FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 668JZ

Calculation Name: 2I5K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I5K

Chain ID: A

ChEMBL ID:

UniProt ID: P32861

Base Structure: X-ray

Registration Date: 2023-06-19

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 OptHSide
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 470
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8877570.551979
FMO2-HF: Nuclear repulsion 8694208.641521
FMO2-HF: Total energy -183361.910458
FMO2-MP2: Total energy -183903.773114


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:22:VAL)


Summations of interaction energy for fragment #1(A:22:VAL)
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.
-2.5080.7470.036-1.19-2.1020.003
Interaction energy analysis for fragmet #1(A:22:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / q_NPA : 0.005
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].
3A24ALA00.0180.0193.059-2.955-0.5310.034-1.040-1.4190.003
4A25SER00.0280.0023.880-0.634-0.2410.003-0.083-0.3140.000
5A26GLN0-0.028-0.0143.9440.1760.4970.000-0.052-0.2680.000
6A27MET00.0490.0435.8460.2610.2610.0000.0000.0000.000
7A28ARG10.8370.8898.3670.2020.2020.0000.0000.0000.000
8A29ASN00.0080.0129.0210.1700.1700.0000.0000.0000.000
9A30ALA00.0000.0059.9610.0790.0790.0000.0000.0000.000
10A31LEU00.0000.00211.6620.0560.0560.0000.0000.0000.000
11A32ASN0-0.025-0.00713.8010.0050.0050.0000.0000.0000.000
12A33LYS10.8070.90513.6210.3380.3380.0000.0000.0000.000
13A34LEU00.0000.00517.4080.0240.0240.0000.0000.0000.000
14A35ALA0-0.068-0.06921.1560.0010.0010.0000.0000.0000.000
15A44ALA00.0450.01528.2310.0010.0010.0000.0000.0000.000
16A45ARG10.8980.93930.2980.0330.0330.0000.0000.0000.000
17A46ALA00.0600.03829.541-0.002-0.0020.0000.0000.0000.000
18A47LYS10.8530.91321.9070.0830.0830.0000.0000.0000.000
19A48PHE00.0710.04321.7340.0040.0040.0000.0000.0000.000
20A49GLU-1-0.762-0.89820.018-0.084-0.0840.0000.0000.0000.000
21A50ASN0-0.036-0.02219.6590.0120.0120.0000.0000.0000.000
22A51GLU-1-0.799-0.88320.9210.0460.0460.0000.0000.0000.000
23A52LEU00.0160.00517.4170.0220.0220.0000.0000.0000.000
24A53ASP-1-0.837-0.90614.795-0.036-0.0360.0000.0000.0000.000
25A54SER00.0250.01215.6210.0360.0360.0000.0000.0000.000
26A55PHE00.0230.00513.6800.0420.0420.0000.0000.0000.000
27A56PHE0-0.008-0.0027.9140.0590.0590.0000.0000.0000.000
28A57THR0-0.028-0.02511.5670.0910.0910.0000.0000.0000.000
29A58LEU00.0530.02813.3550.0690.0690.0000.0000.0000.000
30A59PHE0-0.009-0.0248.2210.0970.0970.0000.0000.0000.000
31A60ARG10.8980.9657.401-0.077-0.0770.0000.0000.0000.000
32A61ARG10.7550.8399.333-0.071-0.0710.0000.0000.0000.000
33A62TYR00.0210.00911.3230.0650.0650.0000.0000.0000.000
34A63LEU00.0020.0064.5930.0380.155-0.001-0.015-0.1010.000
35A64VAL0-0.022-0.0218.7220.0640.0640.0000.0000.0000.000
36A65GLU-1-0.840-0.90810.2270.3650.3650.0000.0000.0000.000
37A66LYS10.8620.9389.804-0.916-0.9160.0000.0000.0000.000
38A67SER0-0.049-0.01310.208-0.034-0.0340.0000.0000.0000.000
39A68SER0-0.039-0.01512.132-0.137-0.1370.0000.0000.0000.000
40A69ARG10.8560.90815.490-0.238-0.2380.0000.0000.0000.000
41A70THR00.0630.03617.1000.0000.0000.0000.0000.0000.000
42A71THR0-0.079-0.05819.828-0.025-0.0250.0000.0000.0000.000
43A72LEU00.0030.02123.4650.0040.0040.0000.0000.0000.000
44A73GLU-1-0.810-0.88725.6600.1700.1700.0000.0000.0000.000
45A74TRP00.0710.01627.793-0.005-0.0050.0000.0000.0000.000
46A75ASP-1-0.913-0.96430.9040.1270.1270.0000.0000.0000.000
47A76LYS10.8230.91128.482-0.149-0.1490.0000.0000.0000.000
48A77ILE0-0.082-0.02531.561-0.004-0.0040.0000.0000.0000.000
49A78LYS10.8460.93033.929-0.105-0.1050.0000.0000.0000.000
50A79SER0-0.013-0.01337.1940.0030.0030.0000.0000.0000.000
51A80PRO0-0.045-0.02338.493-0.002-0.0020.0000.0000.0000.000
52A81ASN0-0.012-0.00340.646-0.005-0.0050.0000.0000.0000.000
53A82PRO0-0.004-0.01843.6070.0010.0010.0000.0000.0000.000
54A83ASP-1-0.903-0.93842.9490.0540.0540.0000.0000.0000.000
55A84GLU-1-0.844-0.92638.1460.0790.0790.0000.0000.0000.000
56A85VAL0-0.056-0.04340.1340.0040.0040.0000.0000.0000.000
57A86VAL00.0210.02942.597-0.002-0.0020.0000.0000.0000.000
58A87LYS10.9020.94545.926-0.047-0.0470.0000.0000.0000.000
59A88TYR00.012-0.02248.471-0.002-0.0020.0000.0000.0000.000
60A89GLU-1-0.882-0.95050.4130.0440.0440.0000.0000.0000.000
61A90ILE0-0.023-0.01249.740-0.002-0.0020.0000.0000.0000.000
62A91ILE00.0430.03446.852-0.001-0.0010.0000.0000.0000.000
63A92SER0-0.094-0.04751.451-0.002-0.0020.0000.0000.0000.000
64A93GLN0-0.057-0.02454.348-0.002-0.0020.0000.0000.0000.000
65A94GLN00.0480.00650.3780.0010.0010.0000.0000.0000.000
66A95PRO0-0.060-0.02153.971-0.001-0.0010.0000.0000.0000.000
67A96GLU-1-0.849-0.90954.4370.0310.0310.0000.0000.0000.000
68A97ASN0-0.014-0.00553.351-0.003-0.0030.0000.0000.0000.000
69A98VAL00.0800.04053.8970.0010.0010.0000.0000.0000.000
70A99SER0-0.040-0.02754.4420.0000.0000.0000.0000.0000.000
71A100ASN00.0390.00949.907-0.001-0.0010.0000.0000.0000.000
72A101LEU00.0780.04849.3370.0010.0010.0000.0000.0000.000
73A102SER0-0.055-0.02748.9990.0010.0010.0000.0000.0000.000
74A103LYS10.8700.92846.304-0.028-0.0280.0000.0000.0000.000
75A104LEU0-0.0120.01244.2630.0020.0020.0000.0000.0000.000
76A105ALA00.0290.00441.821-0.003-0.0030.0000.0000.0000.000
77A106VAL00.0090.00542.2370.0030.0030.0000.0000.0000.000
78A107LEU00.0090.01135.680-0.001-0.0010.0000.0000.0000.000
79A108LYS10.8590.92339.306-0.046-0.0460.0000.0000.0000.000
80A109LEU0-0.024-0.00832.867-0.001-0.0010.0000.0000.0000.000
81A110ASN00.004-0.00735.2270.0000.0000.0000.0000.0000.000
82A111GLY00.0490.03832.284-0.004-0.0040.0000.0000.0000.000
83A112GLY0-0.0380.00032.4580.0020.0020.0000.0000.0000.000
84A113LEU00.0630.02332.298-0.005-0.0050.0000.0000.0000.000
85A114GLY00.0420.00035.5910.0030.0030.0000.0000.0000.000
86A115THR00.0670.04534.5360.0000.0000.0000.0000.0000.000
87A116SER0-0.064-0.01735.816-0.003-0.0030.0000.0000.0000.000
88A117MET00.0410.00737.7130.0010.0010.0000.0000.0000.000
89A118GLY0-0.059-0.04540.451-0.003-0.0030.0000.0000.0000.000
90A119CYS0-0.031-0.01141.634-0.002-0.0020.0000.0000.0000.000
91A120VAL00.0580.02038.6850.0020.0020.0000.0000.0000.000
92A121GLY00.0740.06338.528-0.002-0.0020.0000.0000.0000.000
93A122PRO00.027-0.00637.7360.0040.0040.0000.0000.0000.000
94A123LYS10.7650.85837.905-0.056-0.0560.0000.0000.0000.000
95A124SER0-0.043-0.04439.861-0.002-0.0020.0000.0000.0000.000
96A125VAL00.0490.01342.019-0.001-0.0010.0000.0000.0000.000
97A126ILE0-0.036-0.01041.568-0.002-0.0020.0000.0000.0000.000
98A127GLU-1-0.892-0.94445.4660.0270.0270.0000.0000.0000.000
99A128VAL0-0.012-0.01747.5680.0010.0010.0000.0000.0000.000
100A129ARG10.8260.88049.537-0.029-0.0290.0000.0000.0000.000
101A130GLU-1-0.848-0.90853.1370.0250.0250.0000.0000.0000.000
102A131GLY00.0290.02054.147-0.001-0.0010.0000.0000.0000.000
103A132ASN0-0.046-0.00252.000-0.001-0.0010.0000.0000.0000.000
104A133THR0-0.016-0.02146.8840.0020.0020.0000.0000.0000.000
105A134PHE00.018-0.00844.1060.0010.0010.0000.0000.0000.000
106A135LEU00.0400.01542.5450.0000.0000.0000.0000.0000.000
107A136ASP-1-0.727-0.79746.2270.0240.0240.0000.0000.0000.000
108A137LEU0-0.0050.00148.942-0.001-0.0010.0000.0000.0000.000
109A138SER0-0.017-0.00846.1150.0000.0000.0000.0000.0000.000
110A139VAL00.0190.00947.833-0.001-0.0010.0000.0000.0000.000
111A140ARG10.8870.91949.869-0.024-0.0240.0000.0000.0000.000
112A141GLN00.0010.00648.7450.0000.0000.0000.0000.0000.000
113A142ILE0-0.0030.00247.589-0.001-0.0010.0000.0000.0000.000
114A143GLU-1-0.772-0.84951.0370.0190.0190.0000.0000.0000.000
115A144TYR0-0.046-0.02253.966-0.001-0.0010.0000.0000.0000.000
116A145LEU00.0240.00950.414-0.001-0.0010.0000.0000.0000.000
117A146ASN0-0.034-0.02551.3990.0000.0000.0000.0000.0000.000
118A147ARG10.8210.89555.221-0.021-0.0210.0000.0000.0000.000
119A148GLN0-0.027-0.01058.306-0.001-0.0010.0000.0000.0000.000
120A149TYR0-0.022-0.02855.1070.0000.0000.0000.0000.0000.000
121A150ASP-1-0.902-0.92158.3030.0170.0170.0000.0000.0000.000
122A151SER0-0.060-0.03553.2240.0000.0000.0000.0000.0000.000
123A152ASP-1-0.825-0.90951.1950.0200.0200.0000.0000.0000.000
124A153VAL00.0000.00147.1950.0000.0000.0000.0000.0000.000
125A154PRO0-0.054-0.00744.330-0.001-0.0010.0000.0000.0000.000
126A155LEU0-0.007-0.00143.7260.0020.0020.0000.0000.0000.000
127A156LEU00.021-0.00238.761-0.002-0.0020.0000.0000.0000.000
128A157LEU0-0.038-0.02039.1640.0040.0040.0000.0000.0000.000
129A158MET00.0260.03430.855-0.001-0.0010.0000.0000.0000.000
130A159ASN0-0.042-0.04634.7160.0060.0060.0000.0000.0000.000
131A160SER00.0500.03030.2140.0050.0050.0000.0000.0000.000
132A161PHE00.0900.02826.003-0.006-0.0060.0000.0000.0000.000
133A162ASN0-0.044-0.01128.779-0.009-0.0090.0000.0000.0000.000
134A163THR0-0.014-0.02632.629-0.001-0.0010.0000.0000.0000.000
135A164ASP-1-0.814-0.87634.2900.0210.0210.0000.0000.0000.000
136A165LYS10.9490.96136.286-0.016-0.0160.0000.0000.0000.000
137A166ASP-1-0.869-0.93238.4710.0200.0200.0000.0000.0000.000
138A167THR0-0.046-0.04738.8470.0010.0010.0000.0000.0000.000
139A168GLU-1-0.856-0.90039.9050.0100.0100.0000.0000.0000.000
140A169HIS00.003-0.00441.825-0.001-0.0010.0000.0000.0000.000
141A170LEU0-0.0280.00943.9890.0000.0000.0000.0000.0000.000
142A171ILE00.036-0.00242.0980.0000.0000.0000.0000.0000.000
143A172LYS10.8250.90344.598-0.011-0.0110.0000.0000.0000.000
144A173LYS10.8460.93948.279-0.022-0.0220.0000.0000.0000.000
145A174TYR0-0.110-0.08947.0470.0000.0000.0000.0000.0000.000
146A175SER00.011-0.00651.0730.0000.0000.0000.0000.0000.000
147A176ALA0-0.041-0.02152.7020.0000.0000.0000.0000.0000.000
148A177ASN00.0200.01752.9450.0000.0000.0000.0000.0000.000
149A178ARG10.7920.88352.263-0.019-0.0190.0000.0000.0000.000
150A179ILE00.029-0.01847.6710.0010.0010.0000.0000.0000.000
151A180ARG10.8610.95746.417-0.022-0.0220.0000.0000.0000.000
152A181ILE00.000-0.00544.1600.0020.0020.0000.0000.0000.000
153A182ARG10.8300.90641.426-0.025-0.0250.0000.0000.0000.000
154A183SER0-0.0110.00138.7400.0020.0020.0000.0000.0000.000
155A184PHE00.0370.01332.172-0.002-0.0020.0000.0000.0000.000
156A185ASN0-0.021-0.01331.1570.0080.0080.0000.0000.0000.000
157A186GLN0-0.069-0.04827.052-0.002-0.0020.0000.0000.0000.000
158A187SER0-0.004-0.02023.648-0.011-0.0110.0000.0000.0000.000
159A188ARG10.7680.86624.7250.0000.0000.0000.0000.0000.000
160A189PHE00.0470.01319.407-0.007-0.0070.0000.0000.0000.000
161A190PRO00.0030.01816.660-0.006-0.0060.0000.0000.0000.000
162A191ARG10.8040.88917.823-0.054-0.0540.0000.0000.0000.000
163A192VAL0-0.020-0.01411.554-0.021-0.0210.0000.0000.0000.000
164A193TYR00.0150.01513.1480.0290.0290.0000.0000.0000.000
165A194LYS10.8440.91812.350-0.180-0.1800.0000.0000.0000.000
166A195ASP-1-0.910-0.96512.0730.2150.2150.0000.0000.0000.000
167A196SER0-0.014-0.0299.9510.0690.0690.0000.0000.0000.000
168A197LEU0-0.074-0.0387.2320.0500.0500.0000.0000.0000.000
169A198LEU00.0090.0238.806-0.026-0.0260.0000.0000.0000.000
170A199PRO00.008-0.01710.6810.0570.0570.0000.0000.0000.000
171A200VAL0-0.0190.00013.851-0.022-0.0220.0000.0000.0000.000
172A201PRO0-0.0290.00717.146-0.016-0.0160.0000.0000.0000.000
173A202THR0-0.038-0.02617.102-0.017-0.0170.0000.0000.0000.000
174A203GLU-1-0.843-0.89318.706-0.078-0.0780.0000.0000.0000.000
175A204TYR0-0.034-0.02622.0380.0120.0120.0000.0000.0000.000
176A205ASP-1-0.849-0.93623.9840.0050.0050.0000.0000.0000.000
177A206SER00.0020.01921.9300.0000.0000.0000.0000.0000.000
178A207PRO00.011-0.01323.5240.0040.0040.0000.0000.0000.000
179A208LEU00.0470.04224.9200.0030.0030.0000.0000.0000.000
180A209ASP-1-0.913-0.95124.8690.0350.0350.0000.0000.0000.000
181A210ALA0-0.006-0.00120.7880.0150.0150.0000.0000.0000.000
182A211TRP00.0020.01220.4030.0100.0100.0000.0000.0000.000
183A212TYR0-0.076-0.09318.6650.0060.0060.0000.0000.0000.000
184A213PRO0-0.0080.01523.5890.0000.0000.0000.0000.0000.000
185A214PRO00.0190.02321.7630.0090.0090.0000.0000.0000.000
186A215GLY00.0610.02223.6500.0110.0110.0000.0000.0000.000
187A216HIS0-0.014-0.02026.517-0.001-0.0010.0000.0000.0000.000
188A217GLY00.011-0.03025.876-0.006-0.0060.0000.0000.0000.000
189A218ASP-1-0.786-0.86824.4750.0830.0830.0000.0000.0000.000
190A219LEU0-0.020-0.00926.105-0.010-0.0100.0000.0000.0000.000
191A220PHE00.0460.01127.220-0.008-0.0080.0000.0000.0000.000
192A221GLU-1-0.789-0.90723.3100.0850.0850.0000.0000.0000.000
193A222SER0-0.003-0.00226.599-0.011-0.0110.0000.0000.0000.000
194A223LEU0-0.032-0.00728.766-0.008-0.0080.0000.0000.0000.000
195A224HIS0-0.031-0.02227.417-0.006-0.0060.0000.0000.0000.000
196A225VAL0-0.023-0.00626.322-0.006-0.0060.0000.0000.0000.000
197A226SER0-0.078-0.03729.688-0.006-0.0060.0000.0000.0000.000
198A227GLY00.0650.03633.093-0.005-0.0050.0000.0000.0000.000
199A228GLU-1-0.813-0.91435.2000.0230.0230.0000.0000.0000.000
200A229LEU0-0.0120.01532.1380.0000.0000.0000.0000.0000.000
201A230ASP-1-0.846-0.92834.6720.0240.0240.0000.0000.0000.000
202A231ALA0-0.022-0.01137.488-0.001-0.0010.0000.0000.0000.000
203A232LEU0-0.016-0.01838.244-0.001-0.0010.0000.0000.0000.000
204A233ILE00.0210.02336.999-0.001-0.0010.0000.0000.0000.000
205A234ALA0-0.0210.00241.099-0.001-0.0010.0000.0000.0000.000
206A235GLN0-0.071-0.02643.049-0.001-0.0010.0000.0000.0000.000
207A236GLY0-0.013-0.01144.8040.0000.0000.0000.0000.0000.000
208A237ARG10.7880.89942.649-0.024-0.0240.0000.0000.0000.000
209A238GLU-1-0.837-0.91042.1870.0330.0330.0000.0000.0000.000
210A239ILE0-0.024-0.02140.7740.0030.0030.0000.0000.0000.000
211A240LEU00.0280.01236.129-0.002-0.0020.0000.0000.0000.000
212A241PHE0-0.034-0.01239.7880.0030.0030.0000.0000.0000.000
213A242VAL00.0100.01634.942-0.002-0.0020.0000.0000.0000.000
214A243SER00.0630.04038.4030.0010.0010.0000.0000.0000.000
215A244ASN00.0300.00635.253-0.001-0.0010.0000.0000.0000.000
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