Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 49G8N

Calculation Name: 3AAZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3AAZ

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2432192.082452
FMO2-HF: Nuclear repulsion 2345021.168208
FMO2-HF: Total energy -87170.914244
FMO2-MP2: Total energy -87425.276607


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:GLN)


Summations of interaction energy for fragment #1(A:1:GLN)
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.
-1.4062.4281.722-1.979-3.5750.011
Interaction energy analysis for fragmet #1(A:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.006
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].
3A3THR0-0.013-0.0052.628-1.3132.3331.725-1.915-3.4560.011
4A4LEU0-0.017-0.0225.337-1.126-1.114-0.001-0.006-0.0050.000
5A5LYS10.9550.9818.7151.0621.0620.0000.0000.0000.000
6A6GLU-1-0.741-0.86110.5950.3710.3710.0000.0000.0000.000
7A7SER0-0.093-0.04014.200-0.077-0.0770.0000.0000.0000.000
8A8GLY00.0660.01616.5240.0260.0260.0000.0000.0000.000
9A9PRO0-0.020-0.00920.327-0.010-0.0100.0000.0000.0000.000
10A10THR00.0370.03221.8860.0150.0150.0000.0000.0000.000
11A11LEU0-0.043-0.03123.3570.0190.0190.0000.0000.0000.000
12A12VAL0-0.0040.01627.195-0.015-0.0150.0000.0000.0000.000
13A13LYS10.9350.97729.4670.0470.0470.0000.0000.0000.000
14A14PRO00.0520.01633.1850.0020.0020.0000.0000.0000.000
15A15THR0-0.048-0.03834.922-0.004-0.0040.0000.0000.0000.000
16A16GLN0-0.026-0.01132.557-0.005-0.0050.0000.0000.0000.000
17A17THR00.0190.00629.3520.0140.0140.0000.0000.0000.000
18A18LEU0-0.0210.00723.875-0.015-0.0150.0000.0000.0000.000
19A19THR00.0120.00424.2970.0120.0120.0000.0000.0000.000
20A20LEU0-0.011-0.00619.803-0.022-0.0220.0000.0000.0000.000
21A21THR00.0020.00216.1530.0030.0030.0000.0000.0000.000
22A22CYS0-0.086-0.01813.492-0.015-0.0150.0000.0000.0000.000
23A23THR0-0.002-0.00511.287-0.026-0.0260.0000.0000.0000.000
24A24PHE00.0180.0049.6330.1300.1300.0000.0000.0000.000
25A25SER0-0.009-0.0165.583-0.189-0.1890.0000.0000.0000.000
26A26GLY00.0500.0224.115-0.345-0.313-0.001-0.0490.0190.000
27A27PHE0-0.027-0.0144.7581.3541.498-0.001-0.009-0.1330.000
28A28SER00.0290.0248.127-0.251-0.2510.0000.0000.0000.000
29A29LEU00.0020.00311.7130.1630.1630.0000.0000.0000.000
30A30ARG10.9880.97414.4410.0600.0600.0000.0000.0000.000
31A31THR0-0.010-0.00914.716-0.015-0.0150.0000.0000.0000.000
32A32SER0-0.0530.01113.1630.0790.0790.0000.0000.0000.000
33A33ARG10.9680.96015.152-0.259-0.2590.0000.0000.0000.000
34A34VAL0-0.040-0.01011.8370.0090.0090.0000.0000.0000.000
35A35GLY0-0.0070.00715.259-0.068-0.0680.0000.0000.0000.000
36A36VAL0-0.014-0.01314.3840.0670.0670.0000.0000.0000.000
37A37SER00.003-0.01716.758-0.060-0.0600.0000.0000.0000.000
38A38TRP00.0280.01317.2990.0430.0430.0000.0000.0000.000
39A39ILE0-0.041-0.02317.673-0.013-0.0130.0000.0000.0000.000
40A40ARG10.7950.89119.794-0.153-0.1530.0000.0000.0000.000
41A41GLN00.0050.00120.8070.0390.0390.0000.0000.0000.000
42A42PRO00.0580.03623.062-0.008-0.0080.0000.0000.0000.000
43A43PRO00.0390.00825.0810.0220.0220.0000.0000.0000.000
44A44GLY00.0080.00525.730-0.014-0.0140.0000.0000.0000.000
45A45LYS10.8910.96126.544-0.167-0.1670.0000.0000.0000.000
46A46ALA00.0400.01325.3860.0240.0240.0000.0000.0000.000
47A47LEU0-0.011-0.01019.370-0.011-0.0110.0000.0000.0000.000
48A48GLU-1-0.841-0.92023.3890.1730.1730.0000.0000.0000.000
49A49TRP0-0.044-0.03121.355-0.005-0.0050.0000.0000.0000.000
50A50LEU00.0140.01122.853-0.028-0.0280.0000.0000.0000.000
51A51ALA00.018-0.00723.150-0.030-0.0300.0000.0000.0000.000
52A52HIS0-0.0030.03118.4440.0450.0450.0000.0000.0000.000
53A53ILE0-0.0280.00519.685-0.029-0.0290.0000.0000.0000.000
54A54TYR00.016-0.00619.7580.0530.0530.0000.0000.0000.000
55A55TRP0-0.031-0.01518.569-0.031-0.0310.0000.0000.0000.000
56A56ASP-1-0.858-0.94819.9650.1290.1290.0000.0000.0000.000
57A57ASP-1-0.902-0.95923.2300.0300.0300.0000.0000.0000.000
58A58ASP-1-0.805-0.88724.6360.1350.1350.0000.0000.0000.000
59A59LYS10.7700.88824.712-0.062-0.0620.0000.0000.0000.000
60A60ARG10.8300.92625.585-0.172-0.1720.0000.0000.0000.000
61A61TYR00.0560.01226.1910.0030.0030.0000.0000.0000.000
62A62ASN00.0380.02627.793-0.014-0.0140.0000.0000.0000.000
63A63PRO00.031-0.00129.394-0.014-0.0140.0000.0000.0000.000
64A64SER0-0.033-0.00432.430-0.012-0.0120.0000.0000.0000.000
65A65LEU00.0480.01428.722-0.008-0.0080.0000.0000.0000.000
66A66LYS10.9330.96931.232-0.106-0.1060.0000.0000.0000.000
67A67SER0-0.029-0.01232.256-0.004-0.0040.0000.0000.0000.000
68A68ARG10.9110.96931.592-0.079-0.0790.0000.0000.0000.000
69A69LEU0-0.034-0.01026.205-0.003-0.0030.0000.0000.0000.000
70A70THR0-0.034-0.02127.548-0.007-0.0070.0000.0000.0000.000
71A71ILE0-0.0020.01620.477-0.005-0.0050.0000.0000.0000.000
72A72SER0-0.011-0.01723.047-0.012-0.0120.0000.0000.0000.000
73A73LYS10.9520.97018.158-0.090-0.0900.0000.0000.0000.000
74A74ASP-1-0.770-0.88419.639-0.226-0.2260.0000.0000.0000.000
75A75THR0-0.027-0.01717.499-0.053-0.0530.0000.0000.0000.000
76A76SER0-0.055-0.01117.093-0.045-0.0450.0000.0000.0000.000
77A77LYS10.9540.97917.0700.2320.2320.0000.0000.0000.000
78A78ASN0-0.015-0.00710.7160.0990.0990.0000.0000.0000.000
79A79GLN00.008-0.00413.9330.0630.0630.0000.0000.0000.000
80A80VAL0-0.008-0.01516.3660.0440.0440.0000.0000.0000.000
81A81VAL0-0.014-0.00518.4560.0000.0000.0000.0000.0000.000
82A82LEU0-0.0070.00421.1630.0320.0320.0000.0000.0000.000
83A83THR0-0.006-0.01123.136-0.029-0.0290.0000.0000.0000.000
84A84MET0-0.023-0.00326.5630.0180.0180.0000.0000.0000.000
85A85THR00.0420.02728.497-0.009-0.0090.0000.0000.0000.000
86A86ASN0-0.015-0.01432.1220.0110.0110.0000.0000.0000.000
87A87MET0-0.039-0.01627.3430.0100.0100.0000.0000.0000.000
88A88ASP-1-0.760-0.89432.0990.0550.0550.0000.0000.0000.000
89A89PRO00.008-0.00831.9310.0070.0070.0000.0000.0000.000
90A90VAL0-0.0210.01331.6580.0080.0080.0000.0000.0000.000
91A91ASP-1-0.771-0.87228.5390.1040.1040.0000.0000.0000.000
92A92THR0-0.0140.01727.1700.0000.0000.0000.0000.0000.000
93A93ALA0-0.027-0.02123.8640.0160.0160.0000.0000.0000.000
94A94THR0-0.0220.01717.995-0.029-0.0290.0000.0000.0000.000
95A95TYR0-0.036-0.04719.6240.0240.0240.0000.0000.0000.000
96A96TYR00.0410.00614.255-0.003-0.0030.0000.0000.0000.000
97A98ALA00.0420.01613.0760.1400.1400.0000.0000.0000.000
98A99ARG10.8590.9328.114-1.153-1.1530.0000.0000.0000.000
99A100ARG10.8610.93213.105-0.351-0.3510.0000.0000.0000.000
100A101GLY0-0.0010.00711.899-0.074-0.0740.0000.0000.0000.000
101A102PHE0-0.011-0.02612.889-0.046-0.0460.0000.0000.0000.000
102A103TYR0-0.084-0.0849.8330.1590.1590.0000.0000.0000.000
103A104GLY00.0650.04514.508-0.064-0.0640.0000.0000.0000.000
104A105ARG10.8940.95216.727-0.396-0.3960.0000.0000.0000.000
105A106LYS10.9730.97918.279-0.333-0.3330.0000.0000.0000.000
106A107TYR00.009-0.01216.5800.0280.0280.0000.0000.0000.000
107A108GLU-1-0.838-0.92919.5320.4330.4330.0000.0000.0000.000
108A109VAL00.0170.02616.951-0.010-0.0100.0000.0000.0000.000
109A110ASN00.0300.02616.2220.0390.0390.0000.0000.0000.000
110A111HIS10.8940.92512.532-1.009-1.0090.0000.0000.0000.000
111A112PHE00.029-0.00314.5070.0290.0290.0000.0000.0000.000
112A113ASP-1-0.747-0.8129.6511.1871.1870.0000.0000.0000.000
113A114TYR00.0000.0024.8980.0200.0200.0000.0000.0000.000
114A115TRP00.0390.0089.249-0.409-0.4090.0000.0000.0000.000
115A116GLY00.0240.0109.3750.3610.3610.0000.0000.0000.000
116A117GLN0-0.067-0.0349.8970.0230.0230.0000.0000.0000.000
117A118GLY00.0170.01511.527-0.057-0.0570.0000.0000.0000.000
118A119THR0-0.074-0.04214.873-0.080-0.0800.0000.0000.0000.000
119A120THR0-0.0020.00517.4790.0290.0290.0000.0000.0000.000
120A121VAL00.009-0.00620.880-0.038-0.0380.0000.0000.0000.000
121A122THR00.0390.01723.8690.0230.0230.0000.0000.0000.000
122A123VAL0-0.0200.00427.333-0.019-0.0190.0000.0000.0000.000
123A124SER00.008-0.01330.5330.0030.0030.0000.0000.0000.000
124A125SER00.005-0.00533.185-0.008-0.0080.0000.0000.0000.000
125A126ALA0-0.0060.01433.869-0.008-0.0080.0000.0000.0000.000
126A127SER00.010-0.01033.187-0.002-0.0020.0000.0000.0000.000
127A128THR0-0.0050.00028.0970.0050.0050.0000.0000.0000.000
128A129LYS10.8920.95430.0440.0570.0570.0000.0000.0000.000
129A130GLY00.0570.03128.6210.0040.0040.0000.0000.0000.000
130A131PRO0-0.040-0.01126.4670.0090.0090.0000.0000.0000.000
131A132SER0-0.015-0.00329.773-0.013-0.0130.0000.0000.0000.000
132A133VAL0-0.005-0.00727.8090.0100.0100.0000.0000.0000.000
133A134PHE0-0.008-0.01531.052-0.008-0.0080.0000.0000.0000.000
134A135PRO00.0310.02132.5020.0040.0040.0000.0000.0000.000
135A136LEU0-0.0280.00431.9850.0060.0060.0000.0000.0000.000
136A137ALA00.020-0.00534.3030.0000.0000.0000.0000.0000.000
137A138PRO00.0240.01834.6570.0060.0060.0000.0000.0000.000
138A139SER00.004-0.00137.178-0.004-0.0040.0000.0000.0000.000
139A140SER00.0250.00140.2960.0030.0030.0000.0000.0000.000
140A141LYS10.9650.97142.6880.0010.0010.0000.0000.0000.000
141A142SER0-0.0270.00236.7580.0030.0030.0000.0000.0000.000
142A143THR00.015-0.00537.387-0.002-0.0020.0000.0000.0000.000
143A144SER0-0.055-0.02838.7230.0030.0030.0000.0000.0000.000
144A145GLY00.0420.02338.9640.0020.0020.0000.0000.0000.000
145A146GLY00.0030.00338.7830.0040.0040.0000.0000.0000.000
146A147THR00.0070.01533.564-0.002-0.0020.0000.0000.0000.000
147A148ALA0-0.004-0.00334.6260.0010.0010.0000.0000.0000.000
148A149ALA0-0.0010.00632.6970.0020.0020.0000.0000.0000.000
149A150LEU0-0.0080.01329.878-0.007-0.0070.0000.0000.0000.000
150A151GLY00.042-0.00429.4760.0090.0090.0000.0000.0000.000
151A152CYS0-0.074-0.02724.833-0.030-0.0300.0000.0000.0000.000
152A153LEU00.0050.01329.6270.0130.0130.0000.0000.0000.000
153A154VAL0-0.027-0.01526.398-0.014-0.0140.0000.0000.0000.000
154A155LYS10.9300.95429.6100.0300.0300.0000.0000.0000.000
155A156ASP-1-0.831-0.92231.985-0.039-0.0390.0000.0000.0000.000
156A157TYR0-0.027-0.00726.102-0.013-0.0130.0000.0000.0000.000
157A158PHE00.0220.03729.3360.0170.0170.0000.0000.0000.000
158A159PRO00.0270.00525.610-0.017-0.0170.0000.0000.0000.000
159A160GLU-1-0.822-0.91223.4570.0440.0440.0000.0000.0000.000
160A161PRO00.009-0.00619.600-0.006-0.0060.0000.0000.0000.000
161A162VAL0-0.014-0.01922.215-0.036-0.0360.0000.0000.0000.000
162A163THR0-0.029-0.02216.4710.0140.0140.0000.0000.0000.000
163A164VAL00.0150.00419.776-0.037-0.0370.0000.0000.0000.000
164A165SER0-0.0320.00217.7610.0170.0170.0000.0000.0000.000
165A166TRP0-0.029-0.03319.791-0.009-0.0090.0000.0000.0000.000
166A167ASN00.0580.00721.051-0.006-0.0060.0000.0000.0000.000
167A168SER0-0.023-0.01920.874-0.010-0.0100.0000.0000.0000.000
168A169GLY00.0210.00616.998-0.064-0.0640.0000.0000.0000.000
169A170ALA0-0.089-0.03915.8870.0350.0350.0000.0000.0000.000
170A171LEU00.0640.05317.8130.0020.0020.0000.0000.0000.000
171A172THR0-0.015-0.03418.8370.0140.0140.0000.0000.0000.000
172A173SER0-0.0010.00721.592-0.009-0.0090.0000.0000.0000.000
173A174GLY00.0340.02824.0730.0240.0240.0000.0000.0000.000
174A175VAL0-0.047-0.01721.980-0.013-0.0130.0000.0000.0000.000
175A176HIS00.0060.00623.7560.0320.0320.0000.0000.0000.000
176A177THR00.0110.00121.926-0.031-0.0310.0000.0000.0000.000
177A178PHE0-0.026-0.00524.5700.0250.0250.0000.0000.0000.000
178A179PRO00.0200.00825.682-0.010-0.0100.0000.0000.0000.000
179A180ALA00.0040.00426.531-0.012-0.0120.0000.0000.0000.000
180A181VAL0-0.024-0.01228.3500.0120.0120.0000.0000.0000.000
181A182LEU0-0.0130.00131.863-0.011-0.0110.0000.0000.0000.000
182A183GLN0-0.018-0.02233.4910.0080.0080.0000.0000.0000.000
183A184SER00.0470.01736.6660.0000.0000.0000.0000.0000.000
184A185SER00.000-0.00237.4950.0010.0010.0000.0000.0000.000
185A186GLY00.0270.02236.469-0.004-0.0040.0000.0000.0000.000
186A187LEU0-0.078-0.03033.416-0.004-0.0040.0000.0000.0000.000
187A188TYR00.0240.00529.2890.0050.0050.0000.0000.0000.000
188A189SER0-0.015-0.02631.234-0.017-0.0170.0000.0000.0000.000
189A190LEU0-0.0080.01724.9380.0110.0110.0000.0000.0000.000
190A191SER00.0320.01229.502-0.017-0.0170.0000.0000.0000.000
191A192SER0-0.021-0.00924.2670.0100.0100.0000.0000.0000.000
192A193VAL00.0420.00927.026-0.018-0.0180.0000.0000.0000.000
193A194VAL00.0160.01725.9350.0090.0090.0000.0000.0000.000
194A195THR0-0.018-0.01728.023-0.006-0.0060.0000.0000.0000.000
195A196VAL0-0.020-0.00828.7390.0010.0010.0000.0000.0000.000
196A197PRO00.0590.01830.9540.0050.0050.0000.0000.0000.000
197A198SER00.0200.00934.049-0.007-0.0070.0000.0000.0000.000
198A199SER0-0.017-0.01337.178-0.004-0.0040.0000.0000.0000.000
199A200SER00.0170.01534.133-0.004-0.0040.0000.0000.0000.000
200A201LEU00.025-0.00134.680-0.008-0.0080.0000.0000.0000.000
201A202GLY0-0.012-0.01335.213-0.005-0.0050.0000.0000.0000.000
202A203THR0-0.0240.00434.092-0.001-0.0010.0000.0000.0000.000
203A204GLN0-0.039-0.00829.602-0.010-0.0100.0000.0000.0000.000
204A205THR0-0.0090.00329.4390.0000.0000.0000.0000.0000.000
205A206TYR00.0340.00627.628-0.002-0.0020.0000.0000.0000.000
206A207ILE00.0010.00125.6560.0100.0100.0000.0000.0000.000
207A209ASN00.0330.01320.8870.0030.0030.0000.0000.0000.000
208A210VAL0-0.013-0.00421.8310.0150.0150.0000.0000.0000.000
209A211ASN0-0.004-0.01317.635-0.014-0.0140.0000.0000.0000.000
210A212HIS00.0350.02021.4000.0130.0130.0000.0000.0000.000
211A213LYS10.9820.96715.0390.3440.3440.0000.0000.0000.000
212A214PRO00.0030.01821.056-0.018-0.0180.0000.0000.0000.000
213A215SER0-0.0070.02223.969-0.008-0.0080.0000.0000.0000.000
214A216ASN0-0.039-0.03023.381-0.026-0.0260.0000.0000.0000.000
215A217THR0-0.014-0.01324.516-0.015-0.0150.0000.0000.0000.000
216A218LYS10.9330.95618.6440.3950.3950.0000.0000.0000.000
217A219VAL0-0.016-0.00724.2260.0060.0060.0000.0000.0000.000
218A220ASP-1-0.803-0.86524.069-0.242-0.2420.0000.0000.0000.000
219A221LYS10.8410.91626.7510.1120.1120.0000.0000.0000.000
220A222LYS10.9650.98529.2020.1220.1220.0000.0000.0000.000
221A223VAL0-0.039-0.02030.2530.0080.0080.0000.0000.0000.000
222A224GLU-1-0.928-0.96532.728-0.091-0.0910.0000.0000.0000.000
223A225PRO00.0160.01035.9380.0060.0060.0000.0000.0000.000
224A226LYS10.9280.96838.5730.0450.0450.0000.0000.0000.000
225A227SER0-0.001-0.01541.8050.0000.0000.0000.0000.0000.000
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