# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 06:43:08 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: ~{N}-(4-morpholin-4-ylcyclohexyl)-5-(oxan-4-yl)-7~{H}-pyrrolo[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CC(CCO1)c2c[nH]c3ncnc(N[C@@H]4CC[C@H](CC4)N5CCOCC5)c23
#
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
 6R1  6R1  ~{N}-(4-morpholin-4-ylcyclohexyl)-5-(oxan-4-yl)-7~{H}-pyrrolo[2,3-d]pyrimidin-4-amine  ligand  59  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6R1
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
 6R1  C1   C  CR15  0  -0.081   5.1303  -0.8248   0.5469
 6R1  C3   C  CR56  0   0.475   3.7424  -2.4824   0.0408
 6R1  N6   N  N     0  -0.490   1.1477  -2.6534  -0.5099
 6R1  C7   C  CR6   0   0.466   1.6263  -1.4421  -0.2165
 6R1  C8   C  CR56  0  -0.117   3.0047  -1.2910   0.0575
 6R1  C9   C  CR5   0   0.057   3.9138  -0.2257   0.3780
 6R1  C10  C  CH1   0  -0.403   3.6257   1.2432   0.4331
 6R1  C11  C  CH2   0  -0.444   3.4062   1.8271  -0.9688
 6R1  C12  C  CH2   0  -0.177   3.1686   3.3267  -0.8979
 6R1  C14  C  CH2   0  -0.181   4.3986   3.5330   1.0828
 6R1  C15  C  CH2   0  -0.442   4.7216   2.0482   1.1293
 6R1  C19  C  CH2   0  -0.470  -2.8889  -1.0846   0.6112
 6R1  C20  C  CH1   0  -0.002  -3.5003   0.2336   0.1250
 6R1  C21  C  CH2   0  -0.470  -2.7310   0.7161  -1.1100
 6R1  C22  C  CH2   0  -0.451  -1.2284   0.8108  -0.8692
 6R1  N23  N  NT    0  -0.440  -4.9267   0.0731  -0.1678
 6R1  C24  C  CH2   0  -0.312  -5.5437   1.2837  -0.6907
 6R1  C27  C  CH2   0  -0.185  -7.1513  -0.5640   0.6342
 6R1  N2   N  NR15  0  -0.668   5.0224  -2.1786   0.3454
 6R1  N4   N  N     0  -0.455   3.2676  -3.7019  -0.2349
 6R1  C5   C  CR16  0   0.033   1.9805  -3.6924  -0.5078
 6R1  O13  O  O2    0  -0.483   4.2189   3.9976  -0.2375
 6R1  N16  N  NH1   0  -0.685   0.7729  -0.4010  -0.2125
 6R1  C17  C  CH1   0  -0.045  -0.6592  -0.5203  -0.4037
 6R1  C18  C  CH2   0  -0.433  -1.3888  -0.9735   0.8559
 6R1  C25  C  CH2   0  -0.185  -7.0086   1.0494  -1.0078
 6R1  O26  O  O2    0  -0.483  -7.7333   0.6096   0.1172
 6R1  C28  C  CH2   0  -0.312  -5.6908  -0.3661   0.9911
 6R1  H1   H  HCR5  0   0.286   6.0841  -0.3894   0.7950
 6R1  H2   H  HCH1  0   0.231   2.7064   1.4004   1.0152
 6R1  H3   H  HCH2  0   0.232   4.2879   1.6207  -1.5830
 6R1  H4   H  HCH2  0   0.232   2.5568   1.3531  -1.4687
 6R1  H5   H  HCH2  0   0.238   3.1007   3.7508  -1.9014
 6R1  H6   H  HCH2  0   0.193   2.2100   3.5261  -0.3943
 6R1  H7   H  HCH2  0   0.196   3.4975   3.7306   1.6830
 6R1  H8   H  HCH2  0   0.237   5.2125   4.1164   1.5165
 6R1  H9   H  HCH2  0   0.244   4.8266   1.7359   2.1712
 6R1  H10  H  HCH2  0   0.228   5.6853   1.8716   0.6414
 6R1  H11  H  HCH2  0   0.245  -3.3605  -1.4165   1.5362
 6R1  H12  H  HCH2  0   0.219  -3.0851  -1.8584  -0.1399
 6R1  H13  H  HCH1  0   0.184  -3.3588   0.9871   0.9244
 6R1  H14  H  HCH2  0   0.221  -2.9288   0.0248  -1.9367
 6R1  H15  H  HCH2  0   0.247  -3.0787   1.6990  -1.4292
 6R1  H16  H  HCH2  0   0.246  -0.7288   1.1323  -1.7861
 6R1  H17  H  HCH2  0   0.222  -1.0275   1.5779  -0.1112
 6R1  H19  H  HCH2  0   0.194  -5.4484   2.1266   0.0167
 6R1  H20  H  HCH2  0   0.246  -5.0622   1.5857  -1.6201
 6R1  H21  H  HCH2  0   0.235  -7.7134  -0.8457   1.5262
 6R1  H22  H  HCH2  0   0.198  -7.2368  -1.3857  -0.0920
 6R1  H23  H  HNR5  0   0.409   5.7773  -2.8413   0.4139
 6R1  H24  H  HCR6  0   0.242   1.5325  -4.6497  -0.7553
 6R1  H25  H  HNH1  0   0.393   1.0997   0.4595   0.1953
 6R1  H26  H  HCH1  0   0.238  -0.8240  -1.2625  -1.1886
 6R1  H27  H  HCH2  0   0.216  -1.1962  -0.2521   1.6579
 6R1  H28  H  HCH2  0   0.243  -0.9970  -1.9364   1.1888
 6R1  H29  H  HCH2  0   0.235  -7.4641   1.9800  -1.3497
 6R1  H30  H  HCH2  0   0.198  -7.0866   0.3157  -1.8235
 6R1  H31  H  HCH2  0   0.246  -5.3187  -1.3237   1.3543
 6R1  H32  H  HCH2  0   0.194  -5.6103   0.3526   1.8262

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
 6R1  C25  C24  single    1.517  0.020  1.517
 6R1  C25  O26  single    1.409  0.020  1.409
 6R1  C24  N23  single    1.456  0.020  1.456
 6R1  O26  C27  single    1.408  0.020  1.408
 6R1  N23  C20  single    1.465  0.020  1.465
 6R1  N23  C28  single    1.456  0.020  1.456
 6R1  O13  C14  single    1.411  0.020  1.411
 6R1  O13  C12  single    1.410  0.020  1.410
 6R1  C14  C15  single    1.520  0.020  1.520
 6R1  C20  C21  single    1.533  0.020  1.533
 6R1  C20  C19  single    1.532  0.020  1.532
 6R1  C12  C11  single    1.520  0.020  1.520
 6R1  C27  C28  single    1.516  0.020  1.516
 6R1  C21  C22  single    1.525  0.020  1.525
 6R1  C22  C17  single    1.521  0.020  1.521
 6R1  C19  C18  single    1.524  0.020  1.524
 6R1  C15  C10  single    1.528  0.020  1.528
 6R1  C18  C17  single    1.525  0.020  1.525
 6R1  C11  C10  single    1.534  0.020  1.534
 6R1  C10  C9   single    1.498  0.020  1.498
 6R1  C17  N16  single    1.450  0.020  1.450
 6R1  N16  C7   single    1.346  0.020  1.346
 6R1  C9   C8   aromatic  1.437  0.020  1.437
 6R1  C9   C1   aromatic  1.366  0.020  1.366
 6R1  C7   C8   aromatic  1.413  0.020  1.413
 6R1  C7   N6   aromatic  1.335  0.020  1.335
 6R1  C8   C3   aromatic  1.401  0.020  1.401
 6R1  C1   N2   aromatic  1.373  0.020  1.373
 6R1  N6   C5   aromatic  1.332  0.020  1.332
 6R1  C3   N2   aromatic  1.350  0.020  1.350
 6R1  C3   N4   aromatic  1.337  0.020  1.337
 6R1  C5   N4   aromatic  1.316  0.020  1.316
 6R1  C1   H1   single    0.930  0.020  1.080
 6R1  C10  H2   single    0.970  0.020  1.090
 6R1  C11  H3   single    0.970  0.020  1.090
 6R1  C11  H4   single    0.970  0.020  1.090
 6R1  C12  H5   single    0.970  0.020  1.090
 6R1  C12  H6   single    0.970  0.020  1.090
 6R1  C14  H7   single    0.970  0.020  1.090
 6R1  C14  H8   single    0.970  0.020  1.090
 6R1  C15  H9   single    0.970  0.020  1.090
 6R1  C15  H10  single    0.970  0.020  1.090
 6R1  C19  H11  single    0.970  0.020  1.090
 6R1  C19  H12  single    0.970  0.020  1.090
 6R1  C20  H13  single    0.970  0.020  1.090
 6R1  C21  H14  single    0.970  0.020  1.090
 6R1  C21  H15  single    0.970  0.020  1.090
 6R1  C22  H16  single    0.970  0.020  1.090
 6R1  C22  H17  single    0.970  0.020  1.090
 6R1  C24  H19  single    0.970  0.020  1.090
 6R1  C24  H20  single    0.970  0.020  1.090
 6R1  C27  H21  single    0.970  0.020  1.090
 6R1  C27  H22  single    0.970  0.020  1.090
 6R1  N2   H23  single    0.860  0.020  1.020
 6R1  C5   H24  single    0.930  0.020  1.080
 6R1  N16  H25  single    0.860  0.020  1.020
 6R1  C17  H26  single    0.970  0.020  1.090
 6R1  C18  H27  single    0.970  0.020  1.090
 6R1  C18  H28  single    0.970  0.020  1.090
 6R1  C25  H29  single    0.970  0.020  1.090
 6R1  C25  H30  single    0.970  0.020  1.090
 6R1  C28  H31  single    0.970  0.020  1.090
 6R1  C28  H32  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
 6R1  H1   C1   N2   120.12  3.000
 6R1  H1   C1   C9   129.75  3.000
 6R1  N2   C1   C9   110.13  3.000
 6R1  N4   C3   N2   126.03  3.000
 6R1  N4   C3   C8   126.21  3.000
 6R1  N2   C3   C8   107.76  3.000
 6R1  C5   N6   C7   118.91  3.000
 6R1  N16  C7   C8   122.35  3.000
 6R1  C8   C7   N6   119.28  3.000
 6R1  N16  C7   N6   118.37  3.000
 6R1  C9   C8   C7   137.69  3.000
 6R1  C7   C8   C3   114.85  3.000
 6R1  C9   C8   C3   107.45  3.000
 6R1  C10  C9   C8   127.85  3.000
 6R1  C8   C9   C1   105.41  3.000
 6R1  C10  C9   C1   126.63  3.000
 6R1  H2   C10  C15  106.45  3.000
 6R1  H2   C10  C11  108.04  3.000
 6R1  C15  C10  C11  108.57  3.000
 6R1  H2   C10  C9   108.70  3.000
 6R1  C11  C10  C9   111.54  3.000
 6R1  C15  C10  C9   113.30  3.000
 6R1  H4   C11  H3   106.71  3.000
 6R1  H4   C11  C12  109.12  3.000
 6R1  H3   C11  C12  109.77  3.000
 6R1  H4   C11  C10  111.33  3.000
 6R1  H3   C11  C10  109.02  3.000
 6R1  C12  C11  C10  110.81  3.000
 6R1  H6   C12  H5   107.22  3.000
 6R1  H6   C12  O13  110.36  3.000
 6R1  H5   C12  O13  106.98  3.000
 6R1  H6   C12  C11  109.64  3.000
 6R1  H5   C12  C11  110.50  3.000
 6R1  O13  C12  C11  112.01  3.000
 6R1  H8   C14  H7   107.33  3.000
 6R1  H8   C14  O13  106.91  3.000
 6R1  H7   C14  O13  110.30  3.000
 6R1  H8   C14  C15  110.58  3.000
 6R1  H7   C14  C15  109.43  3.000
 6R1  O13  C14  C15  112.16  3.000
 6R1  H10  C15  H9   107.12  3.000
 6R1  H10  C15  C14  109.33  3.000
 6R1  H9   C15  C14  109.19  3.000
 6R1  H10  C15  C10  110.09  3.000
 6R1  H9   C15  C10  110.66  3.000
 6R1  C14  C15  C10  110.38  3.000
 6R1  H12  C19  H11  106.80  3.000
 6R1  H12  C19  C18  109.74  3.000
 6R1  H11  C19  C18  108.17  3.000
 6R1  H12  C19  C20  108.57  3.000
 6R1  H11  C19  C20  111.01  3.000
 6R1  C18  C19  C20  112.39  3.000
 6R1  H13  C20  N23  110.07  3.000
 6R1  H13  C20  C21  107.65  3.000
 6R1  N23  C20  C21  111.23  3.000
 6R1  H13  C20  C19  107.77  3.000
 6R1  C21  C20  C19  109.04  3.000
 6R1  N23  C20  C19  110.96  3.000
 6R1  H15  C21  H14  106.88  3.000
 6R1  H15  C21  C22  107.73  3.000
 6R1  H14  C21  C22  109.65  3.000
 6R1  H15  C21  C20  111.08  3.000
 6R1  H14  C21  C20  108.58  3.000
 6R1  C22  C21  C20  112.76  3.000
 6R1  H17  C22  H16  106.88  3.000
 6R1  H17  C22  C17  109.39  3.000
 6R1  H16  C22  C17  110.08  3.000
 6R1  H17  C22  C21  109.45  3.000
 6R1  H16  C22  C21  109.66  3.000
 6R1  C17  C22  C21  111.28  3.000
 6R1  C28  N23  C24  108.32  3.000
 6R1  C28  N23  C20  112.64  3.000
 6R1  C24  N23  C20  113.16  3.000
 6R1  H20  C24  H19  107.26  3.000
 6R1  H20  C24  C25  106.93  3.000
 6R1  H19  C24  C25  109.57  3.000
 6R1  H20  C24  N23  110.46  3.000
 6R1  H19  C24  N23  111.60  3.000
 6R1  C25  C24  N23  110.85  3.000
 6R1  H22  C27  H21  107.86  3.000
 6R1  H22  C27  C28  109.13  3.000
 6R1  H21  C27  C28  109.72  3.000
 6R1  H22  C27  O26  110.37  3.000
 6R1  H21  C27  O26  107.59  3.000
 6R1  C28  C27  O26  112.07  3.000
 6R1  H23  N2   C3   125.31  3.000
 6R1  H23  N2   C1   125.45  3.000
 6R1  C3   N2   C1   109.24  3.000
 6R1  C5   N4   C3   112.55  3.000
 6R1  H24  C5   N4   116.40  3.000
 6R1  H24  C5   N6   115.45  3.000
 6R1  N4   C5   N6   128.15  3.000
 6R1  C14  O13  C12  112.11  3.000
 6R1  H25  N16  C17  116.39  3.000
 6R1  H25  N16  C7   117.15  3.000
 6R1  C17  N16  C7   124.21  3.000
 6R1  H26  C17  C18  108.63  3.000
 6R1  H26  C17  N16  107.43  3.000
 6R1  C18  C17  N16  112.84  3.000
 6R1  H26  C17  C22  108.56  3.000
 6R1  N16  C17  C22  109.76  3.000
 6R1  C18  C17  C22  109.51  3.000
 6R1  H28  C18  H27  107.12  3.000
 6R1  H28  C18  C17  110.03  3.000
 6R1  H27  C18  C17  108.96  3.000
 6R1  H28  C18  C19  109.75  3.000
 6R1  H27  C18  C19  109.79  3.000
 6R1  C17  C18  C19  111.10  3.000
 6R1  H30  C25  H29  107.87  3.000
 6R1  H30  C25  O26  110.34  3.000
 6R1  H29  C25  O26  107.57  3.000
 6R1  H30  C25  C24  109.05  3.000
 6R1  H29  C25  C24  109.69  3.000
 6R1  O26  C25  C24  112.22  3.000
 6R1  C25  O26  C27  109.92  3.000
 6R1  H32  C28  H31  107.15  3.000
 6R1  H32  C28  C27  109.45  3.000
 6R1  H31  C28  C27  107.02  3.000
 6R1  H32  C28  N23  111.54  3.000
 6R1  H31  C28  N23  110.56  3.000
 6R1  C27  C28  N23  110.94  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
 6R1  CONST_01  C7   C8   C9   C1    180.00   0.0  0
 6R1  CONST_02  C3   C8   C9   C1      0.00   0.0  0
 6R1  CONST_03  C8   C3   N2   C1      0.00   0.0  0
 6R1  CONST_04  N4   C3   N2   C1    180.00   0.0  0
 6R1  CONST_05  N6   C7   C8   C3      0.00   0.0  0
 6R1  CONST_06  C9   C1   N2   C3      0.00   0.0  0
 6R1  CONST_07  N6   C5   N4   C3      0.00   0.0  0
 6R1  CONST_08  C9   C8   C7   N6    180.00   0.0  0
 6R1  CONST_09  N2   C3   C8   C7    180.00   0.0  0
 6R1  CONST_10  N4   C3   C8   C7      0.00   0.0  0
 6R1  CONST_11  N4   C5   N6   C7      0.00   0.0  0
 6R1  CONST_12  N2   C1   C9   C8      0.00   0.0  0
 6R1  CONST_13  C5   N6   C7   C8      0.00   0.0  0
 6R1  CONST_14  C5   N4   C3   C8      0.00   0.0  0
 6R1  CONST_15  N2   C3   C8   C9      0.00   0.0  0
 6R1  CONST_16  N4   C3   C8   C9    180.00   0.0  0
 6R1  CONST_17  C5   N4   C3   N2    180.00   0.0  0
 6R1  CONST_18  C10  C9   C8   C3    180.00   0.0  0
 6R1  CONST_19  C10  C9   C8   C7      0.00   0.0  0
 6R1  CONST_20  N2   C1   C9   C10   180.00   0.0  0
 6R1  CONST_21  N16  C7   C8   C3    180.00   0.0  0
 6R1  CONST_22  N16  C7   C8   C9      0.00   0.0  0
 6R1  CONST_23  N16  C7   N6   C5    180.00   0.0  0
 6R1  CONST_24  C17  N16  C7   N6      0.00   0.0  0
 6R1  CONST_25  C17  N16  C7   C8    180.00   0.0  0
 6R1  CONST_26  H1   C1   N2   C3    180.00   0.0  0
 6R1  CONST_27  H24  C5   N4   C3    180.00   0.0  0
 6R1  CONST_28  H23  N2   C3   C8    180.00   0.0  0
 6R1  CONST_29  H25  N16  C7   N6    180.00   0.0  0
 6R1  Var_01    O13  C14  C15  C10   -56.78  30.0  1
 6R1  Var_02    O13  C12  C11  C10    55.86  30.0  1
 6R1  Var_03    C15  C14  O13  C12    59.62  30.0  1
 6R1  Var_04    C25  C24  N23  C20   178.57  30.0  1
 6R1  Var_05    C27  C28  N23  C20  -178.11  30.0  1
 6R1  Var_06    C17  C22  C21  C20    56.46  30.0  1
 6R1  Var_07    C17  C18  C19  C20   -57.45  30.0  1
 6R1  Var_08    O26  C25  C24  N23    57.65  30.0  1
 6R1  Var_09    O26  C27  C28  N23   -57.82  30.0  1
 6R1  Var_10    C28  C27  O26  C25    56.86  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 6R1  chir_01  C10  C15  C11  C9   negativ
 6R1  chir_02  C20  N23  C21  C19  positiv
 6R1  chir_03  C17  N16  C22  C18  positiv

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
 6R1  plan-1  C7   0.020
 6R1  plan-1  N16  0.020
 6R1  plan-1  C17  0.020
 6R1  plan-1  H25  0.020
 6R1  plan-2  C1   0.020
 6R1  plan-2  C3   0.020
 6R1  plan-2  N6   0.020
 6R1  plan-2  C7   0.020
 6R1  plan-2  C8   0.020
 6R1  plan-2  C9   0.020
 6R1  plan-2  C10  0.020
 6R1  plan-2  N2   0.020
 6R1  plan-2  N4   0.020
 6R1  plan-2  C5   0.020
 6R1  plan-2  N16  0.020
 6R1  plan-2  H1   0.020
 6R1  plan-2  H23  0.020
 6R1  plan-2  H24  0.020

