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: YY3K2

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 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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2205748.127562
FMO2-HF: Nuclear repulsion 2122834.277644
FMO2-HF: Total energy -82913.849918
FMO2-MP2: Total energy -83151.02411


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.
-141.124-143.6489.835-3.507-3.8020.009
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 : -0.898 / q_NPA : -0.964
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].
3A4GLY00.0440.0153.855-5.035-3.490-0.018-0.686-0.8410.001
4A5THR0-0.009-0.0213.073-4.520-4.1750.071-0.104-0.3120.000
5A6LEU00.0510.0192.024-2.974-7.4179.783-2.708-2.6310.008
6A7GLN00.0250.0154.760-2.887-2.858-0.001-0.009-0.0180.000
7A8THR00.0370.0207.982-3.659-3.6590.0000.0000.0000.000
8A9ILE0-0.0110.0227.000-2.235-2.2350.0000.0000.0000.000
9A10LEU0-0.035-0.01410.118-1.976-1.9760.0000.0000.0000.000
10A11GLY00.0340.01511.333-1.688-1.6880.0000.0000.0000.000
11A12GLY0-0.043-0.02512.997-1.487-1.4870.0000.0000.0000.000
12A13VAL0-0.097-0.04515.006-0.483-0.4830.0000.0000.0000.000
13A14ASN00.022-0.00217.149-0.130-0.1300.0000.0000.0000.000
14A15LYS10.9340.96219.795-11.600-11.6000.0000.0000.0000.000
15A16HIS00.0510.01419.205-1.014-1.0140.0000.0000.0000.000
16A17SER0-0.017-0.01523.754-0.492-0.4920.0000.0000.0000.000
17A18THR0-0.034-0.02825.8980.2870.2870.0000.0000.0000.000
18A19SER00.0260.01327.238-0.441-0.4410.0000.0000.0000.000
19A20ILE00.0190.02426.156-0.035-0.0350.0000.0000.0000.000
20A21GLY00.0850.04624.9660.1770.1770.0000.0000.0000.000
21A22LYS10.7860.89622.103-11.990-11.9900.0000.0000.0000.000
22A23ILE00.0230.01118.8330.6460.6460.0000.0000.0000.000
23A24TRP00.0660.03019.1720.7270.7270.0000.0000.0000.000
24A25LEU00.0240.02818.9860.3580.3580.0000.0000.0000.000
25A26THR00.017-0.01014.3360.7580.7580.0000.0000.0000.000
26A27VAL0-0.006-0.00915.3551.0221.0220.0000.0000.0000.000
27A28LEU0-0.0030.00116.6090.4410.4410.0000.0000.0000.000
28A29PHE0-0.0110.00811.5930.3660.3660.0000.0000.0000.000
29A30ILE00.0130.00911.2360.9510.9510.0000.0000.0000.000
30A31PHE00.0450.01513.3210.4850.4850.0000.0000.0000.000
31A32ARG10.7790.88016.181-15.179-15.1790.0000.0000.0000.000
32A33ILE0-0.005-0.00910.333-0.141-0.1410.0000.0000.0000.000
33A34MET0-0.0110.00010.2091.3021.3020.0000.0000.0000.000
34A35ILE0-0.0120.00314.053-0.181-0.1810.0000.0000.0000.000
35A36LEU00.0190.00313.350-0.354-0.3540.0000.0000.0000.000
36A37VAL0-0.108-0.0479.9040.1480.1480.0000.0000.0000.000
37A38VAL00.0380.01913.1970.2720.2720.0000.0000.0000.000
38A39ALA00.0370.00616.447-0.457-0.4570.0000.0000.0000.000
39A40ALA0-0.049-0.01714.910-0.325-0.3250.0000.0000.0000.000
40A41LYS10.9170.93910.835-24.005-24.0050.0000.0000.0000.000
41A42GLU-1-0.904-0.92416.59414.71314.7130.0000.0000.0000.000
42A43VAL0-0.013-0.01219.678-0.545-0.5450.0000.0000.0000.000
43A44TRP0-0.037-0.04120.277-0.649-0.6490.0000.0000.0000.000
44A45GLY00.0170.02921.011-0.255-0.2550.0000.0000.0000.000
45A46ASP-1-0.824-0.91822.10711.39111.3910.0000.0000.0000.000
46A47GLU-1-0.906-0.92822.66213.02213.0220.0000.0000.0000.000
47A48GLN00.0520.01525.797-0.557-0.5570.0000.0000.0000.000
48A49ALA0-0.003-0.00726.861-0.414-0.4140.0000.0000.0000.000
49A50ASP-1-0.898-0.94528.6449.7469.7460.0000.0000.0000.000
50A51PHE0-0.073-0.01430.596-0.261-0.2610.0000.0000.0000.000
51A52VAL00.010-0.01032.173-0.125-0.1250.0000.0000.0000.000
52A53CYS0-0.004-0.00935.859-0.025-0.0250.0000.0000.0000.000
53A54ASN0-0.060-0.01938.533-0.071-0.0710.0000.0000.0000.000
54A55THR00.0690.02141.149-0.210-0.2100.0000.0000.0000.000
55A56LEU00.0040.00342.1950.1180.1180.0000.0000.0000.000
56A57GLN0-0.048-0.02543.0850.1250.1250.0000.0000.0000.000
57A58PRO00.0460.02040.5890.1730.1730.0000.0000.0000.000
58A59GLY00.006-0.00238.7570.1780.1780.0000.0000.0000.000
59A60CYS0-0.071-0.00937.5210.3210.3210.0000.0000.0000.000
60A61LYS10.9960.98331.900-9.428-9.4280.0000.0000.0000.000
61A62ASN00.004-0.00432.5590.2670.2670.0000.0000.0000.000
62A63VAL0-0.018-0.00932.8430.2150.2150.0000.0000.0000.000
63A64CYS0-0.0070.01934.989-0.042-0.0420.0000.0000.0000.000
64A65TYR00.0060.02825.5070.1770.1770.0000.0000.0000.000
65A66ASP-1-0.919-0.95230.11610.43010.4300.0000.0000.0000.000
66A67HIS0-0.020-0.02231.1840.1900.1900.0000.0000.0000.000
67A68TYR00.002-0.02532.593-0.220-0.2200.0000.0000.0000.000
68A69PHE0-0.140-0.05626.9360.1880.1880.0000.0000.0000.000
69A70PRO00.0350.03927.5230.3640.3640.0000.0000.0000.000
70A71ILE00.0210.01522.2350.4860.4860.0000.0000.0000.000
71A72SER00.0220.05521.6950.0760.0760.0000.0000.0000.000
72A73HIS00.1320.04222.1800.7920.7920.0000.0000.0000.000
73A74ILE0-0.0240.01417.0500.4380.4380.0000.0000.0000.000
74A75ARG10.8400.89117.334-13.857-13.8570.0000.0000.0000.000
75A76LEU00.0330.04818.6710.4290.4290.0000.0000.0000.000
76A77TRP0-0.0060.00018.3410.7590.7590.0000.0000.0000.000
77A78ALA0-0.028-0.00614.5300.6590.6590.0000.0000.0000.000
78A79LEU00.0690.02415.2280.9850.9850.0000.0000.0000.000
79A80GLN0-0.009-0.03317.417-0.166-0.1660.0000.0000.0000.000
80A81LEU0-0.025-0.02613.7810.0640.0640.0000.0000.0000.000
81A82ILE00.0180.01912.3281.1521.1520.0000.0000.0000.000
82A83PHE00.018-0.00514.5350.2900.2900.0000.0000.0000.000
83A84VAL00.008-0.00717.559-0.051-0.0510.0000.0000.0000.000
84A85SER0-0.038-0.01111.219-0.063-0.0630.0000.0000.0000.000
85A86THR0-0.016-0.00113.9060.6310.6310.0000.0000.0000.000
86A87PRO0-0.0040.00515.3380.0720.0720.0000.0000.0000.000
87A88ALA0-0.052-0.03014.337-0.393-0.3930.0000.0000.0000.000
88A89LEU00.0460.0178.7180.1260.1260.0000.0000.0000.000
89A90LEU00.0110.03013.1870.2400.2400.0000.0000.0000.000
90A91VAL00.010-0.00816.053-0.616-0.6160.0000.0000.0000.000
91A92ALA00.0200.00513.485-0.468-0.4680.0000.0000.0000.000
92A93MET00.0450.03011.8740.1900.1900.0000.0000.0000.000
93A94HIS0-0.022-0.01715.074-1.114-1.1140.0000.0000.0000.000
94A95VAL0-0.056-0.04117.076-0.896-0.8960.0000.0000.0000.000
95A96ALA0-0.0030.00115.069-0.772-0.7720.0000.0000.0000.000
96A97TYR00.0630.05717.114-0.121-0.1210.0000.0000.0000.000
97A98ARG10.9450.96318.776-13.149-13.1490.0000.0000.0000.000
98A99ARG10.9060.95120.795-13.931-13.9310.0000.0000.0000.000
99A100HIS0-0.022-0.01419.346-0.430-0.4300.0000.0000.0000.000
100A101GLU-1-0.899-0.95121.40612.48012.4800.0000.0000.0000.000
101A102LYS10.9140.94023.811-11.631-11.6310.0000.0000.0000.000
102A103LYS10.9731.00222.243-13.626-13.6260.0000.0000.0000.000
103A104ARG10.9350.96123.949-12.532-12.5320.0000.0000.0000.000
104A105LYS10.9560.97626.661-11.239-11.2390.0000.0000.0000.000
105A106PHE0-0.0020.00829.186-0.225-0.2250.0000.0000.0000.000
106A107ILE0-0.0280.00028.711-0.138-0.1380.0000.0000.0000.000
107A108LYS10.9300.96928.542-10.813-10.8130.0000.0000.0000.000
108A109GLY00.0540.04332.940-0.143-0.1430.0000.0000.0000.000
109A125LYS10.9950.97228.277-10.414-10.4140.0000.0000.0000.000
110A126VAL00.1650.08031.1410.1470.1470.0000.0000.0000.000
111A127ARG10.9440.96429.897-9.437-9.4370.0000.0000.0000.000
112A128ILE0-0.079-0.03824.4980.3460.3460.0000.0000.0000.000
113A129GLU-1-0.899-0.94626.5509.9689.9680.0000.0000.0000.000
114A130GLY00.0480.03229.063-0.059-0.0590.0000.0000.0000.000
115A131SER0-0.054-0.04426.4960.0400.0400.0000.0000.0000.000
116A132LEU0-0.028-0.02020.5770.1420.1420.0000.0000.0000.000
117A133TRP00.0240.01923.1100.6660.6660.0000.0000.0000.000
118A134TRP00.0570.06026.4580.0300.0300.0000.0000.0000.000
119A135THR0-0.020-0.02023.3460.2910.2910.0000.0000.0000.000
120A136TYR00.0380.02420.4450.1670.1670.0000.0000.0000.000
121A137THR00.0660.02723.3770.2240.2240.0000.0000.0000.000
122A138SER00.0310.00926.093-0.157-0.1570.0000.0000.0000.000
123A139SER0-0.0600.00319.8630.1190.1190.0000.0000.0000.000
124A140ILE00.034-0.01622.7160.3060.3060.0000.0000.0000.000
125A141PHE00.0010.01724.026-0.042-0.0420.0000.0000.0000.000
126A142PHE00.025-0.00122.2280.0100.0100.0000.0000.0000.000
127A143ARG10.8580.94717.531-15.011-15.0110.0000.0000.0000.000
128A144VAL00.0180.00022.0840.1780.1780.0000.0000.0000.000
129A145ILE00.0120.02324.723-0.303-0.3030.0000.0000.0000.000
130A146PHE0-0.026-0.02020.294-0.043-0.0430.0000.0000.0000.000
131A147GLU-1-0.829-0.93821.06114.07314.0730.0000.0000.0000.000
132A148ALA00.0100.00323.570-0.203-0.2030.0000.0000.0000.000
133A149ALA0-0.0010.01325.448-0.364-0.3640.0000.0000.0000.000
134A150PHE0-0.0540.00119.844-0.093-0.0930.0000.0000.0000.000
135A151MET00.0130.02325.138-0.329-0.3290.0000.0000.0000.000
136A152TYR0-0.0200.00826.816-0.363-0.3630.0000.0000.0000.000
137A153VAL00.0870.03626.667-0.272-0.2720.0000.0000.0000.000
138A154PHE0-0.036-0.04321.926-0.148-0.1480.0000.0000.0000.000
139A155TYR0-0.047-0.01827.500-0.083-0.0830.0000.0000.0000.000
140A156VAL0-0.058-0.01631.050-0.311-0.3110.0000.0000.0000.000
141A157MET0-0.078-0.04728.556-0.084-0.0840.0000.0000.0000.000
142A158TYR0-0.067-0.11125.942-0.019-0.0190.0000.0000.0000.000
143A159ASP-1-0.893-0.92231.4138.7808.7800.0000.0000.0000.000
144A160GLY0-0.0120.00434.929-0.174-0.1740.0000.0000.0000.000
145A161PHE0-0.012-0.01632.1270.1980.1980.0000.0000.0000.000
146A162SER0-0.078-0.04030.9120.2330.2330.0000.0000.0000.000
147A163MET00.0260.03327.351-0.017-0.0170.0000.0000.0000.000
148A164GLN00.0020.00232.639-0.046-0.0460.0000.0000.0000.000
149A165ARG10.9510.95934.447-8.049-8.0490.0000.0000.0000.000
150A166LEU00.0010.00935.8320.1380.1380.0000.0000.0000.000
151A167VAL00.0070.01735.789-0.035-0.0350.0000.0000.0000.000
152A168LYS10.8770.92938.169-7.192-7.1920.0000.0000.0000.000
153A170ASN00.010-0.01739.907-0.182-0.1820.0000.0000.0000.000
154A171ALA00.047-0.00837.789-0.038-0.0380.0000.0000.0000.000
155A172TRP00.0820.02339.804-0.050-0.0500.0000.0000.0000.000
156A173PRO0-0.077-0.00439.975-0.132-0.1320.0000.0000.0000.000
157A175PRO00.009-0.00143.392-0.095-0.0950.0000.0000.0000.000
158A176ASN0-0.018-0.00846.931-0.028-0.0280.0000.0000.0000.000
159A177THR0-0.0040.00044.4800.1030.1030.0000.0000.0000.000
160A178VAL00.0130.01741.003-0.109-0.1090.0000.0000.0000.000
161A179ASP-1-0.835-0.92241.6067.2617.2610.0000.0000.0000.000
162A181PHE0-0.009-0.00536.110-0.109-0.1090.0000.0000.0000.000
163A182VAL00.0230.03029.8060.2480.2480.0000.0000.0000.000
164A183SER00.0440.01627.577-0.116-0.1160.0000.0000.0000.000
165A184ARG10.9370.95425.048-11.526-11.5260.0000.0000.0000.000
166A185PRO00.0390.02129.1100.2330.2330.0000.0000.0000.000
167A186THR00.0130.00030.5540.0880.0880.0000.0000.0000.000
168A187GLU-1-0.878-0.93425.24811.95211.9520.0000.0000.0000.000
169A188LYS10.8850.93825.379-10.942-10.9420.0000.0000.0000.000
170A189THR00.0550.03926.0440.2500.2500.0000.0000.0000.000
171A190VAL0-0.0210.00026.2850.1710.1710.0000.0000.0000.000
172A191PHE0-0.003-0.03020.2930.1780.1780.0000.0000.0000.000
173A192THR0-0.012-0.02223.4490.4710.4710.0000.0000.0000.000
174A193VAL00.0350.00925.6200.0100.0100.0000.0000.0000.000
175A194PHE00.0230.02423.3640.1540.1540.0000.0000.0000.000
176A195MET0-0.019-0.00417.8870.3360.3360.0000.0000.0000.000
177A196ILE00.0720.02722.6480.2640.2640.0000.0000.0000.000
178A197ALA0-0.043-0.00925.736-0.224-0.2240.0000.0000.0000.000
179A198VAL0-0.027-0.02720.356-0.048-0.0480.0000.0000.0000.000
180A199SER0-0.028-0.00222.9410.5280.5280.0000.0000.0000.000
181A200GLY00.0800.04523.849-0.080-0.0800.0000.0000.0000.000
182A201ILE00.0110.00124.386-0.082-0.0820.0000.0000.0000.000
183A202CYS0-0.054-0.03620.8990.1210.1210.0000.0000.0000.000
184A203ILE00.0160.02023.4670.1900.1900.0000.0000.0000.000
185A204LEU00.0160.00626.191-0.128-0.1280.0000.0000.0000.000
186A205LEU00.0140.00823.272-0.135-0.1350.0000.0000.0000.000
187A206ASN00.017-0.00221.3510.1280.1280.0000.0000.0000.000
188A207VAL00.0190.01025.201-0.102-0.1020.0000.0000.0000.000
189A208THR0-0.009-0.00128.652-0.464-0.4640.0000.0000.0000.000
190A209GLU-1-0.830-0.94124.82211.36111.3610.0000.0000.0000.000
191A210LEU0-0.038-0.01827.782-0.044-0.0440.0000.0000.0000.000
192A211CYS0-0.0170.00829.383-0.397-0.3970.0000.0000.0000.000
193A212TYR00.029-0.01430.355-0.320-0.3200.0000.0000.0000.000
194A213LEU0-0.101-0.04827.148-0.108-0.1080.0000.0000.0000.000
195A214LEU00.0070.00831.769-0.100-0.1000.0000.0000.0000.000
196A215ILE0-0.049-0.00434.883-0.244-0.2440.0000.0000.0000.000
197A216ARG10.9090.95533.251-9.180-9.1800.0000.0000.0000.000
198A217TYR00.0020.01734.2260.0410.0410.0000.0000.0000.000