CL1   C16  C17   118.33  3.000
 J07  CL1   C16  C15   124.00  3.000
 J07  C17   C16  C15   117.63  3.000
 J07  H17   C17  N18   116.84  3.000
 J07  H17   C17  C16   119.81  3.000
 J07  N18   C17  C16   123.34  3.000
 J07  C17   N18  C13   115.68  3.000
 J07  C28   C20  C21   105.97  3.000
 J07  C28   C20  C15   128.25  3.000
 J07  C21   C20  C15   125.73  3.000
 J07  C26   C21  C22   118.38  3.000
 J07  C26   C21  C20   106.60  3.000
 J07  C22   C21  C20   135.00  3.000
 J07  H22   C22  C23   120.43  3.000
 J07  H22   C22  C21   120.59  3.000
 J07  C23   C22  C21   118.97  3.000
 J07  H23   C23  C24   119.17  3.000
 J07  H23   C23  C22   119.35  3.000
 J07  C24   C23  C22   121.47  3.000
 J07  H24   C24  C25   119.57  3.000
 J07  H24   C24  C23   119.52  3.000
 J07  C25   C24  C23   120.91  3.000
 J07  H25   C25  C26   121.21  3.000
 J07  H25   C25  C24   121.50  3.000
 J07  C26   C25  C24   117.29  3.000
 J07  N27   C26  C25   129.55  3.000
 J07  N27   C26  C21   107.47  3.000
 J07  C25   C26  C21   122.98  3.000
 J07  HN27  N27  C28   124.39  3.000
 J07  HN27  N27  C26   125.62  3.000
 J07  C28   N27  C26   109.99  3.000
 J07  H28   C28  N27   119.71  3.000
 J07  H28   C28  C20   130.29  3.000
 J07  N27   C28  C20   109.96  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
 J07  CONST_01  C20   C15  N14  C13   180.00   0.0  0
 J07  CONST_02  C16   C15  N14  C13     0.00   0.0  0
 J07  CONST_03  C16   C17  N18  C13     0.00   0.0  0
 J07  CONST_04  C17   N18  C13  N14     0.00   0.0  0
 J07  CONST_07  C17   C16  C15  N14     0.00   0.0  0
 J07  CONST_08  N18   C13  N14  C15     0.00   0.0  0
 J07  CONST_09  C22   C21  C20  C15     0.00   0.0  0
 J07  CONST_10  C26   C21  C20  C15   180.00   0.0  0
 J07  CONST_11  N27   C28  C20  C15   180.00   0.0  0
 J07  CONST_12  N18   C17  C16  C15     0.00   0.0  0
 J07  CONST_15  C20   C15  C16  C17   180.00   0.0  0
 J07  CONST_16  C23   C22  C21  C20   180.00   0.0  0
 J07  CONST_17  C25   C26  C21  C20   180.00   0.0  0
 J07  CONST_18  N27   C26  C21  C20     0.00   0.0  0
 J07  CONST_19  C26   N27  C28  C20     0.00   0.0  0
 J07  CONST_20  C24   C23  C22  C21     0.00   0.0  0
 J07  CONST_21  C24   C25  C26  C21     0.00   0.0  0
 J07  CONST_22  C28   N27  C26  C21     0.00   0.0  0
 J07  CONST_23  N27   C28  C20  C21     0.00   0.0  0
 J07  CONST_24  C25   C24  C23  C22     0.00   0.0  0
 J07  CONST_25  C25   C26  C21  C22     0.00   0.0  0
 J07  CONST_26  N27   C26  C21  C22   180.00   0.0  0
 J07  CONST_27  C28   C20  C21  C22   180.00   0.0  0
 J07  CONST_28  C26   C25  C24  C23     0.00   0.0  0
 J07  CONST_29  C26   C21  C22  C23     0.00   0.0  0
 J07  CONST_30  N27   C26  C25  C24   180.00   0.0  0
 J07  CONST_31  C28   N27  C26  C25   180.00   0.0  0
 J07  CONST_32  C28   C20  C21  C26     0.00   0.0  0
 J07  CONST_33  C15   N14  C13  N12   180.00   0.0  0
 J07  CONST_34  C17   N18  C13  N12   180.00   0.0  0
 J07  CONST_35  CL1   C16  C15  N14   180.00   0.0  0
 J07  CONST_36  CL1   C16  C17  N18   180.00   0.0  0
 J07  CONST_37  C20   C15  C16  CL1     0.00   0.0  0
 J07  CONST_38  N14   C13  N12  C09   180.00   0.0  0
 J07  CONST_39  N18   C13  N12  C09     0.00   0.0  0
 J07  CONST_40  H17   C17  N18  C13   180.00   0.0  0
 J07  CONST_41  H28   C28  C20  C15     0.00   0.0  0
 J07  CONST_42  H22   C22  C21  C20     0.00   0.0  0
 J07  CONST_43  HN27  N27  C28  C20   180.00   0.0  0
 J07  CONST_44  H23   C23  C22  C21   180.00   0.0  0
 J07  CONST_45  H25   C25  C26  C21   180.00   0.0  0
 J07  CONST_46  H24   C24  C23  C22   180.00   0.0  0
 J07  CONST_47  C07   N06  C04  O05     0.00   0.0  0
 J07  CONST_49  C07   N06  C04  N03   180.00   0.0  0
 J07  CONST_51  HN12  N12  C13  N14     0.00   0.0  0
 J07  CONST_52  N06   C04  N03  C02   180.00   0.0  0
 J07  CONST_54  O05   C04  N03  C02     0.00   0.0  0
 J07  Var_01    C09   C08  C07  N06    55.16  30.0  1
 J07  Var_02    C09   C10  C11  N06   -57.03  30.0  1
 J07  Var_03    C10   C11  N06  C07    60.42  30.0  1
 J07  Var_04    C11   N06  C07  C08   -59.44  30.0  1
 J07  Var_05    C04   N03  C02  C01  -171.24  30.0  3
 J07  Var_06    H011  C01  C02  N03  -179.31  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
 J07  chir_01  C09  C08  C10  N12  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
 J07  plan-1  N12   0.020
 J07  plan-1  C13   0.020
 J07  plan-1  N14   0.020
 J07  plan-1  C15   0.020
 J07  plan-1  C16   0.020
 J07  plan-1  C17   0.020
 J07  plan-1  N18   0.020
 J07  plan-1  CL1   0.020
 J07  plan-1  C20   0.020
 J07  plan-1  H17   0.020
 J07  plan-2  C15   0.020
 J07  plan-2  C20   0.020
 J07  plan-2  C21   0.020
 J07  plan-2  C22   0.020
 J07  plan-2  C23   0.020
 J07  plan-2  C24   0.020
 J07  plan-2  C25   0.020
 J07  plan-2  C26   0.020
 J07  plan-2  N27   0.020
 J07  plan-2  C28   0.020
 J07  plan-2  H22   0.020
 J07  plan-2  H23   0.020
 J07  plan-2  H24   0.020
 J07  plan-2  H25   0.020
 J07  plan-2  HN27  0.020
 J07  plan-2  H28   0.020
 J07  plan-3  C02   0.020
 J07  plan-3  N03   0.020
 J07  plan-3  C04   0.020
 J07  plan-3  O05   0.020
 J07  plan-3  N06   0.020
 J07  plan-3  C07   0.020
 J07  plan-3  C11   0.020
 J07  plan-3  HN03  0.020
 J07  plan-4  C09   0.020
 J07  plan-4  N12   0.020
 J07  plan-4  C13   0.020
 J07  plan-4  HN12  0.020

