FMODB ID: LZJ39
Calculation Name: 3N7C-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3N7C
Chain ID: A
UniProt ID: Q75DJ0
Base Structure: X-ray
Registration Date: 2023-06-21
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 | OptHSide |
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 | 113 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -899219.764995 |
---|---|
FMO2-HF: Nuclear repulsion | 854879.642078 |
FMO2-HF: Total energy | -44340.122918 |
FMO2-MP2: Total energy | -44469.381571 |
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:503:GLU)
Summations of interaction energy for
fragment #1(A:503:GLU)
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. |
-319.343 | -320.303 | 44.534 | -22.328 | -21.246 | 0.168 |
Interaction energy analysis for fragmet #1(A:503:GLU)
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 | 505 | VAL | 0 | -0.014 | -0.024 | 3.806 | 2.861 | 4.652 | -0.008 | -0.889 | -0.894 | 0.002 |
4 | A | 506 | LEU | 0 | -0.004 | 0.007 | 5.821 | -3.161 | -3.161 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 507 | PHE | 0 | 0.027 | -0.003 | 8.456 | -2.694 | -2.694 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 508 | CYS | 0 | -0.026 | -0.033 | 9.301 | 3.518 | 3.518 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 509 | GLU | -1 | -0.815 | -0.873 | 11.645 | 15.009 | 15.009 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 510 | LYS | 1 | 0.844 | 0.927 | 14.884 | -16.058 | -16.058 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 511 | ALA | 0 | -0.035 | -0.026 | 16.335 | -0.547 | -0.547 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 512 | LYS | 1 | 0.948 | 0.971 | 18.178 | -13.006 | -13.006 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 513 | LEU | 0 | 0.004 | 0.025 | 16.249 | 0.108 | 0.108 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 514 | LEU | 0 | -0.059 | -0.040 | 19.500 | -0.692 | -0.692 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 515 | ILE | 0 | 0.014 | 0.004 | 19.078 | 0.437 | 0.437 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 516 | PHE | 0 | 0.019 | 0.009 | 23.144 | -0.477 | -0.477 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 517 | ASP | -1 | -0.940 | -0.974 | 26.482 | 11.218 | 11.218 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 518 | SER | 0 | 0.015 | -0.017 | 28.968 | -0.167 | -0.167 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 519 | ASP | -1 | -0.822 | -0.893 | 32.236 | 9.256 | 9.256 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 520 | THR | 0 | -0.023 | -0.009 | 34.300 | -0.246 | -0.246 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 521 | LYS | 1 | 0.817 | 0.912 | 32.880 | -9.056 | -9.056 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 522 | GLY | 0 | 0.054 | 0.031 | 31.503 | -0.213 | -0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 523 | TYR | 0 | -0.064 | -0.032 | 23.658 | 0.097 | 0.097 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 524 | THR | 0 | 0.048 | 0.024 | 26.625 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 525 | SER | 0 | -0.007 | -0.019 | 23.906 | 0.684 | 0.684 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 526 | ARG | 1 | 0.917 | 0.960 | 20.499 | -13.643 | -13.643 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 527 | GLY | 0 | 0.017 | 0.011 | 19.835 | 0.285 | 0.285 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 528 | VAL | 0 | -0.069 | -0.040 | 19.306 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 529 | GLY | 0 | 0.076 | 0.019 | 15.467 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 530 | GLU | -1 | -0.860 | -0.909 | 12.350 | 18.594 | 18.594 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 531 | LEU | 0 | -0.046 | -0.034 | 11.639 | 2.238 | 2.238 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 532 | LYS | 1 | 0.980 | 0.969 | 6.996 | -33.718 | -33.718 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 533 | LEU | 0 | -0.001 | 0.016 | 7.746 | 2.219 | 2.219 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 534 | LEU | 0 | -0.054 | -0.026 | 2.579 | -7.013 | -3.835 | 1.310 | -1.630 | -2.858 | 0.019 |
33 | A | 535 | ARG | 1 | 0.948 | 0.986 | 3.527 | -28.691 | -27.662 | 0.011 | -0.238 | -0.801 | 0.000 |
34 | A | 536 | LYS | 1 | 0.910 | 0.946 | 2.209 | -38.895 | -37.666 | 8.521 | -5.299 | -4.451 | -0.030 |
35 | A | 537 | LYS | 1 | 0.903 | 0.949 | 2.675 | -48.316 | -47.365 | 1.731 | 0.126 | -2.809 | 0.009 |
36 | A | 538 | ASP | -1 | -0.828 | -0.901 | 4.413 | 32.515 | 32.645 | 0.000 | -0.028 | -0.102 | 0.000 |
37 | A | 539 | ASP | -1 | -0.873 | -0.940 | 6.308 | 27.865 | 27.865 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 540 | LYS | 1 | 0.843 | 0.906 | 5.762 | -27.949 | -27.949 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 541 | GLY | 0 | 0.064 | 0.032 | 8.724 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 542 | LYS | 1 | 0.886 | 0.958 | 4.740 | -39.971 | -39.865 | -0.001 | -0.004 | -0.100 | 0.000 |
41 | A | 543 | VAL | 0 | 0.025 | 0.000 | 5.085 | 6.810 | 6.889 | -0.001 | -0.004 | -0.074 | 0.000 |
42 | A | 544 | ARG | 1 | 0.773 | 0.842 | 1.654 | -139.397 | -148.850 | 32.971 | -14.362 | -9.157 | 0.168 |
43 | A | 545 | VAL | 0 | 0.012 | 0.011 | 6.138 | 1.192 | 1.192 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 546 | LEU | 0 | -0.042 | -0.021 | 5.212 | 0.245 | 0.245 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 547 | CYS | 0 | -0.038 | 0.000 | 8.245 | -2.207 | -2.207 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 548 | ARG | 1 | 0.899 | 0.949 | 8.234 | -31.144 | -31.144 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 549 | SER | 0 | 0.088 | 0.033 | 12.391 | -0.539 | -0.539 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 550 | GLU | -1 | -0.888 | -0.932 | 16.087 | 16.377 | 16.377 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 551 | GLY | 0 | 0.012 | 0.015 | 18.242 | -0.853 | -0.853 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 552 | MET | 0 | 0.017 | 0.015 | 18.793 | -0.586 | -0.586 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 553 | GLY | 0 | -0.043 | -0.025 | 14.464 | 0.704 | 0.704 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 554 | HIS | 0 | 0.073 | 0.038 | 13.865 | 2.100 | 2.100 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 555 | VAL | 0 | -0.030 | -0.018 | 10.456 | 1.236 | 1.236 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 556 | LEU | 0 | -0.026 | -0.002 | 12.904 | -1.221 | -1.221 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 557 | LEU | 0 | 0.003 | 0.002 | 11.794 | -0.923 | -0.923 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 558 | ASN | 0 | 0.035 | 0.002 | 7.051 | 8.370 | 8.370 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 559 | THR | 0 | 0.004 | 0.015 | 8.941 | -1.054 | -1.054 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 560 | SER | 0 | 0.013 | 0.011 | 8.140 | 4.554 | 4.554 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 561 | VAL | 0 | 0.006 | 0.006 | 8.973 | -2.509 | -2.509 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 562 | VAL | 0 | 0.009 | 0.012 | 11.010 | 0.420 | 0.420 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 563 | LYS | 1 | 0.909 | 0.923 | 14.109 | -18.513 | -18.513 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 564 | SER | 0 | -0.005 | -0.009 | 16.201 | -0.476 | -0.476 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 565 | PHE | 0 | -0.009 | 0.014 | 16.771 | -0.885 | -0.885 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 566 | LYS | 1 | 0.984 | 0.994 | 18.260 | -12.306 | -12.306 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 567 | TYR | 0 | 0.064 | 0.044 | 14.455 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 568 | GLN | 0 | 0.002 | -0.009 | 18.653 | -0.319 | -0.319 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 569 | PRO | 0 | 0.058 | 0.035 | 21.654 | 0.278 | 0.278 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 570 | ILE | 0 | -0.006 | -0.011 | 23.905 | -0.170 | -0.170 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 571 | ASP | -1 | -0.782 | -0.883 | 26.410 | 10.358 | 10.358 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 572 | ALA | 0 | 0.010 | -0.001 | 28.335 | 0.307 | 0.307 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 573 | ASP | -1 | -0.840 | -0.918 | 30.133 | 9.554 | 9.554 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 574 | ASN | 0 | -0.119 | -0.067 | 27.718 | 0.076 | 0.076 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 575 | GLU | -1 | -0.799 | -0.918 | 24.078 | 12.444 | 12.444 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 576 | ASN | 0 | -0.019 | -0.023 | 22.871 | 0.330 | 0.330 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 577 | LEU | 0 | -0.039 | -0.011 | 22.853 | 0.454 | 0.454 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 578 | ILE | 0 | -0.020 | 0.001 | 18.059 | -0.388 | -0.388 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 579 | LYS | 1 | 0.878 | 0.943 | 20.392 | -12.370 | -12.370 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 580 | TRP | 0 | 0.009 | -0.021 | 11.539 | 0.411 | 0.411 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 581 | PRO | 0 | -0.004 | 0.003 | 17.964 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 582 | ILE | 0 | -0.045 | -0.025 | 14.399 | 1.705 | 1.705 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 583 | ILE | 0 | -0.005 | 0.008 | 16.944 | -1.069 | -1.069 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 584 | THR | 0 | 0.008 | -0.020 | 17.607 | 1.445 | 1.445 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 585 | ASP | -1 | -0.847 | -0.910 | 20.044 | 13.568 | 13.568 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 586 | GLY | 0 | -0.006 | -0.011 | 21.437 | -0.605 | -0.605 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 587 | LYS | 1 | 0.854 | 0.924 | 23.091 | -13.826 | -13.826 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 588 | LEU | 0 | -0.048 | -0.024 | 20.705 | 0.720 | 0.720 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 589 | GLU | -1 | -0.831 | -0.894 | 20.711 | 14.200 | 14.200 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 590 | THR | 0 | -0.006 | -0.004 | 20.731 | 0.683 | 0.683 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 591 | PHE | 0 | 0.022 | 0.022 | 16.303 | -0.287 | -0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 592 | ILE | 0 | -0.008 | -0.011 | 20.201 | -0.113 | -0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 593 | ILE | 0 | 0.012 | 0.013 | 14.927 | 0.332 | 0.332 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 594 | LYS | 1 | 0.938 | 0.978 | 19.200 | -12.550 | -12.550 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 595 | VAL | 0 | 0.039 | 0.033 | 18.020 | 0.515 | 0.515 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 596 | LYS | 1 | 0.777 | 0.864 | 19.509 | -16.008 | -16.008 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 597 | GLN | 0 | 0.040 | 0.017 | 22.785 | -0.676 | -0.676 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 598 | LYS | 1 | 0.865 | 0.937 | 22.854 | -10.261 | -10.261 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 599 | ALA | 0 | 0.010 | 0.007 | 23.207 | 0.171 | 0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 600 | ASP | -1 | -0.757 | -0.880 | 18.852 | 15.081 | 15.081 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 601 | GLY | 0 | 0.007 | 0.017 | 18.339 | 0.940 | 0.940 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 602 | ARG | 1 | 0.883 | 0.924 | 19.591 | -11.607 | -11.607 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 603 | ARG | 1 | 0.880 | 0.937 | 16.052 | -15.538 | -15.538 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 604 | LEU | 0 | -0.021 | 0.014 | 13.609 | 0.822 | 0.822 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 605 | VAL | 0 | 0.031 | -0.002 | 15.272 | 0.892 | 0.892 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 606 | GLY | 0 | -0.002 | 0.004 | 17.413 | 0.195 | 0.195 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 607 | ALA | 0 | 0.000 | -0.001 | 12.197 | 0.324 | 0.324 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 608 | VAL | 0 | -0.023 | -0.017 | 12.474 | 1.277 | 1.277 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 609 | ALA | 0 | 0.024 | 0.014 | 13.921 | 0.362 | 0.362 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 610 | ASP | -1 | -0.942 | -0.960 | 13.360 | 19.773 | 19.773 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 611 | ALA | 0 | -0.002 | -0.014 | 10.371 | 0.468 | 0.468 | 0.000 | 0.000 | 0.000 | 0.000 |
110 | A | 612 | GLN | 0 | -0.056 | -0.047 | 12.295 | -0.060 | -0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
111 | A | 613 | GLN | 0 | -0.070 | -0.040 | 14.504 | -1.224 | -1.224 | 0.000 | 0.000 | 0.000 | 0.000 |
112 | A | 614 | ALA | 0 | 0.005 | 0.014 | 12.361 | -0.423 | -0.423 | 0.000 | 0.000 | 0.000 | 0.000 |
113 | A | 615 | MET | 0 | -0.057 | 0.008 | 10.725 | -1.114 | -1.114 | 0.000 | 0.000 | 0.000 | 0.000 |