FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: R8LN8

Calculation Name: 2F4Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2F4Q

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RWH8

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 312
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4553667.577976
FMO2-HF: Nuclear repulsion 4431494.657149
FMO2-HF: Total energy -122172.920827
FMO2-MP2: Total energy -122534.344491


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:2:PRO)


Summations of interaction energy for fragment #1(A:2: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.
-16.602-9.1654.124-4.135-7.425-0.004
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / 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].
3A4ARG10.8650.9032.837-3.639-1.0460.304-1.456-1.441-0.002
4A5THR0-0.005-0.0135.575-0.070-0.0700.0000.0000.0000.000
5A6GLU-1-0.850-0.8882.498-2.826-1.1760.856-1.027-1.479-0.005
6A7LEU00.0090.0082.513-1.980-0.1800.644-0.602-1.842-0.004
7A8LEU00.0080.0033.8340.5570.7530.012-0.028-0.1800.000
8A9ALA0-0.025-0.0086.4170.3250.3250.0000.0000.0000.000
9A10GLU-1-0.981-0.9714.720-2.575-2.432-0.001-0.005-0.1370.000
10A11GLU-1-0.946-0.9718.441-0.631-0.6310.0000.0000.0000.000
11A12TYR0-0.128-0.10410.6410.1670.1670.0000.0000.0000.000
12A13LEU0-0.032-0.00812.7180.0120.0120.0000.0000.0000.000
13A14ARG10.8550.91413.8450.4370.4370.0000.0000.0000.000
14A15ARG10.7670.87315.9830.2890.2890.0000.0000.0000.000
15A16GLU-1-0.832-0.90818.402-0.360-0.3600.0000.0000.0000.000
16A17GLY0-0.030-0.02221.4410.0180.0180.0000.0000.0000.000
17A18HIS00.004-0.01124.554-0.006-0.0060.0000.0000.0000.000
18A19ASP-1-0.854-0.91427.623-0.148-0.1480.0000.0000.0000.000
19A20PRO0-0.039-0.02825.435-0.016-0.0160.0000.0000.0000.000
20A21GLN0-0.0430.00123.780-0.003-0.0030.0000.0000.0000.000
21A22LYS10.8790.93020.4690.2150.2150.0000.0000.0000.000
22A23PHE00.0420.02919.0490.0230.0230.0000.0000.0000.000
23A24ARG11.0371.03215.4140.2540.2540.0000.0000.0000.000
24A39LEU00.0470.01825.502-0.002-0.0020.0000.0000.0000.000
25A40ALA00.0580.01226.416-0.003-0.0030.0000.0000.0000.000
26A41ARG10.8380.92420.1100.2740.2740.0000.0000.0000.000
27A42ILE00.0690.02320.8610.0030.0030.0000.0000.0000.000
28A43ALA00.0020.00123.3640.0000.0000.0000.0000.0000.000
29A44ARG10.9370.96726.4390.1380.1380.0000.0000.0000.000
30A45LEU0-0.0070.01520.0500.0090.0090.0000.0000.0000.000
31A46ALA00.0030.01024.0800.0040.0040.0000.0000.0000.000
32A47VAL00.0160.00319.3170.0080.0080.0000.0000.0000.000
33A48PRO00.0270.01822.0150.0010.0010.0000.0000.0000.000
34A49PRO00.0410.01822.688-0.018-0.0180.0000.0000.0000.000
35A50ALA00.002-0.00223.651-0.009-0.0090.0000.0000.0000.000
36A51TYR0-0.028-0.01218.8970.0050.0050.0000.0000.0000.000
37A52GLN00.0550.01517.901-0.014-0.0140.0000.0000.0000.000
38A53ASP-1-0.807-0.88412.405-0.562-0.5620.0000.0000.0000.000
39A54VAL0-0.043-0.02013.772-0.042-0.0420.0000.0000.0000.000
40A55TYR00.0170.00511.377-0.031-0.0310.0000.0000.0000.000
41A56VAL0-0.058-0.05913.9910.0400.0400.0000.0000.0000.000
42A57SER00.0500.01915.228-0.054-0.0540.0000.0000.0000.000
43A58PRO00.0010.01015.1440.0650.0650.0000.0000.0000.000
44A59ASP-1-0.790-0.89816.782-0.250-0.2500.0000.0000.0000.000
45A60ALA0-0.078-0.03918.665-0.009-0.0090.0000.0000.0000.000
46A61GLU-1-0.816-0.91020.051-0.151-0.1510.0000.0000.0000.000
47A62ASN0-0.0130.02113.9710.0410.0410.0000.0000.0000.000
48A63GLU-1-0.818-0.90916.370-0.203-0.2030.0000.0000.0000.000
49A64LEU0-0.058-0.01711.2990.0410.0410.0000.0000.0000.000
50A65GLN0-0.026-0.01814.923-0.049-0.0490.0000.0000.0000.000
51A66ALA00.000-0.00215.700-0.017-0.0170.0000.0000.0000.000
52A67PHE00.0040.0019.0220.0790.0790.0000.0000.0000.000
53A68GLY00.0550.03514.251-0.027-0.0270.0000.0000.0000.000
54A69ARG10.8680.93510.3960.3310.3310.0000.0000.0000.000
55A70ASP-1-0.768-0.87216.276-0.113-0.1130.0000.0000.0000.000
56A71ALA00.0290.00119.817-0.004-0.0040.0000.0000.0000.000
57A72ALA00.0000.01221.3240.0110.0110.0000.0000.0000.000
58A73GLY00.0220.01317.5750.0150.0150.0000.0000.0000.000
59A74ARG10.8470.93016.0350.0470.0470.0000.0000.0000.000
60A75LEU00.0360.02610.141-0.012-0.0120.0000.0000.0000.000
61A76GLN0-0.055-0.03414.6360.0510.0510.0000.0000.0000.000
62A77TYR00.0150.00211.412-0.005-0.0050.0000.0000.0000.000
63A78ARG10.8670.93816.8720.2010.2010.0000.0000.0000.000
64A79TYR00.028-0.00215.803-0.013-0.0130.0000.0000.0000.000
65A80HIS00.0650.04819.6420.0180.0180.0000.0000.0000.000
66A81PRO00.016-0.00321.6110.0150.0150.0000.0000.0000.000
67A82ASP-1-0.787-0.90124.148-0.104-0.1040.0000.0000.0000.000
68A83PHE0-0.077-0.05820.9030.0150.0150.0000.0000.0000.000
69A84VAL0-0.092-0.03723.8870.0090.0090.0000.0000.0000.000
70A85GLN0-0.0210.00226.2340.0120.0120.0000.0000.0000.000
71A86ALA0-0.005-0.00929.3990.0030.0030.0000.0000.0000.000
72A87GLY0-0.031-0.01030.9700.0020.0020.0000.0000.0000.000
73A88ALA00.0220.01928.5810.0010.0010.0000.0000.0000.000
74A89LEU0-0.0370.00324.261-0.001-0.0010.0000.0000.0000.000
75A90LYS10.9460.96728.6380.0450.0450.0000.0000.0000.000
76A91LYS10.9140.94227.918-0.010-0.0100.0000.0000.0000.000
77A92TRP00.1430.04826.5310.0010.0010.0000.0000.0000.000
78A93GLN00.0600.05725.7070.0030.0030.0000.0000.0000.000
79A94ARG10.8260.89122.1560.0230.0230.0000.0000.0000.000
80A95LEU0-0.015-0.01421.764-0.002-0.0020.0000.0000.0000.000
81A96THR00.0010.00321.1380.0070.0070.0000.0000.0000.000
82A97ARG10.7800.86619.3500.1510.1510.0000.0000.0000.000
83A98PHE0-0.042-0.01917.224-0.013-0.0130.0000.0000.0000.000
84A99ALA00.003-0.00316.2810.0080.0080.0000.0000.0000.000
85A100GLY00.0410.01615.6860.0120.0120.0000.0000.0000.000
86A101ALA0-0.0060.00112.744-0.054-0.0540.0000.0000.0000.000
87A102LEU0-0.052-0.02211.5470.0270.0270.0000.0000.0000.000
88A103PRO00.0470.03210.3790.1310.1310.0000.0000.0000.000
89A104THR00.0590.0236.8060.1320.1320.0000.0000.0000.000
90A105LEU00.0010.0116.6730.1640.1640.0000.0000.0000.000
91A106LYS10.8140.9138.3530.0550.0550.0000.0000.0000.000
92A107VAL00.0400.0382.2390.3960.1671.936-0.450-1.2570.001
93A108ALA00.0340.0214.3572.0542.2200.000-0.043-0.1220.000
94A109THR0-0.005-0.0195.5090.5370.5370.0000.0000.0000.000
95A110THR0-0.037-0.0376.220-0.371-0.3710.0000.0000.0000.000
96A111ALA00.0010.0163.061-2.070-1.0520.374-0.511-0.8810.006
97A112ASP-1-0.734-0.8235.005-0.171-0.071-0.001-0.013-0.0860.000
98A113LEU0-0.073-0.0518.287-0.481-0.4810.0000.0000.0000.000
99A114ARG10.9300.9705.443-2.835-2.8350.0000.0000.0000.000
100A115ALA00.0220.0429.725-0.233-0.2330.0000.0000.0000.000
101A116SER00.0270.01011.283-0.089-0.0890.0000.0000.0000.000
102A117GLY00.0340.01914.873-0.023-0.0230.0000.0000.0000.000
103A118LEU00.0310.00417.0030.0660.0660.0000.0000.0000.000
104A119PRO00.1060.07313.340-0.054-0.0540.0000.0000.0000.000
105A120PRO00.0530.00515.4200.0520.0520.0000.0000.0000.000
106A121ARG10.7750.8138.064-0.564-0.5640.0000.0000.0000.000
107A122LYS10.8510.96212.308-0.747-0.7470.0000.0000.0000.000
108A123VAL0-0.011-0.00213.133-0.007-0.0070.0000.0000.0000.000
109A124MET0-0.013-0.00614.475-0.052-0.0520.0000.0000.0000.000
110A125ALA00.0210.03911.217-0.058-0.0580.0000.0000.0000.000
111A126LEU0-0.003-0.00113.051-0.033-0.0330.0000.0000.0000.000
112A127MET0-0.040-0.01315.874-0.061-0.0610.0000.0000.0000.000
113A128THR00.012-0.01613.375-0.075-0.0750.0000.0000.0000.000
114A129ARG10.8560.9249.484-1.186-1.1860.0000.0000.0000.000
115A130LEU00.0000.01115.652-0.055-0.0550.0000.0000.0000.000
116A131LEU0-0.071-0.03718.269-0.044-0.0440.0000.0000.0000.000
117A132HIS0-0.017-0.00416.054-0.042-0.0420.0000.0000.0000.000
118A133VAL00.0220.01217.437-0.030-0.0300.0000.0000.0000.000
119A134ALA0-0.017-0.00620.014-0.026-0.0260.0000.0000.0000.000
120A135ARG10.8440.91822.125-0.170-0.1700.0000.0000.0000.000
121A136PHE00.0320.01822.825-0.024-0.0240.0000.0000.0000.000
122A137ARG10.8290.90423.963-0.087-0.0870.0000.0000.0000.000
123A138VAL00.0520.04521.9700.0150.0150.0000.0000.0000.000
124A149THR0-0.0070.00435.352-0.004-0.0040.0000.0000.0000.000
125A150TYR0-0.102-0.06131.1230.0000.0000.0000.0000.0000.000
126A151GLY00.0360.01128.378-0.007-0.0070.0000.0000.0000.000
127A152LEU00.0580.02920.819-0.001-0.0010.0000.0000.0000.000
128A153SER0-0.006-0.02423.8370.0050.0050.0000.0000.0000.000
129A154THR0-0.065-0.03025.138-0.001-0.0010.0000.0000.0000.000
130A155LEU00.0170.02826.215-0.011-0.0110.0000.0000.0000.000
131A156ARG10.8820.92728.693-0.111-0.1110.0000.0000.0000.000
132A157GLN00.037-0.00628.263-0.010-0.0100.0000.0000.0000.000
133A158ARG10.9450.97630.637-0.108-0.1080.0000.0000.0000.000
134A159HIS0-0.071-0.02230.3040.0000.0000.0000.0000.0000.000
135A160VAL0-0.008-0.00326.2670.0030.0030.0000.0000.0000.000
136A161VAL00.0300.02729.668-0.005-0.0050.0000.0000.0000.000
137A162VAL0-0.011-0.01126.3410.0080.0080.0000.0000.0000.000
138A163ASP-1-0.890-0.94128.9970.1630.1630.0000.0000.0000.000
139A164GLY00.0440.02428.9620.0030.0030.0000.0000.0000.000
140A165ASN0-0.015-0.03524.2920.0330.0330.0000.0000.0000.000
141A166THR0-0.0030.00424.7930.0270.0270.0000.0000.0000.000
142A167VAL00.0040.02123.475-0.003-0.0030.0000.0000.0000.000
143A168THR00.0280.00726.552-0.005-0.0050.0000.0000.0000.000
144A169PHE0-0.010-0.02423.504-0.004-0.0040.0000.0000.0000.000
145A170ARG10.9330.95329.286-0.123-0.1230.0000.0000.0000.000
146A171PHE0-0.032-0.01828.225-0.002-0.0020.0000.0000.0000.000
147A172LYS10.8880.95933.556-0.082-0.0820.0000.0000.0000.000
148A173GLY00.0800.03032.8570.0040.0040.0000.0000.0000.000
149A174LYS10.9690.96432.905-0.061-0.0610.0000.0000.0000.000
150A175HIS00.030-0.00234.6390.0020.0020.0000.0000.0000.000
151A176GLY00.0460.03637.453-0.003-0.0030.0000.0000.0000.000
152A177VAL0-0.0340.00834.3220.0010.0010.0000.0000.0000.000
153A178SER00.0190.01035.4490.0080.0080.0000.0000.0000.000
154A179GLN0-0.040-0.03229.5310.0060.0060.0000.0000.0000.000
155A180HIS00.0770.04631.8360.0020.0020.0000.0000.0000.000
156A181LYS10.7830.88526.608-0.139-0.1390.0000.0000.0000.000
157A182ALA00.0220.02427.5740.0050.0050.0000.0000.0000.000
158A183THR0-0.015-0.00521.845-0.001-0.0010.0000.0000.0000.000
159A184SER00.0390.02323.909-0.004-0.0040.0000.0000.0000.000
160A185ASP-1-0.769-0.87917.9520.5310.5310.0000.0000.0000.000
161A186ARG10.9941.02119.839-0.374-0.3740.0000.0000.0000.000
162A187THR0-0.081-0.05915.2380.0260.0260.0000.0000.0000.000
163A188LEU0-0.001-0.01018.0110.0160.0160.0000.0000.0000.000
164A189ALA00.0310.01519.309-0.014-0.0140.0000.0000.0000.000
165A190ALA00.0270.01519.762-0.015-0.0150.0000.0000.0000.000
166A191ASN0-0.016-0.00515.668-0.034-0.0340.0000.0000.0000.000
167A192MET0-0.018-0.00319.888-0.008-0.0080.0000.0000.0000.000
168A193GLN00.0290.00622.940-0.028-0.0280.0000.0000.0000.000
169A194LYS10.8910.94218.968-0.472-0.4720.0000.0000.0000.000
170A195LEU0-0.064-0.03620.704-0.014-0.0140.0000.0000.0000.000
171A196LEU0-0.063-0.04224.114-0.022-0.0220.0000.0000.0000.000
172A197ASP-1-0.860-0.90926.3530.2290.2290.0000.0000.0000.000
173A198LEU0-0.078-0.02523.516-0.013-0.0130.0000.0000.0000.000
174A199PRO00.0310.01928.130-0.008-0.0080.0000.0000.0000.000
175A200GLY00.0630.07030.0630.0080.0080.0000.0000.0000.000
176A201PRO0-0.045-0.04631.920-0.006-0.0060.0000.0000.0000.000
177A202TRP0-0.010-0.02128.1410.0000.0000.0000.0000.0000.000
178A203LEU00.0350.03324.9470.0030.0030.0000.0000.0000.000
179A204PHE00.0540.00921.0370.0150.0150.0000.0000.0000.000
180A205GLN0-0.033-0.02222.931-0.027-0.0270.0000.0000.0000.000
181A206THR0-0.068-0.04218.6420.0300.0300.0000.0000.0000.000
182A207VAL00.012-0.00820.414-0.033-0.0330.0000.0000.0000.000
183A208ASP-1-0.825-0.90520.3450.2450.2450.0000.0000.0000.000
184A209ALA0-0.041-0.03121.0700.0020.0020.0000.0000.0000.000
185A210GLY00.0080.01122.609-0.006-0.0060.0000.0000.0000.000
186A211GLY0-0.0050.00325.397-0.009-0.0090.0000.0000.0000.000
187A212GLY0-0.056-0.02526.882-0.007-0.0070.0000.0000.0000.000
188A213GLU-1-0.953-0.96424.2890.1350.1350.0000.0000.0000.000
189A214ARG10.9390.95024.248-0.149-0.1490.0000.0000.0000.000
190A215ARG10.8300.88819.422-0.226-0.2260.0000.0000.0000.000
191A216ARG10.9100.94323.732-0.128-0.1280.0000.0000.0000.000
192A217ILE00.0010.01718.789-0.006-0.0060.0000.0000.0000.000
193A218HIS00.0090.00122.077-0.009-0.0090.0000.0000.0000.000
194A219SER00.029-0.00222.2050.0110.0110.0000.0000.0000.000
195A220THR00.0240.01322.3610.0030.0030.0000.0000.0000.000
196A221GLU-1-0.751-0.84318.2290.2150.2150.0000.0000.0000.000
197A222LEU00.0510.01417.0190.0030.0030.0000.0000.0000.000
198A223ASN0-0.044-0.04217.6610.0020.0020.0000.0000.0000.000
199A224ALA0-0.0060.00917.866-0.025-0.0250.0000.0000.0000.000
200A225TYR0-0.025-0.0449.565-0.106-0.1060.0000.0000.0000.000
201A226LEU0-0.003-0.00813.433-0.016-0.0160.0000.0000.0000.000
202A227ARG10.8940.95314.9420.0620.0620.0000.0000.0000.000
203A228GLU-1-0.852-0.8879.002-0.054-0.0540.0000.0000.0000.000
204A229VAL00.007-0.0039.160-0.129-0.1290.0000.0000.0000.000
205A230ILE0-0.024-0.01310.952-0.041-0.0410.0000.0000.0000.000
206A231GLY00.0170.04713.719-0.016-0.0160.0000.0000.0000.000
207A232PRO0-0.0080.00014.865-0.060-0.0600.0000.0000.0000.000
208A233PHE0-0.035-0.01516.1930.0330.0330.0000.0000.0000.000
209A234THR0-0.017-0.02618.2730.0100.0100.0000.0000.0000.000
210A235ALA00.0720.01119.9530.0100.0100.0000.0000.0000.000
211A236LYS10.9250.96920.875-0.013-0.0130.0000.0000.0000.000
212A237ASP-1-0.740-0.83420.0040.0050.0050.0000.0000.0000.000
213A238PHE00.0950.05215.222-0.003-0.0030.0000.0000.0000.000
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