# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 13:53:20 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: N-[3-({4-[(3-aminopropyl)amino]-5-iodopyrimidin-2-yl}amino)phenyl]pyrrolidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCNc1nc(Nc2cccc(NC(=O)N3CCCC3)c2)ncc1I
#
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
 51W  51W  N-[3-({4-[(3-aminopropyl)amino]-5-iodopyrimidin-2-yl}amino)phenyl]pyrrolidine-1-carboxamide  ligand  51  27  .  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_51W
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
 51W  N12   N  NH1   0  -0.772   0.5371  -0.3689  -0.5030
 51W  C13   C  CR6   0   0.407   1.6879  -1.1472  -0.5669
 51W  C15   C  CR6   0   0.400   4.1050  -1.1232  -0.3453
 51W  C17   C  C     0   0.747   5.6136   0.7990   0.1602
 51W  C20   C  CH2   0  -0.480   8.8742   2.3479   0.3854
 51W  C21   C  CH2   0  -0.476   9.2011   0.9418   0.8762
 51W  C22   C  CH2   0  -0.304   8.0156   0.1131   0.3901
 51W  C24   C  CR16  0  -0.382   4.1255  -2.4941  -0.6330
 51W  C26   C  CR16  0  -0.343   1.7127  -2.5118  -0.8517
 51W  N01   N  NH2   0  -0.799  -4.9277   5.9355   0.2453
 51W  C02   C  CH2   0  -0.274  -3.8400   4.9704   0.2763
 51W  C03   C  CH2   0  -0.483  -4.3075   3.6148  -0.2309
 51W  C04   C  CH2   0  -0.242  -3.1870   2.5895  -0.1986
 51W  C06   C  CR6   0   0.603  -2.8815   0.2362  -0.8113
 51W  C07   C  CR6   0  -0.411  -3.3644  -1.0403  -1.2085
 51W  I08   I  I     0   0.074  -5.3842  -1.4198  -1.6022
 51W  C09   C  CR16  0   0.013  -2.4376  -2.0436  -1.3324
 51W  N10   N  N     0  -0.490  -1.1354  -1.8764  -1.1075
 51W  C11   C  CR6   0   0.611  -0.7718  -0.6523  -0.7478
 51W  C14   C  CR16  0  -0.463   2.8831  -0.4604  -0.3138
 51W  N16   N  NH1   0  -0.810   5.3382  -0.5216  -0.1066
 51W  N18   N  NT    0  -0.516   6.9185   1.0742   0.3693
 51W  C19   C  CH2   0  -0.252   7.3671   2.4446   0.5848
 51W  O23   O  O     0  -0.533   4.7497   1.6685   0.2028
 51W  C25   C  CR16  0  -0.232   2.9411  -3.1593  -0.8780
 51W  N27   N  N     0  -0.529  -1.5814   0.3938  -0.5874
 51W  H121  H  HNH1  0   0.407   0.6870   0.5980  -0.2575
 51W  H201  H  HCH2  0   0.252   9.4113   3.1263   0.9257
 51W  H202  H  HCH2  0   0.239   9.1192   2.4478  -0.6743
 51W  H211  H  HCH2  0   0.255  10.1479   0.5596   0.4979
 51W  H212  H  HCH2  0   0.242   9.2452   0.9231   1.9669
 51W  H222  H  HCH2  0   0.247   8.2035  -0.2950  -0.6090
 51W  H221  H  HCH2  0   0.254   7.8098  -0.7215   1.0644
 51W  H241  H  HCR6  0   0.263   5.0666  -3.0298  -0.6663
 51W  H261  H  HCR6  0   0.280   0.8033  -3.0532  -1.0494
 51W  H012  H  HNH2  0   0.348  -4.6204   6.7984   0.6746
 51W  H011  H  HNH2  0   0.339  -5.1413   6.1710  -0.7161
 51W  H022  H  HCH2  0   0.195  -2.9571   5.2830  -0.2995
 51W  H021  H  HCH2  0   0.219  -3.5070   4.8669   1.3123
 51W  H031  H  HCH2  0   0.233  -5.1457   3.2736   0.3841
 51W  H032  H  HCH2  0   0.233  -4.6804   3.7135  -1.2555
 51W  H042  H  HCH2  0   0.237  -2.3609   2.9154  -0.8345
 51W  H041  H  HCH2  0   0.232  -2.7861   2.5037   0.8164
 51W  H051  H  HNH1  0   0.401  -4.6660   1.1889  -0.7516
 51W  H091  H  HCR6  0   0.279  -2.7441  -3.0409  -1.6281
 51W  H141  H  HCR6  0   0.290   2.8457   0.5961  -0.0991
 51W  H161  H  HNH1  0   0.426   6.1180  -1.1563  -0.1701
 51W  H191  H  HCH2  0   0.232   7.1227   2.7817   1.5971
 51W  H192  H  HCH2  0   0.246   6.8941   3.1313  -0.1167
 51W  H251  H  HCR6  0   0.256   2.9694  -4.2191  -1.0968
 51W  N05   N  NH1   0  -0.667  -3.6702   1.3020  -0.6544

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
 51W  C25  C26   aromatic  1.389  0.020  1.389
 51W  C25  C24   aromatic  1.380  0.020  1.380
 51W  C26  C13   aromatic  1.394  0.020  1.394
 51W  C24  C15   aromatic  1.401  0.020  1.401
 51W  C13  N12   single    1.391  0.020  1.391
 51W  C13  C14   aromatic  1.402  0.020  1.402
 51W  N12  C11   single    1.361  0.020  1.361
 51W  C15  C14   aromatic  1.390  0.020  1.390
 51W  C15  N16   single    1.393  0.020  1.393
 51W  N10  C11   aromatic  1.327  0.020  1.327
 51W  N10  C09   aromatic  1.332  0.020  1.332
 51W  C11  N27   aromatic  1.332  0.020  1.332
 51W  O23  C17   double    1.226  0.020  1.226
 51W  N16  C17   single    1.375  0.020  1.375
 51W  C09  C07   aromatic  1.371  0.020  1.371
 51W  C17  N18   single    1.350  0.020  1.350
 51W  N27  C06   aromatic  1.329  0.020  1.329
 51W  N18  C19   single    1.458  0.020  1.458
 51W  N18  C22   single    1.459  0.020  1.459
 51W  C07  C06   aromatic  1.421  0.020  1.421
 51W  C07  I08   single    2.093  0.020  2.093
 51W  N01  C02   single    1.455  0.020  1.455
 51W  C06  N05   single    1.335  0.020  1.335
 51W  C02  C03   single    1.521  0.020  1.521
 51W  C19  C20   single    1.523  0.020  1.523
 51W  C22  C21   single    1.526  0.020  1.526
 51W  C03  C04   single    1.519  0.020  1.519
 51W  N05  C04   single    1.449  0.020  1.449
 51W  C21  C20   single    1.525  0.020  1.525
 51W  N12  H121  single    0.860  0.020  1.020
 51W  C20  H201  single    0.970  0.020  1.090
 51W  C20  H202  single    0.970  0.020  1.090
 51W  C21  H211  single    0.970  0.020  1.090
 51W  C21  H212  single    0.970  0.020  1.090
 51W  C22  H222  single    0.970  0.020  1.090
 51W  C22  H221  single    0.970  0.020  1.090
 51W  C24  H241  single    0.930  0.020  1.080
 51W  C26  H261  single    0.930  0.020  1.080
 51W  N01  H012  single    0.890  0.020  1.040
 51W  N01  H011  single    0.890  0.020  1.040
 51W  C02  H022  single    0.970  0.020  1.090
 51W  C02  H021  single    0.970  0.020  1.090
 51W  C03  H031  single    0.970  0.020  1.090
 51W  C03  H032  single    0.970  0.020  1.090
 51W  C04  H042  single    0.970  0.020  1.090
 51W  C04  H041  single    0.970  0.020  1.090
 51W  N05  H051  single    0.860  0.020  1.020
 51W  C09  H091  single    0.930  0.020  1.080
 51W  C14  H141  single    0.930  0.020  1.080
 51W  N16  H161  single    0.860  0.020  1.020
 51W  C19  H191  single    0.970  0.020  1.090
 51W  C19  H192  single    0.970  0.020  1.090
 51W  C25  H251  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
 51W  H121  N12  C11   112.72  3.000
 51W  H121  N12  C13   115.12  3.000
 51W  C11   N12  C13   132.13  3.000
 51W  C14   C13  C26   120.09  3.000
 51W  C14   C13  N12   115.03  3.000
 51W  C26   C13  N12   124.88  3.000
 51W  N16   C15  C14   124.64  3.000
 51W  N16   C15  C24   116.42  3.000
 51W  C14   C15  C24   118.94  3.000
 51W  O23   C17  N18   122.07  3.000
 51W  N18   C17  N16   114.80  3.000
 51W  O23   C17  N16   123.13  3.000
 51W  H202  C20  H201  107.78  3.000
 51W  H202  C20  C19   110.07  3.000
 51W  H201  C20  C19   112.18  3.000
 51W  H202  C20  C21   110.40  3.000
 51W  H201  C20  C21   113.18  3.000
 51W  C19   C20  C21   103.21  3.000
 51W  H212  C21  H211  107.82  3.000
 51W  H212  C21  C22   109.90  3.000
 51W  H211  C21  C22   111.98  3.000
 51W  H212  C21  C20   110.24  3.000
 51W  H211  C21  C20   113.47  3.000
 51W  C22   C21  C20   103.40  3.000
 51W  H221  C22  H222  108.10  3.000
 51W  H221  C22  N18   111.75  3.000
 51W  H222  C22  N18   111.19  3.000
 51W  H221  C22  C21   111.38  3.000
 51W  H222  C22  C21   111.07  3.000
 51W  N18   C22  C21   103.36  3.000
 51W  H241  C24  C25   120.10  3.000
 51W  H241  C24  C15   120.19  3.000
 51W  C25   C24  C15   119.70  3.000
 51W  H261  C26  C25   120.60  3.000
 51W  H261  C26  C13   120.98  3.000
 51W  C25   C26  C13   118.42  3.000
 51W  H011  N01  H012  105.58  3.000
 51W  H011  N01  C02   109.40  3.000
 51W  H012  N01  C02   109.26  3.000
 51W  H021  C02  H022  106.18  3.000
 51W  H021  C02  C03   108.98  3.000
 51W  H022  C02  C03   109.00  3.000
 51W  H021  C02  N01   108.10  3.000
 51W  H022  C02  N01   113.62  3.000
 51W  C03   C02  N01   110.76  3.000
 51W  H032  C03  H031  107.05  3.000
 51W  H032  C03  C04   109.39  3.000
 51W  H031  C03  C04   110.04  3.000
 51W  H032  C03  C02   109.66  3.000
 51W  H031  C03  C02   109.02  3.000
 51W  C04   C03  C02   111.57  3.000
 51W  H041  C04  H042  106.63  3.000
 51W  H041  C04  N05   110.13  3.000
 51W  H042  C04  N05   109.52  3.000
 51W  H041  C04  C03   110.05  3.000
 51W  H042  C04  C03   110.13  3.000
 51W  N05   C04  C03   110.31  3.000
 51W  N27   C06  C07   119.08  3.000
 51W  C07   C06  N05   123.30  3.000
 51W  N27   C06  N05   117.62  3.000
 51W  C09   C07  I08   120.18  3.000
 51W  I08   C07  C06   122.91  3.000
 51W  C09   C07  C06   116.91  3.000
 51W  H091  C09  N10   115.96  3.000
 51W  H091  C09  C07   120.42  3.000
 51W  N10   C09  C07   123.61  3.000
 51W  C11   N10  C09   115.44  3.000
 51W  N27   C11  N10   126.19  3.000
 51W  N27   C11  N12   113.52  3.000
 51W  N10   C11  N12   120.29  3.000
 51W  H141  C14  C15   120.12  3.000
 51W  H141  C14  C13   119.10  3.000
 51W  C15   C14  C13   120.78  3.000
 51W  H161  N16  C17   117.53  3.000
 51W  H161  N16  C15   113.74  3.000
 51W  C17   N16  C15   128.71  3.000
 51W  C19   N18  C22   112.69  3.000
 51W  C22   N18  C17   126.51  3.000
 51W  C19   N18  C17   120.79  3.000
 51W  H192  C19  H191  107.72  3.000
 51W  H192  C19  N18   111.32  3.000
 51W  H191  C19  N18   110.95  3.000
 51W  H192  C19  C20   112.65  3.000
 51W  H191  C19  C20   111.20  3.000
 51W  N18   C19  C20   103.03  3.000
 51W  H251  C25  C26   118.91  3.000
 51W  H251  C25  C24   119.03  3.000
 51W  C26   C25  C24   122.06  3.000
 51W  C11   N27  C06   118.76  3.000
 51W  H051  N05  C06   118.90  3.000
 51W  H051  N05  C04   117.39  3.000
 51W  C06   N05  C04   123.32  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
 51W  CONST_01  C24   C25  C26  C13     0.00   0.0  0
 51W  CONST_02  C24   C15  C14  C13     0.00   0.0  0
 51W  CONST_03  C26   C25  C24  C15     0.00   0.0  0
 51W  CONST_04  C26   C13  C14  C15     0.00   0.0  0
 51W  CONST_05  N10   C11  N27  C06     0.00   0.0  0
 51W  CONST_06  N10   C09  C07  C06     0.00   0.0  0
 51W  CONST_07  C11   N10  C09  C07     0.00   0.0  0
 51W  CONST_08  C11   N27  C06  C07     0.00   0.0  0
 51W  CONST_09  N27   C11  N10  C09     0.00   0.0  0
 51W  CONST_10  N27   C06  C07  C09     0.00   0.0  0
 51W  CONST_11  C25   C26  C13  C14     0.00   0.0  0
 51W  CONST_12  C25   C24  C15  C14     0.00   0.0  0
 51W  CONST_13  C25   C26  C13  N12   180.00   0.0  0
 51W  CONST_14  C15   C14  C13  N12   180.00   0.0  0
 51W  CONST_15  C09   N10  C11  N12   180.00   0.0  0
 51W  CONST_16  C06   N27  C11  N12   180.00   0.0  0
 51W  CONST_17  N16   C15  C14  C13   180.00   0.0  0
 51W  CONST_18  C11   N27  C06  N05   180.00   0.0  0
 51W  CONST_19  C09   C07  C06  N05   180.00   0.0  0
 51W  CONST_20  N10   C09  C07  I08   180.00   0.0  0
 51W  CONST_21  N27   C06  C07  I08   180.00   0.0  0
 51W  CONST_22  C25   C24  C15  N16   180.00   0.0  0
 51W  CONST_23  H251  C25  C26  C13   180.00   0.0  0
 51W  CONST_24  H261  C26  C25  C24   180.00   0.0  0
 51W  CONST_25  H141  C14  C15  C24   180.00   0.0  0
 51W  CONST_26  H241  C24  C25  C26   180.00   0.0  0
 51W  CONST_27  H091  C09  C07  C06   180.00   0.0  0
 51W  CONST_28  O23   C17  N18  C22   180.00   0.0  0
 51W  CONST_29  O23   C17  N18  C19     0.00   0.0  0
 51W  CONST_30  N18   C17  N16  C15   180.00   0.0  0
 51W  CONST_31  C24   C15  N16  C17   180.00   0.0  0
 51W  CONST_32  C14   C15  N16  C17     0.00   0.0  0
 51W  CONST_33  N27   C06  N05  C04     0.00   0.0  0
 51W  CONST_34  C07   C06  N05  C04   180.00   0.0  0
 51W  CONST_35  N16   C17  N18  C22     0.00   0.0  0
 51W  CONST_36  C19   N18  C17  N16   180.00   0.0  0
 51W  CONST_37  H161  N16  C15  C24     0.00   0.0  0
 51W  CONST_38  H051  N05  C06  C07     0.00   0.0  0
 51W  CONST_39  O23   C17  N16  C15     0.00   0.0  0
 51W  Var_01    C22   N18  C19  C20    14.29  30.0  1
 51W  Var_02    N18   C22  C21  C20   -29.10  30.0  1
 51W  Var_03    C19   N18  C22  C21     9.34  30.0  1
 51W  Var_04    N18   C19  C20  C21   -31.95  30.0  1
 51W  Var_05    C19   C20  C21  C22    38.08  30.0  1
 51W  Var_06    N10   C11  N12  C13     0.93  30.0  2
 51W  Var_07    C11   N12  C13  C26    -3.97  30.0  2
 51W  Var_08    C06   N05  C04  C03   175.57  30.0  2
 51W  Var_09    C04   C03  C02  N01  -179.66  30.0  3
 51W  Var_10    N05   C04  C03  C02   178.55  30.0  3
 51W  Var_11    H012  N01  C02  C03   174.19  30.0  3

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
 51W  plan-1  N12   0.020
 51W  plan-1  C06   0.020
 51W  plan-1  C07   0.020
 51W  plan-1  I08   0.020
 51W  plan-1  C09   0.020
 51W  plan-1  N10   0.020
 51W  plan-1  C11   0.020
 51W  plan-1  N27   0.020
 51W  plan-1  H091  0.020
 51W  plan-1  N05   0.020
 51W  plan-2  N12   0.020
 51W  plan-2  C13   0.020
 51W  plan-2  C15   0.020
 51W  plan-2  C24   0.020
 51W  plan-2  C26   0.020
 51W  plan-2  C14   0.020
 51W  plan-2  N16   0.020
 51W  plan-2  C25   0.020
 51W  plan-2  H241  0.020
 51W  plan-2  H261  0.020
 51W  plan-2  H141  0.020
 51W  plan-2  H251  0.020
 51W  plan-3  C15   0.020
 51W  plan-3  C17   0.020
 51W  plan-3  C22   0.020
 51W  plan-3  N16   0.020
 51W  plan-3  N18   0.020
 51W  plan-3  C19   0.020
 51W  plan-3  O23   0.020
 51W  plan-3  H161  0.020
 51W  plan-4  C04   0.020
 51W  plan-4  C06   0.020
 51W  plan-4  H051  0.020
 51W  plan-4  N05   0.020

