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: VQQY1

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 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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2388625.793634
FMO2-HF: Nuclear repulsion 2300067.706499
FMO2-HF: Total energy -88558.087135
FMO2-MP2: Total energy -88814.46386


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.
-42.049-36.76814.822-9.216-10.887-0.078
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 : -0.068 / q_NPA : -0.056
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].
3A3THR0-0.014-0.0483.355-0.1431.6670.044-0.976-0.8780.000
4A4GLU-1-0.945-0.9496.1350.7220.7220.0000.0000.0000.000
5A5ASP-1-0.804-0.9277.2980.5310.5310.0000.0000.0000.000
6A6LEU0-0.129-0.0739.245-0.054-0.0540.0000.0000.0000.000
7A7ASP-1-0.983-0.98411.7030.2010.2010.0000.0000.0000.000
8A8ALA00.0080.0259.4150.0020.0020.0000.0000.0000.000
9A9PRO0-0.031-0.0258.571-0.040-0.0400.0000.0000.0000.000
10A10GLN00.0030.02711.555-0.009-0.0090.0000.0000.0000.000
11A11ASP-1-0.800-0.86612.209-0.159-0.1590.0000.0000.0000.000
12A12THR0-0.088-0.06515.048-0.009-0.0090.0000.0000.0000.000
13A13GLY00.0540.02118.7690.0050.0050.0000.0000.0000.000
14A14ASN0-0.092-0.05420.9200.0040.0040.0000.0000.0000.000
15A15ILE00.0370.02823.784-0.007-0.0070.0000.0000.0000.000
16A16GLU-1-0.842-0.93225.165-0.070-0.0700.0000.0000.0000.000
17A17ASN0-0.086-0.04325.5000.0110.0110.0000.0000.0000.000
18A18GLY0-0.0170.00528.5460.0010.0010.0000.0000.0000.000
19A19ALA0-0.050-0.02824.890-0.005-0.0050.0000.0000.0000.000
20A20ALA00.0240.01121.8940.0070.0070.0000.0000.0000.000
21A21ASP-1-0.792-0.86816.130-0.297-0.2970.0000.0000.0000.000
22A22ASN0-0.077-0.05017.371-0.001-0.0010.0000.0000.0000.000
23A23SER0-0.073-0.04012.839-0.062-0.0620.0000.0000.0000.000
24A24PRO0-0.020-0.0149.0900.0630.0630.0000.0000.0000.000
25A25GLN00.0090.0059.206-0.070-0.0700.0000.0000.0000.000
26A26PRO00.0290.0246.158-0.102-0.1020.0000.0000.0000.000
27A27ARG10.8120.8595.0260.3900.3900.0000.0000.0000.000
28A28THR00.0140.0303.058-1.168-0.4210.056-0.226-0.577-0.001
29A29THR0-0.062-0.0352.587-3.562-1.7561.678-1.495-1.9890.010
30A30PHE0-0.044-0.0113.306-3.091-3.3210.0901.073-0.9330.001
31A31ASP-1-0.849-0.9081.761-36.854-35.81312.950-7.569-6.421-0.088
32A32TYR0-0.061-0.0403.9211.6081.7150.004-0.023-0.0890.000
33A33THR0-0.011-0.0056.988-0.085-0.0850.0000.0000.0000.000
34A34GLY0-0.017-0.0049.9330.1780.1780.0000.0000.0000.000
35A35ASN0-0.017-0.02213.539-0.024-0.0240.0000.0000.0000.000
36A36PRO0-0.0030.00716.7270.0360.0360.0000.0000.0000.000
37A37LEU00.0230.00920.3620.0000.0000.0000.0000.0000.000
38A38PRO00.0370.02222.6270.0190.0190.0000.0000.0000.000
39A39PRO00.0130.01125.7050.0100.0100.0000.0000.0000.000
40A40ASP-1-0.873-0.94528.971-0.185-0.1850.0000.0000.0000.000
41A41THR0-0.035-0.02425.8130.0110.0110.0000.0000.0000.000
42A42LYS10.8660.94829.1490.1470.1470.0000.0000.0000.000
43A43LEU00.0440.00931.2050.0080.0080.0000.0000.0000.000
44A44GLU-1-0.876-0.93334.294-0.110-0.1100.0000.0000.0000.000
45A45ASN0-0.016-0.01731.9990.0130.0130.0000.0000.0000.000
46A46PHE00.0500.04733.5990.0070.0070.0000.0000.0000.000
47A47PHE00.018-0.00835.5520.0050.0050.0000.0000.0000.000
48A48SER0-0.034-0.00838.2520.0070.0070.0000.0000.0000.000
49A49PHE0-0.010-0.00135.2080.0050.0050.0000.0000.0000.000
50A50TYR0-0.024-0.02040.9010.0000.0000.0000.0000.0000.000
51A51ARG10.8040.89037.1330.1080.1080.0000.0000.0000.000
52A52LEU0-0.013-0.00344.3710.0030.0030.0000.0000.0000.000
53A53LEU0-0.019-0.02046.709-0.003-0.0030.0000.0000.0000.000
54A54PRO0-0.0260.00247.2850.0020.0020.0000.0000.0000.000
55A55MET00.0080.01050.1500.0010.0010.0000.0000.0000.000
56A56GLY00.0250.00053.9400.0000.0000.0000.0000.0000.000
57A57GLY0-0.0050.00354.8940.0020.0020.0000.0000.0000.000
58A58SER0-0.038-0.03454.0330.0020.0020.0000.0000.0000.000
59A59GLY00.0080.01550.839-0.002-0.0020.0000.0000.0000.000
60A60ALA00.0090.02151.015-0.002-0.0020.0000.0000.0000.000
61A61PRO00.013-0.00451.133-0.001-0.0010.0000.0000.0000.000
62A62SER0-0.026-0.02352.553-0.001-0.0010.0000.0000.0000.000
63A63LEU0-0.042-0.02456.1330.0000.0000.0000.0000.0000.000
64A64SER00.002-0.01259.3100.0000.0000.0000.0000.0000.000
65A65PHE0-0.049-0.03362.2660.0000.0000.0000.0000.0000.000
66A66PRO00.0780.05265.4950.0000.0000.0000.0000.0000.000
67A67ALA0-0.028-0.02568.833-0.001-0.0010.0000.0000.0000.000
68A68ASP-1-0.923-0.95370.772-0.031-0.0310.0000.0000.0000.000
69A69GLU-1-0.934-0.97869.921-0.033-0.0330.0000.0000.0000.000
70A70GLY0-0.017-0.00667.6040.0000.0000.0000.0000.0000.000
71A71THR0-0.033-0.02162.0940.0000.0000.0000.0000.0000.000
72A72ILE0-0.011-0.01761.3120.0000.0000.0000.0000.0000.000
73A73ILE0-0.0040.01355.9640.0000.0000.0000.0000.0000.000
74A74PRO00.0200.01855.6090.0000.0000.0000.0000.0000.000
75A75LEU0-0.029-0.02852.454-0.002-0.0020.0000.0000.0000.000
76A76ASN00.026-0.00451.643-0.003-0.0030.0000.0000.0000.000
77A77PRO00.0430.02246.5740.0000.0000.0000.0000.0000.000
78A78ILE00.0360.02948.711-0.001-0.0010.0000.0000.0000.000
79A79ASN0-0.016-0.00950.5380.0020.0020.0000.0000.0000.000
80A80TRP0-0.021-0.00246.815-0.001-0.0010.0000.0000.0000.000
81A81LEU0-0.016-0.00544.644-0.002-0.0020.0000.0000.0000.000
82A82LYS10.7810.89448.2160.0510.0510.0000.0000.0000.000
83A83GLY00.015-0.00649.4410.0020.0020.0000.0000.0000.000
84A84ALA0-0.0160.00046.328-0.003-0.0030.0000.0000.0000.000
85A85ASP-1-0.897-0.95144.646-0.064-0.0640.0000.0000.0000.000
86A86VAL00.0020.01244.008-0.002-0.0020.0000.0000.0000.000
87A87SER00.0050.00739.560-0.001-0.0010.0000.0000.0000.000
88A88GLY00.000-0.00441.243-0.003-0.0030.0000.0000.0000.000
89A89ILE00.009-0.01741.726-0.003-0.0030.0000.0000.0000.000
90A90ALA00.0280.01942.256-0.002-0.0020.0000.0000.0000.000
91A91ALA00.0620.03940.1260.0000.0000.0000.0000.0000.000
92A92MET0-0.0290.00237.678-0.004-0.0040.0000.0000.0000.000
93A93LEU00.007-0.00638.262-0.003-0.0030.0000.0000.0000.000
94A94SER0-0.034-0.02840.4630.0010.0010.0000.0000.0000.000
95A95CYS0-0.0040.01835.4150.0000.0000.0000.0000.0000.000
96A96PHE00.000-0.00234.214-0.005-0.0050.0000.0000.0000.000
97A97THR0-0.0320.01238.7470.0050.0050.0000.0000.0000.000
98A98TYR00.0080.00441.0630.0040.0040.0000.0000.0000.000
99A99ILE00.0090.01040.678-0.006-0.0060.0000.0000.0000.000
100A100ALA00.0160.00342.4160.0050.0050.0000.0000.0000.000
101A101ALA0-0.0310.00142.785-0.004-0.0040.0000.0000.0000.000
102A102ASP-1-0.777-0.88044.444-0.068-0.0680.0000.0000.0000.000
103A103LEU00.0070.02446.477-0.003-0.0030.0000.0000.0000.000
104A104ARG10.8840.94545.3750.0810.0810.0000.0000.0000.000
105A105ILE00.0310.01248.490-0.002-0.0020.0000.0000.0000.000
106A106THR0-0.014-0.01350.7900.0000.0000.0000.0000.0000.000
107A107LEU00.0000.00652.562-0.001-0.0010.0000.0000.0000.000
108A108ARG10.8950.93055.1750.0550.0550.0000.0000.0000.000
109A109PHE00.0460.01057.4310.0000.0000.0000.0000.0000.000
110A110SER0-0.023-0.03559.8890.0000.0000.0000.0000.0000.000
111A111ASN00.0060.00562.0630.0010.0010.0000.0000.0000.000
112A112PRO0-0.0160.00265.807-0.001-0.0010.0000.0000.0000.000
113A113ASN00.0020.00867.4970.0000.0000.0000.0000.0000.000
114A114ASP-1-0.831-0.92470.247-0.032-0.0320.0000.0000.0000.000
115A115ASN0-0.068-0.03872.6690.0000.0000.0000.0000.0000.000
116A116PRO0-0.036-0.02069.972-0.001-0.0010.0000.0000.0000.000
117A117ALA00.0460.03368.5510.0010.0010.0000.0000.0000.000
118A118THR0-0.090-0.04967.605-0.001-0.0010.0000.0000.0000.000
119A119MET0-0.0110.01363.2760.0010.0010.0000.0000.0000.000
120A120LEU00.0020.01765.203-0.001-0.0010.0000.0000.0000.000
121A121VAL0-0.016-0.01259.7250.0000.0000.0000.0000.0000.000
122A122ALA00.0200.00362.7960.0000.0000.0000.0000.0000.000
123A123PHE0-0.001-0.00256.1000.0000.0000.0000.0000.0000.000
124A124ALA00.0370.01460.4920.0010.0010.0000.0000.0000.000
125A125PRO00.015-0.00558.566-0.001-0.0010.0000.0000.0000.000
126A126PRO0-0.0040.01854.8500.0020.0020.0000.0000.0000.000
127A127GLY0-0.011-0.02657.5540.0000.0000.0000.0000.0000.000
128A128ALA0-0.072-0.01260.6770.0020.0020.0000.0000.0000.000
129A129THR0-0.005-0.01263.6090.0000.0000.0000.0000.0000.000
130A130ILE00.0340.02161.6920.0000.0000.0000.0000.0000.000
131A131PRO0-0.019-0.01766.0640.0010.0010.0000.0000.0000.000
132A132LEU00.0040.00469.0300.0000.0000.0000.0000.0000.000
133A133LYS10.9620.97670.9430.0280.0280.0000.0000.0000.000
134A134PRO00.0680.03767.9830.0010.0010.0000.0000.0000.000
135A135THR00.0200.00570.3970.0010.0010.0000.0000.0000.000
136A136ARG10.8900.90170.4440.0330.0330.0000.0000.0000.000
137A137GLN00.0240.02472.156-0.001-0.0010.0000.0000.0000.000
138A138MET0-0.0050.00071.2320.0000.0000.0000.0000.0000.000
139A139LEU00.0540.00766.3400.0000.0000.0000.0000.0000.000
140A140SER0-0.038-0.02167.613-0.001-0.0010.0000.0000.0000.000
141A141ASN0-0.102-0.03869.4590.0000.0000.0000.0000.0000.000
142A142PHE0-0.057-0.01263.9180.0000.0000.0000.0000.0000.000
143A143TYR00.002-0.00260.9950.0000.0000.0000.0000.0000.000
144A144MET0-0.030-0.00262.269-0.001-0.0010.0000.0000.0000.000
145A145ALA00.0210.00361.385-0.001-0.0010.0000.0000.0000.000
146A146GLU-1-0.778-0.85863.408-0.036-0.0360.0000.0000.0000.000
147A147VAL0-0.022-0.01361.183-0.001-0.0010.0000.0000.0000.000
148A148PRO00.0240.01364.2050.0010.0010.0000.0000.0000.000
149A149VAL0-0.032-0.02163.858-0.002-0.0020.0000.0000.0000.000
150A150SER0-0.009-0.00764.6020.0020.0020.0000.0000.0000.000
151A151ALA00.0190.00466.254-0.001-0.0010.0000.0000.0000.000
152A152ALA0-0.0070.00966.929-0.001-0.0010.0000.0000.0000.000
153A153THR0-0.0010.00461.956-0.002-0.0020.0000.0000.0000.000
154A154SER0-0.009-0.00258.4320.0000.0000.0000.0000.0000.000
155A155THR00.0030.02559.280-0.001-0.0010.0000.0000.0000.000
156A156MET0-0.006-0.01953.870-0.001-0.0010.0000.0000.0000.000
157A157VAL00.0060.02056.4480.0010.0010.0000.0000.0000.000
158A158SER00.0160.00652.094-0.002-0.0020.0000.0000.0000.000
159A159PHE00.0210.01653.1760.0020.0020.0000.0000.0000.000
160A160SER0-0.024-0.01850.761-0.003-0.0030.0000.0000.0000.000
161A161ILE0-0.020-0.00251.1660.0030.0030.0000.0000.0000.000
162A162PRO00.0390.01549.913-0.003-0.0030.0000.0000.0000.000
163A163TYR0-0.051-0.05347.4820.0000.0000.0000.0000.0000.000
164A164THR0-0.023-0.02649.8730.0020.0020.0000.0000.0000.000
165A165SER0-0.035-0.01651.1190.0020.0020.0000.0000.0000.000
166A166PRO0-0.008-0.00352.758-0.001-0.0010.0000.0000.0000.000
167A167LEU00.0030.01650.3340.0010.0010.0000.0000.0000.000
168A168SER00.0070.00347.398-0.001-0.0010.0000.0000.0000.000
169A169ALA0-0.026-0.01344.440-0.003-0.0030.0000.0000.0000.000
170A170ILE0-0.0060.02146.4640.0030.0030.0000.0000.0000.000
171A171PRO0-0.016-0.01045.707-0.004-0.0040.0000.0000.0000.000
172A172THR0-0.054-0.05542.6770.0030.0030.0000.0000.0000.000
173A173SER0-0.028-0.01745.0120.0020.0020.0000.0000.0000.000
174A174TYR0-0.031-0.03746.939-0.001-0.0010.0000.0000.0000.000
175A175PHE0-0.024-0.00648.9000.0010.0010.0000.0000.0000.000
176A176GLY00.0480.02550.8740.0010.0010.0000.0000.0000.000
177A177TRP0-0.0110.00454.343-0.001-0.0010.0000.0000.0000.000
178A178GLU-1-0.813-0.86757.093-0.043-0.0430.0000.0000.0000.000
179A179ASP-1-0.800-0.87358.440-0.033-0.0330.0000.0000.0000.000
180A180TRP00.019-0.00759.8320.0000.0000.0000.0000.0000.000
181A181SER0-0.038-0.01363.4520.0010.0010.0000.0000.0000.000
182A182GLY00.0020.01361.8950.0010.0010.0000.0000.0000.000
183A183THR0-0.081-0.07462.7300.0000.0000.0000.0000.0000.000
184A184ASN0-0.052-0.03559.610-0.001-0.0010.0000.0000.0000.000
185A185PHE00.0000.00253.141-0.001-0.0010.0000.0000.0000.000
186A186GLY00.0060.00353.054-0.001-0.0010.0000.0000.0000.000
187A187GLN0-0.033-0.01052.842-0.004-0.0040.0000.0000.0000.000
188A188LEU00.1040.02951.7350.0010.0010.0000.0000.0000.000
189A189SER0-0.020-0.01754.253-0.002-0.0020.0000.0000.0000.000
190A190SER00.0000.01155.922-0.002-0.0020.0000.0000.0000.000
191A191GLY00.0390.03251.906-0.001-0.0010.0000.0000.0000.000
192A192SER0-0.053-0.05951.424-0.002-0.0020.0000.0000.0000.000
193A193TRP0-0.034-0.02945.8180.0000.0000.0000.0000.0000.000
194A194GLY00.0420.01852.8150.0010.0010.0000.0000.0000.000
195A195ASN0-0.015-0.02656.060-0.001-0.0010.0000.0000.0000.000
196A196LEU0-0.0160.00955.8720.0000.0000.0000.0000.0000.000
197A197MET0-0.028-0.00959.6550.0010.0010.0000.0000.0000.000
198A198LEU0-0.004-0.00660.055-0.001-0.0010.0000.0000.0000.000
199A199ILE00.0050.00164.3110.0010.0010.0000.0000.0000.000
200A200PRO00.0190.01767.407-0.001-0.0010.0000.0000.0000.000
201A201SER0-0.053-0.01669.0530.0010.0010.0000.0000.0000.000
202A202LEU00.0640.01871.432-0.001-0.0010.0000.0000.0000.000
203A203SER0-0.040-0.01874.2130.0000.0000.0000.0000.0000.000
204A204VAL0-0.047-0.02176.2920.0010.0010.0000.0000.0000.000
205A205ASP-1-0.884-0.93477.818-0.027-0.0270.0000.0000.0000.000
206A206SER0-0.017-0.02276.6560.0000.0000.0000.0000.0000.000
207A207ALA0-0.017-0.00978.7470.0000.0000.0000.0000.0000.000
208A208ILE0-0.045-0.01775.6130.0000.0000.0000.0000.0000.000
209A209PRO00.0470.04274.2560.0000.0000.0000.0000.0000.000
210A210PHE0-0.019-0.02769.5280.0000.0000.0000.0000.0000.000
211A211ASP-1-0.802-0.87966.146-0.037-0.0370.0000.0000.0000.000
212A212PHE00.010-0.00464.192-0.001-0.0010.0000.0000.0000.000
213A213GLN0-0.061-0.03360.571-0.001-0.0010.0000.0000.0000.000
214A214LEU00.0100.01657.506-0.001-0.0010.0000.0000.0000.000
215A215SER0-0.033-0.02753.980-0.001-0.0010.0000.0000.0000.000
216A216CYS00.0120.01352.7190.0010.0010.0000.0000.0000.000
217A217TRP00.0190.01747.246-0.001-0.0010.0000.0000.0000.000
218A218VAL0-0.002-0.01045.9170.0020.0020.0000.0000.0000.000
219A219ALA00.0400.02543.492-0.004-0.0040.0000.0000.0000.000
220A220PHE0-0.023-0.02142.1440.0040.0040.0000.0000.0000.000
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