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: 98N32

Calculation Name: 2R3Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2R3Y

Chain ID: A

ChEMBL ID:

UniProt ID: P0AEE3

Base Structure: X-ray

Registration Date: 2023-09-20

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 285
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3466201.432897
FMO2-HF: Nuclear repulsion 3361400.499964
FMO2-HF: Total energy -104800.932933
FMO2-MP2: Total energy -105109.739368


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:42:MET)


Summations of interaction energy for fragment #1(A:42: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.
0.2382.471-0.017-1.15-1.0660.003
Interaction energy analysis for fragmet #1(A:42:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.027
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].
3A44PRO00.0020.0103.890-0.5221.711-0.017-1.150-1.0660.003
4A45ALA00.0340.0256.4490.0290.0290.0000.0000.0000.000
5A46SER00.014-0.0058.8050.0660.0660.0000.0000.0000.000
6A47TYR00.0470.02711.938-0.042-0.0420.0000.0000.0000.000
7A48ASN00.0360.01513.829-0.009-0.0090.0000.0000.0000.000
8A49LEU00.0030.00615.0750.0170.0170.0000.0000.0000.000
9A50ALA00.0280.01816.7740.0280.0280.0000.0000.0000.000
10A51VAL00.0240.00918.8230.0190.0190.0000.0000.0000.000
11A52ARG10.8730.92214.8090.5420.5420.0000.0000.0000.000
12A53ARG10.8490.92019.6570.2710.2710.0000.0000.0000.000
13A54ALA00.0390.02522.8260.0190.0190.0000.0000.0000.000
14A55ALA00.0070.01123.6930.0150.0150.0000.0000.0000.000
15A56PRO00.013-0.00424.4360.0140.0140.0000.0000.0000.000
16A57ALA00.0060.01627.6270.0110.0110.0000.0000.0000.000
17A58VAL0-0.060-0.00728.0790.0130.0130.0000.0000.0000.000
18A59VAL0-0.0030.01230.536-0.007-0.0070.0000.0000.0000.000
19A60ASN00.0450.02331.995-0.002-0.0020.0000.0000.0000.000
20A61VAL0-0.026-0.01734.6580.0010.0010.0000.0000.0000.000
21A62TYR0-0.025-0.03435.6310.0000.0000.0000.0000.0000.000
22A63ASN0-0.0180.01141.1550.0010.0010.0000.0000.0000.000
23A64ARG10.8530.89944.6660.0600.0600.0000.0000.0000.000
24A65GLY00.0360.01347.3150.0010.0010.0000.0000.0000.000
25A66LEU0-0.027-0.02851.018-0.001-0.0010.0000.0000.0000.000
26A67ASN0-0.025-0.02354.2120.0020.0020.0000.0000.0000.000
27A68THR0-0.038-0.00549.3230.0020.0020.0000.0000.0000.000
28A69ASN0-0.032-0.02751.6680.0020.0020.0000.0000.0000.000
29A70SER0-0.006-0.03254.6780.0000.0000.0000.0000.0000.000
30A71HIS0-0.0230.01255.8080.0020.0020.0000.0000.0000.000
31A72ASN0-0.0150.00056.0800.0000.0000.0000.0000.0000.000
32A73GLN0-0.031-0.01052.0100.0000.0000.0000.0000.0000.000
33A74LEU00.0130.00548.9320.0000.0000.0000.0000.0000.000
34A75GLU-1-0.863-0.91447.480-0.047-0.0470.0000.0000.0000.000
35A76ILE0-0.022-0.02441.8790.0010.0010.0000.0000.0000.000
36A77ARG10.8570.92845.3090.0450.0450.0000.0000.0000.000
37A78THR00.002-0.00442.7660.0020.0020.0000.0000.0000.000
38A79LEU0-0.038-0.02036.629-0.002-0.0020.0000.0000.0000.000
39A80GLY0-0.0080.00036.6490.0040.0040.0000.0000.0000.000
40A81SER0-0.0130.00032.902-0.010-0.0100.0000.0000.0000.000
41A82GLY00.0450.02734.2820.0080.0080.0000.0000.0000.000
42A83VAL0-0.026-0.01632.077-0.010-0.0100.0000.0000.0000.000
43A84ILE0-0.0070.00733.4260.0080.0080.0000.0000.0000.000
44A85MET0-0.0140.00133.708-0.009-0.0090.0000.0000.0000.000
45A86ASP-1-0.781-0.88035.216-0.082-0.0820.0000.0000.0000.000
46A87GLN00.0660.01834.5960.0030.0030.0000.0000.0000.000
47A88ARG10.8310.90738.1790.0710.0710.0000.0000.0000.000
48A89GLY0-0.0010.00339.8630.0030.0030.0000.0000.0000.000
49A90TYR0-0.0130.00040.5590.0020.0020.0000.0000.0000.000
50A91ILE0-0.003-0.01437.116-0.006-0.0060.0000.0000.0000.000
51A92ILE00.0060.01537.0970.0050.0050.0000.0000.0000.000
52A93THR00.010-0.01637.530-0.004-0.0040.0000.0000.0000.000
53A94ASN00.015-0.01338.0860.0000.0000.0000.0000.0000.000
54A95LYS10.8540.92740.8740.0370.0370.0000.0000.0000.000
55A96HIS0-0.045-0.05739.585-0.002-0.0020.0000.0000.0000.000
56A97VAL0-0.0090.01139.3480.0000.0000.0000.0000.0000.000
57A98ILE0-0.028-0.01342.7050.0000.0000.0000.0000.0000.000
58A99ASN00.0440.03545.4520.0010.0010.0000.0000.0000.000
59A100ASP-1-0.914-0.96148.812-0.037-0.0370.0000.0000.0000.000
60A101ALA0-0.0270.00547.7800.0000.0000.0000.0000.0000.000
61A102ASP-1-0.813-0.88949.787-0.040-0.0400.0000.0000.0000.000
62A103GLN0-0.014-0.02247.007-0.002-0.0020.0000.0000.0000.000
63A104ILE0-0.0020.00943.0380.0000.0000.0000.0000.0000.000
64A105ILE0-0.033-0.01140.448-0.001-0.0010.0000.0000.0000.000
65A106VAL00.009-0.00137.320-0.001-0.0010.0000.0000.0000.000
66A107ALA0-0.011-0.00435.5640.0010.0010.0000.0000.0000.000
67A108LEU0-0.016-0.01033.048-0.002-0.0020.0000.0000.0000.000
68A109GLN0-0.018-0.02527.855-0.003-0.0030.0000.0000.0000.000
69A110ASP-1-0.849-0.90329.081-0.145-0.1450.0000.0000.0000.000
70A111GLY00.0190.01230.7430.0010.0010.0000.0000.0000.000
71A112ARG10.7420.85233.3330.1320.1320.0000.0000.0000.000
72A113VAL00.001-0.00936.321-0.001-0.0010.0000.0000.0000.000
73A114PHE0-0.015-0.01537.9190.0020.0020.0000.0000.0000.000
74A115GLU-1-0.826-0.89341.975-0.059-0.0590.0000.0000.0000.000
75A116ALA0-0.052-0.03542.604-0.002-0.0020.0000.0000.0000.000
76A117LEU00.0090.01544.6810.0030.0030.0000.0000.0000.000
77A118LEU00.0220.00446.675-0.002-0.0020.0000.0000.0000.000
78A119VAL0-0.043-0.02746.1940.0020.0020.0000.0000.0000.000
79A120GLY00.0810.04047.6290.0030.0030.0000.0000.0000.000
80A121SER0-0.075-0.04446.664-0.002-0.0020.0000.0000.0000.000
81A122ASP-1-0.715-0.81745.974-0.032-0.0320.0000.0000.0000.000
82A123SER00.006-0.01446.535-0.002-0.0020.0000.0000.0000.000
83A124LEU0-0.026-0.00347.7290.0000.0000.0000.0000.0000.000
84A125THR0-0.025-0.04742.4530.0000.0000.0000.0000.0000.000
85A126ASP-1-0.742-0.84842.341-0.045-0.0450.0000.0000.0000.000
86A127LEU0-0.0030.02439.066-0.004-0.0040.0000.0000.0000.000
87A128ALA00.009-0.01342.2440.0040.0040.0000.0000.0000.000
88A129VAL0-0.0050.00741.978-0.004-0.0040.0000.0000.0000.000
89A130LEU00.0180.01741.2730.0030.0030.0000.0000.0000.000
90A131LYS10.8550.91342.7720.0670.0670.0000.0000.0000.000
91A132ILE00.0280.03838.4030.0020.0020.0000.0000.0000.000
92A133ASN0-0.037-0.04242.9810.0020.0020.0000.0000.0000.000
93A134ALA00.0250.02639.4120.0010.0010.0000.0000.0000.000
94A135THR00.003-0.00541.0000.0020.0020.0000.0000.0000.000
95A136GLY00.006-0.00738.463-0.004-0.0040.0000.0000.0000.000
96A137GLY00.0160.03036.206-0.006-0.0060.0000.0000.0000.000
97A138LEU0-0.024-0.01934.7410.0000.0000.0000.0000.0000.000
98A139PRO00.0070.02229.843-0.002-0.0020.0000.0000.0000.000
99A140THR0-0.013-0.01430.8120.0090.0090.0000.0000.0000.000
100A141ILE00.0170.01228.146-0.011-0.0110.0000.0000.0000.000
101A142PRO0-0.0060.00025.0350.0080.0080.0000.0000.0000.000
102A143ILE00.0420.01828.1070.0050.0050.0000.0000.0000.000
103A144ASN0-0.038-0.02726.7020.0080.0080.0000.0000.0000.000
104A145ALA00.0310.00630.0260.0060.0060.0000.0000.0000.000
105A146ARG10.9330.95931.4780.0620.0620.0000.0000.0000.000
106A147ARG10.8140.87923.9580.0990.0990.0000.0000.0000.000
107A148VAL00.0050.00729.748-0.001-0.0010.0000.0000.0000.000
108A149PRO0-0.009-0.01428.303-0.001-0.0010.0000.0000.0000.000
109A150HIS0-0.039-0.01726.7050.0120.0120.0000.0000.0000.000
110A151ILE0-0.019-0.01127.702-0.004-0.0040.0000.0000.0000.000
111A152GLY00.0130.01025.4060.0090.0090.0000.0000.0000.000
112A153ASP-1-0.879-0.93123.215-0.042-0.0420.0000.0000.0000.000
113A154VAL0-0.012-0.01217.951-0.004-0.0040.0000.0000.0000.000
114A155VAL0-0.082-0.03821.197-0.019-0.0190.0000.0000.0000.000
115A156LEU0-0.016-0.02119.084-0.008-0.0080.0000.0000.0000.000
116A157ALA00.0260.02423.1960.0060.0060.0000.0000.0000.000
117A158ILE0-0.042-0.02423.746-0.014-0.0140.0000.0000.0000.000
118A159GLY00.017-0.00727.2160.0120.0120.0000.0000.0000.000
119A160ASN00.007-0.00228.978-0.014-0.0140.0000.0000.0000.000
120A161PRO0-0.0120.02128.9940.0090.0090.0000.0000.0000.000
121A162TYR0-0.006-0.05032.137-0.002-0.0020.0000.0000.0000.000
122A163ASN00.0040.01934.057-0.001-0.0010.0000.0000.0000.000
123A164LEU0-0.016-0.00229.520-0.001-0.0010.0000.0000.0000.000
124A165GLY00.0250.03029.078-0.008-0.0080.0000.0000.0000.000
125A166GLN0-0.074-0.04625.987-0.010-0.0100.0000.0000.0000.000
126A167THR0-0.052-0.02124.667-0.009-0.0090.0000.0000.0000.000
127A168ILE0-0.014-0.02620.527-0.002-0.0020.0000.0000.0000.000
128A169THR0-0.015-0.00622.612-0.001-0.0010.0000.0000.0000.000
129A170GLN00.009-0.01218.443-0.016-0.0160.0000.0000.0000.000
130A171GLY00.0470.02421.8250.0130.0130.0000.0000.0000.000
131A172ILE0-0.018-0.00622.163-0.009-0.0090.0000.0000.0000.000
132A173ILE00.0000.01624.477-0.004-0.0040.0000.0000.0000.000
133A174SER00.018-0.01827.7390.0050.0050.0000.0000.0000.000
134A175ALA0-0.041-0.02229.4530.0070.0070.0000.0000.0000.000
135A176THR00.0080.00632.310-0.006-0.0060.0000.0000.0000.000
136A177GLY00.0090.00234.8140.0040.0040.0000.0000.0000.000
137A178ARG10.8700.93935.6130.0070.0070.0000.0000.0000.000
138A179ILE00.0660.03539.226-0.002-0.0020.0000.0000.0000.000
139A180GLY0-0.0160.01539.603-0.003-0.0030.0000.0000.0000.000
140A181LEU0-0.020-0.01840.4590.0010.0010.0000.0000.0000.000
141A182ASN00.008-0.00243.7240.0000.0000.0000.0000.0000.000
142A183PRO00.0140.01346.7010.0020.0020.0000.0000.0000.000
143A184THR00.022-0.00747.6890.0000.0000.0000.0000.0000.000
144A185GLY00.0560.01646.1950.0000.0000.0000.0000.0000.000
145A186ARG10.9520.98044.9120.0110.0110.0000.0000.0000.000
146A187GLN0-0.090-0.03243.4130.0010.0010.0000.0000.0000.000
147A188ASN0-0.040-0.01939.533-0.004-0.0040.0000.0000.0000.000
148A189PHE00.0350.01336.783-0.005-0.0050.0000.0000.0000.000
149A190LEU0-0.030-0.02430.2140.0050.0050.0000.0000.0000.000
150A191GLN00.0370.01732.3520.0000.0000.0000.0000.0000.000
151A192THR0-0.065-0.05627.095-0.003-0.0030.0000.0000.0000.000
152A193ASP-1-0.734-0.84525.654-0.015-0.0150.0000.0000.0000.000
153A194ALA0-0.050-0.01725.141-0.002-0.0020.0000.0000.0000.000
154A195SER0-0.003-0.00426.0460.0000.0000.0000.0000.0000.000
155A196ILE0-0.0120.01427.958-0.012-0.0120.0000.0000.0000.000
156A197ASN00.0480.03230.2910.0100.0100.0000.0000.0000.000
157A198HIS00.0690.03433.414-0.003-0.0030.0000.0000.0000.000
158A199GLY00.0750.04334.869-0.003-0.0030.0000.0000.0000.000
159A200ASN0-0.024-0.02029.130-0.001-0.0010.0000.0000.0000.000
160A201SER00.0220.01132.921-0.003-0.0030.0000.0000.0000.000
161A202GLY00.0100.01336.188-0.003-0.0030.0000.0000.0000.000
162A203GLY00.0080.00631.957-0.004-0.0040.0000.0000.0000.000
163A204ALA00.004-0.00928.4460.0050.0050.0000.0000.0000.000
164A205LEU0-0.0050.01726.942-0.006-0.0060.0000.0000.0000.000
165A206VAL00.006-0.00723.2330.0040.0040.0000.0000.0000.000
166A207ASN00.0740.01322.939-0.016-0.0160.0000.0000.0000.000
167A208SER00.0390.01717.419-0.022-0.0220.0000.0000.0000.000
168A209LEU0-0.041-0.02018.174-0.042-0.0420.0000.0000.0000.000
169A210GLY00.023-0.00220.455-0.015-0.0150.0000.0000.0000.000
170A211GLU-1-0.802-0.82522.830-0.108-0.1080.0000.0000.0000.000
171A212LEU00.010-0.00326.0120.0040.0040.0000.0000.0000.000
172A213MET0-0.035-0.01126.6880.0100.0100.0000.0000.0000.000
173A214GLY00.019-0.00529.6270.0100.0100.0000.0000.0000.000
174A215ILE0-0.0190.00531.604-0.009-0.0090.0000.0000.0000.000
175A216ASN00.0080.00329.1440.0130.0130.0000.0000.0000.000
176A217THR0-0.010-0.00833.353-0.001-0.0010.0000.0000.0000.000
177A218LEU00.0180.00236.2190.0000.0000.0000.0000.0000.000
178A219SER0-0.019-0.02234.1840.0000.0000.0000.0000.0000.000
179A220PHE0-0.023-0.02735.7730.0010.0010.0000.0000.0000.000
180A221ASP-1-0.811-0.89336.039-0.032-0.0320.0000.0000.0000.000
181A222LYS10.8480.91938.4450.0180.0180.0000.0000.0000.000
182A223SER00.0530.03241.5250.0010.0010.0000.0000.0000.000
183A224ASN0-0.159-0.09242.808-0.004-0.0040.0000.0000.0000.000
184A225ASP-1-0.879-0.94746.230-0.003-0.0030.0000.0000.0000.000
185A226GLY00.0020.01445.4800.0020.0020.0000.0000.0000.000
186A227GLU-1-0.912-0.94340.4740.0040.0040.0000.0000.0000.000
187A228THR0-0.020-0.02236.997-0.003-0.0030.0000.0000.0000.000
188A229PRO0-0.049-0.01136.7070.0020.0020.0000.0000.0000.000
189A230GLU-1-0.916-0.95229.260-0.004-0.0040.0000.0000.0000.000
190A231GLY0-0.013-0.00529.5940.0040.0040.0000.0000.0000.000
191A232ILE0-0.051-0.02730.4020.0020.0020.0000.0000.0000.000
192A233GLY00.0380.03832.324-0.002-0.0020.0000.0000.0000.000
193A234PHE0-0.028-0.01833.2050.0020.0020.0000.0000.0000.000
194A235ALA00.0310.01032.233-0.005-0.0050.0000.0000.0000.000
195A236ILE00.0020.02034.2190.0040.0040.0000.0000.0000.000
196A237PRO00.0300.02034.163-0.007-0.0070.0000.0000.0000.000
197A238PHE00.004-0.00131.7290.0010.0010.0000.0000.0000.000
198A239GLN0-0.0100.01234.5720.0000.0000.0000.0000.0000.000
199A240LEU0-0.0040.01137.2340.0010.0010.0000.0000.0000.000
200A241ALA00.0510.01536.8970.0010.0010.0000.0000.0000.000
201A242THR0-0.015-0.01736.893-0.002-0.0020.0000.0000.0000.000
202A243LYS10.9540.97139.4510.0380.0380.0000.0000.0000.000
203A244ILE0-0.0200.00442.2880.0020.0020.0000.0000.0000.000
204A245MET00.0140.01739.599-0.001-0.0010.0000.0000.0000.000
205A246ASP-1-0.891-0.96241.921-0.059-0.0590.0000.0000.0000.000
206A247LYS10.8050.88244.7790.0360.0360.0000.0000.0000.000
207A248LEU0-0.049-0.01344.6990.0010.0010.0000.0000.0000.000
208A249ILE0-0.036-0.01642.8520.0000.0000.0000.0000.0000.000
209A250ARG10.7170.86547.4080.0420.0420.0000.0000.0000.000
210A251ASP-1-0.802-0.89450.506-0.036-0.0360.0000.0000.0000.000
211A252GLY00.0120.01951.3160.0020.0020.0000.0000.0000.000
212A253ARG10.7800.83850.8340.0300.0300.0000.0000.0000.000
213A254VAL0-0.024-0.00747.9040.0000.0000.0000.0000.0000.000
214A255ILE0-0.031-0.01150.2790.0020.0020.0000.0000.0000.000
215A256ARG10.8410.89547.1390.0300.0300.0000.0000.0000.000
216A257GLY00.0160.00753.7950.0000.0000.0000.0000.0000.000
217A258TYR0-0.007-0.01056.0630.0000.0000.0000.0000.0000.000
218A259ILE00.0330.00058.8140.0000.0000.0000.0000.0000.000
219A260GLY0-0.011-0.00161.4740.0000.0000.0000.0000.0000.000
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