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

tag_button

FMODB ID: VRM11

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 OptHSide
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 -2204481.664346
FMO2-HF: Nuclear repulsion 2121566.115285
FMO2-HF: Total energy -82915.549061
FMO2-MP2: Total energy -83152.553715


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.
-156.156-152.7843.093-2.611-3.8540.019
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 : -0.902 / q_NPA : -0.965
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].
3A4GLY00.0430.0153.855-6.774-5.186-0.019-0.716-0.8530.002
4A5THR00.012-0.0163.013-4.261-3.8730.095-0.125-0.3580.000
5A6LEU00.0120.0102.291-8.935-7.6433.018-1.737-2.5730.017
6A7GLN00.0450.0224.452-5.641-5.537-0.001-0.033-0.0700.000
7A8THR00.0210.0138.135-4.186-4.1860.0000.0000.0000.000
8A9ILE0-0.0060.0216.786-2.439-2.4390.0000.0000.0000.000
9A10LEU0-0.038-0.01310.055-2.207-2.2070.0000.0000.0000.000
10A11GLY00.0300.01311.350-1.816-1.8160.0000.0000.0000.000
11A12GLY0-0.045-0.02812.904-1.613-1.6130.0000.0000.0000.000
12A13VAL0-0.080-0.03414.892-0.526-0.5260.0000.0000.0000.000
13A14ASN00.001-0.00917.038-0.257-0.2570.0000.0000.0000.000
14A15LYS10.9430.95719.577-11.853-11.8530.0000.0000.0000.000
15A16HIS00.0680.03619.310-0.979-0.9790.0000.0000.0000.000
16A17SER0-0.007-0.00523.711-0.490-0.4900.0000.0000.0000.000
17A18THR0-0.044-0.03225.8240.2940.2940.0000.0000.0000.000
18A19SER00.011-0.01027.168-0.434-0.4340.0000.0000.0000.000
19A20ILE00.0190.01826.152-0.046-0.0460.0000.0000.0000.000
20A21GLY00.0890.04724.9570.1750.1750.0000.0000.0000.000
21A22LYS10.7410.86621.956-12.382-12.3820.0000.0000.0000.000
22A23ILE00.0310.00219.1870.7220.7220.0000.0000.0000.000
23A24TRP00.0610.03319.1740.7470.7470.0000.0000.0000.000
24A25LEU00.0280.02419.1310.3850.3850.0000.0000.0000.000
25A26THR0-0.008-0.01314.5460.6880.6880.0000.0000.0000.000
26A27VAL0-0.001-0.00715.3521.0641.0640.0000.0000.0000.000
27A28LEU00.0100.01116.5980.4380.4380.0000.0000.0000.000
28A29PHE0-0.0130.00411.3220.3430.3430.0000.0000.0000.000
29A30ILE00.0160.01011.1981.0121.0120.0000.0000.0000.000
30A31PHE00.0470.01513.3070.4530.4530.0000.0000.0000.000
31A32ARG10.7680.86016.161-15.568-15.5680.0000.0000.0000.000
32A33ILE0-0.008-0.00910.364-0.124-0.1240.0000.0000.0000.000
33A34MET0-0.002-0.00210.2431.3281.3280.0000.0000.0000.000
34A35ILE00.0090.00214.023-0.250-0.2500.0000.0000.0000.000
35A36LEU0-0.0010.00113.661-0.429-0.4290.0000.0000.0000.000
36A37VAL0-0.080-0.0389.9390.0670.0670.0000.0000.0000.000
37A38VAL00.0160.01313.3480.1770.1770.0000.0000.0000.000
38A39ALA00.0260.01116.496-0.448-0.4480.0000.0000.0000.000
39A40ALA0-0.048-0.01315.242-0.391-0.3910.0000.0000.0000.000
40A41LYS10.9370.93811.423-23.760-23.7600.0000.0000.0000.000
41A42GLU-1-0.898-0.92116.90414.25514.2550.0000.0000.0000.000
42A43VAL0-0.001-0.01419.892-0.604-0.6040.0000.0000.0000.000
43A44TRP0-0.023-0.02720.249-0.653-0.6530.0000.0000.0000.000
44A45GLY00.0250.03021.310-0.251-0.2510.0000.0000.0000.000
45A46ASP-1-0.761-0.86722.39611.57311.5730.0000.0000.0000.000
46A47GLU-1-0.865-0.88323.05213.31213.3120.0000.0000.0000.000
47A48GLN00.0500.01626.082-0.710-0.7100.0000.0000.0000.000
48A49ALA00.0280.01327.129-0.448-0.4480.0000.0000.0000.000
49A50ASP-1-0.899-0.94528.9099.9599.9590.0000.0000.0000.000
50A51PHE0-0.050-0.00831.022-0.255-0.2550.0000.0000.0000.000
51A52VAL00.0140.00432.466-0.119-0.1190.0000.0000.0000.000
52A53CYS00.000-0.00136.148-0.021-0.0210.0000.0000.0000.000
53A54ASN0-0.048-0.01538.818-0.052-0.0520.0000.0000.0000.000
54A55THR00.0520.00441.438-0.203-0.2030.0000.0000.0000.000
55A56LEU0-0.0040.00942.4540.1160.1160.0000.0000.0000.000
56A57GLN0-0.032-0.01943.7730.0820.0820.0000.0000.0000.000
57A58PRO00.0470.02140.8060.1770.1770.0000.0000.0000.000
58A59GLY00.002-0.00238.9770.1800.1800.0000.0000.0000.000
59A60CYS0-0.075-0.01137.7550.3080.3080.0000.0000.0000.000
60A61LYS10.9200.94131.632-9.629-9.6290.0000.0000.0000.000
61A62ASN00.011-0.00632.9140.2640.2640.0000.0000.0000.000
62A63VAL0-0.008-0.00633.0950.2230.2230.0000.0000.0000.000
63A64CYS0-0.0010.01835.253-0.011-0.0110.0000.0000.0000.000
64A65TYR00.0080.02325.5030.1020.1020.0000.0000.0000.000
65A66ASP-1-0.923-0.95930.37810.56410.5640.0000.0000.0000.000
66A67HIS0-0.026-0.01931.4480.1580.1580.0000.0000.0000.000
67A68TYR00.001-0.01432.894-0.258-0.2580.0000.0000.0000.000
68A69PHE0-0.107-0.04527.1990.1700.1700.0000.0000.0000.000
69A70PRO00.0180.02927.8040.4010.4010.0000.0000.0000.000
70A71ILE00.0090.00622.6340.5020.5020.0000.0000.0000.000
71A72SER0-0.041-0.02422.8940.1130.1130.0000.0000.0000.000
72A73HIS00.1240.04022.4900.8140.8140.0000.0000.0000.000
73A74ILE0-0.0400.00217.3950.5470.5470.0000.0000.0000.000
74A75ARG10.8430.88217.677-13.962-13.9620.0000.0000.0000.000
75A76LEU00.0230.03718.9740.4950.4950.0000.0000.0000.000
76A77TRP00.0140.00618.6670.8570.8570.0000.0000.0000.000
77A78ALA0-0.0140.00514.7150.7350.7350.0000.0000.0000.000
78A79LEU00.0530.01715.5271.1051.1050.0000.0000.0000.000
79A80GLN0-0.013-0.00217.609-0.168-0.1680.0000.0000.0000.000
80A81LEU00.005-0.01313.9260.1550.1550.0000.0000.0000.000
81A82ILE00.0040.01412.3661.2971.2970.0000.0000.0000.000
82A83PHE00.012-0.00114.3790.3520.3520.0000.0000.0000.000
83A84VAL0-0.015-0.01217.304-0.029-0.0290.0000.0000.0000.000
84A85SER0-0.026-0.00511.9380.8430.8430.0000.0000.0000.000
85A86THR0-0.046-0.02413.8610.8560.8560.0000.0000.0000.000
86A87PRO00.0110.01214.9780.1300.1300.0000.0000.0000.000
87A88ALA0-0.030-0.02114.689-0.363-0.3630.0000.0000.0000.000
88A89LEU00.0330.0129.1620.1100.1100.0000.0000.0000.000
89A90LEU00.0090.02613.1390.2620.2620.0000.0000.0000.000
90A91VAL00.010-0.00815.692-0.708-0.7080.0000.0000.0000.000
91A92ALA00.0170.00613.771-0.534-0.5340.0000.0000.0000.000
92A93MET00.0400.02612.1250.2380.2380.0000.0000.0000.000
93A94HIS00.0010.00814.837-1.246-1.2460.0000.0000.0000.000
94A95VAL0-0.039-0.02817.425-0.953-0.9530.0000.0000.0000.000
95A96ALA00.0010.00315.098-0.865-0.8650.0000.0000.0000.000
96A97TYR00.0610.05017.102-0.221-0.2210.0000.0000.0000.000
97A98ARG10.9210.93918.496-13.699-13.6990.0000.0000.0000.000
98A99ARG10.9150.95920.687-14.426-14.4260.0000.0000.0000.000
99A100HIS00.0470.01719.250-0.746-0.7460.0000.0000.0000.000
100A101GLU-1-0.787-0.88021.34412.31812.3180.0000.0000.0000.000
101A102LYS10.9310.95323.550-11.757-11.7570.0000.0000.0000.000
102A103LYS10.8770.95921.406-14.404-14.4040.0000.0000.0000.000
103A104ARG10.9150.95223.616-12.560-12.5600.0000.0000.0000.000
104A105LYS10.8740.91325.800-12.115-12.1150.0000.0000.0000.000
105A106PHE0-0.0170.00028.950-0.243-0.2430.0000.0000.0000.000
106A107ILE0-0.0290.00628.433-0.157-0.1570.0000.0000.0000.000
107A108LYS10.9380.97029.081-10.645-10.6450.0000.0000.0000.000
108A109GLY00.0580.04532.762-0.149-0.1490.0000.0000.0000.000
109A125LYS10.9950.97228.576-10.403-10.4030.0000.0000.0000.000
110A126VAL00.1530.07431.1130.1480.1480.0000.0000.0000.000
111A127ARG10.9440.96329.942-9.573-9.5730.0000.0000.0000.000
112A128ILE0-0.077-0.03624.2770.3580.3580.0000.0000.0000.000
113A129GLU-1-0.886-0.93426.62310.36110.3610.0000.0000.0000.000
114A130GLY00.0400.02729.137-0.065-0.0650.0000.0000.0000.000
115A131SER0-0.043-0.03826.3630.0460.0460.0000.0000.0000.000
116A132LEU0-0.045-0.02020.7510.1690.1690.0000.0000.0000.000
117A133TRP00.0230.01022.4900.7550.7550.0000.0000.0000.000
118A134TRP00.0810.06326.6140.0040.0040.0000.0000.0000.000
119A135THR0-0.010-0.02823.0230.2640.2640.0000.0000.0000.000
120A136TYR0-0.0090.00120.6160.2720.2720.0000.0000.0000.000
121A137THR00.0680.02923.5310.2390.2390.0000.0000.0000.000
122A138SER00.0110.01025.719-0.186-0.1860.0000.0000.0000.000
123A139SER0-0.061-0.01619.7270.1780.1780.0000.0000.0000.000
124A140ILE00.012-0.00422.6960.3040.3040.0000.0000.0000.000
125A141PHE00.0140.01824.239-0.046-0.0460.0000.0000.0000.000
126A142PHE00.0250.00322.101-0.015-0.0150.0000.0000.0000.000
127A143ARG10.8600.94817.907-15.816-15.8160.0000.0000.0000.000
128A144VAL00.0260.00422.1510.1690.1690.0000.0000.0000.000
129A145ILE0-0.0060.01324.548-0.345-0.3450.0000.0000.0000.000
130A146PHE0-0.026-0.02619.934-0.049-0.0490.0000.0000.0000.000
131A147GLU-1-0.804-0.91020.93914.88014.8800.0000.0000.0000.000
132A148ALA00.0050.00223.627-0.236-0.2360.0000.0000.0000.000
133A149ALA00.0080.01625.149-0.390-0.3900.0000.0000.0000.000
134A150PHE0-0.064-0.03520.110-0.156-0.1560.0000.0000.0000.000
135A151MET00.0250.03425.430-0.392-0.3920.0000.0000.0000.000
136A152TYR0-0.0120.00827.066-0.369-0.3690.0000.0000.0000.000
137A153VAL00.0760.03427.026-0.286-0.2860.0000.0000.0000.000
138A154PHE0-0.041-0.03922.253-0.158-0.1580.0000.0000.0000.000
139A155TYR0-0.037-0.01427.823-0.226-0.2260.0000.0000.0000.000
140A156VAL0-0.063-0.02131.378-0.333-0.3330.0000.0000.0000.000
141A157MET0-0.071-0.04228.863-0.118-0.1180.0000.0000.0000.000
142A158TYR0-0.050-0.07226.448-0.076-0.0760.0000.0000.0000.000
143A159ASP-1-0.888-0.92231.7388.9188.9180.0000.0000.0000.000
144A160GLY0-0.0120.00535.304-0.180-0.1800.0000.0000.0000.000
145A161PHE00.000-0.01132.4830.2210.2210.0000.0000.0000.000
146A162SER0-0.079-0.04131.2710.2390.2390.0000.0000.0000.000
147A163MET00.0210.02927.700-0.001-0.0010.0000.0000.0000.000
148A164GLN0-0.011-0.00232.987-0.085-0.0850.0000.0000.0000.000
149A165ARG10.9460.95734.790-8.075-8.0750.0000.0000.0000.000
150A166LEU0-0.0030.00936.1650.1450.1450.0000.0000.0000.000
151A167VAL00.0130.01235.853-0.037-0.0370.0000.0000.0000.000
152A168LYS10.8250.88938.492-7.284-7.2840.0000.0000.0000.000
153A170ASN00.013-0.01440.205-0.221-0.2210.0000.0000.0000.000
154A171ALA00.0630.01138.068-0.061-0.0610.0000.0000.0000.000
155A172TRP00.0570.00840.071-0.062-0.0620.0000.0000.0000.000
156A173PRO0-0.0510.00540.101-0.135-0.1350.0000.0000.0000.000
157A175PRO00.006-0.00143.650-0.096-0.0960.0000.0000.0000.000
158A176ASN0-0.031-0.01747.207-0.026-0.0260.0000.0000.0000.000
159A177THR00.0050.00544.7530.0910.0910.0000.0000.0000.000
160A178VAL00.0060.01041.402-0.107-0.1070.0000.0000.0000.000
161A179ASP-1-0.795-0.88641.9187.3367.3360.0000.0000.0000.000
162A181PHE00.002-0.00136.427-0.111-0.1110.0000.0000.0000.000
163A182VAL00.0250.01730.3410.2030.2030.0000.0000.0000.000
164A183SER00.0640.03928.666-0.112-0.1120.0000.0000.0000.000
165A184ARG10.8160.86724.185-11.825-11.8250.0000.0000.0000.000
166A185PRO00.0540.03229.4020.2560.2560.0000.0000.0000.000
167A186THR00.0240.01430.8770.0880.0880.0000.0000.0000.000
168A187GLU-1-0.842-0.90625.58511.83811.8380.0000.0000.0000.000
169A188LYS10.8640.92725.480-11.295-11.2950.0000.0000.0000.000
170A189THR00.0340.01626.3630.2750.2750.0000.0000.0000.000
171A190VAL0-0.029-0.00826.3650.1800.1800.0000.0000.0000.000
172A191PHE00.008-0.01720.2940.2090.2090.0000.0000.0000.000
173A192THR0-0.015-0.01723.6920.5330.5330.0000.0000.0000.000
174A193VAL00.0210.00425.9260.0110.0110.0000.0000.0000.000
175A194PHE00.0220.02423.3670.1900.1900.0000.0000.0000.000
176A195MET0-0.0120.00618.0810.2520.2520.0000.0000.0000.000
177A196ILE00.0760.02622.8100.3150.3150.0000.0000.0000.000
178A197ALA0-0.044-0.01225.879-0.218-0.2180.0000.0000.0000.000
179A198VAL0-0.037-0.03720.458-0.068-0.0680.0000.0000.0000.000
180A199SER00.0250.01622.9400.5490.5490.0000.0000.0000.000
181A200GLY00.0230.02223.849-0.086-0.0860.0000.0000.0000.000
182A201ILE00.005-0.00224.840-0.086-0.0860.0000.0000.0000.000
183A202CYS0-0.054-0.02820.8900.0260.0260.0000.0000.0000.000
184A203ILE00.0380.02823.4670.2460.2460.0000.0000.0000.000
185A204LEU00.0150.00826.191-0.131-0.1310.0000.0000.0000.000
186A205LEU00.0080.00823.236-0.117-0.1170.0000.0000.0000.000
187A206ASN00.011-0.02221.4950.1630.1630.0000.0000.0000.000
188A207VAL00.0310.01525.486-0.114-0.1140.0000.0000.0000.000
189A208THR0-0.005-0.00228.868-0.446-0.4460.0000.0000.0000.000
190A209GLU-1-0.801-0.88325.05511.76211.7620.0000.0000.0000.000
191A210LEU0-0.011-0.00527.980-0.050-0.0500.0000.0000.0000.000
192A211CYS0-0.0210.00129.658-0.410-0.4100.0000.0000.0000.000
193A212TYR00.020-0.01430.478-0.354-0.3540.0000.0000.0000.000
194A213LEU0-0.088-0.04627.347-0.124-0.1240.0000.0000.0000.000
195A214LEU00.0110.01331.970-0.107-0.1070.0000.0000.0000.000
196A215ILE0-0.043-0.00235.126-0.258-0.2580.0000.0000.0000.000
197A216ARG10.9310.97433.093-9.518-9.5180.0000.0000.0000.000
198A217TYR0-0.033-0.00834.4320.1960.1960.0000.0000.0000.000