Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 3JLVL

Calculation Name: 1K7K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1K7K

Chain ID: A

ChEMBL ID:

UniProt ID: P52061

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.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
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 209
LigandCharge DGL=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2207252.712487
FMO2-HF: Nuclear repulsion 2129099.475566
FMO2-HF: Total energy -78153.236921
FMO2-MP2: Total energy -78383.5559


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:-11:SER)


Summations of interaction energy for fragment #1(A:-11:SER)
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.
-11.565-9.4647.533-4.31-5.322-0.024
Interaction energy analysis for fragmet #1(A:-11:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.006
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].
3A-9GLY00.0500.0243.860-1.356-0.072-0.010-0.583-0.6910.003
4A-8ARG10.8290.8696.4700.9250.9250.0000.0000.0000.000
5A-7DGL-1-0.761-0.8449.461-0.713-0.7130.0000.0000.0000.000
6A-6ASN00.0260.0146.9750.3920.3920.0000.0000.0000.000
7A-5LEU00.0370.0218.5710.0250.0250.0000.0000.0000.000
8A-4TYR0-0.0010.01212.0070.0060.0060.0000.0000.0000.000
9A-3PHE00.012-0.0079.936-0.021-0.0210.0000.0000.0000.000
10A-2GLN0-0.025-0.01515.7510.0240.0240.0000.0000.0000.000
11A-1GLY0-0.009-0.01218.7640.0300.0300.0000.0000.0000.000
12A0HIS0-0.0340.00920.7580.0180.0180.0000.0000.0000.000
13A1MET0-0.021-0.01518.931-0.020-0.0200.0000.0000.0000.000
14A2GLN0-0.039-0.01516.1580.0170.0170.0000.0000.0000.000
15A3LYS10.8510.91818.5590.1990.1990.0000.0000.0000.000
16A4VAL0-0.015-0.00615.883-0.016-0.0160.0000.0000.0000.000
17A5VAL00.0090.02119.1530.0210.0210.0000.0000.0000.000
18A6LEU0-0.010-0.00918.434-0.016-0.0160.0000.0000.0000.000
19A7ALA00.0210.00820.2420.0190.0190.0000.0000.0000.000
20A8THR0-0.073-0.05122.1690.0190.0190.0000.0000.0000.000
21A9GLY00.1250.05324.875-0.008-0.0080.0000.0000.0000.000
22A10ASN0-0.055-0.02225.853-0.003-0.0030.0000.0000.0000.000
23A11VAL00.0960.03126.030-0.011-0.0110.0000.0000.0000.000
24A12GLY0-0.0090.00526.848-0.008-0.0080.0000.0000.0000.000
25A13LYS10.8620.90221.4190.0830.0830.0000.0000.0000.000
26A14VAL00.0230.02421.690-0.021-0.0210.0000.0000.0000.000
27A15ARG10.9470.96922.5450.0970.0970.0000.0000.0000.000
28A16GLU-1-0.830-0.88419.996-0.159-0.1590.0000.0000.0000.000
29A17LEU00.0340.00915.350-0.015-0.0150.0000.0000.0000.000
30A18ALA00.0370.01118.104-0.036-0.0360.0000.0000.0000.000
31A19SER0-0.046-0.02320.054-0.010-0.0100.0000.0000.0000.000
32A20LEU0-0.050-0.02016.027-0.002-0.0020.0000.0000.0000.000
33A21LEU0-0.004-0.00112.682-0.049-0.0490.0000.0000.0000.000
34A22SER0-0.022-0.01315.863-0.032-0.0320.0000.0000.0000.000
35A23ASP-1-0.946-0.96315.477-0.385-0.3850.0000.0000.0000.000
36A24PHE0-0.007-0.0069.297-0.023-0.0230.0000.0000.0000.000
37A25GLY00.0250.00914.061-0.052-0.0520.0000.0000.0000.000
38A26LEU0-0.059-0.03112.4760.0070.0070.0000.0000.0000.000
39A27ASP-1-0.845-0.90916.964-0.195-0.1950.0000.0000.0000.000
40A28ILE0-0.009-0.00616.5570.0090.0090.0000.0000.0000.000
41A29VAL0-0.010-0.00620.6040.0230.0230.0000.0000.0000.000
42A30ALA0-0.0030.00623.032-0.009-0.0090.0000.0000.0000.000
43A31GLN0-0.031-0.04124.419-0.003-0.0030.0000.0000.0000.000
44A32THR00.0100.00226.0030.0060.0060.0000.0000.0000.000
45A33ASP-1-0.895-0.94827.804-0.120-0.1200.0000.0000.0000.000
46A34LEU0-0.065-0.02824.934-0.001-0.0010.0000.0000.0000.000
47A35GLY0-0.0150.00429.1750.0020.0020.0000.0000.0000.000
48A36VAL0-0.036-0.01326.5290.0050.0050.0000.0000.0000.000
49A37ASP-1-0.860-0.91529.546-0.057-0.0570.0000.0000.0000.000
50A38SER0-0.037-0.03828.172-0.008-0.0080.0000.0000.0000.000
51A39ALA00.0020.01625.5980.0030.0030.0000.0000.0000.000
52A40GLU-1-0.880-0.94027.578-0.005-0.0050.0000.0000.0000.000
53A41GLU-1-0.872-0.91825.849-0.021-0.0210.0000.0000.0000.000
54A42THR0-0.040-0.04627.0310.0060.0060.0000.0000.0000.000
55A43GLY0-0.0140.00423.7220.0070.0070.0000.0000.0000.000
56A44LEU0-0.007-0.02024.318-0.005-0.0050.0000.0000.0000.000
57A45THR0-0.055-0.06520.1710.0080.0080.0000.0000.0000.000
58A46PHE0-0.004-0.01019.034-0.006-0.0060.0000.0000.0000.000
59A47ILE00.0370.01513.170-0.023-0.0230.0000.0000.0000.000
60A48GLU-1-0.810-0.85917.2470.0890.0890.0000.0000.0000.000
61A49ASN00.0430.01119.904-0.022-0.0220.0000.0000.0000.000
62A50ALA0-0.0080.00716.822-0.020-0.0200.0000.0000.0000.000
63A51ILE0-0.006-0.01114.304-0.029-0.0290.0000.0000.0000.000
64A52LEU0-0.021-0.00917.844-0.021-0.0210.0000.0000.0000.000
65A53LYS10.7980.89320.7370.0180.0180.0000.0000.0000.000
66A54ALA00.0010.00017.009-0.013-0.0130.0000.0000.0000.000
67A55ARG10.8660.92317.2080.0110.0110.0000.0000.0000.000
68A56HIS0-0.026-0.01820.519-0.005-0.0050.0000.0000.0000.000
69A57ALA00.0460.01821.362-0.004-0.0040.0000.0000.0000.000
70A58ALA00.0080.01919.448-0.007-0.0070.0000.0000.0000.000
71A59LYS10.8070.88121.5880.0740.0740.0000.0000.0000.000
72A60VAL0-0.027-0.00724.5360.0040.0040.0000.0000.0000.000
73A61THR0-0.014-0.02723.693-0.006-0.0060.0000.0000.0000.000
74A62ALA0-0.065-0.02323.573-0.006-0.0060.0000.0000.0000.000
75A63LEU0-0.0300.00220.696-0.019-0.0190.0000.0000.0000.000
76A64PRO0-0.004-0.00215.5110.0140.0140.0000.0000.0000.000
77A65ALA0-0.0090.00116.3950.0200.0200.0000.0000.0000.000
78A66ILE0-0.0100.00513.779-0.014-0.0140.0000.0000.0000.000
79A67ALA00.0050.00715.9170.0360.0360.0000.0000.0000.000
80A68ASP-1-0.789-0.87616.295-0.112-0.1120.0000.0000.0000.000
81A69ASP-1-0.757-0.86918.3600.0120.0120.0000.0000.0000.000
82A70SER0-0.030-0.02219.6040.0020.0020.0000.0000.0000.000
83A71GLY0-0.013-0.00322.070-0.001-0.0010.0000.0000.0000.000
84A72LEU0-0.043-0.00824.1520.0020.0020.0000.0000.0000.000
85A73ALA0-0.028-0.00324.2690.0020.0020.0000.0000.0000.000
86A74VAL00.0490.00426.2980.0020.0020.0000.0000.0000.000
87A75ASP-1-0.907-0.94625.7200.1070.1070.0000.0000.0000.000
88A76VAL0-0.010-0.00728.4690.0030.0030.0000.0000.0000.000
89A77LEU0-0.035-0.01831.075-0.004-0.0040.0000.0000.0000.000
90A78GLY0-0.0030.00228.981-0.001-0.0010.0000.0000.0000.000
91A79GLY0-0.011-0.00326.1220.0080.0080.0000.0000.0000.000
92A80ALA0-0.0070.00126.831-0.005-0.0050.0000.0000.0000.000
93A81PRO00.031-0.00629.5530.0010.0010.0000.0000.0000.000
94A82GLY00.0750.05325.5860.0000.0000.0000.0000.0000.000
95A83ILE0-0.0030.02523.983-0.011-0.0110.0000.0000.0000.000
96A84TYR00.0130.00526.497-0.010-0.0100.0000.0000.0000.000
97A85SER0-0.024-0.02427.289-0.005-0.0050.0000.0000.0000.000
98A86ALA00.0390.02329.347-0.002-0.0020.0000.0000.0000.000
99A87ARG10.8900.93628.534-0.018-0.0180.0000.0000.0000.000
100A88TYR00.0160.01132.9770.0030.0030.0000.0000.0000.000
101A89SER0-0.059-0.06034.6680.0020.0020.0000.0000.0000.000
102A90GLY0-0.028-0.00337.2960.0000.0000.0000.0000.0000.000
103A91GLU-1-0.871-0.94038.267-0.001-0.0010.0000.0000.0000.000
104A92ASP-1-0.897-0.95340.678-0.003-0.0030.0000.0000.0000.000
105A93ALA0-0.0590.00336.2840.0000.0000.0000.0000.0000.000
106A94THR00.0320.00137.279-0.003-0.0030.0000.0000.0000.000
107A95ASP-1-0.793-0.90133.689-0.009-0.0090.0000.0000.0000.000
108A96GLN00.0370.01836.0530.0030.0030.0000.0000.0000.000
109A97LYS10.8390.91139.3730.0000.0000.0000.0000.0000.000
110A98ASN0-0.0040.01134.1740.0060.0060.0000.0000.0000.000
111A99LEU00.0280.01235.5340.0050.0050.0000.0000.0000.000
112A100GLN00.0160.00236.6450.0020.0020.0000.0000.0000.000
113A101LYS10.8810.96037.297-0.024-0.0240.0000.0000.0000.000
114A102LEU0-0.0210.00832.3550.0030.0030.0000.0000.0000.000
115A103LEU00.0040.00336.7150.0030.0030.0000.0000.0000.000
116A104GLU-1-0.858-0.90939.2650.0260.0260.0000.0000.0000.000
117A105THR0-0.078-0.05936.2630.0020.0020.0000.0000.0000.000
118A106MET00.0130.01733.6320.0040.0040.0000.0000.0000.000
119A107LYS10.8340.93438.616-0.026-0.0260.0000.0000.0000.000
120A108ASP-1-0.892-0.95742.1740.0320.0320.0000.0000.0000.000
121A109VAL0-0.055-0.00836.1430.0020.0020.0000.0000.0000.000
122A110PRO00.0260.00938.981-0.003-0.0030.0000.0000.0000.000
123A111ASP-1-0.785-0.88837.9030.0380.0380.0000.0000.0000.000
124A112ASP-1-0.902-0.92936.0700.0580.0580.0000.0000.0000.000
125A113GLN0-0.076-0.04534.0270.0060.0060.0000.0000.0000.000
126A114ARG10.8150.89133.951-0.037-0.0370.0000.0000.0000.000
127A115GLN0-0.032-0.01928.392-0.005-0.0050.0000.0000.0000.000
128A116ALA00.0340.01427.5000.0010.0010.0000.0000.0000.000
129A117ARG10.9060.94318.911-0.134-0.1340.0000.0000.0000.000
130A118PHE00.0210.03223.465-0.001-0.0010.0000.0000.0000.000
131A119HIS00.0540.01419.4730.0140.0140.0000.0000.0000.000
132A120CYS0-0.083-0.03117.828-0.023-0.0230.0000.0000.0000.000
133A121VAL00.0070.00514.4600.0020.0020.0000.0000.0000.000
134A122LEU00.0400.02411.9460.0000.0000.0000.0000.0000.000
135A123VAL0-0.049-0.02811.9390.0280.0280.0000.0000.0000.000
136A124TYR0-0.010-0.03010.2980.0040.0040.0000.0000.0000.000
137A125LEU0-0.0290.01111.306-0.031-0.0310.0000.0000.0000.000
138A126ARG10.8100.8657.8380.8240.8240.0000.0000.0000.000
139A127HIS00.0360.00814.4770.0320.0320.0000.0000.0000.000
140A128ALA00.0570.03517.5610.0140.0140.0000.0000.0000.000
141A129GLU-1-0.832-0.90519.627-0.045-0.0450.0000.0000.0000.000
142A130ASP-1-0.815-0.87212.873-0.262-0.2620.0000.0000.0000.000
143A131PRO00.003-0.00913.4150.0280.0280.0000.0000.0000.000
144A132THR0-0.091-0.0479.1380.0850.0850.0000.0000.0000.000
145A133PRO00.0220.0239.592-0.133-0.1330.0000.0000.0000.000
146A134LEU00.0000.0134.8070.2460.2460.0000.0000.0000.000
147A135VAL0-0.022-0.0227.7210.0140.0140.0000.0000.0000.000
148A136CYS0-0.044-0.0057.984-0.045-0.0450.0000.0000.0000.000
149A137HIS0-0.006-0.01310.4280.0110.0110.0000.0000.0000.000
150A138GLY00.0260.02413.2120.0170.0170.0000.0000.0000.000
151A139SER0-0.077-0.04515.4760.0120.0120.0000.0000.0000.000
152A140TRP00.0450.00818.796-0.002-0.0020.0000.0000.0000.000
153A141PRO0-0.001-0.00721.741-0.002-0.0020.0000.0000.0000.000
154A142GLY00.0360.00924.511-0.008-0.0080.0000.0000.0000.000
155A143VAL0-0.057-0.02528.2970.0080.0080.0000.0000.0000.000
156A144ILE0-0.011-0.00330.708-0.006-0.0060.0000.0000.0000.000
157A145THR0-0.018-0.01633.8130.0020.0020.0000.0000.0000.000
158A146ARG10.8010.86237.265-0.031-0.0310.0000.0000.0000.000
159A147GLU-1-0.852-0.92740.4810.0200.0200.0000.0000.0000.000
160A148PRO0-0.025-0.00538.9660.0010.0010.0000.0000.0000.000
161A149ALA00.0220.02238.357-0.001-0.0010.0000.0000.0000.000
162A150GLY00.0520.03137.2510.0000.0000.0000.0000.0000.000
163A151THR0-0.041-0.03638.0820.0010.0010.0000.0000.0000.000
164A152GLY0-0.0080.01134.770-0.003-0.0030.0000.0000.0000.000
165A153GLY0-0.023-0.01830.9290.0030.0030.0000.0000.0000.000
166A154PHE0-0.047-0.03226.185-0.004-0.0040.0000.0000.0000.000
167A155GLY00.0060.00231.0700.0030.0030.0000.0000.0000.000
168A156TYR0-0.042-0.06029.8370.0020.0020.0000.0000.0000.000
169A157ASP-1-0.725-0.84129.181-0.008-0.0080.0000.0000.0000.000
170A158PRO00.016-0.00431.8530.0020.0020.0000.0000.0000.000
171A159ILE00.0060.01833.9150.0010.0010.0000.0000.0000.000
172A160PHE0-0.0250.01026.1780.0050.0050.0000.0000.0000.000
173A161PHE00.0620.02531.486-0.004-0.0040.0000.0000.0000.000
174A162VAL00.0300.00827.4280.0060.0060.0000.0000.0000.000
175A163PRO0-0.025-0.02329.269-0.002-0.0020.0000.0000.0000.000
176A164SER0-0.072-0.05927.6250.0010.0010.0000.0000.0000.000
177A165GLU-1-0.865-0.91027.7240.0130.0130.0000.0000.0000.000
178A166GLY0-0.049-0.02031.455-0.004-0.0040.0000.0000.0000.000
179A167LYS10.8390.92233.0230.0000.0000.0000.0000.0000.000
180A168THR00.002-0.01832.8390.0020.0020.0000.0000.0000.000
181A169ALA0-0.016-0.01529.078-0.004-0.0040.0000.0000.0000.000
182A170ALA0-0.057-0.01330.655-0.006-0.0060.0000.0000.0000.000
183A171GLU-1-0.874-0.93933.6800.0020.0020.0000.0000.0000.000
184A172LEU0-0.0500.00728.274-0.002-0.0020.0000.0000.0000.000
185A173THR0-0.011-0.04031.761-0.005-0.0050.0000.0000.0000.000
186A174ARG10.8470.90129.2330.0290.0290.0000.0000.0000.000
187A175GLU-1-0.895-0.94027.121-0.061-0.0610.0000.0000.0000.000
188A176GLU-1-0.749-0.83326.303-0.015-0.0150.0000.0000.0000.000
189A177LYS10.8090.89725.7730.0200.0200.0000.0000.0000.000
190A178SER0-0.011-0.02723.2930.0040.0040.0000.0000.0000.000
191A179ALA0-0.0120.00221.745-0.008-0.0080.0000.0000.0000.000
192A180ILE00.0050.00921.2750.0020.0020.0000.0000.0000.000
193A181SER0-0.0360.00521.2620.0080.0080.0000.0000.0000.000
194A182HIS00.0200.00518.958-0.007-0.0070.0000.0000.0000.000
195A183ARG10.8230.85617.4930.1300.1300.0000.0000.0000.000
196A184GLY00.0680.04217.061-0.029-0.0290.0000.0000.0000.000
197A185GLN0-0.102-0.06815.483-0.009-0.0090.0000.0000.0000.000
198A186ALA00.0180.01313.167-0.019-0.0190.0000.0000.0000.000
199A187LEU0-0.004-0.00412.214-0.075-0.0750.0000.0000.0000.000
200A188LYS10.9520.98112.551-0.046-0.0460.0000.0000.0000.000
201A189LEU0-0.019-0.0119.076-0.044-0.0440.0000.0000.0000.000
202A190LEU00.0170.0007.765-0.218-0.2180.0000.0000.0000.000
203A191LEU0-0.009-0.0138.313-0.263-0.2630.0000.0000.0000.000
204A192ASP-1-0.903-0.9336.733-0.137-0.1370.0000.0000.0000.000
205A193ALA00.006-0.0073.823-0.447-0.2440.001-0.033-0.1710.000
206A194LEU0-0.031-0.0113.799-1.961-1.7850.002-0.126-0.052-0.001
207A195ARG10.9030.9536.0260.5430.5430.0000.0000.0000.000
208A196ASN0-0.090-0.0474.6480.3100.382-0.001-0.038-0.0320.000
209A197GLY00.0130.0122.310-8.606-8.2407.541-3.530-4.376-0.026