# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 15:19:57 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 2-[4,6-dimethyl-3-(1H-pyrrol-1-yl)-1H-pyrazolo[3,4-b]pyridin-1-yl]-N-[3-(morpholin-4-yl)propyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)c2c(n1)n(CC(=O)NCCCN3CCOCC3)nc2n4cccc4
#
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
 O4D  O4D  2-[4,6-dimethyl-3-(1H-pyrrol-1-yl)-1H-pyrazolo[3,4-b]pyridin-1-yl]-N-[3-(morpholin-4-yl)propyl]acetamide  ligand  57  29  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_O4D
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
 O4D  C1   C  CR5   0   0.388  -3.9751   0.9104   0.2981
 O4D  C3   C  CR56  0   0.601  -2.4957  -0.7282   0.4154
 O4D  C12  C  CR16  0  -0.416  -3.8947  -2.7515  -0.5504
 O4D  C13  C  CR6   0   0.252  -2.5486  -2.8874  -0.1356
 O4D  C14  C  CR15  0  -0.062  -5.7851   2.3596   1.1074
 O4D  C15  C  CR15  0  -0.068  -5.6970   1.9797  -1.0944
 O4D  C16  C  CR15  0  -0.356  -6.7642   2.8039  -0.8657
 O4D  C17  C  CR15  0  -0.365  -6.8203   3.0451   0.5340
 O4D  C22  C  CH2   0  -0.253   5.1278   0.3757  -0.8239
 O4D  C23  C  CH2   0  -0.503   3.9990   0.3680   0.1975
 O4D  C24  C  CH2   0  -0.311   6.7508  -0.9320   0.4038
 O4D  C25  C  CH2   0  -0.303   7.4759   0.6583  -1.1978
 O4D  C26  C  CH2   0  -0.233   2.6517   0.5232  -0.4895
 O4D  C27  C  CH2   0  -0.188   8.8410   0.6693  -0.5379
 O4D  C28  C  CH2   0  -0.184   8.1322  -0.8917   1.0289
 O4D  C29  C  CH3   0  -0.737  -1.8814  -4.2230  -0.2390
 O4D  C10  C  C     0   0.540   0.3016   0.7015   0.1673
 O4D  C5   C  CR56  0  -0.186  -3.8116  -0.4709   0.0121
 O4D  C8   C  CR6   0   0.193  -4.5655  -1.5483  -0.4878
 O4D  N11  N  NT    0  -0.427   6.4469   0.3428  -0.2229
 O4D  N2   N  NR5   0  -0.371  -2.0018   0.4266   0.9143
 O4D  N20  N  NH1   0  -0.644   1.5793   0.4764   0.4845
 O4D  N4   N  N     0  -0.237  -2.8896   1.4204   0.8186
 O4D  N6   N  NR5   0  -0.513  -5.1057   1.7086   0.1114
 O4D  N7   N  N     0  -0.465  -1.8438  -1.8836   0.3533
 O4D  O18  O  O     0  -0.484  -0.0875   0.9551  -0.9600
 O4D  O19  O  O2    0  -0.485   9.1264  -0.5640   0.0841
 O4D  H32  H  HCR6  0   0.260  -4.4068  -3.6297  -0.9239
 O4D  H33  H  HCR5  0   0.278  -5.4784   2.2671   2.1364
 O4D  H34  H  HCR5  0   0.281  -5.2957   1.5821  -2.0121
 O4D  H35  H  HCR5  0   0.247  -7.4290   3.1961  -1.6189
 O4D  H36  H  HCR5  0   0.247  -7.5421   3.6505   1.0590
 O4D  H39  H  HCH3  0   0.256  -6.0813  -0.7601  -1.7794
 O4D  H40  H  HCH3  0   0.260  -6.4185  -2.3798  -1.1679
 O4D  H38  H  HCH3  0   0.257  -6.5942  -0.9699  -0.1170
 O4D  H41  H  HCH2  0   0.195   4.9859  -0.4567  -1.5353
 O4D  H42  H  HCH2  0   0.233   5.0573   1.2954  -1.4122
 O4D  H43  H  HCH2  0   0.241   4.0000  -0.5643   0.7690
 O4D  H44  H  HCH2  0   0.240   4.1498   1.1844   0.9086
 O4D  H45  H  HCH2  0   0.244   6.0276  -1.1462   1.1927
 O4D  H48  H  HCH2  0   0.241   7.2817   1.6461  -1.6233
 O4D  H47  H  HCH2  0   0.196   7.4801  -0.0611  -2.0359
 O4D  H50  H  HCH2  0   0.239   2.6139   1.4730  -1.0287
 O4D  H49  H  HCH2  0   0.236   2.5174  -0.2703  -1.2308
 O4D  H51  H  HCH2  0   0.236   9.6161   0.8450  -1.2857
 O4D  H52  H  HCH2  0   0.199   8.8863   1.4890   0.1936
 O4D  H54  H  HCH2  0   0.199   8.1343  -0.1674   1.8562
 O4D  H53  H  HCH2  0   0.236   8.3834  -1.8704   1.4408
 O4D  H55  H  HCH3  0   0.255  -1.9158  -4.5969  -1.2633
 O4D  H57  H  HCH3  0   0.253  -0.8418  -4.1626   0.0748
 O4D  H56  H  HCH3  0   0.256  -2.3895  -4.9595   0.3857
 O4D  H37  H  HNH1  0   0.406   1.8092   0.2118   1.4292
 O4D  C21  C  CH3   0  -0.743  -5.9910  -1.4127  -0.9104
 O4D  C9   C  CH2   0  -0.439  -0.6589   0.6550   1.3522
 O4D  H46  H  HCH2  0   0.197   6.6947  -1.7623  -0.3224
 O4D  H30  H  HCH2  0   0.292  -0.3690  -0.1140   2.0697
 O4D  H31  H  HCH2  0   0.320  -0.6346   1.6127   1.8734

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
 O4D  C16  C17  aromatic  1.421  0.020  1.421
 O4D  C16  C15  aromatic  1.368  0.020  1.368
 O4D  C17  C14  aromatic  1.368  0.020  1.368
 O4D  C15  N6   aromatic  1.370  0.020  1.370
 O4D  C14  N6   aromatic  1.370  0.020  1.370
 O4D  N6   C1   single    1.397  0.020  1.397
 O4D  C21  C8   single    1.493  0.020  1.493
 O4D  C1   C5   aromatic  1.420  0.020  1.420
 O4D  C1   N4   aromatic  1.307  0.020  1.307
 O4D  C8   C5   aromatic  1.407  0.020  1.407
 O4D  C8   C12  aromatic  1.379  0.020  1.379
 O4D  C5   C3   aromatic  1.400  0.020  1.400
 O4D  N4   N2   aromatic  1.336  0.020  1.336
 O4D  O18  C10  double    1.219  0.020  1.219
 O4D  C12  C13  aromatic  1.415  0.020  1.415
 O4D  C26  C23  single    1.520  0.020  1.520
 O4D  C26  N20  single    1.449  0.020  1.449
 O4D  C3   N2   aromatic  1.351  0.020  1.351
 O4D  C3   N7   aromatic  1.328  0.020  1.328
 O4D  N2   C9   single    1.431  0.020  1.431
 O4D  C10  N20  single    1.336  0.020  1.336
 O4D  C10  C9   single    1.526  0.020  1.526
 O4D  C23  C22  single    1.522  0.020  1.522
 O4D  C13  N7   aromatic  1.320  0.020  1.320
 O4D  C13  C29  single    1.497  0.020  1.497
 O4D  C22  N11  single    1.450  0.020  1.450
 O4D  C25  N11  single    1.452  0.020  1.452
 O4D  C25  C27  single    1.516  0.020  1.516
 O4D  N11  C24  single    1.453  0.020  1.453
 O4D  C27  O19  single    1.410  0.020  1.410
 O4D  C24  C28  single    1.517  0.020  1.517
 O4D  O19  C28  single    1.410  0.020  1.410
 O4D  C12  H32  single    0.930  0.020  1.080
 O4D  C14  H33  single    0.930  0.020  1.080
 O4D  C15  H34  single    0.930  0.020  1.080
 O4D  C16  H35  single    0.930  0.020  1.080
 O4D  C17  H36  single    0.930  0.020  1.080
 O4D  C21  H39  single    0.970  0.020  1.090
 O4D  C21  H40  single    0.970  0.020  1.090
 O4D  C21  H38  single    0.970  0.020  1.090
 O4D  C22  H41  single    0.970  0.020  1.090
 O4D  C22  H42  single    0.970  0.020  1.090
 O4D  C23  H43  single    0.970  0.020  1.090
 O4D  C23  H44  single    0.970  0.020  1.090
 O4D  C24  H46  single    0.970  0.020  1.090
 O4D  C24  H45  single    0.970  0.020  1.090
 O4D  C25  H48  single    0.970  0.020  1.090
 O4D  C25  H47  single    0.970  0.020  1.090
 O4D  C26  H50  single    0.970  0.020  1.090
 O4D  C26  H49  single    0.970  0.020  1.090
 O4D  C27  H51  single    0.970  0.020  1.090
 O4D  C27  H52  single    0.970  0.020  1.090
 O4D  C28  H54  single    0.970  0.020  1.090
 O4D  C28  H53  single    0.970  0.020  1.090
 O4D  C29  H55  single    0.970  0.020  1.090
 O4D  C29  H57  single    0.970  0.020  1.090
 O4D  C29  H56  single    0.970  0.020  1.090
 O4D  C9   H30  single    0.970  0.020  1.090
 O4D  C9   H31  single    0.970  0.020  1.090
 O4D  N20  H37  single    0.860  0.020  1.020

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
 O4D  N6   C1   N4   120.16  3.000
 O4D  N4   C1   C5   111.35  3.000
 O4D  N6   C1   C5   128.48  3.000
 O4D  N7   C3   N2   125.53  3.000
 O4D  N7   C3   C5   127.43  3.000
 O4D  N2   C3   C5   107.03  3.000
 O4D  H32  C12  C8   119.55  3.000
 O4D  H32  C12  C13  118.23  3.000
 O4D  C8   C12  C13  122.22  3.000
 O4D  N7   C13  C29  117.78  3.000
 O4D  C29  C13  C12  119.31  3.000
 O4D  N7   C13  C12  122.91  3.000
 O4D  H33  C14  N6   120.81  3.000
 O4D  H33  C14  C17  131.21  3.000
 O4D  N6   C14  C17  107.98  3.000
 O4D  H34  C15  N6   121.04  3.000
 O4D  H34  C15  C16  130.95  3.000
 O4D  N6   C15  C16  107.99  3.000
 O4D  H35  C16  C17  126.98  3.000
 O4D  H35  C16  C15  125.69  3.000
 O4D  C17  C16  C15  107.32  3.000
 O4D  H36  C17  C16  126.95  3.000
 O4D  H36  C17  C14  125.72  3.000
 O4D  C16  C17  C14  107.33  3.000
 O4D  H42  C22  H41  106.21  3.000
 O4D  H42  C22  N11  107.49  3.000
 O4D  H41  C22  N11  111.53  3.000
 O4D  H42  C22  C23  108.50  3.000
 O4D  H41  C22  C23  109.46  3.000
 O4D  N11  C22  C23  113.35  3.000
 O4D  H44  C23  H43  107.25  3.000
 O4D  H44  C23  C26  109.87  3.000
 O4D  H43  C23  C26  108.91  3.000
 O4D  H44  C23  C22  109.29  3.000
 O4D  H43  C23  C22  110.75  3.000
 O4D  C26  C23  C22  110.70  3.000
 O4D  H45  C24  H46  107.10  3.000
 O4D  H45  C24  N11  110.21  3.000
 O4D  H46  C24  N11  111.44  3.000
 O4D  H45  C24  C28  108.10  3.000
 O4D  H46  C24  C28  109.70  3.000
 O4D  N11  C24  C28  110.18  3.000
 O4D  H47  C25  H48  107.10  3.000
 O4D  H47  C25  N11  111.75  3.000
 O4D  H48  C25  N11  109.37  3.000
 O4D  H47  C25  C27  109.36  3.000
 O4D  H48  C25  C27  108.84  3.000
 O4D  N11  C25  C27  110.33  3.000
 O4D  H49  C26  H50  106.96  3.000
 O4D  H49  C26  N20  109.94  3.000
 O4D  H50  C26  N20  109.51  3.000
 O4D  H49  C26  C23  109.93  3.000
 O4D  H50  C26  C23  110.02  3.000
 O4D  N20  C26  C23  110.41  3.000
 O4D  H52  C27  H51  107.86  3.000
 O4D  H52  C27  O19  110.49  3.000
 O4D  H51  C27  O19  107.41  3.000
 O4D  H52  C27  C25  109.39  3.000
 O4D  H51  C27  C25  110.02  3.000
 O4D  O19  C27  C25  111.57  3.000
 O4D  H53  C28  H54  107.85  3.000
 O4D  H53  C28  O19  107.40  3.000
 O4D  H54  C28  O19  110.47  3.000
 O4D  H53  C28  C24  109.97  3.000
 O4D  H54  C28  C24  109.22  3.000
 O4D  O19  C28  C24  111.84  3.000
 O4D  H56  C29  H57  108.51  3.000
 O4D  H56  C29  H55  106.95  3.000
 O4D  H57  C29  H55  108.67  3.000
 O4D  H56  C29  C13  110.80  3.000
 O4D  H57  C29  C13  110.89  3.000
 O4D  H55  C29  C13  110.90  3.000
 O4D  O18  C10  N20  124.06  3.000
 O4D  N20  C10  C9   114.36  3.000
 O4D  O18  C10  C9   121.56  3.000
 O4D  C8   C5   C3   117.73  3.000
 O4D  C3   C5   C1   103.23  3.000
 O4D  C8   C5   C1   139.01  3.000
 O4D  C5   C8   C21  122.87  3.000
 O4D  C5   C8   C12  115.07  3.000
 O4D  C21  C8   C12  122.06  3.000
 O4D  C25  N11  C24  109.39  3.000
 O4D  C24  N11  C22  112.89  3.000
 O4D  C25  N11  C22  111.19  3.000
 O4D  N4   N2   C9   121.79  3.000
 O4D  C9   N2   C3   126.33  3.000
 O4D  N4   N2   C3   111.48  3.000
 O4D  H37  N20  C10  119.03  3.000
 O4D  H37  N20  C26  118.01  3.000
 O4D  C10  N20  C26  122.87  3.000
 O4D  N2   N4   C1   106.86  3.000
 O4D  C15  N6   C14  109.37  3.000
 O4D  C14  N6   C1   125.15  3.000
 O4D  C15  N6   C1   125.46  3.000
 O4D  C13  N7   C3   114.62  3.000
 O4D  C28  O19  C27  110.86  3.000
 O4D  H38  C21  H40  108.40  3.000
 O4D  H38  C21  H39  106.92  3.000
 O4D  H40  C21  H39  108.10  3.000
 O4D  H38  C21  C8   111.04  3.000
 O4D  H40  C21  C8   111.18  3.000
 O4D  H39  C21  C8   111.04  3.000
 O4D  H31  C9   H30  107.39  3.000
 O4D  H31  C9   N2   107.90  3.000
 O4D  H30  C9   N2   109.76  3.000
 O4D  H31  C9   C10  109.29  3.000
 O4D  H30  C9   C10  111.40  3.000
 O4D  N2   C9   C10  110.97  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
 O4D  CONST_01  C16  C15  N6   C1    180.00   0.0  0
 O4D  CONST_02  C17  C14  N6   C1    180.00   0.0  0
 O4D  CONST_03  C12  C8   C5   C1    180.00   0.0  0
 O4D  CONST_04  N2   C3   C5   C1      0.00   0.0  0
 O4D  CONST_05  N7   C3   C5   C1    180.00   0.0  0
 O4D  CONST_06  C3   N2   N4   C1      0.00   0.0  0
 O4D  CONST_07  N6   C1   C5   C3    180.00   0.0  0
 O4D  CONST_08  N4   C1   C5   C3      0.00   0.0  0
 O4D  CONST_09  C12  C8   C5   C3      0.00   0.0  0
 O4D  CONST_10  C12  C13  N7   C3      0.00   0.0  0
 O4D  CONST_11  C5   C8   C12  C13     0.00   0.0  0
 O4D  CONST_12  C5   C3   N7   C13     0.00   0.0  0
 O4D  CONST_13  N2   C3   N7   C13   180.00   0.0  0
 O4D  CONST_14  C15  C16  C17  C14     0.00   0.0  0
 O4D  CONST_15  C16  C15  N6   C14     0.00   0.0  0
 O4D  CONST_18  C17  C14  N6   C15     0.00   0.0  0
 O4D  CONST_21  N6   C14  C17  C16     0.00   0.0  0
 O4D  CONST_22  N6   C15  C16  C17     0.00   0.0  0
 O4D  CONST_23  N2   N4   C1   C5      0.00   0.0  0
 O4D  CONST_24  N4   N2   C3   C5      0.00   0.0  0
 O4D  CONST_25  N6   C1   C5   C8      0.00   0.0  0
 O4D  CONST_26  N4   C1   C5   C8    180.00   0.0  0
 O4D  CONST_27  N2   C3   C5   C8    180.00   0.0  0
 O4D  CONST_28  N7   C3   C5   C8      0.00   0.0  0
 O4D  CONST_29  N7   C13  C12  C8      0.00   0.0  0
 O4D  CONST_30  N6   C1   N4   N2    180.00   0.0  0
 O4D  CONST_31  N7   C3   N2   N4    180.00   0.0  0
 O4D  CONST_32  C21  C8   C5   C1      0.00   0.0  0
 O4D  CONST_33  C9   N2   N4   C1    180.00   0.0  0
 O4D  CONST_34  C21  C8   C5   C3    180.00   0.0  0
 O4D  CONST_35  C29  C13  N7   C3    180.00   0.0  0
 O4D  CONST_36  C21  C8   C12  C13   180.00   0.0  0
 O4D  CONST_37  C8   C12  C13  C29   180.00   0.0  0
 O4D  CONST_38  C9   N2   C3   C5    180.00   0.0  0
 O4D  CONST_39  N7   C3   N2   C9      0.00   0.0  0
 O4D  CONST_40  H34  C15  N6   C1      0.00   0.0  0
 O4D  CONST_41  H33  C14  N6   C1      0.00   0.0  0
 O4D  CONST_42  H35  C16  C17  C14   180.00   0.0  0
 O4D  CONST_43  H36  C17  C16  C15   180.00   0.0  0
 O4D  CONST_44  H32  C12  C8   C5    180.00   0.0  0
 O4D  CONST_45  O18  C10  N20  C26     0.00   0.0  0
 O4D  CONST_46  C9   C10  N20  C26   180.00   0.0  0
 O4D  CONST_47  H37  N20  C10  C9      0.00   0.0  0
 O4D  Var_01    C27  C25  N11  C24   -56.75  30.0  1
 O4D  Var_02    C28  C24  N11  C25    56.48  30.0  1
 O4D  Var_03    O19  C27  C25  N11    57.36  30.0  1
 O4D  Var_04    O19  C28  C24  N11   -57.04  30.0  1
 O4D  Var_05    H54  C28  O19  C27   -65.12  30.0  1
 O4D  Var_06    H51  C27  O19  C28  -177.46  30.0  1
 O4D  Var_07    C10  C9   N2   C3     71.18  30.0  2
 O4D  Var_08    C25  N11  C22  C23  -166.88  30.0  3
 O4D  Var_09    H39  C21  C8   C12  -115.11  30.0  2
 O4D  Var_10    H55  C29  C13  C12    56.72  30.0  2
 O4D  Var_11    N11  C22  C23  C26   175.16  30.0  3
 O4D  Var_12    O18  C10  C9   N2     22.21  30.0  1
 O4D  Var_13    N20  C26  C23  C22   178.36  30.0  1
 O4D  Var_14    C10  N20  C26  C23   174.15  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
 O4D  plan-1  C1   0.020
 O4D  plan-1  C14  0.020
 O4D  plan-1  C15  0.020
 O4D  plan-1  C16  0.020
 O4D  plan-1  C17  0.020
 O4D  plan-1  N6   0.020
 O4D  plan-1  H33  0.020
 O4D  plan-1  H34  0.020
 O4D  plan-1  H35  0.020
 O4D  plan-1  H36  0.020
 O4D  plan-2  C1   0.020
 O4D  plan-2  C3   0.020
 O4D  plan-2  C12  0.020
 O4D  plan-2  C13  0.020
 O4D  plan-2  C29  0.020
 O4D  plan-2  C5   0.020
 O4D  plan-2  C8   0.020
 O4D  plan-2  N2   0.020
 O4D  plan-2  N4   0.020
 O4D  plan-2  N6   0.020
 O4D  plan-2  N7   0.020
 O4D  plan-2  H32  0.020
 O4D  plan-2  C21  0.020
 O4D  plan-2  C9   0.020
 O4D  plan-3  C26  0.020
 O4D  plan-3  C10  0.020
 O4D  plan-3  N20  0.020
 O4D  plan-3  O18  0.020
 O4D  plan-3  H37  0.020
 O4D  plan-3  C9   0.020

