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: 76VVK

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 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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2802936.556118
FMO2-HF: Nuclear repulsion 2714239.90524
FMO2-HF: Total energy -88696.650878
FMO2-MP2: Total energy -88952.834487


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.
-1.9385.4812.149-4.258-5.311-0.025
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 : 0.018 / q_NPA : -0.009
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].
3A33THR00.0400.0353.651-3.2620.727-0.047-2.039-1.904-0.007
4A34LEU00.0520.0185.672-0.015-0.0150.0000.0000.0000.000
5A35ARG10.8170.9046.2361.4891.4890.0000.0000.0000.000
6A36LYS10.9590.9767.303-1.507-1.5070.0000.0000.0000.000
7A37ILE00.0480.0549.647-0.027-0.0270.0000.0000.0000.000
8A38VAL0-0.029-0.02611.4310.0200.0200.0000.0000.0000.000
9A39LEU0-0.076-0.06211.6360.0200.0200.0000.0000.0000.000
10A40GLU-1-0.959-0.97811.7970.4130.4130.0000.0000.0000.000
11A41GLU-1-0.906-0.94112.7490.2420.2420.0000.0000.0000.000
12A42CYS0-0.131-0.06015.848-0.042-0.0420.0000.0000.0000.000
13A43LEU00.0140.01217.1550.0030.0030.0000.0000.0000.000
14A44PRO00.004-0.00617.5320.0000.0000.0000.0000.0000.000
15A45ASN00.0770.05720.2090.0040.0040.0000.0000.0000.000
16A46GLN0-0.026-0.00521.618-0.003-0.0030.0000.0000.0000.000
17A47GLN0-0.040-0.04623.044-0.009-0.0090.0000.0000.0000.000
18A48GLN0-0.0270.01224.432-0.006-0.0060.0000.0000.0000.000
19A49ASN0-0.045-0.04324.9000.0020.0020.0000.0000.0000.000
20A50GLN0-0.065-0.02826.637-0.007-0.0070.0000.0000.0000.000
21A51ASN0-0.0050.04223.702-0.004-0.0040.0000.0000.0000.000
22A52PRO00.014-0.00721.5640.0050.0050.0000.0000.0000.000
23A53SER0-0.038-0.01019.900-0.003-0.0030.0000.0000.0000.000
24A54PRO00.058-0.00615.0860.0010.0010.0000.0000.0000.000
25A56ALA0-0.018-0.01718.4820.0180.0180.0000.0000.0000.000
26A57GLU-1-0.909-0.96620.689-0.094-0.0940.0000.0000.0000.000
27A58VAL00.0140.01719.289-0.025-0.0250.0000.0000.0000.000
28A59LYS10.9420.97521.6070.1040.1040.0000.0000.0000.000
29A60PRO00.0600.02221.978-0.020-0.0200.0000.0000.0000.000
30A61ASN0-0.010-0.00923.045-0.011-0.0110.0000.0000.0000.000
31A62ALA0-0.032-0.00824.2980.0000.0000.0000.0000.0000.000
32A63GLY00.0050.00720.778-0.013-0.0130.0000.0000.0000.000
33A64TYR0-0.042-0.03518.411-0.041-0.0410.0000.0000.0000.000
34A65VAL00.0220.01015.3800.0340.0340.0000.0000.0000.000
35A66VAL00.0090.00517.663-0.034-0.0340.0000.0000.0000.000
36A67LEU00.0280.01212.6180.0260.0260.0000.0000.0000.000
37A68LYS10.7850.89516.3710.0530.0530.0000.0000.0000.000
38A69ASP-1-0.845-0.93113.095-0.217-0.2170.0000.0000.0000.000
39A70LEU0-0.013-0.01411.5080.0330.0330.0000.0000.0000.000
40A71ASN0-0.039-0.01014.4600.0510.0510.0000.0000.0000.000
41A72GLY00.0870.05316.190-0.026-0.0260.0000.0000.0000.000
42A73PRO00.0130.00819.720-0.003-0.0030.0000.0000.0000.000
43A74LEU00.022-0.01122.3070.0010.0010.0000.0000.0000.000
44A75GLN00.0150.03615.401-0.050-0.0500.0000.0000.0000.000
45A76TYR00.0060.00617.4750.0190.0190.0000.0000.0000.000
46A77LEU00.0020.00811.158-0.031-0.0310.0000.0000.0000.000
47A78LEU0-0.0110.01815.3330.0300.0300.0000.0000.0000.000
48A79MET0-0.030-0.01811.250-0.112-0.1120.0000.0000.0000.000
49A80PRO00.0230.02413.0040.0670.0670.0000.0000.0000.000
50A81THR00.0060.00314.747-0.032-0.0320.0000.0000.0000.000
51A82TYR00.0510.01715.4240.0330.0330.0000.0000.0000.000
52A83ARG10.9390.9549.0540.4320.4320.0000.0000.0000.000
53A84ILE00.0390.04711.5500.0320.0320.0000.0000.0000.000
54A85ASN00.015-0.0047.652-0.022-0.0220.0000.0000.0000.000
55A86GLY00.0120.0008.268-0.193-0.1930.0000.0000.0000.000
56A87THR00.0060.00210.7890.0310.0310.0000.0000.0000.000
57A88GLU-1-0.747-0.8509.231-1.089-1.0890.0000.0000.0000.000
58A89SER0-0.087-0.03212.7370.0520.0520.0000.0000.0000.000
59A90PRO00.0970.03014.2430.0360.0360.0000.0000.0000.000
60A91LEU00.0290.02415.9290.0320.0320.0000.0000.0000.000
61A92LEU0-0.0320.00315.0480.0270.0270.0000.0000.0000.000
62A93THR0-0.082-0.03918.9160.0230.0230.0000.0000.0000.000
63A94ASP-1-0.829-0.89221.864-0.185-0.1850.0000.0000.0000.000
64A95PRO0-0.032-0.04723.670-0.004-0.0040.0000.0000.0000.000
65A96SER0-0.027-0.01825.0790.0120.0120.0000.0000.0000.000
66A97THR0-0.098-0.04819.304-0.001-0.0010.0000.0000.0000.000
67A98PRO00.0190.01720.7000.0080.0080.0000.0000.0000.000
68A99ASN00.0360.02421.482-0.040-0.0400.0000.0000.0000.000
69A100PHE00.013-0.02017.7670.0050.0050.0000.0000.0000.000
70A101PHE00.0080.00418.8850.0040.0040.0000.0000.0000.000
71A102TRP00.0210.02221.8330.0080.0080.0000.0000.0000.000
72A103LEU00.0000.00021.8880.0130.0130.0000.0000.0000.000
73A104ALA00.001-0.01219.7630.0100.0100.0000.0000.0000.000
74A105TRP00.0360.01021.5860.0110.0110.0000.0000.0000.000
75A106GLN00.0240.00524.9330.0120.0120.0000.0000.0000.000
76A107ALA0-0.0160.00421.9930.0120.0120.0000.0000.0000.000
77A108ARG10.9000.94323.7570.1030.1030.0000.0000.0000.000
78A109ASP-1-0.898-0.95025.094-0.068-0.0680.0000.0000.0000.000
79A110PHE0-0.073-0.04822.9760.0130.0130.0000.0000.0000.000
80A111MET0-0.0200.01122.9640.0040.0040.0000.0000.0000.000
81A112SER00.0680.02625.1060.0090.0090.0000.0000.0000.000
82A113LYS10.9140.97026.8620.0720.0720.0000.0000.0000.000
83A114LYS10.8650.95622.4640.0370.0370.0000.0000.0000.000
84A115TYR0-0.007-0.02026.8390.0060.0060.0000.0000.0000.000
85A116GLY00.0050.01629.1490.0050.0050.0000.0000.0000.000
86A117GLN0-0.027-0.01131.8870.0050.0050.0000.0000.0000.000
87A118PRO0-0.015-0.02531.952-0.004-0.0040.0000.0000.0000.000
88A119VAL00.0260.02627.9070.0030.0030.0000.0000.0000.000
89A120PRO00.0140.00531.042-0.004-0.0040.0000.0000.0000.000
90A121ASP-1-0.748-0.88330.284-0.087-0.0870.0000.0000.0000.000
91A122ARG10.7840.87829.7060.0590.0590.0000.0000.0000.000
92A123ALA00.0270.01628.787-0.002-0.0020.0000.0000.0000.000
93A124VAL0-0.0030.01224.135-0.005-0.0050.0000.0000.0000.000
94A125SER0-0.027-0.00422.692-0.003-0.0030.0000.0000.0000.000
95A126LEU0-0.010-0.00320.233-0.008-0.0080.0000.0000.0000.000
96A127ALA00.0380.01417.7720.0060.0060.0000.0000.0000.000
97A128ILE0-0.0110.00713.007-0.029-0.0290.0000.0000.0000.000
98A129ASN00.0020.00811.5340.0630.0630.0000.0000.0000.000
99A130SER00.0530.02711.860-0.109-0.1090.0000.0000.0000.000
100A131ARG11.0000.9687.1851.0981.0980.0000.0000.0000.000
101A132THR0-0.077-0.0308.5090.0210.0210.0000.0000.0000.000
102A133GLY00.0070.02210.8530.1300.1300.0000.0000.0000.000
103A134ARG10.7670.8845.9881.5181.5180.0000.0000.0000.000
104A135THR00.0200.0024.831-0.160-0.1600.0000.0000.0000.000
105A136GLN00.0200.0152.634-2.624-0.1811.034-1.493-1.985-0.014
106A137ASN0-0.009-0.0092.3771.0151.9621.163-0.717-1.392-0.004
107A138HIS00.0210.0124.5480.2100.250-0.001-0.009-0.0300.000
108A139PHE0-0.008-0.0117.8160.0630.0630.0000.0000.0000.000
109A140HIS0-0.041-0.0397.6400.1480.1480.0000.0000.0000.000
110A141ILE0-0.0280.01212.206-0.002-0.0020.0000.0000.0000.000
111A142HIS10.8740.92611.7760.3590.3590.0000.0000.0000.000
112A143ILE00.0000.00316.0780.0130.0130.0000.0000.0000.000
113A144SER00.034-0.02419.1720.0170.0170.0000.0000.0000.000
114A145CYS0-0.070-0.03421.1860.0010.0010.0000.0000.0000.000
115A146ILE0-0.0250.00823.059-0.008-0.0080.0000.0000.0000.000
116A147ARG10.8310.88823.3020.0830.0830.0000.0000.0000.000
117A148PRO00.0750.01726.308-0.003-0.0030.0000.0000.0000.000
118A149ASP-1-0.744-0.83728.007-0.072-0.0720.0000.0000.0000.000
119A150VAL0-0.001-0.00325.303-0.002-0.0020.0000.0000.0000.000
120A151ARG10.7760.89528.6550.0830.0830.0000.0000.0000.000
121A152GLU-1-0.910-0.94530.626-0.050-0.0500.0000.0000.0000.000
122A153GLN0-0.023-0.02429.843-0.005-0.0050.0000.0000.0000.000
123A154LEU0-0.025-0.01927.675-0.002-0.0020.0000.0000.0000.000
124A155ASP-1-0.809-0.89132.260-0.071-0.0710.0000.0000.0000.000
125A156ASN0-0.009-0.01135.4180.0030.0030.0000.0000.0000.000
126A157ASN0-0.020-0.00934.8700.0000.0000.0000.0000.0000.000
127A158LEU00.0330.02836.313-0.003-0.0030.0000.0000.0000.000
128A159ALA0-0.039-0.02937.288-0.002-0.0020.0000.0000.0000.000
129A160ASN0-0.051-0.02937.0350.0020.0020.0000.0000.0000.000
130A161ILE0-0.0240.01032.377-0.005-0.0050.0000.0000.0000.000
131A162SER00.0380.01635.3200.0010.0010.0000.0000.0000.000
132A163SER0-0.036-0.01434.133-0.005-0.0050.0000.0000.0000.000
133A164ARG10.9700.98633.6890.0960.0960.0000.0000.0000.000
134A165TRP00.000-0.00725.086-0.002-0.0020.0000.0000.0000.000
135A166LEU0-0.007-0.00831.0210.0040.0040.0000.0000.0000.000
136A167PRO0-0.006-0.00129.961-0.004-0.0040.0000.0000.0000.000
137A168LEU00.0200.01129.2250.0060.0060.0000.0000.0000.000
138A169PRO0-0.005-0.00931.5230.0000.0000.0000.0000.0000.000
139A170GLY00.0060.01332.9650.0020.0020.0000.0000.0000.000
140A171GLY0-0.048-0.01128.9510.0000.0000.0000.0000.0000.000
141A172LEU00.0220.00325.3630.0040.0040.0000.0000.0000.000
142A173ARG10.8720.91721.5010.0860.0860.0000.0000.0000.000
143A174GLY00.0280.02824.8050.0010.0010.0000.0000.0000.000
144A175HIS10.7820.87720.9590.1280.1280.0000.0000.0000.000
145A176GLU-1-0.862-0.92525.360-0.124-0.1240.0000.0000.0000.000
146A177TYR0-0.041-0.06121.090-0.023-0.0230.0000.0000.0000.000
147A178LEU0-0.0180.00925.6680.0120.0120.0000.0000.0000.000
148A179ALA00.024-0.00626.665-0.010-0.0100.0000.0000.0000.000
149A180ARG10.8400.92029.1500.1330.1330.0000.0000.0000.000
150A181ARG10.8560.91230.3850.0790.0790.0000.0000.0000.000
151A182VAL0-0.020-0.01729.085-0.002-0.0020.0000.0000.0000.000
152A183THR00.017-0.00832.4950.0010.0010.0000.0000.0000.000
153A184GLU-1-0.798-0.92832.181-0.102-0.1020.0000.0000.0000.000
154A185SER00.0150.00932.599-0.003-0.0030.0000.0000.0000.000
155A186GLU-1-0.830-0.90732.364-0.111-0.1110.0000.0000.0000.000
156A187LEU00.008-0.00326.769-0.008-0.0080.0000.0000.0000.000
157A188VAL0-0.018-0.00228.559-0.011-0.0110.0000.0000.0000.000
158A189GLN0-0.063-0.01030.5730.0020.0020.0000.0000.0000.000
159A190ARG10.9350.96227.9100.1420.1420.0000.0000.0000.000
160A191SER00.0630.04022.6940.0030.0030.0000.0000.0000.000
161A192PRO00.0690.00522.3420.0030.0030.0000.0000.0000.000
162A193PHE0-0.004-0.00417.102-0.005-0.0050.0000.0000.0000.000
163A194MET0-0.0140.00521.896-0.002-0.0020.0000.0000.0000.000
164A195MET00.0010.01124.9740.0060.0060.0000.0000.0000.000
165A196LEU0-0.0100.00421.0440.0040.0040.0000.0000.0000.000
166A197ALA0-0.004-0.03123.0720.0050.0050.0000.0000.0000.000
167A198GLU-1-0.980-0.99324.848-0.156-0.1560.0000.0000.0000.000
168A199GLU-1-0.886-0.94028.167-0.132-0.1320.0000.0000.0000.000
169A200VAL0-0.063-0.01625.1930.0100.0100.0000.0000.0000.000
170A201PRO00.0550.00527.235-0.011-0.0110.0000.0000.0000.000
171A202GLU-1-0.919-0.95125.905-0.166-0.1660.0000.0000.0000.000
172A203ALA00.0160.02222.989-0.019-0.0190.0000.0000.0000.000
173A204ARG10.9880.97321.7240.1670.1670.0000.0000.0000.000
174A205GLU-1-0.930-0.95321.828-0.219-0.2190.0000.0000.0000.000
175A206HIS10.8230.90819.1190.2250.2250.0000.0000.0000.000
176A207MET00.0600.06217.696-0.004-0.0040.0000.0000.0000.000
177A208GLY00.016-0.00114.206-0.015-0.0150.0000.0000.0000.000
178A209SER0-0.143-0.06314.125-0.021-0.0210.0000.0000.0000.000
179A210TYR00.0720.02416.6490.0350.0350.0000.0000.0000.000
180A211GLY0-0.0190.00815.874-0.058-0.0580.0000.0000.0000.000
181A212LEU0-0.026-0.01417.1430.0310.0310.0000.0000.0000.000
182A213ALA00.0370.00518.934-0.020-0.0200.0000.0000.0000.000
183A214MET0-0.051-0.00921.4610.0010.0010.0000.0000.0000.000
184A215VAL00.0420.02424.4320.0010.0010.0000.0000.0000.000
185A216ARG10.8510.95527.1460.0900.0900.0000.0000.0000.000
186A217GLN0-0.007-0.03430.5320.0040.0040.0000.0000.0000.000
187A218SER00.0340.00433.6100.0010.0010.0000.0000.0000.000
188A219ASP-1-0.742-0.82936.939-0.075-0.0750.0000.0000.0000.000
189A220ASN0-0.050-0.03635.5780.0000.0000.0000.0000.0000.000
190A221SER0-0.052-0.00234.790-0.006-0.0060.0000.0000.0000.000
191A222PHE00.006-0.01728.4510.0000.0000.0000.0000.0000.000
192A223VAL00.0110.01128.2680.0030.0030.0000.0000.0000.000
193A224LEU0-0.062-0.02425.196-0.010-0.0100.0000.0000.0000.000
194A225LEU00.0140.00223.9460.0080.0080.0000.0000.0000.000
195A226ALA00.0360.00421.906-0.022-0.0220.0000.0000.0000.000
196A227THR0-0.042-0.01319.6040.0170.0170.0000.0000.0000.000
197A228GLN00.0380.00619.715-0.015-0.0150.0000.0000.0000.000
198A229ARG10.9030.95213.9940.2970.2970.0000.0000.0000.000
199A230ASN00.0300.00118.7190.0200.0200.0000.0000.0000.000
200A231LEU0-0.002-0.00219.9700.0050.0050.0000.0000.0000.000
201A232LEU00.0250.01921.3320.0100.0100.0000.0000.0000.000
202A233THR00.0370.02123.9580.0050.0050.0000.0000.0000.000
203A234LEU00.0100.00319.4470.0020.0020.0000.0000.0000.000
204A235ASN00.0040.02219.713-0.017-0.0170.0000.0000.0000.000
205A236ARG10.8720.89711.1030.1310.1310.0000.0000.0000.000
206A237ALA00.0480.02314.757-0.055-0.0550.0000.0000.0000.000
207A238SER0-0.015-0.02214.430-0.062-0.0620.0000.0000.0000.000
208A239ALA00.0840.04215.6830.0310.0310.0000.0000.0000.000
209A240GLU-1-0.872-0.92713.471-0.221-0.2210.0000.0000.0000.000
210A241GLU-1-0.856-0.86717.063-0.127-0.1270.0000.0000.0000.000
211A242ILE0-0.010-0.00519.3510.0230.0230.0000.0000.0000.000
212A243GLN0-0.070-0.05017.921-0.007-0.0070.0000.0000.0000.000
213A244ASP-1-0.815-0.91221.269-0.052-0.0520.0000.0000.0000.000
214A245HIS0-0.088-0.05016.1460.0190.0190.0000.0000.0000.000
215A246GLN0-0.022-0.02420.9360.0110.0110.0000.0000.0000.000
216A248GLU-1-0.819-0.90526.172-0.024-0.0240.0000.0000.0000.000
217A249ILE0-0.112-0.04728.5290.0010.0010.0000.0000.0000.000
218A250LEU0-0.059-0.01728.3720.0010.0010.0000.0000.0000.000