# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 17:52:52 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 5-[7-(methylsulfonyl)-2-(morpholin-4-yl)-6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidin-4-yl]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)N1CCc2c1nc(nc2c3cnc(N)nc3)N4CCOCC4
#
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
 MMD  MMD  5-[7-(methylsulfonyl)-2-(morpholin-4-yl)-6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidin-4-yl]pyrimidin-2-amine  ligand  45  26  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MMD
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
 MMD  C1    C  CH2   0  -0.314  -0.0292  -3.5537  -0.4492
 MMD  C2    C  CH2   0  -0.188   0.4483  -4.8129   0.2508
 MMD  O3    O  O2    0  -0.484   1.7800  -5.1294  -0.0854
 MMD  C4    C  CH2   0  -0.187   2.6460  -4.0765   0.2734
 MMD  C5    C  CH2   0  -0.315   2.2813  -2.7818  -0.4288
 MMD  N6    N  NT    0  -0.520   0.8876  -2.4630  -0.1789
 MMD  C7    C  CR6   0   0.645   0.4572  -1.1801  -0.1017
 MMD  N8    N  N     0  -0.535  -0.8511  -0.9585  -0.0722
 MMD  N9    N  N     0  -0.511   1.4057  -0.2266  -0.0484
 MMD  C10   C  CR56  0   0.626   0.9387   0.9884   0.0558
 MMD  N11   N  NR5   0  -0.731   1.7382   2.1151   0.0949
 MMD  S12   S  S     0   1.355   3.3901   2.0898  -0.1132
 MMD  C13   C  CH3   0  -0.798   3.6421   1.4744  -1.7575
 MMD  O14   O  OS    0  -0.652   3.7988   3.4839  -0.0685
 MMD  O15   O  OS    0  -0.641   3.9557   1.1531   0.8367
 MMD  C16   C  CH2   0  -0.270   0.9222   3.3231  -0.1224
 MMD  C17   C  CH2   0  -0.557  -0.5074   2.8496   0.2047
 MMD  C18   C  CR56  0  -0.113  -0.4054   1.3562   0.1035
 MMD  C19   C  CR6   0   0.265  -1.2974   0.3012   0.0388
 MMD  C20   C  CR6   0  -0.133  -2.7535   0.4580   0.0580
 MMD  C21   C  CR16  0  -0.009  -3.5974  -0.5475  -0.4216
 MMD  N22   N  N     0  -0.447  -4.9092  -0.4559  -0.4242
 MMD  C23   C  CR6   0   0.563  -5.4353   0.6725   0.0779
 MMD  N24   N  NH2   0  -0.812  -6.7665   0.7900   0.0625
 MMD  N27   N  N     0  -0.450  -4.7297   1.6907   0.5878
 MMD  C28   C  CR16  0  -0.048  -3.4176   1.5713   0.5690
 MMD  H1    H  HCH2  0   0.232  -0.0991  -3.7284  -1.5304
 MMD  H1A   H  HCH2  0   0.272  -1.0233  -3.2984  -0.0920
 MMD  H2    H  HCH2  0   0.206   0.3469  -4.6836   1.3376
 MMD  H2A   H  HCH2  0   0.243  -0.1766  -5.6560  -0.0475
 MMD  H4    H  HCH2  0   0.206   2.6281  -3.9182   1.3610
 MMD  H4A   H  HCH2  0   0.243   3.6580  -4.3710  -0.0073
 MMD  H5    H  HCH2  0   0.274   2.9163  -1.9797  -0.0612
 MMD  H5A   H  HCH2  0   0.231   2.4577  -2.8804  -1.5078
 MMD  H13   H  HCH3  0   0.296   3.1234   2.1181  -2.4645
 MMD  H13A  H  HCH3  0   0.312   4.7140   1.4982  -1.9498
 MMD  H13B  H  HCH3  0   0.298   3.2740   0.4540  -1.8240
 MMD  H16   H  HCH2  0   0.278   1.2482   4.1309   0.5255
 MMD  H16A  H  HCH2  0   0.266   0.9992   3.6509  -1.1609
 MMD  H17   H  HCH2  0   0.274  -0.7883   3.1657   1.2123
 MMD  H17A  H  HCH2  0   0.276  -1.2255   3.2892  -0.4880
 MMD  H21   H  HCR6  0   0.274  -3.1738  -1.4609  -0.8234
 MMD  HN24  H  HNH2  0   0.405  -7.3404   0.0232  -0.2407
 MMD  HN2A  H  HNH2  0   0.405  -7.2105   1.5834   0.4897
 MMD  H28   H  HCR6  0   0.272  -2.8707   2.3960   1.0102

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
 MMD  C1   C2    single    1.518  0.020  1.518
 MMD  C1   N6    single    1.450  0.020  1.450
 MMD  C2   O3    single    1.410  0.020  1.410
 MMD  O3   C4    single    1.410  0.020  1.410
 MMD  C4   C5    single    1.517  0.020  1.517
 MMD  C5   N6    single    1.451  0.020  1.451
 MMD  N6   C7    single    1.355  0.020  1.355
 MMD  C7   N8    aromatic  1.327  0.020  1.327
 MMD  C7   N9    aromatic  1.346  0.020  1.346
 MMD  N8   C19   aromatic  1.341  0.020  1.341
 MMD  N9   C10   aromatic  1.306  0.020  1.306
 MMD  C10  N11   single    1.382  0.020  1.382
 MMD  C10  C18   aromatic  1.394  0.020  1.394
 MMD  N11  S12   single    1.665  0.020  1.665
 MMD  N11  C16   single    1.474  0.020  1.474
 MMD  S12  C13   single    1.774  0.020  1.774
 MMD  S12  O14   double    1.453  0.020  1.453
 MMD  S12  O15   double    1.449  0.020  1.449
 MMD  C16  C17   single    1.541  0.020  1.541
 MMD  C17  C18   single    1.500  0.020  1.500
 MMD  C18  C19   aromatic  1.383  0.020  1.383
 MMD  C19  C20   single    1.465  0.020  1.465
 MMD  C20  C21   aromatic  1.398  0.020  1.398
 MMD  C20  C28   aromatic  1.393  0.020  1.393
 MMD  C21  N22   aromatic  1.315  0.020  1.315
 MMD  N22  C23   aromatic  1.342  0.020  1.342
 MMD  C23  N24   single    1.336  0.020  1.336
 MMD  C23  N27   aromatic  1.340  0.020  1.340
 MMD  N27  C28   aromatic  1.318  0.020  1.318
 MMD  C1   H1    single    0.970  0.020  1.090
 MMD  C1   H1A   single    0.970  0.020  1.090
 MMD  C2   H2    single    0.970  0.020  1.090
 MMD  C2   H2A   single    0.970  0.020  1.090
 MMD  C4   H4    single    0.970  0.020  1.090
 MMD  C4   H4A   single    0.970  0.020  1.090
 MMD  C5   H5    single    0.970  0.020  1.090
 MMD  C5   H5A   single    0.970  0.020  1.090
 MMD  C13  H13   single    0.970  0.020  1.090
 MMD  C13  H13A  single    0.970  0.020  1.090
 MMD  C13  H13B  single    0.970  0.020  1.090
 MMD  C16  H16   single    0.970  0.020  1.090
 MMD  C16  H16A  single    0.970  0.020  1.090
 MMD  C17  H17   single    0.970  0.020  1.090
 MMD  C17  H17A  single    0.970  0.020  1.090
 MMD  C21  H21   single    0.930  0.020  1.080
 MMD  N24  HN24  single    0.860  0.020  1.020
 MMD  N24  HN2A  single    0.860  0.020  1.020
 MMD  C28  H28   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
 MMD  H1A   C1   H1    107.63  3.000
 MMD  H1A   C1   N6    109.90  3.000
 MMD  H1    C1   N6    110.10  3.000
 MMD  H1A   C1   C2    109.34  3.000
 MMD  H1    C1   C2    110.02  3.000
 MMD  N6    C1   C2    109.83  3.000
 MMD  H2A   C2   H2    107.97  3.000
 MMD  H2A   C2   O3    107.60  3.000
 MMD  H2    C2   O3    110.45  3.000
 MMD  H2A   C2   C1    109.56  3.000
 MMD  H2    C2   C1    109.23  3.000
 MMD  O3    C2   C1    111.93  3.000
 MMD  C4    O3   C2    110.61  3.000
 MMD  H4A   C4   H4    107.98  3.000
 MMD  H4A   C4   C5    109.53  3.000
 MMD  H4    C4   C5    109.34  3.000
 MMD  H4A   C4   O3    107.62  3.000
 MMD  H4    C4   O3    110.45  3.000
 MMD  C5    C4   O3    111.83  3.000
 MMD  H5A   C5   H5    107.75  3.000
 MMD  H5A   C5   N6    110.08  3.000
 MMD  H5    C5   N6    109.92  3.000
 MMD  H5A   C5   C4    109.85  3.000
 MMD  H5    C5   C4    109.43  3.000
 MMD  N6    C5   C4    109.79  3.000
 MMD  C7    N6   C5    121.51  3.000
 MMD  C7    N6   C1    121.45  3.000
 MMD  C5    N6   C1    114.19  3.000
 MMD  N9    C7   N8    125.13  3.000
 MMD  N9    C7   N6    116.68  3.000
 MMD  N8    C7   N6    118.19  3.000
 MMD  C19   N8   C7    119.13  3.000
 MMD  C10   N9   C7    114.22  3.000
 MMD  C18   C10  N11   109.98  3.000
 MMD  C18   C10  N9    126.36  3.000
 MMD  N11   C10  N9    123.64  3.000
 MMD  C16   N11  S12   122.90  3.000
 MMD  C16   N11  C10   110.10  3.000
 MMD  S12   N11  C10   123.91  3.000
 MMD  O15   S12  O14   119.34  3.000
 MMD  O15   S12  C13   109.15  3.000
 MMD  O14   S12  C13   108.74  3.000
 MMD  O15   S12  N11   108.37  3.000
 MMD  O14   S12  N11   105.11  3.000
 MMD  C13   S12  N11   105.20  3.000
 MMD  H13B  C13  H13A  110.06  3.000
 MMD  H13B  C13  H13   110.76  3.000
 MMD  H13A  C13  H13   109.97  3.000
 MMD  H13B  C13  S12   109.53  3.000
 MMD  H13A  C13  S12   107.21  3.000
 MMD  H13   C13  S12   109.23  3.000
 MMD  H16A  C16  H16   108.85  3.000
 MMD  H16A  C16  C17   111.08  3.000
 MMD  H16   C16  C17   112.37  3.000
 MMD  H16A  C16  N11   110.32  3.000
 MMD  H16   C16  N11   110.83  3.000
 MMD  C17   C16  N11   103.33  3.000
 MMD  H17A  C17  H17   107.46  3.000
 MMD  H17A  C17  C18   113.78  3.000
 MMD  H17   C17  C18   111.57  3.000
 MMD  H17A  C17  C16   110.62  3.000
 MMD  H17   C17  C16   110.20  3.000
 MMD  C18   C17  C16   103.20  3.000
 MMD  C19   C18  C17   135.94  3.000
 MMD  C19   C18  C10   114.77  3.000
 MMD  C17   C18  C10   109.29  3.000
 MMD  C20   C19  C18   123.98  3.000
 MMD  C20   C19  N8    115.63  3.000
 MMD  C18   C19  N8    120.38  3.000
 MMD  C28   C20  C21   114.39  3.000
 MMD  C28   C20  C19   124.34  3.000
 MMD  C21   C20  C19   121.25  3.000
 MMD  H21   C21  N22   116.60  3.000
 MMD  H21   C21  C20   119.83  3.000
 MMD  N22   C21  C20   123.57  3.000
 MMD  C23   N22  C21   116.66  3.000
 MMD  N27   C23  N24   117.53  3.000
 MMD  N27   C23  N22   125.08  3.000
 MMD  N24   C23  N22   117.38  3.000
 MMD  HN2A  N24  HN24  118.60  3.000
 MMD  HN2A  N24  C23   120.32  3.000
 MMD  HN24  N24  C23   120.35  3.000
 MMD  C28   N27  C23   116.76  3.000
 MMD  H28   C28  N27   115.33  3.000
 MMD  H28   C28  C20   121.13  3.000
 MMD  N27   C28  C20   123.52  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
 MMD  CONST_01  C18   C19  N8   C7     0.00   0.0  0
 MMD  CONST_02  C20   C19  N8   C7   180.00   0.0  0
 MMD  CONST_03  C18   C10  N9   C7     0.00   0.0  0
 MMD  CONST_04  C10   N9   C7   N8     0.00   0.0  0
 MMD  CONST_05  C10   C18  C19  N8     0.00   0.0  0
 MMD  CONST_08  C19   N8   C7   N9     0.00   0.0  0
 MMD  CONST_09  C19   C18  C10  N9     0.00   0.0  0
 MMD  CONST_10  C20   C19  C18  C10  180.00   0.0  0
 MMD  CONST_13  N22   C21  C20  C19  180.00   0.0  0
 MMD  CONST_14  N27   C28  C20  C19  180.00   0.0  0
 MMD  CONST_15  C23   N22  C21  C20    0.00   0.0  0
 MMD  CONST_16  C23   N27  C28  C20    0.00   0.0  0
 MMD  CONST_17  N27   C28  C20  C21    0.00   0.0  0
 MMD  CONST_18  N27   C23  N22  C21    0.00   0.0  0
 MMD  CONST_19  C28   C20  C21  N22    0.00   0.0  0
 MMD  CONST_20  C28   N27  C23  N22    0.00   0.0  0
 MMD  CONST_21  C19   N8   C7   N6   180.00   0.0  0
 MMD  CONST_22  C10   N9   C7   N6   180.00   0.0  0
 MMD  CONST_23  C20   C19  C18  C17    0.00   0.0  0
 MMD  CONST_24  N24   C23  N22  C21  180.00   0.0  0
 MMD  CONST_25  C28   N27  C23  N24  180.00   0.0  0
 MMD  CONST_26  H21   C21  C20  C19    0.00   0.0  0
 MMD  CONST_27  H28   C28  C20  C19    0.00   0.0  0
 MMD  CONST_28  HN24  N24  C23  N22    0.00   0.0  0
 MMD  CONST_29  HN2A  N24  C23  N22  180.00   0.0  0
 MMD  Var_01    C4    C5   N6   C1   -50.82  30.0  1
 MMD  Var_02    N8    C7   N6   C1    10.29  30.0  2
 MMD  Var_03    C5    N6   C1   C2    50.67  30.0  1
 MMD  Var_04    C5    C4   O3   C2   -59.64  30.0  1
 MMD  Var_05    N6    C1   C2   O3   -54.19  30.0  1
 MMD  Var_06    N6    C5   C4   O3    54.45  30.0  1
 MMD  Var_07    C16   N11  C10  N9   165.94  30.0  1
 MMD  Var_08    C17   C16  N11  C10   19.70  30.0  1
 MMD  Var_09    C16   C17  C18  C10   12.83  30.0  1
 MMD  Var_10    C18   C17  C16  N11  -18.92  30.0  1
 MMD  Var_11    H2    C2   O3   C4   -62.43  30.0  1
 MMD  Var_12    C13   S12  N11  C10   62.23  30.0  3
 MMD  Var_13    H13   C13  S12  N11   57.68  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
 MMD  plan-1  C19   0.020
 MMD  plan-1  C20   0.020
 MMD  plan-1  C21   0.020
 MMD  plan-1  N22   0.020
 MMD  plan-1  C23   0.020
 MMD  plan-1  N24   0.020
 MMD  plan-1  N27   0.020
 MMD  plan-1  C28   0.020
 MMD  plan-1  H21   0.020
 MMD  plan-1  H28   0.020
 MMD  plan-2  N6    0.020
 MMD  plan-2  C7    0.020
 MMD  plan-2  N8    0.020
 MMD  plan-2  N9    0.020
 MMD  plan-2  C10   0.020
 MMD  plan-2  N11   0.020
 MMD  plan-2  C17   0.020
 MMD  plan-2  C18   0.020
 MMD  plan-2  C19   0.020
 MMD  plan-2  C20   0.020
 MMD  plan-3  C23   0.020
 MMD  plan-3  N24   0.020
 MMD  plan-3  HN24  0.020
 MMD  plan-3  HN2A  0.020

