# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 09:59:14 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 2-methyl-N-{2-[4-(methylsulfonyl)piperidin-1-yl]pyrimidin-4-yl}-1-(propan-2-yl)-1H-imidazo[4,5-c]pyridin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)n1c(C)nc2cnc(Nc3ccnc(n3)N4CCC(CC4)[S](C)(=O)=O)cc12
#
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
 4YW  4YW  2-methyl-N-{2-[4-(methylsulfonyl)piperidin-1-yl]pyrimidin-4-yl}-1-(propan-2-yl)-1H-imidazo[4,5-c]pyridin-6-amine  ligand  57  30  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4YW
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
 4YW  C4   C  CR56  0   0.041   3.0426   1.7539   0.4466
 4YW  C5   C  CR16  0  -0.135   1.7403   1.5030   0.8569
 4YW  C11  C  CH1   0  -0.140   6.3273   0.5105  -0.4788
 4YW  C7   C  CR6   0   0.458   2.1214  -0.7566   0.8331
 4YW  C8   C  CR16  0  -0.438   3.4416  -0.6362   0.4157
 4YW  C9   C  CR56  0   0.455   3.8998   0.6630   0.2404
 4YW  C12  C  CH3   0  -0.656   6.8527  -0.2914   0.7038
 4YW  C13  C  CH3   0  -0.652   6.1540  -0.3307  -1.7363
 4YW  N3   N  N     0  -0.477   3.7020   2.9307   0.1974
 4YW  C1   C  CH3   0  -0.778   5.9873   3.5278  -0.5113
 4YW  C2   C  CR5   0   0.434   4.9076   2.5764  -0.1467
 4YW  N6   N  N     0  -0.405   1.3041   0.2731   1.0604
 4YW  N10  N  NR5   0  -0.545   5.0916   1.2139  -0.1391
 4YW  N14  N  NH1   0  -0.757   1.6226  -2.0401   1.0895
 4YW  C15  C  CR6   0   0.539   0.4158  -2.5296   0.6964
 4YW  C16  C  CR16  0  -0.464   0.0078  -3.8064   1.1242
 4YW  C17  C  CR16  0  -0.021  -1.2250  -4.2130   0.6758
 4YW  N18  N  N     0  -0.497  -2.0173  -3.4752  -0.0984
 4YW  C19  C  CR6   0   0.623  -1.5298  -2.2844  -0.4525
 4YW  N20  N  N     0  -0.489  -0.3427  -1.7956  -0.0976
 4YW  N21  N  NT    0  -0.479  -2.2907  -1.5048  -1.2761
 4YW  C22  C  CH2   0  -0.329  -1.9832  -0.0963  -1.4317
 4YW  C23  C  CH2   0  -0.430  -2.7259   0.7405  -0.3926
 4YW  C24  C  CH1   0  -0.458  -4.2256   0.4559  -0.4876
 4YW  C25  C  CH2   0  -0.444  -4.5318  -1.0367  -0.4048
 4YW  C26  C  CH2   0  -0.325  -3.7015  -1.7840  -1.4482
 4YW  S27  S  S     0   1.215  -5.0670   1.3853   0.8091
 4YW  O28  O  OS    0  -0.688  -4.7017   0.8172   2.1098
 4YW  O29  O  OS    0  -0.688  -4.8004   2.8099   0.5927
 4YW  C30  C  CH3   0  -0.793  -6.8031   1.1027   0.5378
 4YW  H1   H  HCR6  0   0.258   1.0452   2.3157   1.0412
 4YW  H2   H  HCH1  0   0.279   7.0579   1.2892  -0.6951
 4YW  H3   H  HCR6  0   0.278   4.0473  -1.5150   0.2448
 4YW  H4   H  HCH3  0   0.248   7.8433  -0.6775   0.4657
 4YW  H5   H  HCH3  0   0.246   6.9374   0.3310   1.5942
 4YW  H6   H  HCH3  0   0.233   6.2194  -1.1455   0.9426
 4YW  H7   H  HCH3  0   0.233   5.4604  -1.1580  -1.5853
 4YW  H8   H  HCH3  0   0.245   5.7887   0.2746  -2.5658
 4YW  H9   H  HCH3  0   0.247   7.1149  -0.7548  -2.0261
 4YW  H10  H  HCH3  0   0.268   6.8443   3.4412   0.1585
 4YW  H11  H  HCH3  0   0.268   6.3459   3.3641  -1.5285
 4YW  H12  H  HCH3  0   0.278   5.6034   4.5424  -0.4444
 4YW  H13  H  HNH1  0   0.412   2.2668  -2.7046   1.4876
 4YW  H14  H  HCR6  0   0.271   0.6145  -4.4223   1.7724
 4YW  H15  H  HCR6  0   0.262  -1.6091  -5.1865   0.9625
 4YW  H16  H  HCH2  0   0.283  -0.9135   0.0621  -1.3380
 4YW  H17  H  HCH2  0   0.248  -2.2828   0.2076  -2.4385
 4YW  H18  H  HCH2  0   0.252  -2.3470   0.4861   0.6011
 4YW  H19  H  HCH2  0   0.265  -2.5229   1.7976  -0.5670
 4YW  H20  H  HCH1  0   0.306  -4.6177   0.8649  -1.4257
 4YW  H21  H  HCH2  0   0.253  -4.2904  -1.4211   0.5894
 4YW  H22  H  HCH2  0   0.265  -5.5896  -1.2306  -0.5904
 4YW  H23  H  HCH2  0   0.251  -3.9916  -1.4614  -2.4520
 4YW  H24  H  HCH2  0   0.276  -3.8824  -2.8523  -1.3813
 4YW  H25  H  HCH3  0   0.294  -7.0477   0.0582   0.7126
 4YW  H26  H  HCH3  0   0.315  -7.3358   1.7283   1.2529
 4YW  H27  H  HCH3  0   0.294  -7.0666   1.3943  -0.4764

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
 4YW  O29  S27  double    1.465  0.020  1.465
 4YW  C23  C22  single    1.527  0.020  1.527
 4YW  C23  C24  single    1.529  0.020  1.529
 4YW  C22  N21  single    1.450  0.020  1.450
 4YW  S27  C30  single    1.780  0.020  1.780
 4YW  S27  C24  single    1.804  0.020  1.804
 4YW  S27  O28  double    1.466  0.020  1.466
 4YW  C24  C25  single    1.526  0.020  1.526
 4YW  N18  C17  aromatic  1.331  0.020  1.331
 4YW  N18  C19  aromatic  1.335  0.020  1.335
 4YW  C17  C16  aromatic  1.373  0.020  1.373
 4YW  N21  C19  single    1.366  0.020  1.366
 4YW  N21  C26  single    1.449  0.020  1.449
 4YW  C19  N20  aromatic  1.332  0.020  1.332
 4YW  C16  C15  aromatic  1.407  0.020  1.407
 4YW  C25  C26  single    1.529  0.020  1.529
 4YW  N20  C15  aromatic  1.321  0.020  1.321
 4YW  C15  N14  single    1.360  0.020  1.360
 4YW  N14  C7   single    1.401  0.020  1.401
 4YW  C7   C8   aromatic  1.390  0.020  1.390
 4YW  C7   N6   aromatic  1.334  0.020  1.334
 4YW  C8   C9   aromatic  1.389  0.020  1.389
 4YW  C12  C11  single    1.522  0.020  1.522
 4YW  C11  C13  single    1.523  0.020  1.523
 4YW  C11  N10  single    1.462  0.020  1.462
 4YW  N6   C5   aromatic  1.321  0.020  1.321
 4YW  C9   N10  aromatic  1.367  0.020  1.367
 4YW  C9   C4   aromatic  1.403  0.020  1.403
 4YW  N10  C2   aromatic  1.375  0.020  1.375
 4YW  C5   C4   aromatic  1.388  0.020  1.388
 4YW  C4   N3   aromatic  1.372  0.020  1.372
 4YW  C2   N3   aromatic  1.303  0.020  1.303
 4YW  C2   C1   single    1.485  0.020  1.485
 4YW  C5   H1   single    0.930  0.020  1.080
 4YW  C11  H2   single    0.970  0.020  1.090
 4YW  C8   H3   single    0.930  0.020  1.080
 4YW  C12  H4   single    0.970  0.020  1.090
 4YW  C12  H5   single    0.970  0.020  1.090
 4YW  C12  H6   single    0.970  0.020  1.090
 4YW  C13  H7   single    0.970  0.020  1.090
 4YW  C13  H8   single    0.970  0.020  1.090
 4YW  C13  H9   single    0.970  0.020  1.090
 4YW  C1   H10  single    0.970  0.020  1.090
 4YW  C1   H11  single    0.970  0.020  1.090
 4YW  C1   H12  single    0.970  0.020  1.090
 4YW  N14  H13  single    0.860  0.020  1.020
 4YW  C16  H14  single    0.930  0.020  1.080
 4YW  C17  H15  single    0.930  0.020  1.080
 4YW  C22  H16  single    0.970  0.020  1.090
 4YW  C22  H17  single    0.970  0.020  1.090
 4YW  C23  H18  single    0.970  0.020  1.090
 4YW  C23  H19  single    0.970  0.020  1.090
 4YW  C24  H20  single    0.970  0.020  1.090
 4YW  C25  H21  single    0.970  0.020  1.090
 4YW  C25  H22  single    0.970  0.020  1.090
 4YW  C26  H23  single    0.970  0.020  1.090
 4YW  C26  H24  single    0.970  0.020  1.090
 4YW  C30  H25  single    0.970  0.020  1.090
 4YW  C30  H26  single    0.970  0.020  1.090
 4YW  C30  H27  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
 4YW  N3   C4   C9   110.29  3.000
 4YW  N3   C4   C5   131.28  3.000
 4YW  C9   C4   C5   118.43  3.000
 4YW  H1   C5   N6   117.36  3.000
 4YW  H1   C5   C4   121.05  3.000
 4YW  N6   C5   C4   121.58  3.000
 4YW  H2   C11  N10  105.60  3.000
 4YW  H2   C11  C13  107.89  3.000
 4YW  N10  C11  C13  111.19  3.000
 4YW  H2   C11  C12  107.41  3.000
 4YW  N10  C11  C12  111.39  3.000
 4YW  C13  C11  C12  112.94  3.000
 4YW  N14  C7   N6   117.25  3.000
 4YW  N6   C7   C8   124.49  3.000
 4YW  N14  C7   C8   118.20  3.000
 4YW  H3   C8   C9   123.76  3.000
 4YW  H3   C8   C7   120.62  3.000
 4YW  C9   C8   C7   115.61  3.000
 4YW  N10  C9   C8   134.41  3.000
 4YW  N10  C9   C4   105.08  3.000
 4YW  C8   C9   C4   120.49  3.000
 4YW  H6   C12  H5   108.28  3.000
 4YW  H6   C12  H4   107.36  3.000
 4YW  H5   C12  H4   108.08  3.000
 4YW  H6   C12  C11  112.49  3.000
 4YW  H5   C12  C11  111.15  3.000
 4YW  H4   C12  C11  109.31  3.000
 4YW  H9   C13  H8   108.02  3.000
 4YW  H9   C13  H7   107.61  3.000
 4YW  H8   C13  H7   108.28  3.000
 4YW  H9   C13  C11  109.53  3.000
 4YW  H8   C13  C11  111.09  3.000
 4YW  H7   C13  C11  112.17  3.000
 4YW  C2   N3   C4   105.04  3.000
 4YW  H12  C1   H11  108.28  3.000
 4YW  H12  C1   H10  108.29  3.000
 4YW  H11  C1   H10  107.59  3.000
 4YW  H12  C1   C2   109.04  3.000
 4YW  H11  C1   C2   111.83  3.000
 4YW  H10  C1   C2   111.69  3.000
 4YW  N10  C2   C1   122.63  3.000
 4YW  C1   C2   N3   124.30  3.000
 4YW  N10  C2   N3   113.07  3.000
 4YW  C7   N6   C5   119.35  3.000
 4YW  C2   N10  C9   106.52  3.000
 4YW  C2   N10  C11  126.06  3.000
 4YW  C9   N10  C11  127.42  3.000
 4YW  H13  N14  C15  116.36  3.000
 4YW  H13  N14  C7   116.68  3.000
 4YW  C15  N14  C7   126.36  3.000
 4YW  N20  C15  C16  121.37  3.000
 4YW  N20  C15  N14  118.89  3.000
 4YW  C16  C15  N14  119.73  3.000
 4YW  H14  C16  C17  122.08  3.000
 4YW  H14  C16  C15  122.46  3.000
 4YW  C17  C16  C15  115.45  3.000
 4YW  H15  C17  N18  116.12  3.000
 4YW  H15  C17  C16  119.81  3.000
 4YW  N18  C17  C16  124.06  3.000
 4YW  C19  N18  C17  115.57  3.000
 4YW  N21  C19  N20  116.60  3.000
 4YW  N20  C19  N18  125.62  3.000
 4YW  N21  C19  N18  117.77  3.000
 4YW  C19  N20  C15  117.91  3.000
 4YW  C26  N21  C22  112.40  3.000
 4YW  C26  N21  C19  120.28  3.000
 4YW  C22  N21  C19  120.07  3.000
 4YW  H17  C22  H16  108.00  3.000
 4YW  H17  C22  C23  109.93  3.000
 4YW  H16  C22  C23  109.92  3.000
 4YW  H17  C22  N21  108.10  3.000
 4YW  H16  C22  N21  109.97  3.000
 4YW  C23  C22  N21  110.86  3.000
 4YW  H19  C23  H18  107.84  3.000
 4YW  H19  C23  C24  110.67  3.000
 4YW  H18  C23  C24  110.67  3.000
 4YW  H19  C23  C22  109.38  3.000
 4YW  H18  C23  C22  108.80  3.000
 4YW  C24  C23  C22  109.44  3.000
 4YW  H20  C24  S27  104.84  3.000
 4YW  H20  C24  C25  109.86  3.000
 4YW  S27  C24  C25  111.80  3.000
 4YW  H20  C24  C23  109.54  3.000
 4YW  C25  C24  C23  112.05  3.000
 4YW  S27  C24  C23  108.48  3.000
 4YW  H22  C25  H21  107.84  3.000
 4YW  H22  C25  C26  108.87  3.000
 4YW  H21  C25  C26  109.21  3.000
 4YW  H22  C25  C24  111.04  3.000
 4YW  H21  C25  C24  110.44  3.000
 4YW  C26  C25  C24  109.40  3.000
 4YW  H24  C26  H23  107.62  3.000
 4YW  H24  C26  C25  110.40  3.000
 4YW  H23  C26  C25  109.78  3.000
 4YW  H24  C26  N21  110.16  3.000
 4YW  H23  C26  N21  108.09  3.000
 4YW  C25  C26  N21  110.71  3.000
 4YW  C30  S27  O29  108.02  3.000
 4YW  C30  S27  O28  108.48  3.000
 4YW  O29  S27  O28  117.55  3.000
 4YW  O28  S27  C24  108.78  3.000
 4YW  C30  S27  C24  105.29  3.000
 4YW  O29  S27  C24  108.05  3.000
 4YW  H27  C30  H26  109.86  3.000
 4YW  H27  C30  H25  110.68  3.000
 4YW  H26  C30  H25  109.65  3.000
 4YW  H27  C30  S27  109.62  3.000
 4YW  H26  C30  S27  106.61  3.000
 4YW  H25  C30  S27  110.34  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
 4YW  CONST_01  C7   C8   C9   C4      0.00   0.0  0
 4YW  CONST_02  C2   N10  C9   C4      0.00   0.0  0
 4YW  CONST_03  C7   N6   C5   C4      0.00   0.0  0
 4YW  CONST_04  N10  C2   N3   C4      0.00   0.0  0
 4YW  CONST_05  C8   C7   N6   C5      0.00   0.0  0
 4YW  CONST_06  C8   C9   C4   C5      0.00   0.0  0
 4YW  CONST_07  N10  C9   C4   C5    180.00   0.0  0
 4YW  CONST_08  C2   N3   C4   C5    180.00   0.0  0
 4YW  CONST_09  N10  C9   C8   C7    180.00   0.0  0
 4YW  CONST_10  C2   N10  C9   C8    180.00   0.0  0
 4YW  CONST_11  N3   C4   C9   C8    180.00   0.0  0
 4YW  CONST_12  N6   C7   C8   C9      0.00   0.0  0
 4YW  CONST_13  N3   C2   N10  C9      0.00   0.0  0
 4YW  CONST_14  N6   C5   C4   C9      0.00   0.0  0
 4YW  CONST_15  C2   N3   C4   C9      0.00   0.0  0
 4YW  CONST_16  N10  C9   C4   N3      0.00   0.0  0
 4YW  CONST_17  N6   C5   C4   N3    180.00   0.0  0
 4YW  CONST_18  N18  C17  C16  C15     0.00   0.0  0
 4YW  CONST_19  N18  C19  N20  C15     0.00   0.0  0
 4YW  CONST_20  C19  N18  C17  C16     0.00   0.0  0
 4YW  CONST_21  C19  N20  C15  C16     0.00   0.0  0
 4YW  CONST_22  N20  C19  N18  C17     0.00   0.0  0
 4YW  CONST_23  N20  C15  C16  C17     0.00   0.0  0
 4YW  CONST_24  N21  C19  N20  C15   180.00   0.0  0
 4YW  CONST_25  N21  C19  N18  C17   180.00   0.0  0
 4YW  CONST_26  C11  N10  C9   C4    180.00   0.0  0
 4YW  CONST_27  C1   C2   N3   C4    180.00   0.0  0
 4YW  CONST_28  N14  C7   N6   C5    180.00   0.0  0
 4YW  CONST_29  C8   C9   N10  C11     0.00   0.0  0
 4YW  CONST_30  N3   C2   N10  C11   180.00   0.0  0
 4YW  CONST_31  N14  C7   C8   C9    180.00   0.0  0
 4YW  CONST_32  C1   C2   N10  C9    180.00   0.0  0
 4YW  CONST_33  C17  C16  C15  N14   180.00   0.0  0
 4YW  CONST_34  C19  N20  C15  N14   180.00   0.0  0
 4YW  CONST_35  H3   C8   C9   C4    180.00   0.0  0
 4YW  CONST_36  H1   C5   N6   C7    180.00   0.0  0
 4YW  CONST_37  H15  C17  C16  C15   180.00   0.0  0
 4YW  CONST_38  H14  C16  C17  N18   180.00   0.0  0
 4YW  Var_01    C22  N21  C19  N18   164.87  30.0  1
 4YW  Var_02    C23  C22  N21  C19   -89.65  30.0  1
 4YW  Var_03    C25  C26  N21  C19    89.41  30.0  1
 4YW  Var_04    C24  C23  C22  N21   -55.39  30.0  1
 4YW  Var_05    C24  C25  C26  N21    55.86  30.0  1
 4YW  Var_06    C16  C15  N14  C7   -174.80  30.0  1
 4YW  Var_07    C15  N14  C7   C8   -135.58  30.0  1
 4YW  Var_08    C12  C11  N10  C9    -61.87  30.0  3
 4YW  Var_09    H10  C1   C2   N3    119.50  30.0  2
 4YW  Var_10    H4   C12  C11  N10  -171.56  30.0  3
 4YW  Var_11    H7   C13  C11  N10   -66.73  30.0  3
 4YW  Var_12    H25  C30  S27  C24    66.11  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
 4YW  chir_01  C24  C23  S27  C25  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
 4YW  plan-1  N14  0.020
 4YW  plan-1  C15  0.020
 4YW  plan-1  C16  0.020
 4YW  plan-1  C17  0.020
 4YW  plan-1  N18  0.020
 4YW  plan-1  C19  0.020
 4YW  plan-1  N20  0.020
 4YW  plan-1  N21  0.020
 4YW  plan-1  H14  0.020
 4YW  plan-1  H15  0.020
 4YW  plan-2  C4   0.020
 4YW  plan-2  C5   0.020
 4YW  plan-2  C11  0.020
 4YW  plan-2  C7   0.020
 4YW  plan-2  C8   0.020
 4YW  plan-2  C9   0.020
 4YW  plan-2  N3   0.020
 4YW  plan-2  C1   0.020
 4YW  plan-2  C2   0.020
 4YW  plan-2  N6   0.020
 4YW  plan-2  N10  0.020
 4YW  plan-2  N14  0.020
 4YW  plan-2  H1   0.020
 4YW  plan-2  H3   0.020

