# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 00:02:56 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 1-{4-[4-amino-5-(3-methoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl]benzyl}piperidin-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)c2cn(c3ccc(CN4CCC(O)CC4)cc3)c5ncnc(N)c25
#
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
 S03  S03  1-{4-[4-amino-5-(3-methoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl]benzyl}piperidin-4-ol  ligand  59  32  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S03
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
 S03  N33   N  NH2   0  -0.824   5.2696   2.5082   0.1770
 S03  C1    C  CR6   0   0.403   3.9627   2.8022   0.1244
 S03  N6    N  N     0  -0.471   3.6163   4.0858   0.2457
 S03  C5    C  CR16  0   0.039   2.3261   4.4060   0.2279
 S03  C2    C  CR56  0  -0.111   2.9556   1.8302  -0.0655
 S03  C9    C  CR5   0  -0.009   2.8731   0.4080  -0.2429
 S03  C10   C  CR6   0   0.042   3.9452  -0.5839  -0.3787
 S03  C11   C  CR16  0  -0.369   5.0230  -0.3683  -1.2451
 S03  C12   C  CR16  0  -0.222   6.0040  -1.3358  -1.3738
 S03  C13   C  CR16  0  -0.395   5.9408  -2.5291  -0.6636
 S03  C14   C  CR6   0   0.407   4.8647  -2.7523   0.1924
 S03  O16   O  O2    0  -0.472   4.6973  -3.8680   0.9255
 S03  C17   C  CH3   0  -0.438   5.6888  -4.8743   0.8634
 S03  C15   C  CR16  0  -0.415   3.8769  -1.7763   0.3323
 S03  C8    C  CR15  0  -0.057   1.5403   0.1178  -0.2853
 S03  C3    C  CR56  0   0.494   1.6465   2.3204  -0.0104
 S03  N4    N  N     0  -0.454   1.2917   3.5975   0.1230
 S03  N7    N  NR5   0  -0.624   0.7911   1.2646  -0.1416
 S03  C18   C  CR6   0   0.319  -0.6201   1.3051  -0.1354
 S03  C19   C  CR16  0  -0.287  -1.3274   0.5625  -1.0761
 S03  C20   C  CR16  0  -0.278  -2.7114   0.5532  -1.0509
 S03  C23   C  CR16  0  -0.268  -1.3056   2.0452   0.8185
 S03  C22   C  CR16  0  -0.314  -2.6933   2.0338   0.8246
 S03  C21   C  CR6   0   0.083  -3.4150   1.2906  -0.1018
 S03  C24   C  CH2   0  -0.317  -4.9213   1.2954  -0.1021
 S03  N26   N  NT    0  -0.413  -5.4753  -0.0285  -0.2940
 S03  C27   C  CH2   0  -0.290  -6.8906   0.0296  -0.6137
 S03  C28   C  CH2   0  -0.461  -7.4482  -1.3531  -0.9139
 S03  C31   C  CH2   0  -0.284  -5.2226  -0.8858   0.8511
 S03  C30   C  CH2   0  -0.475  -5.7344  -2.2970   0.6081
 S03  C29   C  CH1   0   0.066  -7.2165  -2.2838   0.2621
 S03  O32   O  OH1   0  -0.675  -7.7081  -3.5638  -0.0766
 S03  H331  H  HNH2  0   0.399   5.9134   3.2337   0.4439
 S03  H332  H  HNH2  0   0.410   5.5872   1.5590   0.2671
 S03  H5    H  HCR6  0   0.248   2.1036   5.4638   0.3212
 S03  H11   H  HCR6  0   0.262   5.0739   0.5357  -1.8386
 S03  H12   H  HCR6  0   0.262   6.8360  -1.1683  -2.0454
 S03  H13   H  HCR6  0   0.281   6.7280  -3.2598  -0.7900
 S03  H171  H  HCH3  0   0.229   6.6673  -4.5029   1.1786
 S03  H172  H  HCH3  0   0.260   5.3746  -5.6602   1.5458
 S03  H173  H  HCH3  0   0.229   5.7786  -5.2986  -0.1399
 S03  H15   H  HCR6  0   0.256   3.0613  -1.9510   1.0250
 S03  H8    H  HCR5  0   0.304   1.0582  -0.8389  -0.4111
 S03  H19   H  HCR6  0   0.272  -0.7968   0.0009  -1.8350
 S03  H20   H  HCR6  0   0.251  -3.2560  -0.0385  -1.7755
 S03  H23   H  HCR6  0   0.269  -0.7668   2.6095   1.5664
 S03  H22   H  HCR6  0   0.255  -3.2186   2.6043   1.5814
 S03  H241  H  HCH2  0   0.213  -5.2877   1.7675   0.8253
 S03  H242  H  HCH2  0   0.253  -5.2725   1.9289  -0.9228
 S03  H271  H  HCH2  0   0.190  -7.4753   0.4891   0.2036
 S03  H272  H  HCH2  0   0.240  -7.0205   0.6723  -1.4876
 S03  H281  H  HCH2  0   0.238  -8.5148  -1.2704  -1.1358
 S03  H282  H  HCH2  0   0.221  -6.9545  -1.7583  -1.8029
 S03  H311  H  HCH2  0   0.243  -4.1481  -0.9212   1.0395
 S03  H312  H  HCH2  0   0.191  -5.6863  -0.4721   1.7645
 S03  H301  H  HCH2  0   0.235  -5.5521  -2.9023   1.5013
 S03  H302  H  HCH2  0   0.222  -5.1745  -2.7514  -0.2150
 S03  H29   H  HCH1  0   0.186  -7.7677  -1.8808   1.1273
 S03  H32   H  HOH1  0   0.447  -7.6065  -4.1379   0.6889

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
 S03  N33  C1    single    1.341  0.020  1.341
 S03  N33  H331  single    0.890  0.020  1.040
 S03  N33  H332  single    0.890  0.020  1.040
 S03  C1   N6    aromatic  1.335  0.020  1.335
 S03  C1   C2    aromatic  1.412  0.020  1.412
 S03  N6   C5    aromatic  1.329  0.020  1.329
 S03  C5   N4    aromatic  1.317  0.020  1.317
 S03  C5   H5    single    0.930  0.020  1.080
 S03  C2   C9    aromatic  1.436  0.020  1.436
 S03  C2   C3    aromatic  1.399  0.020  1.399
 S03  C9   C10   single    1.467  0.020  1.467
 S03  C9   C8    aromatic  1.365  0.020  1.365
 S03  C10  C11   aromatic  1.400  0.020  1.400
 S03  C10  C15   aromatic  1.390  0.020  1.390
 S03  C11  C12   aromatic  1.384  0.020  1.384
 S03  C11  H11   single    0.930  0.020  1.080
 S03  C12  C13   aromatic  1.390  0.020  1.390
 S03  C12  H12   single    0.930  0.020  1.080
 S03  C13  C14   aromatic  1.393  0.020  1.393
 S03  C13  H13   single    0.930  0.020  1.080
 S03  C14  O16   single    1.345  0.020  1.345
 S03  C14  C15   aromatic  1.396  0.020  1.396
 S03  O16  C17   single    1.414  0.020  1.414
 S03  C17  H171  single    0.970  0.020  1.090
 S03  C17  H172  single    0.970  0.020  1.090
 S03  C17  H173  single    0.970  0.020  1.090
 S03  C15  H15   single    0.930  0.020  1.080
 S03  C8   N7    aromatic  1.377  0.020  1.377
 S03  C8   H8    single    0.930  0.020  1.080
 S03  C3   N4    aromatic  1.332  0.020  1.332
 S03  C3   N7    aromatic  1.365  0.020  1.365
 S03  N7   C18   single    1.412  0.020  1.412
 S03  C18  C19   aromatic  1.392  0.020  1.392
 S03  C18  C23   aromatic  1.388  0.020  1.388
 S03  C19  C20   aromatic  1.384  0.020  1.384
 S03  C19  H19   single    0.930  0.020  1.080
 S03  C20  C21   aromatic  1.393  0.020  1.393
 S03  C20  H20   single    0.930  0.020  1.080
 S03  C23  C22   aromatic  1.388  0.020  1.388
 S03  C23  H23   single    0.930  0.020  1.080
 S03  C22  C21   aromatic  1.390  0.020  1.390
 S03  C22  H22   single    0.930  0.020  1.080
 S03  C21  C24   single    1.506  0.020  1.506
 S03  C24  N26   single    1.448  0.020  1.448
 S03  C24  H241  single    0.970  0.020  1.090
 S03  C24  H242  single    0.970  0.020  1.090
 S03  N26  C27   single    1.452  0.020  1.452
 S03  N26  C31   single    1.453  0.020  1.453
 S03  C27  C28   single    1.521  0.020  1.521
 S03  C27  H271  single    0.970  0.020  1.090
 S03  C27  H272  single    0.970  0.020  1.090
 S03  C28  C29   single    1.517  0.020  1.517
 S03  C28  H281  single    0.970  0.020  1.090
 S03  C28  H282  single    0.970  0.020  1.090
 S03  C31  C30   single    1.521  0.020  1.521
 S03  C31  H311  single    0.970  0.020  1.090
 S03  C31  H312  single    0.970  0.020  1.090
 S03  C30  C29   single    1.522  0.020  1.522
 S03  C30  H301  single    0.970  0.020  1.090
 S03  C30  H302  single    0.970  0.020  1.090
 S03  C29  O32   single    1.412  0.020  1.412
 S03  C29  H29   single    0.970  0.020  1.090
 S03  O32  H32   single    0.850  0.020  0.980

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
 S03  H332  N33  H331  117.07  3.000
 S03  H332  N33  C1    121.25  3.000
 S03  H331  N33  C1    118.44  3.000
 S03  C2    C1   N6    119.27  3.000
 S03  C2    C1   N33   123.33  3.000
 S03  N6    C1   N33   117.40  3.000
 S03  C5    N6   C1    118.83  3.000
 S03  H5    C5   N4    116.38  3.000
 S03  H5    C5   N6    115.64  3.000
 S03  N4    C5   N6    127.98  3.000
 S03  C3    C2   C9    107.35  3.000
 S03  C3    C2   C1    114.88  3.000
 S03  C9    C2   C1    137.67  3.000
 S03  C8    C9   C10   124.54  3.000
 S03  C8    C9   C2    105.70  3.000
 S03  C10   C9   C2    129.74  3.000
 S03  C15   C10  C11   119.12  3.000
 S03  C15   C10  C9    119.79  3.000
 S03  C11   C10  C9    121.06  3.000
 S03  H11   C11  C12   119.97  3.000
 S03  H11   C11  C10   120.28  3.000
 S03  C12   C11  C10   119.72  3.000
 S03  H12   C12  C13   119.00  3.000
 S03  H12   C12  C11   119.64  3.000
 S03  C13   C12  C11   121.36  3.000
 S03  H13   C13  C14   121.73  3.000
 S03  H13   C13  C12   119.15  3.000
 S03  C14   C13  C12   119.11  3.000
 S03  C15   C14  O16   115.92  3.000
 S03  C15   C14  C13   119.76  3.000
 S03  O16   C14  C13   124.32  3.000
 S03  C17   O16  C14   118.61  3.000
 S03  H173  C17  H172  108.63  3.000
 S03  H173  C17  H171  108.84  3.000
 S03  H172  C17  H171  108.87  3.000
 S03  H173  C17  O16   111.97  3.000
 S03  H172  C17  O16   106.51  3.000
 S03  H171  C17  O16   111.92  3.000
 S03  H15   C15  C14   118.93  3.000
 S03  H15   C15  C10   120.13  3.000
 S03  C14   C15  C10   120.92  3.000
 S03  H8    C8   N7    120.50  3.000
 S03  H8    C8   C9    128.96  3.000
 S03  N7    C8   C9    110.54  3.000
 S03  N7    C3   N4    125.74  3.000
 S03  N7    C3   C2    108.16  3.000
 S03  N4    C3   C2    126.09  3.000
 S03  C3    N4   C5    112.79  3.000
 S03  C18   N7   C3    127.14  3.000
 S03  C18   N7   C8    124.61  3.000
 S03  C3    N7   C8    108.24  3.000
 S03  C23   C18  C19   119.86  3.000
 S03  C23   C18  N7    120.79  3.000
 S03  C19   C18  N7    119.33  3.000
 S03  H19   C19  C20   119.94  3.000
 S03  H19   C19  C18   120.09  3.000
 S03  C20   C19  C18   119.96  3.000
 S03  H20   C20  C21   119.43  3.000
 S03  H20   C20  C19   119.64  3.000
 S03  C21   C20  C19   120.93  3.000
 S03  H23   C23  C22   119.98  3.000
 S03  H23   C23  C18   120.50  3.000
 S03  C22   C23  C18   119.50  3.000
 S03  H22   C22  C21   119.70  3.000
 S03  H22   C22  C23   118.91  3.000
 S03  C21   C22  C23   121.38  3.000
 S03  C24   C21  C22   121.18  3.000
 S03  C24   C21  C20   120.45  3.000
 S03  C22   C21  C20   118.36  3.000
 S03  H242  C24  H241  106.02  3.000
 S03  H242  C24  N26   107.88  3.000
 S03  H241  C24  N26   112.06  3.000
 S03  H242  C24  C21   108.84  3.000
 S03  H241  C24  C21   109.47  3.000
 S03  N26   C24  C21   112.32  3.000
 S03  C31   N26  C27   111.51  3.000
 S03  C31   N26  C24   111.63  3.000
 S03  C27   N26  C24   111.44  3.000
 S03  H272  C27  H271  106.50  3.000
 S03  H272  C27  C28   109.47  3.000
 S03  H271  C27  C28   109.27  3.000
 S03  H272  C27  N26   108.39  3.000
 S03  H271  C27  N26   111.69  3.000
 S03  C28   C27  N26   111.37  3.000
 S03  H282  C28  H281  107.65  3.000
 S03  H282  C28  C29   109.48  3.000
 S03  H281  C28  C29   110.66  3.000
 S03  H282  C28  C27   109.36  3.000
 S03  H281  C28  C27   109.22  3.000
 S03  C29   C28  C27   110.41  3.000
 S03  H312  C31  H311  106.42  3.000
 S03  H312  C31  C30   109.78  3.000
 S03  H311  C31  C30   109.20  3.000
 S03  H312  C31  N26   110.96  3.000
 S03  H311  C31  N26   109.06  3.000
 S03  C30   C31  N26   111.30  3.000
 S03  H302  C30  H301  107.40  3.000
 S03  H302  C30  C29   109.32  3.000
 S03  H301  C30  C29   110.65  3.000
 S03  H302  C30  C31   109.47  3.000
 S03  H301  C30  C31   109.08  3.000
 S03  C29   C30  C31   110.85  3.000
 S03  H29   C29  O32   110.21  3.000
 S03  H29   C29  C30   108.16  3.000
 S03  O32   C29  C30   112.68  3.000
 S03  H29   C29  C28   107.92  3.000
 S03  O32   C29  C28   108.47  3.000
 S03  C30   C29  C28   109.28  3.000
 S03  H32   O32  C29   108.25  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
 S03  CONST_01  N4    C5   N6   C1      0.00   0.0  0
 S03  CONST_02  C10   C9   C2   C1      0.00   0.0  0
 S03  CONST_03  C8    C9   C2   C1    180.00   0.0  0
 S03  CONST_04  N4    C3   C2   C1      0.00   0.0  0
 S03  CONST_05  N7    C3   C2   C1    180.00   0.0  0
 S03  CONST_06  C9    C2   C1   N6    180.00   0.0  0
 S03  CONST_07  C3    C2   C1   N6      0.00   0.0  0
 S03  CONST_08  C3    N4   C5   N6      0.00   0.0  0
 S03  CONST_09  C2    C1   N6   C5      0.00   0.0  0
 S03  CONST_10  C2    C3   N4   C5      0.00   0.0  0
 S03  CONST_11  N7    C3   N4   C5    180.00   0.0  0
 S03  CONST_14  N7    C8   C9   C2      0.00   0.0  0
 S03  CONST_15  C8    N7   C3   C2      0.00   0.0  0
 S03  CONST_16  C18   N7   C3   C2    180.00   0.0  0
 S03  CONST_17  N4    C3   C2   C9    180.00   0.0  0
 S03  CONST_18  N7    C3   C2   C9      0.00   0.0  0
 S03  CONST_19  C12   C11  C10  C9    180.00   0.0  0
 S03  CONST_20  C14   C15  C10  C9    180.00   0.0  0
 S03  CONST_21  C3    N7   C8   C9      0.00   0.0  0
 S03  CONST_22  C18   N7   C8   C9    180.00   0.0  0
 S03  CONST_23  C3    C2   C9   C10   180.00   0.0  0
 S03  CONST_24  N7    C8   C9   C10   180.00   0.0  0
 S03  CONST_25  C13   C12  C11  C10     0.00   0.0  0
 S03  CONST_26  C13   C14  C15  C10     0.00   0.0  0
 S03  CONST_28  C14   C15  C10  C11     0.00   0.0  0
 S03  CONST_29  C14   C13  C12  C11     0.00   0.0  0
 S03  CONST_30  C15   C10  C11  C12     0.00   0.0  0
 S03  CONST_31  C15   C14  C13  C12     0.00   0.0  0
 S03  CONST_33  C3    C2   C9   C8      0.00   0.0  0
 S03  CONST_34  N4    C3   N7   C8    180.00   0.0  0
 S03  CONST_39  C18   N7   C3   N4      0.00   0.0  0
 S03  CONST_40  C20   C19  C18  N7    180.00   0.0  0
 S03  CONST_41  C22   C23  C18  N7    180.00   0.0  0
 S03  CONST_42  C21   C20  C19  C18     0.00   0.0  0
 S03  CONST_43  C21   C22  C23  C18     0.00   0.0  0
 S03  CONST_44  C22   C23  C18  C19     0.00   0.0  0
 S03  CONST_45  C22   C21  C20  C19     0.00   0.0  0
 S03  CONST_46  C23   C18  C19  C20     0.00   0.0  0
 S03  CONST_47  C23   C22  C21  C20     0.00   0.0  0
 S03  CONST_48  C5    N6   C1   N33   180.00   0.0  0
 S03  CONST_49  C9    C2   C1   N33     0.00   0.0  0
 S03  CONST_50  C3    C2   C1   N33   180.00   0.0  0
 S03  CONST_51  O16   C14  C15  C10   180.00   0.0  0
 S03  CONST_52  O16   C14  C13  C12   180.00   0.0  0
 S03  CONST_53  C24   C21  C20  C19   180.00   0.0  0
 S03  CONST_54  C24   C21  C22  C23   180.00   0.0  0
 S03  CONST_55  H5    C5   N6   C1    180.00   0.0  0
 S03  CONST_56  H8    C8   C9   C2    180.00   0.0  0
 S03  CONST_57  H11   C11  C10  C9      0.00   0.0  0
 S03  CONST_58  H15   C15  C10  C9      0.00   0.0  0
 S03  CONST_59  H12   C12  C11  C10   180.00   0.0  0
 S03  CONST_60  H13   C13  C12  C11   180.00   0.0  0
 S03  CONST_61  H19   C19  C18  N7      0.00   0.0  0
 S03  CONST_62  H23   C23  C18  N7      0.00   0.0  0
 S03  CONST_63  H20   C20  C19  C18   180.00   0.0  0
 S03  CONST_64  H22   C22  C23  C18   180.00   0.0  0
 S03  CONST_65  H331  N33  C1   N6      0.00   0.0  0
 S03  CONST_66  H332  N33  C1   N6    180.00   0.0  0
 S03  Var_01    C29   C28  C27  N26    57.34  30.0  1
 S03  Var_02    C29   C30  C31  N26   -56.30  30.0  1
 S03  Var_03    C30   C31  N26  C27    58.01  30.0  1
 S03  Var_04    C31   N26  C27  C28   -58.64  30.0  1
 S03  Var_05    N26   C24  C21  C20    44.02  30.0  2
 S03  Var_06    C27   N26  C24  C21  -166.14  30.0  3
 S03  Var_07    C15   C14  O16  C17  -177.80  30.0  2
 S03  Var_08    H171  C17  O16  C14    59.38  30.0  3

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
 S03  chir_01  C29  C28  C30  O32  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
 S03  plan-1  C9    0.020
 S03  plan-1  C10   0.020
 S03  plan-1  C11   0.020
 S03  plan-1  C12   0.020
 S03  plan-1  C13   0.020
 S03  plan-1  C14   0.020
 S03  plan-1  O16   0.020
 S03  plan-1  C15   0.020
 S03  plan-1  H11   0.020
 S03  plan-1  H12   0.020
 S03  plan-1  H13   0.020
 S03  plan-1  H15   0.020
 S03  plan-2  N7    0.020
 S03  plan-2  C18   0.020
 S03  plan-2  C19   0.020
 S03  plan-2  C20   0.020
 S03  plan-2  C23   0.020
 S03  plan-2  C22   0.020
 S03  plan-2  C21   0.020
 S03  plan-2  C24   0.020
 S03  plan-2  H19   0.020
 S03  plan-2  H20   0.020
 S03  plan-2  H23   0.020
 S03  plan-2  H22   0.020
 S03  plan-3  N33   0.020
 S03  plan-3  C1    0.020
 S03  plan-3  N6    0.020
 S03  plan-3  C5    0.020
 S03  plan-3  C2    0.020
 S03  plan-3  C9    0.020
 S03  plan-3  C10   0.020
 S03  plan-3  C8    0.020
 S03  plan-3  C3    0.020
 S03  plan-3  N4    0.020
 S03  plan-3  N7    0.020
 S03  plan-3  C18   0.020
 S03  plan-3  H5    0.020
 S03  plan-3  H8    0.020
 S03  plan-4  N33   0.020
 S03  plan-4  C1    0.020
 S03  plan-4  H331  0.020
 S03  plan-4  H332  0.020

