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: ZYR4N

Calculation Name: 2ZW3-A-Xray320

Preferred Name: Gap junction beta-2 protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZW3

Chain ID: A

ChEMBL ID: CHEMBL4295738

UniProt ID: P29033

Base Structure: X-ray

Registration Date: 2021-09-07

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. 1.20200129
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 -2221292.887706
FMO2-HF: Nuclear repulsion 2138037.175498
FMO2-HF: Total energy -83255.712209
FMO2-MP2: Total energy -83493.952747


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:1:ACE )


Summations of interaction energy for fragment #1(A:1: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.
2.5593.791-0.003-0.556-0.673-0.001
Interaction energy analysis for fragmet #1(A:1:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.009
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].
3A3TRP 0-0.055-0.0223.7470.8112.043-0.003-0.556-0.673-0.001
4A4GLY 00.0450.0155.8010.2420.2420.0000.0000.0000.000
5A5THR 0-0.008-0.0207.0490.1750.1750.0000.0000.0000.000
6A6LEU 00.0570.0217.1160.2020.2020.0000.0000.0000.000
7A7GLN 00.0210.0148.8690.0690.0690.0000.0000.0000.000
8A8THR 00.0380.02012.5890.1280.1280.0000.0000.0000.000
9A9ILE 0-0.0090.02311.4970.0680.0680.0000.0000.0000.000
10A10LEU 0-0.035-0.01315.0940.0600.0600.0000.0000.0000.000
11A11GLY 00.0330.01416.2280.0480.0480.0000.0000.0000.000
12A12GLY 0-0.042-0.02517.5430.0410.0410.0000.0000.0000.000
13A13VAL 0-0.097-0.04419.3900.0040.0040.0000.0000.0000.000
14A14ASN 00.022-0.00221.9950.0030.0030.0000.0000.0000.000
15A15LYS 10.9330.96324.5600.1080.1080.0000.0000.0000.000
16A16HIS 00.0500.01323.6540.0200.0200.0000.0000.0000.000
17A17SER 0-0.015-0.01428.5480.0100.0100.0000.0000.0000.000
18A18THR 0-0.034-0.02830.064-0.006-0.0060.0000.0000.0000.000
19A19SER 00.0320.01530.7950.0060.0060.0000.0000.0000.000
20A20ILE 00.0140.02129.5010.0020.0020.0000.0000.0000.000
21A21GLY 00.0850.04627.9280.0000.0000.0000.0000.0000.000
22A22LYS 10.7830.89525.9130.0920.0920.0000.0000.0000.000
23A23ILE 00.0250.01122.380-0.010-0.0100.0000.0000.0000.000
24A24TRP 00.0650.03022.162-0.006-0.0060.0000.0000.0000.000
25A25LEU 00.0270.02821.6680.0010.0010.0000.0000.0000.000
26A26THR 00.017-0.00917.411-0.005-0.0050.0000.0000.0000.000
27A27VAL 0-0.007-0.00917.972-0.014-0.0140.0000.0000.0000.000
28A28LEU 0-0.0010.00218.6520.0070.0070.0000.0000.0000.000
29A29PHE 0-0.0120.00913.9660.0120.0120.0000.0000.0000.000
30A30ILE 00.0120.00913.1290.0010.0010.0000.0000.0000.000
31A31PHE 00.0470.01614.8100.0280.0280.0000.0000.0000.000
32A32ARG 10.7810.88116.9970.0520.0520.0000.0000.0000.000
33A33ILE 0-0.008-0.01011.1140.0200.0200.0000.0000.0000.000
34A34MET 0-0.0110.00010.1160.0290.0290.0000.0000.0000.000
35A35ILE 0-0.0140.00314.1020.0350.0350.0000.0000.0000.000
36A36LEU 00.0190.00413.5180.0210.0210.0000.0000.0000.000
37A37VAL 0-0.110-0.0489.1430.0450.0450.0000.0000.0000.000
38A38VAL 00.0370.01912.5420.0440.0440.0000.0000.0000.000
39A39ALA 00.0410.00615.3820.0120.0120.0000.0000.0000.000
40A40ALA 0-0.046-0.01614.1530.0130.0130.0000.0000.0000.000
41A41LYS 10.9140.93910.008-0.568-0.5680.0000.0000.0000.000
42A42GLU -1-0.906-0.92415.2450.2170.2170.0000.0000.0000.000
43A43VAL 0-0.010-0.01218.190-0.012-0.0120.0000.0000.0000.000
44A44TRP 0-0.042-0.04319.502-0.017-0.0170.0000.0000.0000.000
45A45GLY 00.0210.03119.793-0.005-0.0050.0000.0000.0000.000
46A46ASP -1-0.827-0.92020.8380.1310.1310.0000.0000.0000.000
47A47GLU -1-0.905-0.92822.0770.1260.1260.0000.0000.0000.000
48A48GLN 00.0500.01424.866-0.014-0.0140.0000.0000.0000.000
49A49ALA 0-0.001-0.00625.711-0.008-0.0080.0000.0000.0000.000
50A50ASP -1-0.896-0.94427.3790.0970.0970.0000.0000.0000.000
51A51PHE 0-0.073-0.01429.621-0.008-0.0080.0000.0000.0000.000
52A52VAL 00.010-0.01031.160-0.001-0.0010.0000.0000.0000.000
53A180CYS 0-0.012-0.01134.774-0.002-0.0020.0000.0000.0000.000
54A54ASN 0-0.054-0.01737.6160.0010.0010.0000.0000.0000.000
55A55THR 00.0660.02040.292-0.003-0.0030.0000.0000.0000.000
56A56LEU 00.0070.00441.1680.0020.0020.0000.0000.0000.000
57A57GLN 0-0.049-0.02642.4470.0020.0020.0000.0000.0000.000
58A58PRO 00.0420.01939.7170.0020.0020.0000.0000.0000.000
59A59GLY 00.010-0.00138.1930.0030.0030.0000.0000.0000.000
60A174CYS 0-0.079-0.01136.9650.0060.0060.0000.0000.0000.000
61A61LYS 10.9950.98230.917-0.087-0.0870.0000.0000.0000.000
62A62ASN 00.012-0.00131.8460.0050.0050.0000.0000.0000.000
63A63VAL 0-0.021-0.01032.4560.0010.0010.0000.0000.0000.000
64A169CYS 0-0.0170.01534.779-0.005-0.0050.0000.0000.0000.000
65A65TYR 00.0080.02725.0160.0010.0010.0000.0000.0000.000
66A66ASP -1-0.918-0.95130.0260.0630.0630.0000.0000.0000.000
67A67HIS 0-0.020-0.02131.076-0.001-0.0010.0000.0000.0000.000
68A68TYR 0-0.006-0.02732.498-0.004-0.0040.0000.0000.0000.000
69A69PHE 0-0.134-0.05526.5960.0010.0010.0000.0000.0000.000
70A70PRO 00.0340.03927.5200.0070.0070.0000.0000.0000.000
71A71ILE 00.0250.01522.7540.0060.0060.0000.0000.0000.000
72A72SER 00.0200.05421.478-0.006-0.0060.0000.0000.0000.000
73A73HIS 00.1270.04022.3940.0040.0040.0000.0000.0000.000
74A74ILE 0-0.0180.01716.804-0.006-0.0060.0000.0000.0000.000
75A75ARG 10.8400.89017.520-0.138-0.1380.0000.0000.0000.000
76A76LEU 00.0340.04819.025-0.013-0.0130.0000.0000.0000.000
77A77TRP 0-0.009-0.00118.747-0.014-0.0140.0000.0000.0000.000
78A78ALA 0-0.028-0.00615.239-0.014-0.0140.0000.0000.0000.000
79A79LEU 00.0700.02416.377-0.025-0.0250.0000.0000.0000.000
80A80GLN 0-0.006-0.03318.640-0.021-0.0210.0000.0000.0000.000
81A81LEU 0-0.021-0.02215.048-0.021-0.0210.0000.0000.0000.000
82A82ILE 00.0130.01714.004-0.036-0.0360.0000.0000.0000.000
83A83PHE 00.019-0.00516.286-0.029-0.0290.0000.0000.0000.000
84A84VAL 00.002-0.00819.787-0.018-0.0180.0000.0000.0000.000
85A85SER 0-0.031-0.01014.037-0.027-0.0270.0000.0000.0000.000
86A86THR 0-0.018-0.00117.234-0.029-0.0290.0000.0000.0000.000
87A87PRO 0-0.0070.00418.780-0.016-0.0160.0000.0000.0000.000
88A88ALA 0-0.050-0.02918.177-0.006-0.0060.0000.0000.0000.000
89A89LEU 00.0470.01713.317-0.020-0.0200.0000.0000.0000.000
90A90LEU 00.0100.02917.754-0.010-0.0100.0000.0000.0000.000
91A91VAL 00.011-0.00720.5130.0030.0030.0000.0000.0000.000
92A92ALA 00.0200.00618.5620.0030.0030.0000.0000.0000.000
93A93MET 00.0440.03116.721-0.018-0.0180.0000.0000.0000.000
94A94HIS 0-0.022-0.01720.1060.0170.0170.0000.0000.0000.000
95A95VAL 0-0.055-0.04122.3810.0120.0120.0000.0000.0000.000
96A96ALA 0-0.0030.00120.3750.0120.0120.0000.0000.0000.000
97A97TYR 00.0570.05622.4490.0010.0010.0000.0000.0000.000
98A98ARG 10.9470.96223.8690.1090.1090.0000.0000.0000.000
99A99ARG 10.9090.95326.1670.1500.1500.0000.0000.0000.000
100A100HIS 0-0.023-0.01424.5240.0020.0020.0000.0000.0000.000
101A101GLU -1-0.904-0.95326.585-0.104-0.1040.0000.0000.0000.000
102A102LYS 10.9180.94128.8340.0960.0960.0000.0000.0000.000
103A103LYS 10.9741.00227.3860.1460.1460.0000.0000.0000.000
104A104ARG 10.9320.95928.6320.1150.1150.0000.0000.0000.000
105A105LYS 10.9600.97931.5630.0890.0890.0000.0000.0000.000
106A106PHE 0-0.0020.01034.0900.0040.0040.0000.0000.0000.000
107A107ILE 0-0.028-0.00133.6300.0010.0010.0000.0000.0000.000
108A108LYS 10.9230.96233.1330.0930.0930.0000.0000.0000.000
109A109GLY 00.0470.02937.7680.0040.0040.0000.0000.0000.000
110A110NME 00.0100.01737.933-0.003-0.0030.0000.0000.0000.000
111A124ACE 00.0640.02237.7770.0010.0010.0000.0000.0000.000
112A125LYS 10.9310.93733.5650.0860.0860.0000.0000.0000.000
113A126VAL 00.1600.08836.533-0.001-0.0010.0000.0000.0000.000
114A127ARG 10.9410.96435.1750.0630.0630.0000.0000.0000.000
115A128ILE 0-0.068-0.03029.883-0.004-0.0040.0000.0000.0000.000
116A129GLU -1-0.901-0.94731.857-0.074-0.0740.0000.0000.0000.000
117A130GLY 00.0490.03234.3250.0020.0020.0000.0000.0000.000
118A131SER 0-0.056-0.04531.5700.0000.0000.0000.0000.0000.000
119A132LEU 0-0.025-0.01825.7350.0000.0000.0000.0000.0000.000
120A133TRP 00.0230.01828.250-0.009-0.0090.0000.0000.0000.000
121A134TRP 00.0590.06231.5320.0010.0010.0000.0000.0000.000
122A135THR 0-0.017-0.02028.051-0.002-0.0020.0000.0000.0000.000
123A136TYR 00.0380.02325.0270.0020.0020.0000.0000.0000.000
124A137THR 00.0620.02628.1210.0000.0000.0000.0000.0000.000
125A138SER 00.0340.01030.2940.0050.0050.0000.0000.0000.000
126A139SER 0-0.0580.00324.1840.0040.0040.0000.0000.0000.000
127A140ILE 00.022-0.01926.6140.0010.0010.0000.0000.0000.000
128A141PHE 00.0120.02027.8090.0050.0050.0000.0000.0000.000
129A142PHE 00.029-0.00125.7100.0040.0040.0000.0000.0000.000
130A143ARG 10.8510.94521.3610.1180.1180.0000.0000.0000.000
131A144VAL 00.0270.00425.1240.0060.0060.0000.0000.0000.000
132A145ILE 00.0080.02227.6520.0060.0060.0000.0000.0000.000
133A146PHE 0-0.025-0.02023.0320.0060.0060.0000.0000.0000.000
134A147GLU -1-0.828-0.93922.544-0.026-0.0260.0000.0000.0000.000
135A148ALA 00.0070.00325.2680.0060.0060.0000.0000.0000.000
136A149ALA 0-0.0010.01227.1280.0040.0040.0000.0000.0000.000
137A150PHE 0-0.0560.00121.2940.0050.0050.0000.0000.0000.000
138A151MET 00.0130.02326.4080.0070.0070.0000.0000.0000.000
139A152TYR 0-0.0190.00927.9140.0040.0040.0000.0000.0000.000
140A153VAL 00.0870.03627.6470.0030.0030.0000.0000.0000.000
141A154PHE 0-0.048-0.04622.6190.0040.0040.0000.0000.0000.000
142A155TYR 0-0.036-0.01428.2260.0030.0030.0000.0000.0000.000
143A156VAL 0-0.059-0.01731.7550.0000.0000.0000.0000.0000.000
144A157MET 0-0.078-0.04729.1700.0010.0010.0000.0000.0000.000
145A158TYR 0-0.067-0.11026.2600.0050.0050.0000.0000.0000.000
146A159ASP -1-0.891-0.92231.7740.0340.0340.0000.0000.0000.000
147A160GLY 0-0.0160.00335.3280.0000.0000.0000.0000.0000.000
148A161PHE 0-0.010-0.01532.4570.0000.0000.0000.0000.0000.000
149A162SER 0-0.078-0.04030.8650.0020.0020.0000.0000.0000.000
150A163MET 00.0270.03227.0020.0030.0030.0000.0000.0000.000
151A164GLN 00.0030.00132.353-0.001-0.0010.0000.0000.0000.000
152A165ARG 10.9480.95933.853-0.043-0.0430.0000.0000.0000.000
153A166LEU 00.0030.01035.0080.0040.0040.0000.0000.0000.000
154A167VAL 00.0080.01735.397-0.003-0.0030.0000.0000.0000.000
155A168LYS 10.8780.92937.687-0.035-0.0350.0000.0000.0000.000
156A170ASN 00.016-0.01539.5790.0000.0000.0000.0000.0000.000
157A171ALA 00.045-0.01037.559-0.001-0.0010.0000.0000.0000.000
158A172TRP 00.0820.02439.6220.0010.0010.0000.0000.0000.000
159A173PRO 0-0.076-0.00439.576-0.001-0.0010.0000.0000.0000.000
160A175PRO 00.0130.00042.903-0.002-0.0020.0000.0000.0000.000
161A176ASN 0-0.018-0.00746.3920.0000.0000.0000.0000.0000.000
162A177THR 0-0.0020.00144.1300.0010.0010.0000.0000.0000.000
163A178VAL 00.0090.01540.3660.0000.0000.0000.0000.0000.000
164A179ASP -1-0.831-0.92040.9140.0390.0390.0000.0000.0000.000
165A181PHE 0-0.009-0.00435.209-0.004-0.0040.0000.0000.0000.000
166A182VAL 00.0210.02929.0040.0060.0060.0000.0000.0000.000
167A183SER 00.0450.01626.363-0.003-0.0030.0000.0000.0000.000
168A184ARG 10.9380.95423.378-0.126-0.1260.0000.0000.0000.000
169A185PRO 00.0400.02228.1880.0000.0000.0000.0000.0000.000
170A186THR 00.0150.00029.932-0.002-0.0020.0000.0000.0000.000
171A187GLU -1-0.878-0.93323.9620.0990.0990.0000.0000.0000.000
172A188LYS 10.8850.93824.614-0.098-0.0980.0000.0000.0000.000
173A189THR 00.0580.03925.632-0.004-0.0040.0000.0000.0000.000
174A190VAL 0-0.023-0.00125.703-0.005-0.0050.0000.0000.0000.000
175A191PHE 0-0.004-0.02919.442-0.006-0.0060.0000.0000.0000.000
176A192THR 0-0.014-0.02323.348-0.002-0.0020.0000.0000.0000.000
177A193VAL 00.0400.01025.599-0.008-0.0080.0000.0000.0000.000
178A194PHE 00.0220.02423.290-0.007-0.0070.0000.0000.0000.000
179A195MET 0-0.020-0.00318.338-0.010-0.0100.0000.0000.0000.000
180A196ILE 00.0760.02722.968-0.008-0.0080.0000.0000.0000.000
181A197ALA 0-0.045-0.00926.274-0.007-0.0070.0000.0000.0000.000
182A198VAL 0-0.027-0.02821.235-0.008-0.0080.0000.0000.0000.000
183A199SER 0-0.028-0.00424.128-0.007-0.0070.0000.0000.0000.000
184A200GLY 00.0810.04624.934-0.004-0.0040.0000.0000.0000.000
185A201ILE 00.0100.00126.162-0.006-0.0060.0000.0000.0000.000
186A202CYS 0-0.056-0.03722.711-0.010-0.0100.0000.0000.0000.000
187A203ILE 00.0190.02125.314-0.007-0.0070.0000.0000.0000.000
188A204LEU 00.0160.00628.114-0.004-0.0040.0000.0000.0000.000
189A205LEU 00.0130.00825.780-0.004-0.0040.0000.0000.0000.000
190A206ASN 00.016-0.00223.983-0.012-0.0120.0000.0000.0000.000
191A207VAL 00.0200.01028.064-0.002-0.0020.0000.0000.0000.000
192A208THR 0-0.008-0.00131.4770.0030.0030.0000.0000.0000.000
193A209GLU -1-0.831-0.94128.544-0.077-0.0770.0000.0000.0000.000
194A210LEU 0-0.037-0.01731.315-0.002-0.0020.0000.0000.0000.000
195A211CYS 0-0.0180.00733.0000.0030.0030.0000.0000.0000.000
196A212TYR 00.030-0.01434.1040.0020.0020.0000.0000.0000.000
197A213LEU 0-0.098-0.04631.395-0.001-0.0010.0000.0000.0000.000
198A214LEU 00.0130.01235.9430.0010.0010.0000.0000.0000.000
199A215ILE 0-0.054-0.00538.6410.0020.0020.0000.0000.0000.000
200A216ARG 10.9250.95937.7640.0560.0560.0000.0000.0000.000
201A217TYR 00.0050.01840.374-0.001-0.0010.0000.0000.0000.000
202A218NME 0-0.026-0.01138.637-0.003-0.0030.0000.0000.0000.000