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: 43Y6N

Calculation Name: 3DR5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DR5

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NRD3

Base Structure: X-ray

Registration Date: 2023-03-14

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2362239.918713
FMO2-HF: Nuclear repulsion 2281412.681318
FMO2-HF: Total energy -80827.237395
FMO2-MP2: Total energy -81065.112803


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:3:ASN)


Summations of interaction energy for fragment #1(A:3:ASN)
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.
-22.387-21.78416.408-9.264-7.748-0.085
Interaction energy analysis for fragmet #1(A:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.031
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].
3A5PHE00.0380.0253.063-2.0250.5140.014-1.199-1.3550.002
4A6GLU-1-0.770-0.8821.822-20.657-23.23716.394-7.902-5.912-0.087
5A7TYR0-0.0160.0124.0650.3681.0120.000-0.163-0.4810.000
6A8LEU0-0.017-0.0056.206-0.036-0.0360.0000.0000.0000.000
7A9ARG10.8860.9277.1860.9710.9710.0000.0000.0000.000
8A10THR0-0.012-0.0167.6960.1400.1400.0000.0000.0000.000
9A11TYR0-0.0450.00210.1880.0270.0270.0000.0000.0000.000
10A12VAL00.0330.00412.297-0.025-0.0250.0000.0000.0000.000
11A13GLU-1-0.858-0.91812.235-0.240-0.2400.0000.0000.0000.000
12A14SER0-0.094-0.06413.6430.0280.0280.0000.0000.0000.000
13A15THR0-0.059-0.02216.0150.0200.0200.0000.0000.0000.000
14A16THR0-0.053-0.02917.447-0.025-0.0250.0000.0000.0000.000
15A17GLU-1-0.972-0.98019.8270.0510.0510.0000.0000.0000.000
16A18THR0-0.022-0.02021.438-0.011-0.0110.0000.0000.0000.000
17A19ASP-1-0.805-0.89623.749-0.010-0.0100.0000.0000.0000.000
18A20ALA00.022-0.00125.570-0.004-0.0040.0000.0000.0000.000
19A21ALA0-0.0020.00527.973-0.002-0.0020.0000.0000.0000.000
20A22VAL0-0.003-0.00922.516-0.006-0.0060.0000.0000.0000.000
21A23ALA0-0.008-0.00623.141-0.010-0.0100.0000.0000.0000.000
22A24ARG10.7930.86824.2040.0100.0100.0000.0000.0000.000
23A25ALA00.003-0.01025.818-0.004-0.0040.0000.0000.0000.000
24A26ARG10.8170.88317.8020.1260.1260.0000.0000.0000.000
25A27GLU-1-0.904-0.93922.631-0.015-0.0150.0000.0000.0000.000
26A28ASP-1-0.856-0.92624.518-0.031-0.0310.0000.0000.0000.000
27A29ALA0-0.037-0.03122.917-0.004-0.0040.0000.0000.0000.000
28A30ALA0-0.0070.00821.428-0.012-0.0120.0000.0000.0000.000
29A31GLU-1-0.977-0.98722.914-0.018-0.0180.0000.0000.0000.000
30A32PHE0-0.079-0.04526.4740.0040.0040.0000.0000.0000.000
31A33GLY0-0.026-0.00223.138-0.004-0.0040.0000.0000.0000.000
32A34LEU0-0.070-0.03323.454-0.012-0.0120.0000.0000.0000.000
33A35PRO0-0.024-0.02720.368-0.010-0.0100.0000.0000.0000.000
34A36ALA00.0300.01619.3480.0160.0160.0000.0000.0000.000
35A37PRO00.0070.01016.761-0.024-0.0240.0000.0000.0000.000
36A38ASP-1-0.766-0.86012.698-0.341-0.3410.0000.0000.0000.000
37A39GLU-1-0.733-0.82214.840-0.050-0.0500.0000.0000.0000.000
38A40MET0-0.021-0.00511.4830.0000.0000.0000.0000.0000.000
39A41THR0-0.030-0.04614.7150.0250.0250.0000.0000.0000.000
40A42GLY00.0030.00416.7780.0240.0240.0000.0000.0000.000
41A43GLN0-0.017-0.03018.0950.0100.0100.0000.0000.0000.000
42A44LEU0-0.0180.01117.9750.0160.0160.0000.0000.0000.000
43A45LEU0-0.015-0.01520.1000.0130.0130.0000.0000.0000.000
44A46THR00.004-0.01422.8000.0080.0080.0000.0000.0000.000
45A47THR0-0.048-0.03122.1470.0110.0110.0000.0000.0000.000
46A48LEU0-0.0070.00622.6740.0060.0060.0000.0000.0000.000
47A49ALA0-0.0220.00425.8880.0050.0050.0000.0000.0000.000
48A50ALA00.0170.01827.9090.0050.0050.0000.0000.0000.000
49A51THR0-0.098-0.05927.2620.0030.0030.0000.0000.0000.000
50A52THR0-0.037-0.03028.7690.0030.0030.0000.0000.0000.000
51A53ASN00.0290.00831.2980.0050.0050.0000.0000.0000.000
52A54GLY00.0440.02635.119-0.001-0.0010.0000.0000.0000.000
53A55ASN0-0.076-0.05337.0090.0040.0040.0000.0000.0000.000
54A56GLY0-0.015-0.00940.224-0.001-0.0010.0000.0000.0000.000
55A57SER0-0.040-0.02736.123-0.002-0.0020.0000.0000.0000.000
56A58THR0-0.022-0.02638.4920.0030.0030.0000.0000.0000.000
57A59GLY00.0040.02235.6130.0020.0020.0000.0000.0000.000
58A60ALA0-0.0060.00230.555-0.003-0.0030.0000.0000.0000.000
59A61ILE0-0.037-0.01931.3470.0040.0040.0000.0000.0000.000
60A62ALA00.0090.00728.112-0.006-0.0060.0000.0000.0000.000
61A63ILE0-0.032-0.01528.4290.0060.0060.0000.0000.0000.000
62A64THR00.0590.00424.135-0.009-0.0090.0000.0000.0000.000
63A65PRO00.0630.03725.8470.0080.0080.0000.0000.0000.000
64A66ALA00.0310.03324.0510.0100.0100.0000.0000.0000.000
65A67ALA0-0.038-0.02726.0050.0010.0010.0000.0000.0000.000
66A68GLY00.0330.00628.4760.0020.0020.0000.0000.0000.000
67A69LEU00.0210.02320.8870.0020.0020.0000.0000.0000.000
68A70VAL0-0.013-0.01322.4930.0010.0010.0000.0000.0000.000
69A71GLY00.027-0.01524.7020.0020.0020.0000.0000.0000.000
70A72LEU0-0.0080.00126.7010.0050.0050.0000.0000.0000.000
71A73TYR0-0.017-0.01219.679-0.002-0.0020.0000.0000.0000.000
72A74ILE0-0.0010.01325.0980.0030.0030.0000.0000.0000.000
73A75LEU0-0.009-0.02727.5630.0040.0040.0000.0000.0000.000
74A76ASN0-0.0110.01926.5140.0060.0060.0000.0000.0000.000
75A77GLY0-0.0020.00628.9100.0030.0030.0000.0000.0000.000
76A78LEU0-0.084-0.02329.8000.0010.0010.0000.0000.0000.000
77A79ALA00.0490.02532.2740.0040.0040.0000.0000.0000.000
78A80ASP-1-0.837-0.92435.725-0.022-0.0220.0000.0000.0000.000
79A81ASN0-0.130-0.04538.4040.0010.0010.0000.0000.0000.000
80A82THR0-0.046-0.02236.212-0.002-0.0020.0000.0000.0000.000
81A83THR0-0.034-0.02936.9980.0010.0010.0000.0000.0000.000
82A84LEU00.0460.04530.239-0.003-0.0030.0000.0000.0000.000
83A85THR0-0.026-0.01834.1390.0040.0040.0000.0000.0000.000
84A86CYS00.0180.02332.014-0.005-0.0050.0000.0000.0000.000
85A87ILE0-0.029-0.02431.9310.0050.0050.0000.0000.0000.000
86A88ASP-1-0.733-0.86030.653-0.078-0.0780.0000.0000.0000.000
87A89PRO0-0.013-0.00632.5280.0050.0050.0000.0000.0000.000
88A90GLU-1-0.882-0.93433.093-0.055-0.0550.0000.0000.0000.000
89A91SER0-0.044-0.03635.4550.0010.0010.0000.0000.0000.000
90A92GLU-1-0.834-0.92931.903-0.049-0.0490.0000.0000.0000.000
91A93HIS10.8920.93830.8840.0680.0680.0000.0000.0000.000
92A94GLN00.0360.04532.7290.0020.0020.0000.0000.0000.000
93A95ARG10.8800.93135.5590.0250.0250.0000.0000.0000.000
94A96GLN00.0490.03130.458-0.001-0.0010.0000.0000.0000.000
95A97ALA00.0220.01231.4750.0020.0020.0000.0000.0000.000
96A98LYS10.8660.91032.4140.0350.0350.0000.0000.0000.000
97A99ALA0-0.052-0.01934.2990.0030.0030.0000.0000.0000.000
98A100LEU00.0530.03628.4640.0030.0030.0000.0000.0000.000
99A101PHE0-0.009-0.02230.1320.0020.0020.0000.0000.0000.000
100A102ARG10.8280.91333.7270.0160.0160.0000.0000.0000.000
101A103GLU-1-0.830-0.88133.580-0.009-0.0090.0000.0000.0000.000
102A104ALA00.0320.03331.6100.0040.0040.0000.0000.0000.000
103A105GLY0-0.012-0.00433.5620.0010.0010.0000.0000.0000.000
104A106TYR0-0.030-0.02630.9290.0000.0000.0000.0000.0000.000
105A107SER0-0.002-0.01236.8280.0010.0010.0000.0000.0000.000
106A108PRO00.038-0.00639.164-0.003-0.0030.0000.0000.0000.000
107A109SER0-0.0390.00240.332-0.002-0.0020.0000.0000.0000.000
108A110ARG10.8590.93435.4040.0280.0280.0000.0000.0000.000
109A111VAL0-0.0060.00534.842-0.004-0.0040.0000.0000.0000.000
110A112ARG10.8760.93336.6740.0440.0440.0000.0000.0000.000
111A113PHE00.009-0.01032.788-0.002-0.0020.0000.0000.0000.000
112A114LEU0-0.040-0.01036.5360.0040.0040.0000.0000.0000.000
113A115LEU0-0.0110.00136.847-0.003-0.0030.0000.0000.0000.000
114A116SER0-0.045-0.02936.8220.0020.0020.0000.0000.0000.000
115A117ARG10.9470.95235.2550.0560.0560.0000.0000.0000.000
116A118PRO00.0440.01031.3920.0030.0030.0000.0000.0000.000
117A119LEU00.0290.01132.8230.0030.0030.0000.0000.0000.000
118A120ASP-1-0.847-0.90235.995-0.051-0.0510.0000.0000.0000.000
119A121VAL0-0.023-0.02036.9620.0040.0040.0000.0000.0000.000
120A122MET00.0260.02332.7340.0020.0020.0000.0000.0000.000
121A123SER0-0.0190.00337.8800.0020.0020.0000.0000.0000.000
122A124ARG10.8380.91341.0530.0450.0450.0000.0000.0000.000
123A125LEU0-0.036-0.00337.0740.0020.0020.0000.0000.0000.000
124A126ALA00.0050.00941.0800.0000.0000.0000.0000.0000.000
125A127ASN00.0600.00240.176-0.004-0.0040.0000.0000.0000.000
126A128ASP-1-0.862-0.91538.894-0.042-0.0420.0000.0000.0000.000
127A129SER0-0.015-0.01238.8660.0030.0030.0000.0000.0000.000
128A130TYR00.0150.02134.5100.0020.0020.0000.0000.0000.000
129A131GLN00.0700.05432.1630.0010.0010.0000.0000.0000.000
130A132LEU00.0140.00626.151-0.003-0.0030.0000.0000.0000.000
131A133VAL0-0.007-0.00728.8600.0050.0050.0000.0000.0000.000
132A134PHE00.0560.02920.992-0.003-0.0030.0000.0000.0000.000
133A135GLY0-0.018-0.01124.7710.0100.0100.0000.0000.0000.000
134A136GLN0-0.040-0.03419.431-0.011-0.0110.0000.0000.0000.000
135A137VAL0-0.029-0.01323.8580.0110.0110.0000.0000.0000.000
136A138SER00.041-0.00524.029-0.014-0.0140.0000.0000.0000.000
137A139PRO00.009-0.00522.5840.0070.0070.0000.0000.0000.000
138A140MET0-0.023-0.02224.8800.0080.0080.0000.0000.0000.000
139A141ASP-1-0.881-0.90728.289-0.089-0.0890.0000.0000.0000.000
140A142LEU00.0090.01622.6520.0060.0060.0000.0000.0000.000
141A143LYS10.8570.93127.3020.0820.0820.0000.0000.0000.000
142A144ALA00.0160.00629.8590.0050.0050.0000.0000.0000.000
143A145LEU0-0.005-0.01227.0790.0050.0050.0000.0000.0000.000
144A146VAL00.0070.00328.3200.0030.0030.0000.0000.0000.000
145A147ASP-1-0.829-0.88130.818-0.068-0.0680.0000.0000.0000.000
146A148ALA0-0.040-0.02034.0010.0040.0040.0000.0000.0000.000
147A149ALA00.0400.00231.3440.0040.0040.0000.0000.0000.000
148A150TRP0-0.0090.01530.1780.0020.0020.0000.0000.0000.000
149A151PRO0-0.006-0.00234.0870.0030.0030.0000.0000.0000.000
150A152LEU0-0.0030.00635.4180.0030.0030.0000.0000.0000.000
151A153LEU00.0050.01830.4610.0030.0030.0000.0000.0000.000
152A154ARG10.8360.92634.9730.0430.0430.0000.0000.0000.000
153A155ARG10.8730.92034.8320.0440.0440.0000.0000.0000.000
154A156GLY0-0.035-0.01433.0330.0030.0030.0000.0000.0000.000
155A157GLY0-0.0130.00431.6460.0000.0000.0000.0000.0000.000
156A158ALA0-0.026-0.02626.641-0.002-0.0020.0000.0000.0000.000
157A159LEU00.0100.01226.7850.0020.0020.0000.0000.0000.000
158A160VAL0-0.008-0.01721.666-0.005-0.0050.0000.0000.0000.000
159A161LEU0-0.005-0.00822.2520.0050.0050.0000.0000.0000.000
160A162ALA00.0590.01818.765-0.014-0.0140.0000.0000.0000.000
161A163ASP-1-0.824-0.90815.950-0.292-0.2920.0000.0000.0000.000
162A164ALA0-0.0080.00217.402-0.001-0.0010.0000.0000.0000.000
163A165LEU0-0.027-0.00815.9650.0160.0160.0000.0000.0000.000
164A166LEU0-0.0100.00116.229-0.002-0.0020.0000.0000.0000.000
165A167ASP-1-0.878-0.94811.123-0.575-0.5750.0000.0000.0000.000
166A168GLY0-0.045-0.01411.931-0.007-0.0070.0000.0000.0000.000
167A169THR0-0.093-0.05614.4590.0230.0230.0000.0000.0000.000
168A170ILE0-0.015-0.00516.8430.0240.0240.0000.0000.0000.000
169A171ALA0-0.008-0.02019.0170.0000.0000.0000.0000.0000.000
170A172ASP-1-0.758-0.81317.919-0.188-0.1880.0000.0000.0000.000
171A173GLN0-0.017-0.01920.4050.0040.0040.0000.0000.0000.000
172A174THR0-0.075-0.06120.1970.0090.0090.0000.0000.0000.000
173A175ARG10.8680.91615.4170.2610.2610.0000.0000.0000.000
174A176LYS10.8560.92122.1000.1140.1140.0000.0000.0000.000
175A177ASP-1-0.767-0.88323.404-0.150-0.1500.0000.0000.0000.000
176A178ARG10.7780.84824.6740.1340.1340.0000.0000.0000.000
177A179ASP-1-0.779-0.87023.261-0.133-0.1330.0000.0000.0000.000
178A180THR00.0210.00021.204-0.009-0.0090.0000.0000.0000.000
179A181GLN0-0.070-0.02222.8020.0050.0050.0000.0000.0000.000
180A182ALA00.0070.00926.2550.0050.0050.0000.0000.0000.000
181A183ALA00.0350.01721.3490.0030.0030.0000.0000.0000.000
182A184ARG00.0460.03522.216-0.007-0.0070.0000.0000.0000.000
183A185ASP-1-0.935-0.95924.563-0.087-0.0870.0000.0000.0000.000
184A186ALA00.008-0.00524.9640.0050.0050.0000.0000.0000.000
185A187ASP-1-0.784-0.87021.857-0.137-0.1370.0000.0000.0000.000
186A188GLU-1-0.861-0.92224.404-0.097-0.0970.0000.0000.0000.000
187A189TYR0-0.030-0.03727.3870.0070.0070.0000.0000.0000.000
188A190ILE0-0.0010.00024.9240.0050.0050.0000.0000.0000.000
189A191ARG10.7080.82423.4990.1140.1140.0000.0000.0000.000
190A192SER0-0.081-0.03727.6620.0050.0050.0000.0000.0000.000
191A193ILE0-0.036-0.00830.3170.0050.0050.0000.0000.0000.000
192A194GLU-1-0.856-0.92132.302-0.061-0.0610.0000.0000.0000.000
193A195GLY0-0.049-0.03234.9910.0010.0010.0000.0000.0000.000
194A196ALA0-0.015-0.01030.1460.0000.0000.0000.0000.0000.000
195A197HIS0-0.034-0.01827.8390.0040.0040.0000.0000.0000.000
196A198VAL00.0380.01923.191-0.003-0.0030.0000.0000.0000.000
197A199ALA0-0.028-0.01120.3670.0020.0020.0000.0000.0000.000
198A200ARG10.8590.91017.6250.1420.1420.0000.0000.0000.000
199A201LEU00.0030.00114.9240.0110.0110.0000.0000.0000.000
200A202PRO0-0.0110.0049.324-0.011-0.0110.0000.0000.0000.000
201A203LEU0-0.004-0.00710.530-0.066-0.0660.0000.0000.0000.000
202A204GLY00.0320.01812.6420.0440.0440.0000.0000.0000.000
203A205ALA00.0240.01911.400-0.091-0.0910.0000.0000.0000.000
204A206GLY0-0.022-0.01913.1660.0410.0410.0000.0000.0000.000
205A207LEU0-0.030-0.00714.5100.0420.0420.0000.0000.0000.000
206A208THR00.0140.00217.0700.0110.0110.0000.0000.0000.000
207A209VAL0-0.037-0.01820.2020.0050.0050.0000.0000.0000.000
208A210VAL00.0320.01722.8740.0020.0020.0000.0000.0000.000
209A211THR0-0.025-0.01426.3590.0030.0030.0000.0000.0000.000
210A212LYS10.8790.93629.1480.0570.0570.0000.0000.0000.000
211A213ALA00.0300.03032.9000.0030.0030.0000.0000.0000.000
212A214LEU00.017-0.00133.8880.0030.0030.0000.0000.0000.000
213A215GLU-1-0.950-0.97936.653-0.041-0.0410.0000.0000.0000.000
214A216HIS0-0.032-0.02133.9880.0020.0020.0000.0000.0000.000
215A217HIS0-0.0050.00639.2830.0010.0010.0000.0000.0000.000
216A218HIS0-0.0120.00737.832-0.002-0.0020.0000.0000.0000.000