# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 19:59:00 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 5-[2-(morpholin-4-yl)-7-(pyridin-3-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: Nc1ncc(cn1)c2nc(nc3N(CCc23)c4cccnc4)N5CCOCC5
#
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
 MMY  MMY  5-[2-(morpholin-4-yl)-7-(pyridin-3-yl)-6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidin-4-yl]pyrimidin-2-amine  ligand  48  28  .  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_MMY
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
 MMY  C1    C  CR16  0  -0.209  -3.8464   0.6333  -0.6386
 MMY  C2    C  CR16  0  -0.314  -5.2287   0.6336  -0.6046
 MMY  C3    C  CR16  0  -0.092  -5.8982   1.7173  -0.0570
 MMY  N4    N  N     0  -0.391  -5.2567   2.7678   0.4357
 MMY  C5    C  CR16  0  -0.147  -3.9326   2.7738   0.4122
 MMY  C6    C  CR6   0   0.278  -3.1576   1.7287  -0.1080
 MMY  N7    N  NR5   0  -0.632  -1.7749   1.8359  -0.1139
 MMY  C8    C  CH2   0  -0.291  -1.0991   3.1009   0.1883
 MMY  C9    C  CH2   0  -0.558   0.3880   2.8303  -0.0883
 MMY  C10   C  CR56  0  -0.135   0.4468   1.3348  -0.1259
 MMY  C11   C  CR56  0   0.599  -0.8579   0.8214  -0.1678
 MMY  N12   N  N     0  -0.533  -1.1607  -0.4543  -0.2172
 MMY  C13   C  CR6   0   0.647  -0.1051  -1.2875  -0.1995
 MMY  N14   N  NT    0  -0.521  -0.3773  -2.6167  -0.2139
 MMY  C15   C  CH2   0  -0.318   0.6656  -3.6124  -0.3572
 MMY  C16   C  CH2   0  -0.186   0.3479  -4.8166   0.5098
 MMY  O17   O  O2    0  -0.484  -0.9343  -5.3371   0.2378
 MMY  C18   C  CH2   0  -0.184  -1.9284  -4.3599   0.4500
 MMY  C19   C  CH2   0  -0.318  -1.7140  -3.1360  -0.4222
 MMY  N20   N  N     0  -0.543   1.1675  -0.9172  -0.1532
 MMY  C21   C  CR6   0   0.261   1.4543   0.3952  -0.1199
 MMY  C22   C  CR6   0  -0.131   2.8809   0.7257  -0.0457
 MMY  C23   C  CR16  0  -0.013   3.8098  -0.1962   0.4428
 MMY  N24   N  N     0  -0.448   5.0993   0.0484   0.5352
 MMY  C25   C  CR6   0   0.559   5.5143   1.2536   0.1170
 MMY  N26   N  NH2   0  -0.814   6.8197   1.5290   0.2301
 MMY  N29   N  N     0  -0.450   4.7232   2.2057  -0.3932
 MMY  C30   C  CR16  0  -0.047   3.4350   1.9333  -0.4638
 MMY  H1    H  HCR6  0   0.292  -3.3155  -0.1995  -1.0705
 MMY  H2    H  HCR6  0   0.270  -5.7819  -0.2028  -1.0100
 MMY  H3    H  HCR6  0   0.261  -6.9812   1.7395  -0.0183
 MMY  H5    H  HCR6  0   0.275  -3.4606   3.6553   0.8293
 MMY  H8    H  HCH2  0   0.267  -1.4963   3.9025  -0.4336
 MMY  H8A   H  HCH2  0   0.260  -1.2598   3.3722   1.2349
 MMY  H9    H  HCH2  0   0.269   0.6831   3.2738  -1.0424
 MMY  H9A   H  HCH2  0   0.272   1.0175   3.2726   0.6846
 MMY  H15   H  HCH2  0   0.231   0.7505  -3.9196  -1.4074
 MMY  H15A  H  HCH2  0   0.274   1.6218  -3.1916  -0.0581
 MMY  H16   H  HCH2  0   0.241   1.0718  -5.6094   0.3159
 MMY  H16A  H  HCH2  0   0.205   0.4317  -4.5330   1.5685
 MMY  H18   H  HCH2  0   0.242  -2.8917  -4.8148   0.2151
 MMY  H18A  H  HCH2  0   0.205  -1.9460  -4.0519   1.5050
 MMY  H19   H  HCH2  0   0.272  -2.4520  -2.3799  -0.1679
 MMY  H19A  H  HCH2  0   0.231  -1.8573  -3.3981  -1.4785
 MMY  H23   H  HCR6  0   0.273   3.4756  -1.1719   0.7772
 MMY  HN26  H  HNH2  0   0.403   7.4637   0.8057   0.4981
 MMY  HN2A  H  HNH2  0   0.403   7.1914   2.3700  -0.1747
 MMY  H30   H  HCR6  0   0.269   2.8200   2.7092  -0.9044

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
 MMY  C1   C2    aromatic  1.383  0.020  1.383
 MMY  C1   C6    aromatic  1.399  0.020  1.399
 MMY  C2   C3    aromatic  1.387  0.020  1.387
 MMY  C3   N4    aromatic  1.326  0.020  1.326
 MMY  N4   C5    aromatic  1.324  0.020  1.324
 MMY  C5   C6    aromatic  1.401  0.020  1.401
 MMY  C6   N7    single    1.387  0.020  1.387
 MMY  N7   C8    single    1.466  0.020  1.466
 MMY  N7   C11   single    1.369  0.020  1.369
 MMY  C8   C9    single    1.537  0.020  1.537
 MMY  C9   C10   single    1.497  0.020  1.497
 MMY  C10  C11   aromatic  1.403  0.020  1.403
 MMY  C10  C21   aromatic  1.378  0.020  1.378
 MMY  C11  N12   aromatic  1.312  0.020  1.312
 MMY  N12  C13   aromatic  1.345  0.020  1.345
 MMY  C13  N14   single    1.357  0.020  1.357
 MMY  C13  N20   aromatic  1.326  0.020  1.326
 MMY  N14  C15   single    1.449  0.020  1.449
 MMY  N14  C19   single    1.449  0.020  1.449
 MMY  C15  C16   single    1.518  0.020  1.518
 MMY  C16  O17   single    1.410  0.020  1.410
 MMY  O17  C18   single    1.410  0.020  1.410
 MMY  C18  C19   single    1.518  0.020  1.518
 MMY  N20  C21   aromatic  1.344  0.020  1.344
 MMY  C21  C22   single    1.466  0.020  1.466
 MMY  C22  C23   aromatic  1.397  0.020  1.397
 MMY  C22  C30   aromatic  1.393  0.020  1.393
 MMY  C23  N24   aromatic  1.316  0.020  1.316
 MMY  N24  C25   aromatic  1.342  0.020  1.342
 MMY  C25  N26   single    1.339  0.020  1.339
 MMY  C25  N29   aromatic  1.339  0.020  1.339
 MMY  N29  C30   aromatic  1.319  0.020  1.319
 MMY  C1   H1    single    0.930  0.020  1.080
 MMY  C2   H2    single    0.930  0.020  1.080
 MMY  C3   H3    single    0.930  0.020  1.080
 MMY  C5   H5    single    0.930  0.020  1.080
 MMY  C8   H8    single    0.970  0.020  1.090
 MMY  C8   H8A   single    0.970  0.020  1.090
 MMY  C9   H9    single    0.970  0.020  1.090
 MMY  C9   H9A   single    0.970  0.020  1.090
 MMY  C15  H15   single    0.970  0.020  1.090
 MMY  C15  H15A  single    0.970  0.020  1.090
 MMY  C16  H16   single    0.970  0.020  1.090
 MMY  C16  H16A  single    0.970  0.020  1.090
 MMY  C18  H18   single    0.970  0.020  1.090
 MMY  C18  H18A  single    0.970  0.020  1.090
 MMY  C19  H19   single    0.970  0.020  1.090
 MMY  C19  H19A  single    0.970  0.020  1.090
 MMY  C23  H23   single    0.930  0.020  1.080
 MMY  N26  HN26  single    0.860  0.020  1.020
 MMY  N26  HN2A  single    0.860  0.020  1.020
 MMY  C30  H30   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
 MMY  H1    C1   C6    120.97  3.000
 MMY  H1    C1   C2    120.16  3.000
 MMY  C6    C1   C2    118.87  3.000
 MMY  H2    C2   C3    120.36  3.000
 MMY  H2    C2   C1    120.13  3.000
 MMY  C3    C2   C1    119.51  3.000
 MMY  H3    C3   N4    116.99  3.000
 MMY  H3    C3   C2    120.84  3.000
 MMY  N4    C3   C2    122.17  3.000
 MMY  C5    N4   C3    118.73  3.000
 MMY  H5    C5   C6    120.59  3.000
 MMY  H5    C5   N4    115.62  3.000
 MMY  C6    C5   N4    123.80  3.000
 MMY  N7    C6   C5    119.69  3.000
 MMY  N7    C6   C1    123.37  3.000
 MMY  C5    C6   C1    116.91  3.000
 MMY  C11   N7   C8    109.81  3.000
 MMY  C11   N7   C6    127.65  3.000
 MMY  C8    N7   C6    121.71  3.000
 MMY  H8A   C8   H8    108.08  3.000
 MMY  H8A   C8   C9    110.99  3.000
 MMY  H8    C8   C9    112.31  3.000
 MMY  H8A   C8   N7    110.11  3.000
 MMY  H8    C8   N7    110.44  3.000
 MMY  C9    C8   N7    104.91  3.000
 MMY  H9A   C9   H9    107.36  3.000
 MMY  H9A   C9   C10   113.60  3.000
 MMY  H9    C9   C10   111.89  3.000
 MMY  H9A   C9   C8    111.08  3.000
 MMY  H9    C9   C8    110.31  3.000
 MMY  C10   C9   C8    102.62  3.000
 MMY  C21   C10  C11   115.51  3.000
 MMY  C21   C10  C9    135.23  3.000
 MMY  C11   C10  C9    109.26  3.000
 MMY  N12   C11  C10   124.87  3.000
 MMY  N12   C11  N7    124.58  3.000
 MMY  C10   C11  N7    110.53  3.000
 MMY  C13   N12  C11   114.88  3.000
 MMY  N20   C13  N14   117.80  3.000
 MMY  N20   C13  N12   125.50  3.000
 MMY  N14   C13  N12   116.69  3.000
 MMY  C19   N14  C15   113.79  3.000
 MMY  C19   N14  C13   122.53  3.000
 MMY  C15   N14  C13   121.99  3.000
 MMY  H15A  C15  H15   107.68  3.000
 MMY  H15A  C15  C16   109.53  3.000
 MMY  H15   C15  C16   109.92  3.000
 MMY  H15A  C15  N14   109.88  3.000
 MMY  H15   C15  N14   110.04  3.000
 MMY  C16   C15  N14   109.76  3.000
 MMY  H16A  C16  H16   107.94  3.000
 MMY  H16A  C16  O17   110.51  3.000
 MMY  H16   C16  O17   107.50  3.000
 MMY  H16A  C16  C15   109.24  3.000
 MMY  H16   C16  C15   109.65  3.000
 MMY  O17   C16  C15   111.90  3.000
 MMY  C18   O17  C16   110.87  3.000
 MMY  H18A  C18  H18   108.02  3.000
 MMY  H18A  C18  C19   109.13  3.000
 MMY  H18   C18  C19   109.70  3.000
 MMY  H18A  C18  O17   110.48  3.000
 MMY  H18   C18  O17   107.53  3.000
 MMY  C19   C18  O17   111.88  3.000
 MMY  H19A  C19  H19   107.62  3.000
 MMY  H19A  C19  C18   109.99  3.000
 MMY  H19   C19  C18   109.30  3.000
 MMY  H19A  C19  N14   110.14  3.000
 MMY  H19   C19  N14   110.09  3.000
 MMY  C18   C19  N14   109.67  3.000
 MMY  C21   N20  C13   118.58  3.000
 MMY  C22   C21  N20   115.40  3.000
 MMY  C22   C21  C10   123.92  3.000
 MMY  N20   C21  C10   120.66  3.000
 MMY  C30   C22  C23   114.37  3.000
 MMY  C30   C22  C21   124.56  3.000
 MMY  C23   C22  C21   121.06  3.000
 MMY  H23   C23  N24   116.60  3.000
 MMY  H23   C23  C22   119.79  3.000
 MMY  N24   C23  C22   123.61  3.000
 MMY  C25   N24  C23   116.64  3.000
 MMY  N29   C25  N26   117.52  3.000
 MMY  N29   C25  N24   125.09  3.000
 MMY  N26   C25  N24   117.39  3.000
 MMY  HN2A  N26  HN26  118.23  3.000
 MMY  HN2A  N26  C25   119.92  3.000
 MMY  HN26  N26  C25   119.96  3.000
 MMY  C30   N29  C25   116.79  3.000
 MMY  H30   C30  N29   115.36  3.000
 MMY  H30   C30  C22   121.13  3.000
 MMY  N29   C30  C22   123.48  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
 MMY  CONST_01  N4    C3   C2   C1      0.00   0.0  0
 MMY  CONST_02  N4    C5   C6   C1      0.00   0.0  0
 MMY  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 MMY  CONST_04  C5    N4   C3   C2      0.00   0.0  0
 MMY  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 MMY  CONST_06  C6    C5   N4   C3      0.00   0.0  0
 MMY  CONST_07  C13   N12  C11  C10     0.00   0.0  0
 MMY  CONST_08  C13   N20  C21  C10     0.00   0.0  0
 MMY  CONST_11  N20   C21  C10  C11     0.00   0.0  0
 MMY  CONST_12  C22   C21  C10  C11   180.00   0.0  0
 MMY  CONST_13  N20   C13  N12  C11     0.00   0.0  0
 MMY  CONST_14  C21   C10  C11  N12     0.00   0.0  0
 MMY  CONST_15  C21   N20  C13  N12     0.00   0.0  0
 MMY  CONST_16  C22   C21  N20  C13   180.00   0.0  0
 MMY  CONST_19  N24   C23  C22  C21   180.00   0.0  0
 MMY  CONST_20  N29   C30  C22  C21   180.00   0.0  0
 MMY  CONST_21  C25   N24  C23  C22     0.00   0.0  0
 MMY  CONST_22  C25   N29  C30  C22     0.00   0.0  0
 MMY  CONST_23  N29   C30  C22  C23     0.00   0.0  0
 MMY  CONST_24  N29   C25  N24  C23     0.00   0.0  0
 MMY  CONST_25  C30   C22  C23  N24     0.00   0.0  0
 MMY  CONST_26  C30   N29  C25  N24     0.00   0.0  0
 MMY  CONST_27  N7    C6   C1   C2    180.00   0.0  0
 MMY  CONST_28  N7    C6   C5   N4    180.00   0.0  0
 MMY  CONST_29  C22   C21  C10  C9      0.00   0.0  0
 MMY  CONST_30  N14   C13  N12  C11   180.00   0.0  0
 MMY  CONST_31  C21   N20  C13  N14   180.00   0.0  0
 MMY  CONST_32  N26   C25  N24  C23   180.00   0.0  0
 MMY  CONST_33  C30   N29  C25  N26   180.00   0.0  0
 MMY  CONST_34  H3    C3   C2   C1    180.00   0.0  0
 MMY  CONST_35  H5    C5   C6   C1    180.00   0.0  0
 MMY  CONST_36  H1    C1   C2   C3    180.00   0.0  0
 MMY  CONST_37  H2    C2   C3   N4    180.00   0.0  0
 MMY  CONST_38  H23   C23  C22  C21     0.00   0.0  0
 MMY  CONST_39  H30   C30  C22  C21     0.00   0.0  0
 MMY  CONST_40  HN26  N26  C25  N24     0.00   0.0  0
 MMY  CONST_41  HN2A  N26  C25  N24   180.00   0.0  0
 MMY  Var_01    C8    N7   C6   C1    166.98  30.0  2
 MMY  Var_02    C9    C8   N7   C6   -173.51  30.0  1
 MMY  Var_03    C10   C11  N7   C6   -178.76  30.0  1
 MMY  Var_04    C10   C9   C8   N7    -16.24  30.0  1
 MMY  Var_05    C11   C10  C9   C8     11.61  30.0  1
 MMY  Var_06    C15   N14  C13  N12   172.54  30.0  2
 MMY  Var_07    C16   C15  N14  C13   142.61  30.0  1
 MMY  Var_08    C18   C19  N14  C13  -142.63  30.0  1
 MMY  Var_09    O17   C16  C15  N14    54.44  30.0  1
 MMY  Var_10    O17   C18  C19  N14   -54.63  30.0  1
 MMY  Var_11    C19   C18  O17  C16    58.90  30.0  1

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
 MMY  plan-1  C1    0.020
 MMY  plan-1  C2    0.020
 MMY  plan-1  C3    0.020
 MMY  plan-1  N4    0.020
 MMY  plan-1  C5    0.020
 MMY  plan-1  C6    0.020
 MMY  plan-1  N7    0.020
 MMY  plan-1  H1    0.020
 MMY  plan-1  H2    0.020
 MMY  plan-1  H3    0.020
 MMY  plan-1  H5    0.020
 MMY  plan-2  N7    0.020
 MMY  plan-2  C9    0.020
 MMY  plan-2  C10   0.020
 MMY  plan-2  C11   0.020
 MMY  plan-2  N12   0.020
 MMY  plan-2  C13   0.020
 MMY  plan-2  N14   0.020
 MMY  plan-2  N20   0.020
 MMY  plan-2  C21   0.020
 MMY  plan-2  C22   0.020
 MMY  plan-3  C21   0.020
 MMY  plan-3  C22   0.020
 MMY  plan-3  C23   0.020
 MMY  plan-3  N24   0.020
 MMY  plan-3  C25   0.020
 MMY  plan-3  N26   0.020
 MMY  plan-3  N29   0.020
 MMY  plan-3  C30   0.020
 MMY  plan-3  H23   0.020
 MMY  plan-3  H30   0.020
 MMY  plan-4  C25   0.020
 MMY  plan-4  N26   0.020
 MMY  plan-4  HN26  0.020
 MMY  plan-4  HN2A  0.020

