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: YVVR2

Calculation Name: 5AOO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5AOO

Chain ID: A

ChEMBL ID:

UniProt ID: O91464

Base Structure: X-ray

Registration Date: 2023-09-21

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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2386269.546583
FMO2-HF: Nuclear repulsion 2297711.946975
FMO2-HF: Total energy -88557.599608
FMO2-MP2: Total energy -88813.879133


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:1:THR)


Summations of interaction energy for fragment #1(A:1:THR)
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.
-28.487-19.2891.93-5.022-6.105-0.037
Interaction energy analysis for fragmet #1(A:1:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.041 / q_NPA : -0.026
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].
3A3THR0-0.022-0.0543.645-0.1311.5290.000-0.851-0.8080.001
4A4GLU-1-0.952-0.9536.3270.6760.6760.0000.0000.0000.000
5A5ASP-1-0.847-0.9497.3200.6160.6160.0000.0000.0000.000
6A6LEU0-0.099-0.0409.331-0.092-0.0920.0000.0000.0000.000
7A7ASP-1-0.995-0.98911.8780.1760.1760.0000.0000.0000.000
8A8ALA00.0140.0239.8030.0210.0210.0000.0000.0000.000
9A9PRO0-0.015-0.0149.098-0.017-0.0170.0000.0000.0000.000
10A10GLN0-0.0020.02112.045-0.058-0.0580.0000.0000.0000.000
11A11ASP-1-0.819-0.90612.811-0.346-0.3460.0000.0000.0000.000
12A12THR0-0.103-0.06715.7970.0040.0040.0000.0000.0000.000
13A13GLY00.0610.02719.5480.0060.0060.0000.0000.0000.000
14A14ASN0-0.095-0.06821.1800.0150.0150.0000.0000.0000.000
15A15ILE00.0180.01124.035-0.008-0.0080.0000.0000.0000.000
16A16GLU-1-0.851-0.93325.794-0.107-0.1070.0000.0000.0000.000
17A17ASN0-0.075-0.03626.0310.0150.0150.0000.0000.0000.000
18A18GLY0-0.0050.00928.5220.0050.0050.0000.0000.0000.000
19A19ALA0-0.050-0.02324.880-0.005-0.0050.0000.0000.0000.000
20A20ALA00.0070.00622.4330.0050.0050.0000.0000.0000.000
21A21ASP-1-0.808-0.88216.874-0.369-0.3690.0000.0000.0000.000
22A22ASN0-0.090-0.05918.044-0.020-0.0200.0000.0000.0000.000
23A23SER0-0.071-0.03713.517-0.067-0.0670.0000.0000.0000.000
24A24PRO0-0.027-0.0159.9500.0530.0530.0000.0000.0000.000
25A25GLN00.0150.00710.260-0.066-0.0660.0000.0000.0000.000
26A26PRO00.0080.0066.724-0.218-0.2180.0000.0000.0000.000
27A27ARG10.9040.9405.7880.7240.7240.0000.0000.0000.000
28A28THR00.0480.0303.623-1.035-0.7310.003-0.049-0.2580.000
29A29THR0-0.077-0.0373.188-2.517-1.2150.125-0.573-0.8540.004
30A30PHE0-0.055-0.0163.918-1.888-1.4950.002-0.045-0.3510.000
31A31ASP-1-0.885-0.9472.637-25.382-19.8781.801-3.497-3.807-0.042
32A32TYR0-0.048-0.0164.5431.3571.392-0.001-0.007-0.0270.000
33A33THR00.0180.0077.552-0.015-0.0150.0000.0000.0000.000
34A34GLY0-0.027-0.00910.1330.1540.1540.0000.0000.0000.000
35A35ASN0-0.015-0.01813.741-0.024-0.0240.0000.0000.0000.000
36A36PRO0-0.0060.00416.9600.0390.0390.0000.0000.0000.000
37A37LEU00.013-0.00420.3450.0020.0020.0000.0000.0000.000
38A38PRO00.0240.02422.9350.0220.0220.0000.0000.0000.000
39A39PRO0-0.037-0.01825.9510.0080.0080.0000.0000.0000.000
40A40ASP-1-0.848-0.93628.946-0.212-0.2120.0000.0000.0000.000
41A41THR00.002-0.00526.4200.0140.0140.0000.0000.0000.000
42A42LYS10.8720.95429.6160.1700.1700.0000.0000.0000.000
43A43LEU00.0480.01931.4290.0090.0090.0000.0000.0000.000
44A44GLU-1-0.892-0.93834.668-0.128-0.1280.0000.0000.0000.000
45A45ASN0-0.027-0.03132.2910.0150.0150.0000.0000.0000.000
46A46PHE00.0610.04333.9640.0080.0080.0000.0000.0000.000
47A47PHE00.004-0.00235.8980.0060.0060.0000.0000.0000.000
48A48SER0-0.0060.01438.4920.0090.0090.0000.0000.0000.000
49A49PHE0-0.018-0.00935.8160.0060.0060.0000.0000.0000.000
50A50TYR0-0.015-0.01641.4670.0010.0010.0000.0000.0000.000
51A51ARG10.8250.90937.4930.1270.1270.0000.0000.0000.000
52A52LEU0-0.030-0.01444.8340.0030.0030.0000.0000.0000.000
53A53LEU0-0.018-0.02047.454-0.003-0.0030.0000.0000.0000.000
54A54PRO0-0.0310.00747.9650.0020.0020.0000.0000.0000.000
55A55MET00.012-0.00250.8930.0010.0010.0000.0000.0000.000
56A56GLY0-0.003-0.01454.6230.0000.0000.0000.0000.0000.000
57A57GLY00.0130.00755.6420.0020.0020.0000.0000.0000.000
58A58SER0-0.003-0.00854.8900.0010.0010.0000.0000.0000.000
59A59GLY00.0180.01551.503-0.002-0.0020.0000.0000.0000.000
60A60ALA0-0.0120.01051.663-0.002-0.0020.0000.0000.0000.000
61A61PRO00.0150.00451.702-0.001-0.0010.0000.0000.0000.000
62A62SER0-0.026-0.02353.145-0.001-0.0010.0000.0000.0000.000
63A63LEU0-0.012-0.00456.6610.0010.0010.0000.0000.0000.000
64A64SER00.0060.00959.6620.0000.0000.0000.0000.0000.000
65A65PHE0-0.078-0.03562.6440.0000.0000.0000.0000.0000.000
66A66PRO00.1130.06665.8570.0000.0000.0000.0000.0000.000
67A67ALA0-0.043-0.03469.241-0.001-0.0010.0000.0000.0000.000
68A68ASP-1-0.931-0.94870.852-0.037-0.0370.0000.0000.0000.000
69A69GLU-1-0.951-0.98769.995-0.039-0.0390.0000.0000.0000.000
70A70GLY0-0.012-0.00367.683-0.001-0.0010.0000.0000.0000.000
71A71THR0-0.030-0.02362.2890.0000.0000.0000.0000.0000.000
72A72ILE0-0.005-0.00661.7420.0000.0000.0000.0000.0000.000
73A73ILE00.0040.00856.335-0.001-0.0010.0000.0000.0000.000
74A74PRO00.0070.01156.251-0.001-0.0010.0000.0000.0000.000
75A75LEU0-0.022-0.02352.735-0.003-0.0030.0000.0000.0000.000
76A76ASN00.023-0.01452.136-0.004-0.0040.0000.0000.0000.000
77A77PRO00.0640.02546.9860.0000.0000.0000.0000.0000.000
78A78ILE00.0260.02448.950-0.001-0.0010.0000.0000.0000.000
79A79ASN0-0.029-0.01950.5440.0010.0010.0000.0000.0000.000
80A80TRP0-0.027-0.00447.259-0.001-0.0010.0000.0000.0000.000
81A81LEU0-0.026-0.01145.251-0.002-0.0020.0000.0000.0000.000
82A82LYS10.8010.91048.6270.0610.0610.0000.0000.0000.000
83A83GLY00.0270.01749.8180.0030.0030.0000.0000.0000.000
84A84ALA0-0.029-0.00847.090-0.004-0.0040.0000.0000.0000.000
85A85ASP-1-0.898-0.95345.086-0.081-0.0810.0000.0000.0000.000
86A86VAL00.0080.01244.423-0.002-0.0020.0000.0000.0000.000
87A87SER0-0.0040.00739.908-0.002-0.0020.0000.0000.0000.000
88A88GLY0-0.006-0.00841.492-0.001-0.0010.0000.0000.0000.000
89A89ILE00.029-0.01241.927-0.004-0.0040.0000.0000.0000.000
90A90ALA00.0310.01542.692-0.002-0.0020.0000.0000.0000.000
91A91ALA00.0590.03540.9510.0000.0000.0000.0000.0000.000
92A92MET0-0.026-0.00437.954-0.004-0.0040.0000.0000.0000.000
93A93LEU00.007-0.00838.848-0.003-0.0030.0000.0000.0000.000
94A94SER0-0.032-0.00941.0730.0010.0010.0000.0000.0000.000
95A95CYS0-0.0020.01736.0780.0000.0000.0000.0000.0000.000
96A96PHE0-0.009-0.01134.672-0.006-0.0060.0000.0000.0000.000
97A97THR0-0.0310.01139.2970.0060.0060.0000.0000.0000.000
98A98TYR00.0070.00141.4800.0040.0040.0000.0000.0000.000
99A99ILE00.0060.00540.863-0.007-0.0070.0000.0000.0000.000
100A100ALA00.0160.00342.7070.0060.0060.0000.0000.0000.000
101A101ALA0-0.032-0.00343.151-0.005-0.0050.0000.0000.0000.000
102A102ASP-1-0.810-0.89444.867-0.078-0.0780.0000.0000.0000.000
103A103LEU00.0140.01946.753-0.004-0.0040.0000.0000.0000.000
104A104ARG10.9360.97744.9180.0940.0940.0000.0000.0000.000
105A105ILE00.0110.00448.824-0.003-0.0030.0000.0000.0000.000
106A106THR00.0020.02150.4410.0030.0030.0000.0000.0000.000
107A107LEU00.0210.01952.867-0.001-0.0010.0000.0000.0000.000
108A108ARG10.9290.95355.3360.0660.0660.0000.0000.0000.000
109A109PHE00.0450.01357.4870.0000.0000.0000.0000.0000.000
110A110SER0-0.030-0.03560.1800.0000.0000.0000.0000.0000.000
111A111ASN0-0.019-0.01262.3490.0010.0010.0000.0000.0000.000
112A112PRO0-0.0220.00066.0670.0000.0000.0000.0000.0000.000
113A113ASN00.0280.02967.9330.0000.0000.0000.0000.0000.000
114A114ASP-1-0.852-0.93070.513-0.038-0.0380.0000.0000.0000.000
115A115ASN0-0.093-0.05572.7890.0010.0010.0000.0000.0000.000
116A116PRO00.0060.00170.101-0.001-0.0010.0000.0000.0000.000
117A117ALA00.0110.01368.7770.0010.0010.0000.0000.0000.000
118A118THR0-0.073-0.02967.963-0.001-0.0010.0000.0000.0000.000
119A119MET0-0.0030.01363.4220.0010.0010.0000.0000.0000.000
120A120LEU0-0.0050.01165.689-0.001-0.0010.0000.0000.0000.000
121A121VAL0-0.005-0.00759.7640.0000.0000.0000.0000.0000.000
122A122ALA00.0110.00462.8770.0000.0000.0000.0000.0000.000
123A123PHE0-0.020-0.01956.360-0.001-0.0010.0000.0000.0000.000
124A124ALA00.0290.01360.7970.0020.0020.0000.0000.0000.000
125A125PRO00.006-0.01058.804-0.002-0.0020.0000.0000.0000.000
126A126PRO0-0.0060.01055.0480.0020.0020.0000.0000.0000.000
127A127GLY0-0.003-0.00857.9590.0000.0000.0000.0000.0000.000
128A128ALA0-0.060-0.01060.7450.0020.0020.0000.0000.0000.000
129A129THR0-0.017-0.01763.6470.0000.0000.0000.0000.0000.000
130A130ILE00.0140.00962.0580.0000.0000.0000.0000.0000.000
131A131PRO0-0.021-0.01766.4200.0010.0010.0000.0000.0000.000
132A132LEU00.0250.01869.182-0.001-0.0010.0000.0000.0000.000
133A133LYS10.9660.97671.4720.0330.0330.0000.0000.0000.000
134A134PRO00.0480.02268.6400.0010.0010.0000.0000.0000.000
135A135THR00.0280.01770.8800.0010.0010.0000.0000.0000.000
136A136ARG10.8950.89370.7800.0390.0390.0000.0000.0000.000
137A137GLN00.0030.01272.275-0.001-0.0010.0000.0000.0000.000
138A138MET00.000-0.00471.5980.0000.0000.0000.0000.0000.000
139A139LEU00.0380.00666.623-0.001-0.0010.0000.0000.0000.000
140A140SER0-0.036-0.03067.615-0.001-0.0010.0000.0000.0000.000
141A141ASN0-0.070-0.01269.0870.0000.0000.0000.0000.0000.000
142A142PHE0-0.060-0.01064.0570.0000.0000.0000.0000.0000.000
143A143TYR00.0130.00661.2760.0000.0000.0000.0000.0000.000
144A144MET0-0.0220.00162.291-0.002-0.0020.0000.0000.0000.000
145A145ALA00.0260.00461.6970.0000.0000.0000.0000.0000.000
146A146GLU-1-0.799-0.86363.686-0.042-0.0420.0000.0000.0000.000
147A147VAL0-0.008-0.01361.384-0.001-0.0010.0000.0000.0000.000
148A148PRO00.0110.00664.3340.0010.0010.0000.0000.0000.000
149A149VAL0-0.032-0.02164.168-0.002-0.0020.0000.0000.0000.000
150A150SER0-0.006-0.00864.7760.0020.0020.0000.0000.0000.000
151A151ALA00.0180.00366.6330.0000.0000.0000.0000.0000.000
152A152ALA00.0070.01767.494-0.001-0.0010.0000.0000.0000.000
153A153THR0-0.0010.00162.224-0.002-0.0020.0000.0000.0000.000
154A154SER0-0.023-0.00358.9810.0000.0000.0000.0000.0000.000
155A155THR0-0.025-0.01360.2170.0000.0000.0000.0000.0000.000
156A156MET0-0.002-0.01153.947-0.001-0.0010.0000.0000.0000.000
157A157VAL00.0160.02156.6060.0010.0010.0000.0000.0000.000
158A158SER0-0.031-0.03252.121-0.001-0.0010.0000.0000.0000.000
159A159PHE00.004-0.00253.4710.0020.0020.0000.0000.0000.000
160A160SER0-0.036-0.02351.319-0.004-0.0040.0000.0000.0000.000
161A161ILE0-0.013-0.00551.6070.0030.0030.0000.0000.0000.000
162A162PRO00.0300.01150.269-0.003-0.0030.0000.0000.0000.000
163A163TYR0-0.051-0.06047.8470.0000.0000.0000.0000.0000.000
164A164THR0-0.017-0.01550.3730.0020.0020.0000.0000.0000.000
165A165SER0-0.019-0.00251.3580.0030.0030.0000.0000.0000.000
166A166PRO0-0.009-0.00252.969-0.001-0.0010.0000.0000.0000.000
167A167LEU00.0070.01950.7400.0010.0010.0000.0000.0000.000
168A168SER00.0120.01147.531-0.001-0.0010.0000.0000.0000.000
169A169ALA0-0.022-0.01644.628-0.003-0.0030.0000.0000.0000.000
170A170ILE00.0010.01946.6920.0030.0030.0000.0000.0000.000
171A171PRO0-0.023-0.00645.980-0.005-0.0050.0000.0000.0000.000
172A172THR0-0.038-0.03443.2300.0040.0040.0000.0000.0000.000
173A173SER0-0.026-0.01745.5090.0020.0020.0000.0000.0000.000
174A174TYR0-0.016-0.03747.298-0.001-0.0010.0000.0000.0000.000
175A175PHE0-0.0080.00648.9250.0010.0010.0000.0000.0000.000
176A176GLY00.0420.01851.0830.0010.0010.0000.0000.0000.000
177A177TRP00.0150.01654.631-0.001-0.0010.0000.0000.0000.000
178A178GLU-1-0.829-0.87857.550-0.052-0.0520.0000.0000.0000.000
179A179ASP-1-0.799-0.88458.725-0.042-0.0420.0000.0000.0000.000
180A180TRP00.011-0.02060.4010.0000.0000.0000.0000.0000.000
181A181SER0-0.042-0.01463.7310.0010.0010.0000.0000.0000.000
182A182GLY0-0.0230.00162.1390.0010.0010.0000.0000.0000.000
183A183THR0-0.075-0.05663.1560.0000.0000.0000.0000.0000.000
184A184ASN0-0.041-0.01759.911-0.002-0.0020.0000.0000.0000.000
185A185PHE00.002-0.00853.609-0.001-0.0010.0000.0000.0000.000
186A186GLY00.0020.00153.440-0.001-0.0010.0000.0000.0000.000
187A187GLN0-0.028-0.01153.500-0.004-0.0040.0000.0000.0000.000
188A188LEU00.0730.02251.8320.0010.0010.0000.0000.0000.000
189A189SER0-0.031-0.02854.682-0.002-0.0020.0000.0000.0000.000
190A190SER0-0.011-0.00256.644-0.001-0.0010.0000.0000.0000.000
191A191GLY00.0520.02652.427-0.001-0.0010.0000.0000.0000.000
192A192SER0-0.067-0.04751.700-0.002-0.0020.0000.0000.0000.000
193A193TRP0-0.026-0.02746.1750.0000.0000.0000.0000.0000.000
194A194GLY00.0380.02253.1960.0010.0010.0000.0000.0000.000
195A195ASN0-0.039-0.03456.490-0.002-0.0020.0000.0000.0000.000
196A196LEU00.0180.02155.9950.0010.0010.0000.0000.0000.000
197A197MET0-0.053-0.01759.9710.0010.0010.0000.0000.0000.000
198A198LEU00.000-0.00660.5460.0000.0000.0000.0000.0000.000
199A199ILE00.0170.01164.7680.0010.0010.0000.0000.0000.000
200A200PRO00.0040.00667.3870.0000.0000.0000.0000.0000.000
201A201SER0-0.039-0.00769.3260.0020.0020.0000.0000.0000.000
202A202LEU00.0530.01471.919-0.001-0.0010.0000.0000.0000.000
203A203SER0-0.020-0.01074.5660.0010.0010.0000.0000.0000.000
204A204VAL0-0.040-0.01376.3430.0010.0010.0000.0000.0000.000
205A205ASP-1-0.907-0.95278.059-0.032-0.0320.0000.0000.0000.000
206A206SER0-0.029-0.00776.8490.0000.0000.0000.0000.0000.000
207A207ALA00.019-0.00478.8740.0000.0000.0000.0000.0000.000
208A208ILE0-0.052-0.02875.8250.0000.0000.0000.0000.0000.000
209A209PRO00.0330.02874.982-0.001-0.0010.0000.0000.0000.000
210A210PHE0-0.009-0.01269.786-0.001-0.0010.0000.0000.0000.000
211A211ASP-1-0.782-0.89766.915-0.044-0.0440.0000.0000.0000.000
212A212PHE0-0.028-0.02564.526-0.001-0.0010.0000.0000.0000.000
213A213GLN0-0.051-0.02660.834-0.002-0.0020.0000.0000.0000.000
214A214LEU0-0.013-0.00757.838-0.001-0.0010.0000.0000.0000.000
215A215SER0-0.008-0.00954.095-0.001-0.0010.0000.0000.0000.000
216A216CYS00.0190.01952.9960.0020.0020.0000.0000.0000.000
217A217TRP00.0180.02447.632-0.001-0.0010.0000.0000.0000.000
218A218VAL00.008-0.00746.2100.0030.0030.0000.0000.0000.000
219A219ALA00.0340.01244.260-0.004-0.0040.0000.0000.0000.000
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