# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 22:52:02 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 8-(1-methyl-1H-imidazol-4-yl)-2-(4,4,4-trifluorobutoxy)pyrido[3,4-d]pyrimidin-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cnc(c1)c2nccc3c(O)nc(OCCCC(F)(F)F)nc23
#
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
 6EB  6EB  8-(1-methyl-1H-imidazol-4-yl)-2-(4,4,4-trifluorobutoxy)pyrido[3,4-d]pyrimidin-4-ol  ligand  39  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_6EB
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
 6EB  C10  C  CR6   0   0.573  -0.1845   0.8389   0.0249
 6EB  C13  C  CH2   0  -0.496  -3.5947  -0.3961  -0.0434
 6EB  C15  C  CT    0   1.003  -6.0897  -0.8064  -0.0613
 6EB  C20  C  CR6   0   0.524   0.7216   2.9035   0.0866
 6EB  C22  C  CR66  0  -0.043   2.0317   2.3295   0.0872
 6EB  C24  C  CR16  0  -0.097   4.4032   2.3557   0.0477
 6EB  N02  N  NR5   0  -0.398   4.5065  -3.0993  -0.1424
 6EB  C03  C  CR15  0   0.076   3.2619  -3.2364   0.3711
 6EB  N04  N  N     0  -0.433   2.6599  -2.0881   0.5163
 6EB  C05  C  CR5   0   0.090   3.5556  -1.1505   0.0832
 6EB  C06  C  CR15  0  -0.053   4.7143  -1.7722  -0.3248
 6EB  C07  C  CR6   0   0.114   3.3544   0.2973   0.0797
 6EB  C08  C  CR66  0   0.189   2.0637   0.9207   0.0728
 6EB  N09  N  N     0  -0.458   0.9396   0.1817   0.0303
 6EB  O11  O  O2    0  -0.452  -1.2741   0.0848  -0.0188
 6EB  C12  C  CH2   0  -0.152  -2.5578   0.7077  -0.0200
 6EB  C14  C  CH2   0  -0.654  -4.9911   0.2185  -0.0367
 6EB  F16  F  F     0  -0.315  -6.0385  -1.5863  -1.1535
 6EB  F17  F  F     0  -0.315  -6.0452  -1.6322   0.9967
 6EB  F18  F  F     0  -0.312  -7.3049  -0.2376  -0.0531
 6EB  N19  N  N     0  -0.478  -0.3498   2.1686   0.0588
 6EB  O21  O  OH1   0  -0.565   0.5110   4.2046   0.1107
 6EB  C23  C  CR16  0  -0.362   3.2307   3.0592   0.0779
 6EB  N25  N  N     0  -0.421   4.4550   1.0172   0.0581
 6EB  H1   H  HCH2  0   0.256  -3.4546  -1.0111  -0.9348
 6EB  H2   H  HCR6  0   0.271   5.3549   2.8721   0.0255
 6EB  H3   H  HCH3  0   0.264   6.2825  -4.1286   0.2774
 6EB  H4   H  HCH3  0   0.265   4.9400  -5.1198  -0.3094
 6EB  H5   H  HCH3  0   0.265   5.8228  -4.0817  -1.4340
 6EB  H6   H  HCR5  0   0.281   2.8504  -4.2037   0.6186
 6EB  H7   H  HCR5  0   0.292   5.6321  -1.3819  -0.7308
 6EB  H8   H  HCH2  0   0.236  -2.6632   1.3562  -0.8933
 6EB  H9   H  HCH2  0   0.236  -2.6773   1.3299   0.8704
 6EB  H10  H  HCH2  0   0.281  -5.1283   0.8383   0.8528
 6EB  H12  H  HCR6  0   0.268   3.2643   4.1409   0.0882
 6EB  H13  H  HCH2  0   0.256  -3.4601  -1.0411   0.8274
 6EB  H14  H  HCH2  0   0.281  -5.1228   0.8732  -0.9016
 6EB  H11  H  HOH1  0   0.500   1.3275   4.7177   0.1406
 6EB  C01  C  CH3   0  -0.518   5.4456  -4.1642  -0.4174

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
 6EB  C03  N02  aromatic  1.353  0.020  1.353
 6EB  C03  N04  aromatic  1.305  0.020  1.305
 6EB  C01  N02  single    1.446  0.020  1.446
 6EB  N02  C06  aromatic  1.356  0.020  1.356
 6EB  N04  C05  aromatic  1.367  0.020  1.367
 6EB  C06  C05  aromatic  1.377  0.020  1.377
 6EB  C05  C07  single    1.462  0.020  1.462
 6EB  N25  C07  aromatic  1.315  0.020  1.315
 6EB  N25  C24  aromatic  1.340  0.020  1.340
 6EB  C07  C08  aromatic  1.433  0.020  1.433
 6EB  C24  C23  aromatic  1.368  0.020  1.368
 6EB  C08  N09  aromatic  1.346  0.020  1.346
 6EB  C08  C22  aromatic  1.409  0.020  1.409
 6EB  N09  C10  aromatic  1.302  0.020  1.302
 6EB  F18  C15  single    1.342  0.020  1.342
 6EB  C23  C22  aromatic  1.404  0.020  1.404
 6EB  C12  C13  single    1.515  0.020  1.515
 6EB  C12  O11  single    1.427  0.020  1.427
 6EB  C22  C20  aromatic  1.430  0.020  1.430
 6EB  C14  C13  single    1.526  0.020  1.526
 6EB  C14  C15  single    1.503  0.020  1.503
 6EB  C10  O11  single    1.326  0.020  1.326
 6EB  C10  N19  aromatic  1.340  0.020  1.340
 6EB  C15  F17  single    1.343  0.020  1.343
 6EB  C15  F16  single    1.343  0.020  1.343
 6EB  C20  N19  aromatic  1.299  0.020  1.299
 6EB  C20  O21  single    1.318  0.020  1.318
 6EB  C13  H1   single    0.970  0.020  1.090
 6EB  C24  H2   single    0.930  0.020  1.080
 6EB  C01  H3   single    0.970  0.020  1.090
 6EB  C01  H4   single    0.970  0.020  1.090
 6EB  C01  H5   single    0.970  0.020  1.090
 6EB  C03  H6   single    0.930  0.020  1.080
 6EB  C06  H7   single    0.930  0.020  1.080
 6EB  C12  H8   single    0.970  0.020  1.090
 6EB  C12  H9   single    0.970  0.020  1.090
 6EB  C14  H10  single    0.970  0.020  1.090
 6EB  C23  H12  single    0.930  0.020  1.080
 6EB  C13  H13  single    0.970  0.020  1.090
 6EB  C14  H14  single    0.970  0.020  1.090
 6EB  O21  H11  single    0.850  0.020  0.980

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
 6EB  N19  C10  O11  117.63  3.000
 6EB  N19  C10  N09  127.38  3.000
 6EB  O11  C10  N09  114.99  3.000
 6EB  H13  C13  H1   107.60  3.000
 6EB  H13  C13  C14  110.32  3.000
 6EB  H1   C13  C14  110.36  3.000
 6EB  H13  C13  C12  109.50  3.000
 6EB  H1   C13  C12  109.59  3.000
 6EB  C14  C13  C12  109.45  3.000
 6EB  F18  C15  F17  106.61  3.000
 6EB  F17  C15  F16  106.40  3.000
 6EB  F18  C15  F16  106.60  3.000
 6EB  F16  C15  C14  112.43  3.000
 6EB  F17  C15  C14  112.48  3.000
 6EB  F18  C15  C14  111.90  3.000
 6EB  O21  C20  N19  115.27  3.000
 6EB  O21  C20  C22  122.85  3.000
 6EB  N19  C20  C22  121.89  3.000
 6EB  C23  C22  C08  120.01  3.000
 6EB  C23  C22  C20  125.02  3.000
 6EB  C08  C22  C20  114.96  3.000
 6EB  H2   C24  N25  116.27  3.000
 6EB  H2   C24  C23  120.57  3.000
 6EB  N25  C24  C23  123.16  3.000
 6EB  C06  N02  C03  106.93  3.000
 6EB  C06  N02  C01  126.57  3.000
 6EB  C03  N02  C01  126.49  3.000
 6EB  H6   C03  N04  125.95  3.000
 6EB  H6   C03  N02  121.88  3.000
 6EB  N04  C03  N02  112.17  3.000
 6EB  C05  N04  C03  105.43  3.000
 6EB  C07  C05  C06  124.22  3.000
 6EB  C07  C05  N04  126.15  3.000
 6EB  C06  C05  N04  109.61  3.000
 6EB  H7   C06  C05  131.72  3.000
 6EB  H7   C06  N02  122.42  3.000
 6EB  C05  C06  N02  105.86  3.000
 6EB  N25  C07  C08  121.02  3.000
 6EB  C08  C07  C05  123.69  3.000
 6EB  N25  C07  C05  115.28  3.000
 6EB  N09  C08  C07  120.89  3.000
 6EB  N09  C08  C22  122.02  3.000
 6EB  C07  C08  C22  117.08  3.000
 6EB  C08  N09  C10  116.36  3.000
 6EB  C12  O11  C10  119.42  3.000
 6EB  H9   C12  H8   107.62  3.000
 6EB  H9   C12  O11  110.26  3.000
 6EB  H8   C12  O11  110.27  3.000
 6EB  H9   C12  C13  110.65  3.000
 6EB  H8   C12  C13  110.74  3.000
 6EB  O11  C12  C13  107.32  3.000
 6EB  H14  C14  H10  106.82  3.000
 6EB  H14  C14  C15  107.92  3.000
 6EB  H10  C14  C15  107.97  3.000
 6EB  H14  C14  C13  110.37  3.000
 6EB  H10  C14  C13  110.30  3.000
 6EB  C15  C14  C13  113.23  3.000
 6EB  C20  N19  C10  117.38  3.000
 6EB  H11  O21  C20  112.97  3.000
 6EB  H12  C23  C24  119.19  3.000
 6EB  H12  C23  C22  123.10  3.000
 6EB  C24  C23  C22  117.71  3.000
 6EB  C07  N25  C24  120.98  3.000
 6EB  H5   C01  H4   108.73  3.000
 6EB  H5   C01  H3   109.12  3.000
 6EB  H4   C01  H3   108.85  3.000
 6EB  H5   C01  N02  110.31  3.000
 6EB  H4   C01  N02  109.06  3.000
 6EB  H3   C01  N02  110.73  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
 6EB  CONST_01  C07  C08  N09  C10   180.00   0.0  0
 6EB  CONST_02  C22  C08  N09  C10     0.00   0.0  0
 6EB  CONST_03  C22  C20  N19  C10     0.00   0.0  0
 6EB  CONST_04  C07  C08  C22  C20   180.00   0.0  0
 6EB  CONST_05  N09  C08  C22  C20     0.00   0.0  0
 6EB  CONST_06  C24  C23  C22  C20   180.00   0.0  0
 6EB  CONST_07  N09  C10  N19  C20     0.00   0.0  0
 6EB  CONST_08  C05  C07  C08  C22   180.00   0.0  0
 6EB  CONST_09  N25  C07  C08  C22     0.00   0.0  0
 6EB  CONST_10  N25  C24  C23  C22     0.00   0.0  0
 6EB  CONST_11  C05  C07  N25  C24   180.00   0.0  0
 6EB  CONST_12  C08  C07  N25  C24     0.00   0.0  0
 6EB  CONST_13  C08  C22  C23  C24     0.00   0.0  0
 6EB  CONST_14  C05  N04  C03  N02     0.00   0.0  0
 6EB  CONST_15  N04  C05  C06  N02     0.00   0.0  0
 6EB  CONST_16  C07  C05  C06  N02   180.00   0.0  0
 6EB  CONST_17  C05  C06  N02  C03     0.00   0.0  0
 6EB  CONST_18  C06  C05  N04  C03     0.00   0.0  0
 6EB  CONST_19  C07  C05  N04  C03   180.00   0.0  0
 6EB  CONST_20  C06  N02  C03  N04     0.00   0.0  0
 6EB  CONST_23  N09  C08  C07  C05     0.00   0.0  0
 6EB  CONST_26  C23  C24  N25  C07     0.00   0.0  0
 6EB  CONST_27  C23  C22  C08  C07     0.00   0.0  0
 6EB  CONST_28  N19  C10  N09  C08     0.00   0.0  0
 6EB  CONST_29  N19  C20  C22  C08     0.00   0.0  0
 6EB  CONST_30  N25  C07  C08  N09   180.00   0.0  0
 6EB  CONST_31  C23  C22  C08  N09   180.00   0.0  0
 6EB  CONST_32  C23  C22  C20  N19   180.00   0.0  0
 6EB  CONST_33  O21  C20  N19  C10   180.00   0.0  0
 6EB  CONST_34  O11  C10  N19  C20   180.00   0.0  0
 6EB  CONST_35  N04  C03  N02  C01   180.00   0.0  0
 6EB  CONST_36  C05  C06  N02  C01   180.00   0.0  0
 6EB  CONST_37  O11  C10  N09  C08   180.00   0.0  0
 6EB  CONST_38  O21  C20  C22  C08   180.00   0.0  0
 6EB  CONST_39  C23  C22  C20  O21     0.00   0.0  0
 6EB  CONST_40  H12  C23  C22  C20     0.00   0.0  0
 6EB  CONST_41  H2   C24  C23  C22   180.00   0.0  0
 6EB  CONST_42  H7   C06  N02  C03   180.00   0.0  0
 6EB  CONST_43  H6   C03  N04  C05   180.00   0.0  0
 6EB  Var_01    N19  C10  O11  C12    -0.37  30.0  1
 6EB  Var_02    H3   C01  N02  C03  -110.05  30.0  2
 6EB  Var_03    C13  C12  O11  C10  -178.77  30.0  1
 6EB  Var_04    F18  C15  C14  C13   179.92  30.0  3
 6EB  Var_05    C12  C13  C14  C15   179.90  30.0  3
 6EB  Var_06    C14  C13  C12  O11   179.65  30.0  3

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
 6EB  plan-1  N02  0.020
 6EB  plan-1  C03  0.020
 6EB  plan-1  N04  0.020
 6EB  plan-1  C05  0.020
 6EB  plan-1  C06  0.020
 6EB  plan-1  C07  0.020
 6EB  plan-1  H6   0.020
 6EB  plan-1  H7   0.020
 6EB  plan-1  C01  0.020
 6EB  plan-2  C10  0.020
 6EB  plan-2  C20  0.020
 6EB  plan-2  C22  0.020
 6EB  plan-2  C24  0.020
 6EB  plan-2  C05  0.020
 6EB  plan-2  C07  0.020
 6EB  plan-2  C08  0.020
 6EB  plan-2  N09  0.020
 6EB  plan-2  O11  0.020
 6EB  plan-2  N19  0.020
 6EB  plan-2  O21  0.020
 6EB  plan-2  C23  0.020
 6EB  plan-2  N25  0.020
 6EB  plan-2  H2   0.020
 6EB  plan-2  H12  0.020

