# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 15:22:53 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (3~{R})-3-[[5-fluoranyl-2-(5-fluoranyl-1~{H}-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]-4,4-dimethyl-pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)[C@@H](CC(O)=O)Nc1nc(ncc1F)c2c[nH]c3ncc(F)cc23
#
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
 6NS  6NS  '(3~{R})-3-[[5-fluoranyl-2-(5-fluoranyl-1~{H}-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]-4,4-dimethyl-pentanoic acid'  ligand  46  27  .  2022-07-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6NS
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
 6NS  F2   F  F     0  -0.307  -1.9309  -3.2533  -0.9982
 6NS  C9   C  CR6   0   0.342  -0.9670  -2.3682  -0.6892
 6NS  C10  C  CR16  0  -0.181   0.3339  -2.7468  -0.5649
 6NS  N2   N  N     0  -0.462   1.2990  -1.8707  -0.2604
 6NS  C11  C  CR6   0   0.323   0.9099  -0.6145  -0.0890
 6NS  N3   N  N     0  -0.478  -0.3375  -0.1611  -0.1939
 6NS  C8   C  CR6   0   0.453  -1.3076  -1.0131  -0.4905
 6NS  N1   N  NH1   0  -0.690  -2.5753  -0.5921  -0.6073
 6NS  C5   C  CH1   0  -0.056  -3.0261   0.7642  -0.3616
 6NS  C6   C  CH2   0  -0.602  -4.1736   0.7142   0.6429
 6NS  C7   C  C     0   0.560  -3.7613   0.0976   1.9540
 6NS  O2   O  OH1   0  -0.594  -4.7841  -0.4868   2.5699
 6NS  O1   O  O     0  -0.434  -2.6521   0.1468   2.4225
 6NS  C2   C  CT    0  -0.076  -3.3796   1.5059  -1.6772
 6NS  C4   C  CH3   0  -0.642  -2.1216   1.5934  -2.5439
 6NS  C3   C  CH3   0  -0.667  -4.4738   0.7781  -2.4590
 6NS  C1   C  CH3   0  -0.659  -3.8442   2.9282  -1.3506
 6NS  C12  C  CR5   0  -0.107   1.9314   0.3665   0.2384
 6NS  C15  C  CR56  0   0.026   3.3407   0.1662   0.3893
 6NS  C16  C  CR16  0  -0.420   4.2216  -0.9103   0.2996
 6NS  C17  C  CR6   0   0.441   5.5482  -0.6247   0.5272
 6NS  F1   F  F     0  -0.314   6.4607  -1.6095   0.4578
 6NS  C18  C  CR16  0  -0.226   5.9956   0.6607   0.8307
 6NS  N5   N  N     0  -0.408   5.1713   1.6924   0.9197
 6NS  C14  C  CR56  0   0.472   3.8972   1.4275   0.7023
 6NS  N4   N  NR15  0  -0.662   2.8757   2.3342   0.7384
 6NS  C13  C  CR15  0   0.004   1.7091   1.7050   0.4622
 6NS  H1   H  HCR6  0   0.283   0.6208  -3.7826  -0.7130
 6NS  H2   H  HNH1  0   0.399  -3.2750  -1.2774  -0.8457
 6NS  H3   H  HCH1  0   0.276  -2.1897   1.2940   0.0960
 6NS  H4   H  HCH2  0   0.303  -4.5185   1.7265   0.8719
 6NS  H5   H  HCH2  0   0.273  -5.0380   0.1818   0.2407
 6NS  H6   H  HOH1  0   0.479  -4.4991  -0.8315   3.4297
 6NS  H7   H  HCH3  0   0.228  -1.7577   0.6077  -2.8354
 6NS  H8   H  HCH3  0   0.229  -2.3364   2.1463  -3.4604
 6NS  H9   H  HCH3  0   0.225  -1.3126   2.1070  -2.0220
 6NS  H10  H  HCH3  0   0.231  -5.3978   0.6782  -1.8865
 6NS  H11  H  HCH3  0   0.237  -4.7177   1.3291  -3.3690
 6NS  H12  H  HCH3  0   0.226  -4.1568  -0.2206  -2.7659
 6NS  H13  H  HCH3  0   0.228  -3.1394   3.4379  -0.6890
 6NS  H14  H  HCH3  0   0.236  -3.9210   3.5177  -2.2655
 6NS  H15  H  HCH3  0   0.230  -4.8251   2.9443  -0.8731
 6NS  H16  H  HCR6  0   0.283   3.8846  -1.9101   0.0649
 6NS  H17  H  HCR6  0   0.278   7.0505   0.8420   1.0025
 6NS  H18  H  HNR5  0   0.419   2.9756   3.3179   0.9325
 6NS  H19  H  HCR5  0   0.299   0.7781   2.2476   0.4420

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
 6NS  N5   C14  aromatic  1.319  0.020  1.319
 6NS  N5   C18  aromatic  1.323  0.020  1.323
 6NS  N4   C14  aromatic  1.366  0.020  1.366
 6NS  N4   C13  aromatic  1.354  0.020  1.354
 6NS  C14  C15  aromatic  1.414  0.020  1.414
 6NS  C18  C17  aromatic  1.395  0.020  1.395
 6NS  C13  C12  aromatic  1.375  0.020  1.375
 6NS  C15  C12  aromatic  1.431  0.020  1.431
 6NS  C15  C16  aromatic  1.394  0.020  1.394
 6NS  C17  C16  aromatic  1.376  0.020  1.376
 6NS  C17  F1   single    1.344  0.020  1.344
 6NS  C12  C11  single    1.454  0.020  1.454
 6NS  N2   C11  aromatic  1.326  0.020  1.326
 6NS  N2   C10  aromatic  1.338  0.020  1.338
 6NS  C11  N3   aromatic  1.331  0.020  1.331
 6NS  O1   C7   double    1.205  0.020  1.205
 6NS  N3   C8   aromatic  1.325  0.020  1.325
 6NS  C10  C9   aromatic  1.361  0.020  1.361
 6NS  C7   O2   single    1.329  0.020  1.329
 6NS  C7   C6   single    1.506  0.020  1.506
 6NS  C8   C9   aromatic  1.411  0.020  1.411
 6NS  C8   N1   single    1.341  0.020  1.341
 6NS  C9   F2   single    1.345  0.020  1.345
 6NS  C5   C6   single    1.526  0.020  1.526
 6NS  C5   N1   single    1.450  0.020  1.450
 6NS  C5   C2   single    1.551  0.020  1.551
 6NS  C3   C2   single    1.529  0.020  1.529
 6NS  C4   C2   single    1.530  0.020  1.530
 6NS  C2   C1   single    1.531  0.020  1.531
 6NS  C10  H1   single    0.930  0.020  1.080
 6NS  N1   H2   single    0.860  0.020  1.020
 6NS  C5   H3   single    0.970  0.020  1.090
 6NS  C6   H4   single    0.970  0.020  1.090
 6NS  C6   H5   single    0.970  0.020  1.090
 6NS  O2   H6   single    0.850  0.020  0.980
 6NS  C4   H7   single    0.970  0.020  1.090
 6NS  C4   H8   single    0.970  0.020  1.090
 6NS  C4   H9   single    0.970  0.020  1.090
 6NS  C3   H10  single    0.970  0.020  1.090
 6NS  C3   H11  single    0.970  0.020  1.090
 6NS  C3   H12  single    0.970  0.020  1.090
 6NS  C1   H13  single    0.970  0.020  1.090
 6NS  C1   H14  single    0.970  0.020  1.090
 6NS  C1   H15  single    0.970  0.020  1.090
 6NS  C16  H16  single    0.930  0.020  1.080
 6NS  C18  H17  single    0.930  0.020  1.080
 6NS  N4   H18  single    0.860  0.020  1.020
 6NS  C13  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
 6NS  C8   C9   C10  119.02  3.000
 6NS  C8   C9   F2   119.43  3.000
 6NS  C10  C9   F2   121.55  3.000
 6NS  H1   C10  N2   117.73  3.000
 6NS  H1   C10  C9   120.40  3.000
 6NS  N2   C10  C9   121.88  3.000
 6NS  C11  N2   C10  115.97  3.000
 6NS  C12  C11  N3   116.51  3.000
 6NS  N3   C11  N2   125.96  3.000
 6NS  C12  C11  N2   117.53  3.000
 6NS  C8   N3   C11  119.00  3.000
 6NS  N1   C8   N3   120.66  3.000
 6NS  N1   C8   C9   121.16  3.000
 6NS  N3   C8   C9   118.18  3.000
 6NS  H2   N1   C5   117.40  3.000
 6NS  H2   N1   C8   117.60  3.000
 6NS  C5   N1   C8   124.94  3.000
 6NS  H3   C5   C2   107.36  3.000
 6NS  H3   C5   C6   108.44  3.000
 6NS  C2   C5   C6   113.74  3.000
 6NS  H3   C5   N1   106.68  3.000
 6NS  C2   C5   N1   111.99  3.000
 6NS  C6   C5   N1   108.34  3.000
 6NS  H5   C6   H4   106.19  3.000
 6NS  H5   C6   C7   109.74  3.000
 6NS  H4   C6   C7   106.44  3.000
 6NS  H5   C6   C5   111.64  3.000
 6NS  H4   C6   C5   110.16  3.000
 6NS  C7   C6   C5   112.37  3.000
 6NS  O1   C7   O2   123.10  3.000
 6NS  O2   C7   C6   111.88  3.000
 6NS  O1   C7   C6   125.00  3.000
 6NS  H6   O2   C7   109.95  3.000
 6NS  C1   C2   C3   109.51  3.000
 6NS  C1   C2   C4   108.49  3.000
 6NS  C3   C2   C4   109.02  3.000
 6NS  C1   C2   C5   109.41  3.000
 6NS  C4   C2   C5   108.69  3.000
 6NS  C3   C2   C5   111.66  3.000
 6NS  H9   C4   H8   108.00  3.000
 6NS  H9   C4   H7   107.81  3.000
 6NS  H8   C4   H7   107.41  3.000
 6NS  H9   C4   C2   111.44  3.000
 6NS  H8   C4   C2   110.05  3.000
 6NS  H7   C4   C2   111.96  3.000
 6NS  H12  C3   H11  107.00  3.000
 6NS  H12  C3   H10  108.03  3.000
 6NS  H11  C3   H10  107.12  3.000
 6NS  H12  C3   C2   111.80  3.000
 6NS  H11  C3   C2   110.24  3.000
 6NS  H10  C3   C2   112.40  3.000
 6NS  H15  C1   H14  107.20  3.000
 6NS  H15  C1   H13  107.94  3.000
 6NS  H14  C1   H13  107.52  3.000
 6NS  H15  C1   C2   112.32  3.000
 6NS  H14  C1   C2   110.14  3.000
 6NS  H13  C1   C2   111.50  3.000
 6NS  C13  C12  C15  106.15  3.000
 6NS  C15  C12  C11  128.40  3.000
 6NS  C13  C12  C11  125.45  3.000
 6NS  C14  C15  C16  117.03  3.000
 6NS  C16  C15  C12  136.34  3.000
 6NS  C14  C15  C12  106.63  3.000
 6NS  H16  C16  C17  121.90  3.000
 6NS  H16  C16  C15  122.09  3.000
 6NS  C17  C16  C15  116.00  3.000
 6NS  C18  C17  F1   117.95  3.000
 6NS  F1   C17  C16  119.60  3.000
 6NS  C18  C17  C16  122.45  3.000
 6NS  H17  C18  N5   117.71  3.000
 6NS  H17  C18  C17  120.06  3.000
 6NS  N5   C18  C17  122.23  3.000
 6NS  C14  N5   C18  115.71  3.000
 6NS  N4   C14  N5   125.76  3.000
 6NS  N4   C14  C15  107.67  3.000
 6NS  N5   C14  C15  126.57  3.000
 6NS  H18  N4   C13  125.34  3.000
 6NS  H18  N4   C14  125.36  3.000
 6NS  C13  N4   C14  109.29  3.000
 6NS  H19  C13  N4   120.94  3.000
 6NS  H19  C13  C12  128.80  3.000
 6NS  N4   C13  C12  110.26  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
 6NS  CONST_01  C11  N2   C10  C9     0.00   0.0  0
 6NS  CONST_02  C11  N3   C8   C9     0.00   0.0  0
 6NS  CONST_03  C12  C11  N2   C10  180.00   0.0  0
 6NS  CONST_04  N3   C11  N2   C10    0.00   0.0  0
 6NS  CONST_05  N3   C8   C9   C10    0.00   0.0  0
 6NS  CONST_06  C13  C12  C11  N2   180.00   0.0  0
 6NS  CONST_07  C15  C12  C11  N2     0.00   0.0  0
 6NS  CONST_08  C8   N3   C11  N2     0.00   0.0  0
 6NS  CONST_09  C8   C9   C10  N2     0.00   0.0  0
 6NS  CONST_10  N4   C13  C12  C11  180.00   0.0  0
 6NS  CONST_11  C14  C15  C12  C11  180.00   0.0  0
 6NS  CONST_12  C16  C15  C12  C11    0.00   0.0  0
 6NS  CONST_13  C13  C12  C11  N3     0.00   0.0  0
 6NS  CONST_14  C15  C12  C11  N3   180.00   0.0  0
 6NS  CONST_15  C12  C11  N3   C8   180.00   0.0  0
 6NS  CONST_16  C14  N4   C13  C12    0.00   0.0  0
 6NS  CONST_17  N5   C14  C15  C12  180.00   0.0  0
 6NS  CONST_18  N4   C14  C15  C12    0.00   0.0  0
 6NS  CONST_19  C17  C16  C15  C12  180.00   0.0  0
 6NS  CONST_20  C18  N5   C14  C15    0.00   0.0  0
 6NS  CONST_21  C13  N4   C14  C15    0.00   0.0  0
 6NS  CONST_22  N4   C13  C12  C15    0.00   0.0  0
 6NS  CONST_23  C18  C17  C16  C15    0.00   0.0  0
 6NS  CONST_24  N5   C14  C15  C16    0.00   0.0  0
 6NS  CONST_25  N4   C14  C15  C16  180.00   0.0  0
 6NS  CONST_26  C13  C12  C15  C16  180.00   0.0  0
 6NS  CONST_27  N5   C18  C17  C16    0.00   0.0  0
 6NS  CONST_28  C14  N5   C18  C17    0.00   0.0  0
 6NS  CONST_29  C14  C15  C16  C17    0.00   0.0  0
 6NS  CONST_30  N4   C14  N5   C18  180.00   0.0  0
 6NS  CONST_31  C13  N4   C14  N5   180.00   0.0  0
 6NS  CONST_32  C13  C12  C15  C14    0.00   0.0  0
 6NS  CONST_33  N2   C10  C9   F2   180.00   0.0  0
 6NS  CONST_34  N3   C8   C9   F2   180.00   0.0  0
 6NS  CONST_35  N1   C8   C9   C10  180.00   0.0  0
 6NS  CONST_36  N1   C8   N3   C11  180.00   0.0  0
 6NS  CONST_37  F1   C17  C16  C15  180.00   0.0  0
 6NS  CONST_38  N5   C18  C17  F1   180.00   0.0  0
 6NS  CONST_39  H19  C13  C12  C11    0.00   0.0  0
 6NS  CONST_40  H1   C10  N2   C11  180.00   0.0  0
 6NS  CONST_41  H18  N4   C13  C12  180.00   0.0  0
 6NS  CONST_42  H16  C16  C15  C12    0.00   0.0  0
 6NS  CONST_43  H17  C18  C17  C16  180.00   0.0  0
 6NS  CONST_44  C5   N1   C8   C9   180.00   0.0  0
 6NS  CONST_45  C5   N1   C8   N3     0.00   0.0  0
 6NS  CONST_46  H2   N1   C8   C9     0.00   0.0  0
 6NS  CONST_47  H6   O2   C7   C6   180.00   0.0  0
 6NS  Var_01    O1   C7   C6   C5    30.02  30.0  2
 6NS  Var_02    H10  C3   C2   C5    59.47  30.0  3
 6NS  Var_03    H7   C4   C2   C5    62.81  30.0  3
 6NS  Var_04    H13  C1   C2   C5    50.40  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
 6NS  chir_01  C5  C6  N1  C2  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
 6NS  plan-1  F2   0.020
 6NS  plan-1  C9   0.020
 6NS  plan-1  C10  0.020
 6NS  plan-1  N2   0.020
 6NS  plan-1  C11  0.020
 6NS  plan-1  N3   0.020
 6NS  plan-1  C8   0.020
 6NS  plan-1  N1   0.020
 6NS  plan-1  C12  0.020
 6NS  plan-1  H1   0.020
 6NS  plan-2  C11  0.020
 6NS  plan-2  C12  0.020
 6NS  plan-2  C15  0.020
 6NS  plan-2  C16  0.020
 6NS  plan-2  C17  0.020
 6NS  plan-2  F1   0.020
 6NS  plan-2  C18  0.020
 6NS  plan-2  N5   0.020
 6NS  plan-2  C14  0.020
 6NS  plan-2  N4   0.020
 6NS  plan-2  C13  0.020
 6NS  plan-2  H16  0.020
 6NS  plan-2  H17  0.020
 6NS  plan-2  H18  0.020
 6NS  plan-2  H19  0.020
 6NS  plan-3  C8   0.020
 6NS  plan-3  N1   0.020
 6NS  plan-3  C5   0.020
 6NS  plan-3  H2   0.020
 6NS  plan-4  C6   0.020
 6NS  plan-4  C7   0.020
 6NS  plan-4  O2   0.020
 6NS  plan-4  O1   0.020
 6NS  plan-4  H6   0.020

