# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 19:41:26 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: [(3R)-1-(5-methyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c[nH]c2ncnc(N3CCC[C@@H](CO)C3)c12
#
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
 A4G  A4G  '[(3R)-1-(5-methyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl]methanol'  ligand  36  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_A4G
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
 A4G  N3   N  N     0  -0.444  -3.3526   0.9724  -1.1477
 A4G  C4   C  CR56  0   0.474  -2.9576  -0.0144  -0.3421
 A4G  N2   N  N     0  -0.478  -1.0718   1.6308  -1.2131
 A4G  C7   C  CR16  0   0.033  -2.3543   1.7232  -1.5589
 A4G  C6   C  CR6   0   0.455  -0.6876   0.6797  -0.3628
 A4G  C9   C  CH2   0  -0.450   2.3140  -0.0632   1.6463
 A4G  C13  C  CH2   0  -0.132   3.0122  -0.5723  -1.3847
 A4G  C8   C  CH2   0  -0.311   0.9662   0.6000   1.4260
 A4G  C2   C  CR5   0  -0.053  -1.6665  -1.5024   0.8205
 A4G  C3   C  CR15  0  -0.055  -2.9725  -1.9008   0.8176
 A4G  N1   N  NR15  0  -0.660  -3.7476  -0.9984   0.1354
 A4G  C5   C  CR56  0  -0.078  -1.6401  -0.2613   0.0911
 A4G  N4   N  NT    0  -0.486   0.6298   0.6405   0.0065
 A4G  C10  C  CH2   0  -0.437   3.3885   0.6412   0.8251
 A4G  C11  C  CH1   0  -0.291   2.9834   0.7589  -0.6463
 A4G  C12  C  CH2   0  -0.304   1.6005   1.3991  -0.7649
 A4G  H1   H  HCR6  0   0.244  -2.6005   2.5244  -2.2486
 A4G  H2   H  HCH2  0   0.240   2.5607  -0.0219   2.7095
 A4G  H3   H  HCH2  0   0.229   2.2512  -1.1210   1.3788
 A4G  H4   H  HCH2  0   0.195   2.3025  -1.2725  -0.9270
 A4G  H5   H  HCH2  0   0.197   2.6688  -0.4073  -2.4156
 A4G  H6   H  HCH2  0   0.257   0.1805   0.0974   1.9822
 A4G  H7   H  HCH2  0   0.232   1.0078   1.6313   1.8070
 A4G  H8   H  HCH3  0   0.239  -0.2000  -1.9185   2.3622
 A4G  H9   H  HCH3  0   0.255  -0.8568  -3.3312   1.5580
 A4G  H10  H  HCH3  0   0.242   0.3187  -2.3155   0.7325
 A4G  H11  H  HCR5  0   0.287  -3.4103  -2.7901   1.2418
 A4G  H12  H  HNR5  0   0.411  -4.7332  -1.0927  -0.0481
 A4G  H13  H  HCH2  0   0.223   3.5358   1.6494   1.2266
 A4G  H14  H  HCH2  0   0.238   4.3471   0.1292   0.9220
 A4G  H15  H  HCH1  0   0.241   3.6836   1.4331  -1.1516
 A4G  H16  H  HCH2  0   0.253   1.2898   1.4271  -1.8084
 A4G  H17  H  HCH2  0   0.228   1.6499   2.4405  -0.4181
 A4G  H18  H  HOH1  0   0.452   4.3225  -1.9365  -1.8084
 A4G  C1   C  CH3   0  -0.774  -0.5438  -2.2996   1.3992
 A4G  O1   O  OH1   0  -0.674   4.3266  -1.0859  -1.3610

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
 A4G  O1   C13  single    1.411  0.020  1.411
 A4G  C13  C11  single    1.523  0.020  1.523
 A4G  C11  C10  single    1.531  0.020  1.531
 A4G  C11  C12  single    1.529  0.020  1.529
 A4G  C10  C9   single    1.525  0.020  1.525
 A4G  C12  N4   single    1.454  0.020  1.454
 A4G  C9   C8   single    1.518  0.020  1.518
 A4G  N4   C8   single    1.459  0.020  1.459
 A4G  N4   C6   single    1.369  0.020  1.369
 A4G  C1   C2   single    1.494  0.020  1.494
 A4G  C6   N2   aromatic  1.332  0.020  1.332
 A4G  C6   C5   aromatic  1.414  0.020  1.414
 A4G  C2   C5   aromatic  1.440  0.020  1.440
 A4G  C2   C3   aromatic  1.365  0.020  1.365
 A4G  N2   C7   aromatic  1.331  0.020  1.331
 A4G  C5   C4   aromatic  1.409  0.020  1.409
 A4G  C3   N1   aromatic  1.371  0.020  1.371
 A4G  C7   N3   aromatic  1.315  0.020  1.315
 A4G  C4   N3   aromatic  1.334  0.020  1.334
 A4G  C4   N1   aromatic  1.349  0.020  1.349
 A4G  C7   H1   single    0.930  0.020  1.080
 A4G  C9   H2   single    0.970  0.020  1.090
 A4G  C9   H3   single    0.970  0.020  1.090
 A4G  C13  H4   single    0.970  0.020  1.090
 A4G  C13  H5   single    0.970  0.020  1.090
 A4G  C8   H6   single    0.970  0.020  1.090
 A4G  C8   H7   single    0.970  0.020  1.090
 A4G  C1   H8   single    0.970  0.020  1.090
 A4G  C1   H9   single    0.970  0.020  1.090
 A4G  C1   H10  single    0.970  0.020  1.090
 A4G  C3   H11  single    0.930  0.020  1.080
 A4G  N1   H12  single    0.860  0.020  1.020
 A4G  C10  H13  single    0.970  0.020  1.090
 A4G  C10  H14  single    0.970  0.020  1.090
 A4G  C11  H15  single    0.970  0.020  1.090
 A4G  C12  H16  single    0.970  0.020  1.090
 A4G  C12  H17  single    0.970  0.020  1.090
 A4G  O1   H18  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
 A4G  C7   N3   C4   112.73  3.000
 A4G  C5   C4   N1   108.12  3.000
 A4G  N1   C4   N3   125.45  3.000
 A4G  C5   C4   N3   126.33  3.000
 A4G  C6   N2   C7   119.54  3.000
 A4G  H1   C7   N2   115.77  3.000
 A4G  H1   C7   N3   116.61  3.000
 A4G  N2   C7   N3   127.62  3.000
 A4G  N4   C6   C5   122.87  3.000
 A4G  C5   C6   N2   119.06  3.000
 A4G  N4   C6   N2   118.05  3.000
 A4G  H3   C9   H2   106.73  3.000
 A4G  H3   C9   C10  110.84  3.000
 A4G  H2   C9   C10  110.35  3.000
 A4G  H3   C9   C8   109.64  3.000
 A4G  H2   C9   C8   108.98  3.000
 A4G  C10  C9   C8   110.22  3.000
 A4G  H5   C13  H4   106.56  3.000
 A4G  H5   C13  O1   111.18  3.000
 A4G  H4   C13  O1   111.30  3.000
 A4G  H5   C13  C11  108.53  3.000
 A4G  H4   C13  C11  110.09  3.000
 A4G  O1   C13  C11  109.13  3.000
 A4G  H7   C8   H6   106.49  3.000
 A4G  H7   C8   N4   108.64  3.000
 A4G  H6   C8   N4   110.14  3.000
 A4G  H7   C8   C9   109.00  3.000
 A4G  H6   C8   C9   111.46  3.000
 A4G  N4   C8   C9   110.97  3.000
 A4G  C5   C2   C3   105.54  3.000
 A4G  C3   C2   C1   124.34  3.000
 A4G  C5   C2   C1   129.98  3.000
 A4G  H11  C3   N1   120.59  3.000
 A4G  H11  C3   C2   128.92  3.000
 A4G  N1   C3   C2   110.47  3.000
 A4G  H12  N1   C3   125.62  3.000
 A4G  H12  N1   C4   125.23  3.000
 A4G  C3   N1   C4   108.96  3.000
 A4G  C2   C5   C6   138.49  3.000
 A4G  C2   C5   C4   106.84  3.000
 A4G  C6   C5   C4   114.50  3.000
 A4G  C12  N4   C8   112.13  3.000
 A4G  C8   N4   C6   119.02  3.000
 A4G  C12  N4   C6   118.98  3.000
 A4G  H14  C10  H13  106.34  3.000
 A4G  H14  C10  C11  110.73  3.000
 A4G  H13  C10  C11  108.50  3.000
 A4G  H14  C10  C9   110.76  3.000
 A4G  H13  C10  C9   108.82  3.000
 A4G  C11  C10  C9   111.52  3.000
 A4G  H15  C11  C12  106.54  3.000
 A4G  H15  C11  C10  108.76  3.000
 A4G  C12  C11  C10  110.26  3.000
 A4G  H15  C11  C13  107.59  3.000
 A4G  C12  C11  C13  110.22  3.000
 A4G  C10  C11  C13  113.20  3.000
 A4G  H17  C12  H16  106.91  3.000
 A4G  H17  C12  C11  109.38  3.000
 A4G  H16  C12  C11  110.08  3.000
 A4G  H17  C12  N4   110.93  3.000
 A4G  H16  C12  N4   109.35  3.000
 A4G  C11  C12  N4   110.15  3.000
 A4G  H10  C1   H9   107.61  3.000
 A4G  H10  C1   H8   107.19  3.000
 A4G  H9   C1   H8   107.01  3.000
 A4G  H10  C1   C2   111.44  3.000
 A4G  H9   C1   C2   110.23  3.000
 A4G  H8   C1   C2   113.10  3.000
 A4G  H18  O1   C13  108.07  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
 A4G  CONST_01  C6   N2   C7  N3     0.00   0.0  0
 A4G  CONST_02  C6   C5   C4  N3     0.00   0.0  0
 A4G  CONST_03  C2   C5   C4  N3   180.00   0.0  0
 A4G  CONST_04  C3   N1   C4  N3   180.00   0.0  0
 A4G  CONST_05  N2   C6   C5  C4     0.00   0.0  0
 A4G  CONST_06  C3   C2   C5  C4     0.00   0.0  0
 A4G  CONST_07  N2   C7   N3  C4     0.00   0.0  0
 A4G  CONST_08  C2   C3   N1  C4     0.00   0.0  0
 A4G  CONST_09  C2   C5   C6  N2   180.00   0.0  0
 A4G  CONST_10  C5   C6   N2  C7     0.00   0.0  0
 A4G  CONST_11  C5   C4   N3  C7     0.00   0.0  0
 A4G  CONST_12  N1   C4   N3  C7   180.00   0.0  0
 A4G  CONST_13  C3   C2   C5  C6   180.00   0.0  0
 A4G  CONST_14  N1   C4   C5  C6   180.00   0.0  0
 A4G  CONST_15  N1   C4   C5  C2     0.00   0.0  0
 A4G  CONST_16  C5   C4   N1  C3     0.00   0.0  0
 A4G  CONST_17  C5   C2   C3  N1     0.00   0.0  0
 A4G  CONST_18  N4   C6   C5  C4   180.00   0.0  0
 A4G  CONST_19  N4   C6   N2  C7   180.00   0.0  0
 A4G  CONST_20  N4   C6   C5  C2     0.00   0.0  0
 A4G  CONST_21  C1   C2   C5  C4   180.00   0.0  0
 A4G  CONST_22  C1   C2   C5  C6     0.00   0.0  0
 A4G  CONST_23  N1   C3   C2  C1   180.00   0.0  0
 A4G  CONST_24  H12  N1   C4  N3     0.00   0.0  0
 A4G  CONST_25  H1   C7   N3  C4   180.00   0.0  0
 A4G  CONST_26  H11  C3   N1  C4   180.00   0.0  0
 A4G  Var_01    C12  N4   C6  N2   -14.75  30.0  3
 A4G  Var_02    C11  C12  N4  C6  -153.80  30.0  1
 A4G  Var_03    C9   C8   N4  C6   153.78  30.0  1
 A4G  Var_04    C11  C10  C9  C8   -52.22  30.0  1
 A4G  Var_05    C10  C9   C8  N4    55.37  30.0  1
 A4G  Var_06    H8   C1   C2  C3  -104.00  30.0  2

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
 A4G  chir_01  C11  C13  C10  C12  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
 A4G  plan-1  N3   0.020
 A4G  plan-1  C4   0.020
 A4G  plan-1  N2   0.020
 A4G  plan-1  C7   0.020
 A4G  plan-1  C6   0.020
 A4G  plan-1  C2   0.020
 A4G  plan-1  C3   0.020
 A4G  plan-1  N1   0.020
 A4G  plan-1  C5   0.020
 A4G  plan-1  N4   0.020
 A4G  plan-1  H1   0.020
 A4G  plan-1  H11  0.020
 A4G  plan-1  H12  0.020
 A4G  plan-1  C1   0.020

