FMODB ID: LJQ89
Calculation Name: 1JNP-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1JNP
Chain ID: A
UniProt ID: P56280
Base Structure: X-ray
Registration Date: 2023-03-13
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 | 101 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -887457.900987 |
---|---|
FMO2-HF: Nuclear repulsion | 844191.899254 |
FMO2-HF: Total energy | -43266.001733 |
FMO2-MP2: Total energy | -43393.133573 |
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:8:ARG)
Summations of interaction energy for
fragment #1(A:8:ARG)
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. |
-57.892 | -60.774 | 21.511 | -9.923 | -8.706 | -0.041 |
Interaction energy analysis for fragmet #1(A:8:ARG)
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 | 10 | GLU | -1 | -0.829 | -0.960 | 3.813 | -28.035 | -26.198 | -0.029 | -0.851 | -0.957 | -0.002 |
4 | A | 11 | THR | 0 | -0.042 | 0.007 | 7.027 | 0.880 | 0.880 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | A | 12 | PRO | 0 | -0.035 | -0.023 | 9.736 | 1.025 | 1.025 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | A | 13 | ALA | 0 | -0.013 | -0.010 | 12.964 | 0.543 | 0.543 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 14 | HIS | 1 | 0.852 | 0.906 | 12.987 | 17.234 | 17.234 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 15 | PRO | 0 | 0.077 | 0.052 | 15.513 | 0.705 | 0.705 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 16 | ASN | 0 | -0.028 | 0.012 | 18.723 | 0.466 | 0.466 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 17 | ARG | 1 | 0.855 | 0.904 | 22.348 | 10.643 | 10.643 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 18 | LEU | 0 | 0.032 | 0.018 | 18.656 | -0.266 | -0.266 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 19 | TRP | 0 | -0.008 | -0.016 | 22.607 | 0.245 | 0.245 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 20 | ILE | 0 | 0.019 | 0.009 | 24.271 | -0.368 | -0.368 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 21 | TRP | 0 | -0.093 | -0.043 | 25.343 | 0.291 | 0.291 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 22 | GLU | -1 | -0.843 | -0.958 | 26.096 | -10.742 | -10.742 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 23 | LYS | 1 | 0.876 | 0.922 | 26.374 | 9.829 | 9.829 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 24 | HIS | 0 | 0.052 | 0.047 | 23.362 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 25 | VAL | 0 | 0.003 | 0.021 | 21.516 | -0.661 | -0.661 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 26 | TYR | 0 | 0.014 | -0.046 | 20.490 | 0.425 | 0.425 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 27 | LEU | 0 | -0.016 | 0.011 | 20.827 | -0.468 | -0.468 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 28 | ASP | -1 | -0.721 | -0.857 | 18.452 | -13.748 | -13.748 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 29 | GLU | -1 | -0.868 | -0.932 | 21.688 | -12.308 | -12.308 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 30 | PHE | 0 | -0.071 | -0.014 | 18.396 | 0.414 | 0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 31 | ARG | 1 | 0.915 | 0.957 | 21.043 | 11.344 | 11.344 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 32 | ARG | 1 | 0.824 | 0.885 | 15.856 | 15.553 | 15.553 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 33 | SER | 0 | 0.003 | -0.009 | 18.940 | -0.052 | -0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 34 | TRP | 0 | 0.009 | -0.012 | 12.395 | -1.186 | -1.186 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 35 | LEU | 0 | 0.028 | 0.000 | 16.647 | 0.978 | 0.978 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 36 | PRO | 0 | -0.033 | 0.016 | 16.864 | -1.175 | -1.175 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | A | 37 | VAL | 0 | -0.011 | -0.002 | 14.935 | 0.411 | 0.411 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 38 | VAL | 0 | -0.061 | -0.036 | 15.973 | 0.185 | 0.185 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 39 | ILE | 0 | 0.031 | 0.004 | 18.632 | -0.200 | -0.200 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 40 | LYS | 1 | 0.887 | 0.953 | 18.560 | 14.885 | 14.885 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 41 | SER | 0 | 0.117 | 0.043 | 20.468 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 42 | ASN | 0 | -0.146 | -0.072 | 23.186 | -0.431 | -0.431 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 43 | GLU | -1 | -0.855 | -0.907 | 25.056 | -10.189 | -10.189 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 44 | LYS | 1 | 0.802 | 0.909 | 20.113 | 15.277 | 15.277 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 45 | PHE | 0 | 0.007 | -0.012 | 22.860 | -0.520 | -0.520 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 46 | GLN | 0 | 0.022 | 0.003 | 17.353 | 0.827 | 0.827 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 47 | VAL | 0 | 0.031 | 0.028 | 18.185 | -0.115 | -0.115 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 48 | ILE | 0 | -0.024 | -0.017 | 12.429 | -0.313 | -0.313 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 49 | LEU | 0 | 0.000 | -0.016 | 14.911 | 0.517 | 0.517 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 50 | ARG | 1 | 0.859 | 0.885 | 9.929 | 25.534 | 25.534 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 51 | GLN | 0 | -0.003 | 0.024 | 12.190 | 1.857 | 1.857 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 52 | GLU | -1 | -0.940 | -0.975 | 13.482 | -17.593 | -17.593 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 53 | ASP | -1 | -0.917 | -0.950 | 16.138 | -13.507 | -13.507 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 54 | VAL | 0 | -0.043 | -0.007 | 18.674 | 0.325 | 0.325 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 55 | THR | 0 | -0.074 | -0.049 | 22.352 | 0.275 | 0.275 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 56 | LEU | 0 | 0.039 | 0.007 | 24.225 | -0.171 | -0.171 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 57 | GLY | 0 | -0.038 | -0.018 | 26.613 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 58 | GLU | -1 | -0.957 | -0.969 | 29.287 | -8.928 | -8.928 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 59 | ALA | 0 | -0.031 | -0.018 | 30.452 | -0.135 | -0.135 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 60 | MET | 0 | 0.014 | 0.046 | 30.115 | 0.287 | 0.287 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 61 | SER | 0 | -0.037 | -0.053 | 31.872 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 62 | PRO | 0 | 0.031 | -0.006 | 33.322 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 63 | SER | 0 | 0.051 | 0.021 | 34.347 | -0.131 | -0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 64 | GLN | 0 | 0.005 | 0.038 | 35.500 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 65 | LEU | 0 | 0.023 | 0.047 | 28.969 | -0.210 | -0.210 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 66 | VAL | 0 | -0.009 | -0.043 | 33.170 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 67 | PRO | 0 | -0.076 | -0.026 | 33.331 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 68 | TYR | 0 | -0.058 | -0.061 | 25.365 | -0.258 | -0.258 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 69 | GLU | -1 | -0.889 | -0.941 | 26.187 | -11.375 | -11.375 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 70 | LEU | 0 | -0.043 | -0.022 | 22.727 | -0.408 | -0.408 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 71 | PRO | 0 | 0.018 | 0.042 | 24.749 | 0.453 | 0.453 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 72 | LEU | 0 | 0.057 | 0.068 | 26.496 | -0.240 | -0.240 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 73 | MET | 0 | 0.006 | -0.016 | 26.782 | -0.139 | -0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 74 | TRP | 0 | 0.103 | 0.034 | 21.577 | -0.073 | -0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 75 | GLN | 0 | -0.065 | -0.030 | 24.048 | 0.071 | 0.071 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 76 | LEU | 0 | 0.022 | 0.034 | 20.493 | 0.180 | 0.180 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 77 | TYR | 0 | -0.016 | -0.005 | 23.626 | 0.584 | 0.584 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 78 | PRO | 0 | -0.005 | -0.019 | 24.756 | -0.362 | -0.362 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 79 | LYS | 1 | 0.854 | 0.941 | 24.498 | 10.837 | 10.837 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 80 | ASP | -1 | -0.838 | -0.926 | 18.521 | -15.408 | -15.408 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 81 | ARG | 1 | 0.900 | 0.962 | 20.552 | 11.022 | 11.022 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 82 | TYR | 0 | 0.036 | -0.030 | 18.077 | 0.255 | 0.255 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 83 | ARG | 1 | 0.841 | 0.935 | 23.041 | 9.663 | 9.663 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 84 | SER | 0 | 0.004 | 0.010 | 26.573 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 85 | ALA | 0 | -0.008 | -0.015 | 27.519 | 0.316 | 0.316 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 86 | ASP | -1 | -0.836 | -0.895 | 30.296 | -9.708 | -9.708 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 87 | SER | 0 | -0.039 | -0.051 | 31.602 | 0.075 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 88 | MET | 0 | 0.006 | 0.031 | 28.213 | 0.051 | 0.051 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 89 | TYR | 0 | -0.067 | -0.073 | 26.206 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 90 | TRP | 0 | 0.062 | 0.027 | 21.122 | -0.119 | -0.119 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 91 | GLN | 0 | -0.060 | -0.025 | 17.728 | 0.489 | 0.489 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 92 | ILE | 0 | 0.032 | 0.027 | 14.004 | -0.277 | -0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 93 | LEU | 0 | -0.053 | -0.018 | 14.288 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 94 | TYR | 0 | -0.014 | -0.016 | 9.802 | -1.539 | -1.539 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 95 | HIS | 0 | 0.029 | 0.031 | 10.472 | 1.540 | 1.540 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 96 | ILE | 0 | 0.104 | 0.084 | 5.109 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 97 | LYN | 0 | -0.016 | 0.008 | 4.436 | 1.401 | 1.834 | 0.000 | -0.182 | -0.251 | 0.000 |
91 | A | 98 | PHE | 0 | -0.127 | -0.044 | 1.832 | -13.412 | -18.480 | 21.508 | -9.689 | -6.751 | -0.038 |
92 | A | 99 | ARG | 1 | 0.882 | 0.938 | 3.026 | 37.017 | 36.884 | 0.033 | 0.806 | -0.706 | -0.001 |
93 | A | 100 | ASP | -1 | -0.901 | -0.950 | 5.036 | -24.510 | -24.461 | -0.001 | -0.007 | -0.041 | 0.000 |
94 | A | 101 | VAL | 0 | 0.065 | 0.029 | 6.323 | 2.086 | 2.086 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 102 | GLU | -1 | -0.882 | -0.925 | 6.200 | -23.701 | -23.701 | 0.000 | 0.000 | 0.000 | 0.000 |
96 | A | 103 | ASP | -1 | -0.754 | -0.830 | 8.082 | -25.535 | -25.535 | 0.000 | 0.000 | 0.000 | 0.000 |
97 | A | 104 | MET | 0 | -0.006 | -0.006 | 9.669 | -0.821 | -0.821 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 105 | LEU | 0 | -0.040 | 0.006 | 12.505 | 0.558 | 0.558 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 106 | LEU | 0 | -0.017 | 0.004 | 14.318 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 107 | GLU | -1 | -0.848 | -0.950 | 17.846 | -16.457 | -16.457 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 108 | LEU | 0 | -0.022 | 0.001 | 20.298 | 0.555 | 0.555 | 0.000 | 0.000 | 0.000 | 0.000 |