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: 49J5N

Calculation Name: 1VZV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VZV

Chain ID: A

ChEMBL ID:

UniProt ID: P09286

Base Structure: X-ray

Registration Date: 2023-06-22

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2489203.390537
FMO2-HF: Nuclear repulsion 2406925.480674
FMO2-HF: Total energy -82277.909863
FMO2-MP2: Total energy -82519.242997


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:11:GLU)


Summations of interaction energy for fragment #1(A:11:GLU)
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.
-88.129-85.1359.931-5.68-7.2420.031
Interaction energy analysis for fragmet #1(A:11:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.929 / q_NPA : -0.973
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].
3A13LEU00.0280.0213.833-1.2091.351-0.028-1.327-1.2050.006
4A14TYR0-0.021-0.0066.082-0.971-0.9710.0000.0000.0000.000
5A15VAL00.0090.0019.8550.0240.0240.0000.0000.0000.000
6A16ALA00.018-0.00513.257-0.364-0.3640.0000.0000.0000.000
7A17GLY00.0440.01816.4490.0380.0380.0000.0000.0000.000
8A18TYR0-0.060-0.01820.0610.0280.0280.0000.0000.0000.000
9A19LEU0-0.063-0.02221.440-0.020-0.0200.0000.0000.0000.000
10A20ALA0-0.020-0.02924.416-0.187-0.1870.0000.0000.0000.000
11A21LEU0-0.0190.00327.9380.0230.0230.0000.0000.0000.000
12A22TYR00.0380.00730.286-0.184-0.1840.0000.0000.0000.000
13A23SER0-0.0210.01133.337-0.153-0.1530.0000.0000.0000.000
14A24LYS10.9020.91932.510-9.107-9.1070.0000.0000.0000.000
15A25ASP-1-0.905-0.96431.1699.1999.1990.0000.0000.0000.000
16A26GLU-1-0.825-0.89033.0717.9817.9810.0000.0000.0000.000
17A27GLY00.0290.01636.2930.0770.0770.0000.0000.0000.000
18A28GLU-1-0.919-0.95736.8797.9137.9130.0000.0000.0000.000
19A29LEU0-0.130-0.08531.5760.2580.2580.0000.0000.0000.000
20A30ASN0-0.008-0.02132.7250.3100.3100.0000.0000.0000.000
21A31ILE0-0.0110.00929.9410.0260.0260.0000.0000.0000.000
22A32THR00.036-0.00233.092-0.053-0.0530.0000.0000.0000.000
23A33PRO00.0850.01333.7870.1190.1190.0000.0000.0000.000
24A34GLU-1-0.915-0.93834.5457.4967.4960.0000.0000.0000.000
25A35ILE0-0.074-0.01032.3920.0480.0480.0000.0000.0000.000
26A36VAL00.0100.00628.8990.2140.2140.0000.0000.0000.000
27A37ARG10.8850.90030.582-8.451-8.4510.0000.0000.0000.000
28A38SER0-0.027-0.03132.3920.0620.0620.0000.0000.0000.000
29A39ALA0-0.042-0.02229.2950.0870.0870.0000.0000.0000.000
30A40LEU0-0.059-0.04125.7400.4490.4490.0000.0000.0000.000
31A41PRO00.0510.01625.780-0.200-0.2000.0000.0000.0000.000
32A42PRO0-0.0270.00123.996-0.221-0.2210.0000.0000.0000.000
33A43THR0-0.017-0.00225.4750.3260.3260.0000.0000.0000.000
34A44SER0-0.014-0.00324.6330.3640.3640.0000.0000.0000.000
35A45LYS10.9030.94217.588-14.752-14.7520.0000.0000.0000.000
36A46ILE00.0150.01520.3410.1280.1280.0000.0000.0000.000
37A47PRO00.0020.00917.4230.7330.7330.0000.0000.0000.000
38A48ILE00.0470.01714.292-0.682-0.6820.0000.0000.0000.000
39A49ASN0-0.0240.00715.7940.7260.7260.0000.0000.0000.000
40A50ILE00.0450.01614.520-0.046-0.0460.0000.0000.0000.000
41A51ASP-1-0.860-0.95118.78211.74711.7470.0000.0000.0000.000
42A52HIS0-0.044-0.03221.874-0.661-0.6610.0000.0000.0000.000
43A53ARG10.8510.92821.130-12.681-12.6810.0000.0000.0000.000
44A54LYS10.9680.98020.812-10.319-10.3190.0000.0000.0000.000
45A55ASP-1-0.831-0.90121.17812.88712.8870.0000.0000.0000.000
46A56CYS0-0.058-0.04317.0370.5970.5970.0000.0000.0000.000
47A57VAL0-0.0030.00215.1660.0950.0950.0000.0000.0000.000
48A58VAL0-0.011-0.02511.6360.3340.3340.0000.0000.0000.000
49A59GLY00.0570.00910.8472.0062.0060.0000.0000.0000.000
50A60GLU-1-0.895-0.93512.27515.14415.1440.0000.0000.0000.000
51A61VAL00.0290.02614.1240.8250.8250.0000.0000.0000.000
52A62ILE0-0.042-0.02212.385-0.585-0.5850.0000.0000.0000.000
53A63ALA00.003-0.00315.956-0.543-0.5430.0000.0000.0000.000
54A64ILE0-0.022-0.00618.9770.3140.3140.0000.0000.0000.000
55A65ILE0-0.0090.00321.870-0.340-0.3400.0000.0000.0000.000
56A66GLU-1-0.803-0.88724.5189.2949.2940.0000.0000.0000.000
57A67ASP-1-0.821-0.91526.30110.43710.4370.0000.0000.0000.000
58A68ILE0-0.009-0.01428.244-0.240-0.2400.0000.0000.0000.000
59A69ARG10.8510.93128.901-10.386-10.3860.0000.0000.0000.000
60A70GLY00.0420.02128.791-0.129-0.1290.0000.0000.0000.000
61A71PRO0-0.0310.00125.6230.2160.2160.0000.0000.0000.000
62A72PHE00.0210.01819.0030.1770.1770.0000.0000.0000.000
63A73PHE0-0.044-0.03916.600-0.055-0.0550.0000.0000.0000.000
64A74LEU00.0670.04313.0720.3090.3090.0000.0000.0000.000
65A75GLY0-0.026-0.02413.813-0.745-0.7450.0000.0000.0000.000
66A76ILE0-0.0310.0107.0881.1621.1620.0000.0000.0000.000
67A77VAL00.0100.0098.877-1.559-1.5590.0000.0000.0000.000
68A78ARG10.9320.9854.319-34.954-34.7260.003-0.074-0.1570.000
69A79CYS0-0.031-0.0046.676-2.289-2.2890.0000.0000.0000.000
70A80PRO0-0.011-0.0046.1770.9000.9000.0000.0000.0000.000
71A81GLN00.0930.0207.1580.5640.5640.0000.0000.0000.000
72A82LEU0-0.004-0.0179.517-0.636-0.6360.0000.0000.0000.000
73A83HIS00.0270.0054.2571.3781.571-0.001-0.019-0.1720.000
74A84ALA0-0.0080.0078.771-0.355-0.3550.0000.0000.0000.000
75A85VAL00.0910.04110.766-1.038-1.0380.0000.0000.0000.000
76A86LEU0-0.038-0.01312.064-1.246-1.2460.0000.0000.0000.000
77A87PHE0-0.040-0.0346.872-0.427-0.4270.0000.0000.0000.000
78A88GLU-1-0.978-0.96512.61016.82516.8250.0000.0000.0000.000
79A89ALA0-0.029-0.01915.501-0.938-0.9380.0000.0000.0000.000
80A90ALA0-0.061-0.01815.521-1.013-1.0130.0000.0000.0000.000
81A91HIS00.0520.02417.4450.1900.1900.0000.0000.0000.000
82A92SER00.016-0.01518.3830.8810.8810.0000.0000.0000.000
83A93ASN0-0.053-0.02819.064-0.094-0.0940.0000.0000.0000.000
84A94PHE0-0.0230.02015.870-0.582-0.5820.0000.0000.0000.000
85A95PHE0-0.011-0.00912.9451.4071.4070.0000.0000.0000.000
86A96GLY00.0140.01417.115-0.613-0.6130.0000.0000.0000.000
87A97ASN00.045-0.00817.3571.4351.4350.0000.0000.0000.000
88A98ARG10.9360.96217.654-15.894-15.8940.0000.0000.0000.000
89A99ASP-1-0.805-0.89613.87519.81919.8190.0000.0000.0000.000
90A100SER0-0.048-0.02613.1482.0832.0830.0000.0000.0000.000
91A101VAL0-0.046-0.03112.9981.6661.6660.0000.0000.0000.000
92A102LEU0-0.027-0.01512.298-1.195-1.1950.0000.0000.0000.000
93A103SER00.0060.0249.5080.5790.5790.0000.0000.0000.000
94A104PRO0-0.009-0.0124.567-1.283-1.201-0.001-0.009-0.0710.000
95A105LEU00.0450.0452.059-3.641-3.7009.959-4.242-5.6580.025
96A106GLU-1-0.868-0.9655.06427.69827.688-0.001-0.0090.0210.000
97A107ARG10.9380.9757.978-33.537-33.5370.0000.0000.0000.000
98A108ALA0-0.0030.0136.189-3.034-3.0340.0000.0000.0000.000
99A109LEU00.032-0.0017.297-3.586-3.5860.0000.0000.0000.000
100A110TYR00.0000.0078.856-2.913-2.9130.0000.0000.0000.000
101A111LEU00.0030.00311.617-2.161-2.1610.0000.0000.0000.000
102A112VAL0-0.030-0.0089.518-1.709-1.7090.0000.0000.0000.000
103A113THR0-0.024-0.00412.179-1.550-1.5500.0000.0000.0000.000
104A114ASN0-0.053-0.03714.301-2.120-2.1200.0000.0000.0000.000
105A115TYR0-0.023-0.01216.178-1.113-1.1130.0000.0000.0000.000
106A116LEU0-0.074-0.03614.766-1.041-1.0410.0000.0000.0000.000
107A117PRO00.0350.04016.8970.3190.3190.0000.0000.0000.000
108A118SER0-0.014-0.01318.710-0.354-0.3540.0000.0000.0000.000
109A119VAL0-0.006-0.00218.2430.4550.4550.0000.0000.0000.000
110A120SER0-0.033-0.03520.822-0.743-0.7430.0000.0000.0000.000
111A121LEU00.0150.02523.2750.2800.2800.0000.0000.0000.000
112A122SER00.0200.00124.624-0.494-0.4940.0000.0000.0000.000
113A123SER0-0.018-0.01526.9200.1130.1130.0000.0000.0000.000
114A124LYS10.9260.97528.973-9.170-9.1700.0000.0000.0000.000
115A125ARG10.8970.95931.030-8.593-8.5930.0000.0000.0000.000
116A126LEU0-0.0410.02029.2360.0010.0010.0000.0000.0000.000
117A137PHE00.0340.00424.647-0.092-0.0920.0000.0000.0000.000
118A138THR00.040-0.01225.319-0.383-0.3830.0000.0000.0000.000
119A139HIS0-0.0400.00021.2890.3650.3650.0000.0000.0000.000
120A140VAL00.0230.03718.575-0.578-0.5780.0000.0000.0000.000
121A141ALA0-0.014-0.01219.3790.5440.5440.0000.0000.0000.000
122A142LEU00.0400.03914.049-0.175-0.1750.0000.0000.0000.000
123A143CYS0-0.050-0.03818.689-0.530-0.5300.0000.0000.0000.000
124A144VAL00.0890.06220.5340.2980.2980.0000.0000.0000.000
125A145VAL00.006-0.00922.5310.1460.1460.0000.0000.0000.000
126A146GLY00.0440.03124.950-0.164-0.1640.0000.0000.0000.000
127A147ARG10.9610.97326.249-9.756-9.7560.0000.0000.0000.000
128A148ARG10.8470.94427.864-10.174-10.1740.0000.0000.0000.000
129A149VAL00.0720.02528.2850.3570.3570.0000.0000.0000.000
130A150GLY00.0190.01726.929-0.041-0.0410.0000.0000.0000.000
131A151THR0-0.104-0.04323.8060.3700.3700.0000.0000.0000.000
132A152VAL00.0290.02220.6180.2540.2540.0000.0000.0000.000
133A153VAL0-0.082-0.04016.801-0.133-0.1330.0000.0000.0000.000
134A154ASN0-0.017-0.01315.046-0.012-0.0120.0000.0000.0000.000
135A155TYR0-0.006-0.03410.5150.1520.1520.0000.0000.0000.000
136A156ASP-1-0.809-0.9209.65125.21825.2180.0000.0000.0000.000
137A157CYS0-0.046-0.0415.1131.4151.4150.0000.0000.0000.000
138A158THR00.0290.0346.5551.2611.2610.0000.0000.0000.000
139A159PRO0-0.0010.0288.988-1.216-1.2160.0000.0000.0000.000
140A160GLU-1-0.889-0.97411.81320.03120.0310.0000.0000.0000.000
141A161SER00.0490.00711.668-1.374-1.3740.0000.0000.0000.000
142A162SER0-0.061-0.02411.480-0.554-0.5540.0000.0000.0000.000
143A163ILE00.015-0.02013.904-1.103-1.1030.0000.0000.0000.000
144A164GLU-1-0.937-0.94616.38915.66115.6610.0000.0000.0000.000
145A165PRO0-0.0010.00517.211-1.060-1.0600.0000.0000.0000.000
146A166PHE0-0.062-0.02718.021-0.732-0.7320.0000.0000.0000.000
147A167ARG10.8630.89722.516-11.780-11.7800.0000.0000.0000.000
148A168VAL0-0.0030.01225.667-0.318-0.3180.0000.0000.0000.000
149A169LEU0-0.0180.01321.476-0.271-0.2710.0000.0000.0000.000
150A170SER00.0950.04825.2590.2470.2470.0000.0000.0000.000
151A171MET00.0700.02421.7620.3810.3810.0000.0000.0000.000
152A172GLU-1-0.920-0.96224.42310.01110.0110.0000.0000.0000.000
153A173SER00.017-0.00224.2230.0930.0930.0000.0000.0000.000
154A174LYS10.8340.92020.566-12.852-12.8520.0000.0000.0000.000
155A175ALA0-0.0020.00320.1470.5680.5680.0000.0000.0000.000
156A176ARG10.9620.98821.041-11.210-11.2100.0000.0000.0000.000
157A177LEU0-0.025-0.01518.1980.1720.1720.0000.0000.0000.000
158A178LEU00.0600.01515.3200.4850.4850.0000.0000.0000.000
159A179SER0-0.0400.00316.9330.5740.5740.0000.0000.0000.000
160A180LEU00.0210.00418.7870.0930.0930.0000.0000.0000.000
161A181VAL0-0.051-0.02912.6170.3480.3480.0000.0000.0000.000
162A182LYS10.9360.97114.882-16.394-16.3940.0000.0000.0000.000
163A183ASP-1-0.939-0.94816.22613.36213.3620.0000.0000.0000.000
164A184TYR0-0.103-0.09211.5340.7680.7680.0000.0000.0000.000
165A185ALA00.0610.04514.1071.1691.1690.0000.0000.0000.000
166A186GLY00.0090.00212.907-0.627-0.6270.0000.0000.0000.000
167A187LEU00.0120.0008.1480.9450.9450.0000.0000.0000.000
168A188ASN0-0.049-0.0427.3531.7991.7990.0000.0000.0000.000
169A189LYS10.9540.9747.547-15.338-15.3380.0000.0000.0000.000
170A190VAL00.0070.0135.8271.6171.6170.0000.0000.0000.000
171A191TRP00.0010.0038.200-1.539-1.5390.0000.0000.0000.000
172A192LYS10.9610.98410.123-21.132-21.1320.0000.0000.0000.000
173A193VAL00.0150.01912.210-1.348-1.3480.0000.0000.0000.000
174A194SER0-0.010-0.03714.3710.5560.5560.0000.0000.0000.000
175A195GLU-1-0.833-0.92314.71819.62319.6230.0000.0000.0000.000
176A196ASP-1-0.819-0.89016.69113.57013.5700.0000.0000.0000.000
177A197LYS10.8340.90518.725-14.384-14.3840.0000.0000.0000.000
178A198LEU0-0.033-0.00713.123-0.354-0.3540.0000.0000.0000.000
179A199ALA00.0650.02617.769-0.097-0.0970.0000.0000.0000.000
180A200LYS10.9280.97019.379-12.327-12.3270.0000.0000.0000.000
181A201VAL0-0.038-0.01719.396-0.498-0.4980.0000.0000.0000.000
182A202LEU00.0320.00215.007-0.324-0.3240.0000.0000.0000.000
183A203LEU00.0320.04719.712-0.195-0.1950.0000.0000.0000.000
184A204SER0-0.027-0.02222.921-0.651-0.6510.0000.0000.0000.000
185A205THR0-0.0130.00820.646-0.395-0.3950.0000.0000.0000.000
186A206ALA00.0360.03423.555-0.282-0.2820.0000.0000.0000.000
187A207VAL00.0840.02224.976-0.422-0.4220.0000.0000.0000.000
188A208ASN0-0.070-0.03627.244-0.748-0.7480.0000.0000.0000.000
189A209ASN0-0.071-0.05825.866-0.094-0.0940.0000.0000.0000.000
190A210MET0-0.045-0.00928.4320.0320.0320.0000.0000.0000.000
191A211LEU0-0.004-0.00630.028-0.105-0.1050.0000.0000.0000.000
192A212LEU0-0.0290.00727.604-0.250-0.2500.0000.0000.0000.000
193A213ARG10.9490.96131.134-8.460-8.4600.0000.0000.0000.000
194A214ASP-1-0.821-0.90231.4909.1909.1900.0000.0000.0000.000
195A215ARG10.9190.97225.003-11.168-11.1680.0000.0000.0000.000
196A216TRP00.045-0.00320.4270.0460.0460.0000.0000.0000.000
197A217ASP-1-0.829-0.89826.56510.10910.1090.0000.0000.0000.000
198A218VAL0-0.089-0.04627.647-0.065-0.0650.0000.0000.0000.000
199A219VAL00.026-0.00622.1890.0110.0110.0000.0000.0000.000
200A220ALA0-0.0040.01824.8840.2600.2600.0000.0000.0000.000
201A221LYS10.8810.92326.824-9.770-9.7700.0000.0000.0000.000
202A222ARG10.8910.95625.498-10.841-10.8410.0000.0000.0000.000
203A223ARG10.9750.99921.693-12.800-12.8000.0000.0000.0000.000
204A224ARG10.9330.95624.574-9.999-9.9990.0000.0000.0000.000
205A225GLU-1-0.820-0.89227.5779.3309.3300.0000.0000.0000.000
206A226ALA0-0.015-0.00223.633-0.149-0.1490.0000.0000.0000.000
207A227GLY00.0520.02225.1410.1080.1080.0000.0000.0000.000
208A228ILE00.0020.03419.4450.1040.1040.0000.0000.0000.000
209A229MET0-0.080-0.05423.024-0.263-0.2630.0000.0000.0000.000
210A230GLY0-0.004-0.01521.773-0.135-0.1350.0000.0000.0000.000
211A231HIS00.0700.05122.4090.2830.2830.0000.0000.0000.000