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: 98G82

Calculation Name: 5XAY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5XAY

Chain ID: A

ChEMBL ID:

UniProt ID: Q9XCC7

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2466999.148337
FMO2-HF: Nuclear repulsion 2383142.789031
FMO2-HF: Total energy -83856.359305
FMO2-MP2: Total energy -84103.243353


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:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-41.581-36.99115.559-10.003-10.145-0.054
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : 0.001
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].
3A4GLN00.0530.0463.227-0.1582.0560.002-1.051-1.1640.000
4A5GLU-1-0.790-0.9011.931-23.556-22.17711.026-6.613-5.791-0.085
5A6ARG10.9340.9622.259-18.789-17.7924.531-2.339-3.1900.031
6A7ALA00.0570.0365.5570.0230.0230.0000.0000.0000.000
7A8ALA00.0350.0047.6590.1530.1530.0000.0000.0000.000
8A9GLN0-0.109-0.0487.5480.2500.2500.0000.0000.0000.000
9A10THR00.012-0.0439.4660.0290.0290.0000.0000.0000.000
10A11ARG10.7080.83111.6040.2080.2080.0000.0000.0000.000
11A12ARG10.9140.9658.9840.3680.3680.0000.0000.0000.000
12A13THR0-0.008-0.01714.1000.0180.0180.0000.0000.0000.000
13A14ILE0-0.031-0.00615.365-0.006-0.0060.0000.0000.0000.000
14A15VAL00.0150.01017.5190.0030.0030.0000.0000.0000.000
15A16ALA00.0200.00818.6260.0000.0000.0000.0000.0000.000
16A17ALA0-0.013-0.00720.0500.0040.0040.0000.0000.0000.000
17A18ALA0-0.012-0.01721.743-0.001-0.0010.0000.0000.0000.000
18A19ALA0-0.0110.00123.198-0.002-0.0020.0000.0000.0000.000
19A20ALA00.0280.01924.700-0.001-0.0010.0000.0000.0000.000
20A21VAL0-0.001-0.00426.1990.0010.0010.0000.0000.0000.000
21A22PHE00.000-0.01025.446-0.002-0.0020.0000.0000.0000.000
22A23ASP-1-0.791-0.86829.137-0.008-0.0080.0000.0000.0000.000
23A24GLU-1-0.804-0.84729.5820.0510.0510.0000.0000.0000.000
24A25LEU0-0.054-0.03331.6190.0000.0000.0000.0000.0000.000
25A26GLY00.0550.03732.795-0.002-0.0020.0000.0000.0000.000
26A27TYR0-0.057-0.03729.5850.0070.0070.0000.0000.0000.000
27A28GLU-1-0.858-0.91832.5670.0060.0060.0000.0000.0000.000
28A29ALA00.0130.00134.6540.0040.0040.0000.0000.0000.000
29A30THR00.0220.01928.1680.0100.0100.0000.0000.0000.000
30A31THR0-0.017-0.01329.7860.0000.0000.0000.0000.0000.000
31A32ILE00.0490.00324.0010.0050.0050.0000.0000.0000.000
32A33ALA0-0.0050.00125.1910.0140.0140.0000.0000.0000.000
33A34GLU-1-0.769-0.87026.4890.1110.1110.0000.0000.0000.000
34A35ILE00.0460.02421.7890.0090.0090.0000.0000.0000.000
35A36LEU0-0.0350.00320.7300.0130.0130.0000.0000.0000.000
36A37LYS10.7980.88122.138-0.081-0.0810.0000.0000.0000.000
37A38ARG10.7590.84523.728-0.066-0.0660.0000.0000.0000.000
38A39SER0-0.026-0.02418.2620.0110.0110.0000.0000.0000.000
39A40GLY00.0140.01118.2960.0400.0400.0000.0000.0000.000
40A41VAL0-0.044-0.01615.3280.0640.0640.0000.0000.0000.000
41A42THR00.0150.01116.050-0.069-0.0690.0000.0000.0000.000
42A43LYS10.9220.94418.683-0.146-0.1460.0000.0000.0000.000
43A44GLY0-0.0230.00118.104-0.031-0.0310.0000.0000.0000.000
44A45ALA00.0480.02414.206-0.044-0.0440.0000.0000.0000.000
45A46LEU00.0220.00415.655-0.061-0.0610.0000.0000.0000.000
46A47TYR00.000-0.01518.446-0.031-0.0310.0000.0000.0000.000
47A48PHE0-0.056-0.01411.646-0.030-0.0300.0000.0000.0000.000
48A49HIS0-0.0030.01411.731-0.110-0.1100.0000.0000.0000.000
49A50PHE0-0.002-0.00416.677-0.039-0.0390.0000.0000.0000.000
50A51THR0-0.004-0.01720.5360.0260.0260.0000.0000.0000.000
51A52SER0-0.002-0.00923.4950.0130.0130.0000.0000.0000.000
52A53LYS10.8570.92325.142-0.014-0.0140.0000.0000.0000.000
53A54GLU-1-0.810-0.88927.166-0.054-0.0540.0000.0000.0000.000
54A55GLN00.0740.05322.0380.0060.0060.0000.0000.0000.000
55A56LEU0-0.020-0.00520.862-0.013-0.0130.0000.0000.0000.000
56A57ALA00.0260.01123.628-0.006-0.0060.0000.0000.0000.000
57A58GLN0-0.024-0.02426.238-0.011-0.0110.0000.0000.0000.000
58A59GLU-1-0.773-0.84518.032-0.227-0.2270.0000.0000.0000.000
59A60VAL0-0.016-0.01522.774-0.010-0.0100.0000.0000.0000.000
60A61LEU0-0.051-0.02323.997-0.006-0.0060.0000.0000.0000.000
61A62THR0-0.010-0.00524.022-0.007-0.0070.0000.0000.0000.000
62A63SER0-0.076-0.04220.905-0.016-0.0160.0000.0000.0000.000
63A64GLN00.0130.01421.271-0.013-0.0130.0000.0000.0000.000
64A65LEU0-0.0370.00022.466-0.012-0.0120.0000.0000.0000.000
65A75ARG10.8660.91733.0890.1080.1080.0000.0000.0000.000
66A76LEU0-0.025-0.00535.0420.0060.0060.0000.0000.0000.000
67A77VAL0-0.022-0.01833.133-0.006-0.0060.0000.0000.0000.000
68A78LEU00.018-0.00634.763-0.002-0.0020.0000.0000.0000.000
69A79GLN0-0.006-0.01634.3400.0080.0080.0000.0000.0000.000
70A80GLN0-0.037-0.01327.9710.0000.0000.0000.0000.0000.000
71A81ILE00.0750.03231.7600.0000.0000.0000.0000.0000.000
72A82ILE0-0.0290.01434.0310.0060.0060.0000.0000.0000.000
73A83ASP-1-0.760-0.85130.472-0.120-0.1200.0000.0000.0000.000
74A84GLU-1-0.791-0.87927.977-0.168-0.1680.0000.0000.0000.000
75A85THR0-0.011-0.01430.1230.0060.0060.0000.0000.0000.000
76A86LEU0-0.019-0.02033.1380.0080.0080.0000.0000.0000.000
77A87LEU0-0.0010.01425.3510.0070.0070.0000.0000.0000.000
78A88LEU00.0120.00427.9220.0070.0070.0000.0000.0000.000
79A89ALA00.0150.00330.3140.0090.0090.0000.0000.0000.000
80A90GLN0-0.045-0.02630.7280.0130.0130.0000.0000.0000.000
81A91LEU0-0.014-0.01125.4230.0090.0090.0000.0000.0000.000
82A92LEU0-0.030-0.00129.0590.0090.0090.0000.0000.0000.000
83A93SER0-0.029-0.01031.4820.0090.0090.0000.0000.0000.000
84A94LYS10.8840.94429.6940.0310.0310.0000.0000.0000.000
85A95GLY00.0030.01130.0520.0070.0070.0000.0000.0000.000
86A96ASP-1-0.784-0.89124.126-0.062-0.0620.0000.0000.0000.000
87A97PRO00.0340.00123.683-0.005-0.0050.0000.0000.0000.000
88A98LEU00.0140.01919.8080.0020.0020.0000.0000.0000.000
89A99VAL0-0.0100.01124.388-0.005-0.0050.0000.0000.0000.000
90A100ARG10.8360.89427.6000.0140.0140.0000.0000.0000.000
91A101GLY00.0180.02327.4130.0020.0020.0000.0000.0000.000
92A102SER0-0.044-0.03626.9450.0000.0000.0000.0000.0000.000
93A103VAL00.0220.01428.7450.0000.0000.0000.0000.0000.000
94A104ARG10.7860.88931.8960.0020.0020.0000.0000.0000.000
95A105LEU0-0.051-0.03028.0150.0020.0020.0000.0000.0000.000
96A106THR0-0.063-0.04332.013-0.004-0.0040.0000.0000.0000.000
97A107VAL0-0.039-0.01234.1270.0000.0000.0000.0000.0000.000
98A108GLU-1-0.816-0.87935.307-0.007-0.0070.0000.0000.0000.000
99A109PRO00.012-0.01337.734-0.003-0.0030.0000.0000.0000.000
100A110GLY00.0320.02238.1220.0030.0030.0000.0000.0000.000
101A111ALA0-0.042-0.02038.805-0.002-0.0020.0000.0000.0000.000
102A112PRO0-0.020-0.02540.5060.0000.0000.0000.0000.0000.000
103A113ARG10.7550.86738.0730.0130.0130.0000.0000.0000.000
104A114ASP-1-0.757-0.85936.485-0.018-0.0180.0000.0000.0000.000
105A115GLY00.0020.01935.9320.0020.0020.0000.0000.0000.000
106A116LEU00.0100.00630.1420.0010.0010.0000.0000.0000.000
107A117ASP-1-0.818-0.90832.991-0.070-0.0700.0000.0000.0000.000
108A118ARG10.8230.88032.1560.0270.0270.0000.0000.0000.000
109A119ARG10.8860.95533.2730.0550.0550.0000.0000.0000.000
110A120ALA0-0.008-0.00530.243-0.005-0.0050.0000.0000.0000.000
111A121PRO00.1020.04528.275-0.006-0.0060.0000.0000.0000.000
112A122MET0-0.0130.01429.923-0.007-0.0070.0000.0000.0000.000
113A123GLN0-0.057-0.04733.1780.0040.0040.0000.0000.0000.000
114A124GLU-1-0.911-0.94926.326-0.162-0.1620.0000.0000.0000.000
115A125TRP00.0160.00930.110-0.005-0.0050.0000.0000.0000.000
116A126ILE0-0.013-0.02330.953-0.001-0.0010.0000.0000.0000.000
117A127GLY0-0.012-0.01332.2250.0010.0010.0000.0000.0000.000
118A128HIS0-0.007-0.01626.912-0.008-0.0080.0000.0000.0000.000
119A129GLY00.0320.01630.601-0.001-0.0010.0000.0000.0000.000
120A130ARG10.8020.89233.9100.1170.1170.0000.0000.0000.000
121A131ASP-1-0.819-0.90831.598-0.140-0.1400.0000.0000.0000.000
122A132LEU0-0.034-0.00729.712-0.005-0.0050.0000.0000.0000.000
123A133LEU00.012-0.00733.3530.0030.0030.0000.0000.0000.000
124A134ARG10.8430.89934.7400.1290.1290.0000.0000.0000.000
125A135ARG10.8780.94329.2070.1800.1800.0000.0000.0000.000
126A136ALA00.0140.01435.7480.0020.0020.0000.0000.0000.000
127A137GLU-1-0.939-0.96738.364-0.084-0.0840.0000.0000.0000.000
128A138ALA0-0.040-0.01937.9040.0030.0030.0000.0000.0000.000
129A139GLY0-0.0170.00139.3110.0000.0000.0000.0000.0000.000
130A140GLY0-0.031-0.01140.0480.0030.0030.0000.0000.0000.000
131A141GLU-1-0.815-0.91737.972-0.113-0.1130.0000.0000.0000.000
132A142LEU0-0.0080.00640.6730.0030.0030.0000.0000.0000.000
133A143LEU0-0.027-0.00844.2330.0020.0020.0000.0000.0000.000
134A144PRO00.0170.00947.149-0.001-0.0010.0000.0000.0000.000
135A145ARG10.9240.94047.6340.0630.0630.0000.0000.0000.000
136A146LEU00.0280.03645.2070.0030.0030.0000.0000.0000.000
137A147ASP-1-0.838-0.91943.588-0.081-0.0810.0000.0000.0000.000
138A148VAL00.0220.00338.9480.0000.0000.0000.0000.0000.000
139A149ASP-1-0.786-0.85838.739-0.095-0.0950.0000.0000.0000.000
140A150ALA00.008-0.00140.4830.0000.0000.0000.0000.0000.000
141A151VAL00.0310.00240.9130.0020.0020.0000.0000.0000.000
142A152ALA00.0040.01036.7350.0000.0000.0000.0000.0000.000
143A153ARG10.8270.89338.1710.0770.0770.0000.0000.0000.000
144A154MET0-0.033-0.00840.0800.0030.0030.0000.0000.0000.000
145A155LEU00.0030.01137.8490.0030.0030.0000.0000.0000.000
146A156VAL00.0180.02034.6020.0030.0030.0000.0000.0000.000
147A157GLY00.0160.01437.1250.0040.0040.0000.0000.0000.000
148A158GLY00.0240.00740.3100.0050.0050.0000.0000.0000.000
149A159PHE00.005-0.00433.1070.0040.0040.0000.0000.0000.000
150A160THR0-0.010-0.02136.9990.0040.0040.0000.0000.0000.000
151A161GLY00.0040.00238.3130.0050.0050.0000.0000.0000.000
152A162ALA0-0.015-0.01340.4780.0040.0040.0000.0000.0000.000
153A163GLN00.0480.01335.6270.0080.0080.0000.0000.0000.000
154A164ILE0-0.0060.00038.9890.0040.0040.0000.0000.0000.000
155A165LEU00.008-0.00840.9980.0040.0040.0000.0000.0000.000
156A166SER0-0.033-0.03240.2860.0030.0030.0000.0000.0000.000
157A167ASN0-0.064-0.03638.1650.0010.0010.0000.0000.0000.000
158A168ILE0-0.030-0.00540.9980.0040.0040.0000.0000.0000.000
159A169LEU0-0.035-0.01444.6760.0020.0020.0000.0000.0000.000
160A170THR0-0.049-0.03342.7340.0020.0020.0000.0000.0000.000
161A171GLY00.0370.02540.8990.0010.0010.0000.0000.0000.000
162A172HIS0-0.021-0.02436.0170.0020.0020.0000.0000.0000.000
163A173ALA00.0030.00538.339-0.003-0.0030.0000.0000.0000.000
164A174ASP-1-0.774-0.84740.570-0.029-0.0290.0000.0000.0000.000
165A175LEU0-0.0130.01735.040-0.004-0.0040.0000.0000.0000.000
166A176LEU00.0340.00935.752-0.004-0.0040.0000.0000.0000.000
167A177GLU-1-0.831-0.86838.327-0.036-0.0360.0000.0000.0000.000
168A178ARG10.7750.84541.6470.0300.0300.0000.0000.0000.000
169A179VAL00.0190.01036.295-0.002-0.0020.0000.0000.0000.000
170A180THR0-0.031-0.03739.340-0.005-0.0050.0000.0000.0000.000
171A181ASP-1-0.823-0.90040.481-0.048-0.0480.0000.0000.0000.000
172A182MET0-0.0140.01341.8380.0000.0000.0000.0000.0000.000
173A183HIS0-0.011-0.02036.1440.0030.0030.0000.0000.0000.000
174A184ARG10.8460.91241.2450.0500.0500.0000.0000.0000.000
175A185HIS0-0.041-0.00843.8280.0000.0000.0000.0000.0000.000
176A186LEU00.0010.00341.9540.0000.0000.0000.0000.0000.000
177A187MET00.0320.02238.762-0.002-0.0020.0000.0000.0000.000
178A188THR0-0.052-0.04343.312-0.001-0.0010.0000.0000.0000.000
179A189SER0-0.114-0.05646.4610.0020.0020.0000.0000.0000.000
180A190VAL0-0.006-0.00442.1210.0000.0000.0000.0000.0000.000
181A191ALA00.0340.01543.292-0.003-0.0030.0000.0000.0000.000
182A192VAL00.0060.00744.8410.0050.0050.0000.0000.0000.000
183A193PRO00.0620.01546.766-0.002-0.0020.0000.0000.0000.000
184A194ALA0-0.006-0.00448.1960.0000.0000.0000.0000.0000.000
185A195VAL0-0.008-0.00541.777-0.003-0.0030.0000.0000.0000.000
186A196LEU00.0400.02943.573-0.002-0.0020.0000.0000.0000.000
187A197VAL0-0.028-0.01444.6700.0000.0000.0000.0000.0000.000
188A198ARG10.8660.93241.7650.0900.0900.0000.0000.0000.000
189A199LEU0-0.0330.00538.924-0.007-0.0070.0000.0000.0000.000
190A200ASP-1-0.827-0.89137.446-0.082-0.0820.0000.0000.0000.000
191A201PHE00.024-0.00437.893-0.005-0.0050.0000.0000.0000.000
192A202SER0-0.033-0.02338.6150.0040.0040.0000.0000.0000.000
193A203ALA00.0460.01637.633-0.004-0.0040.0000.0000.0000.000
194A204GLU-1-0.851-0.93836.369-0.058-0.0580.0000.0000.0000.000
195A205ARG10.7850.87332.4420.1100.1100.0000.0000.0000.000
196A206SER00.0140.01432.857-0.007-0.0070.0000.0000.0000.000
197A207ILE00.003-0.00531.855-0.004-0.0040.0000.0000.0000.000
198A208THR0-0.040-0.02430.241-0.002-0.0020.0000.0000.0000.000
199A209VAL0-0.020-0.01627.949-0.009-0.0090.0000.0000.0000.000
200A210TYR00.018-0.00626.963-0.008-0.0080.0000.0000.0000.000
201A211ASP-1-0.829-0.89326.358-0.089-0.0890.0000.0000.0000.000
202A212GLU-1-0.900-0.94321.910-0.223-0.2230.0000.0000.0000.000
203A213ALA00.0500.02122.622-0.011-0.0110.0000.0000.0000.000
204A214MET0-0.026-0.01121.755-0.007-0.0070.0000.0000.0000.000
205A215ARG10.7750.86920.4150.1260.1260.0000.0000.0000.000
206A216ARG10.7770.88416.3280.2430.2430.0000.0000.0000.000
207A217ARG10.7800.87517.3470.0850.0850.0000.0000.0000.000
208A218GLU-1-0.876-0.92813.467-0.116-0.1160.0000.0000.0000.000
209A219ALA00.010-0.00716.911-0.005-0.0050.0000.0000.0000.000
210A220PRO00.0020.01314.2300.0470.0470.0000.0000.0000.000
211A221LEU00.0340.02913.5890.0220.0220.0000.0000.0000.000
212A222PRO00.0430.03412.0210.0450.0450.0000.0000.0000.000
213A223ALA0-0.030-0.0187.8060.2630.2630.0000.0000.0000.000
214A224ALA00.007-0.0199.561-0.147-0.1470.0000.0000.0000.000
215A225GLY0-0.044-0.01810.059-0.121-0.1210.0000.0000.0000.000
216A226ASP-1-0.825-0.88610.4270.5400.5400.0000.0000.0000.000
217A227LEU0-0.032-0.00613.027-0.129-0.1290.0000.0000.0000.000
218A228GLU-1-0.869-0.94815.7320.3190.3190.0000.0000.0000.000
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