FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 3JJ1L

Calculation Name: 1XFS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XFS

Chain ID: A

ChEMBL ID:

UniProt ID: Q82XK1

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


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 154
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1534971.756534
FMO2-HF: Nuclear repulsion 1472479.673979
FMO2-HF: Total energy -62492.082555
FMO2-MP2: Total energy -62671.881213


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:6:ILE)


Summations of interaction energy for fragment #1(A:6:ILE)
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.
-5.1820.2035.535-3.838-7.081-0.028
Interaction energy analysis for fragmet #1(A:6:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.062 / q_NPA : -0.043
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
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].
3A8ALA0-0.024-0.0193.311-0.3281.5640.064-0.523-1.434-0.001
4A9GLU-1-0.922-0.9564.193-0.457-0.2620.000-0.014-0.1810.000
5A10LEU0-0.048-0.0125.8820.5630.5630.0000.0000.0000.000
6A11ASP-1-0.781-0.9052.289-4.317-2.8704.385-2.775-3.057-0.027
7A12LEU0-0.0370.0043.849-0.560-0.3070.008-0.060-0.2020.000
8A13MET0-0.021-0.0192.915-0.6800.4320.287-0.245-1.1530.000
9A14LEU0-0.0080.0074.813-0.103-0.079-0.001-0.004-0.0180.000
10A15LYS10.9460.9778.5260.0360.0360.0000.0000.0000.000
11A16ARG10.8430.89610.354-0.041-0.0410.0000.0000.0000.000
12A17GLU-1-0.854-0.92514.0740.1320.1320.0000.0000.0000.000
13A18LEU00.0270.02416.457-0.015-0.0150.0000.0000.0000.000
14A19ALA0-0.034-0.00319.7110.0110.0110.0000.0000.0000.000
15A20VAL0-0.006-0.02522.221-0.007-0.0070.0000.0000.0000.000
16A21PRO0-0.0310.01722.0810.0090.0090.0000.0000.0000.000
17A22VAL00.1090.03518.814-0.003-0.0030.0000.0000.0000.000
18A23ASN00.0690.03321.2930.0060.0060.0000.0000.0000.000
19A24LEU0-0.051-0.02823.9560.0000.0000.0000.0000.0000.000
20A25VAL00.0340.01117.667-0.003-0.0030.0000.0000.0000.000
21A26TRP00.0340.02416.6100.0060.0060.0000.0000.0000.000
22A27ARG10.8730.92420.578-0.096-0.0960.0000.0000.0000.000
23A28GLY00.0060.00222.084-0.006-0.0060.0000.0000.0000.000
24A29LEU0-0.033-0.02515.770-0.007-0.0070.0000.0000.0000.000
25A30THR00.004-0.00719.4630.0030.0030.0000.0000.0000.000
26A31GLU-1-0.815-0.87121.8390.0960.0960.0000.0000.0000.000
27A32PRO00.0310.00925.218-0.008-0.0080.0000.0000.0000.000
28A33GLU-1-0.898-0.95726.3820.0450.0450.0000.0000.0000.000
29A34LEU00.0090.00725.010-0.009-0.0090.0000.0000.0000.000
30A35LEU00.0470.01520.024-0.010-0.0100.0000.0000.0000.000
31A36LYS10.8080.89023.524-0.058-0.0580.0000.0000.0000.000
32A37LYS10.8860.93725.637-0.048-0.0480.0000.0000.0000.000
33A38TRP0-0.078-0.03616.918-0.005-0.0050.0000.0000.0000.000
34A39PHE00.0090.00316.910-0.008-0.0080.0000.0000.0000.000
35A40VAL00.0100.02918.974-0.005-0.0050.0000.0000.0000.000
36A41PRO00.0020.01219.0080.0050.0050.0000.0000.0000.000
37A42LYS11.0030.99921.618-0.005-0.0050.0000.0000.0000.000
38A43PRO0-0.034-0.03324.556-0.006-0.0060.0000.0000.0000.000
39A44TRP00.0280.03423.5020.0070.0070.0000.0000.0000.000
40A45SER0-0.010-0.01725.8700.0050.0050.0000.0000.0000.000
41A46ILE0-0.0020.01122.917-0.001-0.0010.0000.0000.0000.000
42A47SER0-0.078-0.04526.910-0.001-0.0010.0000.0000.0000.000
43A48ASP-1-0.853-0.93628.3040.0500.0500.0000.0000.0000.000
44A49CYS0-0.044-0.00724.4570.0040.0040.0000.0000.0000.000
45A50ARG10.9090.96626.227-0.073-0.0730.0000.0000.0000.000
46A51VAL00.0410.01322.9110.0040.0040.0000.0000.0000.000
47A52ASP-1-0.908-0.93324.7910.1330.1330.0000.0000.0000.000
48A53LEU00.013-0.01020.5440.0120.0120.0000.0000.0000.000
49A54ARG10.8840.95223.077-0.157-0.1570.0000.0000.0000.000
50A55PRO00.0220.01620.412-0.005-0.0050.0000.0000.0000.000
51A56GLY00.006-0.00521.037-0.020-0.0200.0000.0000.0000.000
52A57GLY0-0.036-0.01622.753-0.025-0.0250.0000.0000.0000.000
53A58GLU-1-0.949-0.99422.3050.1010.1010.0000.0000.0000.000
54A59PHE0-0.0200.00617.5980.0000.0000.0000.0000.0000.000
55A60TYR0-0.004-0.00922.072-0.007-0.0070.0000.0000.0000.000
56A61THR00.0370.00722.0700.0030.0030.0000.0000.0000.000
57A62VAL0-0.0160.01824.621-0.005-0.0050.0000.0000.0000.000
58A63MET0-0.0030.01320.2500.0010.0010.0000.0000.0000.000
59A64GLN0-0.0010.00125.2740.0030.0030.0000.0000.0000.000
60A65ASP-1-0.689-0.84126.237-0.030-0.0300.0000.0000.0000.000
61A66PRO0-0.052-0.04726.9620.0050.0050.0000.0000.0000.000
62A67GLU-1-0.967-0.98029.179-0.045-0.0450.0000.0000.0000.000
63A68GLY0-0.057-0.01331.0160.0020.0020.0000.0000.0000.000
64A69ASN0-0.094-0.03829.2450.0080.0080.0000.0000.0000.000
65A70LYS10.8890.92628.936-0.008-0.0080.0000.0000.0000.000
66A71PHE0-0.029-0.01724.728-0.002-0.0020.0000.0000.0000.000
67A72PRO0-0.029-0.00225.2260.0050.0050.0000.0000.0000.000
68A73ASN00.038-0.00820.636-0.003-0.0030.0000.0000.0000.000
69A74SER0-0.033-0.02022.3430.0110.0110.0000.0000.0000.000
70A75GLY00.0500.02819.212-0.005-0.0050.0000.0000.0000.000
71A76CYS0-0.099-0.03018.540-0.009-0.0090.0000.0000.0000.000
72A77PHE00.0350.01217.6630.0290.0290.0000.0000.0000.000
73A78LEU0-0.040-0.03513.646-0.013-0.0130.0000.0000.0000.000
74A79GLU-1-0.807-0.88614.1240.6950.6950.0000.0000.0000.000
75A80VAL0-0.012-0.00816.566-0.009-0.0090.0000.0000.0000.000
76A81THR0-0.074-0.04316.528-0.032-0.0320.0000.0000.0000.000
77A82ASP-1-0.841-0.94118.1530.2300.2300.0000.0000.0000.000
78A83GLU-1-0.952-0.99119.4060.1790.1790.0000.0000.0000.000
79A84LYS10.8980.96913.759-0.487-0.4870.0000.0000.0000.000
80A85ARG10.8110.88910.698-0.811-0.8110.0000.0000.0000.000
81A86LEU00.0040.02713.256-0.035-0.0350.0000.0000.0000.000
82A87ILE00.0150.01411.1130.0430.0430.0000.0000.0000.000
83A88TRP00.0450.02113.217-0.028-0.0280.0000.0000.0000.000
84A89THR0-0.005-0.00713.263-0.001-0.0010.0000.0000.0000.000
85A90SER00.0440.02214.885-0.012-0.0120.0000.0000.0000.000
86A91ALA00.0050.00415.327-0.025-0.0250.0000.0000.0000.000
87A92LEU0-0.050-0.02517.240-0.003-0.0030.0000.0000.0000.000
88A93VAL00.0410.02119.775-0.003-0.0030.0000.0000.0000.000
89A94LYS10.9960.97922.622-0.083-0.0830.0000.0000.0000.000
90A95ASN0-0.075-0.04925.0210.0000.0000.0000.0000.0000.000
91A96TYR00.0490.02119.8290.0090.0090.0000.0000.0000.000
92A97ARG10.9230.99022.667-0.091-0.0910.0000.0000.0000.000
93A98PRO00.0240.00221.6350.0020.0020.0000.0000.0000.000
94A99ALA00.0240.01820.720-0.010-0.0100.0000.0000.0000.000
95A100VAL0-0.036-0.01922.577-0.005-0.0050.0000.0000.0000.000
96A101PRO00.0140.01522.924-0.007-0.0070.0000.0000.0000.000
97A113VAL0-0.032-0.02514.3210.0040.0040.0000.0000.0000.000
98A114MET0-0.0010.00810.820-0.041-0.0410.0000.0000.0000.000
99A115THR00.0030.0049.6870.0100.0100.0000.0000.0000.000
100A116ALA0-0.0090.0208.839-0.007-0.0070.0000.0000.0000.000
101A117VAL00.0310.0067.0070.0250.0250.0000.0000.0000.000
102A118ILE0-0.036-0.0118.283-0.041-0.0410.0000.0000.0000.000
103A119GLU-1-0.902-0.9638.8471.0911.0910.0000.0000.0000.000
104A120LEU0-0.042-0.02311.259-0.070-0.0700.0000.0000.0000.000
105A121GLN0-0.030-0.02213.565-0.013-0.0130.0000.0000.0000.000
106A122PRO00.0160.02816.117-0.024-0.0240.0000.0000.0000.000
107A123THR00.011-0.00418.2390.0020.0020.0000.0000.0000.000
108A124SER0-0.020-0.02220.793-0.002-0.0020.0000.0000.0000.000
109A125SER0-0.018-0.01223.047-0.002-0.0020.0000.0000.0000.000
110A126GLY00.000-0.00522.059-0.009-0.0090.0000.0000.0000.000
111A127THR0-0.030-0.01716.7020.0180.0180.0000.0000.0000.000
112A128ARG10.8890.95212.758-0.161-0.1610.0000.0000.0000.000
113A129TYR00.023-0.00511.6550.0430.0430.0000.0000.0000.000
114A130THR00.009-0.0036.708-0.077-0.0770.0000.0000.0000.000
115A131ALA00.0120.0168.3570.0780.0780.0000.0000.0000.000
116A132CYS0-0.013-0.0073.041-0.601-0.3680.792-0.192-0.8320.000
117A133ALA00.0060.0145.5630.1130.1130.0000.0000.0000.000
118A134MET00.004-0.0103.967-0.301-0.0720.000-0.025-0.2040.000
119A135HIS00.0030.0076.6420.2560.2560.0000.0000.0000.000
120A136ASN00.0420.0069.013-0.062-0.0620.0000.0000.0000.000
121A137THR0-0.001-0.00311.742-0.007-0.0070.0000.0000.0000.000
122A138PRO00.0950.03910.8300.0000.0000.0000.0000.0000.000
123A139GLY0-0.016-0.00211.872-0.001-0.0010.0000.0000.0000.000
124A140GLN0-0.018-0.00712.8150.0470.0470.0000.0000.0000.000
125A141ARG10.8340.9226.8151.0711.0710.0000.0000.0000.000
126A142LYS10.9460.96210.2250.4610.4610.0000.0000.0000.000
127A143LEU00.0240.01412.6980.0370.0370.0000.0000.0000.000
128A144HIS0-0.037-0.05010.3530.0730.0730.0000.0000.0000.000
129A145GLU-1-0.892-0.9499.900-0.675-0.6750.0000.0000.0000.000
130A146GLU-1-0.967-0.98212.707-0.236-0.2360.0000.0000.0000.000
131A147MET0-0.054-0.01415.4070.0390.0390.0000.0000.0000.000
132A148GLY00.0240.02115.8320.0240.0240.0000.0000.0000.000
133A149PHE0-0.011-0.0027.8840.0010.0010.0000.0000.0000.000
134A150HIS0-0.005-0.00410.6570.0460.0460.0000.0000.0000.000
135A151GLU-1-0.897-0.95012.356-0.084-0.0840.0000.0000.0000.000
136A152GLY00.0370.01915.8450.0260.0260.0000.0000.0000.000
137A153TRP00.042-0.00110.7370.0390.0390.0000.0000.0000.000
138A154GLY00.0100.01314.1800.0310.0310.0000.0000.0000.000
139A155THR0-0.006-0.00215.2570.0220.0220.0000.0000.0000.000
140A156THR0-0.055-0.02916.0120.0190.0190.0000.0000.0000.000
141A157ILE00.012-0.00214.0700.0170.0170.0000.0000.0000.000
142A158THR0-0.001-0.00117.5010.0090.0090.0000.0000.0000.000
143A159GLN0-0.018-0.00520.500-0.004-0.0040.0000.0000.0000.000
144A160LEU00.0140.01817.9440.0050.0050.0000.0000.0000.000
145A161GLU-1-0.871-0.95120.7650.0420.0420.0000.0000.0000.000
146A162GLU-1-1.000-0.99922.4060.0100.0100.0000.0000.0000.000
147A163LEU0-0.0040.00224.7110.0000.0000.0000.0000.0000.000
148A164LEU0-0.008-0.01221.9590.0020.0020.0000.0000.0000.000
149A165LYS10.8940.95324.712-0.032-0.0320.0000.0000.0000.000
150A166GLN0-0.049-0.02428.144-0.001-0.0010.0000.0000.0000.000
151A167GLU-1-0.916-0.94729.2170.0460.0460.0000.0000.0000.000
152A168LYS10.8850.95328.707-0.059-0.0590.0000.0000.0000.000
153A169ALA0-0.072-0.03330.4930.0030.0030.0000.0000.0000.000
154A170TYR00.0030.01532.4350.0010.0010.0000.0000.0000.000