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: 823RY

Calculation Name: 4E72-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4E72

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HUJ3

Base Structure: X-ray

Registration Date: 2023-06-20

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2589099.871598
FMO2-HF: Nuclear repulsion 2501818.009269
FMO2-HF: Total energy -87281.862329
FMO2-MP2: Total energy -87539.449993


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:26:GLY)


Summations of interaction energy for fragment #1(A:26:GLY)
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.
-7.02-3.2084.071-4.098-3.785-0.028
Interaction energy analysis for fragmet #1(A:26:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.044 / q_NPA : 0.017
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].
3A28ASP-1-0.896-0.9703.672-1.744-0.5600.002-0.532-0.6540.001
4A29ASP-1-0.905-0.9332.293-8.532-6.1304.068-3.425-3.046-0.029
5A30PRO0-0.052-0.0184.3850.2230.154-0.001-0.0190.0890.000
6A31LEU0-0.011-0.0165.8410.0500.0500.0000.0000.0000.000
7A32PRO00.0200.0116.197-0.062-0.0620.0000.0000.0000.000
8A33THR0-0.088-0.0599.4420.1020.1020.0000.0000.0000.000
9A34GLU-1-0.880-0.92812.878-0.018-0.0180.0000.0000.0000.000
10A35ARG10.8070.85916.3810.0710.0710.0000.0000.0000.000
11A36LEU0-0.021-0.01019.6710.0060.0060.0000.0000.0000.000
12A37ALA0-0.004-0.00522.570-0.004-0.0040.0000.0000.0000.000
13A38SER0-0.026-0.00925.3980.0050.0050.0000.0000.0000.000
14A39GLU-1-0.819-0.90229.111-0.028-0.0280.0000.0000.0000.000
15A40HIS0-0.071-0.04330.9730.0010.0010.0000.0000.0000.000
16A41LEU00.0450.00935.531-0.002-0.0020.0000.0000.0000.000
17A42LYS10.8430.93439.277-0.007-0.0070.0000.0000.0000.000
18A43PRO00.020-0.00740.863-0.001-0.0010.0000.0000.0000.000
19A44GLY0-0.034-0.01043.3770.0000.0000.0000.0000.0000.000
20A45CYS0-0.0100.01845.169-0.001-0.0010.0000.0000.0000.000
21A46GLN0-0.052-0.03945.562-0.001-0.0010.0000.0000.0000.000
22A47GLY00.0300.01947.1310.0000.0000.0000.0000.0000.000
23A48GLU-1-0.911-0.96445.104-0.014-0.0140.0000.0000.0000.000
24A49GLN0-0.021-0.01344.743-0.002-0.0020.0000.0000.0000.000
25A50CYS0-0.034-0.01242.2780.0030.0030.0000.0000.0000.000
26A51PRO0-0.0260.00742.159-0.001-0.0010.0000.0000.0000.000
27A52LEU00.0060.00635.4440.0020.0020.0000.0000.0000.000
28A53VAL0-0.026-0.02132.5370.0000.0000.0000.0000.0000.000
29A54ASN0-0.073-0.04229.791-0.001-0.0010.0000.0000.0000.000
30A55ILE00.0100.00526.1250.0000.0000.0000.0000.0000.000
31A56ASP-1-0.762-0.83823.628-0.064-0.0640.0000.0000.0000.000
32A57THR00.0370.00421.826-0.011-0.0110.0000.0000.0000.000
33A58LEU0-0.026-0.00816.126-0.011-0.0110.0000.0000.0000.000
34A59LYS10.8520.92416.305-0.139-0.1390.0000.0000.0000.000
35A60PHE00.0260.00110.930-0.077-0.0770.0000.0000.0000.000
36A61PRO0-0.0010.00010.9860.0940.0940.0000.0000.0000.000
37A62ASP-1-0.871-0.9376.6271.0891.0890.0000.0000.0000.000
38A63GLU-1-0.824-0.8718.4691.1571.1570.0000.0000.0000.000
39A64PRO00.0680.03910.556-0.187-0.1870.0000.0000.0000.000
40A65GLN0-0.023-0.03012.375-0.041-0.0410.0000.0000.0000.000
41A66LEU0-0.003-0.00711.980-0.070-0.0700.0000.0000.0000.000
42A67ASP-1-0.768-0.85715.7640.1750.1750.0000.0000.0000.000
43A68PRO00.005-0.00218.102-0.033-0.0330.0000.0000.0000.000
44A69ILE0-0.039-0.01317.271-0.025-0.0250.0000.0000.0000.000
45A70VAL00.021-0.00117.911-0.026-0.0260.0000.0000.0000.000
46A71GLU-1-0.849-0.90720.7890.0690.0690.0000.0000.0000.000
47A72ARG10.8860.92923.737-0.069-0.0690.0000.0000.0000.000
48A73ALA0-0.012-0.01223.104-0.009-0.0090.0000.0000.0000.000
49A74LEU0-0.003-0.01523.839-0.009-0.0090.0000.0000.0000.000
50A75LEU00.0030.01226.531-0.003-0.0030.0000.0000.0000.000
51A76GLU-1-0.781-0.85328.4760.0280.0280.0000.0000.0000.000
52A77MET0-0.128-0.03727.540-0.006-0.0060.0000.0000.0000.000
53A78THR0-0.076-0.05230.643-0.003-0.0030.0000.0000.0000.000
54A79ARG10.7940.88832.255-0.023-0.0230.0000.0000.0000.000
55A80GLU-1-0.840-0.88735.3360.0080.0080.0000.0000.0000.000
56A81ASN0-0.062-0.04137.774-0.002-0.0020.0000.0000.0000.000
57A82ASN0-0.050-0.06037.0480.0010.0010.0000.0000.0000.000
58A83GLU-1-0.863-0.91637.4170.0170.0170.0000.0000.0000.000
59A84THR0-0.046-0.03239.0020.0040.0040.0000.0000.0000.000
60A85PRO0-0.048-0.01836.3800.0010.0010.0000.0000.0000.000
61A86LEU00.0060.00630.315-0.002-0.0020.0000.0000.0000.000
62A87PRO00.004-0.00232.9010.0050.0050.0000.0000.0000.000
63A88ALA0-0.029-0.02031.4380.0020.0020.0000.0000.0000.000
64A89SER00.0100.00228.0970.0060.0060.0000.0000.0000.000
65A90LEU00.0380.01325.137-0.008-0.0080.0000.0000.0000.000
66A91ALA00.0500.02829.105-0.006-0.0060.0000.0000.0000.000
67A92ALA0-0.106-0.05231.030-0.003-0.0030.0000.0000.0000.000
68A93TYR00.053-0.00531.938-0.003-0.0030.0000.0000.0000.000
69A94GLU-1-0.831-0.90832.4320.0140.0140.0000.0000.0000.000
70A95ARG10.9360.97334.276-0.045-0.0450.0000.0000.0000.000
71A96GLN00.0250.01436.8180.0010.0010.0000.0000.0000.000
72A97PHE00.0120.02037.012-0.002-0.0020.0000.0000.0000.000
73A98LEU0-0.018-0.01736.613-0.002-0.0020.0000.0000.0000.000
74A99ASP-1-0.953-0.98539.9460.0170.0170.0000.0000.0000.000
75A100SER0-0.049-0.04141.630-0.002-0.0020.0000.0000.0000.000
76A101ALA0-0.0210.01241.523-0.001-0.0010.0000.0000.0000.000
77A102GLU-1-0.863-0.92343.640-0.001-0.0010.0000.0000.0000.000
78A103PRO0-0.024-0.03745.445-0.001-0.0010.0000.0000.0000.000
79A104GLY00.0170.01444.887-0.001-0.0010.0000.0000.0000.000
80A105TRP0-0.080-0.03441.704-0.002-0.0020.0000.0000.0000.000
81A106SER0-0.007-0.00737.8620.0000.0000.0000.0000.0000.000
82A107SER00.0040.02033.7940.0000.0000.0000.0000.0000.000
83A108TYR0-0.037-0.02031.4170.0020.0020.0000.0000.0000.000
84A109LEU0-0.015-0.01227.934-0.002-0.0020.0000.0000.0000.000
85A110GLN0-0.046-0.03723.974-0.006-0.0060.0000.0000.0000.000
86A111ALA0-0.010-0.00820.630-0.002-0.0020.0000.0000.0000.000
87A112LYS10.9200.95819.1670.1260.1260.0000.0000.0000.000
88A113VAL00.0170.00113.013-0.001-0.0010.0000.0000.0000.000
89A114ARG10.7240.83916.3150.1800.1800.0000.0000.0000.000
90A115GLU-1-0.816-0.92515.518-0.318-0.3180.0000.0000.0000.000
91A116GLN00.0150.0108.958-0.069-0.0690.0000.0000.0000.000
92A117HIS10.8110.88010.9450.4820.4820.0000.0000.0000.000
93A118ASP-1-0.721-0.8359.584-0.598-0.5980.0000.0000.0000.000
94A119GLY00.0260.0217.5600.1760.1760.0000.0000.0000.000
95A120LEU0-0.072-0.0338.5470.2780.2780.0000.0000.0000.000
96A121VAL00.0120.00210.127-0.136-0.1360.0000.0000.0000.000
97A122ILE0-0.055-0.01612.7020.0840.0840.0000.0000.0000.000
98A123ILE00.0460.02015.250-0.021-0.0210.0000.0000.0000.000
99A124GLU-1-0.829-0.89817.949-0.123-0.1230.0000.0000.0000.000
100A125LEU00.0190.01121.4750.0060.0060.0000.0000.0000.000
101A126SER0-0.071-0.05724.219-0.009-0.0090.0000.0000.0000.000
102A127SER00.0610.04627.6430.0030.0030.0000.0000.0000.000
103A128TYR0-0.022-0.02830.786-0.007-0.0070.0000.0000.0000.000
104A129LEU00.0400.04934.2570.0020.0020.0000.0000.0000.000
105A130PHE0-0.025-0.02137.091-0.002-0.0020.0000.0000.0000.000
106A131THR00.0570.02040.6720.0010.0010.0000.0000.0000.000
107A132GLY00.0460.03243.6070.0010.0010.0000.0000.0000.000
108A133GLY0-0.0110.00645.7640.0000.0000.0000.0000.0000.000
109A134ALA0-0.018-0.02746.509-0.001-0.0010.0000.0000.0000.000
110A135HIS10.8550.91741.9030.0240.0240.0000.0000.0000.000
111A136GLY00.0550.04839.9560.0020.0020.0000.0000.0000.000
112A137MET0-0.031-0.01338.424-0.002-0.0020.0000.0000.0000.000
113A138PRO0-0.039-0.01534.0390.0010.0010.0000.0000.0000.000
114A139GLY00.0740.04832.4970.0010.0010.0000.0000.0000.000
115A140ARG10.7920.89128.1410.0570.0570.0000.0000.0000.000
116A141GLY00.1010.04526.1900.0090.0090.0000.0000.0000.000
117A142PHE0-0.074-0.04121.536-0.017-0.0170.0000.0000.0000.000
118A143ILE00.0210.01918.2330.0200.0200.0000.0000.0000.000
119A144ASN00.0070.00117.461-0.057-0.0570.0000.0000.0000.000
120A145TYR0-0.013-0.03311.538-0.005-0.0050.0000.0000.0000.000
121A146ASP-1-0.749-0.86911.821-0.193-0.1930.0000.0000.0000.000
122A147ARG10.8920.9353.3511.3611.6560.002-0.122-0.1740.000
123A148ARG10.9040.9538.7410.3190.3190.0000.0000.0000.000
124A149GLN0-0.075-0.06410.0060.1380.1380.0000.0000.0000.000
125A150HIS10.7900.8928.302-0.869-0.8690.0000.0000.0000.000
126A151LYS10.8820.94112.958-0.056-0.0560.0000.0000.0000.000
127A152VAL00.0050.01115.917-0.043-0.0430.0000.0000.0000.000
128A153LEU0-0.050-0.02416.3740.0130.0130.0000.0000.0000.000
129A154SER00.021-0.02019.830-0.014-0.0140.0000.0000.0000.000
130A155LEU00.0580.00823.229-0.009-0.0090.0000.0000.0000.000
131A156GLN00.0110.00025.618-0.009-0.0090.0000.0000.0000.000
132A157ASP-1-0.791-0.86020.5780.0190.0190.0000.0000.0000.000
133A158MET0-0.0240.00921.045-0.012-0.0120.0000.0000.0000.000
134A159LEU0-0.0100.01522.488-0.012-0.0120.0000.0000.0000.000
135A160VAL0-0.0100.01025.5730.0100.0100.0000.0000.0000.000
136A161PRO00.0390.00126.7790.0010.0010.0000.0000.0000.000
137A162GLY00.0270.02329.749-0.002-0.0020.0000.0000.0000.000
138A163GLN0-0.057-0.02630.091-0.003-0.0030.0000.0000.0000.000
139A164GLU-1-0.763-0.85430.666-0.040-0.0400.0000.0000.0000.000
140A165GLU-1-0.791-0.88632.058-0.042-0.0420.0000.0000.0000.000
141A166ALA00.0670.03833.310-0.003-0.0030.0000.0000.0000.000
142A167PHE00.019-0.00526.653-0.007-0.0070.0000.0000.0000.000
143A168TRP00.000-0.01730.750-0.007-0.0070.0000.0000.0000.000
144A169LYS10.8490.91533.9460.0390.0390.0000.0000.0000.000
145A170GLN0-0.034-0.01031.388-0.006-0.0060.0000.0000.0000.000
146A171ALA00.0160.01031.826-0.005-0.0050.0000.0000.0000.000
147A172GLU-1-0.827-0.89333.232-0.049-0.0490.0000.0000.0000.000
148A173LEU0-0.056-0.02035.2970.0020.0020.0000.0000.0000.000
149A174ALA00.010-0.00132.424-0.001-0.0010.0000.0000.0000.000
150A175HIS00.0510.01934.388-0.005-0.0050.0000.0000.0000.000
151A176LYS10.8440.90637.0700.0560.0560.0000.0000.0000.000
152A177ALA0-0.0010.00235.3300.0000.0000.0000.0000.0000.000
153A178TRP00.0170.00834.0500.0000.0000.0000.0000.0000.000
154A179LEU00.0180.00936.8230.0010.0010.0000.0000.0000.000
155A180LEU0-0.002-0.00139.8720.0010.0010.0000.0000.0000.000
156A181ALA0-0.044-0.01836.8200.0010.0010.0000.0000.0000.000
157A182ASN0-0.059-0.04337.1170.0010.0010.0000.0000.0000.000
158A183LYS10.9060.94740.6800.0670.0670.0000.0000.0000.000
159A184LEU00.0240.02441.6970.0030.0030.0000.0000.0000.000
160A185ASP-1-0.914-0.93843.644-0.053-0.0530.0000.0000.0000.000
161A186GLN0-0.028-0.02945.1580.0040.0040.0000.0000.0000.000
162A187ASP-1-0.856-0.90847.087-0.039-0.0390.0000.0000.0000.000
163A188ALA00.011-0.01148.1330.0000.0000.0000.0000.0000.000
164A189ASP-1-0.879-0.92750.368-0.030-0.0300.0000.0000.0000.000
165A190PHE00.0580.02441.9660.0010.0010.0000.0000.0000.000
166A191GLN0-0.098-0.06744.9680.0020.0020.0000.0000.0000.000
167A192LYS10.7490.86946.7590.0360.0360.0000.0000.0000.000
168A193THR0-0.0060.00247.0410.0020.0020.0000.0000.0000.000
169A194TRP0-0.053-0.01942.3290.0010.0010.0000.0000.0000.000
170A195PRO0-0.0050.00943.525-0.003-0.0030.0000.0000.0000.000
171A196PHE0-0.019-0.01534.884-0.001-0.0010.0000.0000.0000.000
172A197GLN00.0190.00236.2910.0060.0060.0000.0000.0000.000
173A198ARG10.8440.90433.8440.0280.0280.0000.0000.0000.000
174A199THR00.004-0.00930.0150.0040.0040.0000.0000.0000.000
175A200PRO00.0260.01229.238-0.002-0.0020.0000.0000.0000.000
176A201HIS0-0.040-0.01626.597-0.006-0.0060.0000.0000.0000.000
177A202VAL0-0.017-0.01424.177-0.012-0.0120.0000.0000.0000.000
178A203ALA00.0240.01221.0250.0020.0020.0000.0000.0000.000
179A204LEU00.0240.02317.860-0.001-0.0010.0000.0000.0000.000
180A205THR0-0.0080.00718.032-0.038-0.0380.0000.0000.0000.000
181A206PHE00.0100.00414.8110.0240.0240.0000.0000.0000.000
182A207GLY00.0070.00218.6660.0070.0070.0000.0000.0000.000
183A208ALA0-0.054-0.04322.0690.0190.0190.0000.0000.0000.000
184A209VAL00.0240.04022.765-0.011-0.0110.0000.0000.0000.000
185A210THR0-0.013-0.01523.7620.0140.0140.0000.0000.0000.000
186A211LEU0-0.025-0.01225.6460.0050.0050.0000.0000.0000.000
187A212LYS10.8480.90925.8360.1140.1140.0000.0000.0000.000
188A213TYR0-0.028-0.02529.0590.0050.0050.0000.0000.0000.000
189A214ASP-1-0.769-0.87232.412-0.047-0.0470.0000.0000.0000.000
190A215ALA00.0070.00333.9860.0010.0010.0000.0000.0000.000
191A216TYR0-0.047-0.01836.9010.0030.0030.0000.0000.0000.000
192A217SER0-0.033-0.01636.3770.0020.0020.0000.0000.0000.000
193A218ILE0-0.003-0.01135.4360.0010.0010.0000.0000.0000.000
194A219ALA0-0.0010.00038.703-0.002-0.0020.0000.0000.0000.000
195A220PRO00.0270.02340.3270.0010.0010.0000.0000.0000.000
196A221TYR00.0520.00638.876-0.003-0.0030.0000.0000.0000.000
197A222SER0-0.0190.00139.252-0.002-0.0020.0000.0000.0000.000
198A223TYR0-0.004-0.00637.808-0.002-0.0020.0000.0000.0000.000
199A224ALA0-0.027-0.01934.264-0.005-0.0050.0000.0000.0000.000
200A225HIS00.0240.01431.4880.0040.0040.0000.0000.0000.000
201A226PRO00.0060.01531.504-0.009-0.0090.0000.0000.0000.000
202A227GLU-1-0.724-0.81826.453-0.147-0.1470.0000.0000.0000.000
203A228LEU00.0040.02330.259-0.004-0.0040.0000.0000.0000.000
204A229LYS10.8200.88025.7070.1470.1470.0000.0000.0000.000
205A230ILE00.0300.01427.5990.0080.0080.0000.0000.0000.000
206A231PRO00.0110.00126.411-0.013-0.0130.0000.0000.0000.000
207A232TYR00.0540.01220.3220.0200.0200.0000.0000.0000.000
208A233PRO0-0.025-0.01825.0190.0110.0110.0000.0000.0000.000
209A234ARG10.8810.93527.7050.0990.0990.0000.0000.0000.000
210A235LEU00.0270.01025.9450.0110.0110.0000.0000.0000.000
211A236ASN0-0.015-0.00226.421-0.007-0.0070.0000.0000.0000.000
212A237GLY00.0280.02026.6970.0080.0080.0000.0000.0000.000
213A238ILE0-0.035-0.00727.6340.0090.0090.0000.0000.0000.000
214A239VAL00.0320.01621.9360.0080.0080.0000.0000.0000.000
215A240LYS10.8050.88021.0180.0390.0390.0000.0000.0000.000
216A241PRO00.0410.00120.768-0.019-0.0190.0000.0000.0000.000
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