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: 828VY

Calculation Name: 2JA9-A-Xray319

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2JA9

Chain ID: A

ChEMBL ID:

UniProt ID: Q08285

Base Structure: X-ray

Registration Date: 2021-09-07

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 175
LigandCharge DGL=-1
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1781480.345511
FMO2-HF: Nuclear repulsion 1711931.876623
FMO2-HF: Total energy -69548.468888
FMO2-MP2: Total energy -69748.109815


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:62:LYS )


Summations of interaction energy for fragment #1(A:62:LYS )
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.
-49.38-45.9041.879-1.534-3.823-0.004
Interaction energy analysis for fragmet #1(A:62:LYS )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.959 / q_NPA : 0.974
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].
3A64TYR 0-0.051-0.0753.752-2.965-1.348-0.001-0.669-0.9470.002
4A65ILE 0-0.0020.0075.3063.1823.1820.0000.0000.0000.000
5A66PRO 0-0.001-0.0047.815-0.644-0.6440.0000.0000.0000.000
6A67SER 0-0.0210.01110.4080.8690.8690.0000.0000.0000.000
7A68VAL 00.0590.00612.244-0.008-0.0080.0000.0000.0000.000
8A69ASN 0-0.045-0.03715.1430.0570.0570.0000.0000.0000.000
9A70ASP -1-0.839-0.87510.320-26.338-26.3380.0000.0000.0000.000
10A71PHE 00.0250.01813.5821.1381.1380.0000.0000.0000.000
11A72VAL 0-0.046-0.01811.756-2.159-2.1590.0000.0000.0000.000
12A73ILE 00.0180.00813.8021.3231.3230.0000.0000.0000.000
13A74GLY 00.0000.00114.628-1.271-1.2710.0000.0000.0000.000
14A75VAL 0-0.0210.00716.8730.5240.5240.0000.0000.0000.000
15A76ILE 00.0020.00819.679-0.213-0.2130.0000.0000.0000.000
16A77ILE 0-0.012-0.02019.6610.2220.2220.0000.0000.0000.000
17A78GLY 0-0.001-0.00822.8750.3900.3900.0000.0000.0000.000
18A79THR 0-0.0140.00125.604-0.223-0.2230.0000.0000.0000.000
19A80PHE 00.0090.01125.4240.2350.2350.0000.0000.0000.000
20A81SER 00.0070.00529.8280.0810.0810.0000.0000.0000.000
21A82ASP -1-0.960-0.98629.775-9.529-9.5290.0000.0000.0000.000
22A83SER 00.0390.01925.485-0.275-0.2750.0000.0000.0000.000
23A84TYR 0-0.019-0.00723.9510.3120.3120.0000.0000.0000.000
24A85LYS 10.9310.98320.41312.75412.7540.0000.0000.0000.000
25A86VAL 00.0210.00917.5110.0930.0930.0000.0000.0000.000
26A87SER 0-0.0180.00115.785-0.923-0.9230.0000.0000.0000.000
27A88LEU 00.0620.02511.928-0.201-0.2010.0000.0000.0000.000
28A89GLN 0-0.025-0.0338.429-0.756-0.7560.0000.0000.0000.000
29A90ASN 00.0510.04111.8781.5821.5820.0000.0000.0000.000
30A91PHE 0-0.027-0.02311.304-1.618-1.6180.0000.0000.0000.000
31A92SER 0-0.0250.00110.023-1.427-1.4270.0000.0000.0000.000
32A93SER 00.0260.01112.1790.9290.9290.0000.0000.0000.000
33A94SER 0-0.076-0.02314.136-0.591-0.5910.0000.0000.0000.000
34A95VAL 0-0.012-0.00414.742-0.221-0.2210.0000.0000.0000.000
35A96SER 00.0290.02617.6680.5780.5780.0000.0000.0000.000
36A97LEU 00.0350.02421.127-0.249-0.2490.0000.0000.0000.000
37A98SER 00.0890.04623.0080.6020.6020.0000.0000.0000.000
38A99TYR 0-0.061-0.06426.460-0.119-0.1190.0000.0000.0000.000
39A100MET 0-0.056-0.03729.3080.3930.3930.0000.0000.0000.000
40A101ALA 00.0220.03825.0240.0790.0790.0000.0000.0000.000
41A102PHE 00.026-0.00225.890-0.442-0.4420.0000.0000.0000.000
42A103PRO 00.0490.02228.5520.2730.2730.0000.0000.0000.000
43A104ASN 0-0.045-0.01731.3560.1380.1380.0000.0000.0000.000
44A105ALA 00.0160.05231.6020.3070.3070.0000.0000.0000.000
45A106SER 00.010-0.01633.5950.1980.1980.0000.0000.0000.000
46A107LYS 10.9650.96135.2148.4038.4030.0000.0000.0000.000
47A108LYS 10.9270.97637.3897.0577.0570.0000.0000.0000.000
48A109ASN 0-0.073-0.03735.4410.0330.0330.0000.0000.0000.000
49A110ARG 10.9921.00331.0999.0339.0330.0000.0000.0000.000
50A111PRO 00.0180.02229.3600.1120.1120.0000.0000.0000.000
51A112THR 0-0.021-0.02331.5120.1500.1500.0000.0000.0000.000
52A113LEU 0-0.0140.01025.1840.0120.0120.0000.0000.0000.000
53A114GLN 0-0.016-0.02328.1930.4390.4390.0000.0000.0000.000
54A115VAL 0-0.020-0.02225.356-0.423-0.4230.0000.0000.0000.000
55A116GLY 0-0.017-0.01124.0420.2550.2550.0000.0000.0000.000
56A117ASP -1-0.811-0.88224.268-11.325-11.3250.0000.0000.0000.000
57A118LEU 0-0.028-0.02219.780-0.647-0.6470.0000.0000.0000.000
58A119VAL 0-0.006-0.00419.7750.6000.6000.0000.0000.0000.000
59A120TYR 0-0.014-0.02616.220-0.977-0.9770.0000.0000.0000.000
60A121ALA 00.0330.00118.0540.9180.9180.0000.0000.0000.000
61A122ARG 10.8640.94817.40112.32712.3270.0000.0000.0000.000
62A123VAL 0-0.015-0.00113.2860.7230.7230.0000.0000.0000.000
63A124CYS 0-0.066-0.00316.698-0.154-0.1540.0000.0000.0000.000
64A125THR 00.001-0.01919.0610.0020.0020.0000.0000.0000.000
65A126ALA 00.005-0.01714.141-0.464-0.4640.0000.0000.0000.000
66A127GLU -1-0.929-0.94815.587-14.217-14.2170.0000.0000.0000.000
67A128LYS 10.8320.88913.62815.97115.9710.0000.0000.0000.000
68A129DGL -1-0.848-0.91613.250-16.099-16.0990.0000.0000.0000.000
69A130LEU 0-0.032-0.00416.9660.8290.8290.0000.0000.0000.000
70A131GLU -1-0.946-0.96716.873-14.247-14.2470.0000.0000.0000.000
71A132ALA 00.0010.00815.0880.1820.1820.0000.0000.0000.000
72A133GLU -1-0.857-0.92117.164-12.057-12.0570.0000.0000.0000.000
73A134ILE 0-0.030-0.03416.669-0.726-0.7260.0000.0000.0000.000
74A135GLU -1-0.878-0.96619.481-11.439-11.4390.0000.0000.0000.000
75A136CYS 0-0.045-0.03521.520-0.647-0.6470.0000.0000.0000.000
76A137PHE 0-0.004-0.00723.9730.5230.5230.0000.0000.0000.000
77A138ASP -1-0.838-0.90624.598-12.293-12.2930.0000.0000.0000.000
78A139SER 00.012-0.01424.5040.3530.3530.0000.0000.0000.000
79A140THR 0-0.039-0.00426.8000.4050.4050.0000.0000.0000.000
80A141THR 0-0.056-0.04628.8240.4340.4340.0000.0000.0000.000
81A142GLY 00.0240.02429.6650.3770.3770.0000.0000.0000.000
82A143ARG 10.9160.94730.0419.6749.6740.0000.0000.0000.000
83A144ASP -1-0.818-0.92127.652-11.119-11.1190.0000.0000.0000.000
84A145ALA 0-0.039-0.01025.253-0.453-0.4530.0000.0000.0000.000
85A146GLY 00.0160.01324.137-0.527-0.5270.0000.0000.0000.000
86A147PHE 0-0.088-0.02519.302-0.522-0.5220.0000.0000.0000.000
87A148GLY 00.0280.00222.9370.6510.6510.0000.0000.0000.000
88A149ILE 0-0.019-0.00423.319-0.695-0.6950.0000.0000.0000.000
89A150LEU 0-0.035-0.01019.907-0.126-0.1260.0000.0000.0000.000
90A151GLU -1-0.913-0.96324.187-10.531-10.5310.0000.0000.0000.000
91A152ASP -1-0.883-0.95726.840-10.545-10.5450.0000.0000.0000.000
92A153GLY 0-0.001-0.00523.6640.0680.0680.0000.0000.0000.000
93A154MET 0-0.094-0.04521.1190.1430.1430.0000.0000.0000.000
94A155ILE 00.0270.00815.581-0.505-0.5050.0000.0000.0000.000
95A156ILE 0-0.055-0.01613.3730.3060.3060.0000.0000.0000.000
96A157ASP -1-0.851-0.90211.144-22.739-22.7390.0000.0000.0000.000
97A158VAL 0-0.032-0.0258.544-0.283-0.2830.0000.0000.0000.000
98A159ASN 0-0.006-0.0093.983-8.758-8.5840.000-0.021-0.1540.000
99A160LEU 00.043-0.0042.133-1.986-1.1541.850-0.588-2.094-0.004
100A161ASN 0-0.044-0.0192.9433.8914.6450.030-0.239-0.545-0.002
101A162PHE 00.0390.0204.5116.8966.9950.000-0.017-0.0830.000
102A163ALA 00.0600.0357.7823.5903.5900.0000.0000.0000.000
103A164ARG 10.9670.9826.47936.61136.6110.0000.0000.0000.000
104A165GLN 0-0.011-0.0068.1985.3945.3940.0000.0000.0000.000
105A166LEU 0-0.014-0.00510.3402.4452.4450.0000.0000.0000.000
106A167LEU 0-0.021-0.00112.2961.5611.5610.0000.0000.0000.000
107A168PHE 00.001-0.00710.9610.9910.9910.0000.0000.0000.000
108A169ASN 0-0.036-0.01812.8512.3892.3890.0000.0000.0000.000
109A170ASN 00.0410.00914.774-0.082-0.0820.0000.0000.0000.000
110A171ASP -1-0.876-0.93117.303-15.145-15.1450.0000.0000.0000.000
111A172PHE 0-0.047-0.01611.643-0.165-0.1650.0000.0000.0000.000
112A173PRO 00.0130.00015.8420.7110.7110.0000.0000.0000.000
113A174LEU 0-0.0060.00114.7730.8180.8180.0000.0000.0000.000
114A175LEU 00.0610.02917.7810.8080.8080.0000.0000.0000.000
115A176LYS 10.8820.93918.77116.71216.7120.0000.0000.0000.000
116A177VAL 0-0.045-0.02320.7140.6750.6750.0000.0000.0000.000
117A178LEU 00.007-0.01419.4830.4720.4720.0000.0000.0000.000
118A179ALA 0-0.0110.00323.2150.5460.5460.0000.0000.0000.000
119A180ALA 0-0.059-0.02925.7420.4980.4980.0000.0000.0000.000
120A181HIS 0-0.041-0.00125.5470.5470.5470.0000.0000.0000.000
121A182THR 00.0270.01426.3260.5340.5340.0000.0000.0000.000
122A183LYS 10.9640.98627.3599.3549.3540.0000.0000.0000.000
123A184PHE 0-0.037-0.02421.779-0.127-0.1270.0000.0000.0000.000
124A185GLU -1-0.918-0.94224.572-11.576-11.5760.0000.0000.0000.000
125A186VAL 0-0.031-0.03718.115-0.417-0.4170.0000.0000.0000.000
126A187ALA 00.0350.03518.7920.2590.2590.0000.0000.0000.000
127A188ILE 0-0.006-0.00912.873-0.789-0.7890.0000.0000.0000.000
128A189GLY 00.0470.04413.1790.4880.4880.0000.0000.0000.000
129A190LEU 0-0.017-0.0278.835-2.706-2.7060.0000.0000.0000.000
130A191ASN 0-0.063-0.0537.706-4.404-4.4040.0000.0000.0000.000
131A192GLY 0-0.031-0.0087.886-1.475-1.4750.0000.0000.0000.000
132A193LYS 10.8620.9278.56422.07922.0790.0000.0000.0000.000
133A194ILE 0-0.022-0.00412.042-0.001-0.0010.0000.0000.0000.000
134A195TRP 00.0330.02214.6710.2620.2620.0000.0000.0000.000
135A196VAL 0-0.012-0.01018.3570.0090.0090.0000.0000.0000.000
136A197LYS 10.9600.98821.07611.58511.5850.0000.0000.0000.000
137A198CYS 0-0.079-0.03124.851-0.160-0.1600.0000.0000.0000.000
138A199GLU -1-0.923-0.95427.812-9.090-9.0900.0000.0000.0000.000
139A200GLU -1-0.853-0.91031.354-9.007-9.0070.0000.0000.0000.000
140A201LEU 00.013-0.01328.147-0.461-0.4610.0000.0000.0000.000
141A202SER 00.0370.00528.306-0.356-0.3560.0000.0000.0000.000
142A203ASN 00.0590.01128.135-0.217-0.2170.0000.0000.0000.000
143A204THR 00.0380.02124.240-0.639-0.6390.0000.0000.0000.000
144A205LEU 00.011-0.00823.630-0.758-0.7580.0000.0000.0000.000
145A206ALA 00.0190.03223.538-0.602-0.6020.0000.0000.0000.000
146A207CYS 0-0.0120.02221.561-0.682-0.6820.0000.0000.0000.000
147A208TYR 00.0110.00318.632-1.145-1.1450.0000.0000.0000.000
148A209ARG 10.8870.93718.62911.43811.4380.0000.0000.0000.000
149A210THR 0-0.018-0.02919.059-0.600-0.6000.0000.0000.0000.000
150A211ILE 00.001-0.00114.648-1.027-1.0270.0000.0000.0000.000
151A212MET 00.0010.00314.587-1.645-1.6450.0000.0000.0000.000
152A213GLU -1-0.738-0.86414.324-16.563-16.5630.0000.0000.0000.000
153A214CYS 0-0.061-0.03614.746-0.382-0.3820.0000.0000.0000.000
154A215CYS 0-0.054-0.0199.369-2.493-2.4930.0000.0000.0000.000
155A216GLN 0-0.058-0.0239.973-2.872-2.8720.0000.0000.0000.000
156A217LYS 10.8710.93011.62016.38916.3890.0000.0000.0000.000
157A218ASN 0-0.031-0.0048.043-3.180-3.1800.0000.0000.0000.000
158A219ASP -1-0.806-0.88711.172-21.034-21.0340.0000.0000.0000.000
159A220THR 0-0.039-0.03913.4921.3021.3020.0000.0000.0000.000
160A221ALA 0-0.006-0.00215.8170.9120.9120.0000.0000.0000.000
161A222ALA 00.0160.00817.6650.9490.9490.0000.0000.0000.000
162A223PHE 00.002-0.00712.9840.4450.4450.0000.0000.0000.000
163A224LYS 10.9910.99318.93712.22112.2210.0000.0000.0000.000
164A225ASP -1-0.891-0.94822.529-12.037-12.0370.0000.0000.0000.000
165A226ILE 0-0.107-0.04717.4540.4390.4390.0000.0000.0000.000
166A227ALA 00.0440.01821.6830.3250.3250.0000.0000.0000.000
167A228LYS 10.9760.99623.24811.22311.2230.0000.0000.0000.000
168A229ARG 10.8010.89821.52914.04914.0490.0000.0000.0000.000
169A230GLN 0-0.025-0.01621.4300.8780.8780.0000.0000.0000.000
170A231PHE 00.0500.01123.7910.1190.1190.0000.0000.0000.000
171A232LYS 10.8530.94428.03110.31910.3190.0000.0000.0000.000
172A233GLU -1-0.928-0.96930.112-10.329-10.3290.0000.0000.0000.000
173A234ILE 0-0.016-0.01229.1610.1190.1190.0000.0000.0000.000
174A235LEU 0-0.074-0.02732.919-0.005-0.0050.0000.0000.0000.000
175A236THR -1-0.906-0.95031.410-10.024-10.0240.0000.0000.0000.000