# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 08:52:16 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: N-[3-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)phenyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1cccc(c1)c2ncnc3[nH]ccc23
#
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
 7KX  7KX  N-[3-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)phenyl]propanamide  ligand  34  20  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7KX
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
 7KX  N3   N  N     0  -0.421   3.6365  -1.9727   0.4193
 7KX  C4   C  CR6   0   0.395  -2.0344   0.9966   0.0732
 7KX  N2   N  NR15  0  -0.659   4.9330  -0.2641  -0.6359
 7KX  C7   C  CR16  0  -0.333   0.5055   2.1160   0.4204
 7KX  C6   C  CR16  0  -0.229  -0.6210   2.9255   0.4039
 7KX  C9   C  CR16  0  -0.363  -0.9062   0.1804   0.0986
 7KX  C13  C  CR15  0   0.009   4.6867   1.0004  -1.1035
 7KX  C8   C  CR6   0   0.081   0.3613   0.7409   0.2610
 7KX  C1   C  CH3   0  -0.657  -5.7979  -2.2063  -0.7087
 7KX  C2   C  CH2   0  -0.586  -5.3111  -0.8342  -0.2780
 7KX  C3   C  C     0   0.550  -3.8050  -0.7477  -0.1462
 7KX  O1   O  O     0  -0.466  -3.0925  -1.7308  -0.0633
 7KX  C5   C  CR16  0  -0.350  -1.8776   2.3779   0.2267
 7KX  C10  C  CR6   0   0.206   1.5362  -0.1516   0.2783
 7KX  C11  C  CR56  0   0.000   2.7884   0.2192  -0.2201
 7KX  C12  C  CR15  0  -0.471   3.3872   1.3405  -0.8740
 7KX  C14  C  CR56  0   0.497   3.7970  -0.7664  -0.1035
 7KX  C15  C  CR16  0   0.026   2.4035  -2.2049   0.8314
 7KX  N4   N  N     0  -0.443   1.3677  -1.3711   0.7848
 7KX  H1   H  HNR5  0   0.419   5.8161  -0.7463  -0.6903
 7KX  H2   H  HCR6  0   0.260   1.4786   2.5552   0.5911
 7KX  H3   H  HCR6  0   0.265  -0.5202   3.9945   0.5354
 7KX  H4   H  HCR6  0   0.278  -0.9953  -0.8868  -0.0155
 7KX  H5   H  HCR5  0   0.296   5.4718   1.5688  -1.5742
 7KX  H6   H  HCH3  0   0.230  -5.5079  -2.9788   0.0019
 7KX  H7   H  HCH3  0   0.236  -6.8850  -2.2094  -0.7765
 7KX  H8   H  HCH3  0   0.230  -5.4035  -2.4820  -1.6863
 7KX  H9   H  HCH2  0   0.263  -5.6617  -0.0687  -0.9749
 7KX  H10  H  HCH2  0   0.279  -5.7420  -0.5677   0.6927
 7KX  H11  H  HNH1  0   0.416  -4.0375   1.2537  -0.1764
 7KX  H12  H  HCR6  0   0.275  -2.7474   3.0238   0.2122
 7KX  H13  H  HCR5  0   0.263   2.9287   2.2739  -1.1540
 7KX  H14  H  HCR6  0   0.253   2.2114  -3.1821   1.2602
 7KX  N1   N  NH1   0  -0.750  -3.3378   0.5300  -0.1080

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
 7KX  O1   C3   double    1.217  0.020  1.217
 7KX  C1   C2   single    1.518  0.020  1.518
 7KX  C2   C3   single    1.514  0.020  1.514
 7KX  C3   N1   single    1.361  0.020  1.361
 7KX  N1   C4   single    1.396  0.020  1.396
 7KX  C4   C5   aromatic  1.399  0.020  1.399
 7KX  C4   C9   aromatic  1.393  0.020  1.393
 7KX  C5   C6   aromatic  1.382  0.020  1.382
 7KX  C9   C8   aromatic  1.395  0.020  1.395
 7KX  C6   C7   aromatic  1.387  0.020  1.387
 7KX  C8   C7   aromatic  1.392  0.020  1.392
 7KX  C8   C10  single    1.475  0.020  1.475
 7KX  C12  C13  aromatic  1.363  0.020  1.363
 7KX  C12  C11  aromatic  1.429  0.020  1.429
 7KX  C13  N2   aromatic  1.371  0.020  1.371
 7KX  C11  C10  aromatic  1.398  0.020  1.398
 7KX  C11  C14  aromatic  1.415  0.020  1.415
 7KX  C10  N4   aromatic  1.331  0.020  1.331
 7KX  N2   C14  aromatic  1.351  0.020  1.351
 7KX  C14  N3   aromatic  1.324  0.020  1.324
 7KX  N4   C15  aromatic  1.331  0.020  1.331
 7KX  N3   C15  aromatic  1.321  0.020  1.321
 7KX  N2   H1   single    0.860  0.020  1.020
 7KX  C7   H2   single    0.930  0.020  1.080
 7KX  C6   H3   single    0.930  0.020  1.080
 7KX  C9   H4   single    0.930  0.020  1.080
 7KX  C13  H5   single    0.930  0.020  1.080
 7KX  C1   H6   single    0.970  0.020  1.090
 7KX  C1   H7   single    0.970  0.020  1.090
 7KX  C1   H8   single    0.970  0.020  1.090
 7KX  C2   H9   single    0.970  0.020  1.090
 7KX  C2   H10  single    0.970  0.020  1.090
 7KX  N1   H11  single    0.860  0.020  1.020
 7KX  C5   H12  single    0.930  0.020  1.080
 7KX  C12  H13  single    0.930  0.020  1.080
 7KX  C15  H14  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
 7KX  C15  N3   C14  113.35  3.000
 7KX  C5   C4   N1   116.68  3.000
 7KX  C5   C4   C9   119.08  3.000
 7KX  N1   C4   C9   124.25  3.000
 7KX  H1   N2   C14  125.46  3.000
 7KX  H1   N2   C13  125.50  3.000
 7KX  C14  N2   C13  109.04  3.000
 7KX  H2   C7   C8   120.83  3.000
 7KX  H2   C7   C6   119.72  3.000
 7KX  C8   C7   C6   119.41  3.000
 7KX  H3   C6   C5   119.46  3.000
 7KX  H3   C6   C7   119.97  3.000
 7KX  C5   C6   C7   120.57  3.000
 7KX  H4   C9   C8   119.04  3.000
 7KX  H4   C9   C4   120.78  3.000
 7KX  C8   C9   C4   120.17  3.000
 7KX  H5   C13  C12  129.55  3.000
 7KX  H5   C13  N2   120.32  3.000
 7KX  C12  C13  N2   110.13  3.000
 7KX  C10  C8   C9   118.80  3.000
 7KX  C10  C8   C7   120.92  3.000
 7KX  C9   C8   C7   120.28  3.000
 7KX  H8   C1   H7   107.74  3.000
 7KX  H8   C1   H6   108.02  3.000
 7KX  H7   C1   H6   107.72  3.000
 7KX  H8   C1   C2   111.54  3.000
 7KX  H7   C1   C2   109.89  3.000
 7KX  H6   C1   C2   111.76  3.000
 7KX  H10  C2   H9   105.58  3.000
 7KX  H10  C2   C3   107.48  3.000
 7KX  H9   C2   C3   109.54  3.000
 7KX  H10  C2   C1   110.19  3.000
 7KX  H9   C2   C1   110.44  3.000
 7KX  C3   C2   C1   113.28  3.000
 7KX  N1   C3   O1   123.75  3.000
 7KX  N1   C3   C2   113.42  3.000
 7KX  O1   C3   C2   122.82  3.000
 7KX  H12  C5   C6   119.69  3.000
 7KX  H12  C5   C4   119.82  3.000
 7KX  C6   C5   C4   120.48  3.000
 7KX  N4   C10  C11  119.48  3.000
 7KX  N4   C10  C8   117.25  3.000
 7KX  C11  C10  C8   123.27  3.000
 7KX  C14  C11  C12  106.59  3.000
 7KX  C14  C11  C10  115.11  3.000
 7KX  C12  C11  C10  138.28  3.000
 7KX  H13  C12  C11  128.35  3.000
 7KX  H13  C12  C13  125.34  3.000
 7KX  C11  C12  C13  106.30  3.000
 7KX  C11  C14  N2   107.92  3.000
 7KX  N2   C14  N3   126.58  3.000
 7KX  C11  C14  N3   125.49  3.000
 7KX  H14  C15  N4   116.15  3.000
 7KX  H14  C15  N3   116.57  3.000
 7KX  N4   C15  N3   127.28  3.000
 7KX  C15  N4   C10  119.27  3.000
 7KX  H11  N1   C3   115.69  3.000
 7KX  H11  N1   C4   114.61  3.000
 7KX  C3   N1   C4   129.63  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
 7KX  CONST_01  C12  C11  C14  N3   180.00   0.0  0
 7KX  CONST_02  C10  C11  C14  N3     0.00   0.0  0
 7KX  CONST_03  C13  N2   C14  N3   180.00   0.0  0
 7KX  CONST_04  C10  N4   C15  N3     0.00   0.0  0
 7KX  CONST_05  C7   C6   C5   C4     0.00   0.0  0
 7KX  CONST_06  C7   C8   C9   C4     0.00   0.0  0
 7KX  CONST_07  C10  C8   C9   C4   180.00   0.0  0
 7KX  CONST_08  C11  C12  C13  N2     0.00   0.0  0
 7KX  CONST_09  C12  C11  C14  N2     0.00   0.0  0
 7KX  CONST_10  C10  C11  C14  N2   180.00   0.0  0
 7KX  CONST_11  C15  N3   C14  N2   180.00   0.0  0
 7KX  CONST_14  C9   C4   C5   C6     0.00   0.0  0
 7KX  CONST_15  C9   C8   C7   C6     0.00   0.0  0
 7KX  CONST_16  C10  C8   C7   C6   180.00   0.0  0
 7KX  CONST_19  C10  C11  C12  C13  180.00   0.0  0
 7KX  CONST_20  C14  C11  C12  C13    0.00   0.0  0
 7KX  CONST_21  C11  C14  N2   C13    0.00   0.0  0
 7KX  CONST_22  C5   C4   C9   C8     0.00   0.0  0
 7KX  CONST_23  C5   C6   C7   C8     0.00   0.0  0
 7KX  CONST_24  C12  C11  C10  C8     0.00   0.0  0
 7KX  CONST_25  C14  C11  C10  C8   180.00   0.0  0
 7KX  CONST_26  C15  N4   C10  C8   180.00   0.0  0
 7KX  CONST_27  C15  N4   C10  C11    0.00   0.0  0
 7KX  CONST_28  C15  N3   C14  C11    0.00   0.0  0
 7KX  CONST_29  C14  N2   C13  C12    0.00   0.0  0
 7KX  CONST_30  N4   C10  C11  C12  180.00   0.0  0
 7KX  CONST_31  N4   C10  C11  C14    0.00   0.0  0
 7KX  CONST_32  N4   C15  N3   C14    0.00   0.0  0
 7KX  CONST_33  N1   C4   C5   C6   180.00   0.0  0
 7KX  CONST_34  N1   C4   C9   C8   180.00   0.0  0
 7KX  CONST_35  H1   N2   C14  N3     0.00   0.0  0
 7KX  CONST_36  H3   C6   C5   C4   180.00   0.0  0
 7KX  CONST_37  H13  C12  C13  N2   180.00   0.0  0
 7KX  CONST_38  H12  C5   C6   C7   180.00   0.0  0
 7KX  CONST_39  H4   C9   C8   C7   180.00   0.0  0
 7KX  CONST_40  H2   C7   C8   C9   180.00   0.0  0
 7KX  CONST_41  H14  C15  N4   C10  180.00   0.0  0
 7KX  CONST_42  H5   C13  C12  C11  180.00   0.0  0
 7KX  CONST_43  C3   N1   C4   C9     0.00   0.0  0
 7KX  CONST_44  C5   C4   N1   C3   180.00   0.0  0
 7KX  CONST_45  H11  N1   C4   C9   180.00   0.0  0
 7KX  CONST_46  O1   C3   N1   C4     0.00   0.0  0
 7KX  CONST_47  C2   C3   N1   C4   180.00   0.0  0
 7KX  Var_01    O1   C3   C2   C1   -17.24  30.0  3
 7KX  Var_02    H6   C1   C2   C3    59.92  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
 7KX  plan-1  C4   0.020
 7KX  plan-1  C7   0.020
 7KX  plan-1  C6   0.020
 7KX  plan-1  C9   0.020
 7KX  plan-1  C8   0.020
 7KX  plan-1  C5   0.020
 7KX  plan-1  C10  0.020
 7KX  plan-1  H2   0.020
 7KX  plan-1  H3   0.020
 7KX  plan-1  H4   0.020
 7KX  plan-1  H12  0.020
 7KX  plan-1  N1   0.020
 7KX  plan-2  N3   0.020
 7KX  plan-2  N2   0.020
 7KX  plan-2  C13  0.020
 7KX  plan-2  C8   0.020
 7KX  plan-2  C10  0.020
 7KX  plan-2  C11  0.020
 7KX  plan-2  C12  0.020
 7KX  plan-2  C14  0.020
 7KX  plan-2  C15  0.020
 7KX  plan-2  N4   0.020
 7KX  plan-2  H1   0.020
 7KX  plan-2  H5   0.020
 7KX  plan-2  H13  0.020
 7KX  plan-2  H14  0.020
 7KX  plan-3  C4   0.020
 7KX  plan-3  C2   0.020
 7KX  plan-3  C3   0.020
 7KX  plan-3  O1   0.020
 7KX  plan-3  H11  0.020
 7KX  plan-3  N1   0.020

