# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 03:19:39 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: N,N-dimethyl-N'-[3-(1H-pyrazol-4-yl)pyrazolo[1,5-a]pyrimidin-5-yl]ethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCNc1ccn2ncc(c3c[nH]nc3)c2n1
#
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
 26K  26K  N,N-dimethyl-N'-[3-(1H-pyrazol-4-yl)pyrazolo[1,5-a]pyrimidin-5-yl]ethane-1,2-diamine  ligand  37  20  .  2021-08-04  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_26K
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
 26K  N1   N  NT    0  -0.410   4.7118  -0.9233   0.0285
 26K  N3   N  N     0  -0.385  -2.0619   2.1230  -0.0194
 26K  C4   C  CH2   0  -0.258   2.5359   0.2217  -0.1194
 26K  C5   C  CR6   0   0.542   0.5910   1.7080  -0.0690
 26K  C6   C  CR16  0  -0.458   0.0665   3.0466  -0.1477
 26K  C7   C  CR16  0   0.077  -1.2712   3.2186  -0.1227
 26K  C8   C  CR56  0   0.571  -1.5148   0.8616   0.0574
 26K  C10  C  CR5   0  -0.106  -2.5492  -1.4524   0.2740
 26K  C13  C  CR15  0  -0.100  -3.7140   0.8420   0.1317
 26K  C2   C  CH3   0  -0.526   4.8216  -1.4392  -1.3207
 26K  C1   C  CH3   0  -0.519   6.0164  -0.8581   0.6533
 26K  C3   C  CH2   0  -0.305   4.0385   0.3582   0.0824
 26K  N2   N  NH1   0  -0.680   1.9206   1.5289  -0.0824
 26K  N7   N  N     0  -0.515  -0.1915   0.6542   0.0247
 26K  C9   C  CR5   0  -0.212  -2.5944  -0.0098   0.1601
 26K  C12  C  CR15  0  -0.036  -3.6096  -2.3310   0.3941
 26K  N5   N  NR15  0  -0.427  -3.0800  -3.5630   0.4723
 26K  N4   N  N     0  -0.265  -1.7565  -3.5676   0.4146
 26K  C11  C  CR15  0  -0.155  -1.4161  -2.2970   0.2939
 26K  N6   N  N     0  -0.311  -3.4026   2.1205   0.0238
 26K  H2   H  HCH2  0   0.231   2.3014  -0.2747  -1.0665
 26K  H3   H  HCH2  0   0.241   2.1196  -0.4003   0.6742
 26K  H4   H  HCR6  0   0.294   0.7232   3.9005  -0.2273
 26K  H5   H  HCR6  0   0.320  -1.7639   4.1785  -0.1795
 26K  H6   H  HCR5  0   0.262  -4.7539   0.5536   0.1882
 26K  H7   H  HCH3  0   0.194   5.4134  -0.7868  -1.9820
 26K  H8   H  HCH3  0   0.236   5.3023  -2.4181  -1.3013
 26K  H9   H  HCH3  0   0.234   3.8401  -1.5706  -1.7754
 26K  H10  H  HCH3  0   0.193   6.7110  -0.1712   0.1446
 26K  H11  H  HCH3  0   0.234   5.9221  -0.5309   1.6895
 26K  H12  H  HCH3  0   0.233   6.4755  -1.8479   0.6561
 26K  H13  H  HCH2  0   0.245   4.2089   0.7930   1.0703
 26K  H14  H  HCH2  0   0.200   4.4544   1.0722  -0.6513
 26K  H15  H  HNH1  0   0.403   2.4993   2.3319  -0.2679
 26K  H16  H  HCR5  0   0.281  -4.6747  -2.1691   0.4276
 26K  H17  H  HNR5  0   0.420  -3.5819  -4.4308   0.5705
 26K  H18  H  HCR5  0   0.255  -0.3789  -2.0085   0.2248

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
 26K  C1   N1   single    1.448  0.020  1.448
 26K  N1   C2   single    1.449  0.020  1.449
 26K  N1   C3   single    1.449  0.020  1.449
 26K  C4   C3   single    1.522  0.020  1.522
 26K  C4   N2   single    1.445  0.020  1.445
 26K  N2   C5   single    1.342  0.020  1.342
 26K  C5   C6   aromatic  1.440  0.020  1.440
 26K  C5   N7   aromatic  1.316  0.020  1.316
 26K  C6   C7   aromatic  1.349  0.020  1.349
 26K  N7   C8   aromatic  1.340  0.020  1.340
 26K  C7   N3   aromatic  1.355  0.020  1.355
 26K  C8   N3   aromatic  1.377  0.020  1.377
 26K  C8   C9   aromatic  1.391  0.020  1.391
 26K  N3   N6   aromatic  1.341  0.020  1.341
 26K  C12  C10  aromatic  1.382  0.020  1.382
 26K  C12  N5   aromatic  1.343  0.020  1.343
 26K  N6   C13  aromatic  1.320  0.020  1.320
 26K  C9   C10  single    1.448  0.020  1.448
 26K  C9   C13  aromatic  1.407  0.020  1.407
 26K  C10  C11  aromatic  1.413  0.020  1.413
 26K  N5   N4   aromatic  1.325  0.020  1.325
 26K  C11  N4   aromatic  1.321  0.020  1.321
 26K  C4   H2   single    0.970  0.020  1.090
 26K  C4   H3   single    0.970  0.020  1.090
 26K  C6   H4   single    0.930  0.020  1.080
 26K  C7   H5   single    0.930  0.020  1.080
 26K  C13  H6   single    0.930  0.020  1.080
 26K  C2   H7   single    0.970  0.020  1.090
 26K  C2   H8   single    0.970  0.020  1.090
 26K  C2   H9   single    0.970  0.020  1.090
 26K  C1   H10  single    0.970  0.020  1.090
 26K  C1   H11  single    0.970  0.020  1.090
 26K  C1   H12  single    0.970  0.020  1.090
 26K  C3   H13  single    0.970  0.020  1.090
 26K  C3   H14  single    0.970  0.020  1.090
 26K  N2   H15  single    0.860  0.020  1.020
 26K  C12  H16  single    0.930  0.020  1.080
 26K  N5   H17  single    0.860  0.020  1.020
 26K  C11  H18  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
 26K  C3   N1   C1   111.28  3.000
 26K  C3   N1   C2   112.64  3.000
 26K  C1   N1   C2   110.46  3.000
 26K  N6   N3   C8   113.18  3.000
 26K  N6   N3   C7   125.95  3.000
 26K  C8   N3   C7   120.87  3.000
 26K  H3   C4   H2   106.81  3.000
 26K  H3   C4   N2   109.55  3.000
 26K  H2   C4   N2   109.94  3.000
 26K  H3   C4   C3   109.35  3.000
 26K  H2   C4   C3   111.52  3.000
 26K  N2   C4   C3   109.61  3.000
 26K  N7   C5   N2   118.89  3.000
 26K  N7   C5   C6   122.12  3.000
 26K  N2   C5   C6   118.98  3.000
 26K  H4   C6   C7   120.23  3.000
 26K  H4   C6   C5   121.16  3.000
 26K  C7   C6   C5   118.61  3.000
 26K  H5   C7   C6   124.37  3.000
 26K  H5   C7   N3   117.15  3.000
 26K  C6   C7   N3   118.48  3.000
 26K  C9   C8   N7   132.16  3.000
 26K  C9   C8   N3   105.64  3.000
 26K  N7   C8   N3   122.20  3.000
 26K  C11  C10  C12  103.53  3.000
 26K  C11  C10  C9   128.44  3.000
 26K  C12  C10  C9   128.04  3.000
 26K  H6   C13  N6   119.32  3.000
 26K  H6   C13  C9   127.09  3.000
 26K  N6   C13  C9   113.59  3.000
 26K  H9   C2   H8   107.23  3.000
 26K  H9   C2   H7   107.75  3.000
 26K  H8   C2   H7   107.79  3.000
 26K  H9   C2   N1   111.30  3.000
 26K  H8   C2   N1   109.66  3.000
 26K  H7   C2   N1   112.89  3.000
 26K  H12  C1   H11  107.83  3.000
 26K  H12  C1   H10  107.56  3.000
 26K  H11  C1   H10  107.83  3.000
 26K  H12  C1   N1   109.84  3.000
 26K  H11  C1   N1   110.21  3.000
 26K  H10  C1   N1   113.39  3.000
 26K  H14  C3   H13  106.52  3.000
 26K  H14  C3   C4   109.97  3.000
 26K  H13  C3   C4   108.02  3.000
 26K  H14  C3   N1   111.84  3.000
 26K  H13  C3   N1   108.25  3.000
 26K  C4   C3   N1   111.99  3.000
 26K  H15  N2   C5   117.71  3.000
 26K  H15  N2   C4   118.16  3.000
 26K  C5   N2   C4   122.88  3.000
 26K  C8   N7   C5   117.72  3.000
 26K  C13  C9   C10  129.02  3.000
 26K  C13  C9   C8   103.69  3.000
 26K  C10  C9   C8   127.28  3.000
 26K  H16  C12  N5   121.71  3.000
 26K  H16  C12  C10  131.71  3.000
 26K  N5   C12  C10  106.59  3.000
 26K  H17  N5   N4   119.94  3.000
 26K  H17  N5   C12  126.82  3.000
 26K  N4   N5   C12  113.24  3.000
 26K  C11  N4   N5   104.96  3.000
 26K  H18  C11  N4   120.72  3.000
 26K  H18  C11  C10  127.59  3.000
 26K  N4   C11  C10  111.69  3.000
 26K  C13  N6   N3   103.89  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
 26K  CONST_01  C5   C6   C7   N3      0.00   0.0  0
 26K  CONST_02  C5   N7   C8   N3      0.00   0.0  0
 26K  CONST_03  C10  C9   C8   N3    180.00   0.0  0
 26K  CONST_04  C13  C9   C8   N3      0.00   0.0  0
 26K  CONST_05  C9   C13  N6   N3      0.00   0.0  0
 26K  CONST_06  C9   C8   N7   C5    180.00   0.0  0
 26K  CONST_07  C8   N7   C5   C6      0.00   0.0  0
 26K  CONST_08  C8   N3   C7   C6      0.00   0.0  0
 26K  CONST_09  N6   N3   C7   C6    180.00   0.0  0
 26K  CONST_10  N7   C5   C6   C7      0.00   0.0  0
 26K  CONST_11  N7   C8   N3   C7      0.00   0.0  0
 26K  CONST_12  C9   C8   N3   C7    180.00   0.0  0
 26K  CONST_13  C13  N6   N3   C7    180.00   0.0  0
 26K  CONST_14  C13  N6   N3   C8      0.00   0.0  0
 26K  CONST_15  C12  C10  C9   C8    180.00   0.0  0
 26K  CONST_16  C11  C10  C9   C8      0.00   0.0  0
 26K  CONST_17  N6   C13  C9   C8      0.00   0.0  0
 26K  CONST_18  N4   N5   C12  C10     0.00   0.0  0
 26K  CONST_19  N7   C8   C9   C10     0.00   0.0  0
 26K  CONST_20  N6   C13  C9   C10   180.00   0.0  0
 26K  CONST_21  N5   N4   C11  C10     0.00   0.0  0
 26K  CONST_22  N7   C8   C9   C13   180.00   0.0  0
 26K  CONST_23  C12  C10  C9   C13     0.00   0.0  0
 26K  CONST_24  C11  C10  C9   C13   180.00   0.0  0
 26K  CONST_25  N6   N3   C8   N7    180.00   0.0  0
 26K  CONST_26  N6   N3   C8   C9      0.00   0.0  0
 26K  CONST_27  N5   C12  C10  C9    180.00   0.0  0
 26K  CONST_28  N4   C11  C10  C9    180.00   0.0  0
 26K  CONST_29  N4   C11  C10  C12     0.00   0.0  0
 26K  CONST_30  C11  N4   N5   C12     0.00   0.0  0
 26K  CONST_31  C11  C10  C12  N5      0.00   0.0  0
 26K  CONST_32  N2   C5   C6   C7    180.00   0.0  0
 26K  CONST_33  N2   C5   N7   C8    180.00   0.0  0
 26K  CONST_34  H4   C6   C7   N3    180.00   0.0  0
 26K  CONST_35  H6   C13  N6   N3    180.00   0.0  0
 26K  CONST_36  H5   C7   C6   C5    180.00   0.0  0
 26K  CONST_37  H17  N5   C12  C10   180.00   0.0  0
 26K  CONST_38  H16  C12  C10  C9      0.00   0.0  0
 26K  CONST_39  H18  C11  C10  C9      0.00   0.0  0
 26K  CONST_40  C6   C5   N2   C4    180.00   0.0  0
 26K  CONST_41  N7   C5   N2   C4      0.00   0.0  0
 26K  CONST_42  H15  N2   C5   C6      0.00   0.0  0
 26K  Var_01    C3   C4   N2   C5   -171.65  30.0  2
 26K  Var_02    N2   C4   C3   N1   -178.88  30.0  2
 26K  Var_03    C1   N1   C3   C4   -160.55  30.0  2
 26K  Var_04    H10  C1   N1   C2     62.69  30.0  3
 26K  Var_05    H7   C2   N1   C1    -63.32  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
 26K  plan-1  C10  0.020
 26K  plan-1  C9   0.020
 26K  plan-1  C12  0.020
 26K  plan-1  N5   0.020
 26K  plan-1  N4   0.020
 26K  plan-1  C11  0.020
 26K  plan-1  H16  0.020
 26K  plan-1  H17  0.020
 26K  plan-1  H18  0.020
 26K  plan-2  N3   0.020
 26K  plan-2  C5   0.020
 26K  plan-2  C6   0.020
 26K  plan-2  C7   0.020
 26K  plan-2  C8   0.020
 26K  plan-2  C10  0.020
 26K  plan-2  C13  0.020
 26K  plan-2  N2   0.020
 26K  plan-2  N7   0.020
 26K  plan-2  C9   0.020
 26K  plan-2  N6   0.020
 26K  plan-2  H4   0.020
 26K  plan-2  H5   0.020
 26K  plan-2  H6   0.020
 26K  plan-3  C4   0.020
 26K  plan-3  C5   0.020
 26K  plan-3  N2   0.020
 26K  plan-3  H15  0.020

