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: YYJ52

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 OptAll
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 -2127294.815936
FMO2-HF: Nuclear repulsion 2052310.855239
FMO2-HF: Total energy -74983.960696
FMO2-MP2: Total energy -75202.63412


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.
26.75528.9240.041-1.115-1.0950.002
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 : -0.945 / q_NPA : -0.978
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].
3A561PRO0-0.009-0.0053.3430.0192.1880.041-1.115-1.0950.002
4A562ILE00.0190.0075.517-0.873-0.8730.0000.0000.0000.000
5A563SER0-0.012-0.0017.563-2.130-2.1300.0000.0000.0000.000
6A564LEU0-0.017-0.01211.203-0.127-0.1270.0000.0000.0000.000
7A565LEU0-0.008-0.00513.762-0.607-0.6070.0000.0000.0000.000
8A566GLN00.000-0.01317.5110.5660.5660.0000.0000.0000.000
9A567THR0-0.0010.00019.415-0.179-0.1790.0000.0000.0000.000
10A568LEU00.0260.02020.8940.1730.1730.0000.0000.0000.000
11A569ALA00.0100.01224.610-0.335-0.3350.0000.0000.0000.000
12A570TYR0-0.084-0.04727.880-0.099-0.0990.0000.0000.0000.000
13A571LYS10.8500.92229.093-9.561-9.5610.0000.0000.0000.000
14A572GLN00.0560.03431.3930.1290.1290.0000.0000.0000.000
15A573PRO00.007-0.00231.762-0.169-0.1690.0000.0000.0000.000
16A574LEU0-0.042-0.00334.454-0.140-0.1400.0000.0000.0000.000
17A575GLY00.0360.03137.9150.0760.0760.0000.0000.0000.000
18A576ARG10.8010.85539.139-7.722-7.7220.0000.0000.0000.000
19A577ASN0-0.050-0.03941.937-0.051-0.0510.0000.0000.0000.000
20A578SER0-0.050-0.03743.771-0.018-0.0180.0000.0000.0000.000
21A579ARG10.8510.92344.291-6.862-6.8620.0000.0000.0000.000
22A580ILE00.0130.00744.8930.1130.1130.0000.0000.0000.000
23A581VAL0-0.042-0.01743.527-0.154-0.1540.0000.0000.0000.000
24A582HIS0-0.027-0.01845.1250.0390.0390.0000.0000.0000.000
25A583PHE0-0.004-0.00640.9380.0350.0350.0000.0000.0000.000
26A584THR00.007-0.02944.180-0.040-0.0400.0000.0000.0000.000
27A585ASP-1-0.889-0.94140.5807.2747.2740.0000.0000.0000.000
28A586GLY00.0410.01837.380-0.009-0.0090.0000.0000.0000.000
29A587ALA0-0.021-0.01133.2470.0040.0040.0000.0000.0000.000
30A588LEU00.0510.03533.3070.1190.1190.0000.0000.0000.000
31A589PHE0-0.005-0.01627.2490.3150.3150.0000.0000.0000.000
32A590PRO00.0040.02725.947-0.158-0.1580.0000.0000.0000.000
33A591VAL0-0.018-0.00325.9550.5620.5620.0000.0000.0000.000
34A592VAL0-0.009-0.02422.269-0.208-0.2080.0000.0000.0000.000
35A593ALA0-0.0050.00723.4220.2230.2230.0000.0000.0000.000
36A594PHE0-0.015-0.02120.207-0.116-0.1160.0000.0000.0000.000
37A595GLY00.0340.02623.7750.0140.0140.0000.0000.0000.000
38A596ASP-1-0.860-0.92325.31811.40611.4060.0000.0000.0000.000
39A597ASN0-0.056-0.02726.954-0.397-0.3970.0000.0000.0000.000
40A598HIS00.0040.00028.092-0.322-0.3220.0000.0000.0000.000
41A599SER00.0150.00524.6290.5220.5220.0000.0000.0000.000
42A600THR00.0330.02126.499-0.328-0.3280.0000.0000.0000.000
43A601SER0-0.063-0.06826.6640.4060.4060.0000.0000.0000.000
44A602GLU-1-0.824-0.90228.7128.6718.6710.0000.0000.0000.000
45A603LEU00.0210.01430.1210.3940.3940.0000.0000.0000.000
46A604TYR00.0470.02230.677-0.120-0.1200.0000.0000.0000.000
47A605ILE00.0130.01632.6890.1130.1130.0000.0000.0000.000
48A606ALA0-0.041-0.01931.7700.0680.0680.0000.0000.0000.000
49A607VAL00.0620.02133.908-0.092-0.0920.0000.0000.0000.000
50A608ARG10.8080.90336.725-7.430-7.4300.0000.0000.0000.000
51A609GLY00.0290.00638.025-0.216-0.2160.0000.0000.0000.000
52A610ASP-1-0.920-0.96438.4397.5797.5790.0000.0000.0000.000
53A611HIS00.0500.00739.495-0.237-0.2370.0000.0000.0000.000
54A612ARG10.8570.89637.872-7.698-7.6980.0000.0000.0000.000
55A613ASP-1-0.838-0.91440.5386.7646.7640.0000.0000.0000.000
56A614LEU0-0.024-0.00140.719-0.052-0.0520.0000.0000.0000.000
57A615MET0-0.0280.02634.9210.0430.0430.0000.0000.0000.000
58A616SER00.018-0.00937.715-0.264-0.2640.0000.0000.0000.000
59A617PRO0-0.050-0.05238.3700.1140.1140.0000.0000.0000.000
60A618ASP-1-0.862-0.90536.2177.8477.8470.0000.0000.0000.000
61A619VAL00.0140.01332.2170.2460.2460.0000.0000.0000.000
62A620ARG10.8620.92634.297-7.149-7.1490.0000.0000.0000.000
63A621ASP-1-0.873-0.93235.8377.7267.7260.0000.0000.0000.000
64A622SER0-0.044-0.01429.4280.1860.1860.0000.0000.0000.000
65A623TYR00.009-0.01030.556-0.172-0.1720.0000.0000.0000.000
66A624ALA0-0.0310.01225.8420.2580.2580.0000.0000.0000.000
67A625LEU00.003-0.01327.235-0.359-0.3590.0000.0000.0000.000
68A626THR00.000-0.02826.6270.4600.4600.0000.0000.0000.000
69A627GLY00.001-0.01026.6870.0670.0670.0000.0000.0000.000
70A628ASP-1-0.816-0.90427.3209.2469.2460.0000.0000.0000.000
71A629ASP-1-0.847-0.89830.0999.5919.5910.0000.0000.0000.000
72A630HIS10.8730.94931.575-8.647-8.6470.0000.0000.0000.000
73A631LYS10.8980.95931.351-8.299-8.2990.0000.0000.0000.000
74A632VAL00.0280.01629.023-0.158-0.1580.0000.0000.0000.000
75A633TRP0-0.005-0.01530.8980.2680.2680.0000.0000.0000.000
76A634GLY00.0950.03232.057-0.100-0.1000.0000.0000.0000.000
77A635ALA0-0.053-0.01126.8560.2300.2300.0000.0000.0000.000
78A636THR00.0330.00324.600-0.354-0.3540.0000.0000.0000.000
79A637HIS0-0.0230.00621.4230.6780.6780.0000.0000.0000.000
80A651LYS10.8220.89422.253-10.626-10.6260.0000.0000.0000.000
81A652PHE0-0.025-0.03522.0520.6620.6620.0000.0000.0000.000
82A653ASN0-0.0210.00220.205-0.713-0.7130.0000.0000.0000.000
83A654VAL00.0340.02123.204-0.300-0.3000.0000.0000.0000.000
84A655LYS10.8470.92425.741-11.185-11.1850.0000.0000.0000.000
85A656THR00.0580.01529.878-0.009-0.0090.0000.0000.0000.000
86A657ARG10.8260.89933.076-8.372-8.3720.0000.0000.0000.000
87A658THR0-0.038-0.03135.356-0.349-0.3490.0000.0000.0000.000
88A659ASP-1-0.795-0.87634.8878.5938.5930.0000.0000.0000.000
89A660LEU0-0.0190.00732.148-0.110-0.1100.0000.0000.0000.000
90A661THR0-0.006-0.00134.7230.0470.0470.0000.0000.0000.000
91A662ILE0-0.062-0.02729.3070.0740.0740.0000.0000.0000.000
92A663LEU0-0.0030.00333.571-0.056-0.0560.0000.0000.0000.000
93A664PRO00.0120.02433.9330.1220.1220.0000.0000.0000.000
94A665VAL0-0.018-0.02335.098-0.248-0.2480.0000.0000.0000.000
95A666ALA0-0.050-0.01336.5780.1850.1850.0000.0000.0000.000
96A667ASP-1-0.873-0.94939.0577.3497.3490.0000.0000.0000.000
97A668VAL0-0.062-0.03438.5060.0000.0000.0000.0000.0000.000
98A669PHE0-0.0130.00041.735-0.023-0.0230.0000.0000.0000.000
99A670TRP0-0.015-0.02538.661-0.078-0.0780.0000.0000.0000.000
100A671ARG10.8070.88545.478-6.369-6.3690.0000.0000.0000.000
101A672ALA0-0.013-0.02247.9210.0880.0880.0000.0000.0000.000
102A673ASP-1-0.857-0.88648.7906.3196.3190.0000.0000.0000.000
103A674GLY00.0170.01045.4160.0540.0540.0000.0000.0000.000
104A675SER0-0.046-0.04543.9040.1770.1770.0000.0000.0000.000
105A676ALA00.028-0.00142.658-0.004-0.0040.0000.0000.0000.000
106A677ASP-1-0.841-0.88044.7956.3096.3090.0000.0000.0000.000
107A678VAL0-0.019-0.01639.8620.1100.1100.0000.0000.0000.000
108A679ASP-1-0.808-0.87442.2196.9416.9410.0000.0000.0000.000
109A680VAL0-0.0040.00339.4060.2370.2370.0000.0000.0000.000
110A681VAL0-0.016-0.00337.851-0.180-0.1800.0000.0000.0000.000
111A682TRP0-0.054-0.03738.2140.0950.0950.0000.0000.0000.000
112A683ASN00.025-0.02932.291-0.152-0.1520.0000.0000.0000.000
113A684ASP-1-0.850-0.88835.3367.8967.8960.0000.0000.0000.000
114A685MET0-0.037-0.01028.5970.1600.1600.0000.0000.0000.000
115A686PRO0-0.008-0.00727.161-0.167-0.1670.0000.0000.0000.000
116A687ALA00.0250.01428.599-0.013-0.0130.0000.0000.0000.000
117A688VAL0-0.0010.01325.2200.3970.3970.0000.0000.0000.000
118A689ALA00.0140.00621.6180.0120.0120.0000.0000.0000.000
119A690GLY00.0080.00719.4780.2780.2780.0000.0000.0000.000
120A691GLN00.0430.00919.541-0.580-0.5800.0000.0000.0000.000
121A692SER00.0090.02020.439-0.348-0.3480.0000.0000.0000.000
122A693SER00.1080.06421.965-0.039-0.0390.0000.0000.0000.000
123A694SER0-0.047-0.04423.072-0.399-0.3990.0000.0000.0000.000
124A695ILE00.0440.02924.741-0.313-0.3130.0000.0000.0000.000
125A696ALA00.0500.03527.670-0.329-0.3290.0000.0000.0000.000
126A697LEU0-0.022-0.01226.903-0.325-0.3250.0000.0000.0000.000
127A698ALA00.0310.01529.410-0.297-0.2970.0000.0000.0000.000
128A699LEU00.0330.04131.211-0.310-0.3100.0000.0000.0000.000
129A700ALA00.0260.03333.490-0.303-0.3030.0000.0000.0000.000
130A701SER0-0.097-0.05133.818-0.266-0.2660.0000.0000.0000.000
131A702SER0-0.081-0.05634.948-0.162-0.1620.0000.0000.0000.000
132A703LEU00.0600.04536.054-0.173-0.1730.0000.0000.0000.000
133A704PRO0-0.055-0.01539.273-0.022-0.0220.0000.0000.0000.000
134A705PHE00.0650.02139.108-0.185-0.1850.0000.0000.0000.000
135A706VAL00.0100.01139.0090.2100.2100.0000.0000.0000.000
136A707PRO00.0090.00735.793-0.079-0.0790.0000.0000.0000.000
137A708LYS10.8170.91737.775-7.170-7.1700.0000.0000.0000.000
138A709ALA0-0.016-0.02233.3120.0780.0780.0000.0000.0000.000
139A710ALA0-0.0140.00630.889-0.039-0.0390.0000.0000.0000.000
140A711TYR00.025-0.01328.6630.2740.2740.0000.0000.0000.000
141A712THR0-0.068-0.05523.1350.2380.2380.0000.0000.0000.000
142A713GLY00.0760.02921.1760.1780.1780.0000.0000.0000.000
143A714CYS0-0.086-0.03317.549-0.493-0.4930.0000.0000.0000.000
144A715LEU00.0310.01020.765-0.129-0.1290.0000.0000.0000.000
145A716SER0-0.020-0.01319.4640.6150.6150.0000.0000.0000.000
146A717GLY0-0.034-0.01421.551-0.076-0.0760.0000.0000.0000.000
147A718THR00.023-0.02025.1490.0030.0030.0000.0000.0000.000
148A719ASN00.0010.01121.477-0.448-0.4480.0000.0000.0000.000
149A720VAL00.0190.00721.7640.3210.3210.0000.0000.0000.000
150A721GLN0-0.038-0.02316.5460.4930.4930.0000.0000.0000.000
151A722PRO0-0.0160.00015.355-0.484-0.4840.0000.0000.0000.000
152A723VAL0-0.0010.00616.2381.0271.0270.0000.0000.0000.000
153A724GLN00.0270.00812.966-0.647-0.6470.0000.0000.0000.000
154A725PHE00.0460.00916.916-0.722-0.7220.0000.0000.0000.000
155A726GLY00.0730.02720.292-0.705-0.7050.0000.0000.0000.000
156A727ASN00.0400.01322.261-0.881-0.8810.0000.0000.0000.000
157A728LEU0-0.0170.00223.418-0.486-0.4860.0000.0000.0000.000
158A729LYS10.8400.91721.548-12.992-12.9920.0000.0000.0000.000
159A730ALA00.0390.02226.128-0.407-0.4070.0000.0000.0000.000
160A731ARG10.8100.90626.822-10.995-10.9950.0000.0000.0000.000
161A732ALA00.0020.01329.926-0.338-0.3380.0000.0000.0000.000
162A733ALA00.0300.01830.950-0.261-0.2610.0000.0000.0000.000
163A734HIS10.8350.88531.135-9.766-9.7660.0000.0000.0000.000
164A735LYS10.8570.93234.219-8.460-8.4600.0000.0000.0000.000
165A736ILE00.0120.01236.247-0.175-0.1750.0000.0000.0000.000
166A737GLY0-0.0090.00137.718-0.109-0.1090.0000.0000.0000.000
167A738LEU0-0.0210.00334.845-0.011-0.0110.0000.0000.0000.000
168A739PRO0-0.011-0.00332.3890.2220.2220.0000.0000.0000.000
169A740LEU0-0.043-0.03325.1910.0510.0510.0000.0000.0000.000
170A741VAL0-0.025-0.00928.4550.0930.0930.0000.0000.0000.000
171A742GLY00.0430.02425.4030.1020.1020.0000.0000.0000.000
172A743MET0-0.0200.02219.2480.2090.2090.0000.0000.0000.000
173A744THR0-0.059-0.03919.6230.3160.3160.0000.0000.0000.000
174A745GLN0-0.065-0.05713.3300.8030.8030.0000.0000.0000.000
175A746ASP-1-0.826-0.90016.36015.01615.0160.0000.0000.0000.000
176A747GLY0-0.0130.00618.510-0.418-0.4180.0000.0000.0000.000
177A748GLY0-0.025-0.01721.591-0.468-0.4680.0000.0000.0000.000
178A749GLU-1-0.760-0.84923.04412.76212.7620.0000.0000.0000.000
179A750ASP-1-0.769-0.85126.1549.8999.8990.0000.0000.0000.000
180A751THR0-0.047-0.03228.782-0.347-0.3470.0000.0000.0000.000
181A752ARG10.8200.88918.572-14.167-14.1670.0000.0000.0000.000
182A753ILE00.0090.00825.579-0.271-0.2710.0000.0000.0000.000
183A754CYS0-0.035-0.05522.6620.4090.4090.0000.0000.0000.000
184A755THR0-0.035-0.02324.1060.3390.3390.0000.0000.0000.000
185A756LEU00.010-0.01126.733-0.134-0.1340.0000.0000.0000.000
186A757ASP-1-0.856-0.90629.0149.4849.4840.0000.0000.0000.000
187A758ASP-1-0.829-0.89028.46410.21410.2140.0000.0000.0000.000
188A759ALA0-0.045-0.03429.110-0.165-0.1650.0000.0000.0000.000
189A760ALA0-0.025-0.01231.156-0.209-0.2090.0000.0000.0000.000
190A761ASP-1-0.877-0.93034.5118.1508.1500.0000.0000.0000.000
191A762HIS00.0400.02132.865-0.139-0.1390.0000.0000.0000.000
192A763ALA00.001-0.00134.781-0.171-0.1710.0000.0000.0000.000
193A764PHE0-0.0080.00836.241-0.266-0.2660.0000.0000.0000.000
194A765ASP-1-0.867-0.93137.6687.7987.7980.0000.0000.0000.000
195A766SER0-0.107-0.06237.025-0.168-0.1680.0000.0000.0000.000
196A767MET0-0.0130.01539.093-0.088-0.0880.0000.0000.0000.000
197A768GLU-1-0.858-0.89542.5436.5996.5990.0000.0000.0000.000
198A769SER0-0.144-0.09243.6630.0440.0440.0000.0000.0000.000