# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 07:00:41 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: N~2~-[2-(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-fluoropyrimidin-4-yl]-N,N-dimethyl-L-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Nc1nc(ncc1F)c2c[nH]c3ncc(Cl)cc23)C(=O)N(C)C
#
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
 704  704  N~2~-[2-(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-fluoropyrimidin-4-yl]-N,N-dimethyl-L-alaninamide  ligand  41  25  .  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_704
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
 704  CL1  CL  CL    0  -0.138  -6.4791  -0.8980  -0.2669
 704  C1   C   CH3   0  -0.634   3.4241   0.6891   1.7644
 704  C2   C   CH1   0  -0.201   3.5289   0.2311   0.3064
 704  C4   C   C     0   0.574   5.0006   0.1506  -0.1028
 704  O5   O   O     0  -0.463   5.5505  -0.9446  -0.1506
 704  N6   N   NT    0  -0.451   5.6502   1.3015  -0.3365
 704  C7   C   CH3   0  -0.511   5.0512   2.6203  -0.3606
 704  C8   C   CH3   0  -0.511   7.0814   1.2957  -0.5710
 704  N9   N   NH1   0  -0.679   2.9600  -1.0796   0.1143
 704  C10  C   CR6   0   0.445   1.6432  -1.3030   0.0495
 704  C11  C   CR6   0   0.356   1.1227  -2.6078  -0.0874
 704  C12  C   CR16  0  -0.164  -0.2257  -2.7716  -0.1593
 704  N13  N   N     0  -0.445  -1.0685  -1.7315  -0.1026
 704  C14  C   CR6   0   0.341  -0.5129  -0.5361   0.0258
 704  N15  N   N     0  -0.495   0.7944  -0.2853   0.1037
 704  C16  C   CR5   0  -0.079  -1.3983   0.6147   0.0935
 704  C17  C   CR15  0   0.011  -0.9992   1.9221   0.2351
 704  N18  N   NR15  0  -0.667  -2.0789   2.7411   0.2652
 704  C20  C   CR56  0   0.491  -3.2144   1.9953   0.1441
 704  C21  C   CR56  0   0.019  -2.8289   0.6404   0.0328
 704  C22  C   CR16  0  -0.196  -3.8486  -0.2982  -0.0983
 704  C23  C   CR6   0  -0.105  -5.1407   0.1907  -0.1084
 704  C24  C   CR16  0  -0.042  -5.4044   1.5601   0.0084
 704  N25  N   N     0  -0.392  -4.4486   2.4641   0.1346
 704  H1   H   HCH3  0   0.254   2.3796   0.7013   2.0718
 704  H2   H   HCH3  0   0.234   3.9714   0.0110   2.4196
 704  H3   H   HCH3  0   0.225   3.8237   1.6930   1.9045
 704  H4   H   HCH1  0   0.258   2.9808   0.9296  -0.3279
 704  H5   H   HCH3  0   0.232   5.2785   3.1762   0.5511
 704  H6   H   HCH3  0   0.243   5.4542   3.1779  -1.2061
 704  H7   H   HCH3  0   0.242   3.9743   2.5845  -0.4853
 704  H8   H   HCH3  0   0.274   7.5125   0.3347  -0.3127
 704  H9   H   HCH3  0   0.228   7.3020   1.5125  -1.6179
 704  H10  H   HCH3  0   0.223   7.5516   2.0651   0.0421
 704  H11  H   HNH1  0   0.397   3.6050  -1.8549   0.1068
 704  H12  H   HCR6  0   0.256  -0.6544  -3.7626  -0.2653
 704  H13  H   HCR5  0   0.266  -0.0005   2.3186   0.3180
 704  H14  H   HNR5  0   0.381  -2.0469   3.7443   0.3552
 704  H15  H   HCR6  0   0.273  -3.6360  -1.3540  -0.1869
 704  H16  H   HCR6  0   0.252  -6.4271   1.9182  -0.0018
 704  F27  F   F     0  -0.300   1.9667  -3.6499  -0.1429

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
 704  N18  C20  aromatic  1.364  0.020  1.364
 704  N18  C17  aromatic  1.356  0.020  1.356
 704  N25  C20  aromatic  1.320  0.020  1.320
 704  N25  C24  aromatic  1.322  0.020  1.322
 704  C20  C21  aromatic  1.413  0.020  1.413
 704  C17  C16  aromatic  1.374  0.020  1.374
 704  C24  C23  aromatic  1.399  0.020  1.399
 704  C21  C16  aromatic  1.432  0.020  1.432
 704  C21  C22  aromatic  1.392  0.020  1.392
 704  C16  C14  single    1.454  0.020  1.454
 704  C23  C22  aromatic  1.382  0.020  1.382
 704  C23  CL1  single    1.732  0.020  1.732
 704  N13  C14  aromatic  1.324  0.020  1.324
 704  N13  C12  aromatic  1.340  0.020  1.340
 704  C14  N15  aromatic  1.333  0.020  1.333
 704  C12  C11  aromatic  1.360  0.020  1.360
 704  N15  C10  aromatic  1.326  0.020  1.326
 704  C11  C10  aromatic  1.411  0.020  1.411
 704  C11  F27  single    1.342  0.020  1.342
 704  C10  N9   single    1.337  0.020  1.337
 704  C7   N6   single    1.449  0.020  1.449
 704  O5   C4   double    1.226  0.020  1.226
 704  N6   C4   single    1.342  0.020  1.342
 704  N6   C8   single    1.450  0.020  1.450
 704  N9   C2   single    1.442  0.020  1.442
 704  C4   C2   single    1.530  0.020  1.530
 704  C2   C1   single    1.532  0.020  1.532
 704  C1   H1   single    0.970  0.020  1.090
 704  C1   H2   single    0.970  0.020  1.090
 704  C1   H3   single    0.970  0.020  1.090
 704  C2   H4   single    0.970  0.020  1.090
 704  C7   H5   single    0.970  0.020  1.090
 704  C7   H6   single    0.970  0.020  1.090
 704  C7   H7   single    0.970  0.020  1.090
 704  C8   H8   single    0.970  0.020  1.090
 704  C8   H9   single    0.970  0.020  1.090
 704  C8   H10  single    0.970  0.020  1.090
 704  N9   H11  single    0.860  0.020  1.020
 704  C12  H12  single    0.930  0.020  1.080
 704  C17  H13  single    0.930  0.020  1.080
 704  N18  H14  single    0.860  0.020  1.020
 704  C22  H15  single    0.930  0.020  1.080
 704  C24  H16  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
 704  H3   C1   H2   108.16  3.000
 704  H3   C1   H1   107.77  3.000
 704  H2   C1   H1   108.60  3.000
 704  H3   C1   C2   111.89  3.000
 704  H2   C1   C2   110.59  3.000
 704  H1   C1   C2   109.73  3.000
 704  H4   C2   N9   107.84  3.000
 704  H4   C2   C4   111.19  3.000
 704  N9   C2   C4   107.23  3.000
 704  H4   C2   C1   109.12  3.000
 704  C4   C2   C1   109.64  3.000
 704  N9   C2   C1   111.82  3.000
 704  N6   C4   O5   122.82  3.000
 704  N6   C4   C2   117.85  3.000
 704  O5   C4   C2   119.26  3.000
 704  C8   N6   C7   114.14  3.000
 704  C8   N6   C4   120.16  3.000
 704  C7   N6   C4   125.69  3.000
 704  H7   C7   H6   107.14  3.000
 704  H7   C7   H5   108.64  3.000
 704  H6   C7   H5   108.08  3.000
 704  H7   C7   N6   112.48  3.000
 704  H6   C7   N6   109.01  3.000
 704  H5   C7   N6   111.32  3.000
 704  H10  C8   H9   108.18  3.000
 704  H10  C8   H8   108.66  3.000
 704  H9   C8   H8   108.91  3.000
 704  H10  C8   N6   109.38  3.000
 704  H9   C8   N6   110.72  3.000
 704  H8   C8   N6   110.93  3.000
 704  H11  N9   C10  120.06  3.000
 704  H11  N9   C2   116.58  3.000
 704  C10  N9   C2   123.16  3.000
 704  N15  C10  C11  118.51  3.000
 704  C11  C10  N9   121.49  3.000
 704  N15  C10  N9   120.00  3.000
 704  F27  C11  C12  121.85  3.000
 704  F27  C11  C10  119.33  3.000
 704  C12  C11  C10  118.82  3.000
 704  H12  C12  N13  117.69  3.000
 704  H12  C12  C11  120.45  3.000
 704  N13  C12  C11  121.86  3.000
 704  C14  N13  C12  116.16  3.000
 704  C16  C14  N15  116.45  3.000
 704  N15  C14  N13  125.92  3.000
 704  C16  C14  N13  117.62  3.000
 704  C14  N15  C10  118.73  3.000
 704  C21  C16  C17  106.11  3.000
 704  C21  C16  C14  128.36  3.000
 704  C17  C16  C14  125.53  3.000
 704  H13  C17  N18  120.94  3.000
 704  H13  C17  C16  128.83  3.000
 704  N18  C17  C16  110.23  3.000
 704  H14  N18  C20  125.37  3.000
 704  H14  N18  C17  125.32  3.000
 704  C20  N18  C17  109.31  3.000
 704  N25  C20  C21  126.50  3.000
 704  C21  C20  N18  107.71  3.000
 704  N25  C20  N18  125.78  3.000
 704  C22  C21  C20  117.01  3.000
 704  C22  C21  C16  136.35  3.000
 704  C20  C21  C16  106.64  3.000
 704  H15  C22  C23  121.95  3.000
 704  H15  C22  C21  121.49  3.000
 704  C23  C22  C21  116.56  3.000
 704  C24  C23  C22  121.46  3.000
 704  C22  C23  CL1  120.05  3.000
 704  C24  C23  CL1  118.49  3.000
 704  H16  C24  N25  117.22  3.000
 704  H16  C24  C23  120.03  3.000
 704  N25  C24  C23  122.75  3.000
 704  C24  N25  C20  115.72  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
 704  CONST_01  C16  C14  N15  C10  180.00   0.0  0
 704  CONST_02  N13  C14  N15  C10    0.00   0.0  0
 704  CONST_03  N13  C12  C11  C10    0.00   0.0  0
 704  CONST_04  C14  N13  C12  C11    0.00   0.0  0
 704  CONST_05  C14  N15  C10  C11    0.00   0.0  0
 704  CONST_06  C16  C14  N13  C12  180.00   0.0  0
 704  CONST_07  N15  C14  N13  C12    0.00   0.0  0
 704  CONST_08  N15  C10  C11  C12    0.00   0.0  0
 704  CONST_09  C17  C16  C14  N13  180.00   0.0  0
 704  CONST_10  C21  C16  C14  N13    0.00   0.0  0
 704  CONST_11  N18  C17  C16  C14  180.00   0.0  0
 704  CONST_12  C20  C21  C16  C14  180.00   0.0  0
 704  CONST_13  C22  C21  C16  C14    0.00   0.0  0
 704  CONST_14  C17  C16  C14  N15    0.00   0.0  0
 704  CONST_15  C21  C16  C14  N15  180.00   0.0  0
 704  CONST_16  C20  N18  C17  C16    0.00   0.0  0
 704  CONST_17  N18  C20  C21  C16    0.00   0.0  0
 704  CONST_18  N25  C20  C21  C16  180.00   0.0  0
 704  CONST_19  C23  C22  C21  C16  180.00   0.0  0
 704  CONST_20  N25  C20  N18  C17  180.00   0.0  0
 704  CONST_21  C21  C20  N18  C17    0.00   0.0  0
 704  CONST_22  C20  C21  C16  C17    0.00   0.0  0
 704  CONST_23  C22  C21  C16  C17  180.00   0.0  0
 704  CONST_24  C24  N25  C20  N18  180.00   0.0  0
 704  CONST_25  C22  C21  C20  N18  180.00   0.0  0
 704  CONST_26  C21  C16  C17  N18    0.00   0.0  0
 704  CONST_27  C23  C24  N25  C20    0.00   0.0  0
 704  CONST_28  C23  C22  C21  C20    0.00   0.0  0
 704  CONST_29  C24  N25  C20  C21    0.00   0.0  0
 704  CONST_30  C24  C23  C22  C21    0.00   0.0  0
 704  CONST_31  N25  C20  C21  C22    0.00   0.0  0
 704  CONST_32  N25  C24  C23  C22    0.00   0.0  0
 704  CONST_33  N25  C24  C23  CL1  180.00   0.0  0
 704  CONST_34  C21  C22  C23  CL1  180.00   0.0  0
 704  CONST_35  C14  N15  C10  N9   180.00   0.0  0
 704  CONST_36  C12  C11  C10  N9   180.00   0.0  0
 704  CONST_37  F27  C11  C12  N13  180.00   0.0  0
 704  CONST_38  F27  C11  C10  N15  180.00   0.0  0
 704  CONST_39  H12  C12  C11  C10  180.00   0.0  0
 704  CONST_40  H13  C17  C16  C14    0.00   0.0  0
 704  CONST_41  H14  N18  C17  C16  180.00   0.0  0
 704  CONST_42  H15  C22  C21  C16    0.00   0.0  0
 704  CONST_43  H16  C24  N25  C20  180.00   0.0  0
 704  CONST_44  N15  C10  N9   C2     0.00   0.0  0
 704  CONST_45  C11  C10  N9   C2   180.00   0.0  0
 704  CONST_46  H11  N9   C10  C11    0.00   0.0  0
 704  CONST_47  C7   N6   C4   C2     0.00   0.0  0
 704  CONST_48  C8   N6   C4   C2   180.00   0.0  0
 704  CONST_49  C7   N6   C4   O5   180.00   0.0  0
 704  CONST_50  C8   N6   C4   O5     0.00   0.0  0
 704  Var_01    H5   C7   N6   C4   103.76  30.0  3
 704  Var_02    H8   C8   N6   C4   -12.48  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
 704  chir_01  C2  N9  C4  C1  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
 704  plan-1  N9   0.020
 704  plan-1  C10  0.020
 704  plan-1  C11  0.020
 704  plan-1  C12  0.020
 704  plan-1  N13  0.020
 704  plan-1  C14  0.020
 704  plan-1  N15  0.020
 704  plan-1  C16  0.020
 704  plan-1  H12  0.020
 704  plan-1  F27  0.020
 704  plan-2  CL1  0.020
 704  plan-2  C14  0.020
 704  plan-2  C16  0.020
 704  plan-2  C17  0.020
 704  plan-2  N18  0.020
 704  plan-2  C20  0.020
 704  plan-2  C21  0.020
 704  plan-2  C22  0.020
 704  plan-2  C23  0.020
 704  plan-2  C24  0.020
 704  plan-2  N25  0.020
 704  plan-2  H13  0.020
 704  plan-2  H14  0.020
 704  plan-2  H15  0.020
 704  plan-2  H16  0.020
 704  plan-3  C2   0.020
 704  plan-3  C4   0.020
 704  plan-3  O5   0.020
 704  plan-3  N6   0.020
 704  plan-3  C7   0.020
 704  plan-3  C8   0.020
 704  plan-4  C2   0.020
 704  plan-4  N9   0.020
 704  plan-4  C10  0.020
 704  plan-4  H11  0.020

