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: Q895Y

Calculation Name: 1K4N-A-Xray314

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1K4N

Chain ID: A

ChEMBL ID:

UniProt ID: P52007

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 186
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2020781.111231
FMO2-HF: Nuclear repulsion 1947906.669881
FMO2-HF: Total energy -72874.44135
FMO2-MP2: Total energy -73087.728241


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:1:GLY )


Summations of interaction energy for fragment #1(A:1: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.
-1.094-0.3160.001-0.287-0.4930.001
Interaction energy analysis for fragmet #1(A:1:GLY )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.022
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].
3A3MET 0-0.002-0.0043.798-0.4680.3100.001-0.287-0.4930.001
4A4ILE 0-0.010-0.0076.0320.7160.7160.0000.0000.0000.000
5A5MET 00.0010.0188.1770.1560.1560.0000.0000.0000.000
6A6ALA 00.0190.01511.6170.0450.0450.0000.0000.0000.000
7A7ASN 00.0280.00814.4410.0730.0730.0000.0000.0000.000
8A8TRP 00.1060.02516.7110.0360.0360.0000.0000.0000.000
9A9GLN 0-0.082-0.04320.1310.0250.0250.0000.0000.0000.000
10A10SER 0-0.091-0.05017.1300.0090.0090.0000.0000.0000.000
11A11ILE 0-0.0310.00718.0170.0000.0000.0000.0000.0000.000
12A12ASP -1-0.847-0.91720.932-0.200-0.2000.0000.0000.0000.000
13A13GLU -1-0.928-0.97423.656-0.223-0.2230.0000.0000.0000.000
14A14LEU 0-0.045-0.02522.5830.0170.0170.0000.0000.0000.000
15A15GLN 00.0320.01724.7880.0150.0150.0000.0000.0000.000
16A16ASP -1-0.785-0.87626.734-0.136-0.1360.0000.0000.0000.000
17A17ILE 00.0320.00026.4600.0100.0100.0000.0000.0000.000
18A18ALA 00.0080.01025.0880.0040.0040.0000.0000.0000.000
19A19SER 0-0.054-0.03126.9830.0120.0120.0000.0000.0000.000
20A20ASP -1-0.748-0.84729.918-0.094-0.0940.0000.0000.0000.000
21A21LEU 0-0.0080.01027.0840.0080.0080.0000.0000.0000.000
22A22PRO 00.0260.00329.7090.0080.0080.0000.0000.0000.000
23A23ARG 10.8110.88532.4310.1000.1000.0000.0000.0000.000
24A24PHE 0-0.008-0.00932.5020.0060.0060.0000.0000.0000.000
25A25ILE 00.0210.01730.0780.0040.0040.0000.0000.0000.000
26A26HIS 00.0160.01434.0220.0030.0030.0000.0000.0000.000
27A27ALA 00.0080.00437.3760.0040.0040.0000.0000.0000.000
28A28LEU 0-0.019-0.01733.9770.0040.0040.0000.0000.0000.000
29A29ASP -1-0.848-0.89236.964-0.053-0.0530.0000.0000.0000.000
30A30GLU -1-0.903-0.96838.600-0.042-0.0420.0000.0000.0000.000
31A31LEU 0-0.044-0.02041.1510.0040.0040.0000.0000.0000.000
32A32SER 0-0.012-0.02639.3310.0020.0020.0000.0000.0000.000
33A33ARG 10.8230.92440.4010.0500.0500.0000.0000.0000.000
34A34ARG 10.9020.95144.0230.0490.0490.0000.0000.0000.000
35A35LEU 0-0.009-0.01243.8160.0020.0020.0000.0000.0000.000
36A36GLY 00.0160.02946.0820.0010.0010.0000.0000.0000.000
37A37LEU 0-0.012-0.00440.8990.0010.0010.0000.0000.0000.000
38A38ASN 0-0.015-0.01539.651-0.003-0.0030.0000.0000.0000.000
39A39ILE 00.0570.01435.067-0.001-0.0010.0000.0000.0000.000
40A40THR 0-0.017-0.00334.389-0.005-0.0050.0000.0000.0000.000
41A41PRO 0-0.036-0.01534.526-0.003-0.0030.0000.0000.0000.000
42A42LEU 0-0.0260.00536.193-0.002-0.0020.0000.0000.0000.000
43A43THR 00.0350.01631.189-0.004-0.0040.0000.0000.0000.000
44A44ALA 0-0.011-0.00529.7850.0010.0010.0000.0000.0000.000
45A45ASP -1-0.777-0.87730.254-0.130-0.1300.0000.0000.0000.000
46A46HIS 10.7760.88629.2440.1140.1140.0000.0000.0000.000
47A47ILE 0-0.0020.01428.2960.0140.0140.0000.0000.0000.000
48A48SER 0-0.051-0.07930.834-0.010-0.0100.0000.0000.0000.000
49A49LEU 00.0180.03029.3250.0080.0080.0000.0000.0000.000
50A50ARG 10.8090.89033.7110.1030.1030.0000.0000.0000.000
51A51CYS 00.0020.01635.488-0.002-0.0020.0000.0000.0000.000
52A52HIS 0-0.068-0.04937.5370.0030.0030.0000.0000.0000.000
53A53GLN 0-0.0110.00538.1500.0070.0070.0000.0000.0000.000
54A54ASN 00.0660.00237.385-0.007-0.0070.0000.0000.0000.000
55A55ALA 00.0000.00335.551-0.007-0.0070.0000.0000.0000.000
56A56THR 0-0.036-0.03133.549-0.008-0.0080.0000.0000.0000.000
57A57ALA 00.0570.02632.285-0.009-0.0090.0000.0000.0000.000
58A58GLU -1-0.909-0.96831.316-0.160-0.1600.0000.0000.0000.000
59A59ARG 10.7980.89928.8560.1370.1370.0000.0000.0000.000
60A60TRP 00.024-0.01927.669-0.013-0.0130.0000.0000.0000.000
61A61ARG 10.7890.89626.6440.1690.1690.0000.0000.0000.000
62A62ARG 10.8910.94525.4420.1890.1890.0000.0000.0000.000
63A63GLY 00.0540.02623.235-0.024-0.0240.0000.0000.0000.000
64A64PHE 00.034-0.02421.922-0.025-0.0250.0000.0000.0000.000
65A65GLU -1-0.916-0.95221.703-0.273-0.2730.0000.0000.0000.000
66A66GLN 0-0.067-0.02918.446-0.050-0.0500.0000.0000.0000.000
67A67CYS 0-0.090-0.02017.028-0.040-0.0400.0000.0000.0000.000
68A68GLY 00.0410.01518.2780.0010.0010.0000.0000.0000.000
69A69GLU -1-0.977-0.96818.222-0.446-0.4460.0000.0000.0000.000
70A70LEU 0-0.054-0.03121.5530.0220.0220.0000.0000.0000.000
71A71LEU 0-0.029-0.01324.6240.0000.0000.0000.0000.0000.000
72A72SER 0-0.006-0.00826.8450.0160.0160.0000.0000.0000.000
73A73GLU -1-0.773-0.88330.335-0.161-0.1610.0000.0000.0000.000
74A74ASN 00.0060.01632.7110.0080.0080.0000.0000.0000.000
75A75MET 00.0030.00236.3740.0000.0000.0000.0000.0000.000
76A76ILE 00.0070.01138.7520.0070.0070.0000.0000.0000.000
77A77ASN 0-0.042-0.04041.4050.0000.0000.0000.0000.0000.000
78A78GLY 00.0130.00644.1260.0010.0010.0000.0000.0000.000
79A79ARG 10.8600.92639.1860.0960.0960.0000.0000.0000.000
80A80PRO 00.0330.02235.3750.0020.0020.0000.0000.0000.000
81A81ILE 0-0.032-0.02034.2440.0020.0020.0000.0000.0000.000
82A82CYS 0-0.0210.00629.593-0.002-0.0020.0000.0000.0000.000
83A83LEU 00.0030.01529.3030.0030.0030.0000.0000.0000.000
84A84PHE 00.0440.01424.143-0.003-0.0030.0000.0000.0000.000
85A85LYS 10.9910.99220.8480.2750.2750.0000.0000.0000.000
86A86LEU 0-0.011-0.02420.213-0.025-0.0250.0000.0000.0000.000
87A87HIS 0-0.002-0.00514.812-0.021-0.0210.0000.0000.0000.000
88A88GLU -1-0.887-0.93313.598-0.594-0.5940.0000.0000.0000.000
89A89PRO 0-0.041-0.01917.7390.0200.0200.0000.0000.0000.000
90A90VAL 00.0070.02121.436-0.001-0.0010.0000.0000.0000.000
91A91GLN 0-0.026-0.02723.517-0.005-0.0050.0000.0000.0000.000
92A92VAL 0-0.009-0.01625.3250.0080.0080.0000.0000.0000.000
93A93ALA 00.0230.02129.1250.0060.0060.0000.0000.0000.000
94A94HIS 00.013-0.00628.335-0.005-0.0050.0000.0000.0000.000
95A95TRP 0-0.029-0.02527.862-0.004-0.0040.0000.0000.0000.000
96A96GLN 00.0180.00721.853-0.022-0.0220.0000.0000.0000.000
97A97PHE 0-0.009-0.00125.2110.0000.0000.0000.0000.0000.000
98A98SER 00.0700.02922.357-0.024-0.0240.0000.0000.0000.000
99A99ILE 0-0.0120.01523.616-0.020-0.0200.0000.0000.0000.000
100A100VAL 00.0180.00925.6370.0180.0180.0000.0000.0000.000
101A101GLU -1-0.843-0.89228.107-0.122-0.1220.0000.0000.0000.000
102A102LEU 0-0.010-0.01129.2740.0050.0050.0000.0000.0000.000
103A103PRO 0-0.061-0.02732.1030.0020.0020.0000.0000.0000.000
104A104TRP 00.0470.01631.7490.0010.0010.0000.0000.0000.000
105A105PRO 0-0.0220.00737.4160.0050.0050.0000.0000.0000.000
106A106GLY 00.000-0.00440.6080.0010.0010.0000.0000.0000.000
107A107GLU -1-0.942-0.96143.329-0.062-0.0620.0000.0000.0000.000
108A108LYS 10.8760.95045.0450.0710.0710.0000.0000.0000.000
109A109ARG 10.9910.98844.4930.0600.0600.0000.0000.0000.000
110A110TYR 00.014-0.01141.1790.0040.0040.0000.0000.0000.000
111A111PRO 0-0.006-0.02342.170-0.003-0.0030.0000.0000.0000.000
112A112HIS 0-0.062-0.01235.9500.0050.0050.0000.0000.0000.000
113A113GLU -1-0.756-0.85035.896-0.108-0.1080.0000.0000.0000.000
114A114GLY 00.0460.01933.411-0.003-0.0030.0000.0000.0000.000
115A115TRP 0-0.052-0.02927.4650.0030.0030.0000.0000.0000.000
116A116GLU -1-0.795-0.86834.025-0.085-0.0850.0000.0000.0000.000
117A117HIS 10.7080.81135.7350.1090.1090.0000.0000.0000.000
118A118ILE 00.0390.04332.714-0.009-0.0090.0000.0000.0000.000
119A119GLU -1-0.893-0.94833.982-0.092-0.0920.0000.0000.0000.000
120A120ILE 00.0320.01434.021-0.006-0.0060.0000.0000.0000.000
121A121VAL 00.0410.01733.3170.0030.0030.0000.0000.0000.000
122A122LEU 0-0.037-0.01836.3010.0030.0030.0000.0000.0000.000
123A123PRO 00.0360.01236.5270.0030.0030.0000.0000.0000.000
124A124GLY 00.0070.00039.2200.0040.0040.0000.0000.0000.000
125A125ASP -1-0.829-0.92342.616-0.049-0.0490.0000.0000.0000.000
126A126PRO 0-0.005-0.00142.6200.0000.0000.0000.0000.0000.000
127A127GLU -1-0.922-0.94944.965-0.049-0.0490.0000.0000.0000.000
128A128THR 0-0.025-0.00347.6880.0010.0010.0000.0000.0000.000
129A129LEU 0-0.056-0.00541.9200.0010.0010.0000.0000.0000.000
130A130ASN 00.041-0.00945.737-0.002-0.0020.0000.0000.0000.000
131A131ALA 00.0080.00347.9040.0010.0010.0000.0000.0000.000
132A132ARG 10.8440.89942.4520.0540.0540.0000.0000.0000.000
133A133ALA 00.0120.00544.2930.0000.0000.0000.0000.0000.000
134A134LEU 0-0.025-0.02545.5700.0000.0000.0000.0000.0000.000
135A135ALA 0-0.0100.00548.4800.0010.0010.0000.0000.0000.000
136A136LEU 0-0.058-0.02042.1970.0010.0010.0000.0000.0000.000
137A137LEU 0-0.066-0.02244.818-0.001-0.0010.0000.0000.0000.000
138A138SER 00.0150.01447.8370.0030.0030.0000.0000.0000.000
139A139ASP -1-0.875-0.95350.456-0.032-0.0320.0000.0000.0000.000
140A140GLU -1-0.952-0.96752.634-0.031-0.0310.0000.0000.0000.000
141A141GLY 00.0470.01249.832-0.001-0.0010.0000.0000.0000.000
142A142LEU 0-0.062-0.03649.940-0.002-0.0020.0000.0000.0000.000
143A143SER 0-0.078-0.04152.1200.0000.0000.0000.0000.0000.000
144A144LEU 0-0.0360.00750.2770.0010.0010.0000.0000.0000.000
145A145PRO 00.0240.01353.479-0.001-0.0010.0000.0000.0000.000
146A146GLY 0-0.060-0.04251.636-0.001-0.0010.0000.0000.0000.000
147A147ILE 0-0.0160.00547.374-0.003-0.0030.0000.0000.0000.000
148A148SER 0-0.055-0.02149.0230.0010.0010.0000.0000.0000.000
149A149VAL 00.0510.01248.039-0.003-0.0030.0000.0000.0000.000
150A150LYS 10.9060.95846.6050.0620.0620.0000.0000.0000.000
151A151THR 00.0400.02447.483-0.002-0.0020.0000.0000.0000.000
152A152SER 0-0.020-0.00244.614-0.001-0.0010.0000.0000.0000.000
153A153NME 00.0100.00946.7270.0020.0020.0000.0000.0000.000
154A159ACE 0-0.006-0.01041.3780.0010.0010.0000.0000.0000.000
155A160ARG 11.0121.02140.1590.0620.0620.0000.0000.0000.000
156A161LEU 00.0440.01537.5450.0050.0050.0000.0000.0000.000
157A162PRO 0-0.054-0.04041.526-0.002-0.0020.0000.0000.0000.000
158A163ASN 00.1050.06139.100-0.001-0.0010.0000.0000.0000.000
159A164PRO 0-0.0270.01342.056-0.002-0.0020.0000.0000.0000.000
160A165THR 00.038-0.01640.820-0.003-0.0030.0000.0000.0000.000
161A166LEU 0-0.0360.00043.2360.0020.0020.0000.0000.0000.000
162A167ALA 0-0.043-0.03643.176-0.004-0.0040.0000.0000.0000.000
163A168VAL 00.0620.03843.3490.0040.0040.0000.0000.0000.000
164A169THR 0-0.026-0.01743.604-0.003-0.0030.0000.0000.0000.000
165A170ASP -1-0.718-0.86744.381-0.059-0.0590.0000.0000.0000.000
166A171GLY 0-0.058-0.02146.1840.0020.0020.0000.0000.0000.000
167A172LYS 10.8090.88542.5670.0590.0590.0000.0000.0000.000
168A173THR 00.0160.02438.846-0.007-0.0070.0000.0000.0000.000
169A174THR 0-0.062-0.03339.8470.0060.0060.0000.0000.0000.000
170A175ILE 00.0370.03038.390-0.006-0.0060.0000.0000.0000.000
171A176LYS 10.8930.94338.7020.0890.0890.0000.0000.0000.000
172A177PHE 00.0510.03438.725-0.003-0.0030.0000.0000.0000.000
173A178HIS 10.8250.89335.1000.1000.1000.0000.0000.0000.000
174A179PRO 0-0.016-0.01938.872-0.001-0.0010.0000.0000.0000.000
175A180TRP 0-0.0120.02435.9180.0030.0030.0000.0000.0000.000
176A181SER 00.0320.02930.860-0.001-0.0010.0000.0000.0000.000
177A182ILE 00.010-0.01029.6100.0030.0030.0000.0000.0000.000
178A183GLU -1-0.878-0.95726.169-0.166-0.1660.0000.0000.0000.000
179A184GLU -1-0.894-0.94829.381-0.093-0.0930.0000.0000.0000.000
180A185ILE 0-0.028-0.01232.6110.0060.0060.0000.0000.0000.000
181A186VAL 00.0160.03429.0110.0030.0030.0000.0000.0000.000
182A187ALA 00.004-0.00230.9920.0020.0020.0000.0000.0000.000
183A188SER 0-0.175-0.10932.4000.0080.0080.0000.0000.0000.000
184A189GLU -1-1.001-0.99134.867-0.098-0.0980.0000.0000.0000.000
185A190GLN 0-0.0040.00630.257-0.015-0.0150.0000.0000.0000.000
186A191NME 0-0.034-0.01733.2120.0070.0070.0000.0000.0000.000