Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: 6YVVZ

Calculation Name: 2POF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2POF

Chain ID: A

ChEMBL ID:

UniProt ID: Q8X7A5

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 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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2807094.367476
FMO2-HF: Nuclear repulsion 2718396.271658
FMO2-HF: Total energy -88698.095817
FMO2-MP2: Total energy -88954.146498


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:31:SER)


Summations of interaction energy for fragment #1(A:31:SER)
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.
-3.6052.6674.585-4.761-6.097-0.031
Interaction energy analysis for fragmet #1(A:31:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.012
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].
3A33THR00.0250.0203.095-2.1500.623-0.007-1.349-1.417-0.004
4A34LEU00.0540.0195.0670.4970.609-0.001-0.004-0.1070.000
5A35ARG10.8030.8995.4471.5671.5670.0000.0000.0000.000
6A36LYS10.8000.8927.5250.5900.5900.0000.0000.0000.000
7A37ILE00.0560.0378.8120.1190.1190.0000.0000.0000.000
8A38VAL0-0.009-0.01711.2350.1460.1460.0000.0000.0000.000
9A39LEU0-0.056-0.04111.6260.1070.1070.0000.0000.0000.000
10A40GLU-1-0.859-0.91811.551-0.276-0.2760.0000.0000.0000.000
11A41GLU-1-0.889-0.93512.630-0.447-0.4470.0000.0000.0000.000
12A42CYS0-0.139-0.05715.2950.0040.0040.0000.0000.0000.000
13A43LEU00.0250.01416.9340.0440.0440.0000.0000.0000.000
14A44PRO0-0.011-0.00917.3150.0340.0340.0000.0000.0000.000
15A45ASN00.0210.01619.6460.0510.0510.0000.0000.0000.000
16A46GLN00.0020.00221.2860.0120.0120.0000.0000.0000.000
17A47GLN0-0.056-0.04922.8510.0150.0150.0000.0000.0000.000
18A48GLN0-0.0250.00824.1310.0140.0140.0000.0000.0000.000
19A49ASN0-0.054-0.05023.9120.0240.0240.0000.0000.0000.000
20A50GLN0-0.054-0.01626.7090.0060.0060.0000.0000.0000.000
21A51ASN00.0300.04623.705-0.010-0.0100.0000.0000.0000.000
22A52PRO00.0130.00721.196-0.011-0.0110.0000.0000.0000.000
23A53SER0-0.023-0.02019.394-0.036-0.0360.0000.0000.0000.000
24A54PRO00.0430.01014.6570.0110.0110.0000.0000.0000.000
25A56ALA0-0.003-0.00917.9410.0340.0340.0000.0000.0000.000
26A57GLU-1-0.797-0.88320.432-0.157-0.1570.0000.0000.0000.000
27A58VAL00.0050.00218.950-0.038-0.0380.0000.0000.0000.000
28A59LYS10.8280.91221.3460.1960.1960.0000.0000.0000.000
29A60PRO00.0610.03021.792-0.001-0.0010.0000.0000.0000.000
30A61ASN0-0.028-0.01722.776-0.004-0.0040.0000.0000.0000.000
31A62ALA0-0.014-0.00524.4930.0130.0130.0000.0000.0000.000
32A63GLY00.0140.01320.910-0.002-0.0020.0000.0000.0000.000
33A64TYR0-0.063-0.04018.403-0.024-0.0240.0000.0000.0000.000
34A65VAL00.0260.00915.4820.0180.0180.0000.0000.0000.000
35A66VAL0-0.007-0.00417.515-0.016-0.0160.0000.0000.0000.000
36A67LEU00.0390.02012.3800.0080.0080.0000.0000.0000.000
37A68LYS10.7840.87916.4810.3110.3110.0000.0000.0000.000
38A69ASP-1-0.830-0.92113.517-0.560-0.5600.0000.0000.0000.000
39A70LEU00.0100.00510.9370.0530.0530.0000.0000.0000.000
40A71ASN0-0.055-0.01814.1470.0800.0800.0000.0000.0000.000
41A72GLY00.0950.05416.0180.0120.0120.0000.0000.0000.000
42A73PRO0-0.0030.00419.801-0.024-0.0240.0000.0000.0000.000
43A74LEU00.038-0.00422.567-0.010-0.0100.0000.0000.0000.000
44A75GLN0-0.0110.01015.935-0.002-0.0020.0000.0000.0000.000
45A76TYR0-0.002-0.00617.441-0.022-0.0220.0000.0000.0000.000
46A77LEU00.0030.01111.078-0.003-0.0030.0000.0000.0000.000
47A78LEU0-0.0150.01015.2280.0090.0090.0000.0000.0000.000
48A79MET0-0.024-0.01011.163-0.112-0.1120.0000.0000.0000.000
49A80PRO00.0230.03013.0050.0540.0540.0000.0000.0000.000
50A81THR00.012-0.00814.728-0.071-0.0710.0000.0000.0000.000
51A82TYR00.0400.01415.6850.0060.0060.0000.0000.0000.000
52A83ARG10.9670.9698.5480.3020.3020.0000.0000.0000.000
53A84ILE00.0220.03911.6640.0910.0910.0000.0000.0000.000
54A85ASN0-0.021-0.0127.439-0.290-0.2900.0000.0000.0000.000
55A86GLY00.0420.0057.880-0.166-0.1660.0000.0000.0000.000
56A87THR00.001-0.00610.3870.0340.0340.0000.0000.0000.000
57A88GLU-1-0.759-0.8658.9880.0580.0580.0000.0000.0000.000
58A89SER0-0.055-0.01612.7810.0290.0290.0000.0000.0000.000
59A90PRO00.0980.03314.231-0.013-0.0130.0000.0000.0000.000
60A91LEU00.0390.03515.659-0.005-0.0050.0000.0000.0000.000
61A92LEU0-0.052-0.00314.732-0.011-0.0110.0000.0000.0000.000
62A93THR0-0.070-0.05418.8990.0090.0090.0000.0000.0000.000
63A94ASP-1-0.806-0.87421.616-0.048-0.0480.0000.0000.0000.000
64A95PRO0-0.033-0.03623.377-0.012-0.0120.0000.0000.0000.000
65A96SER0-0.045-0.03524.560-0.003-0.0030.0000.0000.0000.000
66A97THR0-0.096-0.05019.066-0.018-0.0180.0000.0000.0000.000
67A98PRO00.0210.01320.9380.0070.0070.0000.0000.0000.000
68A99ASN00.0140.00121.326-0.020-0.0200.0000.0000.0000.000
69A100PHE00.020-0.01017.733-0.007-0.0070.0000.0000.0000.000
70A101PHE00.0120.00919.087-0.015-0.0150.0000.0000.0000.000
71A102TRP00.0200.01221.634-0.001-0.0010.0000.0000.0000.000
72A103LEU0-0.006-0.00221.7190.0010.0010.0000.0000.0000.000
73A104ALA00.005-0.00619.455-0.005-0.0050.0000.0000.0000.000
74A105TRP0-0.0040.00321.404-0.002-0.0020.0000.0000.0000.000
75A106GLN00.0290.01524.7280.0060.0060.0000.0000.0000.000
76A107ALA0-0.0220.00121.9430.0030.0030.0000.0000.0000.000
77A108ARG10.8480.88823.7480.1000.1000.0000.0000.0000.000
78A109ASP-1-0.807-0.87724.818-0.127-0.1270.0000.0000.0000.000
79A110PHE0-0.039-0.03822.7650.0020.0020.0000.0000.0000.000
80A111MET0-0.0180.01022.951-0.004-0.0040.0000.0000.0000.000
81A112SER00.0550.00925.0840.0060.0060.0000.0000.0000.000
82A113LYS10.8110.90326.6030.1510.1510.0000.0000.0000.000
83A114LYS10.8320.92722.8990.2020.2020.0000.0000.0000.000
84A115TYR00.0180.00226.7740.0020.0020.0000.0000.0000.000
85A116GLY0-0.0060.01029.1410.0070.0070.0000.0000.0000.000
86A117GLN0-0.032-0.00931.8650.0100.0100.0000.0000.0000.000
87A118PRO00.025-0.00931.646-0.007-0.0070.0000.0000.0000.000
88A119VAL00.0380.03027.4700.0040.0040.0000.0000.0000.000
89A120PRO00.0120.00430.6020.0000.0000.0000.0000.0000.000
90A121ASP-1-0.734-0.85529.913-0.093-0.0930.0000.0000.0000.000
91A122ARG10.8190.87129.4580.0490.0490.0000.0000.0000.000
92A123ALA00.0400.03129.0050.0040.0040.0000.0000.0000.000
93A124VAL0-0.0140.00824.415-0.009-0.0090.0000.0000.0000.000
94A125SER0-0.039-0.01622.5030.0120.0120.0000.0000.0000.000
95A126LEU0-0.0080.00019.985-0.022-0.0220.0000.0000.0000.000
96A127ALA00.0140.00517.3360.0270.0270.0000.0000.0000.000
97A128ILE0-0.015-0.00212.490-0.048-0.0480.0000.0000.0000.000
98A129ASN0-0.018-0.01211.4070.0500.0500.0000.0000.0000.000
99A130SER00.0980.04011.6670.0150.0150.0000.0000.0000.000
100A131ARG10.9430.9707.015-1.072-1.0720.0000.0000.0000.000
101A132THR0-0.091-0.0518.6510.3140.3140.0000.0000.0000.000
102A133GLY00.0440.03310.8640.0040.0040.0000.0000.0000.000
103A134ARG10.7610.8696.356-0.054-0.0540.0000.0000.0000.000
104A135THR00.0220.0084.7100.1990.338-0.001-0.033-0.1050.000
105A136GLN00.0110.0092.415-3.606-1.1653.405-2.822-3.024-0.021
106A137ASN0-0.0040.0022.2620.5501.3221.190-0.547-1.416-0.006
107A138HIS00.0290.0074.6430.1470.182-0.001-0.006-0.0280.000
108A139PHE00.0070.0097.936-0.030-0.0300.0000.0000.0000.000
109A140HIS0-0.015-0.0307.3360.0960.0960.0000.0000.0000.000
110A141ILE0-0.041-0.00311.9380.0630.0630.0000.0000.0000.000
111A142HIS10.8660.93112.0900.3320.3320.0000.0000.0000.000
112A143ILE00.0090.01215.8770.0470.0470.0000.0000.0000.000
113A144SER00.032-0.02118.782-0.014-0.0140.0000.0000.0000.000
114A145CYS0-0.063-0.00120.8390.0130.0130.0000.0000.0000.000
115A146ILE0-0.022-0.00223.037-0.002-0.0020.0000.0000.0000.000
116A147ARG10.8500.89323.0290.0520.0520.0000.0000.0000.000
117A148PRO00.0470.01026.2500.0050.0050.0000.0000.0000.000
118A149ASP-1-0.768-0.84427.444-0.032-0.0320.0000.0000.0000.000
119A150VAL0-0.003-0.00825.0630.0040.0040.0000.0000.0000.000
120A151ARG10.7640.86228.3370.0600.0600.0000.0000.0000.000
121A152GLU-1-0.883-0.94030.385-0.025-0.0250.0000.0000.0000.000
122A153GLN0-0.003-0.00729.1740.0040.0040.0000.0000.0000.000
123A154LEU0-0.0020.00027.3580.0040.0040.0000.0000.0000.000
124A155ASP-1-0.764-0.83731.916-0.044-0.0440.0000.0000.0000.000
125A156ASN0-0.057-0.03335.0670.0030.0030.0000.0000.0000.000
126A157ASN0-0.017-0.00733.8550.0060.0060.0000.0000.0000.000
127A158LEU0-0.0210.00335.9810.0010.0010.0000.0000.0000.000
128A159ALA0-0.022-0.01436.9250.0000.0000.0000.0000.0000.000
129A160ASN0-0.040-0.02836.5330.0020.0020.0000.0000.0000.000
130A161ILE0-0.029-0.00432.1210.0030.0030.0000.0000.0000.000
131A162SER00.0520.03334.778-0.003-0.0030.0000.0000.0000.000
132A163SER0-0.021-0.01434.088-0.001-0.0010.0000.0000.0000.000
133A164ARG10.8820.92833.3630.0010.0010.0000.0000.0000.000
134A165TRP00.003-0.01324.9250.0000.0000.0000.0000.0000.000
135A166LEU00.0150.01430.8300.0050.0050.0000.0000.0000.000
136A167PRO0-0.016-0.01729.971-0.003-0.0030.0000.0000.0000.000
137A168LEU00.0170.01929.096-0.003-0.0030.0000.0000.0000.000
138A169PRO0-0.009-0.01031.5610.0050.0050.0000.0000.0000.000
139A170GLY00.0290.02232.868-0.004-0.0040.0000.0000.0000.000
140A171GLY0-0.051-0.01128.8860.0040.0040.0000.0000.0000.000
141A172LEU00.0220.00325.108-0.009-0.0090.0000.0000.0000.000
142A173ARG10.8670.91321.3320.0260.0260.0000.0000.0000.000
143A174GLY00.0240.03125.1480.0040.0040.0000.0000.0000.000
144A175HIS10.7630.86420.643-0.052-0.0520.0000.0000.0000.000
145A176GLU-1-0.722-0.84225.0340.0700.0700.0000.0000.0000.000
146A177TYR0-0.054-0.05120.835-0.001-0.0010.0000.0000.0000.000
147A178LEU0-0.0080.01225.640-0.003-0.0030.0000.0000.0000.000
148A179ALA00.018-0.00426.470-0.007-0.0070.0000.0000.0000.000
149A180ARG10.7890.86728.8640.0280.0280.0000.0000.0000.000
150A181ARG10.8590.92930.1580.0220.0220.0000.0000.0000.000
151A182VAL0-0.014-0.00829.0210.0020.0020.0000.0000.0000.000
152A183THR00.017-0.01732.416-0.003-0.0030.0000.0000.0000.000
153A184GLU-1-0.780-0.89131.495-0.076-0.0760.0000.0000.0000.000
154A185SER00.001-0.00732.420-0.004-0.0040.0000.0000.0000.000
155A186GLU-1-0.812-0.87831.839-0.034-0.0340.0000.0000.0000.000
156A187LEU00.017-0.00826.136-0.002-0.0020.0000.0000.0000.000
157A188VAL0-0.048-0.00528.264-0.007-0.0070.0000.0000.0000.000
158A189GLN00.0050.01630.417-0.004-0.0040.0000.0000.0000.000
159A190ARG10.8730.90727.5330.0410.0410.0000.0000.0000.000
160A191SER00.0570.03522.3690.0000.0000.0000.0000.0000.000
161A192PRO00.0680.01322.0410.0100.0100.0000.0000.0000.000
162A193PHE00.002-0.00416.8650.0080.0080.0000.0000.0000.000
163A194MET00.0540.05721.5590.0140.0140.0000.0000.0000.000
164A195MET0-0.013-0.00224.7790.0070.0070.0000.0000.0000.000
165A196LEU0-0.0080.01721.0910.0060.0060.0000.0000.0000.000
166A197ALA0-0.006-0.01323.0370.0090.0090.0000.0000.0000.000
167A198GLU-1-0.847-0.90124.7940.0060.0060.0000.0000.0000.000
168A199GLU-1-0.865-0.90228.059-0.011-0.0110.0000.0000.0000.000
169A200VAL0-0.018-0.00725.5760.0020.0020.0000.0000.0000.000
170A201PRO00.0380.00527.1750.0030.0030.0000.0000.0000.000
171A202GLU-1-0.859-0.93325.1430.0920.0920.0000.0000.0000.000
172A203ALA0-0.020-0.00722.5160.0110.0110.0000.0000.0000.000
173A204ARG10.8350.87721.400-0.006-0.0060.0000.0000.0000.000
174A205GLU-1-0.889-0.92121.6090.0960.0960.0000.0000.0000.000
175A206HIS10.8000.90219.243-0.094-0.0940.0000.0000.0000.000
176A207MET00.0470.05617.3680.0200.0200.0000.0000.0000.000
177A208GLY00.0250.00513.825-0.008-0.0080.0000.0000.0000.000
178A209SER0-0.129-0.07413.5980.0480.0480.0000.0000.0000.000
179A210TYR00.0480.00216.246-0.005-0.0050.0000.0000.0000.000
180A211GLY0-0.045-0.00815.3850.0050.0050.0000.0000.0000.000
181A212LEU0-0.034-0.01216.7740.0070.0070.0000.0000.0000.000
182A213ALA00.018-0.00818.456-0.026-0.0260.0000.0000.0000.000
183A214MET0-0.0370.00521.0920.0090.0090.0000.0000.0000.000
184A215VAL00.0390.01724.113-0.013-0.0130.0000.0000.0000.000
185A216ARG10.7710.89326.8650.0770.0770.0000.0000.0000.000
186A217GLN00.007-0.01530.3610.0040.0040.0000.0000.0000.000
187A218SER00.0450.00933.422-0.003-0.0030.0000.0000.0000.000
188A219ASP-1-0.754-0.82136.774-0.038-0.0380.0000.0000.0000.000
189A220ASN0-0.066-0.03335.328-0.003-0.0030.0000.0000.0000.000
190A221SER0-0.021-0.02334.747-0.003-0.0030.0000.0000.0000.000
191A222PHE00.003-0.02028.198-0.004-0.0040.0000.0000.0000.000
192A223VAL00.0180.01828.3030.0060.0060.0000.0000.0000.000
193A224LEU0-0.037-0.01024.893-0.010-0.0100.0000.0000.0000.000
194A225LEU00.0110.00023.7120.0100.0100.0000.0000.0000.000
195A226ALA00.016-0.00121.779-0.009-0.0090.0000.0000.0000.000
196A227THR0-0.018-0.00319.2820.0140.0140.0000.0000.0000.000
197A228GLN00.0460.01719.481-0.011-0.0110.0000.0000.0000.000
198A229ARG10.8950.94414.619-0.376-0.3760.0000.0000.0000.000
199A230ASN0-0.005-0.01418.7310.0140.0140.0000.0000.0000.000
200A231LEU0-0.013-0.00920.0390.0030.0030.0000.0000.0000.000
201A232LEU00.0110.01321.848-0.004-0.0040.0000.0000.0000.000
202A233THR0-0.008-0.02024.257-0.003-0.0030.0000.0000.0000.000
203A234LEU0-0.007-0.00819.546-0.005-0.0050.0000.0000.0000.000
204A235ASN00.0220.02519.6620.0100.0100.0000.0000.0000.000
205A236ARG10.8700.90611.242-0.412-0.4120.0000.0000.0000.000
206A237ALA00.0370.02714.7080.0300.0300.0000.0000.0000.000
207A238SER0-0.010-0.01614.1660.0030.0030.0000.0000.0000.000
208A239ALA00.0760.04215.555-0.017-0.0170.0000.0000.0000.000
209A240GLU-1-0.787-0.87213.067-0.255-0.2550.0000.0000.0000.000
210A241GLU-1-0.854-0.87316.9060.0240.0240.0000.0000.0000.000
211A242ILE00.0110.00119.3440.0060.0060.0000.0000.0000.000
212A243GLN0-0.073-0.05017.802-0.019-0.0190.0000.0000.0000.000
213A244ASP-1-0.825-0.93021.338-0.093-0.0930.0000.0000.0000.000
214A245HIS0-0.069-0.02615.7260.0030.0030.0000.0000.0000.000
215A246GLN00.002-0.01520.272-0.015-0.0150.0000.0000.0000.000
216A248GLU-1-0.821-0.89826.144-0.065-0.0650.0000.0000.0000.000
217A249ILE0-0.105-0.04427.7950.0060.0060.0000.0000.0000.000
218A250LEU0-0.105-0.04928.1020.0040.0040.0000.0000.0000.000