# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 03:09:40 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: N-[2-(1,3-benzodioxol-5-yl)ethyl]-1-[2-(1H-imidazol-1-yl)-6-methylpyrimidin-4-yl]-D-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(nc(n1)n2ccnc2)N3CCC[C@@H]3C(=O)NCCc4ccc5OCOc5c4
#
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
 228  228  N-[2-(1,3-benzodioxol-5-yl)ethyl]-1-[2-(1H-imidazol-1-yl)-6-methylpyrimidin-4-yl]-D-prolinamide  ligand  55  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_228
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
 228  C28   C  CR16  0  -0.390  -3.8921   2.2873  -0.9025
 228  C27   C  CR56  0   0.312  -5.0664   2.4170  -1.6001
 228  O31   O  O     0  -0.488  -6.2814   2.8134  -1.1454
 228  C30   C  CH2   0   0.069  -7.1906   2.5992  -2.2165
 228  O29   O  O     0  -0.487  -6.4124   2.4036  -3.3887
 228  C26   C  CR56  0   0.283  -5.1456   2.1681  -2.9611
 228  C25   C  CR16  0  -0.330  -4.0477   1.7789  -3.6859
 228  C24   C  CR16  0  -0.323  -2.8433   1.6432  -2.9837
 228  C23   C  CR6   0   0.111  -2.7507   1.8902  -1.6199
 228  C22   C  CH2   0  -0.524  -1.4500   1.6847  -0.8954
 228  C21   C  CH2   0  -0.278  -1.3653   0.2767  -0.2983
 228  N20   N  NH1   0  -0.638  -0.1258   0.0306   0.4030
 228  C18   C  C     0   0.582   1.0112  -0.3116  -0.2198
 228  O19   O  O     0  -0.489   1.1009  -0.4566  -1.4287
 228  C17   C  CH1   0  -0.223   2.1880  -0.5926   0.7109
 228  C16   C  CH2   0  -0.469   2.3263  -2.0956   0.9917
 228  C15   C  CH2   0  -0.474   3.2478  -2.5921  -0.1172
 228  C14   C  CH2   0  -0.274   4.2207  -1.4361  -0.3167
 228  N13   N  NT    0  -0.492   3.4419  -0.2681   0.0662
 228  C1    C  CR6   0   0.601   3.7817   0.9930  -0.2160
 228  N1    N  N     0  -0.513   2.9092   1.9452   0.1354
 228  C6    C  CR16  0  -0.461   4.9959   1.3390  -0.8449
 228  C5    C  CR6   0   0.294   5.2243   2.6749  -1.0836
 228  C12   C  CH3   0  -0.720   6.4778   3.1517  -1.7405
 228  N4    N  N     0  -0.498   4.3379   3.6214  -0.7305
 228  C3    C  CR6   0   0.627   3.2480   3.1824  -0.1435
 228  N7    N  NR5   0  -0.526   2.3157   4.1585   0.2398
 228  C8    C  CR15  0  -0.084   1.1158   3.9366   0.8734
 228  C9    C  CR15  0  -0.216   0.5658   5.1676   1.0416
 228  NFE   N  N     0  -0.447   1.3933   6.1372   0.5302
 228  C11   C  CR15  0   0.111   2.4279   5.5044   0.0598
 228  H28   H  HCR6  0   0.265  -3.8413   2.4899   0.1603
 228  H301  H  HCH2  0   0.245  -7.8298   3.4732  -2.3389
 228  H302  H  HCH2  0   0.231  -7.7952   1.7072  -2.0174
 228  H25   H  HCR6  0   0.271  -4.1023   1.5935  -4.7501
 228  H24   H  HCR6  0   0.249  -1.9564   1.3374  -3.5251
 228  H221  H  HCH2  0   0.243  -1.3430   2.4217  -0.0963
 228  H222  H  HCH2  0   0.254  -0.6139   1.8311  -1.5816
 228  H211  H  HCH2  0   0.257  -2.1802   0.1236   0.4097
 228  H212  H  HCH2  0   0.246  -1.4826  -0.4654  -1.0891
 228  HN20  H  HNH1  0   0.402  -0.1063   0.1931   1.3965
 228  H17   H  HCH1  0   0.283   2.0718  -0.0273   1.6390
 228  H161  H  HCH2  0   0.264   1.3647  -2.6077   1.0166
 228  H162  H  HCH2  0   0.260   2.7935  -2.2328   1.9683
 228  H151  H  HCH2  0   0.258   3.7611  -3.5158   0.1452
 228  H152  H  HCH2  0   0.247   2.6853  -2.7719  -1.0335
 228  H141  H  HCH2  0   0.245   5.1022  -1.5356   0.3238
 228  H142  H  HCH2  0   0.255   4.5647  -1.3598  -1.3494
 228  H6    H  HCR6  0   0.279   5.7256   0.5948  -1.1276
 228  H121  H  HCH3  0   0.259   7.0586   3.7606  -1.0460
 228  H122  H  HCH3  0   0.249   7.1001   2.3245  -2.0752
 228  H123  H  HCH3  0   0.257   6.2412   3.7804  -2.5993
 228  H8    H  HCR5  0   0.288   0.7819   2.9480   1.1317
 228  H9    H  HCR5  0   0.259  -0.3791   5.4099   1.5022
 228  H11   H  HCR5  0   0.291   3.2859   5.9480  -0.4183

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
 228  C28  C23   aromatic  1.405  0.020  1.405
 228  C28  C27   aromatic  1.372  0.020  1.372
 228  C28  H28   single    0.930  0.020  1.080
 228  C27  O31   single    1.357  0.020  1.357
 228  C27  C26   aromatic  1.386  0.020  1.386
 228  O31  C30   single    1.421  0.020  1.421
 228  C30  O29   single    1.421  0.020  1.421
 228  C30  H301  single    0.970  0.020  1.090
 228  C30  H302  single    0.970  0.020  1.090
 228  O29  C26   single    1.358  0.020  1.358
 228  C26  C25   aromatic  1.372  0.020  1.372
 228  C25  C24   aromatic  1.401  0.020  1.401
 228  C25  H25   single    0.930  0.020  1.080
 228  C24  C23   aromatic  1.389  0.020  1.389
 228  C24  H24   single    0.930  0.020  1.080
 228  C23  C22   single    1.503  0.020  1.503
 228  C22  C21   single    1.532  0.020  1.532
 228  C22  H221  single    0.970  0.020  1.090
 228  C22  H222  single    0.970  0.020  1.090
 228  C21  N20   single    1.445  0.020  1.445
 228  C21  H211  single    0.970  0.020  1.090
 228  C21  H212  single    0.970  0.020  1.090
 228  N20  C18   single    1.341  0.020  1.341
 228  N20  HN20  single    0.860  0.020  1.020
 228  C18  O19   double    1.221  0.020  1.221
 228  C18  C17   single    1.526  0.020  1.526
 228  C17  C16   single    1.535  0.020  1.535
 228  C17  N13   single    1.447  0.020  1.447
 228  C17  H17   single    0.970  0.020  1.090
 228  C16  C15   single    1.525  0.020  1.525
 228  C16  H161  single    0.970  0.020  1.090
 228  C16  H162  single    0.970  0.020  1.090
 228  C15  C14   single    1.524  0.020  1.524
 228  C15  H151  single    0.970  0.020  1.090
 228  C15  H152  single    0.970  0.020  1.090
 228  C14  N13   single    1.455  0.020  1.455
 228  C14  H141  single    0.970  0.020  1.090
 228  C14  H142  single    0.970  0.020  1.090
 228  N13  C1    single    1.336  0.020  1.336
 228  C1   C6    aromatic  1.410  0.020  1.410
 228  C1   N1    aromatic  1.338  0.020  1.338
 228  N1   C3    aromatic  1.313  0.020  1.313
 228  C6   C5    aromatic  1.376  0.020  1.376
 228  C6   H6    single    0.930  0.020  1.080
 228  C5   C12   single    1.493  0.020  1.493
 228  C5   N4    aromatic  1.344  0.020  1.344
 228  C12  H121  single    0.970  0.020  1.090
 228  C12  H122  single    0.970  0.020  1.090
 228  C12  H123  single    0.970  0.020  1.090
 228  N4   C3    aromatic  1.313  0.020  1.313
 228  C3   N7    single    1.403  0.020  1.403
 228  N7   C8    aromatic  1.375  0.020  1.375
 228  N7   C11   aromatic  1.363  0.020  1.363
 228  C8   C9    aromatic  1.359  0.020  1.359
 228  C8   H8    single    0.930  0.020  1.080
 228  C9   NFE   aromatic  1.373  0.020  1.373
 228  C9   H9    single    0.930  0.020  1.080
 228  NFE  C11   aromatic  1.301  0.020  1.301
 228  C11  H11   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
 228  H28   C28  C23   121.04  3.000
 228  H28   C28  C27   121.42  3.000
 228  C23   C28  C27   117.54  3.000
 228  C26   C27  O31   109.30  3.000
 228  C26   C27  C28   122.09  3.000
 228  O31   C27  C28   128.60  3.000
 228  C30   O31  C27   106.04  3.000
 228  H302  C30  H301  110.46  3.000
 228  H302  C30  O29   109.88  3.000
 228  H301  C30  O29   109.82  3.000
 228  H302  C30  O31   109.80  3.000
 228  H301  C30  O31   109.82  3.000
 228  O29   C30  O31   106.99  3.000
 228  C26   O29  C30   105.97  3.000
 228  C25   C26  O29   129.02  3.000
 228  C25   C26  C27   121.60  3.000
 228  O29   C26  C27   109.36  3.000
 228  H25   C25  C24   121.33  3.000
 228  H25   C25  C26   121.87  3.000
 228  C24   C25  C26   116.79  3.000
 228  H24   C24  C23   119.10  3.000
 228  H24   C24  C25   118.74  3.000
 228  C23   C24  C25   122.16  3.000
 228  C22   C23  C24   120.44  3.000
 228  C22   C23  C28   119.69  3.000
 228  C24   C23  C28   119.82  3.000
 228  H222  C22  H221  107.12  3.000
 228  H222  C22  C21   109.03  3.000
 228  H221  C22  C21   109.25  3.000
 228  H222  C22  C23   109.96  3.000
 228  H221  C22  C23   110.19  3.000
 228  C21   C22  C23   111.19  3.000
 228  H212  C21  H211  107.15  3.000
 228  H212  C21  N20   109.16  3.000
 228  H211  C21  N20   107.58  3.000
 228  H212  C21  C22   109.68  3.000
 228  H211  C21  C22   109.93  3.000
 228  N20   C21  C22   113.15  3.000
 228  HN20  N20  C18   118.89  3.000
 228  HN20  N20  C21   117.90  3.000
 228  C18   N20  C21   123.05  3.000
 228  C17   C18  O19   121.68  3.000
 228  C17   C18  N20   114.68  3.000
 228  O19   C18  N20   123.55  3.000
 228  H17   C17  N13   110.77  3.000
 228  H17   C17  C16   111.14  3.000
 228  N13   C17  C16   102.89  3.000
 228  H17   C17  C18   109.92  3.000
 228  N13   C17  C18   110.80  3.000
 228  C16   C17  C18   111.17  3.000
 228  H162  C16  H161  107.35  3.000
 228  H162  C16  C15   110.56  3.000
 228  H161  C16  C15   113.38  3.000
 228  H162  C16  C17   108.98  3.000
 228  H161  C16  C17   112.63  3.000
 228  C15   C16  C17   103.90  3.000
 228  H152  C15  H151  107.81  3.000
 228  H152  C15  C14   110.15  3.000
 228  H151  C15  C14   111.97  3.000
 228  H152  C15  C16   110.68  3.000
 228  H151  C15  C16   112.70  3.000
 228  C14   C15  C16   103.53  3.000
 228  H142  C14  H141  107.84  3.000
 228  H142  C14  N13   111.20  3.000
 228  H141  C14  N13   110.50  3.000
 228  H142  C14  C15   112.22  3.000
 228  H141  C14  C15   111.63  3.000
 228  N13   C14  C15   103.46  3.000
 228  C1    N13  C14   124.46  3.000
 228  C1    N13  C17   121.75  3.000
 228  C14   N13  C17   113.64  3.000
 228  C6    C1   N1    120.25  3.000
 228  N1    C1   N13   116.75  3.000
 228  C6    C1   N13   123.00  3.000
 228  C3    N1   C1    116.52  3.000
 228  H6    C6   C5    120.76  3.000
 228  H6    C6   C1    121.96  3.000
 228  C5    C6   C1    117.28  3.000
 228  N4    C5   C12   116.38  3.000
 228  N4    C5   C6    121.91  3.000
 228  C12   C5   C6    121.71  3.000
 228  H123  C12  H122  108.68  3.000
 228  H123  C12  H121  107.17  3.000
 228  H122  C12  H121  108.40  3.000
 228  H123  C12  C5    110.39  3.000
 228  H122  C12  C5    111.88  3.000
 228  H121  C12  C5    110.18  3.000
 228  C3    N4   C5    115.43  3.000
 228  N7    C3   N4    116.17  3.000
 228  N7    C3   N1    115.22  3.000
 228  N4    C3   N1    128.61  3.000
 228  C11   N7   C8    106.99  3.000
 228  C11   N7   C3    126.61  3.000
 228  C8    N7   C3    126.40  3.000
 228  H8    C8   C9    132.67  3.000
 228  H8    C8   N7    122.02  3.000
 228  C9    C8   N7    105.31  3.000
 228  H9    C9   NFE   121.88  3.000
 228  H9    C9   C8    127.66  3.000
 228  NFE   C9   C8    110.47  3.000
 228  C11   NFE  C9    105.69  3.000
 228  H11   C11  NFE   126.40  3.000
 228  H11   C11  N7    122.05  3.000
 228  NFE   C11  N7    111.54  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
 228  CONST_01  C25   C24  C23  C28     0.00   0.0  0
 228  CONST_02  C25   C26  C27  C28     0.00   0.0  0
 228  CONST_03  C24   C23  C28  C27     0.00   0.0  0
 228  CONST_04  C24   C25  C26  C27     0.00   0.0  0
 228  CONST_05  C23   C28  C27  C26     0.00   0.0  0
 228  CONST_06  C23   C24  C25  C26     0.00   0.0  0
 228  CONST_07  N4    C5   C6   C1      0.00   0.0  0
 228  CONST_08  N4    C3   N1   C1      0.00   0.0  0
 228  CONST_09  N7    C3   N1   C1    180.00   0.0  0
 228  CONST_10  C5    C6   C1   N1      0.00   0.0  0
 228  CONST_11  C5    N4   C3   N1      0.00   0.0  0
 228  CONST_12  C8    N7   C3   N1      0.00   0.0  0
 228  CONST_13  C11   N7   C3   N1    180.00   0.0  0
 228  CONST_14  C3    N1   C1   C6      0.00   0.0  0
 228  CONST_15  C3    N4   C5   C6      0.00   0.0  0
 228  CONST_16  N7    C3   N4   C5    180.00   0.0  0
 228  CONST_17  C8    N7   C3   N4    180.00   0.0  0
 228  CONST_18  C11   N7   C3   N4      0.00   0.0  0
 228  CONST_19  C9    C8   N7   C3    180.00   0.0  0
 228  CONST_20  NFE   C11  N7   C3    180.00   0.0  0
 228  CONST_21  NFE   C9   C8   N7      0.00   0.0  0
 228  CONST_22  C9    NFE  C11  N7      0.00   0.0  0
 228  CONST_23  NFE   C11  N7   C8      0.00   0.0  0
 228  CONST_24  C11   NFE  C9   C8      0.00   0.0  0
 228  CONST_25  C11   N7   C8   C9      0.00   0.0  0
 228  CONST_26  C5    C6   C1   N13   180.00   0.0  0
 228  CONST_27  C3    N1   C1   N13   180.00   0.0  0
 228  CONST_28  C22   C23  C28  C27   180.00   0.0  0
 228  CONST_29  C22   C23  C24  C25   180.00   0.0  0
 228  CONST_30  C12   C5   C6   C1    180.00   0.0  0
 228  CONST_31  C3    N4   C5   C12   180.00   0.0  0
 228  CONST_32  H24   C24  C23  C28   180.00   0.0  0
 228  CONST_33  H25   C25  C26  C27   180.00   0.0  0
 228  CONST_34  H28   C28  C27  O31     0.00   0.0  0
 228  CONST_35  H6    C6   C1   N13     0.00   0.0  0
 228  CONST_36  H8    C8   N7   C3      0.00   0.0  0
 228  CONST_37  H11   C11  N7   C3      0.00   0.0  0
 228  CONST_38  H9    C9   C8   N7    180.00   0.0  0
 228  CONST_39  C17   C18  N20  C21   180.00   0.0  0
 228  CONST_40  HN20  N20  C18  C17     0.00   0.0  0
 228  CONST_41  O19   C18  N20  C21     0.00   0.0  0
 228  Var_01    O29   C30  O31  C27   -14.89  30.0  1
 228  Var_02    C26   C27  O31  C30     9.31  30.0  1
 228  Var_03    C25   C26  O29  C30   172.27  30.0  1
 228  Var_04    C14   C15  C16  C17    35.82  30.0  1
 228  Var_05    C15   C14  N13  C17    10.82  30.0  1
 228  Var_06    C6    C1   N13  C17  -179.93  30.0  2
 228  Var_07    N13   C14  C15  C16   -28.55  30.0  1
 228  Var_08    C21   C22  C23  C28    84.80  30.0  2
 228  Var_09    H121  C12  C5   C6   -115.07  30.0  2
 228  Var_10    N20   C21  C22  C23   179.67  30.0  3
 228  Var_11    C18   N20  C21  C22   -81.50  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
 228  chir_01  C17  C18  C16  N13  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
 228  plan-1  C3    0.020
 228  plan-1  N7    0.020
 228  plan-1  C8    0.020
 228  plan-1  C9    0.020
 228  plan-1  NFE   0.020
 228  plan-1  C11   0.020
 228  plan-1  H8    0.020
 228  plan-1  H9    0.020
 228  plan-1  H11   0.020
 228  plan-2  C28   0.020
 228  plan-2  C27   0.020
 228  plan-2  O31   0.020
 228  plan-2  O29   0.020
 228  plan-2  C26   0.020
 228  plan-2  C25   0.020
 228  plan-2  C24   0.020
 228  plan-2  C23   0.020
 228  plan-2  C22   0.020
 228  plan-2  H28   0.020
 228  plan-2  H25   0.020
 228  plan-2  H24   0.020
 228  plan-3  N13   0.020
 228  plan-3  C1    0.020
 228  plan-3  N1    0.020
 228  plan-3  C6    0.020
 228  plan-3  C5    0.020
 228  plan-3  C12   0.020
 228  plan-3  N4    0.020
 228  plan-3  C3    0.020
 228  plan-3  N7    0.020
 228  plan-3  H6    0.020
 228  plan-4  C21   0.020
 228  plan-4  N20   0.020
 228  plan-4  C18   0.020
 228  plan-4  O19   0.020
 228  plan-4  C17   0.020
 228  plan-4  HN20  0.020

