# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 13:01:55 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: ~{N}-[3-(1,3-benzodioxol-5-yl)pyrazolo[1,5-a]pyrimidin-5-yl]-~{N}',~{N}'-dimethyl-propane-1,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCCNc1ccn2ncc(c3ccc4OCOc4c3)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
 H6W  H6W  ~{N}-[3-(1,3-benzodioxol-5-yl)pyrazolo[1,5-a]pyrimidin-5-yl]-~{N}',~{N}'-dimethyl-propane-1,3-diamine  ligand  46  25  .  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_H6W
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
 H6W  C4   C  CH2   0  -0.496  -4.4490  -0.0257  -0.0225
 H6W  C14  C  CR56  0   0.274   3.2415  -2.6024   0.0406
 H6W  C5   C  CH2   0  -0.240  -2.9752   0.2770  -0.2417
 H6W  C6   C  CR6   0   0.553  -1.5067   2.2386  -0.1620
 H6W  C11  C  CR6   0   0.107   2.4521   0.0550  -0.0131
 H6W  C7   C  CR16  0  -0.459  -1.3728   3.6709  -0.1745
 H6W  C8   C  CR16  0   0.078  -0.1335   4.2010  -0.1417
 H6W  C9   C  CR15  0  -0.080   2.8754   2.5935  -0.0258
 H6W  C10  C  CR5   0  -0.223   2.0436   1.4552  -0.0405
 H6W  C12  C  CR16  0  -0.389   1.5174  -0.9823  -0.0235
 H6W  C13  C  CR16  0  -0.318   1.8984  -2.3285   0.0030
 H6W  N1   N  NT    0  -0.407  -6.1056  -1.8823  -0.0703
 H6W  N2   N  NH1   0  -0.679  -2.7343   1.7009  -0.1742
 H6W  C3   C  CH2   0  -0.251  -4.6990  -1.5273  -0.0601
 H6W  N3   N  N     0  -0.387   0.9287   3.3613  -0.0953
 H6W  C1   C  CH3   0  -0.519  -6.2737  -3.2952  -0.3357
 H6W  C2   C  CH3   0  -0.527  -6.7835  -1.5099   1.1533
 H6W  N4   N  N     0  -0.309   2.2171   3.7340  -0.0587
 H6W  C15  C  CR56  0   0.328   4.1803  -1.5837   0.0505
 H6W  C16  C  CR16  0  -0.446   3.8279  -0.2606   0.0244
 H6W  O1   O  O     0  -0.490   5.4242  -2.1217   0.1128
 H6W  C17  C  CH2   0   0.068   5.2568  -3.5211  -0.0750
 H6W  O2   O  O     0  -0.488   3.8755  -3.8019   0.1002
 H6W  C18  C  CR56  0   0.587   0.7566   1.9954  -0.0876
 H6W  N5   N  N     0  -0.524  -0.4606   1.4386  -0.1263
 H6W  H1   H  HCH2  0   0.241  -4.7579   0.4004   0.9350
 H6W  H2   H  HCH2  0   0.234  -5.0489   0.4541  -0.8019
 H6W  H3   H  HCH2  0   0.238  -2.3716  -0.2209   0.5206
 H6W  H4   H  HCH2  0   0.229  -2.6490  -0.1232  -1.2084
 H6W  H5   H  HCR6  0   0.295  -2.2396   4.3145  -0.2070
 H6W  H6   H  HCR6  0   0.321   0.0770   5.2606  -0.1477
 H6W  H7   H  HCR5  0   0.268   3.9547   2.6135   0.0110
 H6W  H8   H  HCR6  0   0.270   0.4631  -0.7466  -0.0562
 H6W  H9   H  HCR6  0   0.269   1.1557  -3.1148  -0.0009
 H6W  H11  H  HNH1  0   0.405  -3.5148   2.3192  -0.3249
 H6W  H12  H  HCH2  0   0.227  -4.2509  -1.9276  -0.9751
 H6W  H13  H  HCH2  0   0.189  -4.1652  -2.0050   0.7815
 H6W  H14  H  HCH3  0   0.190  -5.8319  -3.9401   0.4407
 H6W  H15  H  HCH3  0   0.232  -7.3347  -3.5395  -0.4039
 H6W  H16  H  HCH3  0   0.231  -5.8092  -3.5564  -1.2877
 H6W  H17  H  HCH3  0   0.237  -6.7605  -0.4307   1.3030
 H6W  H18  H  HCH3  0   0.234  -7.8319  -1.8058   1.0979
 H6W  H19  H  HCH3  0   0.190  -6.3480  -1.9824   2.0487
 H6W  H20  H  HCR6  0   0.264   4.5872   0.5102   0.0342
 H6W  H21  H  HCH2  0   0.231   5.5687  -3.7990  -1.0877
 H6W  H10  H  HCH2  0   0.244   5.8416  -4.0647   0.6666

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
 H6W  N4   C9   aromatic  1.317  0.020  1.317
 H6W  N4   N3   aromatic  1.342  0.020  1.342
 H6W  C9   C10  aromatic  1.410  0.020  1.410
 H6W  N3   C8   aromatic  1.355  0.020  1.355
 H6W  N3   C18  aromatic  1.377  0.020  1.377
 H6W  C8   C7   aromatic  1.348  0.020  1.348
 H6W  C10  C18  aromatic  1.397  0.020  1.397
 H6W  C10  C11  single    1.459  0.020  1.459
 H6W  C12  C11  aromatic  1.396  0.020  1.396
 H6W  C12  C13  aromatic  1.399  0.020  1.399
 H6W  C18  N5   aromatic  1.339  0.020  1.339
 H6W  C7   C6   aromatic  1.439  0.020  1.439
 H6W  C2   N1   single    1.448  0.020  1.448
 H6W  C11  C16  aromatic  1.412  0.020  1.412
 H6W  C13  C14  aromatic  1.371  0.020  1.371
 H6W  N5   C6   aromatic  1.317  0.020  1.317
 H6W  C6   N2   single    1.340  0.020  1.340
 H6W  C16  C15  aromatic  1.369  0.020  1.369
 H6W  C14  C15  aromatic  1.385  0.020  1.385
 H6W  C14  O2   single    1.358  0.020  1.358
 H6W  N1   C3   single    1.451  0.020  1.451
 H6W  N1   C1   single    1.447  0.020  1.447
 H6W  C15  O1   single    1.357  0.020  1.357
 H6W  C4   C3   single    1.523  0.020  1.523
 H6W  C4   C5   single    1.520  0.020  1.520
 H6W  O2   C17  single    1.420  0.020  1.420
 H6W  N2   C5   single    1.446  0.020  1.446
 H6W  O1   C17  single    1.422  0.020  1.422
 H6W  C4   H1   single    0.970  0.020  1.090
 H6W  C4   H2   single    0.970  0.020  1.090
 H6W  C5   H3   single    0.970  0.020  1.090
 H6W  C5   H4   single    0.970  0.020  1.090
 H6W  C7   H5   single    0.930  0.020  1.080
 H6W  C8   H6   single    0.930  0.020  1.080
 H6W  C9   H7   single    0.930  0.020  1.080
 H6W  C12  H8   single    0.930  0.020  1.080
 H6W  C13  H9   single    0.930  0.020  1.080
 H6W  N2   H11  single    0.860  0.020  1.020
 H6W  C3   H12  single    0.970  0.020  1.090
 H6W  C3   H13  single    0.970  0.020  1.090
 H6W  C1   H14  single    0.970  0.020  1.090
 H6W  C1   H15  single    0.970  0.020  1.090
 H6W  C1   H16  single    0.970  0.020  1.090
 H6W  C2   H17  single    0.970  0.020  1.090
 H6W  C2   H18  single    0.970  0.020  1.090
 H6W  C2   H19  single    0.970  0.020  1.090
 H6W  C16  H20  single    0.930  0.020  1.080
 H6W  C17  H21  single    0.970  0.020  1.090
 H6W  C17  H10  single    0.970  0.020  1.090

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
 H6W  H2   C4   H1   107.35  3.000
 H6W  H2   C4   C3   108.95  3.000
 H6W  H1   C4   C3   111.09  3.000
 H6W  H2   C4   C5   109.96  3.000
 H6W  H1   C4   C5   108.82  3.000
 H6W  C3   C4   C5   110.60  3.000
 H6W  O2   C14  C15  109.44  3.000
 H6W  O2   C14  C13  129.41  3.000
 H6W  C15  C14  C13  121.14  3.000
 H6W  H4   C5   H3   106.54  3.000
 H6W  H4   C5   N2   110.56  3.000
 H6W  H3   C5   N2   108.92  3.000
 H6W  H4   C5   C4   110.06  3.000
 H6W  H3   C5   C4   110.14  3.000
 H6W  N2   C5   C4   110.54  3.000
 H6W  N5   C6   N2   118.94  3.000
 H6W  N2   C6   C7   118.98  3.000
 H6W  N5   C6   C7   122.07  3.000
 H6W  C16  C11  C12  119.11  3.000
 H6W  C16  C11  C10  119.20  3.000
 H6W  C12  C11  C10  121.70  3.000
 H6W  H5   C7   C8   120.27  3.000
 H6W  H5   C7   C6   121.26  3.000
 H6W  C8   C7   C6   118.47  3.000
 H6W  H6   C8   N3   117.09  3.000
 H6W  H6   C8   C7   124.37  3.000
 H6W  N3   C8   C7   118.54  3.000
 H6W  H7   C9   N4   118.96  3.000
 H6W  H7   C9   C10  127.21  3.000
 H6W  N4   C9   C10  113.83  3.000
 H6W  C18  C10  C9   103.39  3.000
 H6W  C18  C10  C11  129.05  3.000
 H6W  C9   C10  C11  127.56  3.000
 H6W  H8   C12  C13  118.42  3.000
 H6W  H8   C12  C11  119.42  3.000
 H6W  C13  C12  C11  122.16  3.000
 H6W  H9   C13  C12  120.82  3.000
 H6W  H9   C13  C14  121.84  3.000
 H6W  C12  C13  C14  117.35  3.000
 H6W  C2   N1   C1   110.59  3.000
 H6W  C1   N1   C3   110.65  3.000
 H6W  C2   N1   C3   112.65  3.000
 H6W  H11  N2   C6   117.71  3.000
 H6W  H11  N2   C5   117.94  3.000
 H6W  C6   N2   C5   123.24  3.000
 H6W  H13  C3   H12  106.31  3.000
 H6W  H13  C3   N1   111.59  3.000
 H6W  H12  C3   N1   107.55  3.000
 H6W  H13  C3   C4   109.16  3.000
 H6W  H12  C3   C4   108.30  3.000
 H6W  N1   C3   C4   113.62  3.000
 H6W  C18  N3   N4   113.29  3.000
 H6W  C18  N3   C8   121.14  3.000
 H6W  N4   N3   C8   125.57  3.000
 H6W  H16  C1   H15  107.81  3.000
 H6W  H16  C1   H14  107.70  3.000
 H6W  H15  C1   H14  107.63  3.000
 H6W  H16  C1   N1   110.14  3.000
 H6W  H15  C1   N1   110.06  3.000
 H6W  H14  C1   N1   113.31  3.000
 H6W  H19  C2   H18  107.74  3.000
 H6W  H19  C2   H17  107.74  3.000
 H6W  H18  C2   H17  107.21  3.000
 H6W  H19  C2   N1   113.04  3.000
 H6W  H18  C2   N1   109.72  3.000
 H6W  H17  C2   N1   111.16  3.000
 H6W  N3   N4   C9   103.89  3.000
 H6W  O1   C15  C16  128.31  3.000
 H6W  O1   C15  C14  109.27  3.000
 H6W  C16  C15  C14  122.40  3.000
 H6W  H20  C16  C15  120.50  3.000
 H6W  H20  C16  C11  121.65  3.000
 H6W  C15  C16  C11  117.85  3.000
 H6W  C17  O1   C15  106.04  3.000
 H6W  H10  C17  H21  110.47  3.000
 H6W  H10  C17  O2   109.84  3.000
 H6W  H21  C17  O2   109.92  3.000
 H6W  H10  C17  O1   109.75  3.000
 H6W  H21  C17  O1   109.77  3.000
 H6W  O2   C17  O1   107.02  3.000
 H6W  C17  O2   C14  105.90  3.000
 H6W  N5   C18  N3   121.74  3.000
 H6W  N5   C18  C10  132.67  3.000
 H6W  N3   C18  C10  105.59  3.000
 H6W  C18  N5   C6   118.04  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
 H6W  CONST_01  C11  C12  C13  C14     0.00   0.0  0
 H6W  CONST_02  C11  C16  C15  C14     0.00   0.0  0
 H6W  CONST_03  N3   C8   C7   C6      0.00   0.0  0
 H6W  CONST_04  N3   C18  N5   C6      0.00   0.0  0
 H6W  CONST_05  C10  C18  N5   C6    180.00   0.0  0
 H6W  CONST_06  N4   C9   C10  C11   180.00   0.0  0
 H6W  CONST_07  N3   C18  C10  C11   180.00   0.0  0
 H6W  CONST_08  N5   C18  C10  C11     0.00   0.0  0
 H6W  CONST_09  N4   N3   C8   C7    180.00   0.0  0
 H6W  CONST_10  C18  N3   C8   C7      0.00   0.0  0
 H6W  CONST_11  C18  N5   C6   C7      0.00   0.0  0
 H6W  CONST_12  C9   N4   N3   C8    180.00   0.0  0
 H6W  CONST_13  C10  C18  N3   C8    180.00   0.0  0
 H6W  CONST_14  N5   C18  N3   C8      0.00   0.0  0
 H6W  CONST_15  N5   C6   C7   C8      0.00   0.0  0
 H6W  CONST_16  C18  N3   N4   C9      0.00   0.0  0
 H6W  CONST_17  N3   C18  C10  C9      0.00   0.0  0
 H6W  CONST_18  N5   C18  C10  C9    180.00   0.0  0
 H6W  CONST_19  C12  C11  C10  C9    180.00   0.0  0
 H6W  CONST_20  C16  C11  C10  C9      0.00   0.0  0
 H6W  CONST_21  N3   N4   C9   C10     0.00   0.0  0
 H6W  CONST_22  N4   N3   C18  C10     0.00   0.0  0
 H6W  CONST_23  C13  C12  C11  C10   180.00   0.0  0
 H6W  CONST_24  C15  C16  C11  C10   180.00   0.0  0
 H6W  CONST_25  C18  C10  C11  C12     0.00   0.0  0
 H6W  CONST_26  C15  C16  C11  C12     0.00   0.0  0
 H6W  CONST_27  C15  C14  C13  C12     0.00   0.0  0
 H6W  CONST_28  C16  C11  C12  C13     0.00   0.0  0
 H6W  CONST_29  C16  C15  C14  C13     0.00   0.0  0
 H6W  CONST_30  C18  C10  C9   N4      0.00   0.0  0
 H6W  CONST_31  N5   C18  N3   N4    180.00   0.0  0
 H6W  CONST_32  C18  C10  C11  C16   180.00   0.0  0
 H6W  CONST_33  N2   C6   C7   C8    180.00   0.0  0
 H6W  CONST_34  C18  N5   C6   N2    180.00   0.0  0
 H6W  CONST_35  H8   C12  C13  C14   180.00   0.0  0
 H6W  CONST_36  H20  C16  C15  C14   180.00   0.0  0
 H6W  CONST_37  H6   C8   C7   C6    180.00   0.0  0
 H6W  CONST_38  H7   C9   C10  C11     0.00   0.0  0
 H6W  CONST_39  H9   C13  C12  C11   180.00   0.0  0
 H6W  CONST_40  H5   C7   C8   N3    180.00   0.0  0
 H6W  CONST_41  C7   C6   N2   C5    180.00   0.0  0
 H6W  CONST_42  N5   C6   N2   C5      0.00   0.0  0
 H6W  CONST_43  H11  N2   C6   C7      0.00   0.0  0
 H6W  Var_01    O1   C17  O2   C14    14.87  30.0  1
 H6W  Var_02    O2   C17  O1   C15   -14.80  30.0  1
 H6W  Var_03    C6   N2   C5   C4    171.26  30.0  1
 H6W  Var_04    C2   N1   C3   C4    -65.40  30.0  2
 H6W  Var_05    N1   C3   C4   C5   -170.78  30.0  3
 H6W  Var_06    C3   C4   C5   N2   -178.64  30.0  1
 H6W  Var_07    H17  C2   N1   C3     62.10  30.0  3
 H6W  Var_08    H14  C1   N1   C3     63.01  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
 H6W  plan-1  C6   0.020
 H6W  plan-1  C11  0.020
 H6W  plan-1  C7   0.020
 H6W  plan-1  C8   0.020
 H6W  plan-1  C9   0.020
 H6W  plan-1  C10  0.020
 H6W  plan-1  N2   0.020
 H6W  plan-1  N3   0.020
 H6W  plan-1  N4   0.020
 H6W  plan-1  C18  0.020
 H6W  plan-1  N5   0.020
 H6W  plan-1  H5   0.020
 H6W  plan-1  H6   0.020
 H6W  plan-1  H7   0.020
 H6W  plan-2  C14  0.020
 H6W  plan-2  C11  0.020
 H6W  plan-2  C10  0.020
 H6W  plan-2  C12  0.020
 H6W  plan-2  C13  0.020
 H6W  plan-2  C15  0.020
 H6W  plan-2  C16  0.020
 H6W  plan-2  O1   0.020
 H6W  plan-2  O2   0.020
 H6W  plan-2  H8   0.020
 H6W  plan-2  H9   0.020
 H6W  plan-2  H20  0.020
 H6W  plan-3  C5   0.020
 H6W  plan-3  C6   0.020
 H6W  plan-3  N2   0.020
 H6W  plan-3  H11  0.020

