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: Q1MKY

Calculation Name: 2AXO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2AXO

Chain ID: A

ChEMBL ID:

UniProt ID: A9CHH7

Base Structure: X-ray

Registration Date: 2023-03-13

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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2545419.193085
FMO2-HF: Nuclear repulsion 2460625.454997
FMO2-HF: Total energy -84793.738088
FMO2-MP2: Total energy -85039.775548


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:38:ALA)


Summations of interaction energy for fragment #1(A:38:ALA)
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.
-0.0920000000000012.184-0.011-1.295-0.970.004
Interaction energy analysis for fragmet #1(A:38:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.016
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].
3A40GLU-1-0.953-0.9613.821-1.5610.715-0.011-1.295-0.9700.004
4A41ALA0-0.023-0.0065.7100.1370.1370.0000.0000.0000.000
5A42VAL00.0160.0086.548-0.063-0.0630.0000.0000.0000.000
6A43LYS10.9050.9429.2440.5370.5370.0000.0000.0000.000
7A44GLY0-0.018-0.01012.5370.0280.0280.0000.0000.0000.000
8A45VAL0-0.0010.00714.769-0.002-0.0020.0000.0000.0000.000
9A46VAL00.000-0.00217.313-0.004-0.0040.0000.0000.0000.000
10A47GLU-1-0.749-0.83520.1040.0080.0080.0000.0000.0000.000
11A48LEU00.000-0.00123.009-0.003-0.0030.0000.0000.0000.000
12A49PHE00.0000.01925.7470.0060.0060.0000.0000.0000.000
13A50THR00.012-0.03728.808-0.004-0.0040.0000.0000.0000.000
14A51SER00.0710.02931.2180.0050.0050.0000.0000.0000.000
15A52GLN00.0200.02133.897-0.001-0.0010.0000.0000.0000.000
16A53GLY0-0.023-0.01035.467-0.001-0.0010.0000.0000.0000.000
17A54CYS0-0.0400.01332.108-0.005-0.0050.0000.0000.0000.000
18A55ALA00.0410.00036.204-0.003-0.0030.0000.0000.0000.000
19A56SER0-0.037-0.02236.183-0.002-0.0020.0000.0000.0000.000
20A58PRO00.0560.04731.043-0.006-0.0060.0000.0000.0000.000
21A59PRO0-0.014-0.01730.142-0.006-0.0060.0000.0000.0000.000
22A60ALA00.012-0.00427.817-0.009-0.0090.0000.0000.0000.000
23A61ASP-1-0.789-0.88726.287-0.055-0.0550.0000.0000.0000.000
24A62GLU-1-0.961-0.97825.643-0.111-0.1110.0000.0000.0000.000
25A63ALA0-0.015-0.01924.322-0.013-0.0130.0000.0000.0000.000
26A64LEU00.0530.02120.536-0.017-0.0170.0000.0000.0000.000
27A65ARG10.9490.98620.5650.0780.0780.0000.0000.0000.000
28A66LYS10.8540.92720.4040.1280.1280.0000.0000.0000.000
29A67MET0-0.0060.01617.634-0.025-0.0250.0000.0000.0000.000
30A68ILE0-0.014-0.00316.011-0.024-0.0240.0000.0000.0000.000
31A69GLN0-0.078-0.03915.8070.0100.0100.0000.0000.0000.000
32A70LYS10.8950.94713.5720.3310.3310.0000.0000.0000.000
33A71GLY00.0240.02012.044-0.067-0.0670.0000.0000.0000.000
34A72ASP-1-0.819-0.88810.414-0.381-0.3810.0000.0000.0000.000
35A73VAL0-0.028-0.01211.4940.0140.0140.0000.0000.0000.000
36A74VAL00.0130.01612.9280.0090.0090.0000.0000.0000.000
37A75GLY0-0.003-0.00714.9900.0000.0000.0000.0000.0000.000
38A76LEU0-0.017-0.00818.3490.0130.0130.0000.0000.0000.000
39A77SER00.0070.00921.491-0.008-0.0080.0000.0000.0000.000
40A78TYR0-0.009-0.02423.3770.0120.0120.0000.0000.0000.000
41A79HIS0-0.021-0.00627.967-0.006-0.0060.0000.0000.0000.000
42A80VAL00.005-0.00531.2970.0050.0050.0000.0000.0000.000
43A81ASP-1-0.803-0.90234.111-0.001-0.0010.0000.0000.0000.000
44A82TYR0-0.059-0.03934.928-0.002-0.0020.0000.0000.0000.000
45A83TRP0-0.035-0.02836.645-0.002-0.0020.0000.0000.0000.000
46A84ASN0-0.056-0.02438.2320.0010.0010.0000.0000.0000.000
47A85TYR00.0380.00441.7320.0010.0010.0000.0000.0000.000
48A86LEU0-0.016-0.01845.1840.0010.0010.0000.0000.0000.000
49A87GLY0-0.0080.02145.5400.0010.0010.0000.0000.0000.000
50A88TRP0-0.052-0.01438.9980.0000.0000.0000.0000.0000.000
51A89THR0-0.027-0.03440.026-0.002-0.0020.0000.0000.0000.000
52A90ASP-1-0.734-0.88134.629-0.011-0.0110.0000.0000.0000.000
53A91SER0-0.046-0.02736.0660.0020.0020.0000.0000.0000.000
54A92LEU0-0.072-0.04430.1120.0030.0030.0000.0000.0000.000
55A93ALA0-0.0090.01531.9530.0010.0010.0000.0000.0000.000
56A94SER00.0120.00332.3900.0020.0020.0000.0000.0000.000
57A95LYS10.9600.99734.804-0.012-0.0120.0000.0000.0000.000
58A96GLU-1-0.847-0.93832.2840.0200.0200.0000.0000.0000.000
59A97ASN0-0.029-0.01429.7330.0030.0030.0000.0000.0000.000
60A98THR0-0.047-0.05031.541-0.004-0.0040.0000.0000.0000.000
61A99GLU-1-0.914-0.97134.2060.0160.0160.0000.0000.0000.000
62A100ARG10.8440.92523.754-0.022-0.0220.0000.0000.0000.000
63A101GLN00.0100.00430.7010.0010.0010.0000.0000.0000.000
64A102TYR0-0.037-0.02131.678-0.002-0.0020.0000.0000.0000.000
65A103GLY00.0270.01332.091-0.001-0.0010.0000.0000.0000.000
66A104TYR00.003-0.02624.0200.0020.0020.0000.0000.0000.000
67A105MET0-0.081-0.01630.756-0.004-0.0040.0000.0000.0000.000
68A106ARG10.8440.91834.050-0.012-0.0120.0000.0000.0000.000
69A107ALA00.0050.01430.558-0.001-0.0010.0000.0000.0000.000
70A108LEU0-0.073-0.04428.356-0.002-0.0020.0000.0000.0000.000
71A109GLY0-0.0020.01332.330-0.003-0.0030.0000.0000.0000.000
72A110ARG10.8710.94733.0450.0270.0270.0000.0000.0000.000
73A111ASN00.015-0.00436.9680.0010.0010.0000.0000.0000.000
74A112GLY00.023-0.00338.1560.0010.0010.0000.0000.0000.000
75A113VAL0-0.030-0.01034.952-0.001-0.0010.0000.0000.0000.000
76A114TYR0-0.093-0.05831.814-0.001-0.0010.0000.0000.0000.000
77A115THR00.0390.05532.9970.0010.0010.0000.0000.0000.000
78A116PRO0-0.003-0.01530.0010.0000.0000.0000.0000.0000.000
79A117GLN0-0.011-0.00729.2940.0000.0000.0000.0000.0000.000
80A118ALA00.0100.00924.3640.0030.0030.0000.0000.0000.000
81A119ILE0-0.013-0.00124.386-0.002-0.0020.0000.0000.0000.000
82A120LEU00.003-0.00821.208-0.003-0.0030.0000.0000.0000.000
83A121ASN00.0680.03017.3160.0030.0030.0000.0000.0000.000
84A122GLY00.0420.01920.1970.0110.0110.0000.0000.0000.000
85A123ARG10.8690.93620.6970.0250.0250.0000.0000.0000.000
86A124ASP-1-0.802-0.89524.928-0.055-0.0550.0000.0000.0000.000
87A125HIS0-0.0080.00925.942-0.001-0.0010.0000.0000.0000.000
88A126VAL00.0250.01825.302-0.004-0.0040.0000.0000.0000.000
89A127LYS10.9640.97328.4630.0610.0610.0000.0000.0000.000
90A128GLY00.0480.01927.113-0.007-0.0070.0000.0000.0000.000
91A129ALA00.007-0.00626.529-0.006-0.0060.0000.0000.0000.000
92A130ASP-1-0.925-0.93727.458-0.115-0.1150.0000.0000.0000.000
93A131VAL00.017-0.03122.037-0.006-0.0060.0000.0000.0000.000
94A132ARG10.9310.95722.7190.1420.1420.0000.0000.0000.000
95A133GLY00.1010.06323.586-0.008-0.0080.0000.0000.0000.000
96A134ILE0-0.045-0.01221.4360.0000.0000.0000.0000.0000.000
97A135TYR0-0.059-0.05815.4900.0110.0110.0000.0000.0000.000
98A136ASP-1-0.882-0.93519.364-0.194-0.1940.0000.0000.0000.000
99A137ARG10.8320.92121.8950.0860.0860.0000.0000.0000.000
100A138LEU0-0.033-0.02216.4980.0080.0080.0000.0000.0000.000
101A139ASP-1-0.905-0.94717.318-0.265-0.2650.0000.0000.0000.000
102A140ALA0-0.019-0.01718.3640.0030.0030.0000.0000.0000.000
103A141PHE0-0.027-0.01819.0520.0130.0130.0000.0000.0000.000
104A142LYS10.9821.00011.9730.3390.3390.0000.0000.0000.000
105A143ARG10.8570.93216.7700.2080.2080.0000.0000.0000.000
106A144GLU-1-0.910-0.94318.909-0.077-0.0770.0000.0000.0000.000
107A145GLY0-0.027-0.00117.3040.0180.0180.0000.0000.0000.000
108A146GLN0-0.076-0.04718.3800.0220.0220.0000.0000.0000.000
109A147GLY00.0200.00015.442-0.005-0.0050.0000.0000.0000.000
110A148LEU0-0.056-0.02012.2570.0230.0230.0000.0000.0000.000
111A149ASN0-0.020-0.02312.198-0.009-0.0090.0000.0000.0000.000
112A150VAL0-0.0350.00213.3610.0300.0300.0000.0000.0000.000
113A151PRO0-0.0160.0029.700-0.012-0.0120.0000.0000.0000.000
114A152VAL00.0450.00610.820-0.018-0.0180.0000.0000.0000.000
115A153SER0-0.0120.0009.4870.0920.0920.0000.0000.0000.000
116A154SER00.0140.00611.253-0.069-0.0690.0000.0000.0000.000
117A155LYS10.9840.99612.754-0.500-0.5000.0000.0000.0000.000
118A156PHE00.0240.00914.893-0.031-0.0310.0000.0000.0000.000
119A157ALA0-0.055-0.03217.8070.0340.0340.0000.0000.0000.000
120A158GLY00.0090.00319.793-0.014-0.0140.0000.0000.0000.000
121A159ASP-1-0.929-0.96122.4420.1520.1520.0000.0000.0000.000
122A160GLU-1-0.945-0.98322.7610.1780.1780.0000.0000.0000.000
123A161VAL0-0.066-0.02818.6350.0160.0160.0000.0000.0000.000
124A162GLU-1-0.919-0.95716.4750.3820.3820.0000.0000.0000.000
125A163ILE0-0.015-0.01715.8510.0260.0260.0000.0000.0000.000
126A164ASP-1-0.833-0.91913.1780.4790.4790.0000.0000.0000.000
127A165ILE0-0.036-0.01913.6430.0160.0160.0000.0000.0000.000
128A166GLY00.0220.00713.9300.0160.0160.0000.0000.0000.000
129A167ALA0-0.017-0.01714.728-0.041-0.0410.0000.0000.0000.000
130A168GLY0-0.013-0.03516.436-0.001-0.0010.0000.0000.0000.000
131A169ASN0-0.025-0.00718.997-0.002-0.0020.0000.0000.0000.000
132A170GLY0-0.0030.00222.471-0.007-0.0070.0000.0000.0000.000
133A171LYS10.9420.96224.650-0.063-0.0630.0000.0000.0000.000
134A172ALA0-0.022-0.01022.147-0.010-0.0100.0000.0000.0000.000
135A173ASP-1-0.870-0.91424.2390.0860.0860.0000.0000.0000.000
136A174VAL0-0.016-0.01719.9060.0020.0020.0000.0000.0000.000
137A175VAL0-0.018-0.00721.621-0.003-0.0030.0000.0000.0000.000
138A176VAL00.0060.00420.5690.0080.0080.0000.0000.0000.000
139A177ALA00.0070.01121.201-0.009-0.0090.0000.0000.0000.000
140A178TYR0-0.030-0.03621.5840.0080.0080.0000.0000.0000.000
141A179PHE00.0220.01017.988-0.012-0.0120.0000.0000.0000.000
142A180THR00.0090.01823.6110.0070.0070.0000.0000.0000.000
143A181ARG10.9470.96517.2520.0490.0490.0000.0000.0000.000
144A182GLU-1-0.909-0.98122.743-0.044-0.0440.0000.0000.0000.000
145A183GLN00.0360.02625.5320.0100.0100.0000.0000.0000.000
146A184THR0-0.020-0.01129.179-0.005-0.0050.0000.0000.0000.000
147A185VAL00.0050.00532.1610.0050.0050.0000.0000.0000.000
148A186ASP-1-0.886-0.94535.293-0.017-0.0170.0000.0000.0000.000
149A187VAL0-0.051-0.02437.3200.0000.0000.0000.0000.0000.000
150A195LYS10.9910.99238.9930.0350.0350.0000.0000.0000.000
151A196LYS10.9180.94435.2680.0200.0200.0000.0000.0000.000
152A197MET0-0.0290.00533.101-0.004-0.0040.0000.0000.0000.000
153A198SER0-0.029-0.00928.0190.0020.0020.0000.0000.0000.000
154A199TYR00.0130.01727.696-0.006-0.0060.0000.0000.0000.000
155A200TRP00.014-0.01121.3810.0000.0000.0000.0000.0000.000
156A201HIS0-0.009-0.01616.912-0.005-0.0050.0000.0000.0000.000
157A202SER00.0090.01222.599-0.001-0.0010.0000.0000.0000.000
158A203VAL0-0.023-0.02523.6410.0080.0080.0000.0000.0000.000
159A204TYR0-0.033-0.01726.057-0.001-0.0010.0000.0000.0000.000
160A205ASP-1-0.872-0.95127.3770.0570.0570.0000.0000.0000.000
161A206VAL00.0060.01525.3030.0030.0030.0000.0000.0000.000
162A207GLN00.0190.01825.8140.0090.0090.0000.0000.0000.000
163A208THR00.0250.01125.3090.0050.0050.0000.0000.0000.000
164A209VAL0-0.038-0.01923.557-0.001-0.0010.0000.0000.0000.000
165A210GLY00.0350.02025.0160.0080.0080.0000.0000.0000.000
166A211MET0-0.018-0.00525.328-0.011-0.0110.0000.0000.0000.000
167A212TRP00.0310.02318.514-0.009-0.0090.0000.0000.0000.000
168A213ASP-1-0.888-0.95023.1450.1280.1280.0000.0000.0000.000
169A214GLY00.0150.01421.340-0.010-0.0100.0000.0000.0000.000
170A215SER0-0.022-0.02520.6030.0180.0180.0000.0000.0000.000
171A216PRO0-0.077-0.03716.9100.0020.0020.0000.0000.0000.000
172A217MET0-0.0350.00017.924-0.025-0.0250.0000.0000.0000.000
173A218THR00.0260.01417.1650.0140.0140.0000.0000.0000.000
174A219VAL0-0.056-0.02419.165-0.027-0.0270.0000.0000.0000.000
175A220LYS10.9360.96720.376-0.250-0.2500.0000.0000.0000.000
176A221LEU0-0.009-0.00321.697-0.022-0.0220.0000.0000.0000.000
177A222PRO00.0830.03424.2390.0080.0080.0000.0000.0000.000
178A223ALA00.1260.05526.099-0.001-0.0010.0000.0000.0000.000
179A224SER0-0.053-0.02927.693-0.002-0.0020.0000.0000.0000.000
180A225VAL00.0320.00623.287-0.010-0.0100.0000.0000.0000.000
181A226VAL00.0200.03522.827-0.005-0.0050.0000.0000.0000.000
182A227ALA0-0.016-0.01524.359-0.006-0.0060.0000.0000.0000.000
183A228LYS10.8560.94025.848-0.084-0.0840.0000.0000.0000.000
184A229VAL00.0230.01419.409-0.011-0.0110.0000.0000.0000.000
185A230LYS10.8680.92320.907-0.141-0.1410.0000.0000.0000.000
186A231LYS10.8540.95523.796-0.052-0.0520.0000.0000.0000.000
187A232GLY0-0.039-0.04222.962-0.014-0.0140.0000.0000.0000.000
188A233GLY00.0080.02319.3640.0050.0050.0000.0000.0000.000
189A234CYS0-0.044-0.00718.4410.0000.0000.0000.0000.0000.000
190A235ALA00.0220.01616.7440.0050.0050.0000.0000.0000.000
191A236VAL00.0060.00315.775-0.003-0.0030.0000.0000.0000.000
192A237LEU0-0.027-0.03216.376-0.004-0.0040.0000.0000.0000.000
193A238LEU00.0270.02217.4960.0030.0030.0000.0000.0000.000
194A239GLN0-0.063-0.04219.264-0.009-0.0090.0000.0000.0000.000
195A240THR0-0.009-0.00222.3060.0030.0030.0000.0000.0000.000
196A241ALA00.0570.02024.950-0.005-0.0050.0000.0000.0000.000
197A242ASN00.0270.01828.5370.0050.0050.0000.0000.0000.000
198A243ALA00.013-0.01531.4090.0030.0030.0000.0000.0000.000
199A244SER0-0.052-0.02634.8330.0010.0010.0000.0000.0000.000
200A245GLY00.0110.02132.4920.0010.0010.0000.0000.0000.000
201A246ASP-1-0.861-0.91631.8060.0160.0160.0000.0000.0000.000
202A247PRO0-0.052-0.02226.9490.0020.0020.0000.0000.0000.000
203A248ALA00.0350.01226.510-0.008-0.0080.0000.0000.0000.000
204A249ALA0-0.012-0.00622.2340.0000.0000.0000.0000.0000.000
205A250ILE00.0050.01717.6370.0130.0130.0000.0000.0000.000
206A251VAL0-0.011-0.01417.903-0.017-0.0170.0000.0000.0000.000
207A252GLY00.0450.02114.2380.0100.0100.0000.0000.0000.000
208A253ALA0-0.025-0.02013.102-0.019-0.0190.0000.0000.0000.000
209A254SER0-0.0050.01311.7320.0240.0240.0000.0000.0000.000
210A255ILE00.0000.00612.049-0.034-0.0340.0000.0000.0000.000
211A256LEU0-0.0270.01912.6940.0310.0310.0000.0000.0000.000
212A257LEU00.001-0.01914.986-0.038-0.0380.0000.0000.0000.000
213A258GLY00.0640.02516.9390.0220.0220.0000.0000.0000.000
214A259ASN0-0.0530.00418.7820.0270.0270.0000.0000.0000.000
215A260GLU-1-0.879-0.93614.7850.2450.2450.0000.0000.0000.000
216A261THR0-0.075-0.07016.4910.0210.0210.0000.0000.0000.000
217A262GLN00.0020.00512.712-0.054-0.0540.0000.0000.0000.000
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