FMODB ID: 179VZ
Calculation Name: 5HRJ-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 5HRJ
Chain ID: A
UniProt ID: Q2VL90
Base Structure: X-ray
Registration Date: 2023-06-22
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 2.20220422 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 97 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -687059.30627 |
---|---|
FMO2-HF: Nuclear repulsion | 648137.171375 |
FMO2-HF: Total energy | -38922.134896 |
FMO2-MP2: Total energy | -39029.754572 |
3D Structure
Ligand structure
Ligand Interaction
Ligand binding energy
"IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
---|---|---|---|---|---|
IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
N/A | N/A | N/A | N/A | N/A | N/A |
Interactive mode: IFIE and PIEDA for fragment #1(A:477:PRO)
Summations of interaction energy for
fragment #1(A:477:PRO)
IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
---|---|---|---|---|---|
IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
-18.153 | -5.669 | 8.884 | -7.767 | -13.6 | -0.04 |
Interaction energy analysis for fragmet #1(A:477:PRO)
frag_NumFragment number. | ChainChain species. | Res #Residue number. | RES3-letter code of amino acid residue, ligand and solvent molecule. | FCHARGEFormal charge [e]. | q_MullikenFragment charge evaluated by Mulliken charge [e]. | q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. | DISTDistance from Ligand [Å]. | TotalIFIE at MP2 level [kcal/mol]. | ESElectro static interaction energy by PIEDA [kcal/mol]. | EXExchange-repulsion energy by PIEDA [kcal/mol]. | CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. | DI(MP2)Dispersion energy by PIEDA [kcal/mol]. | q(I=>J)Charge transfer value from I to J fragmens [e]. |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3 | A | 479 | LEU | 0 | 0.003 | 0.019 | 3.801 | -1.453 | 1.487 | -0.025 | -1.538 | -1.376 | 0.006 |
4 | A | 480 | VAL | 0 | -0.059 | -0.024 | 6.203 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 481 | GLY | 0 | 0.019 | -0.002 | 9.495 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 482 | GLY | 0 | 0.016 | 0.024 | 11.893 | 0.035 | 0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 483 | ASP | -1 | -0.960 | -0.980 | 13.374 | -0.281 | -0.281 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 484 | ILE | 0 | -0.032 | -0.015 | 13.601 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 485 | PRO | 0 | 0.019 | -0.013 | 10.541 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 486 | CYS | 0 | -0.059 | -0.022 | 8.047 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 487 | SER | 0 | -0.021 | -0.006 | 10.098 | 0.088 | 0.088 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 488 | GLY | 0 | 0.047 | 0.013 | 9.555 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 489 | ARG | 1 | 0.823 | 0.915 | 8.892 | -0.310 | -0.310 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 490 | VAL | 0 | 0.017 | 0.011 | 3.977 | -0.209 | -0.099 | 0.000 | -0.018 | -0.092 | 0.000 |
15 | A | 491 | GLU | -1 | -0.818 | -0.912 | 4.476 | 0.762 | 0.893 | -0.001 | -0.031 | -0.100 | 0.000 |
16 | A | 492 | VAL | 0 | 0.037 | 0.008 | 2.300 | -1.035 | 0.973 | 3.069 | -2.229 | -2.849 | -0.013 |
17 | A | 493 | GLN | 0 | -0.041 | -0.021 | 3.354 | -1.994 | -2.023 | 0.010 | 0.182 | -0.162 | 0.000 |
18 | A | 494 | HIS | 0 | 0.009 | 0.005 | 5.449 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 495 | GLY | 0 | -0.022 | -0.012 | 8.884 | -0.318 | -0.318 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 496 | ASP | -1 | -0.873 | -0.926 | 10.405 | 1.097 | 1.097 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 497 | THR | 0 | -0.083 | -0.037 | 10.711 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 498 | TRP | 0 | 0.024 | -0.002 | 2.440 | -0.339 | 0.267 | 0.605 | -0.452 | -0.759 | 0.002 |
23 | A | 499 | GLY | 0 | 0.016 | 0.019 | 6.789 | -0.459 | -0.459 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 500 | THR | 0 | -0.039 | -0.026 | 6.808 | 0.405 | 0.405 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 501 | VAL | 0 | 0.053 | 0.023 | 6.659 | 0.081 | 0.081 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 502 | CYS | 0 | -0.065 | -0.009 | 9.763 | -0.199 | -0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 503 | ASP | -1 | -0.840 | -0.943 | 12.833 | 0.124 | 0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 504 | SER | 0 | -0.078 | -0.057 | 14.368 | -0.043 | -0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 505 | ASP | -1 | -0.702 | -0.823 | 12.592 | 0.333 | 0.333 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 506 | PHE | 0 | -0.011 | 0.000 | 6.165 | 0.033 | 0.033 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 507 | SER | 0 | 0.037 | 0.022 | 11.572 | -0.063 | -0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 508 | LEU | 0 | 0.036 | -0.013 | 11.552 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 509 | GLU | -1 | -0.866 | -0.928 | 11.730 | -0.427 | -0.427 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 510 | ALA | 0 | 0.019 | 0.005 | 8.338 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 511 | ALA | 0 | 0.003 | -0.008 | 6.977 | -0.263 | -0.263 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 512 | SER | 0 | -0.033 | -0.017 | 7.656 | -0.280 | -0.280 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 513 | VAL | 0 | -0.012 | 0.004 | 5.313 | -0.167 | -0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 514 | LEU | 0 | 0.029 | 0.016 | 2.779 | -1.775 | -0.554 | 0.549 | -0.365 | -1.405 | 0.001 |
39 | A | 515 | CYS | 0 | -0.119 | -0.060 | 4.156 | -0.609 | -0.468 | -0.001 | -0.016 | -0.124 | 0.000 |
40 | A | 516 | ARG | 1 | 0.861 | 0.923 | 6.991 | 0.909 | 0.909 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 517 | GLU | -1 | -0.862 | -0.940 | 2.599 | -10.294 | -7.051 | 3.162 | -2.532 | -3.874 | -0.034 |
42 | A | 518 | LEU | 0 | -0.079 | -0.039 | 2.582 | -1.440 | -0.196 | 0.563 | -0.400 | -1.406 | 0.000 |
43 | A | 519 | GLN | 0 | -0.023 | -0.007 | 5.020 | 0.264 | 0.279 | -0.001 | -0.003 | -0.011 | 0.000 |
44 | A | 521 | GLY | 0 | -0.031 | -0.006 | 9.632 | 0.163 | 0.163 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 522 | THR | 0 | 0.002 | -0.008 | 10.887 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 523 | VAL | 0 | 0.014 | 0.000 | 10.743 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 524 | VAL | 0 | -0.003 | 0.016 | 12.110 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 525 | SER | 0 | -0.056 | -0.046 | 13.629 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 526 | LEU | 0 | 0.021 | 0.024 | 10.822 | -0.053 | -0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 527 | LEU | 0 | -0.060 | -0.035 | 12.801 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 528 | GLY | 0 | 0.052 | 0.019 | 13.719 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 529 | GLY | 0 | -0.048 | -0.022 | 16.239 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 530 | ALA | 0 | 0.012 | 0.010 | 15.021 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 531 | HIS | 0 | -0.006 | 0.015 | 15.018 | -0.009 | -0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 532 | PHE | 0 | -0.027 | -0.012 | 12.036 | -0.028 | -0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 533 | GLY | 0 | -0.002 | 0.011 | 14.821 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 534 | GLU | -1 | -0.929 | -0.970 | 14.407 | 0.171 | 0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 535 | GLY | 0 | -0.028 | -0.013 | 12.467 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 536 | SER | 0 | -0.074 | -0.048 | 13.033 | -0.041 | -0.041 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 537 | GLY | 0 | -0.014 | -0.017 | 12.897 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 538 | GLN | 0 | 0.043 | 0.023 | 11.392 | -0.155 | -0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 539 | ILE | 0 | -0.055 | -0.028 | 11.610 | 0.058 | 0.058 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 540 | TRP | 0 | -0.027 | -0.015 | 6.569 | -0.152 | -0.152 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 541 | ALA | 0 | 0.011 | 0.004 | 11.356 | -0.127 | -0.127 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 542 | GLU | -1 | -0.950 | -0.980 | 12.138 | 0.684 | 0.684 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 543 | GLU | -1 | -0.891 | -0.962 | 11.526 | 0.323 | 0.323 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 544 | PHE | 0 | 0.005 | -0.017 | 6.532 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 545 | GLN | 0 | -0.054 | -0.034 | 10.148 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 546 | CYS | 0 | -0.167 | -0.048 | 8.871 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 547 | GLU | -1 | -0.919 | -0.971 | 11.742 | -0.215 | -0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 548 | GLY | 0 | 0.073 | 0.048 | 11.871 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 549 | HIS | 0 | -0.107 | -0.046 | 11.473 | -0.142 | -0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 550 | GLU | -1 | -0.760 | -0.875 | 9.120 | -0.398 | -0.398 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 551 | SER | 0 | -0.043 | -0.039 | 9.051 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 552 | HIS | 0 | 0.004 | 0.008 | 4.591 | -0.235 | -0.126 | -0.001 | -0.008 | -0.099 | 0.000 |
76 | A | 553 | LEU | 0 | 0.059 | 0.013 | 2.301 | -0.096 | 0.649 | 0.955 | -0.357 | -1.343 | -0.002 |
77 | A | 554 | SER | 0 | -0.067 | -0.031 | 5.098 | 0.414 | 0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 555 | LEU | 0 | -0.036 | -0.015 | 6.855 | 0.106 | 0.106 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 557 | PRO | 0 | 0.006 | 0.015 | 10.683 | 0.133 | 0.133 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 558 | VAL | 0 | 0.007 | 0.009 | 11.129 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 559 | ALA | 0 | -0.006 | 0.000 | 13.666 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 560 | PRO | 0 | -0.017 | 0.003 | 15.243 | 0.055 | 0.055 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 561 | ARG | 1 | 0.827 | 0.908 | 15.275 | -0.375 | -0.375 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 562 | PRO | 0 | -0.086 | -0.033 | 17.130 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 563 | ASP | -1 | -0.953 | -0.990 | 20.384 | 0.200 | 0.200 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 564 | GLY | 0 | 0.036 | 0.029 | 22.448 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 565 | THR | 0 | -0.035 | -0.018 | 17.603 | 0.038 | 0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 567 | SER | 0 | 0.053 | 0.025 | 18.436 | 0.031 | 0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 568 | HIS | 1 | 0.894 | 0.931 | 13.243 | -0.515 | -0.515 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 569 | SER | 0 | -0.024 | -0.014 | 16.272 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 570 | ARG | 1 | 0.889 | 0.938 | 16.870 | -0.214 | -0.214 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 571 | ASP | -1 | -0.729 | -0.839 | 11.867 | 0.483 | 0.483 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 572 | VAL | 0 | 0.004 | 0.002 | 8.964 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 573 | GLY | 0 | 0.010 | -0.002 | 9.413 | 0.063 | 0.063 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 574 | VAL | 0 | -0.007 | -0.001 | 6.881 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 575 | VAL | 0 | 0.036 | 0.014 | 10.012 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 577 | SER | 0 | 0.004 | 0.015 | 11.463 | 0.062 | 0.062 | 0.000 | 0.000 | 0.000 | 0.000 |