# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 18:06:14 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 1-(5-cyanopyrazin-2-yl)-3-(5-phenyl-1H-pyrazol-3-yl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1cc([nH]n1)c2ccccc2)Nc3cnc(cn3)C#N
#
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
 H6K  H6K  1-(5-cyanopyrazin-2-yl)-3-(5-phenyl-1H-pyrazol-3-yl)urea  ligand  34  23  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_H6K
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
 H6K  N4   N  NS    0  -0.238  -8.3682   1.2195   0.1690
 H6K  C6   C  CSP   0   0.063  -7.3024   0.7844   0.1376
 H6K  C4   C  CR6   0   0.132  -5.9733   0.2610   0.0987
 H6K  N2   N  N     0  -0.344  -5.8322  -1.0689   0.0555
 H6K  C3   C  CR16  0  -0.161  -4.6166  -1.5378   0.0175
 H6K  C5   C  CR16  0  -0.040  -4.8756   1.1038   0.1052
 H6K  N3   N  N     0  -0.380  -3.6381   0.6337   0.0658
 H6K  C2   C  CR6   0   0.518  -3.4898  -0.6773   0.0205
 H6K  N1   N  NH1   0  -0.774  -2.2560  -1.2611  -0.0292
 H6K  C1   C  C     0   0.745  -1.0129  -0.6413  -0.0240
 H6K  O    O  O     0  -0.460  -0.8503   0.5558   0.0426
 H6K  N5   N  NH1   0  -0.776  -0.0010  -1.5464  -0.0988
 H6K  C7   C  CR5   0   0.472   1.3500  -1.2307  -0.1332
 H6K  N7   N  N     0  -0.305   2.1995  -2.2200  -0.3376
 H6K  N6   N  NR15  0  -0.513   3.4000  -1.6483  -0.2984
 H6K  C9   C  CR5   0   0.441   3.3516  -0.3220  -0.0862
 H6K  C8   C  CR15  0  -0.548   2.0108  -0.0007   0.0320
 H6K  C10  C  CR6   0   0.075   4.5387   0.5237   0.0006
 H6K  C15  C  CR16  0  -0.301   5.7881  -0.0073   0.3268
 H6K  C14  C  CR16  0  -0.239   6.9031   0.8137   0.4018
 H6K  C13  C  CR16  0  -0.261   6.7871   2.1765   0.1628
 H6K  C12  C  CR16  0  -0.236   5.5460   2.7138  -0.1550
 H6K  C11  C  CR16  0  -0.317   4.4316   1.8946  -0.2396
 H6K  H3   H  HCR6  0   0.302  -4.4918  -2.6145  -0.0167
 H6K  H4   H  HCR6  0   0.299  -4.9976   2.1796   0.1412
 H6K  H2   H  HNH1  0   0.432  -2.2689  -2.2694  -0.0743
 H6K  H5   H  HNH1  0   0.416  -0.2064  -2.5322  -0.1777
 H6K  H1   H  HNR5  0   0.422   4.2141  -2.2120  -0.4835
 H6K  H6   H  HCR5  0   0.278   1.5913   0.9672   0.2346
 H6K  H11  H  HCR6  0   0.252   5.9009  -1.0628   0.5421
 H6K  H10  H  HCR6  0   0.263   7.8637   0.3865   0.6575
 H6K  H9   H  HCR6  0   0.262   7.6570   2.8170   0.2250
 H6K  H8   H  HCR6  0   0.263   5.4455   3.7745  -0.3439
 H6K  H7   H  HCR6  0   0.259   3.4736   2.3223  -0.5064

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
 H6K  C12  C13  aromatic  1.389  0.020  1.389
 H6K  C12  C11  aromatic  1.386  0.020  1.386
 H6K  C13  C14  aromatic  1.388  0.020  1.388
 H6K  C11  C10  aromatic  1.396  0.020  1.396
 H6K  C14  C15  aromatic  1.387  0.020  1.387
 H6K  O    C1   double    1.210  0.020  1.210
 H6K  C10  C15  aromatic  1.396  0.020  1.396
 H6K  C10  C9   single    1.460  0.020  1.460
 H6K  C8   C9   aromatic  1.384  0.020  1.384
 H6K  C8   C7   aromatic  1.406  0.020  1.406
 H6K  C9   N6   aromatic  1.344  0.020  1.344
 H6K  C1   N1   single    1.389  0.020  1.389
 H6K  C1   N5   single    1.360  0.020  1.360
 H6K  N1   C2   single    1.366  0.020  1.366
 H6K  C7   N5   single    1.388  0.020  1.388
 H6K  C7   N7   aromatic  1.320  0.020  1.320
 H6K  N6   N7   aromatic  1.330  0.020  1.330
 H6K  C2   C3   aromatic  1.418  0.020  1.418
 H6K  C2   N3   aromatic  1.320  0.020  1.320
 H6K  C3   N2   aromatic  1.303  0.020  1.303
 H6K  N3   C5   aromatic  1.324  0.020  1.324
 H6K  N2   C4   aromatic  1.338  0.020  1.338
 H6K  C5   C4   aromatic  1.384  0.020  1.384
 H6K  C4   C6   single    1.429  0.020  1.429
 H6K  C6   N4   triple    1.152  0.020  1.152
 H6K  C3   H3   single    0.930  0.020  1.080
 H6K  C5   H4   single    0.930  0.020  1.080
 H6K  N1   H2   single    0.860  0.020  1.020
 H6K  N5   H5   single    0.860  0.020  1.020
 H6K  N6   H1   single    0.860  0.020  1.020
 H6K  C8   H6   single    0.930  0.020  1.080
 H6K  C15  H11  single    0.930  0.020  1.080
 H6K  C14  H10  single    0.930  0.020  1.080
 H6K  C13  H9   single    0.930  0.020  1.080
 H6K  C12  H8   single    0.930  0.020  1.080
 H6K  C11  H7   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
 H6K  C4   C6   N4   180.00  3.000
 H6K  C5   C4   N2   121.45  3.000
 H6K  C5   C4   C6   120.97  3.000
 H6K  N2   C4   C6   117.58  3.000
 H6K  C3   N2   C4   117.18  3.000
 H6K  H3   C3   C2   120.74  3.000
 H6K  H3   C3   N2   117.74  3.000
 H6K  C2   C3   N2   121.52  3.000
 H6K  H4   C5   N3   117.31  3.000
 H6K  H4   C5   C4   121.04  3.000
 H6K  N3   C5   C4   121.65  3.000
 H6K  C2   N3   C5   117.29  3.000
 H6K  N1   C2   N3   121.82  3.000
 H6K  N3   C2   C3   120.90  3.000
 H6K  N1   C2   C3   117.29  3.000
 H6K  H2   N1   C1   117.22  3.000
 H6K  H2   N1   C2   114.65  3.000
 H6K  C1   N1   C2   128.14  3.000
 H6K  N5   C1   O    124.17  3.000
 H6K  N5   C1   N1   111.64  3.000
 H6K  O    C1   N1   124.19  3.000
 H6K  H5   N5   C7   114.72  3.000
 H6K  H5   N5   C1   120.17  3.000
 H6K  C7   N5   C1   125.06  3.000
 H6K  C8   C7   N7   111.80  3.000
 H6K  N7   C7   N5   117.38  3.000
 H6K  C8   C7   N5   130.82  3.000
 H6K  N6   N7   C7   104.72  3.000
 H6K  H1   N6   C9   127.61  3.000
 H6K  H1   N6   N7   118.91  3.000
 H6K  C9   N6   N7   113.34  3.000
 H6K  C10  C9   C8   130.40  3.000
 H6K  C8   C9   N6   106.11  3.000
 H6K  C10  C9   N6   123.48  3.000
 H6K  H6   C8   C9   127.14  3.000
 H6K  H6   C8   C7   128.82  3.000
 H6K  C9   C8   C7   104.02  3.000
 H6K  C11  C10  C15  118.84  3.000
 H6K  C15  C10  C9   121.41  3.000
 H6K  C11  C10  C9   119.75  3.000
 H6K  H11  C15  C14  118.84  3.000
 H6K  H11  C15  C10  120.69  3.000
 H6K  C14  C15  C10  120.46  3.000
 H6K  H10  C14  C13  120.16  3.000
 H6K  H10  C14  C15  119.53  3.000
 H6K  C13  C14  C15  120.31  3.000
 H6K  H9   C13  C12  120.16  3.000
 H6K  H9   C13  C14  120.26  3.000
 H6K  C12  C13  C14  119.58  3.000
 H6K  H8   C12  C11  119.61  3.000
 H6K  H8   C12  C13  120.14  3.000
 H6K  C11  C12  C13  120.25  3.000
 H6K  H7   C11  C12  119.55  3.000
 H6K  H7   C11  C10  119.88  3.000
 H6K  C12  C11  C10  120.56  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
 H6K  CONST_01  C2   C3   N2   C4     0.00  0.0  0
 H6K  CONST_02  C2   N3   C5   C4     0.00  0.0  0
 H6K  CONST_03  N3   C2   C3   N2     0.00  0.0  0
 H6K  CONST_04  N3   C5   C4   N2     0.00  0.0  0
 H6K  CONST_05  C5   N3   C2   C3     0.00  0.0  0
 H6K  CONST_06  C5   C4   N2   C3     0.00  0.0  0
 H6K  CONST_07  C10  C9   C8   C7   180.00  0.0  0
 H6K  CONST_08  N6   C9   C8   C7     0.00  0.0  0
 H6K  CONST_09  C9   N6   N7   C7     0.00  0.0  0
 H6K  CONST_10  C9   C8   C7   N7     0.00  0.0  0
 H6K  CONST_11  C10  C9   N6   N7   180.00  0.0  0
 H6K  CONST_12  C8   C9   N6   N7     0.00  0.0  0
 H6K  CONST_15  C8   C7   N7   N6     0.00  0.0  0
 H6K  CONST_16  C12  C11  C10  C9   180.00  0.0  0
 H6K  CONST_17  C14  C15  C10  C9   180.00  0.0  0
 H6K  CONST_20  C13  C12  C11  C10    0.00  0.0  0
 H6K  CONST_21  C13  C14  C15  C10    0.00  0.0  0
 H6K  CONST_22  C12  C13  C14  C15    0.00  0.0  0
 H6K  CONST_23  C12  C11  C10  C15    0.00  0.0  0
 H6K  CONST_24  C11  C12  C13  C14    0.00  0.0  0
 H6K  CONST_25  C11  C10  C15  C14    0.00  0.0  0
 H6K  CONST_26  C3   N2   C4   C6   180.00  0.0  0
 H6K  CONST_27  N3   C5   C4   C6   180.00  0.0  0
 H6K  CONST_28  N1   C2   C3   N2   180.00  0.0  0
 H6K  CONST_29  N1   C2   N3   C5   180.00  0.0  0
 H6K  CONST_30  C9   C8   C7   N5   180.00  0.0  0
 H6K  CONST_31  N6   N7   C7   N5   180.00  0.0  0
 H6K  CONST_32  H3   C3   N2   C4   180.00  0.0  0
 H6K  CONST_33  H4   C5   C4   N2   180.00  0.0  0
 H6K  CONST_34  H1   N6   N7   C7   180.00  0.0  0
 H6K  CONST_35  H6   C8   C7   N7   180.00  0.0  0
 H6K  CONST_36  H7   C11  C10  C9     0.00  0.0  0
 H6K  CONST_37  H11  C15  C10  C9     0.00  0.0  0
 H6K  CONST_38  H8   C12  C11  C10  180.00  0.0  0
 H6K  CONST_39  H10  C14  C15  C10  180.00  0.0  0
 H6K  CONST_40  H9   C13  C14  C15  180.00  0.0  0
 H6K  CONST_41  C1   N1   C2   C3   180.00  0.0  0
 H6K  CONST_42  C1   N1   C2   N3     0.00  0.0  0
 H6K  CONST_43  C8   C7   N5   C1     0.00  0.0  0
 H6K  CONST_44  N7   C7   N5   C1   180.00  0.0  0
 H6K  CONST_45  H2   N1   C2   C3     0.00  0.0  0
 H6K  CONST_46  H5   N5   C7   N7     0.00  0.0  0
 H6K  CONST_47  O    C1   N1   C2     0.00  0.0  0
 H6K  CONST_48  C7   N5   C1   O      0.00  0.0  0
 H6K  CONST_49  N5   C1   N1   C2   180.00  0.0  0
 H6K  CONST_50  C7   N5   C1   N1   180.00  0.0  0

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
 H6K  plan-1  N5   0.020
 H6K  plan-1  C7   0.020
 H6K  plan-1  N7   0.020
 H6K  plan-1  N6   0.020
 H6K  plan-1  C9   0.020
 H6K  plan-1  C8   0.020
 H6K  plan-1  C10  0.020
 H6K  plan-1  H1   0.020
 H6K  plan-1  H6   0.020
 H6K  plan-2  N4   0.020
 H6K  plan-2  C6   0.020
 H6K  plan-2  C4   0.020
 H6K  plan-2  N2   0.020
 H6K  plan-2  C3   0.020
 H6K  plan-2  C5   0.020
 H6K  plan-2  N3   0.020
 H6K  plan-2  C2   0.020
 H6K  plan-2  N1   0.020
 H6K  plan-2  H3   0.020
 H6K  plan-2  H4   0.020
 H6K  plan-3  C9   0.020
 H6K  plan-3  C10  0.020
 H6K  plan-3  C15  0.020
 H6K  plan-3  C14  0.020
 H6K  plan-3  C13  0.020
 H6K  plan-3  C12  0.020
 H6K  plan-3  C11  0.020
 H6K  plan-3  H11  0.020
 H6K  plan-3  H10  0.020
 H6K  plan-3  H9   0.020
 H6K  plan-3  H8   0.020
 H6K  plan-3  H7   0.020
 H6K  plan-4  C2   0.020
 H6K  plan-4  N1   0.020
 H6K  plan-4  C1   0.020
 H6K  plan-4  O    0.020
 H6K  plan-4  N5   0.020
 H6K  plan-4  C7   0.020
 H6K  plan-4  H2   0.020
 H6K  plan-4  H5   0.020

