Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: G6361

Calculation Name: 2FYI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FYI

Chain ID: A

ChEMBL ID:

UniProt ID: Q47083

Base Structure: X-ray

Registration Date: 2023-09-20

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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2638354.642832
FMO2-HF: Nuclear repulsion 2551552.25178
FMO2-HF: Total energy -86802.391052
FMO2-MP2: Total energy -87060.438323


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:85:SER)


Summations of interaction energy for fragment #1(A:85: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.
-17.162-12.4175.72-4.187-6.2780.008
Interaction energy analysis for fragmet #1(A:85:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.014
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].
3A87MET0-0.081-0.0392.416-7.367-4.4753.055-2.535-3.4120.019
4A88THR0-0.026-0.0262.738-2.930-1.2990.682-0.936-1.377-0.009
5A89ASN00.0320.0154.516-1.487-1.439-0.001-0.013-0.0340.000
6A90ASP-1-0.867-0.9196.483-0.148-0.1480.0000.0000.0000.000
7A91THR0-0.122-0.0507.6340.2770.2770.0000.0000.0000.000
8A92SER00.0840.0419.397-0.123-0.1230.0000.0000.0000.000
9A93GLY00.009-0.00812.7530.1170.1170.0000.0000.0000.000
10A94VAL00.0170.01215.517-0.080-0.0800.0000.0000.0000.000
11A95LEU0-0.0230.00913.7170.0320.0320.0000.0000.0000.000
12A96THR00.0440.02316.850-0.032-0.0320.0000.0000.0000.000
13A97ILE0-0.030-0.01316.0790.0230.0230.0000.0000.0000.000
14A98ALA00.0360.02920.5790.0060.0060.0000.0000.0000.000
15A99THR0-0.018-0.03422.655-0.003-0.0030.0000.0000.0000.000
16A100THR00.0320.01125.0130.0090.0090.0000.0000.0000.000
17A101HIS00.0320.01526.355-0.022-0.0220.0000.0000.0000.000
18A102THR00.010-0.00327.164-0.016-0.0160.0000.0000.0000.000
19A103GLN00.0240.00822.7160.0070.0070.0000.0000.0000.000
20A104ALA00.0290.01422.514-0.038-0.0380.0000.0000.0000.000
21A105ARG10.7670.86722.6900.2520.2520.0000.0000.0000.000
22A106TYR0-0.015-0.00323.968-0.006-0.0060.0000.0000.0000.000
23A107SER0-0.057-0.02820.7490.0130.0130.0000.0000.0000.000
24A108LEU00.0070.00217.796-0.042-0.0420.0000.0000.0000.000
25A109PRO00.0220.03516.850-0.091-0.0910.0000.0000.0000.000
26A110GLU-1-0.871-0.92814.944-0.793-0.7930.0000.0000.0000.000
27A111VAL00.0630.02412.762-0.145-0.1450.0000.0000.0000.000
28A112ILE0-0.036-0.01912.114-0.182-0.1820.0000.0000.0000.000
29A113LYS10.8530.91612.0940.7060.7060.0000.0000.0000.000
30A114ALA00.0530.0299.051-0.241-0.2410.0000.0000.0000.000
31A115PHE0-0.002-0.0127.509-0.623-0.6230.0000.0000.0000.000
32A116ARG10.9260.9577.9210.7340.7340.0000.0000.0000.000
33A117GLU-1-0.958-0.9596.374-2.305-2.3050.0000.0000.0000.000
34A118LEU0-0.044-0.0172.403-1.212-1.2351.985-0.663-1.299-0.002
35A119PHE0-0.038-0.0524.206-0.682-0.485-0.001-0.040-0.1560.000
36A120PRO00.0180.0345.7870.5830.5830.0000.0000.0000.000
37A121GLU-1-0.914-0.9578.828-0.437-0.4370.0000.0000.0000.000
38A122VAL0-0.104-0.04310.1320.2470.2470.0000.0000.0000.000
39A123ARG10.8110.89912.4010.3180.3180.0000.0000.0000.000
40A124LEU0-0.006-0.00314.1990.0330.0330.0000.0000.0000.000
41A125GLU-1-0.832-0.89916.207-0.313-0.3130.0000.0000.0000.000
42A126LEU0-0.019-0.01918.357-0.003-0.0030.0000.0000.0000.000
43A127ILE00.0090.01321.9520.0200.0200.0000.0000.0000.000
44A128GLN0-0.007-0.01425.495-0.009-0.0090.0000.0000.0000.000
45A129GLY00.0130.00327.5790.0140.0140.0000.0000.0000.000
46A130THR0-0.062-0.07330.170-0.003-0.0030.0000.0000.0000.000
47A131PRO00.0440.00130.337-0.002-0.0020.0000.0000.0000.000
48A132GLN00.0340.02531.2040.0040.0040.0000.0000.0000.000
49A133GLU-1-0.799-0.86231.920-0.152-0.1520.0000.0000.0000.000
50A134ILE0-0.0300.00726.2380.0000.0000.0000.0000.0000.000
51A135ALA00.0230.01028.274-0.002-0.0020.0000.0000.0000.000
52A136THR0-0.033-0.01930.2260.0090.0090.0000.0000.0000.000
53A137LEU0-0.008-0.00827.4630.0050.0050.0000.0000.0000.000
54A138LEU0-0.0240.00323.4000.0010.0010.0000.0000.0000.000
55A139GLN0-0.093-0.05427.0750.0120.0120.0000.0000.0000.000
56A140ASN0-0.005-0.01129.9770.0180.0180.0000.0000.0000.000
57A141GLY0-0.0160.00825.6440.0060.0060.0000.0000.0000.000
58A142GLU-1-0.939-0.96325.217-0.162-0.1620.0000.0000.0000.000
59A143ALA0-0.058-0.03023.332-0.024-0.0240.0000.0000.0000.000
60A144ASP-1-0.812-0.87818.776-0.273-0.2730.0000.0000.0000.000
61A145ILE0-0.036-0.03015.9200.0220.0220.0000.0000.0000.000
62A146GLY00.0080.01520.630-0.010-0.0100.0000.0000.0000.000
63A147ILE0-0.036-0.02018.8640.0040.0040.0000.0000.0000.000
64A148ALA00.0480.01523.446-0.001-0.0010.0000.0000.0000.000
65A149SER00.0210.00426.6920.0020.0020.0000.0000.0000.000
66A150GLU-1-0.910-0.95628.994-0.117-0.1170.0000.0000.0000.000
67A151ARG10.8570.91230.5850.1010.1010.0000.0000.0000.000
68A152LEU00.0690.04525.6490.0010.0010.0000.0000.0000.000
69A153SER0-0.002-0.01328.9370.0030.0030.0000.0000.0000.000
70A154ASN0-0.057-0.02729.9220.0050.0050.0000.0000.0000.000
71A155ASP-1-0.780-0.87231.246-0.086-0.0860.0000.0000.0000.000
72A156PRO00.002-0.00531.7590.0000.0000.0000.0000.0000.000
73A157GLN0-0.040-0.02631.4380.0060.0060.0000.0000.0000.000
74A158LEU0-0.045-0.00827.155-0.007-0.0070.0000.0000.0000.000
75A159VAL00.0140.00924.6320.0140.0140.0000.0000.0000.000
76A160ALA0-0.022-0.01224.353-0.018-0.0180.0000.0000.0000.000
77A161PHE00.0230.01120.8350.0160.0160.0000.0000.0000.000
78A162PRO0-0.019-0.00422.711-0.023-0.0230.0000.0000.0000.000
79A163TRP00.006-0.00317.3140.0040.0040.0000.0000.0000.000
80A164PHE00.001-0.00520.9520.0030.0030.0000.0000.0000.000
81A165ARG10.9100.94223.3510.1240.1240.0000.0000.0000.000
82A166TRP0-0.0130.00826.929-0.010-0.0100.0000.0000.0000.000
83A167HIS00.0480.01729.1780.0120.0120.0000.0000.0000.000
84A168HIS0-0.025-0.01932.613-0.009-0.0090.0000.0000.0000.000
85A169SER0-0.054-0.02234.7980.0030.0030.0000.0000.0000.000
86A170LEU00.0260.00136.6990.0000.0000.0000.0000.0000.000
87A171LEU0-0.0180.00637.163-0.002-0.0020.0000.0000.0000.000
88A172VAL0-0.017-0.02039.9410.0050.0050.0000.0000.0000.000
89A173PRO00.0550.00842.599-0.003-0.0030.0000.0000.0000.000
90A174HIS00.0320.02440.4060.0060.0060.0000.0000.0000.000
91A175ASP-1-0.917-0.94645.040-0.088-0.0880.0000.0000.0000.000
92A176HIS0-0.0010.01847.1440.0050.0050.0000.0000.0000.000
93A177PRO00.0520.01449.0090.0000.0000.0000.0000.0000.000
94A178LEU0-0.009-0.01546.6840.0020.0020.0000.0000.0000.000
95A179THR0-0.062-0.02744.8460.0000.0000.0000.0000.0000.000
96A180GLN0-0.033-0.02347.0460.0040.0040.0000.0000.0000.000
97A181ILE0-0.069-0.01749.7740.0040.0040.0000.0000.0000.000
98A182SER0-0.009-0.02848.417-0.004-0.0040.0000.0000.0000.000
99A183PRO0-0.0670.00447.4550.0020.0020.0000.0000.0000.000
100A184LEU00.0730.04543.2670.0020.0020.0000.0000.0000.000
101A185THR00.0450.00846.299-0.001-0.0010.0000.0000.0000.000
102A186LEU00.0310.01744.095-0.002-0.0020.0000.0000.0000.000
103A187GLU-1-0.729-0.87547.675-0.062-0.0620.0000.0000.0000.000
104A188SER0-0.060-0.02749.5030.0020.0020.0000.0000.0000.000
105A189ILE00.0310.01643.903-0.001-0.0010.0000.0000.0000.000
106A190ALA0-0.034-0.02848.145-0.001-0.0010.0000.0000.0000.000
107A191LYS10.8240.92050.0320.0630.0630.0000.0000.0000.000
108A192TRP0-0.008-0.00348.8740.0010.0010.0000.0000.0000.000
109A193PRO00.0620.02849.363-0.001-0.0010.0000.0000.0000.000
110A194LEU0-0.036-0.01344.407-0.004-0.0040.0000.0000.0000.000
111A195ILE0-0.0230.01341.5030.0000.0000.0000.0000.0000.000
112A196THR00.010-0.02139.090-0.005-0.0050.0000.0000.0000.000
113A197TYR00.0350.03632.9760.0020.0020.0000.0000.0000.000
114A198ARG10.9710.99038.3090.1330.1330.0000.0000.0000.000
115A199GLN0-0.020-0.03238.907-0.003-0.0030.0000.0000.0000.000
116A200GLY0-0.012-0.00537.847-0.001-0.0010.0000.0000.0000.000
117A201ILE0-0.071-0.03834.002-0.007-0.0070.0000.0000.0000.000
118A202THR00.008-0.00231.3200.0010.0010.0000.0000.0000.000
119A203GLY00.1250.07733.2380.0020.0020.0000.0000.0000.000
120A204ARG10.7930.89134.9850.1050.1050.0000.0000.0000.000
121A205SER00.0340.00538.0620.0030.0030.0000.0000.0000.000
122A206ARG10.9590.99033.5530.1150.1150.0000.0000.0000.000
123A207ILE00.0010.00638.3530.0050.0050.0000.0000.0000.000
124A208ASP-1-0.803-0.88041.223-0.085-0.0850.0000.0000.0000.000
125A209ASP-1-0.907-0.95141.730-0.072-0.0720.0000.0000.0000.000
126A210ALA0-0.030-0.00842.2130.0050.0050.0000.0000.0000.000
127A211PHE0-0.006-0.01844.1420.0040.0040.0000.0000.0000.000
128A212ALA00.0270.02346.9350.0040.0040.0000.0000.0000.000
129A213ARG10.8030.88941.1380.0760.0760.0000.0000.0000.000
130A214LYS10.7920.87948.9320.0610.0610.0000.0000.0000.000
131A215GLY0-0.0060.00051.2700.0010.0010.0000.0000.0000.000
132A216LEU0-0.065-0.02950.6630.0010.0010.0000.0000.0000.000
133A217LEU0-0.006-0.00549.821-0.001-0.0010.0000.0000.0000.000
134A218ALA00.0000.00146.6680.0000.0000.0000.0000.0000.000
135A219ASP-1-0.858-0.93048.606-0.077-0.0770.0000.0000.0000.000
136A220ILE0-0.085-0.03544.394-0.005-0.0050.0000.0000.0000.000
137A221VAL00.0470.02647.3270.0020.0020.0000.0000.0000.000
138A222LEU0-0.027-0.01342.136-0.002-0.0020.0000.0000.0000.000
139A223SER0-0.035-0.01842.569-0.001-0.0010.0000.0000.0000.000
140A224ALA0-0.0020.00038.390-0.001-0.0010.0000.0000.0000.000
141A225GLN0-0.021-0.03835.7780.0080.0080.0000.0000.0000.000
142A226ASP-1-0.825-0.91432.831-0.188-0.1880.0000.0000.0000.000
143A227SER00.0560.00932.2380.0060.0060.0000.0000.0000.000
144A228ASP-1-0.753-0.85731.477-0.227-0.2270.0000.0000.0000.000
145A229VAL00.0130.01134.8870.0090.0090.0000.0000.0000.000
146A230ILE0-0.036-0.02236.5700.0070.0070.0000.0000.0000.000
147A231LYS10.8710.94631.4170.2220.2220.0000.0000.0000.000
148A232THR0-0.017-0.00138.3740.0050.0050.0000.0000.0000.000
149A233TYR0-0.016-0.02340.6550.0080.0080.0000.0000.0000.000
150A234VAL0-0.024-0.00141.3080.0070.0070.0000.0000.0000.000
151A235ALA00.0080.00541.5320.0050.0050.0000.0000.0000.000
152A236LEU0-0.081-0.02943.5460.0050.0050.0000.0000.0000.000
153A237GLY00.0320.01746.3780.0050.0050.0000.0000.0000.000
154A238LEU0-0.104-0.04146.3330.0040.0040.0000.0000.0000.000
155A239GLY00.0310.00647.2420.0040.0040.0000.0000.0000.000
156A240ILE0-0.0040.01444.466-0.004-0.0040.0000.0000.0000.000
157A241GLY00.0450.01840.7180.0000.0000.0000.0000.0000.000
158A242LEU0-0.051-0.00239.1430.0000.0000.0000.0000.0000.000
159A243VAL00.011-0.00234.429-0.003-0.0030.0000.0000.0000.000
160A244ALA00.022-0.00230.3380.0040.0040.0000.0000.0000.000
161A245GLU-1-0.766-0.85829.374-0.176-0.1760.0000.0000.0000.000
162A246GLN00.041-0.00325.8360.0110.0110.0000.0000.0000.000
163A247SER0-0.061-0.02927.455-0.014-0.0140.0000.0000.0000.000
164A248SER00.011-0.00229.8160.0000.0000.0000.0000.0000.000
165A249GLY0-0.018-0.00626.839-0.003-0.0030.0000.0000.0000.000
166A250GLU-1-0.854-0.92025.645-0.287-0.2870.0000.0000.0000.000
167A251GLN0-0.083-0.05427.9110.0010.0010.0000.0000.0000.000
168A252GLU-1-0.959-0.95731.024-0.177-0.1770.0000.0000.0000.000
169A253GLU-1-0.753-0.87932.759-0.176-0.1760.0000.0000.0000.000
170A254GLU-1-0.856-0.90736.414-0.138-0.1380.0000.0000.0000.000
171A255ASN0-0.071-0.05138.9150.0070.0070.0000.0000.0000.000
172A256LEU0-0.039-0.01139.0890.0070.0070.0000.0000.0000.000
173A257ILE00.0610.03038.910-0.004-0.0040.0000.0000.0000.000
174A258ARG10.7490.84533.0060.1840.1840.0000.0000.0000.000
175A259LEU00.0070.00238.0520.0030.0030.0000.0000.0000.000
176A260ASP-1-0.867-0.94536.903-0.121-0.1210.0000.0000.0000.000
177A261THR00.024-0.00737.9530.0070.0070.0000.0000.0000.000
178A262ARG10.8620.91731.7680.1460.1460.0000.0000.0000.000
179A263HIS0-0.090-0.02237.3300.0010.0010.0000.0000.0000.000
180A264LEU0-0.074-0.03540.2720.0060.0060.0000.0000.0000.000
181A265PHE0-0.002-0.00138.1190.0030.0030.0000.0000.0000.000
182A266ASP-1-0.841-0.90036.853-0.081-0.0810.0000.0000.0000.000
183A267ALA0-0.047-0.01831.527-0.006-0.0060.0000.0000.0000.000
184A268ASN0-0.038-0.03130.7950.0130.0130.0000.0000.0000.000
185A269THR0-0.014-0.02626.350-0.002-0.0020.0000.0000.0000.000
186A270VAL0-0.0240.01723.3900.0040.0040.0000.0000.0000.000
187A271TRP00.015-0.00723.975-0.001-0.0010.0000.0000.0000.000
188A272LEU00.0270.01217.869-0.020-0.0200.0000.0000.0000.000
189A273GLY0-0.016-0.00421.6770.0290.0290.0000.0000.0000.000
190A274LEU00.0440.01518.671-0.025-0.0250.0000.0000.0000.000
191A275LYS10.9030.94223.0040.1000.1000.0000.0000.0000.000
192A276ARG10.9120.94924.6230.0500.0500.0000.0000.0000.000
193A277GLY0-0.0020.00226.0930.0000.0000.0000.0000.0000.000
194A278GLN0-0.058-0.01322.4500.0130.0130.0000.0000.0000.000
195A279LEU00.005-0.00720.8170.0030.0030.0000.0000.0000.000
196A280GLN00.028-0.01516.792-0.029-0.0290.0000.0000.0000.000
197A281ARG10.8500.94212.3380.2790.2790.0000.0000.0000.000
198A282ASN00.015-0.0168.366-0.082-0.0820.0000.0000.0000.000
199A283TYR00.046-0.0029.7360.0090.0090.0000.0000.0000.000
200A284VAL00.0060.01810.690-0.101-0.1010.0000.0000.0000.000
201A285TRP0-0.017-0.01712.557-0.016-0.0160.0000.0000.0000.000
202A286ARG10.8550.9145.4770.0500.0500.0000.0000.0000.000
203A287PHE00.0400.01810.283-0.067-0.0670.0000.0000.0000.000
204A288LEU00.0260.01011.960-0.001-0.0010.0000.0000.0000.000
205A289GLU-1-0.854-0.9058.677-0.251-0.2510.0000.0000.0000.000
206A290LEU0-0.019-0.0087.826-0.004-0.0040.0000.0000.0000.000
207A291CYS0-0.073-0.02110.669-0.012-0.0120.0000.0000.0000.000
208A292ASN0-0.044-0.04214.1640.0480.0480.0000.0000.0000.000
209A293ALA00.0310.02314.0710.0260.0260.0000.0000.0000.000
210A294GLY0-0.047-0.01115.0870.0560.0560.0000.0000.0000.000
211A295LEU0-0.041-0.01716.4600.0450.0450.0000.0000.0000.000
212A296SER00.0510.00914.552-0.002-0.0020.0000.0000.0000.000
213A297VAL00.027-0.00611.256-0.027-0.0270.0000.0000.0000.000
214A298GLU-1-0.839-0.92314.1900.2910.2910.0000.0000.0000.000
215A299ASP-1-0.822-0.88017.1960.0920.0920.0000.0000.0000.000
216A300ILE0-0.0020.01015.416-0.017-0.0170.0000.0000.0000.000
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