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: 5272Z

Calculation Name: 4AB5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4AB5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9JXG8

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2546092.545185
FMO2-HF: Nuclear repulsion 2460427.09683
FMO2-HF: Total energy -85665.448355
FMO2-MP2: Total energy -85913.171267


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:92:GLY)


Summations of interaction energy for fragment #1(A:92: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.
-6.536-2.8497.321-6.37-4.637-0.034
Interaction energy analysis for fragmet #1(A:92:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / 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].
3A94ALA0-0.061-0.0343.854-0.7720.333-0.007-0.522-0.5740.001
4A95GLY00.0210.0174.0911.0531.171-0.001-0.022-0.0950.000
5A96GLU-1-0.926-0.9624.003-2.417-2.2150.001-0.041-0.1610.000
6A97LEU0-0.047-0.0276.5550.3000.3000.0000.0000.0000.000
7A98ARG10.8430.9219.6240.9680.9680.0000.0000.0000.000
8A99ILE00.000-0.02211.6450.0530.0530.0000.0000.0000.000
9A100ALA00.0080.01614.8810.0180.0180.0000.0000.0000.000
10A101VAL0-0.011-0.01918.1070.0200.0200.0000.0000.0000.000
11A102GLU-1-0.764-0.87221.003-0.189-0.1890.0000.0000.0000.000
12A103CYS0-0.0240.00523.2810.0220.0220.0000.0000.0000.000
13A104HIS00.027-0.01524.803-0.005-0.0050.0000.0000.0000.000
14A105THR0-0.018-0.01426.195-0.001-0.0010.0000.0000.0000.000
15A107PHE00.0290.01019.7540.0000.0000.0000.0000.0000.000
16A108ASP-1-0.905-0.94822.485-0.048-0.0480.0000.0000.0000.000
17A109TRP00.0310.00921.4420.0050.0050.0000.0000.0000.000
18A110LEU0-0.031-0.01517.9960.0030.0030.0000.0000.0000.000
19A111MET0-0.0060.00317.395-0.007-0.0070.0000.0000.0000.000
20A112PRO0-0.015-0.01617.7360.0120.0120.0000.0000.0000.000
21A113ALA00.0190.02318.1830.0170.0170.0000.0000.0000.000
22A114MET0-0.002-0.00612.5260.0090.0090.0000.0000.0000.000
23A115GLY0-0.064-0.03513.3280.0290.0290.0000.0000.0000.000
24A116GLU-1-0.890-0.94115.3280.0490.0490.0000.0000.0000.000
25A117PHE00.0280.0078.9110.0430.0430.0000.0000.0000.000
26A118ARG10.9830.9878.870-0.040-0.0400.0000.0000.0000.000
27A119PRO0-0.038-0.0199.4430.0960.0960.0000.0000.0000.000
28A120MET0-0.0150.00111.4080.0770.0770.0000.0000.0000.000
29A121TRP0-0.040-0.0258.166-0.029-0.0290.0000.0000.0000.000
30A122PRO0-0.009-0.0106.562-0.066-0.0660.0000.0000.0000.000
31A123GLN0-0.058-0.0322.6774.3295.7001.308-1.084-1.596-0.003
32A124VAL0-0.0160.0102.778-2.743-2.3990.923-0.630-0.637-0.008
33A125GLU-1-0.911-0.9521.945-6.079-5.5165.098-4.052-1.610-0.024
34A126LEU0-0.074-0.0404.552-0.020-0.036-0.001-0.0190.0360.000
35A127ASP-1-0.863-0.9358.361-0.539-0.5390.0000.0000.0000.000
36A128ILE0-0.068-0.02511.0140.0370.0370.0000.0000.0000.000
37A129VAL0-0.017-0.00514.3650.0040.0040.0000.0000.0000.000
38A130SER0-0.041-0.05116.7480.0260.0260.0000.0000.0000.000
39A131GLY00.0090.01220.267-0.003-0.0030.0000.0000.0000.000
40A132PHE0-0.055-0.04019.4610.0030.0030.0000.0000.0000.000
41A133GLN0-0.077-0.03924.8530.0140.0140.0000.0000.0000.000
42A134ALA0-0.007-0.00726.2630.0100.0100.0000.0000.0000.000
43A135ASP-1-0.820-0.93025.611-0.178-0.1780.0000.0000.0000.000
44A136PRO0-0.006-0.00321.201-0.012-0.0120.0000.0000.0000.000
45A137VAL00.0340.02421.262-0.034-0.0340.0000.0000.0000.000
46A138GLY00.0140.00022.550-0.015-0.0150.0000.0000.0000.000
47A139LEU0-0.007-0.01718.543-0.013-0.0130.0000.0000.0000.000
48A140LEU0-0.0040.02917.279-0.041-0.0410.0000.0000.0000.000
49A141LEU00.0000.00718.840-0.029-0.0290.0000.0000.0000.000
50A142GLN0-0.040-0.02320.462-0.015-0.0150.0000.0000.0000.000
51A143HIS0-0.0060.01315.566-0.055-0.0550.0000.0000.0000.000
52A144ARG10.8540.92314.8910.2370.2370.0000.0000.0000.000
53A145ALA00.0220.01214.158-0.016-0.0160.0000.0000.0000.000
54A146ASP-1-0.779-0.86510.939-0.871-0.8710.0000.0000.0000.000
55A147LEU00.009-0.00213.9540.0450.0450.0000.0000.0000.000
56A148ALA00.0010.01116.323-0.003-0.0030.0000.0000.0000.000
57A149ILE0-0.0240.00319.3500.0170.0170.0000.0000.0000.000
58A150VAL0-0.012-0.01121.9750.0030.0030.0000.0000.0000.000
59A151SER00.033-0.00325.4280.0050.0050.0000.0000.0000.000
60A152GLU-1-0.959-0.97828.688-0.094-0.0940.0000.0000.0000.000
61A153ALA0-0.027-0.00428.379-0.010-0.0100.0000.0000.0000.000
62A154GLU-1-0.940-0.96529.113-0.135-0.1350.0000.0000.0000.000
63A155LYS10.9330.95029.6430.0920.0920.0000.0000.0000.000
64A156GLN00.0970.04427.3750.0030.0030.0000.0000.0000.000
65A157ASN0-0.063-0.04128.2160.0010.0010.0000.0000.0000.000
66A158GLY00.0250.01224.906-0.006-0.0060.0000.0000.0000.000
67A159ILE0-0.0090.02621.831-0.027-0.0270.0000.0000.0000.000
68A160SER0-0.021-0.00621.7470.0210.0210.0000.0000.0000.000
69A161PHE00.0100.00122.824-0.013-0.0130.0000.0000.0000.000
70A162GLN00.0160.00320.9500.0270.0270.0000.0000.0000.000
71A163PRO00.0100.01324.550-0.004-0.0040.0000.0000.0000.000
72A164LEU0-0.026-0.00721.8610.0000.0000.0000.0000.0000.000
73A165PHE00.031-0.00625.0620.0090.0090.0000.0000.0000.000
74A166ALA0-0.0160.00729.358-0.006-0.0060.0000.0000.0000.000
75A167TYR00.0380.00629.0170.0070.0070.0000.0000.0000.000
76A168GLU-1-0.912-0.95134.415-0.043-0.0430.0000.0000.0000.000
77A169MET0-0.058-0.02434.6990.0000.0000.0000.0000.0000.000
78A170VAL00.0190.01337.5910.0020.0020.0000.0000.0000.000
79A171GLY00.0260.01139.940-0.002-0.0020.0000.0000.0000.000
80A172ILE0-0.035-0.01739.4150.0030.0030.0000.0000.0000.000
81A173CYS0-0.021-0.02143.030-0.001-0.0010.0000.0000.0000.000
82A174ALA00.0220.01546.0760.0010.0010.0000.0000.0000.000
83A175PRO00.0230.00047.477-0.001-0.0010.0000.0000.0000.000
84A176ASP-1-0.897-0.93550.202-0.015-0.0150.0000.0000.0000.000
85A177HIS0-0.111-0.04749.5600.0010.0010.0000.0000.0000.000
86A178PRO00.035-0.00952.0970.0000.0000.0000.0000.0000.000
87A179LEU00.0350.01848.7730.0010.0010.0000.0000.0000.000
88A180ALA00.0180.02250.630-0.001-0.0010.0000.0000.0000.000
89A181ALA0-0.022-0.00151.5780.0010.0010.0000.0000.0000.000
90A182LYS10.8060.90552.2410.0300.0300.0000.0000.0000.000
91A183ASN00.028-0.00251.0350.0000.0000.0000.0000.0000.000
92A184VAL0-0.011-0.00148.557-0.001-0.0010.0000.0000.0000.000
93A185TRP0-0.038-0.02744.7350.0000.0000.0000.0000.0000.000
94A186THR00.001-0.00947.956-0.002-0.0020.0000.0000.0000.000
95A187ALA00.0570.00847.4870.0000.0000.0000.0000.0000.000
96A188GLU-1-0.857-0.95048.477-0.039-0.0390.0000.0000.0000.000
97A189ASP-1-0.825-0.88250.078-0.031-0.0310.0000.0000.0000.000
98A190PHE0-0.011-0.02243.7980.0000.0000.0000.0000.0000.000
99A191ILE0-0.054-0.01248.438-0.001-0.0010.0000.0000.0000.000
100A192GLY0-0.015-0.00250.811-0.001-0.0010.0000.0000.0000.000
101A193GLU-1-0.887-0.95347.735-0.030-0.0300.0000.0000.0000.000
102A194THR0-0.029-0.00244.459-0.002-0.0020.0000.0000.0000.000
103A195LEU0-0.006-0.01340.6970.0010.0010.0000.0000.0000.000
104A196ILE0-0.045-0.04038.264-0.002-0.0020.0000.0000.0000.000
105A197THR0-0.015-0.00235.9810.0010.0010.0000.0000.0000.000
106A198TYR00.036-0.01131.0260.0020.0020.0000.0000.0000.000
107A199PRO0-0.076-0.03231.1170.0020.0020.0000.0000.0000.000
108A200VAL00.0370.02228.969-0.006-0.0060.0000.0000.0000.000
109A201PRO00.0100.00831.2050.0070.0070.0000.0000.0000.000
110A202ASP-1-0.768-0.91433.989-0.071-0.0710.0000.0000.0000.000
111A203GLU-1-0.955-0.96332.891-0.097-0.0970.0000.0000.0000.000
112A204MET0-0.033-0.01927.123-0.003-0.0030.0000.0000.0000.000
113A205LEU0-0.038-0.01631.7720.0030.0030.0000.0000.0000.000
114A206ASP-1-0.772-0.88033.775-0.082-0.0820.0000.0000.0000.000
115A207LEU0-0.0070.00636.0050.0020.0020.0000.0000.0000.000
116A208PRO00.003-0.02037.7410.0020.0020.0000.0000.0000.000
117A209LYS10.9811.01732.8970.1040.1040.0000.0000.0000.000
118A210LYS10.8560.92335.2980.0790.0790.0000.0000.0000.000
119A211ILE0-0.041-0.02040.4340.0040.0040.0000.0000.0000.000
120A212LEU0-0.045-0.02042.7490.0020.0020.0000.0000.0000.000
121A213ILE00.0400.02840.8310.0020.0020.0000.0000.0000.000
122A214PRO0-0.016-0.00242.8970.0020.0020.0000.0000.0000.000
123A215LYS10.8960.94745.8420.0450.0450.0000.0000.0000.000
124A216ASN0-0.058-0.02247.6380.0010.0010.0000.0000.0000.000
125A217ILE0-0.038-0.01346.9790.0020.0020.0000.0000.0000.000
126A218ASN00.0290.01644.410-0.003-0.0030.0000.0000.0000.000
127A219PRO00.0260.03744.4590.0010.0010.0000.0000.0000.000
128A220PRO00.0240.01845.206-0.003-0.0030.0000.0000.0000.000
129A221ARG10.8180.89240.3490.0590.0590.0000.0000.0000.000
130A222ARG10.9360.96740.8470.0400.0400.0000.0000.0000.000
131A223HIS00.0020.00235.7210.0000.0000.0000.0000.0000.000
132A224SER0-0.030-0.02834.9010.0040.0040.0000.0000.0000.000
133A225GLU-1-0.781-0.88828.667-0.094-0.0940.0000.0000.0000.000
134A226LEU0-0.029-0.00729.301-0.001-0.0010.0000.0000.0000.000
135A227THR00.1390.06230.7580.0010.0010.0000.0000.0000.000
136A228ILE00.0190.01132.5810.0030.0030.0000.0000.0000.000
137A229ALA0-0.0120.00534.8130.0030.0030.0000.0000.0000.000
138A230ILE00.0110.01034.3710.0020.0020.0000.0000.0000.000
139A231ILE00.0250.01536.3690.0020.0020.0000.0000.0000.000
140A232GLN00.0120.00739.2150.0030.0030.0000.0000.0000.000
141A233LEU0-0.037-0.00139.4220.0020.0020.0000.0000.0000.000
142A234VAL0-0.0020.01041.0550.0010.0010.0000.0000.0000.000
143A235ALA00.0340.01243.3260.0010.0010.0000.0000.0000.000
144A236SER0-0.072-0.03344.9380.0020.0020.0000.0000.0000.000
145A237ARG10.9010.94147.1200.0220.0220.0000.0000.0000.000
146A238ARG10.8420.92644.8330.0250.0250.0000.0000.0000.000
147A239GLY00.0310.01344.959-0.002-0.0020.0000.0000.0000.000
148A240ILE00.0040.01044.2290.0020.0020.0000.0000.0000.000
149A241ALA00.0140.00938.778-0.002-0.0020.0000.0000.0000.000
150A242ALA00.0050.00938.6350.0030.0030.0000.0000.0000.000
151A243LEU0-0.025-0.01833.858-0.003-0.0030.0000.0000.0000.000
152A244PRO00.0740.03631.5300.0020.0020.0000.0000.0000.000
153A245TYR0-0.018-0.00734.6860.0040.0040.0000.0000.0000.000
154A246TRP00.0310.00628.1740.0050.0050.0000.0000.0000.000
155A247THR0-0.0020.00131.4080.0020.0020.0000.0000.0000.000
156A248VAL0-0.012-0.01733.4510.0040.0040.0000.0000.0000.000
157A249MET00.0060.02136.0680.0020.0020.0000.0000.0000.000
158A250PRO00.0520.02334.1710.0030.0030.0000.0000.0000.000
159A251TYR0-0.036-0.04034.1260.0020.0020.0000.0000.0000.000
160A252LEU0-0.043-0.00639.7010.0010.0010.0000.0000.0000.000
161A253GLU-1-0.930-0.96139.183-0.008-0.0080.0000.0000.0000.000
162A254LYS10.8690.93637.9520.0090.0090.0000.0000.0000.000
163A255GLY00.0140.02043.3160.0010.0010.0000.0000.0000.000
164A256TYR0-0.053-0.02439.7800.0000.0000.0000.0000.0000.000
165A257VAL00.002-0.00741.203-0.001-0.0010.0000.0000.0000.000
166A258VAL0-0.0170.00244.5140.0020.0020.0000.0000.0000.000
167A259HIS00.0460.00942.395-0.003-0.0030.0000.0000.0000.000
168A260ARG10.8220.90544.2730.0270.0270.0000.0000.0000.000
169A261GLN00.0660.04944.228-0.002-0.0020.0000.0000.0000.000
170A262ILE0-0.0110.00140.9090.0010.0010.0000.0000.0000.000
171A263THR0-0.036-0.03044.358-0.001-0.0010.0000.0000.0000.000
172A264ALA0-0.020-0.02046.9790.0010.0010.0000.0000.0000.000
173A265ASP-1-0.895-0.93945.386-0.041-0.0410.0000.0000.0000.000
174A266GLY0-0.0220.00643.465-0.001-0.0010.0000.0000.0000.000
175A267LEU0-0.022-0.01337.525-0.002-0.0020.0000.0000.0000.000
176A268GLN00.0040.00835.779-0.002-0.0020.0000.0000.0000.000
177A269SER0-0.029-0.02631.980-0.002-0.0020.0000.0000.0000.000
178A270LYS10.9190.95131.6790.0770.0770.0000.0000.0000.000
179A271LEU00.0350.01825.393-0.005-0.0050.0000.0000.0000.000
180A272TYR00.0180.00325.5090.0090.0090.0000.0000.0000.000
181A273ALA00.0140.01719.978-0.006-0.0060.0000.0000.0000.000
182A274ALA0-0.004-0.00821.2180.0080.0080.0000.0000.0000.000
183A275ILE00.0430.01516.958-0.025-0.0250.0000.0000.0000.000
184A276ARG10.8590.92113.8310.5630.5630.0000.0000.0000.000
185A277THR0-0.035-0.04319.495-0.004-0.0040.0000.0000.0000.000
186A278GLU-1-0.900-0.96017.173-0.399-0.3990.0000.0000.0000.000
187A279ASP-1-0.850-0.92414.641-0.583-0.5830.0000.0000.0000.000
188A280THR0-0.046-0.02616.862-0.002-0.0020.0000.0000.0000.000
189A281ASP-1-0.892-0.94718.562-0.189-0.1890.0000.0000.0000.000
190A282LYS10.8380.94011.3000.7080.7080.0000.0000.0000.000
191A283SER00.021-0.00913.9770.0120.0120.0000.0000.0000.000
192A284TYR00.0390.0179.5100.0460.0460.0000.0000.0000.000
193A285LEU00.0190.02512.4820.0280.0280.0000.0000.0000.000
194A286ASN00.0160.00814.5330.0560.0560.0000.0000.0000.000
195A287ASN0-0.020-0.01914.7220.0360.0360.0000.0000.0000.000
196A288PHE00.0470.02113.9660.0260.0260.0000.0000.0000.000
197A289CYS0-0.036-0.01615.8880.0210.0210.0000.0000.0000.000
198A290GLN0-0.015-0.00219.1260.0030.0030.0000.0000.0000.000
199A291ILE00.0480.04615.4890.0110.0110.0000.0000.0000.000
200A292ILE0-0.018-0.01118.5300.0140.0140.0000.0000.0000.000
201A293ARG10.8190.91021.2180.1210.1210.0000.0000.0000.000
202A294GLU-1-0.957-0.97222.103-0.018-0.0180.0000.0000.0000.000
203A295ARG10.8870.94320.1240.0100.0100.0000.0000.0000.000
204A296GLY00.0270.01324.1860.0050.0050.0000.0000.0000.000
205A297PHE0-0.035-0.03526.5340.0040.0040.0000.0000.0000.000
206A298ALA0-0.045-0.00127.3840.0040.0040.0000.0000.0000.000
207A299ASP-1-0.972-0.97627.225-0.010-0.0100.0000.0000.0000.000
208A300LEU0-0.045-0.02127.393-0.001-0.0010.0000.0000.0000.000
209A301PRO0-0.019-0.00331.065-0.001-0.0010.0000.0000.0000.000
210A302GLY00.002-0.02434.717-0.003-0.0030.0000.0000.0000.000
211A303LEU0-0.049-0.00328.977-0.004-0.0040.0000.0000.0000.000
212A304SER0-0.043-0.02233.3900.0030.0030.0000.0000.0000.000
213A305GLU-1-0.909-0.96031.773-0.053-0.0530.0000.0000.0000.000
214A306LEU0-0.066-0.03129.5440.0010.0010.0000.0000.0000.000
215A307GLU-1-0.981-0.98431.484-0.068-0.0680.0000.0000.0000.000