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: R1J78

Calculation Name: 2GEF-A-Xray311

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: 2021-09-06

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 202
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2142022.801866
FMO2-HF: Nuclear repulsion 2066700.752008
FMO2-HF: Total energy -75322.049858
FMO2-MP2: Total energy -75541.962656


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:558:ACE )


Summations of interaction energy for fragment #1(A:558:ACE )
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.
1.5762.159-0.004-0.298-0.280.001
Interaction energy analysis for fragmet #1(A:558:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.056 / q_NPA : -0.041
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].
3A560LEU 00.0020.0013.8751.4952.078-0.004-0.298-0.2800.001
4A561PRO 0-0.041-0.0177.0250.0120.0120.0000.0000.0000.000
5A562ILE 00.0450.0399.481-0.048-0.0480.0000.0000.0000.000
6A563SER 0-0.012-0.01611.8660.0830.0830.0000.0000.0000.000
7A564LEU 0-0.015-0.01813.990-0.003-0.0030.0000.0000.0000.000
8A565LEU 00.0190.00917.1430.0180.0180.0000.0000.0000.000
9A566GLN 0-0.035-0.02419.803-0.001-0.0010.0000.0000.0000.000
10A567THR 0-0.013-0.00521.8020.0040.0040.0000.0000.0000.000
11A568LEU 00.0100.02022.5290.0060.0060.0000.0000.0000.000
12A569ALA 00.0070.00426.163-0.004-0.0040.0000.0000.0000.000
13A570TYR 0-0.025-0.01829.1760.0040.0040.0000.0000.0000.000
14A571LYS 10.9420.97730.665-0.021-0.0210.0000.0000.0000.000
15A572GLN 0-0.004-0.01232.5920.0000.0000.0000.0000.0000.000
16A573PRO 00.0290.01532.9650.0000.0000.0000.0000.0000.000
17A574LEU 0-0.0310.00635.479-0.003-0.0030.0000.0000.0000.000
18A575GLY 00.0150.01138.1710.0030.0030.0000.0000.0000.000
19A576ARG 10.8890.92139.934-0.035-0.0350.0000.0000.0000.000
20A577ASN 0-0.063-0.04742.523-0.001-0.0010.0000.0000.0000.000
21A578SER 0-0.039-0.02444.5900.0000.0000.0000.0000.0000.000
22A579ARG 10.9790.98644.989-0.023-0.0230.0000.0000.0000.000
23A580ILE 00.0130.02145.4800.0000.0000.0000.0000.0000.000
24A581VAL 0-0.038-0.02044.2020.0010.0010.0000.0000.0000.000
25A582HIS 0-0.0240.00645.8140.0000.0000.0000.0000.0000.000
26A583PHE 00.000-0.00241.7450.0020.0020.0000.0000.0000.000
27A584THR 00.008-0.02944.787-0.002-0.0020.0000.0000.0000.000
28A585ASP -1-0.943-0.96140.8540.0180.0180.0000.0000.0000.000
29A586GLY 00.0430.01237.8010.0020.0020.0000.0000.0000.000
30A587ALA 0-0.021-0.00333.805-0.003-0.0030.0000.0000.0000.000
31A588LEU 00.0260.02834.0160.0040.0040.0000.0000.0000.000
32A589PHE 00.001-0.00328.012-0.001-0.0010.0000.0000.0000.000
33A590PRO 0-0.0320.00026.9010.0020.0020.0000.0000.0000.000
34A591VAL 00.0070.00126.8300.0050.0050.0000.0000.0000.000
35A592VAL 0-0.032-0.01723.054-0.005-0.0050.0000.0000.0000.000
36A593ALA 00.0060.00524.4930.0110.0110.0000.0000.0000.000
37A594PHE 0-0.029-0.02721.128-0.011-0.0110.0000.0000.0000.000
38A595GLY 00.0390.02824.3960.0090.0090.0000.0000.0000.000
39A596ASP -1-0.884-0.93025.6650.0570.0570.0000.0000.0000.000
40A597ASN 0-0.128-0.07626.871-0.003-0.0030.0000.0000.0000.000
41A598HIS 0-0.007-0.01828.945-0.009-0.0090.0000.0000.0000.000
42A599SER 00.0500.03125.6900.0060.0060.0000.0000.0000.000
43A600THR 0-0.052-0.01627.506-0.003-0.0030.0000.0000.0000.000
44A601SER 0-0.005-0.05127.8070.0030.0030.0000.0000.0000.000
45A602GLU -1-0.816-0.90129.7200.0310.0310.0000.0000.0000.000
46A603LEU 0-0.002-0.00631.1540.0010.0010.0000.0000.0000.000
47A604TYR 00.0560.03231.5590.0030.0030.0000.0000.0000.000
48A605ILE 0-0.0040.00833.514-0.002-0.0020.0000.0000.0000.000
49A606ALA 0-0.006-0.00532.2420.0040.0040.0000.0000.0000.000
50A607VAL 00.0290.01834.277-0.004-0.0040.0000.0000.0000.000
51A608ARG 10.8750.91137.014-0.017-0.0170.0000.0000.0000.000
52A609GLY 00.0360.02538.099-0.002-0.0020.0000.0000.0000.000
53A610ASP -1-1.000-1.01638.5310.0400.0400.0000.0000.0000.000
54A611HIS 00.0980.05039.434-0.002-0.0020.0000.0000.0000.000
55A612ARG 10.9670.95237.760-0.049-0.0490.0000.0000.0000.000
56A613ASP -1-0.967-0.97440.3470.0300.0300.0000.0000.0000.000
57A614LEU 00.0070.00541.473-0.001-0.0010.0000.0000.0000.000
58A615MET 0-0.085-0.00234.8870.0000.0000.0000.0000.0000.000
59A616SER 00.0470.01837.611-0.001-0.0010.0000.0000.0000.000
60A617PRO 0-0.020-0.04638.5920.0020.0020.0000.0000.0000.000
61A618ASP -1-0.912-0.92435.8020.0510.0510.0000.0000.0000.000
62A619VAL 0-0.022-0.02132.3740.0050.0050.0000.0000.0000.000
63A620ARG 10.8740.93834.112-0.036-0.0360.0000.0000.0000.000
64A621ASP -1-0.920-0.94434.7790.0580.0580.0000.0000.0000.000
65A622SER 0-0.044-0.01629.4510.0070.0070.0000.0000.0000.000
66A623TYR 00.018-0.01030.054-0.006-0.0060.0000.0000.0000.000
67A624ALA 0-0.0240.01525.6320.0090.0090.0000.0000.0000.000
68A625LEU 0-0.044-0.04726.506-0.008-0.0080.0000.0000.0000.000
69A626THR 00.0290.01226.1400.0070.0070.0000.0000.0000.000
70A627GLY 00.0430.00926.0250.0050.0050.0000.0000.0000.000
71A628ASP -1-0.885-0.93626.7900.0480.0480.0000.0000.0000.000
72A629ASP -1-0.893-0.93229.2870.0760.0760.0000.0000.0000.000
73A630HIS 10.8520.94630.836-0.050-0.0500.0000.0000.0000.000
74A631LYS 10.9620.97830.929-0.057-0.0570.0000.0000.0000.000
75A632VAL 00.0290.03828.859-0.006-0.0060.0000.0000.0000.000
76A633TRP 00.015-0.02230.8240.0080.0080.0000.0000.0000.000
77A634GLY 00.0740.01932.027-0.004-0.0040.0000.0000.0000.000
78A635ALA 0-0.056-0.00727.0310.0000.0000.0000.0000.0000.000
79A636THR 00.009-0.01524.3440.0070.0070.0000.0000.0000.000
80A637HIS 00.0210.01422.523-0.004-0.0040.0000.0000.0000.000
81A638NME 00.0010.01720.8760.0200.0200.0000.0000.0000.000
82A650ACE 00.012-0.00621.1120.0050.0050.0000.0000.0000.000
83A651LYS 10.8190.88321.534-0.109-0.1090.0000.0000.0000.000
84A652PHE 0-0.031-0.00721.6630.0080.0080.0000.0000.0000.000
85A653ASN 0-0.0060.00120.550-0.011-0.0110.0000.0000.0000.000
86A654VAL 00.0070.00423.019-0.004-0.0040.0000.0000.0000.000
87A655LYS 10.9530.99426.393-0.049-0.0490.0000.0000.0000.000
88A656THR 00.0530.00029.635-0.003-0.0030.0000.0000.0000.000
89A657ARG 10.9220.95332.577-0.028-0.0280.0000.0000.0000.000
90A658THR 0-0.059-0.03134.803-0.003-0.0030.0000.0000.0000.000
91A659ASP -1-0.861-0.91234.4760.0510.0510.0000.0000.0000.000
92A660LEU 0-0.016-0.00832.023-0.004-0.0040.0000.0000.0000.000
93A661THR 00.0080.01534.5350.0050.0050.0000.0000.0000.000
94A662ILE 0-0.078-0.02829.614-0.004-0.0040.0000.0000.0000.000
95A663LEU 0-0.003-0.00533.9180.0020.0020.0000.0000.0000.000
96A664PRO 0-0.0130.01434.638-0.002-0.0020.0000.0000.0000.000
97A665VAL 00.023-0.01235.683-0.001-0.0010.0000.0000.0000.000
98A666ALA 0-0.092-0.04337.464-0.001-0.0010.0000.0000.0000.000
99A667ASP -1-0.827-0.92539.9390.0050.0050.0000.0000.0000.000
100A668VAL 0-0.077-0.03139.6910.0020.0020.0000.0000.0000.000
101A669PHE 0-0.0100.01842.845-0.002-0.0020.0000.0000.0000.000
102A670TRP 0-0.011-0.02539.9800.0000.0000.0000.0000.0000.000
103A671ARG 10.8250.92146.616-0.010-0.0100.0000.0000.0000.000
104A672ALA 0-0.035-0.04448.8270.0000.0000.0000.0000.0000.000
105A673ASP -1-0.845-0.88450.1710.0070.0070.0000.0000.0000.000
106A674GLY 00.0180.02045.9510.0000.0000.0000.0000.0000.000
107A675SER 0-0.047-0.04644.6080.0010.0010.0000.0000.0000.000
108A676ALA 00.011-0.01643.572-0.001-0.0010.0000.0000.0000.000
109A677ASP -1-0.863-0.92745.6700.0120.0120.0000.0000.0000.000
110A678VAL 0-0.027-0.02140.377-0.001-0.0010.0000.0000.0000.000
111A679ASP -1-0.833-0.90343.1100.0170.0170.0000.0000.0000.000
112A680VAL 0-0.0060.00139.9460.0010.0010.0000.0000.0000.000
113A681VAL 00.0110.00338.341-0.001-0.0010.0000.0000.0000.000
114A682TRP 0-0.071-0.04338.8110.0030.0030.0000.0000.0000.000
115A683ASN 00.029-0.00432.8060.0000.0000.0000.0000.0000.000
116A684ASP -1-0.900-0.96435.6290.0380.0380.0000.0000.0000.000
117A685MET 0-0.052-0.01129.1640.0030.0030.0000.0000.0000.000
118A686PRO 0-0.019-0.00227.2270.0000.0000.0000.0000.0000.000
119A687ALA 00.016-0.00228.631-0.003-0.0030.0000.0000.0000.000
120A688VAL 00.0090.01125.8490.0060.0060.0000.0000.0000.000
121A689ALA 00.0050.01621.5120.0060.0060.0000.0000.0000.000
122A690GLY 0-0.0030.00519.852-0.006-0.0060.0000.0000.0000.000
123A691GLN 00.0500.00619.967-0.017-0.0170.0000.0000.0000.000
124A692SER 0-0.0190.01221.604-0.010-0.0100.0000.0000.0000.000
125A693SER 00.0760.04322.784-0.007-0.0070.0000.0000.0000.000
126A694SER 0-0.043-0.05123.378-0.001-0.0010.0000.0000.0000.000
127A695ILE 00.0630.03025.716-0.002-0.0020.0000.0000.0000.000
128A696ALA 00.0340.03228.024-0.001-0.0010.0000.0000.0000.000
129A697LEU 0-0.055-0.02827.1720.0000.0000.0000.0000.0000.000
130A698ALA 00.0510.01729.6480.0000.0000.0000.0000.0000.000
131A699LEU 00.0580.04631.476-0.001-0.0010.0000.0000.0000.000
132A700ALA 0-0.0230.01333.761-0.001-0.0010.0000.0000.0000.000
133A701SER 0-0.082-0.03533.9230.0000.0000.0000.0000.0000.000
134A702SER 0-0.090-0.07335.175-0.001-0.0010.0000.0000.0000.000
135A703LEU 00.0140.00936.942-0.001-0.0010.0000.0000.0000.000
136A704PRO 0-0.054-0.01539.6280.0020.0020.0000.0000.0000.000
137A705PHE 00.0900.04039.971-0.001-0.0010.0000.0000.0000.000
138A706VAL 0-0.0220.00639.3850.0020.0020.0000.0000.0000.000
139A707PRO 00.0300.01436.408-0.002-0.0020.0000.0000.0000.000
140A708LYS 10.9640.98538.6540.0020.0020.0000.0000.0000.000
141A709ALA 00.002-0.00334.521-0.003-0.0030.0000.0000.0000.000
142A710ALA 0-0.040-0.00831.9170.0030.0030.0000.0000.0000.000
143A711TYR 00.027-0.03829.404-0.002-0.0020.0000.0000.0000.000
144A712THR 0-0.035-0.04424.5610.0070.0070.0000.0000.0000.000
145A713GLY 00.0430.00722.582-0.009-0.0090.0000.0000.0000.000
146A714CYS 0-0.052-0.01618.1390.0090.0090.0000.0000.0000.000
147A715LEU 00.0310.01921.329-0.012-0.0120.0000.0000.0000.000
148A716SER 0-0.030-0.00419.3800.0190.0190.0000.0000.0000.000
149A717GLY 00.011-0.00721.311-0.010-0.0100.0000.0000.0000.000
150A718THR 00.0260.01224.6880.0030.0030.0000.0000.0000.000
151A719ASN 0-0.0100.00422.335-0.008-0.0080.0000.0000.0000.000
152A720VAL 00.0260.00522.6730.0090.0090.0000.0000.0000.000
153A721GLN 0-0.057-0.04216.2790.0000.0000.0000.0000.0000.000
154A722PRO 00.0060.00917.1060.0100.0100.0000.0000.0000.000
155A723VAL 0-0.026-0.01717.6400.0100.0100.0000.0000.0000.000
156A724GLN 00.0650.02415.5050.0130.0130.0000.0000.0000.000
157A725PHE 00.012-0.01217.8930.0060.0060.0000.0000.0000.000
158A726GLY 00.0930.04822.0020.0050.0050.0000.0000.0000.000
159A727ASN 0-0.0120.00024.3010.0090.0090.0000.0000.0000.000
160A728LEU 00.0290.01524.7330.0020.0020.0000.0000.0000.000
161A729LYS 10.8980.98722.614-0.023-0.0230.0000.0000.0000.000
162A730ALA 00.0610.03627.5820.0030.0030.0000.0000.0000.000
163A731ARG 10.8480.92830.1380.0140.0140.0000.0000.0000.000
164A732ALA 00.0300.03330.9410.0010.0010.0000.0000.0000.000
165A733ALA 00.0080.00432.3550.0010.0010.0000.0000.0000.000
166A734HIS 10.8310.87632.9290.0140.0140.0000.0000.0000.000
167A735LYS 10.8810.95835.882-0.010-0.0100.0000.0000.0000.000
168A736ILE 00.000-0.00537.6950.0010.0010.0000.0000.0000.000
169A737GLY 00.0000.01239.3560.0000.0000.0000.0000.0000.000
170A738LEU 0-0.0110.00836.352-0.001-0.0010.0000.0000.0000.000
171A739PRO 00.0020.00734.376-0.001-0.0010.0000.0000.0000.000
172A740LEU 0-0.030-0.02026.8750.0040.0040.0000.0000.0000.000
173A741VAL 00.0170.03030.410-0.005-0.0050.0000.0000.0000.000
174A742GLY 00.0360.00626.7990.0070.0070.0000.0000.0000.000
175A743MET 0-0.048-0.00120.890-0.008-0.0080.0000.0000.0000.000
176A744THR 0-0.050-0.04521.1990.0080.0080.0000.0000.0000.000
177A745GLN 0-0.077-0.05714.640-0.027-0.0270.0000.0000.0000.000
178A746ASP -1-0.872-0.93519.030-0.059-0.0590.0000.0000.0000.000
179A747GLY 00.0010.01521.7410.0000.0000.0000.0000.0000.000
180A748GLY 0-0.039-0.01724.4850.0040.0040.0000.0000.0000.000
181A749GLU -1-0.908-0.94325.372-0.040-0.0400.0000.0000.0000.000
182A750ASP -1-0.748-0.85128.304-0.023-0.0230.0000.0000.0000.000
183A751THR 0-0.054-0.03131.055-0.002-0.0020.0000.0000.0000.000
184A752ARG 10.9520.97821.6690.0740.0740.0000.0000.0000.000
185A753ILE 00.0200.01727.406-0.001-0.0010.0000.0000.0000.000
186A754CYS 0-0.044-0.04024.893-0.002-0.0020.0000.0000.0000.000
187A755THR 00.0060.00725.4210.0040.0040.0000.0000.0000.000
188A756LEU 00.016-0.02627.8500.0010.0010.0000.0000.0000.000
189A757ASP -1-0.898-0.93729.7320.0010.0010.0000.0000.0000.000
190A758ASP -1-0.849-0.90530.845-0.021-0.0210.0000.0000.0000.000
191A759ALA 0-0.087-0.04730.1520.0000.0000.0000.0000.0000.000
192A760ALA 00.006-0.00432.2640.0020.0020.0000.0000.0000.000
193A761ASP -1-0.888-0.95435.309-0.008-0.0080.0000.0000.0000.000
194A762HIS 00.0200.03034.3490.0020.0020.0000.0000.0000.000
195A763ALA 00.016-0.00635.7620.0010.0010.0000.0000.0000.000
196A764PHE 0-0.0110.01837.4690.0010.0010.0000.0000.0000.000
197A765ASP -1-0.858-0.93139.282-0.011-0.0110.0000.0000.0000.000
198A766SER 0-0.153-0.09138.5900.0000.0000.0000.0000.0000.000
199A767MET 0-0.111-0.04740.6960.0010.0010.0000.0000.0000.000
200A768GLU -1-0.945-0.95743.997-0.009-0.0090.0000.0000.0000.000
201A769SER 0-0.055-0.02746.2240.0010.0010.0000.0000.0000.000
202A770NME 0-0.033-0.01143.653-0.001-0.0010.0000.0000.0000.000