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: 5JNKZ

Calculation Name: 2VZN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VZN

Chain ID: A

ChEMBL ID:

UniProt ID: P35778

Base Structure: X-ray

Registration Date: 2023-09-22

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2633477.630527
FMO2-HF: Nuclear repulsion 2544463.393707
FMO2-HF: Total energy -89014.23682
FMO2-MP2: Total energy -89266.214351


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:2:ASN)


Summations of interaction energy for fragment #1(A:2:ASN)
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.
-21.647-19.7379.093-5.308-5.693-0.04
Interaction energy analysis for fragmet #1(A:2:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.021
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].
3A4CYS0-0.104-0.0313.273-1.1161.6880.067-1.262-1.6090.005
4A5ASN00.0160.0023.413-0.3110.4550.006-0.262-0.5090.000
5A6LEU00.0250.0264.2620.6890.968-0.001-0.047-0.2310.000
6A7GLN00.0330.0057.3810.3860.3860.0000.0000.0000.000
7A8SER0-0.024-0.02410.1660.2640.2640.0000.0000.0000.000
8A9CYS0-0.0060.0058.863-0.211-0.2110.0000.0000.0000.000
9A10LYS10.9380.9657.8760.9550.9550.0000.0000.0000.000
10A11ARG10.9200.96212.2170.9150.9150.0000.0000.0000.000
11A12ASN0-0.038-0.01414.6670.0930.0930.0000.0000.0000.000
12A13ASN0-0.019-0.00615.4180.0520.0520.0000.0000.0000.000
13A14ALA00.0040.01914.0460.0620.0620.0000.0000.0000.000
14A15ILE00.005-0.0029.160-0.114-0.1140.0000.0000.0000.000
15A16HIS00.0120.0006.3960.3850.3850.0000.0000.0000.000
16A17THR00.025-0.0099.3730.3510.3510.0000.0000.0000.000
17A18MET0-0.032-0.0255.8770.4350.4350.0000.0000.0000.000
18A20GLN00.0290.0167.5760.1280.1280.0000.0000.0000.000
19A21TYR00.0020.00610.9900.1260.1260.0000.0000.0000.000
20A22THR00.0530.0258.844-0.167-0.1670.0000.0000.0000.000
21A23SER00.005-0.00110.4540.0070.0070.0000.0000.0000.000
22A24PRO0-0.014-0.01312.853-0.097-0.0970.0000.0000.0000.000
23A25THR0-0.009-0.00114.246-0.027-0.0270.0000.0000.0000.000
24A26PRO00.001-0.00117.416-0.011-0.0110.0000.0000.0000.000
25A27GLY00.0270.02719.5840.0370.0370.0000.0000.0000.000
26A28PRO0-0.009-0.02320.860-0.005-0.0050.0000.0000.0000.000
27A29MET00.0240.01523.6110.0130.0130.0000.0000.0000.000
28A30CYS0-0.178-0.05919.4170.0210.0210.0000.0000.0000.000
29A31LEU00.0290.00825.3800.0120.0120.0000.0000.0000.000
30A32GLU-1-0.841-0.93228.773-0.090-0.0900.0000.0000.0000.000
31A33TYR0-0.0070.00923.562-0.010-0.0100.0000.0000.0000.000
32A34SER0-0.027-0.02126.7270.0130.0130.0000.0000.0000.000
33A35ASN0-0.027-0.05025.871-0.020-0.0200.0000.0000.0000.000
34A36VAL00.0230.02819.951-0.020-0.0200.0000.0000.0000.000
35A37GLY0-0.0050.01719.7310.0130.0130.0000.0000.0000.000
36A38PHE0-0.035-0.03519.7550.0080.0080.0000.0000.0000.000
37A39THR00.007-0.02022.2670.0000.0000.0000.0000.0000.000
38A40ASP-1-0.807-0.91821.768-0.301-0.3010.0000.0000.0000.000
39A41ALA00.0670.04124.205-0.012-0.0120.0000.0000.0000.000
40A42GLU-1-0.806-0.87425.192-0.233-0.2330.0000.0000.0000.000
41A43LYS10.7870.90019.4510.3210.3210.0000.0000.0000.000
42A44ASP-1-0.841-0.92422.974-0.288-0.2880.0000.0000.0000.000
43A45ALA0-0.062-0.01525.4880.0010.0010.0000.0000.0000.000
44A46ILE00.0360.01321.9540.0010.0010.0000.0000.0000.000
45A47VAL0-0.0180.00021.634-0.013-0.0130.0000.0000.0000.000
46A48ASN0-0.041-0.03524.2600.0110.0110.0000.0000.0000.000
47A49LYS10.8270.91127.7010.2300.2300.0000.0000.0000.000
48A50HIS00.0280.00923.565-0.014-0.0140.0000.0000.0000.000
49A51ASN00.0440.02424.791-0.009-0.0090.0000.0000.0000.000
50A52GLU-1-0.845-0.89128.045-0.201-0.2010.0000.0000.0000.000
51A53LEU0-0.023-0.01029.2780.0160.0160.0000.0000.0000.000
52A54ARG10.8050.88923.6870.4050.4050.0000.0000.0000.000
53A55GLN00.011-0.00829.6160.0180.0180.0000.0000.0000.000
54A56ARG10.8250.91532.3070.1940.1940.0000.0000.0000.000
55A57VAL00.0460.02932.1610.0130.0130.0000.0000.0000.000
56A58ALA00.0400.02031.6200.0100.0100.0000.0000.0000.000
57A59SER0-0.086-0.04833.6680.0140.0140.0000.0000.0000.000
58A60GLY0-0.009-0.00136.7970.0100.0100.0000.0000.0000.000
59A61LYS10.9030.94938.0830.1650.1650.0000.0000.0000.000
60A62GLU-1-0.737-0.80835.925-0.174-0.1740.0000.0000.0000.000
61A63MET00.0320.00238.5120.0000.0000.0000.0000.0000.000
62A64ARG10.8210.89436.3490.1850.1850.0000.0000.0000.000
63A65GLY00.1290.06338.869-0.008-0.0080.0000.0000.0000.000
64A66THR0-0.050-0.02438.9410.0120.0120.0000.0000.0000.000
65A67ASN0-0.089-0.04440.8340.0050.0050.0000.0000.0000.000
66A68GLY00.0160.01842.4920.0040.0040.0000.0000.0000.000
67A69PRO0-0.026-0.00540.974-0.007-0.0070.0000.0000.0000.000
68A70GLN00.0240.00935.453-0.013-0.0130.0000.0000.0000.000
69A71PRO0-0.0040.01336.7140.0050.0050.0000.0000.0000.000
70A72PRO00.0420.02336.271-0.011-0.0110.0000.0000.0000.000
71A73ALA0-0.0170.00231.636-0.003-0.0030.0000.0000.0000.000
72A74VAL0-0.108-0.04933.0090.0090.0090.0000.0000.0000.000
73A75LYS10.8010.87728.3590.2140.2140.0000.0000.0000.000
74A76MET00.0170.00927.576-0.018-0.0180.0000.0000.0000.000
75A77PRO0-0.0480.01423.5050.0170.0170.0000.0000.0000.000
76A78ASN00.0280.00224.946-0.025-0.0250.0000.0000.0000.000
77A79LEU0-0.016-0.00320.565-0.020-0.0200.0000.0000.0000.000
78A80THR00.0240.00919.3200.0280.0280.0000.0000.0000.000
79A81TRP00.0840.02916.476-0.067-0.0670.0000.0000.0000.000
80A82ASP-1-0.781-0.87111.732-1.359-1.3590.0000.0000.0000.000
81A83PRO00.0390.01511.850-0.055-0.0550.0000.0000.0000.000
82A84GLU-1-0.744-0.8215.246-4.947-4.9470.0000.0000.0000.000
83A85LEU0-0.021-0.0109.390-0.090-0.0900.0000.0000.0000.000
84A86ALA00.0490.02311.3880.0780.0780.0000.0000.0000.000
85A87THR0-0.065-0.0369.8490.0040.0040.0000.0000.0000.000
86A88ILE00.0000.0006.5130.1510.1510.0000.0000.0000.000
87A89ALA0-0.0150.00510.3140.1880.1880.0000.0000.0000.000
88A90GLN0-0.022-0.03514.0450.1070.1070.0000.0000.0000.000
89A91ARG10.8250.9079.8020.4660.4660.0000.0000.0000.000
90A92TRP00.0220.01213.8310.0750.0750.0000.0000.0000.000
91A93ALA00.0360.02115.3130.0830.0830.0000.0000.0000.000
92A94ASN0-0.009-0.01516.7720.0510.0510.0000.0000.0000.000
93A95GLN00.0090.00015.6140.1110.1110.0000.0000.0000.000
94A97THR00.0540.04320.1370.0270.0270.0000.0000.0000.000
95A98PHE0-0.063-0.02421.706-0.043-0.0430.0000.0000.0000.000
96A99GLU-1-0.898-0.94820.760-0.285-0.2850.0000.0000.0000.000
97A100HIS0-0.038-0.03918.4030.0020.0020.0000.0000.0000.000
98A101ASP-1-0.730-0.81713.262-0.977-0.9770.0000.0000.0000.000
99A102ALA00.0190.00314.938-0.045-0.0450.0000.0000.0000.000
100A103CYS0-0.070-0.02111.314-0.169-0.1690.0000.0000.0000.000
101A104ARG10.8590.9269.6150.9120.9120.0000.0000.0000.000
102A105ASN0-0.021-0.0149.023-0.202-0.2020.0000.0000.0000.000
103A106VAL00.0270.0185.902-0.724-0.7240.0000.0000.0000.000
104A107GLU-1-0.836-0.9301.841-22.096-24.0359.021-3.737-3.344-0.045
105A108ARG10.7350.8396.2102.8052.8050.0000.0000.0000.000
106A109PHE0-0.004-0.0119.3350.4050.4050.0000.0000.0000.000
107A110ALA00.0010.00810.523-0.303-0.3030.0000.0000.0000.000
108A111VAL0-0.013-0.01110.3360.0800.0800.0000.0000.0000.000
109A112GLY00.0440.03813.4120.0440.0440.0000.0000.0000.000
110A113GLN0-0.022-0.04315.253-0.016-0.0160.0000.0000.0000.000
111A114ASN00.0210.03218.0820.0330.0330.0000.0000.0000.000
112A115ILE00.0170.01119.214-0.037-0.0370.0000.0000.0000.000
113A116ALA00.0050.01722.6320.0330.0330.0000.0000.0000.000
114A117ALA00.0430.00825.043-0.012-0.0120.0000.0000.0000.000
115A118THR0-0.0190.01127.6220.0150.0150.0000.0000.0000.000
116A119SER0-0.022-0.04330.710-0.009-0.0090.0000.0000.0000.000
117A120SER0-0.0100.00333.3610.0060.0060.0000.0000.0000.000
118A121SER00.0310.01136.2750.0000.0000.0000.0000.0000.000
119A122GLY00.0280.01037.0090.0080.0080.0000.0000.0000.000
120A123LYS10.9020.94134.0800.0810.0810.0000.0000.0000.000
121A124ASN00.0270.00931.7810.0030.0030.0000.0000.0000.000
122A125LYS10.8870.93233.4220.1340.1340.0000.0000.0000.000
123A126SER00.0530.05231.6560.0040.0040.0000.0000.0000.000
124A127THR0-0.041-0.07029.985-0.011-0.0110.0000.0000.0000.000
125A128PRO00.041-0.00525.355-0.003-0.0030.0000.0000.0000.000
126A129ASN00.0180.01027.438-0.026-0.0260.0000.0000.0000.000
127A130GLU-1-0.787-0.85629.988-0.190-0.1900.0000.0000.0000.000
128A131MET0-0.0050.00827.154-0.002-0.0020.0000.0000.0000.000
129A132ILE00.0210.01624.938-0.008-0.0080.0000.0000.0000.000
130A133LEU0-0.015-0.01628.0140.0010.0010.0000.0000.0000.000
131A134LEU0-0.051-0.02630.8930.0090.0090.0000.0000.0000.000
132A135TRP00.008-0.01522.467-0.005-0.0050.0000.0000.0000.000
133A136TYR0-0.003-0.03529.0340.0040.0040.0000.0000.0000.000
134A137ASN0-0.033-0.03230.8910.0200.0200.0000.0000.0000.000
135A138GLU-1-0.726-0.84729.228-0.287-0.2870.0000.0000.0000.000
136A139VAL0-0.052-0.02533.2850.0070.0070.0000.0000.0000.000
137A140LYS10.8600.92634.8870.1700.1700.0000.0000.0000.000
138A141ASP-1-0.818-0.89335.462-0.174-0.1740.0000.0000.0000.000
139A142PHE0-0.026-0.00131.627-0.001-0.0010.0000.0000.0000.000
140A143ASP-1-0.735-0.83235.645-0.149-0.1490.0000.0000.0000.000
141A144ASN00.036-0.00536.074-0.018-0.0180.0000.0000.0000.000
142A145ARG10.7930.85136.8520.1450.1450.0000.0000.0000.000
143A146TRP00.0350.01132.600-0.006-0.0060.0000.0000.0000.000
144A147ILE0-0.0180.00132.003-0.016-0.0160.0000.0000.0000.000
145A148SER0-0.011-0.00931.320-0.012-0.0120.0000.0000.0000.000
146A149SER0-0.041-0.02730.3790.0020.0020.0000.0000.0000.000
147A150PHE00.0270.01326.9670.0100.0100.0000.0000.0000.000
148A151PRO00.0350.01029.406-0.004-0.0040.0000.0000.0000.000
149A152SER0-0.015-0.01428.914-0.013-0.0130.0000.0000.0000.000
150A153ASP-1-0.840-0.90029.902-0.210-0.2100.0000.0000.0000.000
151A154ASP-1-0.828-0.92827.502-0.305-0.3050.0000.0000.0000.000
152A155ASN0-0.052-0.04029.774-0.001-0.0010.0000.0000.0000.000
153A156ILE0-0.042-0.01231.2090.0040.0040.0000.0000.0000.000
154A157LEU0-0.026-0.00924.158-0.010-0.0100.0000.0000.0000.000
155A158MET0-0.009-0.02028.073-0.010-0.0100.0000.0000.0000.000
156A159LYS10.8490.93329.5750.1950.1950.0000.0000.0000.000
157A160VAL0-0.052-0.02330.1710.0080.0080.0000.0000.0000.000
158A161GLY00.0830.05626.222-0.009-0.0090.0000.0000.0000.000
159A162HIS0-0.047-0.01923.716-0.062-0.0620.0000.0000.0000.000
160A163TYR0-0.022-0.01925.955-0.017-0.0170.0000.0000.0000.000
161A164THR0-0.028-0.04026.1760.0010.0010.0000.0000.0000.000
162A165GLN00.0180.00719.747-0.061-0.0610.0000.0000.0000.000
163A166ILE0-0.029-0.00423.457-0.020-0.0200.0000.0000.0000.000
164A167VAL0-0.032-0.01425.397-0.001-0.0010.0000.0000.0000.000
165A168TRP00.0490.06121.6370.0220.0220.0000.0000.0000.000
166A169ALA0-0.002-0.00723.651-0.028-0.0280.0000.0000.0000.000
167A170LYS10.9130.94920.9420.3510.3510.0000.0000.0000.000
168A171THR0-0.0030.00618.381-0.014-0.0140.0000.0000.0000.000
169A172THR0-0.013-0.02318.0990.0490.0490.0000.0000.0000.000
170A173LYS10.8330.92014.5860.6420.6420.0000.0000.0000.000
171A174ILE00.0370.01817.093-0.024-0.0240.0000.0000.0000.000
172A175GLY00.0100.00814.8460.0170.0170.0000.0000.0000.000
173A176CYS0-0.103-0.03815.760-0.050-0.0500.0000.0000.0000.000
174A177GLY00.0340.00917.081-0.011-0.0110.0000.0000.0000.000
175A178ARG10.8200.88717.9270.2860.2860.0000.0000.0000.000
176A179ILE0-0.0050.01821.2210.0090.0090.0000.0000.0000.000
177A180MET00.0050.02823.270-0.001-0.0010.0000.0000.0000.000
178A181PHE00.0070.00125.6980.0020.0020.0000.0000.0000.000
179A182LYS10.7840.89828.5560.0850.0850.0000.0000.0000.000
180A183GLU-1-0.705-0.80630.617-0.168-0.1680.0000.0000.0000.000
181A184PRO00.021-0.01831.0850.0090.0090.0000.0000.0000.000
182A185ASP-1-0.838-0.89833.970-0.108-0.1080.0000.0000.0000.000
183A186ASN0-0.061-0.03135.5560.0080.0080.0000.0000.0000.000
184A187TRP00.0120.00835.316-0.002-0.0020.0000.0000.0000.000
185A188THR0-0.048-0.02431.554-0.002-0.0020.0000.0000.0000.000
186A189LYS10.8550.91327.7060.1850.1850.0000.0000.0000.000
187A190HIS0-0.059-0.03226.545-0.006-0.0060.0000.0000.0000.000
188A191TYR0-0.008-0.01220.733-0.010-0.0100.0000.0000.0000.000
189A192LEU00.0110.00021.500-0.008-0.0080.0000.0000.0000.000
190A193VAL00.0230.02316.8000.0000.0000.0000.0000.0000.000
191A195ASN00.0530.03012.0490.1220.1220.0000.0000.0000.000
192A196TYR0-0.031-0.04615.5240.0400.0400.0000.0000.0000.000
193A197GLY00.0360.02714.220-0.116-0.1160.0000.0000.0000.000
194A198PRO0-0.018-0.02014.8100.0860.0860.0000.0000.0000.000
195A199ALA00.004-0.00215.7010.0780.0780.0000.0000.0000.000
196A200GLY00.009-0.00317.3930.0510.0510.0000.0000.0000.000
197A201ASN0-0.032-0.02120.806-0.008-0.0080.0000.0000.0000.000
198A202VAL0-0.0240.00120.2590.0030.0030.0000.0000.0000.000
199A203LEU00.0310.00622.9330.0340.0340.0000.0000.0000.000
200A204GLY00.0090.01825.9520.0000.0000.0000.0000.0000.000
201A205ALA0-0.040-0.01824.9710.0190.0190.0000.0000.0000.000
202A206PRO0-0.039-0.01226.9670.0020.0020.0000.0000.0000.000
203A207ILE0-0.0090.01326.874-0.024-0.0240.0000.0000.0000.000
204A208TYR0-0.024-0.04727.050-0.023-0.0230.0000.0000.0000.000
205A209GLU-1-0.816-0.88729.409-0.199-0.1990.0000.0000.0000.000
206A210ILE00.0480.02531.7660.0090.0090.0000.0000.0000.000
207A211LYS10.9520.97835.2750.1650.1650.0000.0000.0000.000
208A212LYS10.8690.92237.4400.1540.1540.0000.0000.0000.000
209A213HIS00.0590.02641.2680.0000.0000.0000.0000.0000.000
210A214HIS00.0210.00744.0240.0020.0020.0000.0000.0000.000
211A215HIS00.0300.00646.2740.0030.0030.0000.0000.0000.000
212A216HIS00.0270.00349.5050.0040.0040.0000.0000.0000.000
213A217HIS0-0.058-0.00946.7380.0000.0000.0000.0000.0000.000
214A218HIS0-0.0130.00749.918-0.001-0.0010.0000.0000.0000.000