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: 14RGZ

Calculation Name: 2ZW3-A-Xray372

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: 2023-06-20

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 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 -2202262.169056
FMO2-HF: Nuclear repulsion 2119345.140229
FMO2-HF: Total energy -82917.028828
FMO2-MP2: Total energy -83153.780902


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:ASP)


Summations of interaction energy for fragment #1(A:2: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.
-203.73-199.659.126-5.789-7.4180.071
Interaction energy analysis for fragmet #1(A:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.846 / q_NPA : -0.938
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].
3A4GLY00.0810.0423.882-12.256-10.718-0.008-0.650-0.8810.002
4A5THR00.0110.0143.167-6.532-6.0670.056-0.117-0.4040.000
5A6LEU00.0000.0022.187-12.917-10.7582.938-1.914-3.1830.019
6A7GLN00.0120.0001.881-28.737-28.8196.140-3.108-2.9500.050
7A8THR00.005-0.0076.621-6.697-6.6970.0000.0000.0000.000
8A9ILE0-0.042-0.0126.466-3.414-3.4140.0000.0000.0000.000
9A10LEU0-0.034-0.0079.112-3.031-3.0310.0000.0000.0000.000
10A11GLY00.0220.00510.444-2.374-2.3740.0000.0000.0000.000
11A12GLY0-0.028-0.00512.342-2.052-2.0520.0000.0000.0000.000
12A13VAL0-0.051-0.02814.427-1.010-1.0100.0000.0000.0000.000
13A14ASN0-0.017-0.02116.758-0.607-0.6070.0000.0000.0000.000
14A15LYS10.9270.96019.290-12.548-12.5480.0000.0000.0000.000
15A16HIS00.0540.03818.458-1.242-1.2420.0000.0000.0000.000
16A17SER00.0120.01122.699-0.517-0.5170.0000.0000.0000.000
17A18THR0-0.060-0.05125.3810.1540.1540.0000.0000.0000.000
18A19SER00.020-0.00225.843-0.441-0.4410.0000.0000.0000.000
19A20ILE00.0730.05025.702-0.082-0.0820.0000.0000.0000.000
20A21GLY00.0620.01824.1090.4890.4890.0000.0000.0000.000
21A22LYS10.7430.85521.342-13.295-13.2950.0000.0000.0000.000
22A23ILE00.0220.01319.0040.9420.9420.0000.0000.0000.000
23A24TRP00.0470.02619.1360.7970.7970.0000.0000.0000.000
24A25LEU00.0170.02018.1630.4090.4090.0000.0000.0000.000
25A26THR0-0.011-0.00914.0440.7710.7710.0000.0000.0000.000
26A27VAL00.0120.00115.1551.2711.2710.0000.0000.0000.000
27A28LEU00.0160.01116.7360.4680.4680.0000.0000.0000.000
28A29PHE0-0.017-0.00710.2080.1580.1580.0000.0000.0000.000
29A30ILE00.0160.00311.4471.0701.0700.0000.0000.0000.000
30A31PHE00.0070.00113.3530.5930.5930.0000.0000.0000.000
31A32ARG10.7370.83916.027-16.612-16.6120.0000.0000.0000.000
32A33ILE00.0200.00310.058-0.142-0.1420.0000.0000.0000.000
33A34MET0-0.0050.00010.5431.0201.0200.0000.0000.0000.000
34A35ILE00.010-0.00213.587-0.419-0.4190.0000.0000.0000.000
35A36LEU0-0.0140.00413.579-0.569-0.5690.0000.0000.0000.000
36A37VAL0-0.022-0.0279.832-0.316-0.3160.0000.0000.0000.000
37A38VAL00.0140.01713.176-0.190-0.1900.0000.0000.0000.000
38A39ALA00.0410.01716.079-0.515-0.5150.0000.0000.0000.000
39A40ALA0-0.064-0.04114.634-0.598-0.5980.0000.0000.0000.000
40A41LYS10.8900.94311.814-22.694-22.6940.0000.0000.0000.000
41A42GLU-1-0.899-0.92016.77513.74713.7470.0000.0000.0000.000
42A43VAL00.000-0.00619.878-0.658-0.6580.0000.0000.0000.000
43A44TRP0-0.018-0.03419.963-0.714-0.7140.0000.0000.0000.000
44A45GLY00.0420.03421.721-0.110-0.1100.0000.0000.0000.000
45A46ASP-1-0.769-0.86222.49311.68611.6860.0000.0000.0000.000
46A47GLU-1-0.847-0.85122.50113.45313.4530.0000.0000.0000.000
47A48GLN00.0370.01926.328-0.689-0.6890.0000.0000.0000.000
48A49ALA00.0130.00827.425-0.409-0.4090.0000.0000.0000.000
49A50ASP-1-0.869-0.94729.23010.08310.0830.0000.0000.0000.000
50A51PHE0-0.0330.00330.749-0.267-0.2670.0000.0000.0000.000
51A52VAL00.0170.01632.427-0.128-0.1280.0000.0000.0000.000
52A53CYS0-0.0030.00236.0520.0410.0410.0000.0000.0000.000
53A54ASN0-0.034-0.01238.895-0.067-0.0670.0000.0000.0000.000
54A55THR00.008-0.01841.678-0.226-0.2260.0000.0000.0000.000
55A56LEU00.0300.01842.2670.1390.1390.0000.0000.0000.000
56A57GLN0-0.0210.00143.6000.0580.0580.0000.0000.0000.000
57A58PRO00.0300.00940.4580.1800.1800.0000.0000.0000.000
58A59GLY0-0.0020.00238.4430.2120.2120.0000.0000.0000.000
59A60CYS0-0.0410.00137.6640.3200.3200.0000.0000.0000.000
60A61LYS10.8870.92131.761-9.581-9.5810.0000.0000.0000.000
61A62ASN00.006-0.00732.8870.2650.2650.0000.0000.0000.000
62A63VAL00.0290.01032.7830.2540.2540.0000.0000.0000.000
63A64CYS0-0.0060.02334.819-0.010-0.0100.0000.0000.0000.000
64A65TYR0-0.0180.00425.2070.1640.1640.0000.0000.0000.000
65A66ASP-1-0.950-0.98230.10610.64210.6420.0000.0000.0000.000
66A67HIS0-0.003-0.01331.1430.1790.1790.0000.0000.0000.000
67A68TYR0-0.029-0.01732.475-0.237-0.2370.0000.0000.0000.000
68A69PHE0-0.070-0.02927.0890.1790.1790.0000.0000.0000.000
69A70PRO00.0500.04227.0140.4710.4710.0000.0000.0000.000
70A71ILE0-0.019-0.01522.2690.5760.5760.0000.0000.0000.000
71A72SER0-0.018-0.00922.1670.1540.1540.0000.0000.0000.000
72A73HIS00.0810.03421.9270.9410.9410.0000.0000.0000.000
73A74ILE0-0.0200.00417.0680.6340.6340.0000.0000.0000.000
74A75ARG10.8450.89217.450-14.167-14.1670.0000.0000.0000.000
75A76LEU00.0470.03618.2570.8240.8240.0000.0000.0000.000
76A77TRP00.005-0.00418.0950.6990.6990.0000.0000.0000.000
77A78ALA00.0030.00113.9330.8850.8850.0000.0000.0000.000
78A79LEU00.003-0.00114.4821.3411.3410.0000.0000.0000.000
79A80GLN00.0510.04016.431-0.054-0.0540.0000.0000.0000.000
80A81LEU00.005-0.00612.9340.1990.1990.0000.0000.0000.000
81A82ILE0-0.0030.00511.0501.3571.3570.0000.0000.0000.000
82A83PHE0-0.0020.00212.9080.3280.3280.0000.0000.0000.000
83A84VAL0-0.014-0.01116.053-0.180-0.1800.0000.0000.0000.000
84A85SER0-0.009-0.00810.2730.8170.8170.0000.0000.0000.000
85A86THR0-0.028-0.01012.2741.1781.1780.0000.0000.0000.000
86A87PRO00.0070.00513.6920.1750.1750.0000.0000.0000.000
87A88ALA0-0.0230.00613.279-0.652-0.6520.0000.0000.0000.000
88A89LEU00.0360.0137.802-0.104-0.1040.0000.0000.0000.000
89A90LEU00.0070.02511.775-0.134-0.1340.0000.0000.0000.000
90A91VAL00.010-0.01514.672-0.752-0.7520.0000.0000.0000.000
91A92ALA00.0170.01412.215-0.854-0.8540.0000.0000.0000.000
92A93MET00.0390.01612.403-0.104-0.1040.0000.0000.0000.000
93A94HIS0-0.0010.01713.943-1.637-1.6370.0000.0000.0000.000
94A95VAL0-0.021-0.02616.658-1.097-1.0970.0000.0000.0000.000
95A96ALA00.0100.01114.364-0.908-0.9080.0000.0000.0000.000
96A97TYR00.0340.02016.309-0.691-0.6910.0000.0000.0000.000
97A98ARG10.8960.92818.124-14.642-14.6420.0000.0000.0000.000
98A99ARG10.9310.96920.204-15.283-15.2830.0000.0000.0000.000
99A100HIS00.0450.03519.036-0.846-0.8460.0000.0000.0000.000
100A101GLU-1-0.746-0.86421.10412.36212.3620.0000.0000.0000.000
101A102LYS10.9230.95823.402-12.183-12.1830.0000.0000.0000.000
102A103LYS10.8660.94121.348-14.920-14.9200.0000.0000.0000.000
103A104ARG10.9290.95423.996-12.600-12.6000.0000.0000.0000.000
104A105LYS10.8590.92625.953-12.406-12.4060.0000.0000.0000.000
105A106PHE00.032-0.00228.901-0.256-0.2560.0000.0000.0000.000
106A107ILE0-0.056-0.01028.292-0.252-0.2520.0000.0000.0000.000
107A108LYS10.9100.95229.682-10.533-10.5330.0000.0000.0000.000
108A109GLY00.0410.03932.723-0.148-0.1480.0000.0000.0000.000
109A125LYS11.0180.98828.852-10.700-10.7000.0000.0000.0000.000
110A126VAL00.1270.06329.9750.3270.3270.0000.0000.0000.000
111A127ARG10.9290.96429.189-10.094-10.0940.0000.0000.0000.000
112A128ILE0-0.055-0.02523.3350.3980.3980.0000.0000.0000.000
113A129GLU-1-0.833-0.91525.72710.95210.9520.0000.0000.0000.000
114A130GLY00.0760.03427.6890.1980.1980.0000.0000.0000.000
115A131SER0-0.127-0.08726.292-0.222-0.2220.0000.0000.0000.000
116A132LEU0-0.0460.00219.6380.2560.2560.0000.0000.0000.000
117A133TRP00.0410.01921.2030.8490.8490.0000.0000.0000.000
118A134TRP00.0720.05725.0110.1150.1150.0000.0000.0000.000
119A135THR00.015-0.01621.7590.3040.3040.0000.0000.0000.000
120A136TYR0-0.025-0.00419.1160.4030.4030.0000.0000.0000.000
121A137THR00.0540.01921.9870.3380.3380.0000.0000.0000.000
122A138SER0-0.011-0.00623.902-0.160-0.1600.0000.0000.0000.000
123A139SER0-0.055-0.03617.9070.0850.0850.0000.0000.0000.000
124A140ILE00.0130.00220.7920.3760.3760.0000.0000.0000.000
125A141PHE00.0150.01222.3960.0150.0150.0000.0000.0000.000
126A142PHE00.0130.00120.834-0.066-0.0660.0000.0000.0000.000
127A143ARG10.8720.94217.165-16.973-16.9730.0000.0000.0000.000
128A144VAL0-0.006-0.00120.5680.0740.0740.0000.0000.0000.000
129A145ILE00.0050.00623.218-0.189-0.1890.0000.0000.0000.000
130A146PHE0-0.010-0.01118.784-0.136-0.1360.0000.0000.0000.000
131A147GLU-1-0.727-0.86019.62616.39416.3940.0000.0000.0000.000
132A148ALA0-0.015-0.00622.114-0.368-0.3680.0000.0000.0000.000
133A149ALA0-0.005-0.00124.208-0.354-0.3540.0000.0000.0000.000
134A150PHE0-0.016-0.01220.280-0.142-0.1420.0000.0000.0000.000
135A151MET0-0.0050.00923.862-0.268-0.2680.0000.0000.0000.000
136A152TYR0-0.015-0.01026.025-0.329-0.3290.0000.0000.0000.000
137A153VAL00.0190.00425.774-0.281-0.2810.0000.0000.0000.000
138A154PHE0-0.034-0.03821.926-0.171-0.1710.0000.0000.0000.000
139A155TYR0-0.044-0.01427.357-0.294-0.2940.0000.0000.0000.000
140A156VAL0-0.051-0.01430.681-0.395-0.3950.0000.0000.0000.000
141A157MET0-0.060-0.02428.326-0.167-0.1670.0000.0000.0000.000
142A158TYR0-0.018-0.05025.9250.0290.0290.0000.0000.0000.000
143A159ASP-1-0.913-0.94331.5959.1559.1550.0000.0000.0000.000
144A160GLY00.0020.00234.003-0.308-0.3080.0000.0000.0000.000
145A161PHE0-0.013-0.00531.5840.2290.2290.0000.0000.0000.000
146A162SER0-0.062-0.03030.7330.2500.2500.0000.0000.0000.000
147A163MET0-0.0080.01727.444-0.059-0.0590.0000.0000.0000.000
148A164GLN0-0.012-0.00932.513-0.133-0.1330.0000.0000.0000.000
149A165ARG10.9410.95434.469-8.175-8.1750.0000.0000.0000.000
150A166LEU0-0.0070.00936.3530.0710.0710.0000.0000.0000.000
151A167VAL00.0330.01735.685-0.003-0.0030.0000.0000.0000.000
152A168LYS10.8310.89938.604-7.323-7.3230.0000.0000.0000.000
153A170ASN00.0510.01140.081-0.328-0.3280.0000.0000.0000.000
154A171ALA00.0650.03037.882-0.049-0.0490.0000.0000.0000.000
155A172TRP00.0320.00539.917-0.060-0.0600.0000.0000.0000.000
156A173PRO0-0.0260.00339.409-0.176-0.1760.0000.0000.0000.000
157A175PRO0-0.022-0.01643.470-0.112-0.1120.0000.0000.0000.000
158A176ASN0-0.022-0.00847.177-0.134-0.1340.0000.0000.0000.000
159A177THR0-0.007-0.01644.3490.1080.1080.0000.0000.0000.000
160A178VAL0-0.020-0.00941.424-0.133-0.1330.0000.0000.0000.000
161A179ASP-1-0.820-0.89441.7907.4817.4810.0000.0000.0000.000
162A181PHE00.009-0.00636.370-0.088-0.0880.0000.0000.0000.000
163A182VAL00.0450.02230.4370.2100.2100.0000.0000.0000.000
164A183SER00.028-0.00228.595-0.128-0.1280.0000.0000.0000.000
165A184ARG10.7980.85523.900-12.010-12.0100.0000.0000.0000.000
166A185PRO00.0580.02929.0330.3260.3260.0000.0000.0000.000
167A186THR00.0060.00730.3270.1600.1600.0000.0000.0000.000
168A187GLU-1-0.826-0.90025.46312.01312.0130.0000.0000.0000.000
169A188LYS10.8710.92925.128-11.541-11.5410.0000.0000.0000.000
170A189THR00.0130.00726.0250.3040.3040.0000.0000.0000.000
171A190VAL0-0.007-0.00126.3930.1220.1220.0000.0000.0000.000
172A191PHE00.0290.00320.2150.2570.2570.0000.0000.0000.000
173A192THR0-0.019-0.01023.4390.6380.6380.0000.0000.0000.000
174A193VAL00.0140.00025.2820.0740.0740.0000.0000.0000.000
175A194PHE0-0.010-0.01123.2110.0640.0640.0000.0000.0000.000
176A195MET0-0.0210.00417.5440.3410.3410.0000.0000.0000.000
177A196ILE00.0330.03022.6720.3380.3380.0000.0000.0000.000
178A197ALA00.0180.01225.423-0.186-0.1860.0000.0000.0000.000
179A198VAL0-0.015-0.02020.0700.0060.0060.0000.0000.0000.000
180A199SER00.0520.02822.2020.4380.4380.0000.0000.0000.000
181A200GLY00.0180.01923.143-0.088-0.0880.0000.0000.0000.000
182A201ILE0-0.007-0.00824.167-0.166-0.1660.0000.0000.0000.000
183A202CYS0-0.026-0.01220.3360.2160.2160.0000.0000.0000.000
184A203ILE00.0000.01222.3960.1140.1140.0000.0000.0000.000
185A204LEU00.0270.01524.955-0.167-0.1670.0000.0000.0000.000
186A205LEU0-0.0120.01022.705-0.213-0.2130.0000.0000.0000.000
187A206ASN00.001-0.01619.9280.3020.3020.0000.0000.0000.000
188A207VAL00.0350.01123.785-0.197-0.1970.0000.0000.0000.000
189A208THR0-0.005-0.00627.490-0.545-0.5450.0000.0000.0000.000
190A209GLU-1-0.816-0.88423.63912.73712.7370.0000.0000.0000.000
191A210LEU0-0.008-0.01226.665-0.178-0.1780.0000.0000.0000.000
192A211CYS0-0.0050.00728.077-0.444-0.4440.0000.0000.0000.000
193A212TYR00.000-0.01229.129-0.384-0.3840.0000.0000.0000.000
194A213LEU0-0.078-0.03625.769-0.135-0.1350.0000.0000.0000.000
195A214LEU00.0200.00830.424-0.234-0.2340.0000.0000.0000.000
196A215ILE0-0.019-0.00433.390-0.274-0.2740.0000.0000.0000.000
197A216ARG10.9030.96731.488-10.113-10.1130.0000.0000.0000.000
198A217TYR0-0.062-0.02533.0300.2170.2170.0000.0000.0000.000