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: VRM81

Calculation Name: 4EJS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EJS

Chain ID: A

ChEMBL ID:

UniProt ID: Q02884

Base Structure: X-ray

Registration Date: 2023-06-20

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2875746.988109
FMO2-HF: Nuclear repulsion 2787102.891246
FMO2-HF: Total energy -88644.096863
FMO2-MP2: Total energy -88902.953241


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:67:GLY)


Summations of interaction energy for fragment #1(A:67: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.
-1.4592.6580.76-2.214-2.6630.001
Interaction energy analysis for fragmet #1(A:67:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.010
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].
3A69ASP-1-0.832-0.8973.816-1.406-0.068-0.013-0.716-0.6090.002
4A70SER00.0380.0117.1770.1810.1810.0000.0000.0000.000
5A71SER0-0.114-0.0439.4470.1210.1210.0000.0000.0000.000
6A72HIS00.0590.0169.2190.0620.0620.0000.0000.0000.000
7A73VAL0-0.029-0.03111.6490.0550.0550.0000.0000.0000.000
8A74GLY00.0030.00113.2510.0310.0310.0000.0000.0000.000
9A75VAL0-0.043-0.0248.7700.0520.0520.0000.0000.0000.000
10A76ARG10.8850.94212.072-0.077-0.0770.0000.0000.0000.000
11A77PRO0-0.0030.00513.5780.0270.0270.0000.0000.0000.000
12A78SER0-0.016-0.01514.912-0.025-0.0250.0000.0000.0000.000
13A79PRO00.008-0.00817.586-0.002-0.0020.0000.0000.0000.000
14A80ALA00.0000.01720.674-0.003-0.0030.0000.0000.0000.000
15A81THR0-0.062-0.03916.1630.0080.0080.0000.0000.0000.000
16A82SER00.0350.02414.932-0.003-0.0030.0000.0000.0000.000
17A83GLN0-0.024-0.01312.390-0.024-0.0240.0000.0000.0000.000
18A84PRO00.0430.0208.190-0.046-0.0460.0000.0000.0000.000
19A85THR0-0.0110.00511.1320.0480.0480.0000.0000.0000.000
20A86THR00.0490.02612.576-0.026-0.0260.0000.0000.0000.000
21A87SER0-0.0060.00314.4260.0070.0070.0000.0000.0000.000
22A88THR0-0.003-0.06217.8820.0050.0050.0000.0000.0000.000
23A89GLY0-0.019-0.02419.955-0.001-0.0010.0000.0000.0000.000
24A90SER0-0.034-0.01021.768-0.011-0.0110.0000.0000.0000.000
25A91ALA00.0370.01724.2960.0050.0050.0000.0000.0000.000
26A92ASP-1-0.877-0.93525.4350.0390.0390.0000.0000.0000.000
27A93LEU00.0620.02723.1170.0050.0050.0000.0000.0000.000
28A94ASP-1-0.736-0.81020.8510.0810.0810.0000.0000.0000.000
29A95SER0-0.095-0.07422.6100.0060.0060.0000.0000.0000.000
30A96ILE00.0240.01925.1130.0030.0030.0000.0000.0000.000
31A97LEU00.0010.01119.8630.0060.0060.0000.0000.0000.000
32A98GLY0-0.029-0.02022.7860.0090.0090.0000.0000.0000.000
33A99HIS0-0.0210.00217.860-0.002-0.0020.0000.0000.0000.000
34A100MET0-0.017-0.00518.749-0.002-0.0020.0000.0000.0000.000
35A101GLY00.0390.04317.818-0.010-0.0100.0000.0000.0000.000
36A102LEU0-0.017-0.01115.4420.0040.0040.0000.0000.0000.000
37A103PRO0-0.037-0.03513.5560.0120.0120.0000.0000.0000.000
38A104LEU0-0.005-0.0137.211-0.005-0.0050.0000.0000.0000.000
39A105GLY00.0410.01510.4480.0120.0120.0000.0000.0000.000
40A106ASN0-0.067-0.01711.055-0.033-0.0330.0000.0000.0000.000
41A107SER0-0.019-0.02514.7400.0070.0070.0000.0000.0000.000
42A108VAL0-0.014-0.00717.567-0.011-0.0110.0000.0000.0000.000
43A109LEU0-0.0100.00120.9510.0030.0030.0000.0000.0000.000
44A110VAL0-0.006-0.01724.156-0.005-0.0050.0000.0000.0000.000
45A111GLU-1-0.796-0.88326.7330.0780.0780.0000.0000.0000.000
46A112GLU-1-0.776-0.90830.3110.0500.0500.0000.0000.0000.000
47A113GLN0-0.023-0.01633.209-0.001-0.0010.0000.0000.0000.000
48A114SER0-0.024-0.04036.3000.0000.0000.0000.0000.0000.000
49A115THR0-0.078-0.05137.905-0.001-0.0010.0000.0000.0000.000
50A116THR0-0.0120.03335.5630.0010.0010.0000.0000.0000.000
51A117GLU-1-0.741-0.87632.5240.0390.0390.0000.0000.0000.000
52A118PHE00.0230.01732.3810.0010.0010.0000.0000.0000.000
53A119HIS00.0380.01129.1220.0060.0060.0000.0000.0000.000
54A120SER0-0.107-0.07427.8050.0070.0070.0000.0000.0000.000
55A121ILE0-0.004-0.00328.2530.0000.0000.0000.0000.0000.000
56A122LEU00.0380.02125.4550.0000.0000.0000.0000.0000.000
57A123GLY00.0300.01823.7120.0070.0070.0000.0000.0000.000
58A124LYS10.7910.88823.166-0.037-0.0370.0000.0000.0000.000
59A125LEU00.0180.01924.016-0.004-0.0040.0000.0000.0000.000
60A126PHE00.0420.02616.282-0.002-0.0020.0000.0000.0000.000
61A127ALA0-0.049-0.03819.1820.0050.0050.0000.0000.0000.000
62A128ALA00.0150.00119.932-0.007-0.0070.0000.0000.0000.000
63A129GLN00.006-0.01218.205-0.009-0.0090.0000.0000.0000.000
64A130GLY00.0100.00116.299-0.011-0.0110.0000.0000.0000.000
65A131ILE0-0.035-0.00816.675-0.022-0.0220.0000.0000.0000.000
66A132VAL00.008-0.00419.273-0.019-0.0190.0000.0000.0000.000
67A133HIS0-0.0350.00214.960-0.008-0.0080.0000.0000.0000.000
68A134ASN0-0.0030.00515.272-0.049-0.0490.0000.0000.0000.000
69A135ARG10.7010.83616.4330.0140.0140.0000.0000.0000.000
70A136ILE00.0170.01718.4340.0090.0090.0000.0000.0000.000
71A145ARG10.9380.97415.0210.1790.1790.0000.0000.0000.000
72A146ASN0-0.077-0.05411.073-0.025-0.0250.0000.0000.0000.000
73A147GLY00.1150.03112.6750.0040.0040.0000.0000.0000.000
74A148ASP-1-0.878-0.91110.601-0.268-0.2680.0000.0000.0000.000
75A149THR0-0.055-0.03910.7060.0090.0090.0000.0000.0000.000
76A150HIS0-0.014-0.01412.517-0.015-0.0150.0000.0000.0000.000
77A151VAL00.0230.02014.0030.0590.0590.0000.0000.0000.000
78A152ILE00.0110.00213.752-0.017-0.0170.0000.0000.0000.000
79A153VAL0-0.018-0.00917.8900.0080.0080.0000.0000.0000.000
80A154LEU00.0010.01121.471-0.007-0.0070.0000.0000.0000.000
81A155SER00.020-0.01923.282-0.007-0.0070.0000.0000.0000.000
82A156LEU00.007-0.00126.8220.0000.0000.0000.0000.0000.000
83A157ASN00.0150.01029.578-0.009-0.0090.0000.0000.0000.000
84A158GLN00.021-0.00427.2960.0060.0060.0000.0000.0000.000
85A159MET0-0.041-0.01928.953-0.004-0.0040.0000.0000.0000.000
86A160PHE00.0380.01823.314-0.002-0.0020.0000.0000.0000.000
87A161ALA00.017-0.00525.406-0.001-0.0010.0000.0000.0000.000
88A162LYS10.8790.93426.738-0.017-0.0170.0000.0000.0000.000
89A163GLU-1-0.786-0.86229.5310.0180.0180.0000.0000.0000.000
90A164LEU0-0.069-0.01923.5590.0020.0020.0000.0000.0000.000
91A165PRO00.0210.01926.493-0.005-0.0050.0000.0000.0000.000
92A166GLY00.0170.01027.122-0.002-0.0020.0000.0000.0000.000
93A167ILE0-0.044-0.02525.3030.0020.0020.0000.0000.0000.000
94A168TYR0-0.034-0.01828.253-0.001-0.0010.0000.0000.0000.000
95A235LYS10.8500.89118.9250.0660.0660.0000.0000.0000.000
96A236ASP-1-0.840-0.88820.189-0.059-0.0590.0000.0000.0000.000
97A237TYR0-0.048-0.03715.142-0.004-0.0040.0000.0000.0000.000
98A238ASN0-0.015-0.02118.7260.0080.0080.0000.0000.0000.000
99A239HIS00.0020.01920.388-0.002-0.0020.0000.0000.0000.000
100A240GLN00.0450.02224.3190.0060.0060.0000.0000.0000.000
101A241PHE0-0.018-0.01322.696-0.005-0.0050.0000.0000.0000.000
102A242ASP-1-0.704-0.82228.4450.0100.0100.0000.0000.0000.000
103A243ILE0-0.034-0.01130.9110.0000.0000.0000.0000.0000.000
104A244THR0-0.070-0.04932.6630.0000.0000.0000.0000.0000.000
105A245THR0-0.039-0.02032.856-0.002-0.0020.0000.0000.0000.000
106A246ARG10.7850.86830.936-0.015-0.0150.0000.0000.0000.000
107A247LEU00.001-0.00523.953-0.004-0.0040.0000.0000.0000.000
108A248MET0-0.016-0.01628.552-0.003-0.0030.0000.0000.0000.000
109A249PRO00.0140.02725.8330.0010.0010.0000.0000.0000.000
110A250ALA00.0350.00126.7940.0030.0030.0000.0000.0000.000
111A251PRO00.001-0.00322.574-0.006-0.0060.0000.0000.0000.000
112A252ILE0-0.0070.00621.9460.0050.0050.0000.0000.0000.000
113A253ALA00.0120.00221.4350.0050.0050.0000.0000.0000.000
114A254SER0-0.014-0.00817.8320.0120.0120.0000.0000.0000.000
115A255GLU-1-0.775-0.86116.758-0.040-0.0400.0000.0000.0000.000
116A256LEU0-0.016-0.00617.4870.0170.0170.0000.0000.0000.000
117A257THR00.0000.00217.348-0.015-0.0150.0000.0000.0000.000
118A258PHE0-0.026-0.00520.1270.0150.0150.0000.0000.0000.000
119A259ILE0-0.011-0.00518.687-0.001-0.0010.0000.0000.0000.000
120A260ALA00.0370.02023.1980.0010.0010.0000.0000.0000.000
121A261PRO00.0200.00926.2320.0050.0050.0000.0000.0000.000
122A262THR00.0020.00227.482-0.001-0.0010.0000.0000.0000.000
123A263GLN0-0.072-0.04324.494-0.011-0.0110.0000.0000.0000.000
124A264PRO00.0450.01027.5860.0040.0040.0000.0000.0000.000
125A265VAL00.1040.05923.9570.0060.0060.0000.0000.0000.000
126A266SER0-0.003-0.00823.2970.0110.0110.0000.0000.0000.000
127A267THR0-0.044-0.01622.2280.0060.0060.0000.0000.0000.000
128A268ILE00.0560.03221.3870.0070.0070.0000.0000.0000.000
129A269LEU00.0070.01218.6940.0160.0160.0000.0000.0000.000
130A270SER0-0.0220.00217.4200.0290.0290.0000.0000.0000.000
131A271GLN00.0190.01017.3550.0150.0150.0000.0000.0000.000
132A272ILE00.0520.03814.7300.0070.0070.0000.0000.0000.000
133A273GLU-1-0.728-0.83011.8790.4130.4130.0000.0000.0000.000
134A274GLN0-0.021-0.00812.5150.0310.0310.0000.0000.0000.000
135A275THR0-0.030-0.04313.343-0.035-0.0350.0000.0000.0000.000
136A276ILE00.0250.0098.576-0.026-0.0260.0000.0000.0000.000
137A277LYS10.8390.9158.614-0.179-0.1790.0000.0000.0000.000
138A278ARG10.8900.9618.948-0.172-0.1720.0000.0000.0000.000
139A279ASN0-0.106-0.0429.889-0.149-0.1490.0000.0000.0000.000
140A280ASP-1-0.760-0.8853.7770.3480.5660.002-0.072-0.1480.000
141A281LYS10.8230.9154.2121.0241.196-0.001-0.051-0.1210.000
142A282LYS10.8120.9185.065-0.0400.018-0.001-0.007-0.0500.000
143A283LEU0-0.018-0.0107.6750.3510.3510.0000.0000.0000.000
144A284ILE0-0.028-0.0238.854-0.066-0.0660.0000.0000.0000.000
145A285ARG10.8170.94111.055-0.062-0.0620.0000.0000.0000.000
146A286ILE00.0090.00513.809-0.027-0.0270.0000.0000.0000.000
147A287VAL00.0230.01116.625-0.005-0.0050.0000.0000.0000.000
148A288ILE0-0.022-0.02020.176-0.007-0.0070.0000.0000.0000.000
149A289PRO0-0.003-0.00523.129-0.003-0.0030.0000.0000.0000.000
150A290SER0-0.003-0.00226.015-0.007-0.0070.0000.0000.0000.000
151A291LEU00.0370.01924.672-0.004-0.0040.0000.0000.0000.000
152A292LEU0-0.020-0.01528.066-0.005-0.0050.0000.0000.0000.000
153A293HIS00.0870.05131.146-0.005-0.0050.0000.0000.0000.000
154A294PRO00.0600.01333.2140.0010.0010.0000.0000.0000.000
155A295ALA0-0.047-0.01035.921-0.002-0.0020.0000.0000.0000.000
156A296MET0-0.070-0.02829.621-0.001-0.0010.0000.0000.0000.000
157A297TYR00.0140.01226.6600.0070.0070.0000.0000.0000.000
158A298PRO00.0370.01331.887-0.004-0.0040.0000.0000.0000.000
159A299PRO00.0920.03734.4840.0030.0030.0000.0000.0000.000
160A300LYS10.8580.91432.990-0.058-0.0580.0000.0000.0000.000
161A301MET0-0.025-0.00128.1770.0040.0040.0000.0000.0000.000
162A302PHE0-0.012-0.01831.5230.0060.0060.0000.0000.0000.000
163A303GLU-1-0.876-0.89633.9520.0650.0650.0000.0000.0000.000
164A304SER00.046-0.00332.1820.0040.0040.0000.0000.0000.000
165A305SER0-0.069-0.05330.0560.0080.0080.0000.0000.0000.000
166A306GLU-1-0.861-0.90828.6380.0810.0810.0000.0000.0000.000
167A307ILE00.0310.02226.9060.0110.0110.0000.0000.0000.000
168A308ILE00.014-0.00226.3530.0110.0110.0000.0000.0000.000
169A309GLY00.0430.03525.0880.0120.0120.0000.0000.0000.000
170A310LEU0-0.040-0.03622.2140.0150.0150.0000.0000.0000.000
171A311MET0-0.016-0.00821.3420.0180.0180.0000.0000.0000.000
172A312HIS00.0160.01220.9040.0260.0260.0000.0000.0000.000
173A313GLY00.0120.00219.2280.0220.0220.0000.0000.0000.000
174A314VAL0-0.001-0.02217.2800.0350.0350.0000.0000.0000.000
175A315ARG10.8640.92316.062-0.168-0.1680.0000.0000.0000.000
176A316SER0-0.030-0.02315.6090.0530.0530.0000.0000.0000.000
177A317LEU0-0.031-0.01612.5670.0510.0510.0000.0000.0000.000
178A318VAL0-0.021-0.00411.1680.1380.1380.0000.0000.0000.000
179A319LYS10.8150.88510.904-0.242-0.2420.0000.0000.0000.000
180A320LYS10.8500.9349.315-0.324-0.3240.0000.0000.0000.000
181A321TYR0-0.057-0.0525.761-0.122-0.1220.0000.0000.0000.000
182A322TYR00.0580.0177.3400.1870.1870.0000.0000.0000.000
183A323GLU-1-0.923-0.9572.5753.7135.1600.697-0.951-1.192-0.004
184A324ARG10.7310.8463.388-5.595-4.7110.076-0.417-0.5430.003
185A325VAL00.0090.0246.134-0.288-0.2880.0000.0000.0000.000
186A326VAL0-0.0120.0139.571-0.037-0.0370.0000.0000.0000.000
187A327LEU0-0.030-0.01312.908-0.013-0.0130.0000.0000.0000.000
188A328PHE00.0440.03016.474-0.010-0.0100.0000.0000.0000.000
189A329ALA0-0.019-0.01519.843-0.001-0.0010.0000.0000.0000.000
190A330SER00.0700.04623.081-0.001-0.0010.0000.0000.0000.000
191A331ILE0-0.058-0.03226.7240.0020.0020.0000.0000.0000.000
192A332SER00.0370.03029.843-0.001-0.0010.0000.0000.0000.000
193A333ILE00.010-0.01631.7980.0000.0000.0000.0000.0000.000
194A334ASP-1-0.831-0.89735.1400.0460.0460.0000.0000.0000.000
195A335ILE0-0.045-0.02134.300-0.002-0.0020.0000.0000.0000.000
196A336ILE0-0.060-0.01832.7670.0020.0020.0000.0000.0000.000
197A337THR00.0100.00835.994-0.001-0.0010.0000.0000.0000.000
198A338PRO00.0920.02436.0120.0040.0040.0000.0000.0000.000
199A339PRO00.005-0.00235.4270.0030.0030.0000.0000.0000.000
200A340LEU00.0280.02331.3850.0040.0040.0000.0000.0000.000
201A341LEU00.0340.01930.7670.0070.0070.0000.0000.0000.000
202A342VAL0-0.020-0.01030.6180.0060.0060.0000.0000.0000.000
203A343LEU0-0.028-0.01829.9020.0060.0060.0000.0000.0000.000
204A344LEU00.005-0.00827.0850.0100.0100.0000.0000.0000.000
205A345ARG10.7580.83125.809-0.070-0.0700.0000.0000.0000.000
206A346ASN0-0.050-0.01025.4500.0100.0100.0000.0000.0000.000
207A347MET0-0.047-0.01522.3070.0140.0140.0000.0000.0000.000
208A348PHE00.0150.00820.7430.0260.0260.0000.0000.0000.000
209A349ASP-1-0.847-0.88817.2840.2550.2550.0000.0000.0000.000
210A350SER0-0.033-0.01420.418-0.013-0.0130.0000.0000.0000.000
211A351VAL00.0110.01222.7860.0070.0070.0000.0000.0000.000
212A352ILE00.0090.00724.112-0.004-0.0040.0000.0000.0000.000
213A353ASN0-0.035-0.00827.766-0.004-0.0040.0000.0000.0000.000
214A354LEU00.0180.01329.470-0.002-0.0020.0000.0000.0000.000
215A355GLU-1-0.796-0.90133.0110.0390.0390.0000.0000.0000.000
216A356PRO0-0.0030.02436.760-0.001-0.0010.0000.0000.0000.000
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