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: 5JJGZ

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 OptH
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 -2385887.839168
FMO2-HF: Nuclear repulsion 2297330.830485
FMO2-HF: Total energy -88557.008683
FMO2-MP2: Total energy -88813.301332


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.
-26.262-18.0691.351-4.257-5.285-0.029
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 : -0.017 / q_NPA : -0.017
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].
3A3THR0-0.015-0.0343.519-0.7280.9760.010-0.879-0.8340.001
4A4GLU-1-0.973-0.9776.1800.3550.3550.0000.0000.0000.000
5A5ASP-1-0.837-0.9467.3790.2860.2860.0000.0000.0000.000
6A6LEU0-0.099-0.0449.349-0.064-0.0640.0000.0000.0000.000
7A7ASP-1-1.002-0.98911.9630.1010.1010.0000.0000.0000.000
8A8ALA00.0230.0279.7750.0160.0160.0000.0000.0000.000
9A9PRO0-0.038-0.0269.1400.0130.0130.0000.0000.0000.000
10A10GLN0-0.028-0.00212.153-0.067-0.0670.0000.0000.0000.000
11A11ASP-1-0.865-0.93312.931-0.467-0.4670.0000.0000.0000.000
12A12THR0-0.108-0.05615.7840.0150.0150.0000.0000.0000.000
13A13GLY00.0750.03519.4740.0090.0090.0000.0000.0000.000
14A14ASN0-0.063-0.04621.1070.0130.0130.0000.0000.0000.000
15A15ILE00.0190.01124.212-0.005-0.0050.0000.0000.0000.000
16A16GLU-1-0.904-0.96825.736-0.121-0.1210.0000.0000.0000.000
17A17ASN0-0.057-0.02525.8810.0170.0170.0000.0000.0000.000
18A18GLY0-0.0130.00528.4820.0070.0070.0000.0000.0000.000
19A19ALA0-0.052-0.02424.783-0.003-0.0030.0000.0000.0000.000
20A20ALA00.0030.00122.3710.0030.0030.0000.0000.0000.000
21A21ASP-1-0.854-0.91716.957-0.365-0.3650.0000.0000.0000.000
22A22ASN0-0.072-0.05018.002-0.024-0.0240.0000.0000.0000.000
23A23SER0-0.059-0.02213.377-0.060-0.0600.0000.0000.0000.000
24A24PRO0-0.043-0.0209.9400.0400.0400.0000.0000.0000.000
25A25GLN00.0590.02710.216-0.088-0.0880.0000.0000.0000.000
26A26PRO0-0.021-0.0016.659-0.252-0.2520.0000.0000.0000.000
27A27ARG10.9810.9915.7390.9850.9850.0000.0000.0000.000
28A28THR00.0460.0313.553-1.225-0.9110.004-0.055-0.2630.000
29A29THR0-0.078-0.0423.103-1.687-0.5830.077-0.453-0.7280.002
30A30PHE0-0.045-0.0184.009-1.174-0.8140.001-0.048-0.3120.000
31A31ASP-1-0.890-0.9432.784-23.535-18.8551.260-2.816-3.124-0.032
32A32TYR0-0.034-0.0174.6061.4451.476-0.001-0.006-0.0240.000
33A33THR0-0.004-0.0057.5810.1520.1520.0000.0000.0000.000
34A34GLY0-0.0060.00210.1730.1250.1250.0000.0000.0000.000
35A35ASN00.002-0.00713.771-0.039-0.0390.0000.0000.0000.000
36A36PRO0-0.018-0.00417.0020.0390.0390.0000.0000.0000.000
37A37LEU00.014-0.00420.387-0.001-0.0010.0000.0000.0000.000
38A38PRO00.0190.01922.9470.0230.0230.0000.0000.0000.000
39A39PRO0-0.030-0.01925.9910.0060.0060.0000.0000.0000.000
40A40ASP-1-0.856-0.94129.016-0.189-0.1890.0000.0000.0000.000
41A41THR00.000-0.00726.6240.0120.0120.0000.0000.0000.000
42A42LYS10.9290.99029.6400.1540.1540.0000.0000.0000.000
43A43LEU00.0390.01931.4480.0080.0080.0000.0000.0000.000
44A44GLU-1-0.929-0.97134.682-0.110-0.1100.0000.0000.0000.000
45A45ASN0-0.023-0.01732.3360.0140.0140.0000.0000.0000.000
46A46PHE00.0420.03134.0100.0070.0070.0000.0000.0000.000
47A47PHE0-0.001-0.01235.9250.0050.0050.0000.0000.0000.000
48A48SER0-0.0040.01238.5210.0080.0080.0000.0000.0000.000
49A49PHE0-0.033-0.01536.0620.0060.0060.0000.0000.0000.000
50A50TYR0-0.004-0.01041.5010.0010.0010.0000.0000.0000.000
51A51ARG10.8620.93837.6170.1180.1180.0000.0000.0000.000
52A52LEU0-0.024-0.01244.8650.0030.0030.0000.0000.0000.000
53A53LEU0-0.018-0.02347.479-0.003-0.0030.0000.0000.0000.000
54A54PRO0-0.0390.00647.9870.0020.0020.0000.0000.0000.000
55A55MET00.0220.00150.9120.0010.0010.0000.0000.0000.000
56A56GLY0-0.006-0.01654.6410.0000.0000.0000.0000.0000.000
57A57GLY00.0140.00755.6480.0020.0020.0000.0000.0000.000
58A58SER0-0.003-0.00854.9190.0010.0010.0000.0000.0000.000
59A59GLY00.0180.01551.517-0.002-0.0020.0000.0000.0000.000
60A60ALA0-0.0100.00951.681-0.002-0.0020.0000.0000.0000.000
61A61PRO00.0110.00351.718-0.001-0.0010.0000.0000.0000.000
62A62SER0-0.013-0.01753.1710.0000.0000.0000.0000.0000.000
63A63LEU0-0.0080.00256.6880.0000.0000.0000.0000.0000.000
64A64SER00.0280.01859.6850.0000.0000.0000.0000.0000.000
65A65PHE0-0.067-0.02962.5020.0000.0000.0000.0000.0000.000
66A66PRO00.1190.06465.8810.0000.0000.0000.0000.0000.000
67A67ALA0-0.048-0.03969.265-0.001-0.0010.0000.0000.0000.000
68A68ASP-1-0.928-0.94170.879-0.034-0.0340.0000.0000.0000.000
69A69GLU-1-0.953-0.98370.113-0.037-0.0370.0000.0000.0000.000
70A70GLY0-0.020-0.00967.6990.0000.0000.0000.0000.0000.000
71A71THR0-0.029-0.02162.4010.0000.0000.0000.0000.0000.000
72A72ILE0-0.004-0.00461.6770.0000.0000.0000.0000.0000.000
73A73ILE0-0.0080.00556.608-0.001-0.0010.0000.0000.0000.000
74A74PRO00.0090.00856.312-0.001-0.0010.0000.0000.0000.000
75A75LEU0-0.016-0.01752.658-0.003-0.0030.0000.0000.0000.000
76A76ASN00.016-0.02052.097-0.004-0.0040.0000.0000.0000.000
77A77PRO00.0690.03247.0260.0000.0000.0000.0000.0000.000
78A78ILE00.0300.02548.951-0.002-0.0020.0000.0000.0000.000
79A79ASN0-0.064-0.05250.5400.0010.0010.0000.0000.0000.000
80A80TRP0-0.0180.00247.170-0.001-0.0010.0000.0000.0000.000
81A81LEU0-0.035-0.01745.408-0.002-0.0020.0000.0000.0000.000
82A82LYS10.8550.95248.6290.0600.0600.0000.0000.0000.000
83A83GLY00.0260.01649.8160.0030.0030.0000.0000.0000.000
84A84ALA0-0.027-0.00747.148-0.003-0.0030.0000.0000.0000.000
85A85ASP-1-0.896-0.95345.096-0.082-0.0820.0000.0000.0000.000
86A86VAL00.0110.01644.190-0.002-0.0020.0000.0000.0000.000
87A87SER0-0.0020.00939.550-0.001-0.0010.0000.0000.0000.000
88A88GLY0-0.009-0.01641.237-0.001-0.0010.0000.0000.0000.000
89A89ILE00.030-0.00941.944-0.004-0.0040.0000.0000.0000.000
90A90ALA00.0320.01342.705-0.002-0.0020.0000.0000.0000.000
91A91ALA00.0700.03840.7240.0000.0000.0000.0000.0000.000
92A92MET0-0.047-0.00537.897-0.003-0.0030.0000.0000.0000.000
93A93LEU00.005-0.00638.853-0.003-0.0030.0000.0000.0000.000
94A94SER0-0.031-0.01441.0600.0010.0010.0000.0000.0000.000
95A95CYS00.0110.02336.062-0.001-0.0010.0000.0000.0000.000
96A96PHE0-0.007-0.00834.846-0.005-0.0050.0000.0000.0000.000
97A97THR0-0.0370.00339.2890.0060.0060.0000.0000.0000.000
98A98TYR0-0.012-0.00141.4630.0040.0040.0000.0000.0000.000
99A99ILE00.0090.00740.843-0.006-0.0060.0000.0000.0000.000
100A100ALA00.0130.00042.7050.0050.0050.0000.0000.0000.000
101A101ALA0-0.0250.00043.154-0.004-0.0040.0000.0000.0000.000
102A102ASP-1-0.828-0.91044.875-0.068-0.0680.0000.0000.0000.000
103A103LEU00.0170.01846.771-0.004-0.0040.0000.0000.0000.000
104A104ARG10.9460.98144.4240.0850.0850.0000.0000.0000.000
105A105ILE00.0120.00748.849-0.003-0.0030.0000.0000.0000.000
106A106THR00.0040.01950.5170.0030.0030.0000.0000.0000.000
107A107LEU00.0120.01052.900-0.002-0.0020.0000.0000.0000.000
108A108ARG10.9540.97855.2910.0620.0620.0000.0000.0000.000
109A109PHE00.0430.01457.5230.0000.0000.0000.0000.0000.000
110A110SER0-0.036-0.03459.9850.0000.0000.0000.0000.0000.000
111A111ASN0-0.007-0.01262.3870.0010.0010.0000.0000.0000.000
112A112PRO0-0.035-0.01066.1070.0000.0000.0000.0000.0000.000
113A113ASN00.0470.03967.9740.0000.0000.0000.0000.0000.000
114A114ASP-1-0.878-0.95370.557-0.035-0.0350.0000.0000.0000.000
115A115ASN0-0.072-0.03272.7640.0010.0010.0000.0000.0000.000
116A116PRO0-0.0030.00070.141-0.001-0.0010.0000.0000.0000.000
117A117ALA00.0220.01668.8400.0010.0010.0000.0000.0000.000
118A118THR0-0.077-0.03167.9970.0000.0000.0000.0000.0000.000
119A119MET00.0010.01363.4310.0010.0010.0000.0000.0000.000
120A120LEU00.0060.02065.7200.0000.0000.0000.0000.0000.000
121A121VAL0-0.010-0.00959.7830.0000.0000.0000.0000.0000.000
122A122ALA00.0090.00262.9010.0000.0000.0000.0000.0000.000
123A123PHE0-0.031-0.02356.379-0.001-0.0010.0000.0000.0000.000
124A124ALA00.0190.01160.8130.0020.0020.0000.0000.0000.000
125A125PRO00.010-0.00958.815-0.002-0.0020.0000.0000.0000.000
126A126PRO0-0.0030.01055.0770.0010.0010.0000.0000.0000.000
127A127GLY0-0.002-0.00857.9600.0000.0000.0000.0000.0000.000
128A128ALA0-0.058-0.01060.7410.0020.0020.0000.0000.0000.000
129A129THR0-0.013-0.01363.6470.0000.0000.0000.0000.0000.000
130A130ILE00.0060.00962.0430.0000.0000.0000.0000.0000.000
131A131PRO0-0.019-0.01966.4240.0010.0010.0000.0000.0000.000
132A132LEU00.0270.01969.190-0.001-0.0010.0000.0000.0000.000
133A133LYS10.9610.97571.4810.0310.0310.0000.0000.0000.000
134A134PRO00.0460.02268.6440.0010.0010.0000.0000.0000.000
135A135THR00.0370.02070.8940.0010.0010.0000.0000.0000.000
136A136ARG10.9980.98371.3300.0350.0350.0000.0000.0000.000
137A137GLN0-0.0140.00372.296-0.001-0.0010.0000.0000.0000.000
138A138MET00.005-0.00271.6290.0000.0000.0000.0000.0000.000
139A139LEU00.0320.00166.4960.0000.0000.0000.0000.0000.000
140A140SER0-0.035-0.02967.633-0.001-0.0010.0000.0000.0000.000
141A141ASN0-0.0380.00069.1060.0000.0000.0000.0000.0000.000
142A142PHE0-0.061-0.00964.1540.0000.0000.0000.0000.0000.000
143A143TYR00.0080.00461.3080.0010.0010.0000.0000.0000.000
144A144MET0-0.0160.00062.310-0.002-0.0020.0000.0000.0000.000
145A145ALA00.0170.00061.7340.0000.0000.0000.0000.0000.000
146A146GLU-1-0.894-0.94763.715-0.039-0.0390.0000.0000.0000.000
147A147VAL0-0.010-0.01561.3930.0000.0000.0000.0000.0000.000
148A148PRO00.0020.00064.2980.0010.0010.0000.0000.0000.000
149A149VAL0-0.030-0.01664.279-0.002-0.0020.0000.0000.0000.000
150A150SER0-0.008-0.01264.8320.0020.0020.0000.0000.0000.000
151A151ALA00.0270.00666.6790.0000.0000.0000.0000.0000.000
152A152ALA00.0020.01867.542-0.001-0.0010.0000.0000.0000.000
153A153THR00.0020.00762.103-0.002-0.0020.0000.0000.0000.000
154A154SER0-0.036-0.01559.1790.0000.0000.0000.0000.0000.000
155A155THR0-0.0050.00160.3200.0000.0000.0000.0000.0000.000
156A156MET0-0.020-0.02354.325-0.002-0.0020.0000.0000.0000.000
157A157VAL00.0130.02156.6440.0010.0010.0000.0000.0000.000
158A158SER0-0.027-0.03052.138-0.001-0.0010.0000.0000.0000.000
159A159PHE00.0140.00453.4930.0020.0020.0000.0000.0000.000
160A160SER0-0.037-0.01951.429-0.003-0.0030.0000.0000.0000.000
161A161ILE0-0.017-0.00851.6250.0030.0030.0000.0000.0000.000
162A162PRO00.0180.00750.279-0.003-0.0030.0000.0000.0000.000
163A163TYR0-0.031-0.03347.7430.0000.0000.0000.0000.0000.000
164A164THR0-0.013-0.01350.3790.0020.0020.0000.0000.0000.000
165A165SER0-0.0200.00051.3190.0020.0020.0000.0000.0000.000
166A166PRO0-0.008-0.00152.9640.0000.0000.0000.0000.0000.000
167A167LEU00.0080.01850.6700.0010.0010.0000.0000.0000.000
168A168SER00.0110.00047.3770.0000.0000.0000.0000.0000.000
169A169ALA0-0.023-0.01644.630-0.003-0.0030.0000.0000.0000.000
170A170ILE00.0000.01846.6810.0020.0020.0000.0000.0000.000
171A171PRO0-0.027-0.01045.973-0.004-0.0040.0000.0000.0000.000
172A172THR0-0.019-0.02843.1860.0030.0030.0000.0000.0000.000
173A173SER0-0.031-0.01945.4830.0010.0010.0000.0000.0000.000
174A174TYR0-0.011-0.02147.283-0.001-0.0010.0000.0000.0000.000
175A175PHE00.0160.01448.9140.0010.0010.0000.0000.0000.000
176A176GLY00.0250.01151.0560.0010.0010.0000.0000.0000.000
177A177TRP00.0140.00854.605-0.001-0.0010.0000.0000.0000.000
178A178GLU-1-0.915-0.95257.527-0.048-0.0480.0000.0000.0000.000
179A179ASP-1-0.796-0.89158.706-0.040-0.0400.0000.0000.0000.000
180A180TRP00.002-0.02160.7050.0000.0000.0000.0000.0000.000
181A181SER0-0.041-0.01363.7050.0010.0010.0000.0000.0000.000
182A182GLY0-0.037-0.00562.1100.0000.0000.0000.0000.0000.000
183A183THR0-0.078-0.05063.1310.0000.0000.0000.0000.0000.000
184A184ASN0-0.0060.00559.819-0.001-0.0010.0000.0000.0000.000
185A185PHE0-0.006-0.01653.559-0.001-0.0010.0000.0000.0000.000
186A186GLY0-0.015-0.00453.417-0.001-0.0010.0000.0000.0000.000
187A187GLN0-0.046-0.03453.487-0.003-0.0030.0000.0000.0000.000
188A188LEU00.0870.03051.8810.0010.0010.0000.0000.0000.000
189A189SER0-0.0150.00754.674-0.002-0.0020.0000.0000.0000.000
190A190SER00.0100.01356.557-0.001-0.0010.0000.0000.0000.000
191A191GLY00.0490.02152.417-0.001-0.0010.0000.0000.0000.000
192A192SER0-0.059-0.04651.693-0.002-0.0020.0000.0000.0000.000
193A193TRP0-0.023-0.02646.3540.0000.0000.0000.0000.0000.000
194A194GLY00.0390.02153.2030.0020.0020.0000.0000.0000.000
195A195ASN0-0.034-0.03256.498-0.002-0.0020.0000.0000.0000.000
196A196LEU00.0170.02155.9810.0010.0010.0000.0000.0000.000
197A197MET0-0.057-0.02059.9870.0000.0000.0000.0000.0000.000
198A198LEU00.007-0.00860.5540.0000.0000.0000.0000.0000.000
199A199ILE00.0140.01364.7900.0010.0010.0000.0000.0000.000
200A200PRO00.0030.00867.5530.0000.0000.0000.0000.0000.000
201A201SER0-0.025-0.00369.3550.0020.0020.0000.0000.0000.000
202A202LEU00.0420.00771.953-0.001-0.0010.0000.0000.0000.000
203A203SER0-0.024-0.00974.6010.0010.0010.0000.0000.0000.000
204A204VAL0-0.037-0.00776.5250.0010.0010.0000.0000.0000.000
205A205ASP-1-0.910-0.95678.095-0.030-0.0300.0000.0000.0000.000
206A206SER0-0.033-0.01476.8420.0000.0000.0000.0000.0000.000
207A207ALA00.020-0.00178.9100.0000.0000.0000.0000.0000.000
208A208ILE0-0.056-0.02875.4590.0000.0000.0000.0000.0000.000
209A209PRO00.0310.02475.091-0.001-0.0010.0000.0000.0000.000
210A210PHE0-0.007-0.00869.684-0.001-0.0010.0000.0000.0000.000
211A211ASP-1-0.850-0.93767.173-0.041-0.0410.0000.0000.0000.000
212A212PHE0-0.018-0.02064.524-0.001-0.0010.0000.0000.0000.000
213A213GLN0-0.028-0.01560.809-0.002-0.0020.0000.0000.0000.000
214A214LEU0-0.032-0.01757.7880.0000.0000.0000.0000.0000.000
215A215SER0-0.016-0.01154.098-0.001-0.0010.0000.0000.0000.000
216A216CYS00.0160.00952.9100.0020.0020.0000.0000.0000.000
217A217TRP00.0160.02547.716-0.002-0.0020.0000.0000.0000.000
218A218VAL00.005-0.00746.3390.0030.0030.0000.0000.0000.000
219A219ALA00.0370.00944.270-0.004-0.0040.0000.0000.0000.000
220A220PHE0-0.047-0.03142.2270.0040.0040.0000.0000.0000.000
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