# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 06:01:03 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: N'-(3-{[5-(2-cyclopropylpyrimidin-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]carbonyl}-2,4-difluorophenyl)-N-ethyl-N-methylsulfuric diamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(C)[S](=O)(=O)Nc1ccc(F)c(c1F)C(=O)c2c[nH]c3ncc(cc23)c4cnc(nc4)C5CC5
#
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
 904  904  'N'-(3-{[5-(2-cyclopropylpyrimidin-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]carbonyl}-2,4-difluorophenyl)-N-ethyl-N-methylsulfuric diamide'  ligand  58  36  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_904
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
 904  S1   S  S     0   1.507  -6.0382  -0.8278   0.9604
 904  C2   C  CR5   0  -0.196   0.1265   1.5774  -0.3705
 904  C4   C  CR6   0  -0.496  -2.1411   0.8664  -1.1742
 904  C5   C  CR56  0   0.068   1.5277   1.5133  -0.0627
 904  N6   N  NC1   0  -0.811  -5.2246   0.6382   0.8922
 904  C8   C  CR15  0   0.044  -0.3187   2.7961   0.1046
 904  C10  C  CR6   0   0.092  -4.3749   0.8578  -0.2091
 904  C11  C  CR6   0   0.610  -2.9996   0.6934  -0.1068
 904  C12  C  CR56  0   0.477   1.8451   2.7171   0.5929
 904  N13  N  NR15  0  -0.657   0.6992   3.4669   0.6708
 904  C15  C  CR6   0   0.426   7.0298  -1.6827  -0.0964
 904  C16  C  CR16  0  -0.289   2.5543   0.5932  -0.2280
 904  N18  N  N     0  -0.408   3.0274   3.0704   1.0561
 904  N19  N  N     0  -0.422   6.1800  -1.6061  -1.1180
 904  N20  N  N     0  -0.423   6.9210  -0.9803   1.0284
 904  C21  C  CH1   0  -0.364   8.1628  -2.6143  -0.2314
 904  C23  C  CR6   0  -0.009   3.8131   0.9325   0.2572
 904  N24  N  N     0  -0.585  -4.9486  -2.0194   0.7925
 904  C25  C  CH2   0  -0.467   8.6495  -3.3753   0.9772
 904  C28  C  CH2   0  -0.467   9.4833  -2.2827   0.4165
 904  C31  C  CR6   0  -0.065   4.9496   0.0121   0.1303
 904  C32  C  CR6   0   0.577  -2.7102   1.2019  -2.3906
 904  O33  O  OS    0  -0.657  -6.5956  -0.8431   2.2996
 904  O34  O  OS    0  -0.645  -6.9050  -0.8698  -0.1993
 904  O35  O  O     0  -0.382  -0.2137  -0.4446  -1.4985
 904  C36  C  CR16  0  -0.043   5.8971  -0.1537   1.1374
 904  C38  C  CR16  0  -0.053   5.1626  -0.7680  -1.0012
 904  C40  C  CR16  0  -0.111   3.9897   2.1810   0.8794
 904  C42  C  CR16  0  -0.239  -4.8935   1.2198  -1.4470
 904  C44  C  CR16  0  -0.437  -4.0683   1.3886  -2.5473
 904  F46  F  F     0  -0.288  -2.4748   0.3468   1.0723
 904  F47  F  F     0  -0.292  -1.8979   1.3679  -3.4376
 904  C48  C  CH2   0  -0.290  -4.8944  -2.8906  -0.3813
 904  C51  C  CH3   0  -0.519  -4.0671  -2.3394   1.9038
 904  C55  C  CH3   0  -0.657  -3.8150  -2.5043  -1.3758
 904  H1   H  HNC1  0   0.421  -4.8679   0.9256   1.7968
 904  H2   H  HCR5  0   0.315  -1.3061   3.2285   0.0631
 904  H3   H  HNR5  0   0.430   0.6296   4.3811   1.0920
 904  H4   H  HCR6  0   0.269   2.3792  -0.3646  -0.6993
 904  H5   H  HCH1  0   0.274   8.1961  -3.1325  -1.1814
 904  H6   H  HCH2  0   0.257   8.1357  -3.1939   1.9123
 904  H7   H  HCH2  0   0.263   8.9579  -4.3999   0.8161
 904  H8   H  HCH2  0   0.263  10.3778  -2.5403  -0.1352
 904  H9   H  HCH2  0   0.257   9.5372  -1.3534   0.9685
 904  H10  H  HCR6  0   0.272   5.8138   0.3941   2.0711
 904  H11  H  HCR6  0   0.273   4.4902  -0.7011  -1.8508
 904  H12  H  HCR6  0   0.267   4.9734   2.4670   1.2350
 904  H13  H  HCR6  0   0.295  -5.9585   1.3720  -1.5480
 904  H14  H  HCR6  0   0.297  -4.4752   1.6725  -3.5081
 904  H15  H  HCH2  0   0.253  -4.7178  -3.9002  -0.0046
 904  H16  H  HCH2  0   0.265  -5.8668  -2.9135  -0.8672
 904  H17  H  HCH3  0   0.255  -4.4136  -3.2281   2.4329
 904  H18  H  HCH3  0   0.254  -3.0623  -2.5256   1.5275
 904  H19  H  HCH3  0   0.255  -3.9984  -1.5215   2.6168
 904  H20  H  HCH3  0   0.227  -4.0205  -1.5360  -1.8313
 904  H21  H  HCH3  0   0.228  -2.8297  -2.4601  -0.9109
 904  H22  H  HCH3  0   0.241  -3.7693  -3.2458  -2.1739
 904  C3   C  C     0   0.344  -0.6685   0.5861  -1.0425

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
 904  C28  C21  single    1.508  0.020  1.508
 904  C28  C25  single    1.484  0.020  1.484
 904  C21  C25  single    1.509  0.020  1.509
 904  C21  C15  single    1.473  0.020  1.473
 904  N20  C15  aromatic  1.331  0.020  1.331
 904  N20  C36  aromatic  1.320  0.020  1.320
 904  C15  N19  aromatic  1.331  0.020  1.331
 904  O35  C3   double    1.215  0.020  1.215
 904  O34  S1   double    1.448  0.020  1.448
 904  C36  C31  aromatic  1.393  0.020  1.393
 904  N19  C38  aromatic  1.323  0.020  1.323
 904  F47  C32  single    1.335  0.020  1.335
 904  C32  C44  aromatic  1.380  0.020  1.380
 904  C32  C4   aromatic  1.384  0.020  1.384
 904  C44  C42  aromatic  1.386  0.020  1.386
 904  C3   C4   single    1.505  0.020  1.505
 904  C3   C2   single    1.438  0.020  1.438
 904  C4   C11  aromatic  1.381  0.020  1.381
 904  C42  C10  aromatic  1.390  0.020  1.390
 904  C11  C10  aromatic  1.389  0.020  1.389
 904  C11  F46  single    1.336  0.020  1.336
 904  C10  N6   single    1.408  0.020  1.408
 904  N6   S1   single    1.678  0.020  1.678
 904  C38  C31  aromatic  1.391  0.020  1.391
 904  C31  C23  single    1.468  0.020  1.468
 904  S1   O33  double    1.451  0.020  1.451
 904  S1   N24  single    1.623  0.020  1.623
 904  C16  C23  aromatic  1.391  0.020  1.391
 904  C16  C5   aromatic  1.388  0.020  1.388
 904  C23  C40  aromatic  1.406  0.020  1.406
 904  C2   C5   aromatic  1.436  0.020  1.436
 904  C2   C8   aromatic  1.382  0.020  1.382
 904  C5   C12  aromatic  1.407  0.020  1.407
 904  N24  C51  single    1.454  0.020  1.454
 904  N24  C48  single    1.463  0.020  1.463
 904  C8   N13  aromatic  1.344  0.020  1.344
 904  C40  N18  aromatic  1.322  0.020  1.322
 904  C12  N18  aromatic  1.318  0.020  1.318
 904  C12  N13  aromatic  1.372  0.020  1.372
 904  C48  C55  single    1.518  0.020  1.518
 904  N6   H1   single    0.890  0.020  1.040
 904  C8   H2   single    0.930  0.020  1.080
 904  N13  H3   single    0.860  0.020  1.020
 904  C16  H4   single    0.930  0.020  1.080
 904  C21  H5   single    0.970  0.020  1.090
 904  C25  H6   single    0.970  0.020  1.090
 904  C25  H7   single    0.970  0.020  1.090
 904  C28  H8   single    0.970  0.020  1.090
 904  C28  H9   single    0.970  0.020  1.090
 904  C36  H10  single    0.930  0.020  1.080
 904  C38  H11  single    0.930  0.020  1.080
 904  C40  H12  single    0.930  0.020  1.080
 904  C42  H13  single    0.930  0.020  1.080
 904  C44  H14  single    0.930  0.020  1.080
 904  C48  H15  single    0.970  0.020  1.090
 904  C48  H16  single    0.970  0.020  1.090
 904  C51  H17  single    0.970  0.020  1.090
 904  C51  H18  single    0.970  0.020  1.090
 904  C51  H19  single    0.970  0.020  1.090
 904  C55  H20  single    0.970  0.020  1.090
 904  C55  H21  single    0.970  0.020  1.090
 904  C55  H22  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
 904  O34  S1   O33  120.59  3.000
 904  O33  S1   N24  110.22  3.000
 904  O34  S1   N24  107.31  3.000
 904  N24  S1   N6   108.16  3.000
 904  O33  S1   N6   103.48  3.000
 904  O34  S1   N6   106.44  3.000
 904  C8   C2   C5   106.26  3.000
 904  C8   C2   C3   126.21  3.000
 904  C5   C2   C3   127.52  3.000
 904  C32  C4   C11  117.01  3.000
 904  C11  C4   C3   121.16  3.000
 904  C32  C4   C3   121.63  3.000
 904  C16  C5   C12  117.11  3.000
 904  C12  C5   C2   106.37  3.000
 904  C16  C5   C2   136.51  3.000
 904  H1   N6   C10  116.19  3.000
 904  H1   N6   S1   112.45  3.000
 904  C10  N6   S1   117.42  3.000
 904  H2   C8   N13  120.62  3.000
 904  H2   C8   C2   129.44  3.000
 904  N13  C8   C2   109.94  3.000
 904  C42  C10  C11  117.77  3.000
 904  C11  C10  N6   121.42  3.000
 904  C42  C10  N6   120.80  3.000
 904  F46  C11  C10  118.99  3.000
 904  F46  C11  C4   118.07  3.000
 904  C10  C11  C4   122.95  3.000
 904  N18  C12  N13  125.65  3.000
 904  N13  C12  C5   107.81  3.000
 904  N18  C12  C5   126.54  3.000
 904  H3   N13  C12  125.22  3.000
 904  H3   N13  C8   125.16  3.000
 904  C12  N13  C8   109.63  3.000
 904  C21  C15  N20  118.31  3.000
 904  N20  C15  N19  124.49  3.000
 904  C21  C15  N19  117.20  3.000
 904  H4   C16  C23  120.95  3.000
 904  H4   C16  C5   121.26  3.000
 904  C23  C16  C5   117.77  3.000
 904  C40  N18  C12  115.18  3.000
 904  C38  N19  C15  117.36  3.000
 904  C36  N20  C15  117.62  3.000
 904  H5   C21  C28  117.09  3.000
 904  H5   C21  C25  116.84  3.000
 904  C28  C21  C25   58.96  3.000
 904  H5   C21  C15  114.01  3.000
 904  C25  C21  C15  119.58  3.000
 904  C28  C21  C15  119.68  3.000
 904  C40  C23  C31  119.85  3.000
 904  C40  C23  C16  118.98  3.000
 904  C31  C23  C16  121.17  3.000
 904  C51  N24  C48  117.38  3.000
 904  C48  N24  S1   123.02  3.000
 904  C51  N24  S1   119.30  3.000
 904  H7   C25  H6   115.01  3.000
 904  H7   C25  C28  118.72  3.000
 904  H6   C25  C28  118.01  3.000
 904  H7   C25  C21  116.76  3.000
 904  H6   C25  C21  117.03  3.000
 904  C28  C25  C21   60.48  3.000
 904  H9   C28  H8   115.04  3.000
 904  H9   C28  C25  117.86  3.000
 904  H8   C28  C25  118.80  3.000
 904  H9   C28  C21  116.85  3.000
 904  H8   C28  C21  116.91  3.000
 904  C25  C28  C21   60.56  3.000
 904  C38  C31  C36  114.67  3.000
 904  C38  C31  C23  122.72  3.000
 904  C36  C31  C23  122.61  3.000
 904  F47  C32  C44  119.53  3.000
 904  C44  C32  C4   122.50  3.000
 904  F47  C32  C4   117.97  3.000
 904  H10  C36  C31  120.64  3.000
 904  H10  C36  N20  116.51  3.000
 904  C31  C36  N20  122.84  3.000
 904  H11  C38  C31  120.49  3.000
 904  H11  C38  N19  116.49  3.000
 904  C31  C38  N19  123.01  3.000
 904  H12  C40  C23  119.55  3.000
 904  H12  C40  N18  116.04  3.000
 904  C23  C40  N18  124.41  3.000
 904  H13  C42  C44  119.70  3.000
 904  H13  C42  C10  119.19  3.000
 904  C44  C42  C10  121.11  3.000
 904  H14  C44  C42  120.90  3.000
 904  H14  C44  C32  120.45  3.000
 904  C42  C44  C32  118.65  3.000
 904  H16  C48  H15  106.22  3.000
 904  H16  C48  C55  110.40  3.000
 904  H15  C48  C55  110.26  3.000
 904  H16  C48  N24  109.76  3.000
 904  H15  C48  N24  106.25  3.000
 904  C55  C48  N24  113.62  3.000
 904  H19  C51  H18  107.28  3.000
 904  H19  C51  H17  108.36  3.000
 904  H18  C51  H17  108.75  3.000
 904  H19  C51  N24  111.96  3.000
 904  H18  C51  N24  109.44  3.000
 904  H17  C51  N24  110.94  3.000
 904  H22  C55  H21  107.57  3.000
 904  H22  C55  H20  107.84  3.000
 904  H21  C55  H20  108.21  3.000
 904  H22  C55  C48  109.66  3.000
 904  H21  C55  C48  111.94  3.000
 904  H20  C55  C48  111.46  3.000
 904  O35  C3   C4   119.43  3.000
 904  C4   C3   C2   116.98  3.000
 904  O35  C3   C2   123.59  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
 904  CONST_01  C23  C16  C5   C2   180.00   0.0  0
 904  CONST_02  N18  C12  C5   C2   180.00   0.0  0
 904  CONST_03  N13  C12  C5   C2     0.00   0.0  0
 904  CONST_04  C12  N13  C8   C2     0.00   0.0  0
 904  CONST_05  C42  C44  C32  C4     0.00   0.0  0
 904  CONST_06  C42  C10  C11  C4     0.00   0.0  0
 904  CONST_07  C31  C23  C16  C5   180.00   0.0  0
 904  CONST_08  C40  C23  C16  C5     0.00   0.0  0
 904  CONST_09  N13  C8   C2   C5     0.00   0.0  0
 904  CONST_10  C40  N18  C12  C5     0.00   0.0  0
 904  CONST_11  C8   N13  C12  C5     0.00   0.0  0
 904  CONST_12  C16  C5   C2   C8   180.00   0.0  0
 904  CONST_13  C12  C5   C2   C8     0.00   0.0  0
 904  CONST_14  N18  C12  N13  C8   180.00   0.0  0
 904  CONST_15  C32  C44  C42  C10    0.00   0.0  0
 904  CONST_16  C32  C4   C11  C10    0.00   0.0  0
 904  CONST_17  C44  C32  C4   C11    0.00   0.0  0
 904  CONST_18  C44  C42  C10  C11    0.00   0.0  0
 904  CONST_19  C23  C16  C5   C12    0.00   0.0  0
 904  CONST_20  C23  C40  N18  C12    0.00   0.0  0
 904  CONST_21  C16  C5   C12  N13  180.00   0.0  0
 904  CONST_22  C40  N18  C12  N13  180.00   0.0  0
 904  CONST_23  C31  C36  N20  C15    0.00   0.0  0
 904  CONST_24  C31  C38  N19  C15    0.00   0.0  0
 904  CONST_27  N18  C40  C23  C16    0.00   0.0  0
 904  CONST_28  N18  C12  C5   C16    0.00   0.0  0
 904  CONST_29  C31  C23  C40  N18  180.00   0.0  0
 904  CONST_30  C36  N20  C15  N19    0.00   0.0  0
 904  CONST_31  C36  C31  C38  N19    0.00   0.0  0
 904  CONST_32  C23  C31  C38  N19  180.00   0.0  0
 904  CONST_33  C38  N19  C15  N20    0.00   0.0  0
 904  CONST_34  C38  C31  C36  N20    0.00   0.0  0
 904  CONST_35  C23  C31  C36  N20  180.00   0.0  0
 904  CONST_38  C36  N20  C15  C21  180.00   0.0  0
 904  CONST_39  C38  N19  C15  C21  180.00   0.0  0
 904  CONST_40  C44  C32  C4   C3   180.00   0.0  0
 904  CONST_41  C10  C11  C4   C3   180.00   0.0  0
 904  CONST_42  C16  C5   C2   C3     0.00   0.0  0
 904  CONST_43  C12  C5   C2   C3   180.00   0.0  0
 904  CONST_44  N13  C8   C2   C3   180.00   0.0  0
 904  CONST_45  N6   C10  C11  C4   180.00   0.0  0
 904  CONST_46  C44  C42  C10  N6   180.00   0.0  0
 904  CONST_47  F47  C32  C4   C11  180.00   0.0  0
 904  CONST_48  F46  C11  C4   C32  180.00   0.0  0
 904  CONST_49  F47  C32  C44  C42  180.00   0.0  0
 904  CONST_50  F46  C11  C10  C42  180.00   0.0  0
 904  CONST_51  H4   C16  C5   C2     0.00   0.0  0
 904  CONST_52  H3   N13  C8   C2   180.00   0.0  0
 904  CONST_53  H14  C44  C32  C4   180.00   0.0  0
 904  CONST_54  H2   C8   C2   C5   180.00   0.0  0
 904  CONST_55  H13  C42  C10  C11  180.00   0.0  0
 904  CONST_56  H12  C40  N18  C12  180.00   0.0  0
 904  CONST_57  H10  C36  N20  C15  180.00   0.0  0
 904  CONST_58  H11  C38  N19  C15  180.00   0.0  0
 904  Var_01    C25  C28  C21  C15  108.67  30.0  1
 904  Var_02    C28  C21  C15  N19  147.26  30.0  3
 904  Var_03    C32  C4   C3   C2   107.89  30.0  2
 904  Var_04    C5   C2   C3   C4   176.67  30.0  2
 904  Var_05    O34  S1   N6   C10  -62.66  30.0  3
 904  Var_06    C55  C48  N24  S1   100.50  30.0  3
 904  Var_07    C51  N24  S1   N6    74.38  30.0  3
 904  Var_08    H17  C51  N24  S1   101.32  30.0  3
 904  Var_09    H20  C55  C48  N24  -65.96  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
 904  chir_01  C21  C28  C25  C15  both

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
 904  plan-1  C15  0.020
 904  plan-1  N19  0.020
 904  plan-1  N20  0.020
 904  plan-1  C21  0.020
 904  plan-1  C23  0.020
 904  plan-1  C31  0.020
 904  plan-1  C36  0.020
 904  plan-1  C38  0.020
 904  plan-1  H10  0.020
 904  plan-1  H11  0.020
 904  plan-2  C4   0.020
 904  plan-2  N6   0.020
 904  plan-2  C10  0.020
 904  plan-2  C11  0.020
 904  plan-2  C32  0.020
 904  plan-2  C42  0.020
 904  plan-2  C44  0.020
 904  plan-2  F46  0.020
 904  plan-2  F47  0.020
 904  plan-2  H13  0.020
 904  plan-2  H14  0.020
 904  plan-2  C3   0.020
 904  plan-3  C2   0.020
 904  plan-3  C5   0.020
 904  plan-3  C8   0.020
 904  plan-3  C12  0.020
 904  plan-3  N13  0.020
 904  plan-3  C16  0.020
 904  plan-3  N18  0.020
 904  plan-3  C23  0.020
 904  plan-3  C31  0.020
 904  plan-3  C40  0.020
 904  plan-3  H2   0.020
 904  plan-3  H3   0.020
 904  plan-3  H4   0.020
 904  plan-3  H12  0.020
 904  plan-3  C3   0.020
 904  plan-4  S1   0.020
 904  plan-4  N6   0.020
 904  plan-4  C10  0.020
 904  plan-4  H1   0.020
 904  plan-5  C2   0.020
 904  plan-5  C4   0.020
 904  plan-5  O35  0.020
 904  plan-5  C3   0.020

