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: 4382N

Calculation Name: 2GEF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GEF

Chain ID: A

ChEMBL ID:

UniProt ID: Q8AZM0

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 OptH
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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2125528.660451
FMO2-HF: Nuclear repulsion 2050548.408114
FMO2-HF: Total energy -74980.252336
FMO2-MP2: Total energy -75199.079004


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:559:ASP)


Summations of interaction energy for fragment #1(A:559:ASP)
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.
29.39731.3630.028-1.004-0.990.002
Interaction energy analysis for fragmet #1(A:559:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.957 / q_NPA : -0.985
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].
3A561PRO0-0.039-0.0183.4420.6782.6440.028-1.004-0.9900.002
4A562ILE00.0430.0385.8140.5900.5900.0000.0000.0000.000
5A563SER0-0.013-0.0177.856-2.110-2.1100.0000.0000.0000.000
6A564LEU0-0.014-0.01811.152-0.282-0.2820.0000.0000.0000.000
7A565LEU00.0180.00913.826-0.610-0.6100.0000.0000.0000.000
8A566GLN0-0.035-0.02417.5560.7100.7100.0000.0000.0000.000
9A567THR0-0.012-0.00419.538-0.482-0.4820.0000.0000.0000.000
10A568LEU00.0100.02021.2210.1730.1730.0000.0000.0000.000
11A569ALA00.0060.00424.572-0.332-0.3320.0000.0000.0000.000
12A570TYR0-0.026-0.01827.8700.0850.0850.0000.0000.0000.000
13A571LYS10.9410.97829.453-9.072-9.0720.0000.0000.0000.000
14A572GLN00.000-0.01031.4580.1610.1610.0000.0000.0000.000
15A573PRO00.0340.01731.961-0.134-0.1340.0000.0000.0000.000
16A574LEU0-0.0360.00434.514-0.168-0.1680.0000.0000.0000.000
17A575GLY00.0150.01137.3660.1460.1460.0000.0000.0000.000
18A576ARG10.8890.92239.044-7.493-7.4930.0000.0000.0000.000
19A577ASN0-0.064-0.04841.764-0.051-0.0510.0000.0000.0000.000
20A578SER0-0.039-0.02543.727-0.025-0.0250.0000.0000.0000.000
21A579ARG10.9810.98744.201-6.649-6.6490.0000.0000.0000.000
22A580ILE00.0130.02044.6960.1190.1190.0000.0000.0000.000
23A581VAL0-0.041-0.02043.550-0.132-0.1320.0000.0000.0000.000
24A582HIS0-0.0220.00745.0440.0510.0510.0000.0000.0000.000
25A583PHE0-0.002-0.00241.2460.0110.0110.0000.0000.0000.000
26A584THR00.013-0.02844.166-0.049-0.0490.0000.0000.0000.000
27A585ASP-1-0.949-0.96440.4067.1377.1370.0000.0000.0000.000
28A586GLY00.0440.01337.288-0.010-0.0100.0000.0000.0000.000
29A587ALA0-0.017-0.00133.1570.0170.0170.0000.0000.0000.000
30A588LEU00.0250.02833.0700.1140.1140.0000.0000.0000.000
31A589PHE0-0.003-0.00527.1760.2570.2570.0000.0000.0000.000
32A590PRO0-0.0240.00325.652-0.101-0.1010.0000.0000.0000.000
33A591VAL00.000-0.00325.8150.3930.3930.0000.0000.0000.000
34A592VAL0-0.033-0.01721.766-0.176-0.1760.0000.0000.0000.000
35A593ALA00.0090.00623.7060.2290.2290.0000.0000.0000.000
36A594PHE0-0.031-0.02820.151-0.174-0.1740.0000.0000.0000.000
37A595GLY00.0400.03023.7890.0320.0320.0000.0000.0000.000
38A596ASP-1-0.883-0.93025.20211.39611.3960.0000.0000.0000.000
39A597ASN0-0.128-0.07726.571-0.357-0.3570.0000.0000.0000.000
40A598HIS0-0.004-0.01828.232-0.155-0.1550.0000.0000.0000.000
41A599SER00.0480.03124.6880.4600.4600.0000.0000.0000.000
42A600THR0-0.056-0.01826.539-0.388-0.3880.0000.0000.0000.000
43A601SER0-0.003-0.04926.6710.3780.3780.0000.0000.0000.000
44A602GLU-1-0.816-0.90128.4458.8148.8140.0000.0000.0000.000
45A603LEU0-0.001-0.00629.9630.3410.3410.0000.0000.0000.000
46A604TYR00.0580.03230.773-0.115-0.1150.0000.0000.0000.000
47A605ILE0-0.0070.00732.6390.1520.1520.0000.0000.0000.000
48A606ALA0-0.006-0.00531.7750.0310.0310.0000.0000.0000.000
49A607VAL00.0320.01833.807-0.060-0.0600.0000.0000.0000.000
50A608ARG10.8740.91136.839-7.332-7.3320.0000.0000.0000.000
51A609GLY00.0340.02438.049-0.206-0.2060.0000.0000.0000.000
52A610ASP-1-1.000-1.01738.5687.3477.3470.0000.0000.0000.000
53A611HIS00.0980.05239.302-0.210-0.2100.0000.0000.0000.000
54A612ARG10.9680.95238.127-7.540-7.5400.0000.0000.0000.000
55A613ASP-1-0.967-0.97540.3536.8046.8040.0000.0000.0000.000
56A614LEU00.0040.00441.163-0.109-0.1090.0000.0000.0000.000
57A615MET0-0.086-0.00234.7750.0620.0620.0000.0000.0000.000
58A616SER00.0510.01937.296-0.251-0.2510.0000.0000.0000.000
59A617PRO0-0.017-0.04538.4640.0950.0950.0000.0000.0000.000
60A618ASP-1-0.917-0.92735.7037.8637.8630.0000.0000.0000.000
61A619VAL0-0.018-0.01932.2270.2300.2300.0000.0000.0000.000
62A620ARG10.8720.93834.192-6.946-6.9460.0000.0000.0000.000
63A621ASP-1-0.921-0.94535.1917.7737.7730.0000.0000.0000.000
64A622SER0-0.037-0.01429.5310.2090.2090.0000.0000.0000.000
65A623TYR00.019-0.01030.498-0.193-0.1930.0000.0000.0000.000
66A624ALA0-0.0280.01325.9610.2460.2460.0000.0000.0000.000
67A625LEU0-0.033-0.04127.193-0.320-0.3200.0000.0000.0000.000
68A626THR00.0210.00826.6970.4090.4090.0000.0000.0000.000
69A627GLY00.0380.00826.7940.0430.0430.0000.0000.0000.000
70A628ASP-1-0.885-0.93627.4929.1289.1280.0000.0000.0000.000
71A629ASP-1-0.884-0.91930.0999.2339.2330.0000.0000.0000.000
72A630HIS10.8570.94731.709-8.636-8.6360.0000.0000.0000.000
73A631LYS10.9570.97631.525-8.034-8.0340.0000.0000.0000.000
74A632VAL00.0360.04028.967-0.180-0.1800.0000.0000.0000.000
75A633TRP00.009-0.02431.0110.2650.2650.0000.0000.0000.000
76A634GLY00.0730.01931.962-0.048-0.0480.0000.0000.0000.000
77A635ALA0-0.056-0.00626.9930.1910.1910.0000.0000.0000.000
78A636THR00.020-0.01624.468-0.247-0.2470.0000.0000.0000.000
79A637HIS00.0080.02221.4550.5990.5990.0000.0000.0000.000
80A651LYS10.8570.90122.532-10.438-10.4380.0000.0000.0000.000
81A652PHE0-0.073-0.04222.3370.6030.6030.0000.0000.0000.000
82A653ASN0-0.0040.00021.082-0.610-0.6100.0000.0000.0000.000
83A654VAL00.0070.00523.441-0.275-0.2750.0000.0000.0000.000
84A655LYS10.9510.99226.690-10.631-10.6310.0000.0000.0000.000
85A656THR00.0560.00130.029-0.007-0.0070.0000.0000.0000.000
86A657ARG10.9220.95432.813-8.253-8.2530.0000.0000.0000.000
87A658THR0-0.062-0.03235.146-0.356-0.3560.0000.0000.0000.000
88A659ASP-1-0.860-0.91134.7718.2958.2950.0000.0000.0000.000
89A660LEU0-0.015-0.00832.020-0.086-0.0860.0000.0000.0000.000
90A661THR00.0060.01434.6220.0720.0720.0000.0000.0000.000
91A662ILE0-0.075-0.02729.2890.0030.0030.0000.0000.0000.000
92A663LEU0-0.007-0.00533.558-0.061-0.0610.0000.0000.0000.000
93A664PRO0-0.0110.01433.8140.1080.1080.0000.0000.0000.000
94A665VAL00.022-0.01334.899-0.222-0.2220.0000.0000.0000.000
95A666ALA0-0.087-0.04236.3470.1950.1950.0000.0000.0000.000
96A667ASP-1-0.829-0.92638.7667.3237.3230.0000.0000.0000.000
97A668VAL0-0.075-0.03038.603-0.008-0.0080.0000.0000.0000.000
98A669PHE0-0.0100.01941.677-0.023-0.0230.0000.0000.0000.000
99A670TRP0-0.010-0.02538.739-0.049-0.0490.0000.0000.0000.000
100A671ARG10.8250.92145.481-6.254-6.2540.0000.0000.0000.000
101A672ALA0-0.037-0.04547.7600.1030.1030.0000.0000.0000.000
102A673ASP-1-0.844-0.88449.3136.2366.2360.0000.0000.0000.000
103A674GLY00.0200.02244.9860.0440.0440.0000.0000.0000.000
104A675SER0-0.048-0.04743.7370.1830.1830.0000.0000.0000.000
105A676ALA00.012-0.01542.653-0.019-0.0190.0000.0000.0000.000
106A677ASP-1-0.862-0.92644.8136.2496.2490.0000.0000.0000.000
107A678VAL0-0.028-0.02239.5560.0960.0960.0000.0000.0000.000
108A679ASP-1-0.836-0.90442.0236.8716.8710.0000.0000.0000.000
109A680VAL0-0.0070.00039.3100.2320.2320.0000.0000.0000.000
110A681VAL00.0110.00337.452-0.148-0.1480.0000.0000.0000.000
111A682TRP0-0.071-0.04238.1750.0670.0670.0000.0000.0000.000
112A683ASN00.032-0.00332.020-0.175-0.1750.0000.0000.0000.000
113A684ASP-1-0.904-0.96535.1957.8027.8020.0000.0000.0000.000
114A685MET0-0.052-0.01228.5660.1290.1290.0000.0000.0000.000
115A686PRO0-0.020-0.00226.965-0.173-0.1730.0000.0000.0000.000
116A687ALA00.011-0.00128.405-0.023-0.0230.0000.0000.0000.000
117A688VAL00.0150.01725.3850.3580.3580.0000.0000.0000.000
118A689ALA00.0070.01821.3460.0210.0210.0000.0000.0000.000
119A690GLY00.0060.00719.6520.1980.1980.0000.0000.0000.000
120A691GLN00.0480.00719.802-0.438-0.4380.0000.0000.0000.000
121A692SER00.0240.02720.704-0.060-0.0600.0000.0000.0000.000
122A693SER00.0400.03022.054-0.067-0.0670.0000.0000.0000.000
123A694SER0-0.044-0.05023.086-0.420-0.4200.0000.0000.0000.000
124A695ILE00.0720.03324.836-0.268-0.2680.0000.0000.0000.000
125A696ALA00.0230.02827.421-0.298-0.2980.0000.0000.0000.000
126A697LEU0-0.054-0.02827.063-0.337-0.3370.0000.0000.0000.000
127A698ALA00.0560.02029.398-0.284-0.2840.0000.0000.0000.000
128A699LEU00.0590.04531.214-0.272-0.2720.0000.0000.0000.000
129A700ALA0-0.0340.00933.323-0.294-0.2940.0000.0000.0000.000
130A701SER0-0.073-0.03333.863-0.288-0.2880.0000.0000.0000.000
131A702SER0-0.094-0.07534.929-0.149-0.1490.0000.0000.0000.000
132A703LEU00.0180.01236.266-0.178-0.1780.0000.0000.0000.000
133A704PRO0-0.057-0.01639.170-0.008-0.0080.0000.0000.0000.000
134A705PHE00.0860.03939.084-0.183-0.1830.0000.0000.0000.000
135A706VAL0-0.0210.00638.5280.2240.2240.0000.0000.0000.000
136A707PRO00.0320.01535.562-0.090-0.0900.0000.0000.0000.000
137A708LYS10.9650.98537.581-7.007-7.0070.0000.0000.0000.000
138A709ALA00.001-0.00333.2120.0740.0740.0000.0000.0000.000
139A710ALA0-0.039-0.00830.669-0.016-0.0160.0000.0000.0000.000
140A711TYR00.025-0.03928.4170.2070.2070.0000.0000.0000.000
141A712THR0-0.047-0.04923.2130.3050.3050.0000.0000.0000.000
142A713GLY00.0550.01121.5770.1760.1760.0000.0000.0000.000
143A714CYS0-0.051-0.01517.629-0.467-0.4670.0000.0000.0000.000
144A715LEU00.0270.01820.782-0.078-0.0780.0000.0000.0000.000
145A716SER0-0.029-0.00319.3680.2380.2380.0000.0000.0000.000
146A717GLY00.012-0.00721.340-0.097-0.0970.0000.0000.0000.000
147A718THR00.0260.01124.870-0.062-0.0620.0000.0000.0000.000
148A719ASN0-0.0120.00421.640-0.398-0.3980.0000.0000.0000.000
149A720VAL00.0310.00721.6920.3150.3150.0000.0000.0000.000
150A721GLN0-0.064-0.04516.1830.2520.2520.0000.0000.0000.000
151A722PRO00.0090.01115.682-0.472-0.4720.0000.0000.0000.000
152A723VAL0-0.024-0.01516.4230.8300.8300.0000.0000.0000.000
153A724GLN00.0640.02314.064-0.287-0.2870.0000.0000.0000.000
154A725PHE00.011-0.01216.708-0.696-0.6960.0000.0000.0000.000
155A726GLY00.0910.04820.315-0.601-0.6010.0000.0000.0000.000
156A727ASN0-0.0120.00022.325-0.894-0.8940.0000.0000.0000.000
157A728LEU00.0270.01523.381-0.406-0.4060.0000.0000.0000.000
158A729LYS10.8970.98721.226-13.062-13.0620.0000.0000.0000.000
159A730ALA00.0570.03625.966-0.390-0.3900.0000.0000.0000.000
160A731ARG10.8540.93028.349-10.451-10.4510.0000.0000.0000.000
161A732ALA00.0220.03129.459-0.305-0.3050.0000.0000.0000.000
162A733ALA00.0150.00630.760-0.274-0.2740.0000.0000.0000.000
163A734HIS10.8260.87330.614-9.796-9.7960.0000.0000.0000.000
164A735LYS10.8840.95834.187-8.427-8.4270.0000.0000.0000.000
165A736ILE0-0.001-0.00636.103-0.173-0.1730.0000.0000.0000.000
166A737GLY0-0.0010.01237.665-0.109-0.1090.0000.0000.0000.000
167A738LEU0-0.0110.00934.860-0.048-0.0480.0000.0000.0000.000
168A739PRO00.0020.00732.7070.2230.2230.0000.0000.0000.000
169A740LEU0-0.027-0.01925.2790.0480.0480.0000.0000.0000.000
170A741VAL00.0140.02928.8980.1360.1360.0000.0000.0000.000
171A742GLY00.0360.00725.5380.0580.0580.0000.0000.0000.000
172A743MET0-0.045-0.00219.3060.1290.1290.0000.0000.0000.000
173A744THR0-0.051-0.04419.6100.2800.2800.0000.0000.0000.000
174A745GLN0-0.077-0.05713.1550.7560.7560.0000.0000.0000.000
175A746ASP-1-0.872-0.93516.73414.37814.3780.0000.0000.0000.000
176A747GLY00.0020.01418.727-0.383-0.3830.0000.0000.0000.000
177A748GLY0-0.037-0.01621.774-0.495-0.4950.0000.0000.0000.000
178A749GLU-1-0.914-0.94523.27012.27212.2720.0000.0000.0000.000
179A750ASP-1-0.743-0.84926.2229.7439.7430.0000.0000.0000.000
180A751THR0-0.058-0.03229.095-0.239-0.2390.0000.0000.0000.000
181A752ARG10.9550.97919.409-13.563-13.5630.0000.0000.0000.000
182A753ILE00.0210.01625.838-0.152-0.1520.0000.0000.0000.000
183A754CYS0-0.041-0.03923.4030.5190.5190.0000.0000.0000.000
184A755THR00.0040.00624.3920.2600.2600.0000.0000.0000.000
185A756LEU00.015-0.02526.971-0.117-0.1170.0000.0000.0000.000
186A757ASP-1-0.897-0.93729.1748.9988.9980.0000.0000.0000.000
187A758ASP-1-0.851-0.90629.6759.7509.7500.0000.0000.0000.000
188A759ALA0-0.088-0.04729.261-0.137-0.1370.0000.0000.0000.000
189A760ALA00.009-0.00331.353-0.185-0.1850.0000.0000.0000.000
190A761ASP-1-0.889-0.95534.5668.1878.1870.0000.0000.0000.000
191A762HIS00.0200.03033.220-0.137-0.1370.0000.0000.0000.000
192A763ALA00.016-0.00634.848-0.179-0.1790.0000.0000.0000.000
193A764PHE0-0.0090.01836.471-0.269-0.2690.0000.0000.0000.000
194A765ASP-1-0.867-0.93537.9417.7877.7870.0000.0000.0000.000
195A766SER0-0.150-0.08937.364-0.186-0.1860.0000.0000.0000.000
196A767MET0-0.111-0.04739.442-0.067-0.0670.0000.0000.0000.000
197A768GLU-1-0.951-0.95842.8416.5926.5920.0000.0000.0000.000
198A769SER0-0.075-0.03243.670-0.053-0.0530.0000.0000.0000.000