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: MNM6Z

Calculation Name: 3AUF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3AUF

Chain ID: A

ChEMBL ID:

UniProt ID: E5RXD0

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2378995.609339
FMO2-HF: Nuclear repulsion 2298169.572646
FMO2-HF: Total energy -80826.036692
FMO2-MP2: Total energy -81062.229398


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:-11:SER)


Summations of interaction energy for fragment #1(A:-11:SER)
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.
0.6532.323-0.02-0.829-0.820.001
Interaction energy analysis for fragmet #1(A:-11:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.013
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].
3A-9GLY00.0150.0173.8810.8692.417-0.019-0.824-0.7050.001
4A-8GLU-1-0.776-0.8725.3770.6280.750-0.001-0.005-0.1150.000
5A-7ASN0-0.037-0.0355.982-0.093-0.0930.0000.0000.0000.000
6A-6LEU0-0.0060.0018.5610.0020.0020.0000.0000.0000.000
7A-5TYR0-0.003-0.00312.092-0.038-0.0380.0000.0000.0000.000
8A-4PHE0-0.045-0.01510.379-0.051-0.0510.0000.0000.0000.000
9A-3GLN00.009-0.00210.0050.0140.0140.0000.0000.0000.000
10A-2GLY0-0.010-0.0079.838-0.121-0.1210.0000.0000.0000.000
11A-1HIS0-0.087-0.0578.481-0.227-0.2270.0000.0000.0000.000
12A1MET0-0.0220.00611.005-0.114-0.1140.0000.0000.0000.000
13A2ILE0-0.0220.00614.080-0.052-0.0520.0000.0000.0000.000
14A3ARG10.8460.90116.554-0.218-0.2180.0000.0000.0000.000
15A4ILE00.0610.01919.027-0.010-0.0100.0000.0000.0000.000
16A5GLY00.0320.02321.989-0.006-0.0060.0000.0000.0000.000
17A6VAL0-0.055-0.02625.678-0.002-0.0020.0000.0000.0000.000
18A7LEU00.0280.02527.937-0.004-0.0040.0000.0000.0000.000
19A8ILE0-0.053-0.02731.214-0.003-0.0030.0000.0000.0000.000
20A9SER00.055-0.01033.9330.0000.0000.0000.0000.0000.000
21A10GLY00.014-0.00737.049-0.003-0.0030.0000.0000.0000.000
22A11SER00.0090.01137.1950.0020.0020.0000.0000.0000.000
23A12GLY00.0650.03833.5000.0010.0010.0000.0000.0000.000
24A13THR0-0.026-0.01832.2290.0030.0030.0000.0000.0000.000
25A14ASN00.0620.00828.0100.0010.0010.0000.0000.0000.000
26A15LEU00.0070.01227.4720.0040.0040.0000.0000.0000.000
27A16GLN0-0.043-0.01127.6940.0030.0030.0000.0000.0000.000
28A17ALA00.0530.03625.4810.0030.0030.0000.0000.0000.000
29A18ILE00.0000.00822.2000.0050.0050.0000.0000.0000.000
30A19LEU00.0090.00823.1520.0110.0110.0000.0000.0000.000
31A20ASP-1-0.805-0.90124.7290.0560.0560.0000.0000.0000.000
32A21GLY0-0.019-0.01121.5010.0000.0000.0000.0000.0000.000
33A22CYS0-0.061-0.03119.9880.0170.0170.0000.0000.0000.000
34A23ARG10.7770.87820.854-0.049-0.0490.0000.0000.0000.000
35A24GLU-1-0.799-0.87321.8000.0480.0480.0000.0000.0000.000
36A25GLY00.0110.01017.793-0.009-0.0090.0000.0000.0000.000
37A26ARG10.8100.89116.080-0.036-0.0360.0000.0000.0000.000
38A27ILE0-0.044-0.00916.226-0.009-0.0090.0000.0000.0000.000
39A28PRO00.0490.03511.693-0.014-0.0140.0000.0000.0000.000
40A29GLY00.0590.00714.0750.0300.0300.0000.0000.0000.000
41A30ARG10.9130.95816.950-0.193-0.1930.0000.0000.0000.000
42A31VAL0-0.006-0.00520.7920.0030.0030.0000.0000.0000.000
43A32ALA0-0.048-0.01523.812-0.003-0.0030.0000.0000.0000.000
44A33VAL00.0200.01225.438-0.007-0.0070.0000.0000.0000.000
45A34VAL0-0.019-0.00828.0630.0030.0030.0000.0000.0000.000
46A35ILE00.0080.00330.722-0.003-0.0030.0000.0000.0000.000
47A36SER00.001-0.00733.6630.0000.0000.0000.0000.0000.000
48A37ASP-1-0.781-0.85736.5230.0410.0410.0000.0000.0000.000
49A38ARG10.8490.90839.307-0.038-0.0380.0000.0000.0000.000
50A39ALA00.0450.02840.4040.0020.0020.0000.0000.0000.000
51A40ASP-1-0.903-0.94741.7510.0310.0310.0000.0000.0000.000
52A41ALA0-0.043-0.00637.741-0.001-0.0010.0000.0000.0000.000
53A42TYR00.0430.01337.2110.0020.0020.0000.0000.0000.000
54A43GLY0-0.012-0.01634.4640.0010.0010.0000.0000.0000.000
55A44LEU00.017-0.00433.7800.0040.0040.0000.0000.0000.000
56A45GLU-1-0.786-0.86335.5050.0400.0400.0000.0000.0000.000
57A46ARG10.7950.88632.141-0.040-0.0400.0000.0000.0000.000
58A47ALA00.0160.01130.9950.0020.0020.0000.0000.0000.000
59A48ARG10.9360.95731.981-0.041-0.0410.0000.0000.0000.000
60A49ARG10.8190.89134.270-0.035-0.0350.0000.0000.0000.000
61A50ALA0-0.037-0.01028.619-0.001-0.0010.0000.0000.0000.000
62A51GLY0-0.0110.01029.2330.0060.0060.0000.0000.0000.000
63A52VAL0-0.052-0.02927.2350.0050.0050.0000.0000.0000.000
64A53ASP-1-0.828-0.89130.1480.0690.0690.0000.0000.0000.000
65A54ALA0-0.011-0.01231.6910.0020.0020.0000.0000.0000.000
66A55LEU00.0020.00833.636-0.005-0.0050.0000.0000.0000.000
67A56HIS0-0.063-0.05236.145-0.002-0.0020.0000.0000.0000.000
68A57MET0-0.033-0.00536.7680.0010.0010.0000.0000.0000.000
69A58ASP-1-0.774-0.89339.8250.0350.0350.0000.0000.0000.000
70A59PRO0-0.082-0.06441.1700.0010.0010.0000.0000.0000.000
71A60ALA0-0.025-0.00943.2270.0000.0000.0000.0000.0000.000
72A61ALA0-0.0100.01544.512-0.001-0.0010.0000.0000.0000.000
73A62TYR00.004-0.00740.6870.0020.0020.0000.0000.0000.000
74A63PRO00.0170.01944.696-0.001-0.0010.0000.0000.0000.000
75A64SER00.008-0.00943.7350.0000.0000.0000.0000.0000.000
76A65ARG11.0080.98941.068-0.033-0.0330.0000.0000.0000.000
77A66THR00.007-0.00138.7080.0020.0020.0000.0000.0000.000
78A67ALA00.0300.02138.7900.0030.0030.0000.0000.0000.000
79A68PHE00.0110.01737.4040.0020.0020.0000.0000.0000.000
80A69ASP-1-0.742-0.89534.4510.0610.0610.0000.0000.0000.000
81A70ALA0-0.025-0.01834.5360.0050.0050.0000.0000.0000.000
82A71ALA00.0310.02635.2150.0030.0030.0000.0000.0000.000
83A72LEU0-0.015-0.00932.9480.0020.0020.0000.0000.0000.000
84A73ALA00.018-0.00730.7710.0050.0050.0000.0000.0000.000
85A74GLU-1-0.848-0.88430.6600.0680.0680.0000.0000.0000.000
86A75ARG10.8570.89032.081-0.058-0.0580.0000.0000.0000.000
87A76LEU0-0.006-0.01527.5360.0040.0040.0000.0000.0000.000
88A77GLN0-0.018-0.01627.2360.0040.0040.0000.0000.0000.000
89A78ALA0-0.0200.00628.0900.0050.0050.0000.0000.0000.000
90A79TYR0-0.078-0.06027.4040.0000.0000.0000.0000.0000.000
91A80GLY0-0.051-0.02024.6610.0090.0090.0000.0000.0000.000
92A81VAL0-0.072-0.03422.8350.0150.0150.0000.0000.0000.000
93A82ASP-1-0.817-0.87718.4160.2370.2370.0000.0000.0000.000
94A83LEU0-0.001-0.00418.2240.0000.0000.0000.0000.0000.000
95A84VAL00.0440.02721.321-0.007-0.0070.0000.0000.0000.000
96A85CYS0-0.020-0.00222.9180.0020.0020.0000.0000.0000.000
97A86LEU00.0030.00425.514-0.005-0.0050.0000.0000.0000.000
98A87ALA00.0320.01628.125-0.002-0.0020.0000.0000.0000.000
99A88GLY00.013-0.01229.897-0.004-0.0040.0000.0000.0000.000
100A89TYR0-0.0010.00232.789-0.004-0.0040.0000.0000.0000.000
101A90MET0-0.0190.00634.489-0.001-0.0010.0000.0000.0000.000
102A91ARG10.8420.91836.253-0.047-0.0470.0000.0000.0000.000
103A92LEU00.0020.00835.4590.0020.0020.0000.0000.0000.000
104A93VAL00.0490.02530.680-0.001-0.0010.0000.0000.0000.000
105A94ARG10.8660.93934.025-0.048-0.0480.0000.0000.0000.000
106A95GLY00.0550.02133.5510.0040.0040.0000.0000.0000.000
107A96PRO00.0080.01432.9230.0040.0040.0000.0000.0000.000
108A97MET00.0260.03629.4740.0060.0060.0000.0000.0000.000
109A98LEU0-0.014-0.00928.9420.0060.0060.0000.0000.0000.000
110A99THR0-0.054-0.03628.3610.0040.0040.0000.0000.0000.000
111A100ALA0-0.040-0.01028.3260.0050.0050.0000.0000.0000.000
112A101PHE0-0.013-0.01024.0440.0070.0070.0000.0000.0000.000
113A102PRO00.0340.02823.985-0.001-0.0010.0000.0000.0000.000
114A103ASN0-0.051-0.03920.8110.0030.0030.0000.0000.0000.000
115A104ARG10.8730.93417.168-0.199-0.1990.0000.0000.0000.000
116A105ILE0-0.0060.00621.919-0.003-0.0030.0000.0000.0000.000
117A106LEU00.0010.00719.772-0.003-0.0030.0000.0000.0000.000
118A107ASN0-0.023-0.02924.311-0.002-0.0020.0000.0000.0000.000
119A108ILE0-0.0050.01825.7590.0000.0000.0000.0000.0000.000
120A109HIS10.7860.87928.049-0.034-0.0340.0000.0000.0000.000
121A110PRO00.0180.01830.917-0.002-0.0020.0000.0000.0000.000
122A111SER0-0.022-0.04032.332-0.001-0.0010.0000.0000.0000.000
123A112LEU00.0060.03130.2170.0020.0020.0000.0000.0000.000
124A113LEU00.0070.01729.3600.0000.0000.0000.0000.0000.000
125A114PRO00.003-0.01530.713-0.001-0.0010.0000.0000.0000.000
126A115ALA00.0060.01133.4400.0000.0000.0000.0000.0000.000
127A116PHE00.0100.01635.3510.0010.0010.0000.0000.0000.000
128A117PRO00.0550.04735.4800.0010.0010.0000.0000.0000.000
129A118GLY00.0160.00736.428-0.002-0.0020.0000.0000.0000.000
130A119LEU0-0.022-0.02937.5380.0000.0000.0000.0000.0000.000
131A120GLU-1-0.819-0.88839.6580.0190.0190.0000.0000.0000.000
132A121ALA00.0240.03136.752-0.002-0.0020.0000.0000.0000.000
133A122GLN00.0570.01436.517-0.001-0.0010.0000.0000.0000.000
134A123ARG10.7630.84139.696-0.019-0.0190.0000.0000.0000.000
135A124GLN0-0.023-0.02139.937-0.002-0.0020.0000.0000.0000.000
136A125ALA00.0000.00739.190-0.001-0.0010.0000.0000.0000.000
137A126LEU0-0.011-0.01441.315-0.001-0.0010.0000.0000.0000.000
138A127GLU-1-0.887-0.92844.3290.0130.0130.0000.0000.0000.000
139A128HIS0-0.038-0.02043.1750.0000.0000.0000.0000.0000.000
140A129GLY00.0110.01645.320-0.001-0.0010.0000.0000.0000.000
141A130VAL0-0.067-0.02839.457-0.001-0.0010.0000.0000.0000.000
142A131LYS10.8860.90541.578-0.002-0.0020.0000.0000.0000.000
143A132VAL0-0.039-0.01234.844-0.002-0.0020.0000.0000.0000.000
144A133ALA00.0270.01635.9580.0020.0020.0000.0000.0000.000
145A134GLY00.017-0.00531.949-0.003-0.0030.0000.0000.0000.000
146A135CYS0-0.058-0.00729.0550.0020.0020.0000.0000.0000.000
147A136THR00.016-0.00226.489-0.004-0.0040.0000.0000.0000.000
148A137VAL00.0110.01322.5880.0040.0040.0000.0000.0000.000
149A138HIS0-0.013-0.00823.921-0.006-0.0060.0000.0000.0000.000
150A139PHE00.0750.02618.1550.0030.0030.0000.0000.0000.000
151A140VAL0-0.056-0.01924.228-0.009-0.0090.0000.0000.0000.000
152A141THR00.018-0.00327.0950.0050.0050.0000.0000.0000.000
153A142ALA0-0.007-0.01929.565-0.002-0.0020.0000.0000.0000.000
154A143GLY00.0180.03332.504-0.003-0.0030.0000.0000.0000.000
155A144VAL0-0.053-0.03733.0520.0020.0020.0000.0000.0000.000
156A145ASP-1-0.793-0.89531.4860.0370.0370.0000.0000.0000.000
157A146GLU-1-0.873-0.93331.1550.0420.0420.0000.0000.0000.000
158A147GLY0-0.0040.01827.7820.0000.0000.0000.0000.0000.000
159A148PRO0-0.023-0.02023.123-0.005-0.0050.0000.0000.0000.000
160A149ILE00.0120.01024.0190.0050.0050.0000.0000.0000.000
161A150ILE0-0.037-0.01118.6150.0020.0020.0000.0000.0000.000
162A151LEU00.0220.00318.699-0.008-0.0080.0000.0000.0000.000
163A152GLN0-0.066-0.04122.2750.0030.0030.0000.0000.0000.000
164A153ALA00.0130.02125.026-0.006-0.0060.0000.0000.0000.000
165A154ALA00.0080.00127.5690.0040.0040.0000.0000.0000.000
166A155VAL0-0.025-0.01131.159-0.003-0.0030.0000.0000.0000.000
167A156PRO00.0210.01334.2020.0010.0010.0000.0000.0000.000
168A157VAL0-0.019-0.00237.8580.0020.0020.0000.0000.0000.000
169A158LEU0-0.018-0.01740.747-0.002-0.0020.0000.0000.0000.000
170A159GLU-1-0.830-0.90243.7380.0020.0020.0000.0000.0000.000
171A160GLY0-0.004-0.01347.1470.0000.0000.0000.0000.0000.000
172A161ASP-1-0.783-0.83341.9090.0050.0050.0000.0000.0000.000
173A162THR00.0200.01445.1900.0010.0010.0000.0000.0000.000
174A163VAL00.006-0.02342.2270.0000.0000.0000.0000.0000.000
175A164GLU-1-0.812-0.88641.5380.0190.0190.0000.0000.0000.000
176A165ASP-1-0.838-0.90440.7220.0080.0080.0000.0000.0000.000
177A166LEU00.0070.00837.9680.0000.0000.0000.0000.0000.000
178A167ARG10.8660.93037.353-0.019-0.0190.0000.0000.0000.000
179A168ARG10.8390.89535.998-0.014-0.0140.0000.0000.0000.000
180A169ARG10.7720.84735.136-0.003-0.0030.0000.0000.0000.000
181A170ILE00.0150.01432.363-0.001-0.0010.0000.0000.0000.000
182A171LEU0-0.021-0.01231.4110.0010.0010.0000.0000.0000.000
183A172ALA0-0.017-0.00830.7130.0030.0030.0000.0000.0000.000
184A173GLU-1-0.750-0.85327.238-0.004-0.0040.0000.0000.0000.000
185A174GLU-1-0.890-0.94926.6790.0340.0340.0000.0000.0000.000
186A175HIS0-0.011-0.03226.1160.0070.0070.0000.0000.0000.000
187A176ARG10.7920.89122.0940.0110.0110.0000.0000.0000.000
188A177ILE00.035-0.00322.1150.0040.0040.0000.0000.0000.000
189A178TYR0-0.022-0.03221.5720.0090.0090.0000.0000.0000.000
190A179PRO0-0.008-0.01820.6000.0120.0120.0000.0000.0000.000
191A180GLU-1-0.879-0.93017.633-0.003-0.0030.0000.0000.0000.000
192A181ALA00.0270.00816.7380.0050.0050.0000.0000.0000.000
193A182ILE0-0.013-0.01017.1440.0180.0180.0000.0000.0000.000
194A183ARG10.8600.92612.2920.0110.0110.0000.0000.0000.000
195A184LEU0-0.016-0.00812.4630.0340.0340.0000.0000.0000.000
196A185PHE0-0.016-0.01612.6430.0240.0240.0000.0000.0000.000
197A186ALA0-0.0040.00313.0080.0320.0320.0000.0000.0000.000
198A187GLU-1-0.798-0.8908.6000.0930.0930.0000.0000.0000.000
199A188GLY0-0.0090.0088.0190.0310.0310.0000.0000.0000.000
200A189ARG10.7500.8568.4220.1830.1830.0000.0000.0000.000
201A190LEU0-0.0010.00711.059-0.047-0.0470.0000.0000.0000.000
202A191VAL00.0060.00413.2690.0250.0250.0000.0000.0000.000
203A192ILE0-0.0060.00016.037-0.024-0.0240.0000.0000.0000.000
204A193GLU-1-0.818-0.89019.1710.1010.1010.0000.0000.0000.000
205A194GLY00.0100.00621.893-0.012-0.0120.0000.0000.0000.000
206A195ARG10.8440.90825.567-0.046-0.0460.0000.0000.0000.000
207A196ARG10.8650.92021.656-0.060-0.0600.0000.0000.0000.000
208A197VAL00.0370.00517.6600.0130.0130.0000.0000.0000.000
209A198ARG10.8570.93513.628-0.160-0.1600.0000.0000.0000.000
210A199ILE00.0470.02113.7460.0280.0280.0000.0000.0000.000
211A200LEU0-0.032-0.0069.1170.0000.0000.0000.0000.0000.000
212A201ASP-1-0.911-0.9407.534-0.262-0.2620.0000.0000.0000.000