![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: 1NK4Z
Calculation Name: 3FQ4-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 3FQ4
Chain ID: A
UniProt ID: P16144
Base Structure: X-ray
Registration Date: 2023-09-23
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 | 109 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -865761.251519 |
---|---|
FMO2-HF: Nuclear repulsion | 822870.461835 |
FMO2-HF: Total energy | -42890.789685 |
FMO2-MP2: Total energy | -43018.65615 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F037443/ligand_interaction/ligand_F037443.png)
Ligand Interaction
![ligand interaction](./Kdata/F037443/ligand_interaction/ligand_interaction_F037443.png)
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:988:MET)
Summations of interaction energy for
fragment #1(A:988:MET)
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. |
-4.389 | -2.268 | 7.465 | -2.559 | -7.026 | -0.003 |
Interaction energy analysis for fragmet #1(A:988:MET)
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 | 990 | ASP | -1 | -0.852 | -0.926 | 3.668 | -0.354 | 1.665 | -0.012 | -0.944 | -1.064 | 0.001 |
4 | A | 991 | VAL | 0 | -0.052 | -0.023 | 2.669 | -0.366 | 0.209 | 0.496 | -0.207 | -0.864 | -0.001 |
5 | A | 992 | VAL | 0 | 0.015 | -0.004 | 5.233 | 0.015 | 0.053 | -0.001 | -0.002 | -0.035 | 0.000 |
6 | A | 993 | SER | 0 | -0.010 | -0.001 | 8.645 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | A | 994 | PHE | 0 | -0.003 | -0.003 | 11.020 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | A | 995 | GLU | -1 | -0.949 | -0.968 | 13.829 | -0.467 | -0.467 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | A | 996 | GLN | 0 | -0.017 | -0.013 | 15.614 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | A | 997 | PRO | 0 | 0.020 | 0.005 | 17.095 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | A | 998 | GLU | -1 | -0.926 | -0.956 | 18.522 | -0.225 | -0.225 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | A | 999 | PHE | 0 | 0.019 | 0.017 | 18.927 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | A | 1000 | SER | 0 | 0.000 | -0.006 | 24.151 | 0.012 | 0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | A | 1001 | VAL | 0 | 0.000 | 0.010 | 27.616 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | A | 1002 | SER | 0 | 0.039 | 0.027 | 30.243 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | A | 1003 | ARG | 1 | 0.874 | 0.907 | 33.749 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | A | 1004 | GLY | 0 | 0.014 | 0.006 | 35.340 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | A | 1005 | ASP | -1 | -0.892 | -0.939 | 32.480 | -0.101 | -0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | A | 1006 | GLN | 0 | -0.070 | -0.026 | 34.130 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | A | 1007 | VAL | 0 | -0.055 | -0.034 | 28.420 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | A | 1008 | ALA | 0 | -0.005 | 0.010 | 26.314 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | A | 1009 | ARG | 1 | 0.920 | 0.956 | 25.139 | 0.104 | 0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | A | 1010 | ILE | 0 | -0.014 | -0.011 | 19.468 | -0.015 | -0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | A | 1011 | PRO | 0 | 0.047 | 0.044 | 18.298 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | A | 1012 | VAL | 0 | -0.033 | -0.023 | 13.424 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | A | 1013 | ILE | 0 | 0.049 | 0.024 | 11.148 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | A | 1014 | ARG | 1 | 0.791 | 0.870 | 8.685 | -0.077 | -0.077 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | A | 1015 | ARG | 1 | 0.968 | 0.979 | 6.445 | 1.763 | 1.763 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | A | 1016 | VAL | 0 | -0.042 | -0.034 | 4.657 | -0.242 | -0.142 | -0.001 | -0.016 | -0.082 | 0.000 |
30 | A | 1017 | LEU | 0 | 0.024 | 0.020 | 6.874 | -0.013 | -0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | A | 1018 | ASP | -1 | -0.873 | -0.933 | 7.456 | 1.391 | 1.391 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | A | 1019 | GLY | 0 | 0.010 | 0.014 | 9.335 | 0.039 | 0.039 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | A | 1020 | GLY | 0 | 0.006 | 0.010 | 11.839 | -0.037 | -0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | A | 1021 | LYS | 1 | 0.916 | 0.970 | 12.866 | -0.441 | -0.441 | 0.000 | 0.000 | 0.000 | 0.000 |
35 | A | 1022 | SER | 0 | 0.032 | 0.022 | 9.586 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
36 | A | 1023 | GLN | 0 | -0.014 | -0.014 | 11.561 | -0.083 | -0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | A | 1024 | VAL | 0 | 0.004 | 0.020 | 10.366 | 0.104 | 0.104 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | A | 1025 | SER | 0 | 0.044 | 0.023 | 13.054 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | A | 1026 | TYR | 0 | -0.026 | -0.023 | 15.430 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | A | 1027 | ARG | 1 | 0.974 | 0.993 | 17.964 | 0.113 | 0.113 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | A | 1028 | THR | 0 | 0.053 | 0.034 | 20.942 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | A | 1029 | GLN | 0 | -0.046 | -0.016 | 22.762 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | A | 1030 | ASP | -1 | -0.754 | -0.846 | 24.852 | -0.099 | -0.099 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | A | 1031 | GLY | 0 | -0.017 | -0.011 | 27.053 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | A | 1032 | THR | 0 | -0.011 | -0.006 | 28.486 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | A | 1033 | ALA | 0 | -0.061 | -0.025 | 30.019 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | A | 1034 | GLN | 0 | 0.022 | -0.014 | 30.599 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | A | 1035 | GLY | 0 | 0.066 | 0.024 | 31.452 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | A | 1036 | ASN | 0 | -0.056 | -0.042 | 32.254 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | A | 1037 | ARG | 1 | 0.868 | 0.951 | 35.146 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
51 | A | 1038 | ASP | -1 | -0.768 | -0.889 | 33.143 | -0.087 | -0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
52 | A | 1039 | TYR | 0 | -0.028 | -0.035 | 27.561 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
53 | A | 1040 | ILE | 0 | 0.013 | 0.011 | 30.732 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
54 | A | 1041 | PRO | 0 | -0.024 | -0.010 | 27.978 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
55 | A | 1042 | VAL | 0 | -0.017 | -0.011 | 24.061 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
56 | A | 1043 | GLU | -1 | -0.964 | -0.991 | 22.483 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
57 | A | 1044 | GLY | 0 | 0.094 | 0.068 | 21.064 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
58 | A | 1045 | GLU | -1 | -0.952 | -0.984 | 17.870 | 0.079 | 0.079 | 0.000 | 0.000 | 0.000 | 0.000 |
59 | A | 1046 | LEU | 0 | -0.041 | -0.012 | 14.957 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
60 | A | 1047 | LEU | 0 | -0.030 | -0.024 | 15.011 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
61 | A | 1048 | PHE | 0 | -0.013 | -0.007 | 12.969 | -0.030 | -0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
62 | A | 1049 | GLN | 0 | 0.049 | 0.004 | 14.841 | 0.083 | 0.083 | 0.000 | 0.000 | 0.000 | 0.000 |
63 | A | 1050 | PRO | 0 | 0.028 | 0.013 | 15.190 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
64 | A | 1051 | GLY | 0 | 0.016 | 0.012 | 14.976 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
65 | A | 1052 | GLU | -1 | -0.809 | -0.879 | 15.750 | -0.050 | -0.050 | 0.000 | 0.000 | 0.000 | 0.000 |
66 | A | 1053 | ALA | 0 | 0.034 | 0.003 | 13.531 | -0.010 | -0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
67 | A | 1054 | TRP | 0 | -0.027 | -0.017 | 14.117 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
68 | A | 1055 | LYS | 1 | 0.827 | 0.909 | 16.043 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
69 | A | 1056 | GLU | -1 | -0.830 | -0.921 | 18.366 | -0.157 | -0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
70 | A | 1057 | LEU | 0 | -0.041 | -0.011 | 18.680 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
71 | A | 1058 | GLN | 0 | 0.003 | -0.006 | 22.000 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
72 | A | 1059 | VAL | 0 | -0.024 | 0.010 | 24.435 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
73 | A | 1060 | LYS | 1 | 0.979 | 0.982 | 27.109 | 0.042 | 0.042 | 0.000 | 0.000 | 0.000 | 0.000 |
74 | A | 1061 | LEU | 0 | -0.027 | -0.014 | 29.592 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
75 | A | 1062 | LEU | 0 | -0.004 | 0.004 | 32.831 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
76 | A | 1063 | GLU | -1 | -0.915 | -0.959 | 36.265 | -0.072 | -0.072 | 0.000 | 0.000 | 0.000 | 0.000 |
77 | A | 1064 | LEU | 0 | -0.049 | -0.015 | 38.057 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
78 | A | 1074 | ARG | 1 | 0.959 | 0.974 | 41.113 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
79 | A | 1075 | GLN | 0 | -0.038 | -0.011 | 37.587 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
80 | A | 1076 | VAL | 0 | 0.024 | 0.004 | 32.449 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
81 | A | 1077 | ARG | 1 | 0.781 | 0.896 | 32.666 | 0.089 | 0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
82 | A | 1078 | ARG | 1 | 0.983 | 0.999 | 26.998 | 0.179 | 0.179 | 0.000 | 0.000 | 0.000 | 0.000 |
83 | A | 1079 | PHE | 0 | -0.007 | 0.015 | 25.088 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
84 | A | 1080 | HIS | 0 | 0.009 | 0.006 | 21.520 | -0.029 | -0.029 | 0.000 | 0.000 | 0.000 | 0.000 |
85 | A | 1081 | VAL | 0 | 0.010 | 0.007 | 19.211 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
86 | A | 1082 | GLN | 0 | -0.018 | -0.022 | 16.792 | -0.025 | -0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
87 | A | 1083 | LEU | 0 | 0.019 | 0.019 | 11.955 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
88 | A | 1084 | SER | 0 | -0.027 | -0.023 | 12.926 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
89 | A | 1085 | ASN | 0 | 0.009 | 0.003 | 12.911 | 0.080 | 0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
90 | A | 1086 | PRO | 0 | 0.025 | 0.020 | 8.450 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
91 | A | 1087 | LYS | 1 | 0.963 | 0.979 | 10.541 | -0.213 | -0.213 | 0.000 | 0.000 | 0.000 | 0.000 |
92 | A | 1088 | PHE | 0 | -0.045 | -0.052 | 10.789 | -0.018 | -0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
93 | A | 1089 | GLY | 0 | 0.075 | 0.050 | 8.063 | -0.061 | -0.061 | 0.000 | 0.000 | 0.000 | 0.000 |
94 | A | 1090 | ALA | 0 | -0.019 | 0.009 | 6.105 | 0.567 | 0.567 | 0.000 | 0.000 | 0.000 | 0.000 |
95 | A | 1091 | HIS | 1 | 0.879 | 0.935 | 2.935 | -5.579 | -6.233 | 6.984 | -1.383 | -4.947 | -0.003 |
96 | A | 1092 | LEU | 0 | 0.012 | 0.026 | 4.885 | -0.599 | -0.556 | -0.001 | -0.007 | -0.034 | 0.000 |
97 | A | 1093 | GLY | 0 | -0.004 | -0.013 | 5.575 | -0.487 | -0.487 | 0.000 | 0.000 | 0.000 | 0.000 |
98 | A | 1094 | GLN | 0 | -0.063 | -0.011 | 7.218 | 0.414 | 0.414 | 0.000 | 0.000 | 0.000 | 0.000 |
99 | A | 1095 | PRO | 0 | 0.025 | 0.019 | 10.240 | -0.059 | -0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
100 | A | 1096 | HIS | 0 | 0.074 | 0.013 | 9.853 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
101 | A | 1097 | SER | 0 | -0.041 | -0.024 | 12.416 | 0.101 | 0.101 | 0.000 | 0.000 | 0.000 | 0.000 |
102 | A | 1098 | THR | 0 | -0.002 | -0.015 | 16.069 | -0.032 | -0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
103 | A | 1099 | THR | 0 | 0.002 | -0.003 | 18.995 | 0.027 | 0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
104 | A | 1100 | ILE | 0 | 0.000 | 0.007 | 22.493 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
105 | A | 1101 | ILE | 0 | -0.051 | -0.038 | 25.471 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
106 | A | 1102 | ILE | 0 | 0.012 | 0.008 | 28.603 | 0.002 | 0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
107 | A | 1103 | ARG | 1 | 0.912 | 0.936 | 29.954 | 0.157 | 0.157 | 0.000 | 0.000 | 0.000 | 0.000 |
108 | A | 1104 | ASP | -1 | -0.818 | -0.916 | 34.556 | -0.085 | -0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
109 | A | 1105 | PRO | 0 | -0.010 | 0.005 | 37.850 | -0.005 | -0.005 | 0.000 | 0.000 | 0.000 | 0.000 |