FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 3KNYL

Calculation Name: 3JTG-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3JTG

Chain ID: A

ChEMBL ID:

UniProt ID: Q3UPW2

Base Structure: X-ray

Registration Date: 2025-07-11

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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 182
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -795815.241659
FMO2-HF: Nuclear repulsion 755507.921242
FMO2-HF: Total energy -40307.320418
FMO2-MP2: Total energy -40425.567254


3D Structure Molmil
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:272:GLY)


Summations of interaction energy for fragment #1(A:272:GLY)
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.
-0.625-0.0438.275-4.652-4.207-0.022
Interaction energy analysis for fragmet #1(A:272:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.002
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].
3A273THR0-0.0370.0853.506-0.1000.3190.003-0.154-0.2680.000
4A274HIS00.083-0.1083.1860.3562.1510.005-0.942-0.8580.003
5A274HIS0-0.1140.1034.635-0.0500.034-0.001-0.014-0.0690.000
6A275LEU00.140-0.0905.023-0.210-0.199-0.002-0.005-0.0050.000
7A275LEU0-0.1150.0909.2230.0310.0310.0000.0000.0000.000
8A276TRP00.104-0.0787.3440.0930.0930.0000.0000.0000.000
9A276TRP0-0.0400.0896.938-0.024-0.0240.0000.0000.0000.000
10A277GLU00.061-0.1173.0591.1790.4790.1650.703-0.169-0.001
11A277GLU-1-0.911-0.8192.241-3.609-5.0958.096-4.084-2.527-0.024
12A278PHE00.153-0.0454.3380.3700.422-0.001-0.011-0.0390.000
13A278PHE0-0.1030.0705.7600.0390.0390.0000.0000.0000.000
14A279ILE00.035-0.1205.5860.2980.2980.0000.0000.0000.000
15A279ILE0-0.0940.0769.1360.0040.0040.0000.0000.0000.000
16A280ARG00.141-0.0887.4730.1000.1000.0000.0000.0000.000
17A280ARG10.7551.0363.442-0.456-0.2590.010-0.074-0.1320.000
18A281ASP00.092-0.1086.130-0.051-0.0510.0000.0000.0000.000
19A281ASP-1-0.983-0.8284.0111.5121.7220.000-0.071-0.1400.000
20A282ILE00.072-0.1007.2030.0870.0870.0000.0000.0000.000
21A282ILE0-0.1010.0669.304-0.010-0.0100.0000.0000.0000.000
22A283LEU0-0.002-0.11510.3920.0190.0190.0000.0000.0000.000
23A283LEU0-0.0910.09611.387-0.010-0.0100.0000.0000.0000.000
24A284ILE00.010-0.10510.564-0.033-0.0330.0000.0000.0000.000
25A284ILE0-0.1090.0927.939-0.014-0.0140.0000.0000.0000.000
26A285HIS0-0.009-0.10211.9580.0050.0050.0000.0000.0000.000
27A285HIS10.8151.0289.099-0.596-0.5960.0000.0000.0000.000
28A286PRO00.088-0.08412.8990.0010.0010.0000.0000.0000.000
29A287GLU00.039-0.01316.198-0.021-0.0210.0000.0000.0000.000
30A287GLU-1-0.845-0.79414.5560.3300.3300.0000.0000.0000.000
31A288LEU00.044-0.12214.558-0.022-0.0220.0000.0000.0000.000
32A288LEU0-0.0780.11012.9030.0220.0220.0000.0000.0000.000
33A289ASN00.128-0.07915.2300.0240.0240.0000.0000.0000.000
34A289ASN0-0.1330.07814.949-0.016-0.0160.0000.0000.0000.000
35A290GLU00.142-0.03116.147-0.020-0.0200.0000.0000.0000.000
36A290GLU-1-1.028-0.88118.1190.1360.1360.0000.0000.0000.000
37A291GLY00.072-0.10018.959-0.021-0.0210.0000.0000.0000.000
38A292LEU00.037-0.03916.023-0.023-0.0230.0000.0000.0000.000
39A292LEU0-0.0700.11014.235-0.004-0.0040.0000.0000.0000.000
40A293MET00.078-0.12715.490-0.024-0.0240.0000.0000.0000.000
41A293MET0-0.0810.11011.613-0.013-0.0130.0000.0000.0000.000
42A294LYS00.052-0.07716.8360.0230.0230.0000.0000.0000.000
43A294LYS10.9021.08019.604-0.021-0.0210.0000.0000.0000.000
44A295TRP00.055-0.11817.869-0.018-0.0180.0000.0000.0000.000
45A295TRP0-0.0290.11813.016-0.014-0.0140.0000.0000.0000.000
46A296GLU00.028-0.10118.5290.0090.0090.0000.0000.0000.000
47A296GLU-1-0.982-0.87421.017-0.006-0.0060.0000.0000.0000.000
48A297ASN00.108-0.08520.2680.0050.0050.0000.0000.0000.000
49A297ASN0-0.0830.08921.7870.0010.0010.0000.0000.0000.000
50A298ARG00.088-0.12518.064-0.014-0.0140.0000.0000.0000.000
51A298ARG10.8191.06814.639-0.058-0.0580.0000.0000.0000.000
52A299HIS00.135-0.07718.105-0.002-0.0020.0000.0000.0000.000
53A299HIS0-0.0310.12122.1570.0030.0030.0000.0000.0000.000
54A300GLU00.026-0.12420.137-0.005-0.0050.0000.0000.0000.000
55A300GLU-1-1.031-0.86721.401-0.035-0.0350.0000.0000.0000.000
56A301GLY00.028-0.09316.323-0.014-0.0140.0000.0000.0000.000
57A302VAL00.114-0.01716.403-0.022-0.0220.0000.0000.0000.000
58A302VAL0-0.0890.12020.2710.0010.0010.0000.0000.0000.000
59A303PHE00.054-0.09515.9040.0190.0190.0000.0000.0000.000
60A303PHE0-0.0530.11313.214-0.005-0.0050.0000.0000.0000.000
61A304LYS00.073-0.09617.395-0.017-0.0170.0000.0000.0000.000
62A304LYS10.8451.05220.3100.0100.0100.0000.0000.0000.000
63A305PHE00.080-0.09217.3670.0160.0160.0000.0000.0000.000
64A305PHE0-0.1200.06313.813-0.001-0.0010.0000.0000.0000.000
65A306LEU00.051-0.12918.240-0.009-0.0090.0000.0000.0000.000
66A306LEU0-0.0930.11719.8440.0000.0000.0000.0000.0000.000
67A307ARG00.087-0.10019.147-0.007-0.0070.0000.0000.0000.000
68A307ARG10.7341.03119.244-0.079-0.0790.0000.0000.0000.000
69A308SER00.067-0.05418.4060.0060.0060.0000.0000.0000.000
70A308SER0-0.0320.06420.0320.0030.0030.0000.0000.0000.000
71A309GLU00.120-0.13318.011-0.013-0.0130.0000.0000.0000.000
72A309GLU-1-0.908-0.80121.405-0.042-0.0420.0000.0000.0000.000
73A310ALA00.089-0.08218.724-0.005-0.0050.0000.0000.0000.000
74A310ALA0-0.0500.10118.8460.0020.0020.0000.0000.0000.000
75A311VAL00.019-0.10914.7540.0270.0270.0000.0000.0000.000
76A311VAL0-0.0490.10812.870-0.005-0.0050.0000.0000.0000.000
77A312ALA00.093-0.09413.884-0.013-0.0130.0000.0000.0000.000
78A312ALA0-0.0630.10217.064-0.002-0.0020.0000.0000.0000.000
79A313GLN00.069-0.10715.186-0.028-0.0280.0000.0000.0000.000
80A313GLN0-0.0900.11017.644-0.004-0.0040.0000.0000.0000.000
81A314LEU00.103-0.11313.361-0.009-0.0090.0000.0000.0000.000
82A314LEU0-0.0560.12912.4290.0000.0000.0000.0000.0000.000
83A315TRP00.105-0.07010.7340.0570.0570.0000.0000.0000.000
84A315TRP0-0.0930.0826.9030.0320.0320.0000.0000.0000.000
85A316GLY0-0.005-0.12211.749-0.044-0.0440.0000.0000.0000.000
86A317GLN00.1210.00114.252-0.025-0.0250.0000.0000.0000.000
87A317GLN0-0.1060.09513.8230.0470.0470.0000.0000.0000.000
88A318LYS00.055-0.1099.6720.0480.0480.0000.0000.0000.000
89A318LYS10.8681.0967.112-1.165-1.1650.0000.0000.0000.000
90A319LYS00.019-0.10910.6220.0270.0270.0000.0000.0000.000
91A319LYS10.8371.0668.8480.5600.5600.0000.0000.0000.000
92A320LYS00.037-0.10711.977-0.022-0.0220.0000.0000.0000.000
93A320LYS10.8621.06914.203-0.050-0.0500.0000.0000.0000.000
94A321ASN00.193-0.08115.376-0.012-0.0120.0000.0000.0000.000
95A321ASN0-0.1420.06615.8930.0140.0140.0000.0000.0000.000
96A322SER00.070-0.07817.354-0.007-0.0070.0000.0000.0000.000
97A322SER0-0.0250.10820.7810.0080.0080.0000.0000.0000.000
98A323ASN00.103-0.05419.8290.0080.0080.0000.0000.0000.000
99A323ASN0-0.1270.06021.2810.0050.0050.0000.0000.0000.000
100A324MET00.103-0.09216.824-0.012-0.0120.0000.0000.0000.000
101A324MET0-0.1050.11514.159-0.006-0.0060.0000.0000.0000.000
102A325THR00.021-0.06218.2990.0180.0180.0000.0000.0000.000
103A325THR00.0170.07321.209-0.007-0.0070.0000.0000.0000.000
104A326TYR00.163-0.07918.044-0.027-0.0270.0000.0000.0000.000
105A326TYR00.0060.14117.664-0.002-0.0020.0000.0000.0000.000
106A327GLU00.105-0.09818.843-0.020-0.0200.0000.0000.0000.000
107A327GLU-1-1.013-0.84422.383-0.089-0.0890.0000.0000.0000.000
108A328LYS00.075-0.11519.089-0.009-0.0090.0000.0000.0000.000
109A328LYS10.7741.03118.5100.1050.1050.0000.0000.0000.000
110A329LEU00.119-0.09815.103-0.038-0.0380.0000.0000.0000.000
111A329LEU0-0.0820.12412.9770.0020.0020.0000.0000.0000.000
112A330SER00.030-0.10815.355-0.044-0.0440.0000.0000.0000.000
113A330SER0-0.0520.07819.0130.0070.0070.0000.0000.0000.000
114A331ARG00.042-0.14017.749-0.005-0.0050.0000.0000.0000.000
115A331ARG10.8461.08518.7570.1780.1780.0000.0000.0000.000
116A332ALA00.080-0.11114.2610.0160.0160.0000.0000.0000.000
117A332ALA0-0.0450.12613.327-0.011-0.0110.0000.0000.0000.000
118A333MET00.044-0.11414.079-0.050-0.0500.0000.0000.0000.000
119A333MET0-0.0780.10312.825-0.020-0.0200.0000.0000.0000.000
120A334ARG00.109-0.04915.074-0.007-0.0070.0000.0000.0000.000
121A334ARG10.8391.03719.6550.1380.1380.0000.0000.0000.000
122A335TYR0-0.006-0.13516.4740.0250.0250.0000.0000.0000.000
123A335TYR0-0.0810.09315.7300.0040.0040.0000.0000.0000.000
124A336TYR00.034-0.14914.191-0.006-0.0060.0000.0000.0000.000
125A336TYR0-0.0200.1319.264-0.039-0.0390.0000.0000.0000.000
126A337TYR00.090-0.04515.123-0.004-0.0040.0000.0000.0000.000
127A337TYR0-0.0680.08818.0210.0090.0090.0000.0000.0000.000
128A338LYS00.110-0.06818.4940.0100.0100.0000.0000.0000.000
129A338LYS10.8611.06918.9460.1430.1430.0000.0000.0000.000
130A339ARG00.108-0.07515.1550.0220.0220.0000.0000.0000.000
131A339ARG10.8501.05010.0830.4910.4910.0000.0000.0000.000
132A340GLU00.104-0.07015.767-0.020-0.0200.0000.0000.0000.000
133A340GLU-1-0.937-0.84217.551-0.141-0.1410.0000.0000.0000.000
134A341ILE00.121-0.06512.3880.0210.0210.0000.0000.0000.000
135A341ILE0-0.1320.0639.943-0.011-0.0110.0000.0000.0000.000
136A342LEU00.021-0.13513.176-0.002-0.0020.0000.0000.0000.000
137A342LEU0-0.0790.07512.480-0.004-0.0040.0000.0000.0000.000
138A343GLU00.063-0.12415.426-0.009-0.0090.0000.0000.0000.000
139A343GLU-1-0.926-0.79618.620-0.100-0.1000.0000.0000.0000.000
140A344ARG00.102-0.09119.0790.0020.0020.0000.0000.0000.000
141A344ARG10.8281.04021.5230.1100.1100.0000.0000.0000.000
142A345VAL00.077-0.11221.1680.0030.0030.0000.0000.0000.000
143A345VAL0-0.0960.11420.4740.0020.0020.0000.0000.0000.000
144A346ASP00.019-0.17222.967-0.003-0.0030.0000.0000.0000.000
145A346ASP-1-0.930-0.77226.675-0.068-0.0680.0000.0000.0000.000
146A347GLY00.007-0.10726.3310.0050.0050.0000.0000.0000.000
147A348ARG0-0.028-0.04525.0120.0070.0070.0000.0000.0000.000
148A348ARG10.9261.09924.2940.0320.0320.0000.0000.0000.000
149A349ARG00.195-0.05923.678-0.008-0.0080.0000.0000.0000.000
150A349ARG10.8871.06725.3240.0370.0370.0000.0000.0000.000
151A350LEU00.008-0.11220.5210.0030.0030.0000.0000.0000.000
152A350LEU0-0.0780.10420.5200.0000.0000.0000.0000.0000.000
153A351VAL00.119-0.09619.5150.0010.0010.0000.0000.0000.000
154A351VAL0-0.0890.09420.7730.0020.0020.0000.0000.0000.000
155A352TYR00.042-0.08616.732-0.002-0.0020.0000.0000.0000.000
156A352TYR0-0.1280.04916.097-0.015-0.0150.0000.0000.0000.000
157A353LYS00.170-0.10516.9690.0150.0150.0000.0000.0000.000
158A353LYS10.8221.09318.1950.0760.0760.0000.0000.0000.000
159A354PHE00.033-0.10713.786-0.025-0.0250.0000.0000.0000.000
160A354PHE0-0.0860.1119.7140.0000.0000.0000.0000.0000.000
161A355GLY00.043-0.07714.2330.0210.0210.0000.0000.0000.000
162A356LYS00.1480.04314.707-0.013-0.0130.0000.0000.0000.000
163A356LYS10.8711.06517.7630.1320.1320.0000.0000.0000.000
164A357ASN00.086-0.07013.9640.0140.0140.0000.0000.0000.000
165A357ASN0-0.2120.02613.2220.0050.0050.0000.0000.0000.000
166A358SER0-0.014-0.07710.359-0.059-0.0590.0000.0000.0000.000
167A358SER0-0.0780.02710.3100.0120.0120.0000.0000.0000.000
168A359SER00.002-0.1109.3250.0280.0280.0000.0000.0000.000
169A359SER0-0.0060.0939.360-0.006-0.0060.0000.0000.0000.000
170A360GLY00.064-0.0738.680-0.010-0.0100.0000.0000.0000.000
171A361TRP00.1100.0129.6790.0620.0620.0000.0000.0000.000
172A361TRP0-0.0620.10810.6340.0080.0080.0000.0000.0000.000
173A362LYS00.088-0.09611.7960.0150.0150.0000.0000.0000.000
174A362LYS10.9151.10415.1300.0580.0580.0000.0000.0000.000
175A363GLU00.010-0.14415.2630.0180.0180.0000.0000.0000.000
176A363GLU-1-0.941-0.83218.6430.0270.0270.0000.0000.0000.000
177A364GLU00.018-0.12217.6320.0150.0150.0000.0000.0000.000
178A364GLU-1-0.973-0.83119.4960.0190.0190.0000.0000.0000.000
179A365GLU00.105-0.10014.418-0.006-0.0060.0000.0000.0000.000
180A365GLU-1-1.056-0.87812.384-0.082-0.0820.0000.0000.0000.000
181A366VAL0-0.117-0.14711.905-0.008-0.0080.0000.0000.0000.000
182A366VAL00.0360.03211.0560.0080.0080.0000.0000.0000.000