# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 16:06:36 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (3S)-1-[2-(pyrido[2,3-b]pyrazin-7-ylsulfanyl)-9H-pyrimido[4,5-b]indol-4-yl]pyrrolidin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CCN(C1)c2nc(Sc3cnc4nccnc4c3)nc5[nH]c6ccccc6c25
#
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
 MJU  MJU  (3S)-1-[2-(pyrido[2,3-b]pyrazin-7-ylsulfanyl)-9H-pyrimido[4,5-b]indol-4-yl]pyrrolidin-3-amine  ligand  48  30  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MJU
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
 MJU  N19  N  NH2   0  -0.794   5.0185  -2.5359   1.7210
 MJU  C17  C  CH1   0  -0.134   5.3935  -2.0676   0.3972
 MJU  C16  C  CH2   0  -0.490   4.8754  -3.0351  -0.6602
 MJU  C15  C  CH2   0  -0.248   3.3833  -2.7375  -0.7076
 MJU  C18  C  CH2   0  -0.293   4.6061  -0.8071   0.0576
 MJU  N14  N  NT    0  -0.484   3.3170  -1.3105  -0.3886
 MJU  C10  C  CR6   0   0.471   2.1431  -0.6823  -0.2789
 MJU  C7   C  CR56  0  -0.102   1.9371   0.7011  -0.0208
 MJU  C3   C  CR56  0   0.064   2.6869   1.9409   0.0822
 MJU  C4   C  CR16  0  -0.397   4.0108   2.3492  -0.1069
 MJU  C5   C  CR16  0  -0.254   4.3541   3.6800   0.0609
 MJU  C6   C  CR16  0  -0.282   3.3988   4.6381   0.4080
 MJU  C1   C  CR16  0  -0.302   2.0741   4.2782   0.5760
 MJU  N11  N  N     0  -0.501   1.0627  -1.4712  -0.4374
 MJU  C12  C  CR6   0   0.209  -0.1373  -0.9703  -0.2431
 MJU  N13  N  N     0  -0.441  -0.4713   0.2487   0.1094
 MJU  C8   C  CR56  0   0.482   0.5886   1.0517   0.1897
 MJU  N9   N  NR15  0  -0.752   0.4951   2.3694   0.4691
 MJU  C2   C  CR56  0   0.344   1.7400   2.9421   0.4009
 MJU  S20  S  S2    0   0.105  -1.4126  -2.1780  -0.4811
 MJU  C21  C  CR6   0  -0.206  -2.8647  -1.1833  -0.4259
 MJU  C26  C  CR16  0  -0.013  -3.0789  -0.1842  -1.4123
 MJU  N25  N  N     0  -0.405  -4.1492   0.5517  -1.4808
 MJU  C24  C  CR66  0   0.349  -5.1240   0.3444  -0.5708
 MJU  N27  N  N     0  -0.357  -6.2251   1.1140  -0.6704
 MJU  C28  C  CR16  0  -0.091  -7.1680   0.9083   0.2069
 MJU  C29  C  CR16  0  -0.117  -7.0578  -0.0718   1.2224
 MJU  N30  N  N     0  -0.373  -6.0040  -0.8300   1.3394
 MJU  C23  C  CR66  0   0.150  -5.0162  -0.6348   0.4408
 MJU  C22  C  CR16  0  -0.174  -3.8374  -1.4092   0.5043
 MJU  H1   H  HNH2  0   0.349   5.4940  -3.4081   1.9174
 MJU  H2   H  HNH2  0   0.348   5.3461  -1.8804   2.4198
 MJU  H4   H  HCH1  0   0.239   6.4678  -1.8793   0.2802
 MJU  H5   H  HCH2  0   0.245   5.3435  -2.8119  -1.6211
 MJU  H6   H  HCH2  0   0.257   5.0818  -4.0794  -0.4244
 MJU  H7   H  HCH2  0   0.246   2.9423  -2.9419  -1.6833
 MJU  H8   H  HCH2  0   0.236   2.8345  -3.3220   0.0324
 MJU  H9   H  HCH2  0   0.260   4.5007  -0.1452   0.9174
 MJU  H10  H  HCH2  0   0.252   5.1172  -0.2649  -0.7419
 MJU  H11  H  HCR6  0   0.253   4.7810   1.6528  -0.3964
 MJU  H12  H  HCR6  0   0.253   5.3829   3.9803  -0.0883
 MJU  H13  H  HCR6  0   0.256   3.6923   5.6719   0.5340
 MJU  H14  H  HCR6  0   0.266   1.3178   5.0119   0.8240
 MJU  H15  H  HNR5  0   0.414  -0.3699   2.8565   0.6423
 MJU  H16  H  HCR6  0   0.285  -2.3159  -0.0156  -2.1644
 MJU  H17  H  HCR6  0   0.290  -8.0625   1.5168   0.1428
 MJU  H18  H  HCR6  0   0.287  -7.8664  -0.2091   1.9302
 MJU  H19  H  HCR6  0   0.300  -3.7307  -2.1560   1.2806

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
 MJU  C28  N27  aromatic  1.304  0.020  1.304
 MJU  C28  C29  aromatic  1.416  0.020  1.416
 MJU  N27  C24  aromatic  1.347  0.020  1.347
 MJU  C29  N30  aromatic  1.303  0.020  1.303
 MJU  C24  N25  aromatic  1.350  0.020  1.350
 MJU  C24  C23  aromatic  1.412  0.020  1.412
 MJU  N25  C26  aromatic  1.301  0.020  1.301
 MJU  N30  C23  aromatic  1.350  0.020  1.350
 MJU  C23  C22  aromatic  1.412  0.020  1.412
 MJU  C26  C21  aromatic  1.420  0.020  1.420
 MJU  C22  C21  aromatic  1.365  0.020  1.365
 MJU  C21  S20  single    1.761  0.020  1.761
 MJU  N19  C17  single    1.453  0.020  1.453
 MJU  S20  C12  single    1.772  0.020  1.772
 MJU  C17  C18  single    1.524  0.020  1.524
 MJU  C17  C16  single    1.524  0.020  1.524
 MJU  C18  N14  single    1.454  0.020  1.454
 MJU  N11  C12  aromatic  1.315  0.020  1.315
 MJU  N11  C10  aromatic  1.347  0.020  1.347
 MJU  C12  N13  aromatic  1.312  0.020  1.312
 MJU  C16  C15  single    1.522  0.020  1.522
 MJU  N14  C10  single    1.336  0.020  1.336
 MJU  N14  C15  single    1.464  0.020  1.464
 MJU  N13  C8   aromatic  1.332  0.020  1.332
 MJU  C10  C7   aromatic  1.422  0.020  1.422
 MJU  C8   C7   aromatic  1.409  0.020  1.409
 MJU  C8   N9   aromatic  1.350  0.020  1.350
 MJU  C7   C3   aromatic  1.453  0.020  1.453
 MJU  N9   C2   aromatic  1.372  0.020  1.372
 MJU  C3   C4   aromatic  1.398  0.020  1.398
 MJU  C3   C2   aromatic  1.414  0.020  1.414
 MJU  C4   C5   aromatic  1.385  0.020  1.385
 MJU  C2   C1   aromatic  1.388  0.020  1.388
 MJU  C1   C6   aromatic  1.383  0.020  1.383
 MJU  C5   C6   aromatic  1.397  0.020  1.397
 MJU  N19  H1   single    0.890  0.020  1.040
 MJU  N19  H2   single    0.890  0.020  1.040
 MJU  C17  H4   single    0.970  0.020  1.090
 MJU  C16  H5   single    0.970  0.020  1.090
 MJU  C16  H6   single    0.970  0.020  1.090
 MJU  C15  H7   single    0.970  0.020  1.090
 MJU  C15  H8   single    0.970  0.020  1.090
 MJU  C18  H9   single    0.970  0.020  1.090
 MJU  C18  H10  single    0.970  0.020  1.090
 MJU  C4   H11  single    0.930  0.020  1.080
 MJU  C5   H12  single    0.930  0.020  1.080
 MJU  C6   H13  single    0.930  0.020  1.080
 MJU  C1   H14  single    0.930  0.020  1.080
 MJU  N9   H15  single    0.860  0.020  1.020
 MJU  C26  H16  single    0.930  0.020  1.080
 MJU  C28  H17  single    0.930  0.020  1.080
 MJU  C29  H18  single    0.930  0.020  1.080
 MJU  C22  H19  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
 MJU  H2   N19  H1   105.76  3.000
 MJU  H2   N19  C17  109.67  3.000
 MJU  H1   N19  C17  109.46  3.000
 MJU  H4   C17  C18  109.89  3.000
 MJU  H4   C17  C16  111.58  3.000
 MJU  C18  C17  C16  101.23  3.000
 MJU  H4   C17  N19  113.90  3.000
 MJU  C16  C17  N19  109.86  3.000
 MJU  C18  C17  N19  109.64  3.000
 MJU  H6   C16  H5   107.76  3.000
 MJU  H6   C16  C15  112.30  3.000
 MJU  H5   C16  C15  110.66  3.000
 MJU  H6   C16  C17  113.18  3.000
 MJU  H5   C16  C17  109.58  3.000
 MJU  C15  C16  C17  103.34  3.000
 MJU  H8   C15  H7   107.64  3.000
 MJU  H8   C15  N14  110.59  3.000
 MJU  H7   C15  N14  111.08  3.000
 MJU  H8   C15  C16  111.55  3.000
 MJU  H7   C15  C16  112.81  3.000
 MJU  N14  C15  C16  103.19  3.000
 MJU  H10  C18  H9   108.72  3.000
 MJU  H10  C18  N14  111.22  3.000
 MJU  H9   C18  N14  111.50  3.000
 MJU  H10  C18  C17  109.37  3.000
 MJU  H9   C18  C17  112.10  3.000
 MJU  N14  C18  C17  103.89  3.000
 MJU  C10  N14  C18  126.23  3.000
 MJU  C10  N14  C15  121.07  3.000
 MJU  C18  N14  C15  111.36  3.000
 MJU  N11  C10  C7   118.35  3.000
 MJU  C7   C10  N14  126.84  3.000
 MJU  N11  C10  N14  114.81  3.000
 MJU  C8   C7   C3   105.73  3.000
 MJU  C3   C7   C10  140.20  3.000
 MJU  C8   C7   C10  114.06  3.000
 MJU  C2   C3   C4   117.24  3.000
 MJU  C2   C3   C7   105.93  3.000
 MJU  C4   C3   C7   136.75  3.000
 MJU  H11  C4   C5   118.45  3.000
 MJU  H11  C4   C3   121.61  3.000
 MJU  C5   C4   C3   119.93  3.000
 MJU  H12  C5   C6   119.61  3.000
 MJU  H12  C5   C4   119.06  3.000
 MJU  C6   C5   C4   121.33  3.000
 MJU  H13  C6   C1   119.62  3.000
 MJU  H13  C6   C5   119.92  3.000
 MJU  C1   C6   C5   120.45  3.000
 MJU  H14  C1   C2   120.86  3.000
 MJU  H14  C1   C6   121.38  3.000
 MJU  C2   C1   C6   117.75  3.000
 MJU  C12  N11  C10  119.44  3.000
 MJU  S20  C12  N13  119.07  3.000
 MJU  N13  C12  N11  128.75  3.000
 MJU  S20  C12  N11  112.16  3.000
 MJU  C8   N13  C12  111.94  3.000
 MJU  N9   C8   N13  123.07  3.000
 MJU  N9   C8   C7   109.87  3.000
 MJU  N13  C8   C7   127.05  3.000
 MJU  H15  N9   C2   125.85  3.000
 MJU  H15  N9   C8   124.52  3.000
 MJU  C2   N9   C8   109.52  3.000
 MJU  N9   C2   C1   127.87  3.000
 MJU  C1   C2   C3   123.26  3.000
 MJU  N9   C2   C3   108.86  3.000
 MJU  C21  S20  C12  101.79  3.000
 MJU  C22  C21  C26  118.84  3.000
 MJU  C22  C21  S20  121.04  3.000
 MJU  C26  C21  S20  119.99  3.000
 MJU  H16  C26  N25  117.02  3.000
 MJU  H16  C26  C21  119.01  3.000
 MJU  N25  C26  C21  123.96  3.000
 MJU  C24  N25  C26  118.16  3.000
 MJU  C23  C24  N27  120.76  3.000
 MJU  C23  C24  N25  122.31  3.000
 MJU  N27  C24  N25  116.92  3.000
 MJU  C28  N27  C24  116.82  3.000
 MJU  H17  C28  C29  119.69  3.000
 MJU  H17  C28  N27  117.93  3.000
 MJU  C29  C28  N27  122.37  3.000
 MJU  H18  C29  N30  118.10  3.000
 MJU  H18  C29  C28  119.89  3.000
 MJU  N30  C29  C28  122.01  3.000
 MJU  C23  N30  C29  116.61  3.000
 MJU  C22  C23  N30  120.12  3.000
 MJU  C22  C23  C24  118.45  3.000
 MJU  N30  C23  C24  121.43  3.000
 MJU  H19  C22  C23  119.54  3.000
 MJU  H19  C22  C21  122.19  3.000
 MJU  C23  C22  C21  118.27  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
 MJU  CONST_01  N13  C12  N11  C10    0.00   0.0  0
 MJU  CONST_02  N13  C8   C7   C10    0.00   0.0  0
 MJU  CONST_03  N9   C8   C7   C10  180.00   0.0  0
 MJU  CONST_04  C4   C3   C7   C10    0.00   0.0  0
 MJU  CONST_05  C2   C3   C7   C10  180.00   0.0  0
 MJU  CONST_06  C12  N11  C10  C7     0.00   0.0  0
 MJU  CONST_07  C12  N13  C8   C7     0.00   0.0  0
 MJU  CONST_08  C2   N9   C8   C7     0.00   0.0  0
 MJU  CONST_09  C5   C4   C3   C7   180.00   0.0  0
 MJU  CONST_10  N9   C2   C3   C7     0.00   0.0  0
 MJU  CONST_11  C1   C2   C3   C7   180.00   0.0  0
 MJU  CONST_12  N11  C10  C7   C3   180.00   0.0  0
 MJU  CONST_13  N13  C8   C7   C3   180.00   0.0  0
 MJU  CONST_14  N9   C8   C7   C3     0.00   0.0  0
 MJU  CONST_15  C6   C5   C4   C3     0.00   0.0  0
 MJU  CONST_16  C8   N9   C2   C3     0.00   0.0  0
 MJU  CONST_17  C6   C1   C2   C3     0.00   0.0  0
 MJU  CONST_18  C8   C7   C3   C4   180.00   0.0  0
 MJU  CONST_19  N9   C2   C3   C4   180.00   0.0  0
 MJU  CONST_20  C1   C2   C3   C4     0.00   0.0  0
 MJU  CONST_21  C1   C6   C5   C4     0.00   0.0  0
 MJU  CONST_22  C2   C3   C4   C5     0.00   0.0  0
 MJU  CONST_23  C2   C1   C6   C5     0.00   0.0  0
 MJU  CONST_24  N9   C2   C1   C6   180.00   0.0  0
 MJU  CONST_25  C8   N9   C2   C1   180.00   0.0  0
 MJU  CONST_26  C8   N13  C12  N11    0.00   0.0  0
 MJU  CONST_27  C8   C7   C10  N11    0.00   0.0  0
 MJU  CONST_28  N9   C8   N13  C12  180.00   0.0  0
 MJU  CONST_29  C2   N9   C8   N13  180.00   0.0  0
 MJU  CONST_30  C2   C3   C7   C8     0.00   0.0  0
 MJU  CONST_31  C24  N25  C26  C21    0.00   0.0  0
 MJU  CONST_32  C24  C23  C22  C21    0.00   0.0  0
 MJU  CONST_33  N30  C23  C22  C21  180.00   0.0  0
 MJU  CONST_34  N27  C24  N25  C26  180.00   0.0  0
 MJU  CONST_35  C23  C24  N25  C26    0.00   0.0  0
 MJU  CONST_36  C23  C22  C21  C26    0.00   0.0  0
 MJU  CONST_37  C28  N27  C24  N25  180.00   0.0  0
 MJU  CONST_38  N30  C23  C24  N25  180.00   0.0  0
 MJU  CONST_39  C22  C23  C24  N25    0.00   0.0  0
 MJU  CONST_40  C22  C21  C26  N25    0.00   0.0  0
 MJU  CONST_41  C29  C28  N27  C24    0.00   0.0  0
 MJU  CONST_42  C29  N30  C23  C24    0.00   0.0  0
 MJU  CONST_43  N30  C29  C28  N27    0.00   0.0  0
 MJU  CONST_44  N30  C23  C24  N27    0.00   0.0  0
 MJU  CONST_45  C22  C23  C24  N27  180.00   0.0  0
 MJU  CONST_46  C23  C24  N27  C28    0.00   0.0  0
 MJU  CONST_47  C23  N30  C29  C28    0.00   0.0  0
 MJU  CONST_48  C22  C23  N30  C29  180.00   0.0  0
 MJU  CONST_49  C12  N11  C10  N14  180.00   0.0  0
 MJU  CONST_50  C8   C7   C10  N14  180.00   0.0  0
 MJU  CONST_51  C3   C7   C10  N14    0.00   0.0  0
 MJU  CONST_52  S20  C12  N11  C10  180.00   0.0  0
 MJU  CONST_53  S20  C12  N13  C8   180.00   0.0  0
 MJU  CONST_54  N25  C26  C21  S20  180.00   0.0  0
 MJU  CONST_55  C23  C22  C21  S20  180.00   0.0  0
 MJU  CONST_56  H15  N9   C8   C7   180.00   0.0  0
 MJU  CONST_57  H11  C4   C3   C7     0.00   0.0  0
 MJU  CONST_58  H12  C5   C4   C3   180.00   0.0  0
 MJU  CONST_59  H14  C1   C2   C3   180.00   0.0  0
 MJU  CONST_60  H13  C6   C5   C4   180.00   0.0  0
 MJU  CONST_61  H19  C22  C21  C26  180.00   0.0  0
 MJU  CONST_62  H17  C28  N27  C24  180.00   0.0  0
 MJU  CONST_63  H16  C26  N25  C24  180.00   0.0  0
 MJU  CONST_64  H18  C29  C28  N27  180.00   0.0  0
 MJU  Var_01    C10  N14  C18  C17  150.64  30.0  1
 MJU  Var_02    N14  C15  C16  C17   31.55  30.0  1
 MJU  Var_03    C18  N14  C15  C16   -9.61  30.0  1
 MJU  Var_04    N11  C10  N14  C15    2.19  30.0  2
 MJU  Var_05    C26  C21  S20  C12   63.40  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
 MJU  chir_01  C17  N19  C18  C16  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
 MJU  plan-1  S20  0.020
 MJU  plan-1  C21  0.020
 MJU  plan-1  C26  0.020
 MJU  plan-1  N25  0.020
 MJU  plan-1  C24  0.020
 MJU  plan-1  N27  0.020
 MJU  plan-1  C28  0.020
 MJU  plan-1  C29  0.020
 MJU  plan-1  N30  0.020
 MJU  plan-1  C23  0.020
 MJU  plan-1  C22  0.020
 MJU  plan-1  H16  0.020
 MJU  plan-1  H17  0.020
 MJU  plan-1  H18  0.020
 MJU  plan-1  H19  0.020
 MJU  plan-2  N14  0.020
 MJU  plan-2  C10  0.020
 MJU  plan-2  C7   0.020
 MJU  plan-2  C3   0.020
 MJU  plan-2  C4   0.020
 MJU  plan-2  C5   0.020
 MJU  plan-2  C6   0.020
 MJU  plan-2  C1   0.020
 MJU  plan-2  N11  0.020
 MJU  plan-2  C12  0.020
 MJU  plan-2  N13  0.020
 MJU  plan-2  C8   0.020
 MJU  plan-2  N9   0.020
 MJU  plan-2  C2   0.020
 MJU  plan-2  S20  0.020
 MJU  plan-2  H11  0.020
 MJU  plan-2  H12  0.020
 MJU  plan-2  H13  0.020
 MJU  plan-2  H14  0.020
 MJU  plan-2  H15  0.020

