# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 14:07:14 2022
#   Inital geometry file: a 134 line input string
#   Ligand name: 4-(2-bromoanilino)-2-[(6-methoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-7-yl)amino]pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2CCN(C)Cc2cc1Nc3ncc(C(N)=O)c(Nc4ccccc4Br)n3
#
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
 YK4  YK4  4-(2-bromoanilino)-2-[(6-methoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-7-yl)amino]pyrimidine-5-carboxamide  ligand  54  31  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_YK4
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
 YK4  C2    C   CR6   0   0.611   8.1949   4.2937   4.5250
 YK4  C4    C   CR6   0   0.584   8.5303   3.4932   2.4198
 YK4  C5    C   CR6   0  -0.278   8.0946   4.7298   1.8708
 YK4  C6    C   CR16  0  -0.033   7.7041   5.6713   2.8172
 YK4  C7    C   C     0   0.532   8.0328   4.9642   0.4152
 YK4  N10   N   NH1   0  -0.777   8.9031   2.4655   1.6340
 YK4  C11   C   CR6   0   0.373   9.4623   1.2677   2.1019
 YK4  C12   C   CR6   0  -0.169   8.8808   0.0363   1.8029
 YK4  C15   C   CR16  0  -0.252  11.2170   0.0946   3.2786
 YK4  C16   C   CR16  0  -0.267  10.6426   1.2752   2.8439
 YK4  C19   C   CR6   0   0.263   8.5736   3.0324   6.6490
 YK4  C21   C   CR16  0  -0.433   8.9457   2.2057   8.8929
 YK4  C23   C   CR6   0   0.042   9.1106   0.6989   7.0354
 YK4  C24   C   CR16  0  -0.354   8.8058   1.7512   6.1726
 YK4  C27   C   CH2   0  -0.293  10.1180  -1.3858   8.6020
 YK4  C31   C   CH3   0  -0.431   8.4841   4.8276   9.8188
 YK4  N1    N   N     0  -0.482   7.7420   5.4929   4.1209
 YK4  N3    N   N     0  -0.516   8.5756   3.3065   3.7339
 YK4  O8    O   O     0  -0.504   8.1331   4.0348  -0.3898
 YK4  N9    N   NH2   0  -0.819   7.8464   6.2250  -0.0054
 YK4  C13   C   CR16  0  -0.241   9.4615  -1.1556   2.2182
 YK4  C14   C   CR16  0  -0.252  10.6303  -1.1237   2.9604
 YK4  BR17  BR  BR    0  -0.032   7.2664  -0.0300   0.8288
 YK4  N18   N   NH1   0  -0.757   8.2347   4.1371   5.8672
 YK4  C20   C   CR6   0   0.325   8.6519   3.2545   8.0423
 YK4  C22   C   CR6   0   0.064   9.1789   0.9189   8.4009
 YK4  C25   C   CH2   0  -0.304   9.4005  -0.6563   6.4494
 YK4  N26   N   NT    0  -0.415   9.3245  -1.7132   7.4331
 YK4  C28   C   CH2   0  -0.495   9.4903  -0.2144   9.3381
 YK4  C29   C   CH3   0  -0.518   9.7046  -2.9787   6.8498
 YK4  O30   O   O2    0  -0.485   8.4217   4.5242   8.4405
 YK4  H1    H   HCR6  0   0.264   7.3180   6.6360   2.5040
 YK4  H2    H   HNH1  0   0.426   8.7370   2.6037   0.6400
 YK4  H3    H   HCR6  0   0.268  12.1299   0.1248   3.8582
 YK4  H4    H   HCR6  0   0.273  11.1130   2.2228   3.0693
 YK4  H5    H   HCR6  0   0.271   9.0032   2.3676   9.9623
 YK4  H6    H   HCR6  0   0.293   8.7617   1.5655   5.1105
 YK4  H7    H   HCH2  0   0.237  10.1530  -2.2573   9.2583
 YK4  H8    H   HCH2  0   0.195  11.1612  -1.1458   8.3315
 YK4  H9    H   HCH3  0   0.261   8.2867   5.8927   9.9097
 YK4  H10   H   HCH3  0   0.229   7.7321   4.2780  10.3909
 YK4  H11   H   HCH3  0   0.229   9.4713   4.6143  10.2363
 YK4  H12   H   HNH2  0   0.406   7.8221   6.4071  -0.9955
 YK4  H13   H   HNH2  0   0.412   7.9056   7.0267   0.5968
 YK4  H14   H   HCR6  0   0.281   9.0013  -2.1034   1.9730
 YK4  H15   H   HCR6  0   0.268  11.0772  -2.0515   3.2913
 YK4  H16   H   HNH1  0   0.408   7.9524   4.9617   6.3757
 YK4  H17   H   HCH2  0   0.241   8.6914  -0.8702   5.6443
 YK4  H18   H   HCH2  0   0.208  10.3972  -0.6247   5.9713
 YK4  H20   H   HCH2  0   0.241  10.1574   0.1255  10.1340
 YK4  H21   H   HCH2  0   0.242   8.5710  -0.5477   9.8295
 YK4  H22   H   HCH3  0   0.235   9.5963  -3.7789   7.5831
 YK4  H23   H   HCH3  0   0.232   9.0560  -3.2100   6.0030
 YK4  H24   H   HCH3  0   0.191  10.7437  -2.9946   6.4839

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
 YK4  BR17  C12  single    1.887  0.020  1.887
 YK4  O8    C7   double    1.234  0.020  1.234
 YK4  N9    C7   single    1.342  0.020  1.342
 YK4  C7    C5   single    1.476  0.020  1.476
 YK4  C12   C13  aromatic  1.389  0.020  1.389
 YK4  C12   C11  aromatic  1.394  0.020  1.394
 YK4  C13   C14  aromatic  1.385  0.020  1.385
 YK4  N10   C11  single    1.402  0.020  1.402
 YK4  N10   C4   single    1.346  0.020  1.346
 YK4  C11   C16  aromatic  1.394  0.020  1.394
 YK4  C5    C4   aromatic  1.421  0.020  1.421
 YK4  C5    C6   aromatic  1.391  0.020  1.391
 YK4  C14   C15  aromatic  1.389  0.020  1.389
 YK4  C4    N3   aromatic  1.328  0.020  1.328
 YK4  C6    N1   aromatic  1.316  0.020  1.316
 YK4  C16   C15  aromatic  1.383  0.020  1.383
 YK4  N3    C2   aromatic  1.321  0.020  1.321
 YK4  N1    C2   aromatic  1.344  0.020  1.344
 YK4  C2    N18  single    1.352  0.020  1.352
 YK4  N18   C19  single    1.395  0.020  1.395
 YK4  C24   C19  aromatic  1.387  0.020  1.387
 YK4  C24   C23  aromatic  1.395  0.020  1.395
 YK4  C25   C23  single    1.505  0.020  1.505
 YK4  C25   N26  single    1.446  0.020  1.446
 YK4  C19   C20  aromatic  1.413  0.020  1.413
 YK4  C29   N26  single    1.444  0.020  1.444
 YK4  C23   C22  aromatic  1.385  0.020  1.385
 YK4  N26   C27  single    1.450  0.020  1.450
 YK4  C20   O30  single    1.350  0.020  1.350
 YK4  C20   C21  aromatic  1.382  0.020  1.382
 YK4  O30   C31  single    1.413  0.020  1.413
 YK4  C22   C21  aromatic  1.397  0.020  1.397
 YK4  C22   C28  single    1.503  0.020  1.503
 YK4  C27   C28  single    1.519  0.020  1.519
 YK4  C6    H1   single    0.930  0.020  1.080
 YK4  N10   H2   single    0.860  0.020  1.020
 YK4  C15   H3   single    0.930  0.020  1.080
 YK4  C16   H4   single    0.930  0.020  1.080
 YK4  C21   H5   single    0.930  0.020  1.080
 YK4  C24   H6   single    0.930  0.020  1.080
 YK4  C27   H7   single    0.970  0.020  1.090
 YK4  C27   H8   single    0.970  0.020  1.090
 YK4  C31   H9   single    0.970  0.020  1.090
 YK4  C31   H10  single    0.970  0.020  1.090
 YK4  C31   H11  single    0.970  0.020  1.090
 YK4  N9    H12  single    0.860  0.020  1.020
 YK4  N9    H13  single    0.860  0.020  1.020
 YK4  C13   H14  single    0.930  0.020  1.080
 YK4  C14   H15  single    0.930  0.020  1.080
 YK4  N18   H16  single    0.860  0.020  1.020
 YK4  C25   H17  single    0.970  0.020  1.090
 YK4  C25   H18  single    0.970  0.020  1.090
 YK4  C28   H20  single    0.970  0.020  1.090
 YK4  C28   H21  single    0.970  0.020  1.090
 YK4  C29   H22  single    0.970  0.020  1.090
 YK4  C29   H23  single    0.970  0.020  1.090
 YK4  C29   H24  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
 YK4  N18   C2   N3   119.96  3.000
 YK4  N18   C2   N1   114.32  3.000
 YK4  N3    C2   N1   125.72  3.000
 YK4  N3    C4   N10  117.44  3.000
 YK4  N3    C4   C5   120.99  3.000
 YK4  N10   C4   C5   121.57  3.000
 YK4  C7    C5   C6   123.50  3.000
 YK4  C6    C5   C4   114.34  3.000
 YK4  C7    C5   C4   122.14  3.000
 YK4  H1    C6   N1   114.62  3.000
 YK4  H1    C6   C5   120.34  3.000
 YK4  N1    C6   C5   125.03  3.000
 YK4  N9    C7   O8   120.97  3.000
 YK4  N9    C7   C5   117.65  3.000
 YK4  O8    C7   C5   121.38  3.000
 YK4  H2    N10  C11  120.47  3.000
 YK4  H2    N10  C4   114.92  3.000
 YK4  C11   N10  C4   124.59  3.000
 YK4  C16   C11  C12  118.17  3.000
 YK4  C16   C11  N10  120.70  3.000
 YK4  C12   C11  N10  121.10  3.000
 YK4  BR17  C12  C13  118.81  3.000
 YK4  C13   C12  C11  121.28  3.000
 YK4  BR17  C12  C11  119.91  3.000
 YK4  H3    C15  C14  120.24  3.000
 YK4  H3    C15  C16  119.67  3.000
 YK4  C14   C15  C16  120.08  3.000
 YK4  H4    C16  C15  120.11  3.000
 YK4  H4    C16  C11  118.93  3.000
 YK4  C15   C16  C11  120.95  3.000
 YK4  C20   C19  N18  116.21  3.000
 YK4  C20   C19  C24  118.35  3.000
 YK4  N18   C19  C24  125.43  3.000
 YK4  H5    C21  C22  118.46  3.000
 YK4  H5    C21  C20  120.37  3.000
 YK4  C22   C21  C20  121.17  3.000
 YK4  C25   C23  C22  121.17  3.000
 YK4  C22   C23  C24  120.07  3.000
 YK4  C25   C23  C24  118.74  3.000
 YK4  H6    C24  C23  119.21  3.000
 YK4  H6    C24  C19  119.37  3.000
 YK4  C23   C24  C19  121.42  3.000
 YK4  H8    C27  H7   106.89  3.000
 YK4  H8    C27  C28  109.97  3.000
 YK4  H7    C27  C28  109.72  3.000
 YK4  H8    C27  N26  111.63  3.000
 YK4  H7    C27  N26  108.78  3.000
 YK4  C28   C27  N26  109.79  3.000
 YK4  H11   C31  H10  108.87  3.000
 YK4  H11   C31  H9   108.86  3.000
 YK4  H10   C31  H9   108.90  3.000
 YK4  H11   C31  O30  111.76  3.000
 YK4  H10   C31  O30  111.85  3.000
 YK4  H9    C31  O30  106.50  3.000
 YK4  C6    N1   C2   115.37  3.000
 YK4  C4    N3   C2   118.53  3.000
 YK4  H13   N9   H12  116.53  3.000
 YK4  H13   N9   C7   123.62  3.000
 YK4  H12   N9   C7   118.77  3.000
 YK4  H14   C13  C14  120.05  3.000
 YK4  H14   C13  C12  120.40  3.000
 YK4  C14   C13  C12  119.55  3.000
 YK4  H15   C14  C13  119.53  3.000
 YK4  H15   C14  C15  120.51  3.000
 YK4  C13   C14  C15  119.97  3.000
 YK4  H16   N18  C19  115.63  3.000
 YK4  H16   N18  C2   113.42  3.000
 YK4  C19   N18  C2   130.94  3.000
 YK4  O30   C20  C21  124.63  3.000
 YK4  C21   C20  C19  119.96  3.000
 YK4  O30   C20  C19  115.41  3.000
 YK4  C28   C22  C23  120.35  3.000
 YK4  C28   C22  C21  120.62  3.000
 YK4  C23   C22  C21  119.03  3.000
 YK4  H18   C25  H17  105.76  3.000
 YK4  H18   C25  N26  111.25  3.000
 YK4  H17   C25  N26  108.89  3.000
 YK4  H18   C25  C23  108.44  3.000
 YK4  H17   C25  C23  109.75  3.000
 YK4  N26   C25  C23  112.54  3.000
 YK4  C29   N26  C25  110.60  3.000
 YK4  C29   N26  C27  112.29  3.000
 YK4  C25   N26  C27  110.77  3.000
 YK4  H21   C28  H20  106.30  3.000
 YK4  H21   C28  C22  109.61  3.000
 YK4  H20   C28  C22  110.25  3.000
 YK4  H21   C28  C27  109.26  3.000
 YK4  H20   C28  C27  109.91  3.000
 YK4  C22   C28  C27  111.39  3.000
 YK4  H24   C29  H23  107.45  3.000
 YK4  H24   C29  H22  107.84  3.000
 YK4  H23   C29  H22  107.89  3.000
 YK4  H24   C29  N26  113.26  3.000
 YK4  H23   C29  N26  110.03  3.000
 YK4  H22   C29  N26  110.19  3.000
 YK4  C20   O30  C31  118.82  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
 YK4  CONST_01  C5    C4   N3   C2      0.00   0.0  0
 YK4  CONST_02  C5    C6   N1   C2      0.00   0.0  0
 YK4  CONST_03  N1    C6   C5   C4      0.00   0.0  0
 YK4  CONST_04  N1    C2   N3   C4      0.00   0.0  0
 YK4  CONST_05  N3    C4   C5   C6      0.00   0.0  0
 YK4  CONST_06  N3    C2   N1   C6      0.00   0.0  0
 YK4  CONST_07  C14   C13  C12  C11     0.00   0.0  0
 YK4  CONST_08  C14   C15  C16  C11     0.00   0.0  0
 YK4  CONST_09  C15   C14  C13  C12     0.00   0.0  0
 YK4  CONST_10  C15   C16  C11  C12     0.00   0.0  0
 YK4  CONST_11  C13   C12  C11  C16     0.00   0.0  0
 YK4  CONST_12  C13   C14  C15  C16     0.00   0.0  0
 YK4  CONST_13  C22   C23  C24  C19     0.00   0.0  0
 YK4  CONST_14  C22   C21  C20  C19     0.00   0.0  0
 YK4  CONST_15  C24   C19  C20  C21     0.00   0.0  0
 YK4  CONST_16  C24   C23  C22  C21     0.00   0.0  0
 YK4  CONST_17  C20   C19  C24  C23     0.00   0.0  0
 YK4  CONST_18  C20   C21  C22  C23     0.00   0.0  0
 YK4  CONST_19  N10   C4   N3   C2    180.00   0.0  0
 YK4  CONST_20  N18   C2   N3   C4    180.00   0.0  0
 YK4  CONST_21  N10   C4   C5   C6    180.00   0.0  0
 YK4  CONST_22  N18   C2   N1   C6    180.00   0.0  0
 YK4  CONST_23  N3    C4   C5   C7    180.00   0.0  0
 YK4  CONST_24  N1    C6   C5   C7    180.00   0.0  0
 YK4  CONST_25  C13   C12  C11  N10   180.00   0.0  0
 YK4  CONST_26  C15   C16  C11  N10   180.00   0.0  0
 YK4  CONST_27  BR17  C12  C11  C16   180.00   0.0  0
 YK4  CONST_28  N18   C19  C20  C21   180.00   0.0  0
 YK4  CONST_29  N18   C19  C24  C23   180.00   0.0  0
 YK4  CONST_30  O30   C20  C19  C24   180.00   0.0  0
 YK4  CONST_31  BR17  C12  C13  C14   180.00   0.0  0
 YK4  CONST_32  O30   C20  C21  C22   180.00   0.0  0
 YK4  CONST_33  H1    C6   N1   C2    180.00   0.0  0
 YK4  CONST_34  H14   C13  C12  C11   180.00   0.0  0
 YK4  CONST_35  H3    C15  C16  C11   180.00   0.0  0
 YK4  CONST_36  H15   C14  C13  C12   180.00   0.0  0
 YK4  CONST_37  H4    C16  C11  C12   180.00   0.0  0
 YK4  CONST_38  H5    C21  C20  C19   180.00   0.0  0
 YK4  CONST_39  H6    C24  C19  C20   180.00   0.0  0
 YK4  CONST_40  H12   N9   C7   C5    180.00   0.0  0
 YK4  CONST_41  H13   N9   C7   C5      0.00   0.0  0
 YK4  Var_01    C27   C28  C22  C21  -162.43  30.0  1
 YK4  Var_02    C27   N26  C25  C23   -50.64  30.0  1
 YK4  Var_03    N26   C25  C23  C24  -163.56  30.0  1
 YK4  Var_04    N26   C27  C28  C22   -49.49  30.0  1
 YK4  Var_05    C28   C27  N26  C25    67.81  30.0  1
 YK4  Var_06    C24   C19  N18  C2     -8.27  30.0  2
 YK4  Var_07    C12   C11  N10  C4    123.65  30.0  2
 YK4  Var_08    C11   N10  C4   C5    173.59  30.0  2
 YK4  Var_09    N3    C2   N18  C19    -3.24  30.0  2
 YK4  Var_10    O8    C7   C5   C4     12.69  30.0  2
 YK4  Var_11    H22   C29  N26  C27    58.57  30.0  3
 YK4  Var_12    H9    C31  O30  C20   179.04  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
 YK4  plan-1  C2    0.020
 YK4  plan-1  C4    0.020
 YK4  plan-1  C5    0.020
 YK4  plan-1  C6    0.020
 YK4  plan-1  C7    0.020
 YK4  plan-1  N10   0.020
 YK4  plan-1  N1    0.020
 YK4  plan-1  N3    0.020
 YK4  plan-1  N18   0.020
 YK4  plan-1  H1    0.020
 YK4  plan-2  N10   0.020
 YK4  plan-2  C11   0.020
 YK4  plan-2  C12   0.020
 YK4  plan-2  C15   0.020
 YK4  plan-2  C16   0.020
 YK4  plan-2  C13   0.020
 YK4  plan-2  C14   0.020
 YK4  plan-2  BR17  0.020
 YK4  plan-2  H3    0.020
 YK4  plan-2  H4    0.020
 YK4  plan-2  H14   0.020
 YK4  plan-2  H15   0.020
 YK4  plan-3  C19   0.020
 YK4  plan-3  C21   0.020
 YK4  plan-3  C23   0.020
 YK4  plan-3  C24   0.020
 YK4  plan-3  N18   0.020
 YK4  plan-3  C20   0.020
 YK4  plan-3  C22   0.020
 YK4  plan-3  C25   0.020
 YK4  plan-3  C28   0.020
 YK4  plan-3  O30   0.020
 YK4  plan-3  H5    0.020
 YK4  plan-3  H6    0.020
 YK4  plan-4  C5    0.020
 YK4  plan-4  C7    0.020
 YK4  plan-4  O8    0.020
 YK4  plan-4  N9    0.020
 YK4  plan-4  H12   0.020
 YK4  plan-4  H13   0.020

