# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 09:46:17 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 2-{2-[(3,5-dimethylphenyl)amino]pyrimidin-4-yl}-N-[(1S)-2-hydroxy-1-methylethyl]-4-methyl-1,3-thiazole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CO)NC(=O)c1sc(nc1C)c2ccnc(Nc3cc(C)cc(C)c3)n2
#
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
 685  685  2-{2-[(3,5-dimethylphenyl)amino]pyrimidin-4-yl}-N-[(1S)-2-hydroxy-1-methylethyl]-4-methyl-1,3-thiazole-5-carboxamide  ligand  51  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_685
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
 685  C1    C  CH3   0  -0.653  -6.7461  -1.6967  -1.2223
 685  C2    C  CH1   0  -0.114  -5.7959  -1.9090  -0.0483
 685  C4    C  CH2   0  -0.165  -5.2565  -3.3275   0.0279
 685  O5    O  OH1   0  -0.673  -4.4877  -3.5826  -1.1267
 685  N6    N  NH1   0  -0.647  -4.6730  -0.9877  -0.0907
 685  C7    C  C     0   0.541  -4.7206   0.2602   0.4029
 685  O8    O  O     0  -0.476  -5.7059   0.7440   0.9413
 685  C9    C  CR5   0  -0.422  -3.4668   1.0396   0.2800
 685  S10   S  S2    0   0.309  -1.9142   0.3006   0.2708
 685  C11   C  CR5   0  -0.008  -1.2107   1.8597   0.1499
 685  N12   N  N     0  -0.397  -2.0578   2.8411   0.1237
 685  C13   C  CR5   0   0.373  -3.3440   2.4063   0.2034
 685  C14   C  CH3   0  -0.729  -4.4486   3.4084   0.1935
 685  C15   C  CR6   0   0.303   0.2423   2.0043   0.0939
 685  C16   C  CR16  0  -0.373   0.8511   3.2484  -0.0284
 685  C17   C  CR16  0   0.017   2.2325   3.2247  -0.0752
 685  N18   N  N     0  -0.461   2.9457   2.1101  -0.0043
 685  C19   C  CR6   0   0.616   2.2635   0.9738   0.1174
 685  N20   N  NH1   0  -0.777   2.9100  -0.2166   0.2054
 685  C21   C  CR6   0   0.400   4.2636  -0.5458   0.2121
 685  C22   C  CR16  0  -0.386   5.3094   0.3666   0.0805
 685  C23   C  CR6   0   0.131   6.6306  -0.0769   0.0941
 685  C24   C  CH3   0  -0.724   7.7491   0.9194  -0.0206
 685  C25   C  CR16  0  -0.373   6.9048  -1.4312   0.2363
 685  C26   C  CR6   0   0.130   5.8718  -2.3570   0.3732
 685  C27   C  CH3   0  -0.725   6.1740  -3.8157   0.5608
 685  C28   C  CR16  0  -0.431   4.5615  -1.9059   0.3563
 685  N29   N  N     0  -0.503   0.9314   0.8794   0.1648
 685  H1    H  HCH3  0   0.229  -6.2399  -1.8340  -2.1776
 685  H1A   H  HCH3  0   0.230  -7.5765  -2.4025  -1.1726
 685  H1B   H  HCH3  0   0.238  -7.1627  -0.6902  -1.2014
 685  H2    H  HCH1  0   0.259  -6.3373  -1.7302   0.8825
 685  H4    H  HCH2  0   0.219  -4.6576  -3.4307   0.9405
 685  H4A   H  HCH2  0   0.210  -6.1058  -4.0164   0.1134
 685  HO5   H  HOH1  0   0.462  -4.0053  -4.4037  -0.9977
 685  HN6   H  HNH1  0   0.396  -3.9057  -1.2530  -0.6907
 685  H14   H  HCH3  0   0.259  -4.7713   3.6414   1.2089
 685  H14A  H  HCH3  0   0.251  -4.1022   4.3308  -0.2681
 685  H14B  H  HCH3  0   0.253  -5.3198   3.0519  -0.3504
 685  H16   H  HCR6  0   0.281   0.2872   4.1664  -0.0873
 685  H17   H  HCR6  0   0.281   2.7933   4.1468  -0.1764
 685  HN20  H  HNH1  0   0.410   2.2795  -0.9988   0.2996
 685  H22   H  HCR6  0   0.276   5.1043   1.4183  -0.0384
 685  H24   H  HCH3  0   0.248   8.0808   1.2471   0.9669
 685  H24A  H  HCH3  0   0.243   8.6152   0.4942  -0.5269
 685  H24B  H  HCH3  0   0.242   7.4398   1.8084  -0.5695
 685  H25   H  HCR6  0   0.236   7.9341  -1.7738   0.2386
 685  H27   H  HCH3  0   0.249   6.4430  -4.0257   1.5978
 685  H27A  H  HCH3  0   0.243   5.3164  -4.4404   0.3138
 685  H27B  H  HCH3  0   0.244   7.0132  -4.1327  -0.0583
 685  H28   H  HCR6  0   0.257   3.7515  -2.6218   0.4500

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
 685  C1   C2    single    1.525  0.020  1.525
 685  C1   H1    single    0.970  0.020  1.090
 685  C1   H1A   single    0.970  0.020  1.090
 685  C1   H1B   single    0.970  0.020  1.090
 685  C2   C4    single    1.520  0.020  1.520
 685  C2   N6    single    1.453  0.020  1.453
 685  C2   H2    single    0.970  0.020  1.090
 685  O5   C4    single    1.410  0.020  1.410
 685  C4   H4    single    0.970  0.020  1.090
 685  C4   H4A   single    0.970  0.020  1.090
 685  O5   HO5   single    0.850  0.020  0.980
 685  N6   C7    single    1.343  0.020  1.343
 685  N6   HN6   single    0.860  0.020  1.020
 685  O8   C7    double    1.223  0.020  1.223
 685  C7   C9    single    1.481  0.020  1.481
 685  C9   C13   aromatic  1.374  0.020  1.374
 685  C9   S10   aromatic  1.720  0.020  1.720
 685  S10  C11   aromatic  1.715  0.020  1.715
 685  N12  C11   aromatic  1.297  0.020  1.297
 685  C11  C15   single    1.461  0.020  1.461
 685  C13  N12   aromatic  1.360  0.020  1.360
 685  C14  C13   single    1.491  0.020  1.491
 685  C14  H14   single    0.970  0.020  1.090
 685  C14  H14A  single    0.970  0.020  1.090
 685  C14  H14B  single    0.970  0.020  1.090
 685  C15  N29   aromatic  1.321  0.020  1.321
 685  C15  C16   aromatic  1.390  0.020  1.390
 685  C16  C17   aromatic  1.382  0.020  1.382
 685  C16  H16   single    0.930  0.020  1.080
 685  C17  N18   aromatic  1.325  0.020  1.325
 685  C17  H17   single    0.930  0.020  1.080
 685  C19  N18   aromatic  1.331  0.020  1.331
 685  N29  C19   aromatic  1.336  0.020  1.336
 685  C19  N20   single    1.357  0.020  1.357
 685  C21  N20   single    1.393  0.020  1.393
 685  N20  HN20  single    0.860  0.020  1.020
 685  C22  C21   aromatic  1.394  0.020  1.394
 685  C21  C28   aromatic  1.400  0.020  1.400
 685  C23  C22   aromatic  1.394  0.020  1.394
 685  C22  H22   single    0.930  0.020  1.080
 685  C24  C23   single    1.502  0.020  1.502
 685  C23  C25   aromatic  1.389  0.020  1.389
 685  C24  H24   single    0.970  0.020  1.090
 685  C24  H24A  single    0.970  0.020  1.090
 685  C24  H24B  single    0.970  0.020  1.090
 685  C25  C26   aromatic  1.394  0.020  1.394
 685  C25  H25   single    0.930  0.020  1.080
 685  C26  C27   single    1.501  0.020  1.501
 685  C26  C28   aromatic  1.386  0.020  1.386
 685  C27  H27   single    0.970  0.020  1.090
 685  C27  H27A  single    0.970  0.020  1.090
 685  C27  H27B  single    0.970  0.020  1.090
 685  C28  H28   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
 685  H1B   C1   H1A   107.80  3.000
 685  H1B   C1   H1    108.11  3.000
 685  H1A   C1   H1    108.18  3.000
 685  H1B   C1   C2    110.61  3.000
 685  H1A   C1   C2    110.43  3.000
 685  H1    C1   C2    111.58  3.000
 685  H2    C2   N6    107.72  3.000
 685  H2    C2   C4    106.63  3.000
 685  N6    C2   C4    108.60  3.000
 685  H2    C2   C1    108.94  3.000
 685  N6    C2   C1    111.76  3.000
 685  C4    C2   C1    112.94  3.000
 685  H4A   C4   H4    107.40  3.000
 685  H4A   C4   O5    111.85  3.000
 685  H4    C4   O5    111.51  3.000
 685  H4A   C4   C2    108.38  3.000
 685  H4    C4   C2    108.88  3.000
 685  O5    C4   C2    108.74  3.000
 685  HO5   O5   C4    108.56  3.000
 685  HN6   N6   C7    119.32  3.000
 685  HN6   N6   C2    115.98  3.000
 685  C7    N6   C2    123.44  3.000
 685  C9    C7   O8    120.69  3.000
 685  C9    C7   N6    115.36  3.000
 685  O8    C7   N6    123.93  3.000
 685  C13   C9   S10   110.27  3.000
 685  S10   C9   C7    122.58  3.000
 685  C13   C9   C7    127.12  3.000
 685  C11   S10  C9     88.86  3.000
 685  C15   C11  N12   125.02  3.000
 685  C15   C11  S10   120.04  3.000
 685  N12   C11  S10   114.93  3.000
 685  C13   N12  C11   112.00  3.000
 685  C14   C13  N12   119.03  3.000
 685  C14   C13  C9    127.03  3.000
 685  N12   C13  C9    113.94  3.000
 685  H14B  C14  H14A  108.72  3.000
 685  H14B  C14  H14   107.39  3.000
 685  H14A  C14  H14   107.94  3.000
 685  H14B  C14  C13   112.12  3.000
 685  H14A  C14  C13   109.67  3.000
 685  H14   C14  C13   110.88  3.000
 685  N29   C15  C16   122.56  3.000
 685  C16   C15  C11   121.82  3.000
 685  N29   C15  C11   115.62  3.000
 685  H16   C16  C17   122.34  3.000
 685  H16   C16  C15   122.49  3.000
 685  C17   C16  C15   115.16  3.000
 685  H17   C17  N18   116.24  3.000
 685  H17   C17  C16   120.37  3.000
 685  N18   C17  C16   123.39  3.000
 685  C19   N18  C17   116.56  3.000
 685  N29   C19  N20   114.24  3.000
 685  N20   C19  N18   120.70  3.000
 685  N29   C19  N18   125.06  3.000
 685  HN20  N20  C21   115.06  3.000
 685  HN20  N20  C19   112.85  3.000
 685  C21   N20  C19   132.09  3.000
 685  C28   C21  C22   119.08  3.000
 685  C28   C21  N20   115.90  3.000
 685  C22   C21  N20   125.02  3.000
 685  H22   C22  C23   119.47  3.000
 685  H22   C22  C21   120.40  3.000
 685  C23   C22  C21   120.12  3.000
 685  C25   C23  C24   120.49  3.000
 685  C25   C23  C22   119.90  3.000
 685  C24   C23  C22   119.60  3.000
 685  H24B  C24  H24A  108.05  3.000
 685  H24B  C24  H24   107.28  3.000
 685  H24A  C24  H24   107.21  3.000
 685  H24B  C24  C23   111.61  3.000
 685  H24A  C24  C23   111.62  3.000
 685  H24   C24  C23   110.86  3.000
 685  H25   C25  C26   119.55  3.000
 685  H25   C25  C23   119.70  3.000
 685  C26   C25  C23   120.75  3.000
 685  C28   C26  C27   120.53  3.000
 685  C28   C26  C25   118.90  3.000
 685  C27   C26  C25   120.56  3.000
 685  H27B  C27  H27A  108.09  3.000
 685  H27B  C27  H27   107.09  3.000
 685  H27A  C27  H27   107.40  3.000
 685  H27B  C27  C26   111.50  3.000
 685  H27A  C27  C26   111.74  3.000
 685  H27   C27  C26   110.80  3.000
 685  H28   C28  C26   119.34  3.000
 685  H28   C28  C21   119.41  3.000
 685  C26   C28  C21   121.24  3.000
 685  C19   N29  C15   117.26  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
 685  CONST_01  C11  N12  C13  C9     0.00   0.0  0
 685  CONST_02  N12  C11  S10  C9     0.00   0.0  0
 685  CONST_03  C15  C11  S10  C9   180.00   0.0  0
 685  CONST_04  N12  C13  C9   S10    0.00   0.0  0
 685  CONST_05  C13  N12  C11  S10    0.00   0.0  0
 685  CONST_06  N29  C15  C11  S10    0.00   0.0  0
 685  CONST_07  C16  C15  C11  S10  180.00   0.0  0
 685  CONST_08  C13  C9   S10  C11    0.00   0.0  0
 685  CONST_09  C19  N29  C15  C11  180.00   0.0  0
 685  CONST_10  C17  C16  C15  C11  180.00   0.0  0
 685  CONST_11  N29  C15  C11  N12  180.00   0.0  0
 685  CONST_12  C16  C15  C11  N12    0.00   0.0  0
 685  CONST_13  C15  C11  N12  C13  180.00   0.0  0
 685  CONST_14  N18  C19  N29  C15    0.00   0.0  0
 685  CONST_15  N18  C17  C16  C15    0.00   0.0  0
 685  CONST_16  C19  N29  C15  C16    0.00   0.0  0
 685  CONST_17  C19  N18  C17  C16    0.00   0.0  0
 685  CONST_18  N29  C15  C16  C17    0.00   0.0  0
 685  CONST_19  N29  C19  N18  C17    0.00   0.0  0
 685  CONST_20  C25  C23  C22  C21    0.00   0.0  0
 685  CONST_21  C25  C26  C28  C21    0.00   0.0  0
 685  CONST_22  C26  C28  C21  C22    0.00   0.0  0
 685  CONST_23  C26  C25  C23  C22    0.00   0.0  0
 685  CONST_24  C28  C21  C22  C23    0.00   0.0  0
 685  CONST_25  C28  C26  C25  C23    0.00   0.0  0
 685  CONST_26  N12  C13  C9   C7   180.00   0.0  0
 685  CONST_27  C11  S10  C9   C7   180.00   0.0  0
 685  CONST_28  C14  C13  C9   S10  180.00   0.0  0
 685  CONST_29  C14  C13  N12  C11  180.00   0.0  0
 685  CONST_30  N20  C19  N29  C15  180.00   0.0  0
 685  CONST_31  N20  C19  N18  C17  180.00   0.0  0
 685  CONST_32  C23  C22  C21  N20  180.00   0.0  0
 685  CONST_33  C26  C28  C21  N20  180.00   0.0  0
 685  CONST_34  C24  C23  C22  C21  180.00   0.0  0
 685  CONST_35  C27  C26  C28  C21  180.00   0.0  0
 685  CONST_36  C27  C26  C25  C23  180.00   0.0  0
 685  CONST_37  C26  C25  C23  C24  180.00   0.0  0
 685  CONST_38  H16  C16  C15  C11    0.00   0.0  0
 685  CONST_39  H17  C17  C16  C15  180.00   0.0  0
 685  CONST_40  H28  C28  C21  C22  180.00   0.0  0
 685  CONST_41  H25  C25  C23  C22  180.00   0.0  0
 685  CONST_42  H22  C22  C23  C25  180.00   0.0  0
 685  CONST_43  C9   C7   N6   C2   180.00   0.0  0
 685  CONST_44  HN6  N6   C7   C9     0.00   0.0  0
 685  CONST_45  O8   C7   N6   C2     0.00   0.0  0
 685  Var_01    C21  N20  C19  N18    0.91  30.0  2
 685  Var_02    C22  C21  N20  C19   -2.05  30.0  3
 685  Var_03    C13  C9   C7   N6   152.99  30.0  2
 685  Var_04    H14  C14  C13  C9    83.80  30.0  2
 685  Var_05    H24  C24  C23  C22   91.79  30.0  2
 685  Var_06    H27  C27  C26  C25   79.84  30.0  2

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
 685  chir_01  C2  C1  C4  N6  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
 685  plan-1  C7   0.020
 685  plan-1  C9   0.020
 685  plan-1  S10  0.020
 685  plan-1  C11  0.020
 685  plan-1  N12  0.020
 685  plan-1  C13  0.020
 685  plan-1  C14  0.020
 685  plan-1  C15  0.020
 685  plan-2  C11  0.020
 685  plan-2  C15  0.020
 685  plan-2  C16  0.020
 685  plan-2  C17  0.020
 685  plan-2  N18  0.020
 685  plan-2  C19  0.020
 685  plan-2  N20  0.020
 685  plan-2  N29  0.020
 685  plan-2  H16  0.020
 685  plan-2  H17  0.020
 685  plan-3  N20  0.020
 685  plan-3  C21  0.020
 685  plan-3  C22  0.020
 685  plan-3  C23  0.020
 685  plan-3  C24  0.020
 685  plan-3  C25  0.020
 685  plan-3  C26  0.020
 685  plan-3  C27  0.020
 685  plan-3  C28  0.020
 685  plan-3  H22  0.020
 685  plan-3  H25  0.020
 685  plan-3  H28  0.020
 685  plan-4  C2   0.020
 685  plan-4  N6   0.020
 685  plan-4  C7   0.020
 685  plan-4  O8   0.020
 685  plan-4  C9   0.020
 685  plan-4  HN6  0.020

