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

tag_button

FMODB ID: R8488

Calculation Name: 4ERN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ERN

Chain ID: A

ChEMBL ID:

UniProt ID: P19447

Base Structure: X-ray

Registration Date: 2023-09-23

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3087010.052596
FMO2-HF: Nuclear repulsion 2993853.58883
FMO2-HF: Total energy -93156.463766
FMO2-MP2: Total energy -93427.870829


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:502:ILE)


Summations of interaction energy for fragment #1(A:502:ILE)
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.
-1.22.340.444-1.341-2.643-0.006
Interaction energy analysis for fragmet #1(A:502:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.006
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].
3A504LYS10.8660.9352.789-0.8621.7720.436-1.151-1.920-0.006
4A505VAL00.025-0.0045.411-0.065-0.0650.0000.0000.0000.000
5A506GLN00.0170.0237.8350.0880.0880.0000.0000.0000.000
6A507CYS0-0.039-0.00911.074-0.006-0.0060.0000.0000.0000.000
7A508ALA00.004-0.00613.526-0.003-0.0030.0000.0000.0000.000
8A509GLU-1-0.751-0.78217.2480.0470.0470.0000.0000.0000.000
9A510VAL0-0.016-0.01120.462-0.004-0.0040.0000.0000.0000.000
10A511TRP0-0.022-0.02123.1220.0000.0000.0000.0000.0000.000
11A512CYS00.0020.00426.523-0.004-0.0040.0000.0000.0000.000
12A513PRO00.0700.03529.3060.0020.0020.0000.0000.0000.000
13A514MET00.0040.03633.012-0.001-0.0010.0000.0000.0000.000
14A515SER00.0160.01835.153-0.001-0.0010.0000.0000.0000.000
15A516PRO00.0470.01837.8320.0010.0010.0000.0000.0000.000
16A517GLU-1-0.802-0.90941.0610.0030.0030.0000.0000.0000.000
17A518PHE00.025-0.00436.6190.0010.0010.0000.0000.0000.000
18A519TYR0-0.039-0.02637.7200.0010.0010.0000.0000.0000.000
19A520ARG10.9270.94739.525-0.004-0.0040.0000.0000.0000.000
20A521GLU-1-0.818-0.89841.5450.0070.0070.0000.0000.0000.000
21A522TYR0-0.0170.00035.4820.0020.0020.0000.0000.0000.000
22A523VAL0-0.0120.00439.7740.0010.0010.0000.0000.0000.000
23A524ALA00.0120.00442.0660.0010.0010.0000.0000.0000.000
24A525ILE00.0110.02041.5550.0000.0000.0000.0000.0000.000
25A526LYS10.8840.93341.669-0.012-0.0120.0000.0000.0000.000
26A527THR00.0120.02441.2830.0010.0010.0000.0000.0000.000
27A528LYS10.9040.94435.220-0.019-0.0190.0000.0000.0000.000
28A529LYS10.9400.96736.259-0.008-0.0080.0000.0000.0000.000
29A530ARG10.8010.89836.758-0.016-0.0160.0000.0000.0000.000
30A531ILE00.001-0.00331.3320.0000.0000.0000.0000.0000.000
31A532LEU00.0280.02232.7030.0000.0000.0000.0000.0000.000
32A533LEU0-0.0260.00734.241-0.001-0.0010.0000.0000.0000.000
33A534TYR0-0.014-0.02329.465-0.001-0.0010.0000.0000.0000.000
34A535THR0-0.046-0.01628.5170.0010.0010.0000.0000.0000.000
35A536MET0-0.020-0.01130.017-0.001-0.0010.0000.0000.0000.000
36A537ASN00.0020.00931.698-0.003-0.0030.0000.0000.0000.000
37A538PRO00.0660.02831.9440.0000.0000.0000.0000.0000.000
38A539ASN0-0.036-0.03831.767-0.003-0.0030.0000.0000.0000.000
39A540LYS10.7740.88426.676-0.018-0.0180.0000.0000.0000.000
40A541PHE00.0110.00327.565-0.002-0.0020.0000.0000.0000.000
41A542ARG10.9290.95928.3730.0070.0070.0000.0000.0000.000
42A543ALA00.0460.03225.425-0.003-0.0030.0000.0000.0000.000
43A544CYS0-0.040-0.01623.750-0.004-0.0040.0000.0000.0000.000
44A545GLN00.0610.03824.068-0.003-0.0030.0000.0000.0000.000
45A546PHE00.0330.01323.962-0.004-0.0040.0000.0000.0000.000
46A547LEU0-0.014-0.01419.993-0.007-0.0070.0000.0000.0000.000
47A548ILE0-0.015-0.00320.895-0.009-0.0090.0000.0000.0000.000
48A549LYS10.9730.99521.6770.0200.0200.0000.0000.0000.000
49A550PHE0-0.0050.00218.509-0.009-0.0090.0000.0000.0000.000
50A551HIS10.8070.85915.7360.0800.0800.0000.0000.0000.000
51A552GLU-1-0.769-0.84918.270-0.051-0.0510.0000.0000.0000.000
52A553ARG10.8610.94520.3850.0510.0510.0000.0000.0000.000
53A554ARG10.8340.92813.7160.1640.1640.0000.0000.0000.000
54A555ASN0-0.007-0.01016.719-0.014-0.0140.0000.0000.0000.000
55A556ASP-1-0.837-0.89513.746-0.193-0.1930.0000.0000.0000.000
56A557LYS10.8690.95112.9700.0650.0650.0000.0000.0000.000
57A558ILE0-0.027-0.02013.904-0.001-0.0010.0000.0000.0000.000
58A559ILE00.0360.01214.1000.0040.0040.0000.0000.0000.000
59A560VAL0-0.008-0.00417.1500.0020.0020.0000.0000.0000.000
60A561PHE0-0.010-0.01418.6050.0020.0020.0000.0000.0000.000
61A562ALA00.008-0.00420.430-0.001-0.0010.0000.0000.0000.000
62A563ASP-1-0.881-0.94624.0490.0290.0290.0000.0000.0000.000
63A564ASN00.0570.03025.336-0.002-0.0020.0000.0000.0000.000
64A565VAL00.0570.01528.796-0.002-0.0020.0000.0000.0000.000
65A566PHE00.0270.02330.327-0.002-0.0020.0000.0000.0000.000
66A567ALA00.040-0.00328.799-0.002-0.0020.0000.0000.0000.000
67A568LEU0-0.045-0.01725.033-0.002-0.0020.0000.0000.0000.000
68A569LYS10.9480.97727.996-0.006-0.0060.0000.0000.0000.000
69A570GLU-1-0.806-0.89530.925-0.001-0.0010.0000.0000.0000.000
70A571TYR0-0.022-0.04426.689-0.002-0.0020.0000.0000.0000.000
71A572ALA0-0.0070.01226.947-0.002-0.0020.0000.0000.0000.000
72A573ILE0-0.002-0.00228.198-0.002-0.0020.0000.0000.0000.000
73A574ARG10.8660.95431.7080.0020.0020.0000.0000.0000.000
74A575LEU0-0.051-0.02326.280-0.002-0.0020.0000.0000.0000.000
75A576ASN0-0.018-0.00128.415-0.002-0.0020.0000.0000.0000.000
76A577LYS10.8080.90023.9170.0250.0250.0000.0000.0000.000
77A578PRO00.0260.01624.0650.0030.0030.0000.0000.0000.000
78A579TYR00.012-0.00824.5090.0010.0010.0000.0000.0000.000
79A580ILE0-0.021-0.00121.2380.0000.0000.0000.0000.0000.000
80A581TYR00.011-0.03024.5940.0020.0020.0000.0000.0000.000
81A582GLY00.0310.01426.549-0.001-0.0010.0000.0000.0000.000
82A583PRO0-0.020-0.02028.4250.0000.0000.0000.0000.0000.000
83A584THR0-0.0200.02626.707-0.001-0.0010.0000.0000.0000.000
84A585SER00.0780.04428.4650.0010.0010.0000.0000.0000.000
85A586GLN00.0500.00025.3890.0000.0000.0000.0000.0000.000
86A587GLY00.0340.02526.2970.0000.0000.0000.0000.0000.000
87A588GLU-1-0.894-0.95227.262-0.002-0.0020.0000.0000.0000.000
88A589ARG10.8890.94022.640-0.014-0.0140.0000.0000.0000.000
89A590MET00.0160.00420.902-0.001-0.0010.0000.0000.0000.000
90A591GLN00.0080.01422.794-0.003-0.0030.0000.0000.0000.000
91A592ILE00.0100.00721.822-0.003-0.0030.0000.0000.0000.000
92A593LEU0-0.013-0.00317.728-0.003-0.0030.0000.0000.0000.000
93A594GLN00.001-0.01118.636-0.005-0.0050.0000.0000.0000.000
94A595ASN00.019-0.00420.154-0.007-0.0070.0000.0000.0000.000
95A596PHE0-0.0170.00214.389-0.006-0.0060.0000.0000.0000.000
96A597LYS10.8820.94114.130-0.010-0.0100.0000.0000.0000.000
97A598HIS00.013-0.00316.248-0.012-0.0120.0000.0000.0000.000
98A599ASN0-0.0030.01418.969-0.008-0.0080.0000.0000.0000.000
99A600PRO00.017-0.00219.9430.0010.0010.0000.0000.0000.000
100A601LYS10.9390.97021.0020.0350.0350.0000.0000.0000.000
101A602ILE0-0.051-0.01721.6980.0030.0030.0000.0000.0000.000
102A603ASN00.0610.02917.8780.0050.0050.0000.0000.0000.000
103A604THR00.014-0.02418.013-0.003-0.0030.0000.0000.0000.000
104A605ILE0-0.040-0.00817.9000.0020.0020.0000.0000.0000.000
105A606PHE00.0060.00320.3340.0020.0020.0000.0000.0000.000
106A607ILE0-0.017-0.01117.8710.0000.0000.0000.0000.0000.000
107A608SER00.014-0.04621.8590.0020.0020.0000.0000.0000.000
108A609LYS10.9270.96321.371-0.042-0.0420.0000.0000.0000.000
109A610VAL0-0.0110.00322.5980.0030.0030.0000.0000.0000.000
110A611GLY0-0.020-0.00419.1850.0000.0000.0000.0000.0000.000
111A612ASP-1-0.933-0.96716.9030.0610.0610.0000.0000.0000.000
112A613THR00.001-0.01317.6270.0010.0010.0000.0000.0000.000
113A614SER00.016-0.00618.776-0.001-0.0010.0000.0000.0000.000
114A615PHE00.0250.02818.273-0.004-0.0040.0000.0000.0000.000
115A616ASP-1-0.910-0.97314.9220.0280.0280.0000.0000.0000.000
116A617LEU0-0.065-0.02613.158-0.003-0.0030.0000.0000.0000.000
117A618PRO0-0.0110.01612.9410.0050.0050.0000.0000.0000.000
118A619GLU-1-0.910-0.9687.6120.1250.1250.0000.0000.0000.000
119A620ALA0-0.032-0.0249.903-0.029-0.0290.0000.0000.0000.000
120A621ASN0-0.0050.0058.5840.0360.0360.0000.0000.0000.000
121A622VAL00.006-0.00210.561-0.019-0.0190.0000.0000.0000.000
122A623LEU0-0.0150.00812.8390.0120.0120.0000.0000.0000.000
123A624ILE00.004-0.00314.5720.0000.0000.0000.0000.0000.000
124A625GLN0-0.012-0.00417.5460.0080.0080.0000.0000.0000.000
125A626ILE00.0390.02020.009-0.001-0.0010.0000.0000.0000.000
126A627SER00.0440.02523.405-0.002-0.0020.0000.0000.0000.000
127A628SER0-0.0320.00822.9070.0070.0070.0000.0000.0000.000
128A629HIS10.9040.94224.181-0.040-0.0400.0000.0000.0000.000
129A630GLY00.0090.03925.2830.0050.0050.0000.0000.0000.000
130A631GLY00.1410.01925.632-0.003-0.0030.0000.0000.0000.000
131A632SER0-0.107-0.04021.6290.0060.0060.0000.0000.0000.000
132A633ARG10.9450.96919.428-0.061-0.0610.0000.0000.0000.000
133A634ARG10.9980.99816.803-0.105-0.1050.0000.0000.0000.000
134A635GLN00.0200.02116.4950.0070.0070.0000.0000.0000.000
135A636GLU-1-0.802-0.89616.2690.0690.0690.0000.0000.0000.000
136A637ALA00.0250.02012.6450.0030.0030.0000.0000.0000.000
137A638GLN00.0110.01411.5710.0210.0210.0000.0000.0000.000
138A639ARG10.8420.93211.687-0.049-0.0490.0000.0000.0000.000
139A640LEU00.0090.0028.9110.0000.0000.0000.0000.0000.000
140A641GLY00.0080.0037.4870.0200.0200.0000.0000.0000.000
141A642ARG10.8900.9447.066-0.031-0.0310.0000.0000.0000.000
142A643VAL0-0.0090.0068.9010.0030.0030.0000.0000.0000.000
143A644LEU0-0.0220.0037.515-0.013-0.0130.0000.0000.0000.000
144A645ARG10.8650.9393.594-0.458-0.1050.006-0.045-0.3140.000
145A646ALA00.001-0.0063.806-0.494-0.1480.004-0.106-0.2440.000
146A647LYS10.8720.9595.3310.2890.404-0.001-0.004-0.1090.000
147A648LYS10.8990.9848.1730.0110.0110.0000.0000.0000.000
148A649GLY00.054-0.0109.4540.0780.0780.0000.0000.0000.000
149A650MET0-0.020-0.0108.9810.1000.1000.0000.0000.0000.000
150A651VAL0-0.004-0.0115.313-0.140-0.1400.0000.0000.0000.000
151A652ALA00.0030.0037.4110.0150.0150.0000.0000.0000.000
152A653GLU-1-0.913-0.9489.870-0.202-0.2020.0000.0000.0000.000
153A654GLU-1-0.907-0.9428.568-0.208-0.2080.0000.0000.0000.000
154A655TYR0-0.010-0.0308.7300.0070.0070.0000.0000.0000.000
155A656ASN00.0100.0224.2470.3440.436-0.001-0.035-0.0560.000
156A657ALA00.0300.0077.4570.0270.0270.0000.0000.0000.000
157A658PHE0-0.033-0.0129.4480.0340.0340.0000.0000.0000.000
158A659PHE00.0630.02912.0870.0110.0110.0000.0000.0000.000
159A660TYR00.0430.03813.617-0.009-0.0090.0000.0000.0000.000
160A661SER00.0050.00317.3650.0050.0050.0000.0000.0000.000
161A662LEU0-0.026-0.00919.867-0.002-0.0020.0000.0000.0000.000
162A663VAL0-0.023-0.00823.4270.0020.0020.0000.0000.0000.000
163A664SER0-0.009-0.02926.014-0.004-0.0040.0000.0000.0000.000
164A665GLN00.007-0.01129.7710.0020.0020.0000.0000.0000.000
165A666ASP-1-0.896-0.94131.5490.0120.0120.0000.0000.0000.000
166A667THR0-0.022-0.02831.4220.0000.0000.0000.0000.0000.000
167A668GLN00.026-0.00331.3310.0030.0030.0000.0000.0000.000
168A669GLU-1-0.770-0.88127.1420.0250.0250.0000.0000.0000.000
169A670MET00.0330.02727.0330.0030.0030.0000.0000.0000.000
170A671ALA00.0040.02127.3510.0030.0030.0000.0000.0000.000
171A672TYR0-0.115-0.05924.5730.0050.0050.0000.0000.0000.000
172A673SER00.024-0.05123.0180.0050.0050.0000.0000.0000.000
173A674THR00.0130.01222.4780.0050.0050.0000.0000.0000.000
174A675LYS10.8780.94122.874-0.047-0.0470.0000.0000.0000.000
175A676ARG10.7940.84317.959-0.048-0.0480.0000.0000.0000.000
176A677GLN00.0180.02918.0820.0060.0060.0000.0000.0000.000
177A678ARG10.9600.97817.938-0.062-0.0620.0000.0000.0000.000
178A679PHE00.008-0.00615.7510.0090.0090.0000.0000.0000.000
179A680LEU00.017-0.00912.7300.0150.0150.0000.0000.0000.000
180A681VAL0-0.0110.00713.0970.0270.0270.0000.0000.0000.000
181A682ASP-1-0.878-0.92914.1870.1480.1480.0000.0000.0000.000
182A683GLN0-0.162-0.08211.8140.0000.0000.0000.0000.0000.000
183A684GLY00.0100.00810.3400.0460.0460.0000.0000.0000.000
184A685TYR0-0.058-0.0316.9050.0460.0460.0000.0000.0000.000
185A686SER00.0110.01010.446-0.032-0.0320.0000.0000.0000.000
186A687PHE00.006-0.00812.466-0.015-0.0150.0000.0000.0000.000
187A688LYS10.9490.98315.4090.0050.0050.0000.0000.0000.000
188A689VAL00.0290.01618.6440.0000.0000.0000.0000.0000.000
189A690ILE0-0.036-0.01719.291-0.005-0.0050.0000.0000.0000.000
190A691THR00.0230.00223.2220.0000.0000.0000.0000.0000.000
191A692LYS10.9960.98326.5090.0020.0020.0000.0000.0000.000
192A693LEU0-0.044-0.00822.358-0.001-0.0010.0000.0000.0000.000
193A694ALA0-0.001-0.01025.0420.0000.0000.0000.0000.0000.000
194A695GLY00.1180.05626.520-0.004-0.0040.0000.0000.0000.000
195A696MET0-0.045-0.02427.660-0.001-0.0010.0000.0000.0000.000
196A697GLU-1-0.979-0.99229.750-0.012-0.0120.0000.0000.0000.000
197A698GLU-1-0.967-0.96529.801-0.033-0.0330.0000.0000.0000.000
198A699GLU-1-0.914-0.95728.013-0.040-0.0400.0000.0000.0000.000
199A700ASP-1-0.928-0.94631.626-0.015-0.0150.0000.0000.0000.000
200A701LEU0-0.091-0.05929.3050.0000.0000.0000.0000.0000.000
201A702ALA00.011-0.00832.6120.0010.0010.0000.0000.0000.000
202A703PHE0-0.027-0.02633.3030.0010.0010.0000.0000.0000.000
203A704SER00.0350.03036.9740.0010.0010.0000.0000.0000.000
204A705THR00.0280.01738.5670.0010.0010.0000.0000.0000.000
205A706LYS10.9030.92840.9270.0000.0000.0000.0000.0000.000
206A707GLU-1-0.889-0.93643.202-0.003-0.0030.0000.0000.0000.000
207A708GLU-1-0.823-0.91539.581-0.007-0.0070.0000.0000.0000.000
208A709GLN0-0.061-0.04438.0120.0020.0020.0000.0000.0000.000
209A710GLN0-0.009-0.01240.0520.0010.0010.0000.0000.0000.000
210A711GLN00.0180.00641.7080.0010.0010.0000.0000.0000.000
211A712LEU0-0.053-0.01234.8690.0010.0010.0000.0000.0000.000
212A713LEU0-0.017-0.01139.3930.0010.0010.0000.0000.0000.000
213A714GLN00.0150.01340.8860.0010.0010.0000.0000.0000.000
214A715LYS10.9010.95437.9150.0000.0000.0000.0000.0000.000
215A716VAL0-0.026-0.02136.5840.0010.0010.0000.0000.0000.000
216A717LEU0-0.018-0.01439.3190.0010.0010.0000.0000.0000.000
217A718ALA0-0.0110.01242.6360.0000.0000.0000.0000.0000.000
218A719ALA0-0.0050.02638.7590.0000.0000.0000.0000.0000.000
219A720THR0-0.017-0.02640.1990.0000.0000.0000.0000.0000.000
220A721ASP-1-0.792-0.93639.0200.0130.0130.0000.0000.0000.000
221A722LEU00.0260.01837.4860.0010.0010.0000.0000.0000.000
222A723ASP-1-0.852-0.91035.9830.0100.0100.0000.0000.0000.000
223A724ALA0-0.057-0.03434.0150.0000.0000.0000.0000.0000.000
224A725GLU-1-0.933-0.96833.0730.0190.0190.0000.0000.0000.000
225A726GLU-1-0.947-0.96926.6680.0330.0330.0000.0000.0000.000
226A727GLU-1-0.758-0.86026.9680.0180.0180.0000.0000.0000.000
227A728VAL0-0.0120.00527.9240.0030.0030.0000.0000.0000.000
228A729VAL0-0.007-0.02525.905-0.002-0.0020.0000.0000.0000.000
229A730ALA0-0.0100.01327.6940.0020.0020.0000.0000.0000.000