# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:11:27 2022
#   Inital geometry file: a 106 line input string
#   Ligand name: 3-{(3R,4R)-4-methyl-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl}-3-oxopropanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CCN(C[C@@H]1N(C)c2ncnc3[nH]ccc23)C(=O)CC#N
#
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
 MI1  MI1  3-{(3R,4R)-4-methyl-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl}-3-oxopropanenitrile  ligand  43  23  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MI1
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
 MI1  C1    C  CH1   0  -0.053  -0.3405  -0.1731  -0.3168
 MI1  C2    C  CH2   0  -0.341  -1.5283   0.7074  -0.7159
 MI1  C4    C  CH2   0  -0.333  -2.9104  -1.2437  -1.1358
 MI1  C5    C  CH2   0  -0.431  -1.7468  -2.1769  -0.8296
 MI1  C6    C  CH1   0  -0.262  -0.3807  -1.5196  -1.0609
 MI1  N3    N  NT    0  -0.456  -2.7553  -0.0007  -0.3947
 MI1  O21   O  O     0  -0.481  -3.3320   1.4276   1.2636
 MI1  C20   C  C     0   0.585  -3.5464   0.4247   0.6023
 MI1  C22   C  CH2   0  -0.712  -4.7900  -0.4163   0.8833
 MI1  C23   C  CSP   0   0.148  -5.5792   0.1931   1.9380
 MI1  N24   N  NS    0  -0.262  -6.2319   0.6454   2.7689
 MI1  C7    C  CH3   0  -0.675  -0.0406  -1.3986  -2.5439
 MI1  N8    N  NT    0  -0.497   0.9432   0.5119  -0.4463
 MI1  C9    C  CH3   0  -0.567   1.1744   1.4789  -1.4992
 MI1  C10   C  CR6   0   0.514   1.9680   0.1331   0.3533
 MI1  C15   C  CR56  0  -0.079   3.2975   0.6174   0.2344
 MI1  C16   C  CR15  0  -0.440   4.0656   1.4940  -0.6046
 MI1  C11   C  CR15  0  -0.018   5.3403   1.4788  -0.1264
 MI1  N12   N  NR15  0  -0.656   5.4126   0.6438   0.9572
 MI1  C14   C  CR56  0   0.468   4.1954   0.1071   1.1927
 MI1  N17   N  N     0  -0.453   3.9168  -0.7656   2.1636
 MI1  C18   C  CR16  0   0.036   2.6568  -1.1430   2.1497
 MI1  N19   N  N     0  -0.500   1.6994  -0.7556   1.3173
 MI1  H1    H  HCH1  0   0.269  -0.4693  -0.3852   0.7451
 MI1  H2    H  HCH2  0   0.286  -1.5017   1.6602  -0.1926
 MI1  H2A   H  HCH2  0   0.254  -1.5516   0.9129  -1.7890
 MI1  H4    H  HCH2  0   0.259  -2.9547  -1.0035  -2.2017
 MI1  H4A   H  HCH2  0   0.284  -3.8537  -1.7242  -0.8916
 MI1  H5    H  HCH2  0   0.241  -1.8259  -2.5015   0.2120
 MI1  H5A   H  HCH2  0   0.246  -1.8355  -3.0727  -1.4483
 MI1  H6    H  HCH1  0   0.252   0.3723  -2.1645  -0.5998
 MI1  H22   H  HCH2  0   0.348  -5.4180  -0.5106  -0.0055
 MI1  H22A  H  HCH2  0   0.346  -4.5254  -1.4293   1.1957
 MI1  H7    H  HCH3  0   0.238   0.9879  -1.0692  -2.6922
 MI1  H7A   H  HCH3  0   0.241  -0.1389  -2.3693  -3.0319
 MI1  H7B   H  HCH3  0   0.221  -0.6885  -0.7022  -3.0797
 MI1  H9    H  HCH3  0   0.277   0.2394   1.7601  -1.9696
 MI1  H9A   H  HCH3  0   0.260   1.6068   2.3948  -1.0987
 MI1  H9B   H  HCH3  0   0.245   1.8287   1.0956  -2.2849
 MI1  H16   H  HCR5  0   0.258   3.7425   2.0623  -1.4584
 MI1  H11   H  HCR5  0   0.286   6.2138   2.0034  -0.4765
 MI1  H18   H  HCR6  0   0.242   2.3571  -1.8597   2.9081
 MI1  HN12  H  HNR5  0   0.412   6.2438   0.4526   1.4934

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
 MI1  C2   C1    single    1.531  0.020  1.531
 MI1  C1   C6    single    1.539  0.020  1.539
 MI1  C1   N8    single    1.461  0.020  1.461
 MI1  C1   H1    single    0.970  0.020  1.090
 MI1  N3   C2    single    1.453  0.020  1.453
 MI1  C2   H2    single    0.970  0.020  1.090
 MI1  C2   H2A   single    0.970  0.020  1.090
 MI1  N3   C4    single    1.455  0.020  1.455
 MI1  C4   C5    single    1.523  0.020  1.523
 MI1  C4   H4    single    0.970  0.020  1.090
 MI1  C4   H4A   single    0.970  0.020  1.090
 MI1  C5   C6    single    1.534  0.020  1.534
 MI1  C5   H5    single    0.970  0.020  1.090
 MI1  C5   H5A   single    0.970  0.020  1.090
 MI1  C7   C6    single    1.526  0.020  1.526
 MI1  C6   H6    single    0.970  0.020  1.090
 MI1  C20  N3    single    1.342  0.020  1.342
 MI1  O21  C20   double    1.220  0.020  1.220
 MI1  C22  C20   single    1.527  0.020  1.527
 MI1  C23  C22   single    1.451  0.020  1.451
 MI1  C22  H22   single    0.970  0.020  1.090
 MI1  C22  H22A  single    0.970  0.020  1.090
 MI1  N24  C23   triple    1.149  0.020  1.149
 MI1  C7   H7    single    0.970  0.020  1.090
 MI1  C7   H7A   single    0.970  0.020  1.090
 MI1  C7   H7B   single    0.970  0.020  1.090
 MI1  C9   N8    single    1.448  0.020  1.448
 MI1  N8   C10   single    1.354  0.020  1.354
 MI1  C9   H9    single    0.970  0.020  1.090
 MI1  C9   H9A   single    0.970  0.020  1.090
 MI1  C9   H9B   single    0.970  0.020  1.090
 MI1  C10  N19   aromatic  1.338  0.020  1.338
 MI1  C10  C15   aromatic  1.420  0.020  1.420
 MI1  C15  C16   aromatic  1.436  0.020  1.436
 MI1  C15  C14   aromatic  1.409  0.020  1.409
 MI1  C16  C11   aromatic  1.362  0.020  1.362
 MI1  C16  H16   single    0.930  0.020  1.080
 MI1  C11  N12   aromatic  1.370  0.020  1.370
 MI1  C11  H11   single    0.930  0.020  1.080
 MI1  C14  N12   aromatic  1.351  0.020  1.351
 MI1  C14  N17   aromatic  1.335  0.020  1.335
 MI1  C18  N17   aromatic  1.315  0.020  1.315
 MI1  N19  C18   aromatic  1.326  0.020  1.326
 MI1  C18  H18   single    0.930  0.020  1.080
 MI1  N12  HN12  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
 MI1  H1    C1   N8   106.34  3.000
 MI1  H1    C1   C6   107.31  3.000
 MI1  N8    C1   C6   112.98  3.000
 MI1  H1    C1   C2   105.90  3.000
 MI1  N8    C1   C2   112.88  3.000
 MI1  C6    C1   C2   110.90  3.000
 MI1  H2A   C2   H2   107.96  3.000
 MI1  H2A   C2   N3   106.90  3.000
 MI1  H2    C2   N3   109.96  3.000
 MI1  H2A   C2   C1   112.37  3.000
 MI1  H2    C2   C1   111.07  3.000
 MI1  N3    C2   C1   108.50  3.000
 MI1  H4A   C4   H4   106.33  3.000
 MI1  H4A   C4   N3   110.84  3.000
 MI1  H4    C4   N3   108.24  3.000
 MI1  H4A   C4   C5   110.32  3.000
 MI1  H4    C4   C5   111.20  3.000
 MI1  N3    C4   C5   109.85  3.000
 MI1  H5A   C5   H5   106.86  3.000
 MI1  H5A   C5   C6   109.78  3.000
 MI1  H5    C5   C6   109.59  3.000
 MI1  H5A   C5   C4   109.06  3.000
 MI1  H5    C5   C4   108.55  3.000
 MI1  C6    C5   C4   112.81  3.000
 MI1  H6    C6   C7   107.65  3.000
 MI1  H6    C6   C5   107.28  3.000
 MI1  C7    C6   C5   112.27  3.000
 MI1  H6    C6   C1   107.11  3.000
 MI1  C7    C6   C1   113.24  3.000
 MI1  C5    C6   C1   108.99  3.000
 MI1  C20   N3   C4   125.89  3.000
 MI1  C20   N3   C2   120.51  3.000
 MI1  C4    N3   C2   113.19  3.000
 MI1  C22   C20  O21  119.73  3.000
 MI1  C22   C20  N3   116.24  3.000
 MI1  O21   C20  N3   124.03  3.000
 MI1  H22A  C22  H22  106.97  3.000
 MI1  H22A  C22  C23  108.25  3.000
 MI1  H22   C22  C23  108.36  3.000
 MI1  H22A  C22  C20  111.46  3.000
 MI1  H22   C22  C20  111.47  3.000
 MI1  C23   C22  C20  110.20  3.000
 MI1  N24   C23  C22  180.00  3.000
 MI1  H7B   C7   H7A  107.13  3.000
 MI1  H7B   C7   H7   107.49  3.000
 MI1  H7A   C7   H7   107.04  3.000
 MI1  H7B   C7   C6   113.28  3.000
 MI1  H7A   C7   C6   110.12  3.000
 MI1  H7    C7   C6   111.49  3.000
 MI1  C10   N8   C9   119.69  3.000
 MI1  C10   N8   C1   118.79  3.000
 MI1  C9    N8   C1   121.19  3.000
 MI1  H9B   C9   H9A  108.78  3.000
 MI1  H9B   C9   H9   107.20  3.000
 MI1  H9A   C9   H9   106.50  3.000
 MI1  H9B   C9   N8   112.61  3.000
 MI1  H9A   C9   N8   110.95  3.000
 MI1  H9    C9   N8   110.55  3.000
 MI1  N19   C10  C15  118.34  3.000
 MI1  C15   C10  N8   124.32  3.000
 MI1  N19   C10  N8   117.34  3.000
 MI1  C14   C15  C16  106.12  3.000
 MI1  C14   C15  C10  114.60  3.000
 MI1  C16   C15  C10  139.28  3.000
 MI1  H16   C16  C11  124.47  3.000
 MI1  H16   C16  C15  128.74  3.000
 MI1  C11   C16  C15  106.78  3.000
 MI1  H11   C11  N12  120.74  3.000
 MI1  H11   C11  C16  129.75  3.000
 MI1  N12   C11  C16  109.51  3.000
 MI1  HN12  N12  C14  125.12  3.000
 MI1  HN12  N12  C11  125.46  3.000
 MI1  C14   N12  C11  109.42  3.000
 MI1  N17   C14  N12  125.07  3.000
 MI1  N17   C14  C15  126.76  3.000
 MI1  N12   C14  C15  108.17  3.000
 MI1  C18   N17  C14  112.32  3.000
 MI1  H18   C18  N19  115.59  3.000
 MI1  H18   C18  N17  116.51  3.000
 MI1  N19   C18  N17  127.90  3.000
 MI1  C18   N19  C10  120.07  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
 MI1  CONST_01  N17   C18  N19  C10     0.00   0.0  0
 MI1  CONST_02  C11   C16  C15  C10   180.00   0.0  0
 MI1  CONST_03  N12   C14  C15  C10   180.00   0.0  0
 MI1  CONST_04  N17   C14  C15  C10     0.00   0.0  0
 MI1  CONST_05  C18   N19  C10  C15     0.00   0.0  0
 MI1  CONST_06  N12   C11  C16  C15     0.00   0.0  0
 MI1  CONST_07  C11   N12  C14  C15     0.00   0.0  0
 MI1  CONST_08  C18   N17  C14  C15     0.00   0.0  0
 MI1  CONST_09  N19   C10  C15  C16   180.00   0.0  0
 MI1  CONST_10  N12   C14  C15  C16     0.00   0.0  0
 MI1  CONST_11  N17   C14  C15  C16   180.00   0.0  0
 MI1  CONST_12  C14   N12  C11  C16     0.00   0.0  0
 MI1  CONST_13  C14   C15  C16  C11     0.00   0.0  0
 MI1  CONST_14  N17   C14  N12  C11   180.00   0.0  0
 MI1  CONST_15  C18   N17  C14  N12   180.00   0.0  0
 MI1  CONST_16  N19   C10  C15  C14     0.00   0.0  0
 MI1  CONST_17  N19   C18  N17  C14     0.00   0.0  0
 MI1  CONST_18  C18   N19  C10  N8    180.00   0.0  0
 MI1  CONST_19  C16   C15  C10  N8      0.00   0.0  0
 MI1  CONST_20  C14   C15  C10  N8    180.00   0.0  0
 MI1  CONST_21  N19   C10  N8   C1      0.00   0.0  0
 MI1  CONST_22  C15   C10  N8   C1    180.00   0.0  0
 MI1  CONST_23  H18   C18  N19  C10   180.00   0.0  0
 MI1  CONST_24  H16   C16  C15  C10     0.00   0.0  0
 MI1  CONST_25  H11   C11  C16  C15   180.00   0.0  0
 MI1  CONST_26  HN12  N12  C14  C15   180.00   0.0  0
 MI1  CONST_27  O21   C20  N3   C2      0.00   0.0  0
 MI1  CONST_28  C22   C20  N3   C2    180.00   0.0  0
 MI1  CONST_29  O21   C20  N3   C4    180.00   0.0  0
 MI1  CONST_30  C22   C20  N3   C4      0.00   0.0  0
 MI1  CONST_31  N19   C10  N8   C9    180.00   0.0  0
 MI1  CONST_32  C15   C10  N8   C9      0.00   0.0  0
 MI1  Var_01    C4    N3   C2   C1    -62.64  30.0  1
 MI1  Var_02    C5    C4   N3   C2     59.72  30.0  1
 MI1  Var_03    N3    C4   C5   C6    -53.49  30.0  1
 MI1  Var_04    C23   C22  C20  N3   -177.33  30.0  2
 MI1  Var_05    H9    C9   N8   C1     13.21  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
 MI1  chir_01  C1  C2  C6  N8  negativ
 MI1  chir_02  C6  C1  C5  C7  negativ

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
 MI1  plan-1  N8    0.020
 MI1  plan-1  C10   0.020
 MI1  plan-1  C15   0.020
 MI1  plan-1  C16   0.020
 MI1  plan-1  C11   0.020
 MI1  plan-1  N12   0.020
 MI1  plan-1  C14   0.020
 MI1  plan-1  N17   0.020
 MI1  plan-1  C18   0.020
 MI1  plan-1  N19   0.020
 MI1  plan-1  H16   0.020
 MI1  plan-1  H11   0.020
 MI1  plan-1  H18   0.020
 MI1  plan-1  HN12  0.020
 MI1  plan-2  C1    0.020
 MI1  plan-2  N8    0.020
 MI1  plan-2  C9    0.020
 MI1  plan-2  C10   0.020
 MI1  plan-3  C2    0.020
 MI1  plan-3  C4    0.020
 MI1  plan-3  N3    0.020
 MI1  plan-3  O21   0.020
 MI1  plan-3  C20   0.020
 MI1  plan-3  C22   0.020

