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: 98VN2

Calculation Name: 1V8E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1V8E

Chain ID: A

ChEMBL ID:

UniProt ID: Q53W25

Base Structure: X-ray

Registration Date: 2023-09-23

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2510147.663007
FMO2-HF: Nuclear repulsion 2429493.151326
FMO2-HF: Total energy -80654.51168
FMO2-MP2: Total energy -80896.253542


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:8:PRO)


Summations of interaction energy for fragment #1(A:8:PRO)
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.
-7.462-2.8149.75-4.548-9.85-0.032
Interaction energy analysis for fragmet #1(A:8:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.026
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].
3A10ARG10.7910.8723.5700.9392.8440.005-0.839-1.0720.001
4A11LEU0-0.033-0.0285.7560.7100.7100.0000.0000.0000.000
5A12GLY00.0690.0218.5530.0510.0510.0000.0000.0000.000
6A13HIS0-0.066-0.05711.9860.0940.0940.0000.0000.0000.000
7A14ARG10.8480.91813.7580.3600.3600.0000.0000.0000.000
8A15GLY0-0.0110.00115.4010.0560.0560.0000.0000.0000.000
9A16ALA0-0.010-0.01714.948-0.084-0.0840.0000.0000.0000.000
10A17PRO00.0520.02316.2030.0490.0490.0000.0000.0000.000
11A18LEU0-0.040-0.00718.1870.0330.0330.0000.0000.0000.000
12A19LYS10.8440.92718.0720.3430.3430.0000.0000.0000.000
13A20ALA00.0430.02721.6470.0250.0250.0000.0000.0000.000
14A21LYS10.8490.92122.2700.1480.1480.0000.0000.0000.000
15A22GLU-1-0.806-0.88520.532-0.276-0.2760.0000.0000.0000.000
16A23ASN0-0.042-0.04720.0340.0090.0090.0000.0000.0000.000
17A24THR00.0340.01221.5550.0250.0250.0000.0000.0000.000
18A25LEU00.017-0.01122.123-0.023-0.0230.0000.0000.0000.000
19A26GLU-1-0.931-0.96222.424-0.202-0.2020.0000.0000.0000.000
20A27SER00.0200.01619.415-0.028-0.0280.0000.0000.0000.000
21A28PHE00.007-0.01117.020-0.037-0.0370.0000.0000.0000.000
22A29ARG10.9230.97617.7060.1480.1480.0000.0000.0000.000
23A30LEU00.0080.00218.839-0.016-0.0160.0000.0000.0000.000
24A31ALA0-0.035-0.01214.283-0.030-0.0300.0000.0000.0000.000
25A32LEU0-0.009-0.00713.537-0.072-0.0720.0000.0000.0000.000
26A33GLU-1-0.911-0.96514.955-0.212-0.2120.0000.0000.0000.000
27A34ALA0-0.088-0.03514.5070.0230.0230.0000.0000.0000.000
28A35GLY0-0.009-0.00412.230-0.016-0.0160.0000.0000.0000.000
29A36LEU0-0.080-0.0309.196-0.126-0.1260.0000.0000.0000.000
30A37ASP-1-0.764-0.8445.529-2.320-2.3200.0000.0000.0000.000
31A38GLY00.0440.0048.8710.2640.2640.0000.0000.0000.000
32A39VAL0-0.055-0.01111.299-0.106-0.1060.0000.0000.0000.000
33A40GLH0-0.037-0.02412.1770.0230.0230.0000.0000.0000.000
34A41LEU0-0.005-0.00913.8440.0170.0170.0000.0000.0000.000
35A42ASP-1-0.740-0.84217.625-0.299-0.2990.0000.0000.0000.000
36A43VAL0-0.003-0.02020.1840.0160.0160.0000.0000.0000.000
37A44TRP0-0.007-0.00623.2910.0080.0080.0000.0000.0000.000
38A45PRO0-0.067-0.02726.6810.0020.0020.0000.0000.0000.000
39A46THR00.007-0.03629.5210.0000.0000.0000.0000.0000.000
40A47ARG10.8040.88132.6620.0650.0650.0000.0000.0000.000
41A48ASP-1-0.874-0.90835.362-0.072-0.0720.0000.0000.0000.000
42A49GLY0-0.078-0.03932.7330.0030.0030.0000.0000.0000.000
43A50VAL0-0.0330.00029.9600.0000.0000.0000.0000.0000.000
44A51PHE00.003-0.00425.414-0.001-0.0010.0000.0000.0000.000
45A52ALA00.0230.01526.677-0.005-0.0050.0000.0000.0000.000
46A53VAL0-0.030-0.02021.617-0.007-0.0070.0000.0000.0000.000
47A54ARG10.8110.85823.9670.1420.1420.0000.0000.0000.000
48A55HIS00.0450.01921.794-0.007-0.0070.0000.0000.0000.000
49A56ASP-1-0.872-0.92523.526-0.143-0.1430.0000.0000.0000.000
50A57PRO0-0.0020.02127.0310.0040.0040.0000.0000.0000.000
51A58ASP-1-0.881-0.94629.324-0.097-0.0970.0000.0000.0000.000
52A59THR0-0.031-0.03631.772-0.006-0.0060.0000.0000.0000.000
53A60PRO0-0.011-0.01634.0210.0050.0050.0000.0000.0000.000
54A61LEU0-0.026-0.00936.8980.0050.0050.0000.0000.0000.000
55A62GLY00.0080.02037.1750.0050.0050.0000.0000.0000.000
56A63PRO00.0230.01833.849-0.006-0.0060.0000.0000.0000.000
57A64VAL00.0280.00129.4800.0050.0050.0000.0000.0000.000
58A65PHE0-0.039-0.01332.5550.0060.0060.0000.0000.0000.000
59A66GLN0-0.064-0.03633.8910.0060.0060.0000.0000.0000.000
60A67VAL00.0080.00935.7410.0050.0050.0000.0000.0000.000
61A68ASP-1-0.762-0.84335.567-0.066-0.0660.0000.0000.0000.000
62A69TYR00.019-0.03230.0290.0010.0010.0000.0000.0000.000
63A70ALA0-0.024-0.01934.480-0.004-0.0040.0000.0000.0000.000
64A71ASP-1-0.876-0.93237.126-0.068-0.0680.0000.0000.0000.000
65A72LEU0-0.019-0.02132.175-0.003-0.0030.0000.0000.0000.000
66A73LYS10.8080.90730.4800.1140.1140.0000.0000.0000.000
67A74ALA0-0.023-0.00934.549-0.001-0.0010.0000.0000.0000.000
68A75GLN0-0.071-0.03035.9830.0040.0040.0000.0000.0000.000
69A76GLU-1-0.840-0.89630.054-0.142-0.1420.0000.0000.0000.000
70A77PRO00.0460.02132.403-0.006-0.0060.0000.0000.0000.000
71A78ASP-1-0.856-0.91128.732-0.151-0.1510.0000.0000.0000.000
72A79LEU00.0150.01827.398-0.013-0.0130.0000.0000.0000.000
73A80PRO00.0040.02124.2460.0130.0130.0000.0000.0000.000
74A81ARG10.8270.89527.1130.0910.0910.0000.0000.0000.000
75A82LEU00.019-0.00821.154-0.005-0.0050.0000.0000.0000.000
76A83GLU-1-0.842-0.90623.480-0.107-0.1070.0000.0000.0000.000
77A84GLU-1-0.860-0.93024.967-0.123-0.1230.0000.0000.0000.000
78A85VAL0-0.003-0.00319.291-0.006-0.0060.0000.0000.0000.000
79A86LEU0-0.023-0.01619.003-0.010-0.0100.0000.0000.0000.000
80A87ALA00.0230.02121.0280.0080.0080.0000.0000.0000.000
81A88LEU0-0.0020.00219.7480.0090.0090.0000.0000.0000.000
82A89LYS10.8080.90115.2710.0760.0760.0000.0000.0000.000
83A90GLU-1-0.972-0.98219.444-0.049-0.0490.0000.0000.0000.000
84A91ALA0-0.056-0.02021.2700.0150.0150.0000.0000.0000.000
85A92PHE0-0.022-0.01615.961-0.002-0.0020.0000.0000.0000.000
86A93PRO00.0610.02616.876-0.018-0.0180.0000.0000.0000.000
87A94GLN0-0.040-0.02512.5360.0010.0010.0000.0000.0000.000
88A95ALA0-0.0020.03012.258-0.019-0.0190.0000.0000.0000.000
89A96VAL0-0.043-0.0139.0800.1010.1010.0000.0000.0000.000
90A97PHE0-0.005-0.01712.415-0.100-0.1000.0000.0000.0000.000
91A98ASN00.0430.03411.8080.1150.1150.0000.0000.0000.000
92A99VAL0-0.002-0.01313.890-0.017-0.0170.0000.0000.0000.000
93A100GLU-1-0.759-0.87816.732-0.257-0.2570.0000.0000.0000.000
94A101LEU0-0.045-0.02518.2000.0140.0140.0000.0000.0000.000
95A102LYS10.7950.91119.3130.2560.2560.0000.0000.0000.000
96A103SER0-0.046-0.05323.7190.0100.0100.0000.0000.0000.000
97A104PHE00.0830.06126.738-0.004-0.0040.0000.0000.0000.000
98A105PRO0-0.015-0.02628.1130.0070.0070.0000.0000.0000.000
99A106GLY00.0420.02930.3320.0040.0040.0000.0000.0000.000
100A107LEU0-0.031-0.03231.8860.0060.0060.0000.0000.0000.000
101A108GLY00.0030.01428.334-0.002-0.0020.0000.0000.0000.000
102A109GLU-1-0.870-0.95128.261-0.062-0.0620.0000.0000.0000.000
103A110GLU-1-0.897-0.94130.163-0.053-0.0530.0000.0000.0000.000
104A111ALA00.0320.01828.1180.0020.0020.0000.0000.0000.000
105A112ALA00.0510.02026.097-0.002-0.0020.0000.0000.0000.000
106A113ARG10.9020.95526.8650.0490.0490.0000.0000.0000.000
107A114ARG10.8410.91029.3880.0650.0650.0000.0000.0000.000
108A115LEU00.0290.02221.9540.0030.0030.0000.0000.0000.000
109A116ALA00.001-0.00424.7140.0010.0010.0000.0000.0000.000
110A117ALA0-0.050-0.02525.7830.0070.0070.0000.0000.0000.000
111A118LEU0-0.0080.00725.8920.0060.0060.0000.0000.0000.000
112A119LEU00.0140.00020.3930.0010.0010.0000.0000.0000.000
113A120ARG10.9590.98522.9820.0170.0170.0000.0000.0000.000
114A121GLY0-0.033-0.02423.4940.0000.0000.0000.0000.0000.000
115A122ARG10.8760.95720.8880.0790.0790.0000.0000.0000.000
116A123GLU-1-0.899-0.94717.5670.0800.0800.0000.0000.0000.000
117A124GLY0-0.040-0.02514.074-0.021-0.0210.0000.0000.0000.000
118A125VAL0-0.012-0.00514.572-0.063-0.0630.0000.0000.0000.000
119A126TRP0-0.024-0.0119.2220.0510.0510.0000.0000.0000.000
120A127VAL0-0.0020.00315.264-0.040-0.0400.0000.0000.0000.000
121A128SER00.003-0.00414.6040.0050.0050.0000.0000.0000.000
122A129SER00.013-0.02316.6880.0070.0070.0000.0000.0000.000
123A130PHE00.0350.03017.6380.0060.0060.0000.0000.0000.000
124A131ASP-1-0.791-0.88320.698-0.082-0.0820.0000.0000.0000.000
125A132PRO00.0330.00223.3880.0050.0050.0000.0000.0000.000
126A133LEU00.0110.00324.3500.0110.0110.0000.0000.0000.000
127A134ALA00.0010.01024.2720.0080.0080.0000.0000.0000.000
128A135LEU00.0110.00619.4180.0070.0070.0000.0000.0000.000
129A136LEU0-0.0180.00123.2480.0130.0130.0000.0000.0000.000
130A137ALA0-0.060-0.03026.0810.0100.0100.0000.0000.0000.000
131A138LEU00.0100.00021.4700.0080.0080.0000.0000.0000.000
132A139ARG10.7910.87418.2660.0000.0000.0000.0000.0000.000
133A140LYS10.9190.95924.1920.0210.0210.0000.0000.0000.000
134A141ALA0-0.055-0.03127.4180.0060.0060.0000.0000.0000.000
135A142ALA0-0.004-0.00423.9500.0030.0030.0000.0000.0000.000
136A143PRO0-0.025-0.02123.191-0.001-0.0010.0000.0000.0000.000
137A144GLY0-0.016-0.00321.3800.0090.0090.0000.0000.0000.000
138A145LEU0-0.0080.02118.7230.0090.0090.0000.0000.0000.000
139A146PRO00.0240.01314.506-0.004-0.0040.0000.0000.0000.000
140A147LEU0-0.019-0.01516.299-0.035-0.0350.0000.0000.0000.000
141A148GLY00.0230.01014.1770.0170.0170.0000.0000.0000.000
142A149PHE0-0.028-0.02715.099-0.004-0.0040.0000.0000.0000.000
143A150LEU0-0.0190.00814.036-0.020-0.0200.0000.0000.0000.000
144A151MET0-0.057-0.01515.7270.0440.0440.0000.0000.0000.000
145A152ALA00.0380.00916.738-0.031-0.0310.0000.0000.0000.000
146A153GLU-1-0.902-0.94119.262-0.128-0.1280.0000.0000.0000.000
147A154ASP-1-0.812-0.89419.009-0.126-0.1260.0000.0000.0000.000
148A155HIS0-0.022-0.00720.0640.0270.0270.0000.0000.0000.000
149A156SER00.035-0.03818.0280.0100.0100.0000.0000.0000.000
150A157ALA0-0.058-0.02619.8710.0160.0160.0000.0000.0000.000
151A158LEU00.0140.00022.3800.0120.0120.0000.0000.0000.000
152A159LEU00.0130.01416.6920.0090.0090.0000.0000.0000.000
153A160PRO0-0.103-0.05820.4080.0130.0130.0000.0000.0000.000
154A161CYS0-0.051-0.02122.8130.0100.0100.0000.0000.0000.000
155A162LEU0-0.0070.01820.748-0.003-0.0030.0000.0000.0000.000
156A163GLY0-0.021-0.00621.3850.0120.0120.0000.0000.0000.000
157A164VAL0-0.031-0.02816.597-0.009-0.0090.0000.0000.0000.000
158A165GLU-1-0.759-0.84113.3850.0410.0410.0000.0000.0000.000
159A166ALA00.0060.00110.9570.0370.0370.0000.0000.0000.000
160A167VAL0-0.0080.00311.4810.0030.0030.0000.0000.0000.000
161A168HIS0-0.018-0.02610.903-0.062-0.0620.0000.0000.0000.000
162A169PRO00.0220.02810.6140.0230.0230.0000.0000.0000.000
163A170HIS00.1180.06412.013-0.080-0.0800.0000.0000.0000.000
164A171HIS0-0.023-0.06411.5050.0320.0320.0000.0000.0000.000
165A172ALA0-0.022-0.00812.6100.0200.0200.0000.0000.0000.000
166A173LEU0-0.067-0.02915.1870.0370.0370.0000.0000.0000.000
167A174VAL0-0.054-0.0089.8190.0290.0290.0000.0000.0000.000
168A175THR00.0540.02513.203-0.008-0.0080.0000.0000.0000.000
169A176GLU-1-0.902-0.95813.546-0.008-0.0080.0000.0000.0000.000
170A177GLU-1-0.960-0.98714.571-0.038-0.0380.0000.0000.0000.000
171A178ALA00.0200.02014.8720.0200.0200.0000.0000.0000.000
172A179VAL00.0190.0069.7920.0140.0140.0000.0000.0000.000
173A180ALA00.0060.01012.5950.0510.0510.0000.0000.0000.000
174A181GLY0-0.024-0.01115.0210.0310.0310.0000.0000.0000.000
175A182TRP00.004-0.03011.3090.0090.0090.0000.0000.0000.000
176A183ARG10.7960.8656.206-0.276-0.2760.0000.0000.0000.000
177A184LYS10.9200.98213.271-0.030-0.0300.0000.0000.0000.000
178A185ARG10.8880.94616.110-0.027-0.0270.0000.0000.0000.000
179A186GLY0-0.018-0.00713.853-0.003-0.0030.0000.0000.0000.000
180A187LEU0-0.068-0.01812.5770.0200.0200.0000.0000.0000.000
181A188PHE00.0060.0025.1820.0260.0260.0000.0000.0000.000
182A189VAL00.000-0.0107.352-0.084-0.0840.0000.0000.0000.000
183A190VAL0-0.024-0.0106.019-0.198-0.1980.0000.0000.0000.000
184A191ALA00.0260.0196.7740.1570.1570.0000.0000.0000.000
185A192TRP0-0.063-0.0148.497-0.151-0.1510.0000.0000.0000.000
186A193THR00.0190.01311.1770.0700.0700.0000.0000.0000.000
187A194VAL00.009-0.0018.7350.0720.0720.0000.0000.0000.000
188A195ASN0-0.008-0.02211.023-0.143-0.1430.0000.0000.0000.000
189A196GLU-1-0.920-0.96312.810-0.301-0.3010.0000.0000.0000.000
190A197GLU-1-0.847-0.91910.974-0.442-0.4420.0000.0000.0000.000
191A198GLY00.0100.00110.973-0.026-0.0260.0000.0000.0000.000
192A199GLU-1-0.701-0.80711.423-0.405-0.4050.0000.0000.0000.000
193A200ALA00.0120.0017.363-0.041-0.0410.0000.0000.0000.000
194A201ARG10.8690.9096.7070.2590.2590.0000.0000.0000.000
195A202ARG10.7580.8508.2090.3980.3980.0000.0000.0000.000
196A203LEU0-0.001-0.0087.1480.0430.0430.0000.0000.0000.000
197A204LEU00.0250.0042.1200.346-1.1234.889-0.730-2.691-0.001
198A205ALA0-0.051-0.0034.5630.1230.198-0.001-0.006-0.0680.000
199A206LEU0-0.037-0.0217.5290.1300.1300.0000.0000.0000.000
200A207GLY0-0.020-0.0055.6560.1190.1190.0000.0000.0000.000
201A208LEU0-0.042-0.0224.6560.0120.243-0.001-0.064-0.1660.000
202A209ASP-1-0.735-0.8242.462-3.320-1.1241.706-1.641-2.261-0.022
203A210GLY0-0.011-0.0022.570-2.232-0.2181.529-1.564-1.979-0.014
204A211LEU0-0.035-0.0123.3670.6690.746-0.0020.303-0.3770.000
205A212ILE00.0160.0165.367-0.101-0.131-0.001-0.0010.0320.000
206A213GLY00.0290.0018.8620.1080.1080.0000.0000.0000.000
207A214ASP-1-0.785-0.87511.076-0.470-0.4700.0000.0000.0000.000
208A215ARG10.8450.92213.1180.4570.4570.0000.0000.0000.000
209A216PRO00.0530.01511.574-0.091-0.0910.0000.0000.0000.000
210A217GLU-1-0.840-0.92110.925-0.614-0.6140.0000.0000.0000.000
211A218VAL0-0.042-0.0169.6300.0060.0060.0000.0000.0000.000
212A219LEU00.007-0.0046.873-0.093-0.0930.0000.0000.0000.000
213A220LEU0-0.024-0.0056.248-0.426-0.4260.0000.0000.0000.000
214A221PRO0-0.038-0.0147.743-0.068-0.0680.0000.0000.0000.000
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