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: 8N92Y

Calculation Name: 1P2F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1P2F

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WXY0

Base Structure: X-ray

Registration Date: 2023-09-27

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2653193.772167
FMO2-HF: Nuclear repulsion 2565871.261719
FMO2-HF: Total energy -87322.510447
FMO2-MP2: Total energy -87580.046986


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-9.137-6.5669.194-3.915-7.849-0.014
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : 0.000
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].
3A3TRP00.0590.0342.660-5.795-1.9791.313-2.307-2.821-0.019
4A4LYS10.9170.9542.2040.3630.2352.650-0.517-2.0050.004
5A5ILE00.002-0.0045.4910.3590.3590.0000.0000.0000.000
6A6ALA00.0480.0389.2630.0130.0130.0000.0000.0000.000
7A7VAL0-0.038-0.02612.052-0.004-0.0040.0000.0000.0000.000
8A8VAL00.0130.00115.6560.0160.0160.0000.0000.0000.000
9A9ASP-1-0.798-0.93018.460-0.205-0.2050.0000.0000.0000.000
10A10ASP-1-0.846-0.92221.903-0.148-0.1480.0000.0000.0000.000
11A11ASP-1-0.824-0.89624.957-0.172-0.1720.0000.0000.0000.000
12A12LYS10.9810.95923.5640.1150.1150.0000.0000.0000.000
13A13ASN0-0.102-0.04823.844-0.020-0.0200.0000.0000.0000.000
14A14ILE00.0160.00821.470-0.024-0.0240.0000.0000.0000.000
15A15LEU0-0.0020.01218.591-0.041-0.0410.0000.0000.0000.000
16A16LYS10.9280.98319.1760.1910.1910.0000.0000.0000.000
17A17LYS10.8900.94520.4340.1920.1920.0000.0000.0000.000
18A18VAL00.0050.00416.808-0.033-0.0330.0000.0000.0000.000
19A19SER0-0.006-0.01015.698-0.065-0.0650.0000.0000.0000.000
20A20GLU-1-0.898-0.96715.887-0.395-0.3950.0000.0000.0000.000
21A21LYS10.7730.88717.7420.3900.3900.0000.0000.0000.000
22A22LEU00.041-0.00313.088-0.057-0.0570.0000.0000.0000.000
23A23GLN0-0.0090.00312.219-0.146-0.1460.0000.0000.0000.000
24A24GLN0-0.086-0.02812.152-0.108-0.1080.0000.0000.0000.000
25A25LEU0-0.026-0.0159.752-0.037-0.0370.0000.0000.0000.000
26A26GLY00.003-0.0027.308-0.745-0.7450.0000.0000.0000.000
27A27ARG10.8680.9285.9031.4691.4690.0000.0000.0000.000
28A28VAL00.0210.0178.217-0.036-0.0360.0000.0000.0000.000
29A29LYS10.8820.9589.3980.5310.5310.0000.0000.0000.000
30A30THR0-0.038-0.02412.450-0.002-0.0020.0000.0000.0000.000
31A31PHE00.0530.03013.0400.0070.0070.0000.0000.0000.000
32A32LEU0-0.017-0.01618.363-0.006-0.0060.0000.0000.0000.000
33A33THR00.0000.00621.3620.0050.0050.0000.0000.0000.000
34A34GLY00.0350.00120.379-0.012-0.0120.0000.0000.0000.000
35A35GLU-1-0.964-0.98919.939-0.047-0.0470.0000.0000.0000.000
36A36ASP-1-0.953-0.97518.802-0.130-0.1300.0000.0000.0000.000
37A37PHE0-0.052-0.03612.653-0.002-0.0020.0000.0000.0000.000
38A38LEU0-0.067-0.03915.3920.0110.0110.0000.0000.0000.000
39A39ASN00.0100.01917.4670.0330.0330.0000.0000.0000.000
40A40ASH0-0.108-0.08711.6430.0410.0410.0000.0000.0000.000
41A41GLU-1-0.892-0.94212.2590.1170.1170.0000.0000.0000.000
42A42GLU-1-0.990-0.9457.255-0.321-0.3210.0000.0000.0000.000
43A43ALA0-0.018-0.0106.161-0.023-0.0230.0000.0000.0000.000
44A44PHE0-0.008-0.0255.744-0.147-0.1470.0000.0000.0000.000
45A45HIS00.0580.0292.276-3.807-4.9245.231-1.091-3.0230.001
46A46VAL0-0.005-0.0047.653-0.055-0.0550.0000.0000.0000.000
47A47VAL00.0110.01310.723-0.050-0.0500.0000.0000.0000.000
48A48VAL0-0.036-0.02613.3990.0200.0200.0000.0000.0000.000
49A49LEU00.0030.04816.3090.0090.0090.0000.0000.0000.000
50A50ASP-1-0.749-0.83819.210-0.172-0.1720.0000.0000.0000.000
51A51VAL0-0.006-0.01322.8360.0130.0130.0000.0000.0000.000
52A52MET0-0.074-0.03625.4440.0190.0190.0000.0000.0000.000
53A53LEU00.0090.01421.573-0.010-0.0100.0000.0000.0000.000
54A54PRO0-0.028-0.02625.6220.0090.0090.0000.0000.0000.000
55A55ASP-1-0.769-0.88524.600-0.085-0.0850.0000.0000.0000.000
56A56TYR00.0010.01223.8540.0100.0100.0000.0000.0000.000
57A57SER00.0200.01726.060-0.012-0.0120.0000.0000.0000.000
58A58GLY00.057-0.03622.7840.0020.0020.0000.0000.0000.000
59A59TYR0-0.025-0.03522.259-0.003-0.0030.0000.0000.0000.000
60A60GLU-1-0.897-0.95723.621-0.047-0.0470.0000.0000.0000.000
61A61ILE00.0300.02618.3050.0090.0090.0000.0000.0000.000
62A62CYS0-0.062-0.02618.8390.0000.0000.0000.0000.0000.000
63A63ARG10.9270.96319.1890.0340.0340.0000.0000.0000.000
64A64MET00.0170.00619.5500.0130.0130.0000.0000.0000.000
65A65ILE0-0.030-0.00313.8360.0210.0210.0000.0000.0000.000
66A66LYS10.8060.88615.5320.1450.1450.0000.0000.0000.000
67A67GLU-1-0.916-0.94417.8530.0180.0180.0000.0000.0000.000
68A68THR0-0.065-0.03115.2300.0210.0210.0000.0000.0000.000
69A69ARG10.8840.94210.845-0.141-0.1410.0000.0000.0000.000
70A70PRO00.0430.02813.390-0.026-0.0260.0000.0000.0000.000
71A71GLU-1-0.924-0.9689.7420.2860.2860.0000.0000.0000.000
72A72THR0-0.086-0.03210.660-0.022-0.0220.0000.0000.0000.000
73A73TRP0-0.0030.00110.418-0.009-0.0090.0000.0000.0000.000
74A74VAL00.0180.00013.506-0.028-0.0280.0000.0000.0000.000
75A75ILE0-0.068-0.02516.2220.0030.0030.0000.0000.0000.000
76A76LEU00.0240.00818.436-0.005-0.0050.0000.0000.0000.000
77A77LEU0-0.029-0.01020.407-0.014-0.0140.0000.0000.0000.000
78A78THR00.0620.02123.3190.0200.0200.0000.0000.0000.000
79A79LEU00.0230.00226.981-0.009-0.0090.0000.0000.0000.000
80A80LEU0-0.0220.00130.4750.0030.0030.0000.0000.0000.000
81A81SER00.010-0.00930.478-0.007-0.0070.0000.0000.0000.000
82A82ASP-1-0.866-0.90331.600-0.102-0.1020.0000.0000.0000.000
83A83ASP-1-0.736-0.88033.263-0.101-0.1010.0000.0000.0000.000
84A84GLU-1-0.957-0.96633.739-0.075-0.0750.0000.0000.0000.000
85A85SER0-0.016-0.03330.7170.0020.0020.0000.0000.0000.000
86A86VAL0-0.035-0.01428.432-0.005-0.0050.0000.0000.0000.000
87A87LEU0-0.050-0.02828.903-0.001-0.0010.0000.0000.0000.000
88A88LYS11.0061.01829.3000.0860.0860.0000.0000.0000.000
89A89GLY00.0030.00225.6590.0010.0010.0000.0000.0000.000
90A90PHE0-0.057-0.05424.859-0.002-0.0020.0000.0000.0000.000
91A91GLU-1-0.973-0.98125.872-0.062-0.0620.0000.0000.0000.000
92A92ALA0-0.029-0.00523.6760.0090.0090.0000.0000.0000.000
93A93GLY00.0200.01821.9420.0060.0060.0000.0000.0000.000
94A94ALA0-0.006-0.00420.075-0.008-0.0080.0000.0000.0000.000
95A95ASP-1-0.795-0.88116.745-0.184-0.1840.0000.0000.0000.000
96A96ASP-1-0.768-0.88019.472-0.311-0.3110.0000.0000.0000.000
97A97TYR0-0.049-0.03921.0710.0060.0060.0000.0000.0000.000
98A98VAL0-0.011-0.02221.221-0.016-0.0160.0000.0000.0000.000
99A99THR0-0.0010.01424.1010.0070.0070.0000.0000.0000.000
100A100LYS10.7840.89525.3720.1630.1630.0000.0000.0000.000
101A101PRO00.007-0.00528.3340.0110.0110.0000.0000.0000.000
102A102PHE00.0380.00321.849-0.002-0.0020.0000.0000.0000.000
103A103ASN00.0220.01525.111-0.019-0.0190.0000.0000.0000.000
104A104PRO00.0660.01120.964-0.012-0.0120.0000.0000.0000.000
105A105GLU-1-0.834-0.90620.442-0.463-0.4630.0000.0000.0000.000
106A106ILE0-0.0200.00120.934-0.026-0.0260.0000.0000.0000.000
107A107LEU00.0280.01817.483-0.013-0.0130.0000.0000.0000.000
108A108LEU00.008-0.00114.960-0.046-0.0460.0000.0000.0000.000
109A109ALA0-0.015-0.00916.233-0.069-0.0690.0000.0000.0000.000
110A110ARG10.8800.92917.8140.2650.2650.0000.0000.0000.000
111A111VAL00.0560.03612.1120.0010.0010.0000.0000.0000.000
112A112LYS10.9560.97913.0620.6810.6810.0000.0000.0000.000
113A113ARG10.7630.88914.1080.3050.3050.0000.0000.0000.000
114A114PHE00.0160.01412.7700.0310.0310.0000.0000.0000.000
115A115LEU0-0.0050.0048.1400.0690.0690.0000.0000.0000.000
116A116GLU-1-0.948-0.98410.567-1.134-1.1340.0000.0000.0000.000
117A117ARG10.8510.92112.7100.5680.5680.0000.0000.0000.000
118A118GLU-1-0.914-0.93511.355-0.438-0.4380.0000.0000.0000.000
119A119LYS10.8530.93814.7330.3860.3860.0000.0000.0000.000
120A120LYS10.9180.95217.1440.1240.1240.0000.0000.0000.000
121A121GLY0-0.018-0.00619.4070.0090.0090.0000.0000.0000.000
122A122LEU0-0.043-0.00222.0950.0190.0190.0000.0000.0000.000
123A123TYR0-0.015-0.01521.640-0.003-0.0030.0000.0000.0000.000
124A124ASP-1-0.824-0.91924.750-0.068-0.0680.0000.0000.0000.000
125A125PHE0-0.002-0.01425.5540.0060.0060.0000.0000.0000.000
126A126GLY00.0210.01228.9370.0080.0080.0000.0000.0000.000
127A127ASP-1-0.876-0.94131.256-0.046-0.0460.0000.0000.0000.000
128A128LEU0-0.0230.01132.063-0.003-0.0030.0000.0000.0000.000
129A129LYS10.8890.96529.2110.0710.0710.0000.0000.0000.000
130A130ILE0-0.006-0.00928.0810.0020.0020.0000.0000.0000.000
131A131ASP-1-0.705-0.82527.141-0.178-0.1780.0000.0000.0000.000
132A132ALA0-0.035-0.04124.5700.0050.0050.0000.0000.0000.000
133A133THR0-0.100-0.07323.351-0.019-0.0190.0000.0000.0000.000
134A134GLY00.0090.00326.124-0.001-0.0010.0000.0000.0000.000
135A135PHE0-0.104-0.04328.4100.0090.0090.0000.0000.0000.000
136A136THR0-0.013-0.00130.9110.0130.0130.0000.0000.0000.000
137A137VAL0-0.0020.00131.532-0.005-0.0050.0000.0000.0000.000
138A138PHE00.001-0.00831.4960.0050.0050.0000.0000.0000.000
139A139LEU00.011-0.00134.5940.0000.0000.0000.0000.0000.000
140A140LYS10.9200.93736.3130.0420.0420.0000.0000.0000.000
141A141GLY00.0240.02035.6160.0020.0020.0000.0000.0000.000
142A142LYS10.9400.97836.6330.0570.0570.0000.0000.0000.000
143A143ARG10.8860.93235.1920.1030.1030.0000.0000.0000.000
144A144ILE0-0.022-0.00137.1790.0050.0050.0000.0000.0000.000
145A145HIS0-0.022-0.02038.743-0.007-0.0070.0000.0000.0000.000
146A146LEU00.010-0.01335.4370.0040.0040.0000.0000.0000.000
147A147PRO0-0.048-0.00638.134-0.005-0.0050.0000.0000.0000.000
148A148LYS11.0141.00634.1120.1350.1350.0000.0000.0000.000
149A149LYS10.9130.96535.2610.0970.0970.0000.0000.0000.000
150A150GLU-1-0.838-0.94735.573-0.086-0.0860.0000.0000.0000.000
151A151PHE00.0010.01229.705-0.001-0.0010.0000.0000.0000.000
152A152GLU-1-0.901-0.96231.079-0.146-0.1460.0000.0000.0000.000
153A153ILE0-0.0110.00130.598-0.005-0.0050.0000.0000.0000.000
154A154LEU0-0.004-0.00631.4570.0010.0010.0000.0000.0000.000
155A155LEU00.0090.01325.5290.0030.0030.0000.0000.0000.000
156A156PHE00.0300.02025.924-0.004-0.0040.0000.0000.0000.000
157A157LEU0-0.049-0.03226.8800.0000.0000.0000.0000.0000.000
158A158ALA0-0.006-0.00527.1560.0050.0050.0000.0000.0000.000
159A159GLU-1-0.912-0.97122.701-0.222-0.2220.0000.0000.0000.000
160A160ASN0-0.122-0.05322.444-0.014-0.0140.0000.0000.0000.000
161A161ALA00.0370.01824.6850.0170.0170.0000.0000.0000.000
162A162GLY0-0.052-0.02624.9330.0020.0020.0000.0000.0000.000
163A163LYS10.9500.97220.5610.1440.1440.0000.0000.0000.000
164A164VAL0-0.027-0.01327.431-0.002-0.0020.0000.0000.0000.000
165A165VAL00.0180.01728.671-0.005-0.0050.0000.0000.0000.000
166A166THR00.0430.00831.1350.0030.0030.0000.0000.0000.000
167A167ARG10.8780.91934.2330.0460.0460.0000.0000.0000.000
168A168GLU-1-0.916-0.95535.446-0.071-0.0710.0000.0000.0000.000
169A169LYS11.0071.01527.1780.1380.1380.0000.0000.0000.000
170A170LEU0-0.020-0.01132.148-0.008-0.0080.0000.0000.0000.000
171A171LEU0-0.065-0.03634.234-0.003-0.0030.0000.0000.0000.000
172A172GLU-1-0.915-0.95333.537-0.092-0.0920.0000.0000.0000.000
173A173THR0-0.083-0.03529.481-0.010-0.0100.0000.0000.0000.000
174A174PHE0-0.023-0.02029.543-0.006-0.0060.0000.0000.0000.000
175A175TRP0-0.045-0.04234.5600.0050.0050.0000.0000.0000.000
176A176GLU-1-0.907-0.93136.117-0.118-0.1180.0000.0000.0000.000
177A177ASP-1-0.904-0.93438.040-0.081-0.0810.0000.0000.0000.000
178A178PRO0-0.007-0.01741.0090.0000.0000.0000.0000.0000.000
179A179VAL0-0.011-0.00141.1370.0030.0030.0000.0000.0000.000
180A180SER0-0.025-0.01143.4840.0010.0010.0000.0000.0000.000
181A181PRO00.1340.03242.341-0.002-0.0020.0000.0000.0000.000
182A182ARG10.9810.99842.6870.0460.0460.0000.0000.0000.000
183A183VAL0-0.034-0.01841.9480.0010.0010.0000.0000.0000.000
184A184VAL00.0490.02837.851-0.002-0.0020.0000.0000.0000.000
185A185ASP-1-0.857-0.92240.302-0.053-0.0530.0000.0000.0000.000
186A186THR0-0.083-0.04742.4940.0020.0020.0000.0000.0000.000
187A187VAL00.0140.01637.8300.0010.0010.0000.0000.0000.000
188A188ILE00.0280.01836.196-0.001-0.0010.0000.0000.0000.000
189A189LYS10.9190.96339.5980.0460.0460.0000.0000.0000.000
190A190ARG10.9030.94141.8930.0670.0670.0000.0000.0000.000
191A191ILE00.0580.03835.4390.0010.0010.0000.0000.0000.000
192A192ARG10.8380.88538.8330.0510.0510.0000.0000.0000.000
193A193LYS10.8910.93940.4990.0500.0500.0000.0000.0000.000
194A194ALA0-0.0060.01339.7430.0020.0020.0000.0000.0000.000
195A195ILE00.0020.00235.419-0.001-0.0010.0000.0000.0000.000
196A196GLU-1-0.804-0.91037.839-0.050-0.0500.0000.0000.0000.000
197A197ASP-1-0.931-0.95940.698-0.038-0.0380.0000.0000.0000.000
198A198ASP-1-0.886-0.95043.356-0.030-0.0300.0000.0000.0000.000
199A199PRO0-0.042-0.00943.3050.0010.0010.0000.0000.0000.000
200A200ASN0-0.090-0.05344.392-0.001-0.0010.0000.0000.0000.000
201A201ARG10.9280.97043.2340.0260.0260.0000.0000.0000.000
202A202PRO0-0.031-0.00538.6930.0000.0000.0000.0000.0000.000
203A203ARG10.8890.93734.3300.0430.0430.0000.0000.0000.000
204A204TYR0-0.029-0.01032.3710.0010.0010.0000.0000.0000.000
205A205ILE00.0300.03733.454-0.003-0.0030.0000.0000.0000.000
206A206LYS10.9190.97434.9930.0410.0410.0000.0000.0000.000
207A207THR00.0160.00636.146-0.005-0.0050.0000.0000.0000.000
208A208ILE00.0100.00934.1370.0040.0040.0000.0000.0000.000
209A209TRP00.0430.00733.699-0.004-0.0040.0000.0000.0000.000
210A210GLY00.0140.01539.9240.0000.0000.0000.0000.0000.000
211A211VAL00.000-0.00236.685-0.002-0.0020.0000.0000.0000.000
212A212GLY00.0180.00435.298-0.005-0.0050.0000.0000.0000.000
213A213TYR0-0.032-0.00534.3230.0060.0060.0000.0000.0000.000
214A214MET00.0120.01830.004-0.004-0.0040.0000.0000.0000.000
215A215PHE00.0230.02628.5840.0050.0050.0000.0000.0000.000
216A216THR0-0.042-0.03129.3700.0010.0010.0000.0000.0000.000
217A217GLY00.0610.03028.3040.0010.0010.0000.0000.0000.000