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: K38K3

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 OptHSide
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 -2546767.9163
FMO2-HF: Nuclear repulsion 2461973.106249
FMO2-HF: Total energy -84794.810051
FMO2-MP2: Total energy -85040.78122


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.
-0.1252.234-0.016-1.354-0.9890.005
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 : 0.034 / 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].
3A40GLU-1-0.855-0.8973.821-1.6390.720-0.016-1.354-0.9890.005
4A41ALA0-0.0080.0035.8370.1460.1460.0000.0000.0000.000
5A42VAL00.0100.0056.689-0.063-0.0630.0000.0000.0000.000
6A43LYS10.8180.8829.3480.5480.5480.0000.0000.0000.000
7A44GLY0-0.007-0.00612.6680.0240.0240.0000.0000.0000.000
8A45VAL0-0.0120.00014.8450.0000.0000.0000.0000.0000.000
9A46VAL00.007-0.00317.378-0.005-0.0050.0000.0000.0000.000
10A47GLU-1-0.760-0.81220.1750.0130.0130.0000.0000.0000.000
11A48LEU0-0.008-0.00223.059-0.003-0.0030.0000.0000.0000.000
12A49PHE0-0.0030.01725.8020.0060.0060.0000.0000.0000.000
13A50THR0-0.004-0.06728.787-0.005-0.0050.0000.0000.0000.000
14A51SER00.0570.02931.2640.0050.0050.0000.0000.0000.000
15A52GLN00.0120.01033.930-0.002-0.0020.0000.0000.0000.000
16A53GLY0-0.011-0.00635.497-0.001-0.0010.0000.0000.0000.000
17A54CYS0-0.0540.00832.185-0.005-0.0050.0000.0000.0000.000
18A55ALA00.037-0.00336.262-0.003-0.0030.0000.0000.0000.000
19A56SER0-0.031-0.01736.240-0.002-0.0020.0000.0000.0000.000
20A58PRO00.0540.04331.115-0.005-0.0050.0000.0000.0000.000
21A59PRO0-0.010-0.01330.215-0.005-0.0050.0000.0000.0000.000
22A60ALA00.009-0.00527.906-0.008-0.0080.0000.0000.0000.000
23A61ASP-1-0.775-0.86726.363-0.048-0.0480.0000.0000.0000.000
24A62GLU-1-0.915-0.93625.703-0.101-0.1010.0000.0000.0000.000
25A63ALA0-0.024-0.02224.444-0.012-0.0120.0000.0000.0000.000
26A64LEU00.0470.02120.439-0.015-0.0150.0000.0000.0000.000
27A65ARG10.9640.99220.6280.0660.0660.0000.0000.0000.000
28A66LYS10.8320.89820.4610.1120.1120.0000.0000.0000.000
29A67MET0-0.0110.01417.732-0.024-0.0240.0000.0000.0000.000
30A68ILE0-0.013-0.00716.088-0.021-0.0210.0000.0000.0000.000
31A69GLN0-0.088-0.04115.8450.0090.0090.0000.0000.0000.000
32A70LYS10.7890.88514.0860.3110.3110.0000.0000.0000.000
33A71GLY00.0230.02412.092-0.060-0.0600.0000.0000.0000.000
34A72ASP-1-0.755-0.84010.516-0.345-0.3450.0000.0000.0000.000
35A73VAL0-0.022-0.01111.5990.0110.0110.0000.0000.0000.000
36A74VAL00.0080.01912.7480.0090.0090.0000.0000.0000.000
37A75GLY0-0.002-0.00815.026-0.001-0.0010.0000.0000.0000.000
38A76LEU0-0.021-0.00918.3870.0130.0130.0000.0000.0000.000
39A77SER00.0130.01021.511-0.008-0.0080.0000.0000.0000.000
40A78TYR0-0.015-0.03823.5230.0110.0110.0000.0000.0000.000
41A79HIS0-0.022-0.01727.982-0.006-0.0060.0000.0000.0000.000
42A80VAL00.011-0.00331.3110.0040.0040.0000.0000.0000.000
43A81ASP-1-0.804-0.87934.1310.0010.0010.0000.0000.0000.000
44A82TYR0-0.058-0.05034.963-0.002-0.0020.0000.0000.0000.000
45A83TRP0-0.012-0.01536.818-0.003-0.0030.0000.0000.0000.000
46A84ASN0-0.060-0.03038.0880.0010.0010.0000.0000.0000.000
47A85TYR00.0290.00341.7480.0010.0010.0000.0000.0000.000
48A86LEU0-0.002-0.01545.1950.0010.0010.0000.0000.0000.000
49A87GLY0-0.0090.02345.5490.0010.0010.0000.0000.0000.000
50A88TRP0-0.052-0.01539.1050.0000.0000.0000.0000.0000.000
51A89THR0-0.024-0.02840.318-0.002-0.0020.0000.0000.0000.000
52A90ASP-1-0.722-0.84734.575-0.011-0.0110.0000.0000.0000.000
53A91SER0-0.051-0.03236.0940.0020.0020.0000.0000.0000.000
54A92LEU0-0.055-0.03729.9580.0030.0030.0000.0000.0000.000
55A93ALA0-0.0190.00931.9410.0010.0010.0000.0000.0000.000
56A94SER00.0190.00732.3350.0020.0020.0000.0000.0000.000
57A95LYS10.9130.95234.801-0.014-0.0140.0000.0000.0000.000
58A96GLU-1-0.864-0.94932.4000.0190.0190.0000.0000.0000.000
59A97ASN0-0.032-0.01529.7190.0040.0040.0000.0000.0000.000
60A98THR0-0.034-0.05931.541-0.004-0.0040.0000.0000.0000.000
61A99GLU-1-0.863-0.92034.2280.0150.0150.0000.0000.0000.000
62A100ARG10.8290.90323.720-0.022-0.0220.0000.0000.0000.000
63A101GLN0-0.0010.00530.7290.0000.0000.0000.0000.0000.000
64A102TYR0-0.028-0.02331.714-0.002-0.0020.0000.0000.0000.000
65A103GLY00.0310.01632.122-0.001-0.0010.0000.0000.0000.000
66A104TYR00.000-0.02823.9600.0010.0010.0000.0000.0000.000
67A105MET0-0.077-0.01130.805-0.004-0.0040.0000.0000.0000.000
68A106ARG10.8210.88234.111-0.013-0.0130.0000.0000.0000.000
69A107ALA0-0.0020.00830.596-0.001-0.0010.0000.0000.0000.000
70A108LEU0-0.072-0.04328.361-0.002-0.0020.0000.0000.0000.000
71A109GLY0-0.0040.01332.407-0.003-0.0030.0000.0000.0000.000
72A110ARG10.8630.94533.1970.0240.0240.0000.0000.0000.000
73A111ASN00.013-0.00437.0480.0010.0010.0000.0000.0000.000
74A112GLY00.0330.00038.2300.0010.0010.0000.0000.0000.000
75A113VAL0-0.024-0.01234.730-0.001-0.0010.0000.0000.0000.000
76A114TYR0-0.077-0.04532.019-0.002-0.0020.0000.0000.0000.000
77A115THR00.0390.04732.9920.0010.0010.0000.0000.0000.000
78A116PRO0-0.007-0.01230.0570.0000.0000.0000.0000.0000.000
79A117GLN0-0.025-0.02029.4940.0000.0000.0000.0000.0000.000
80A118ALA00.0170.01124.4800.0030.0030.0000.0000.0000.000
81A119ILE0-0.016-0.00724.640-0.002-0.0020.0000.0000.0000.000
82A120LEU00.0110.00120.863-0.002-0.0020.0000.0000.0000.000
83A121ASN00.0480.01517.2870.0020.0020.0000.0000.0000.000
84A122GLY00.0500.02220.2730.0100.0100.0000.0000.0000.000
85A123ARG10.8730.94620.2630.0240.0240.0000.0000.0000.000
86A124ASP-1-0.782-0.86625.013-0.054-0.0540.0000.0000.0000.000
87A125HIS0-0.0180.00726.0350.0010.0010.0000.0000.0000.000
88A126VAL00.0350.01425.497-0.004-0.0040.0000.0000.0000.000
89A127LYS10.9610.97928.5750.0550.0550.0000.0000.0000.000
90A128GLY00.0450.01927.207-0.006-0.0060.0000.0000.0000.000
91A129ALA0-0.001-0.01126.628-0.006-0.0060.0000.0000.0000.000
92A130ASP-1-0.913-0.93727.705-0.107-0.1070.0000.0000.0000.000
93A131VAL00.013-0.01622.130-0.005-0.0050.0000.0000.0000.000
94A132ARG10.9400.96222.8600.1340.1340.0000.0000.0000.000
95A133GLY00.0880.05823.742-0.008-0.0080.0000.0000.0000.000
96A134ILE0-0.027-0.01621.4160.0000.0000.0000.0000.0000.000
97A135TYR0-0.057-0.06615.6420.0040.0040.0000.0000.0000.000
98A136ASP-1-0.891-0.93819.523-0.184-0.1840.0000.0000.0000.000
99A137ARG10.8040.88922.0570.0760.0760.0000.0000.0000.000
100A138LEU0-0.032-0.01916.4890.0060.0060.0000.0000.0000.000
101A139ASP-1-0.816-0.89417.032-0.261-0.2610.0000.0000.0000.000
102A140ALA0-0.013-0.01418.5130.0010.0010.0000.0000.0000.000
103A141PHE0-0.014-0.01619.2890.0110.0110.0000.0000.0000.000
104A142LYS10.9330.96812.7540.3240.3240.0000.0000.0000.000
105A143ARG10.8130.90916.8590.2010.2010.0000.0000.0000.000
106A144GLU-1-0.935-0.95719.020-0.073-0.0730.0000.0000.0000.000
107A145GLY0-0.0120.00517.3740.0170.0170.0000.0000.0000.000
108A146GLN0-0.068-0.03518.4490.0280.0280.0000.0000.0000.000
109A147GLY00.0200.00215.495-0.004-0.0040.0000.0000.0000.000
110A148LEU0-0.056-0.02012.4150.0210.0210.0000.0000.0000.000
111A149ASN0-0.035-0.03812.206-0.009-0.0090.0000.0000.0000.000
112A150VAL0-0.0180.00613.3470.0260.0260.0000.0000.0000.000
113A151PRO0-0.0090.0009.423-0.010-0.0100.0000.0000.0000.000
114A152VAL00.0330.00610.782-0.018-0.0180.0000.0000.0000.000
115A153SER0-0.028-0.0099.2630.0980.0980.0000.0000.0000.000
116A154SER00.0180.01211.264-0.062-0.0620.0000.0000.0000.000
117A155LYS10.9070.94712.678-0.429-0.4290.0000.0000.0000.000
118A156PHE00.0160.00114.832-0.035-0.0350.0000.0000.0000.000
119A157ALA0-0.054-0.03217.7050.0310.0310.0000.0000.0000.000
120A158GLY00.0150.00719.691-0.014-0.0140.0000.0000.0000.000
121A159ASP-1-0.941-0.97122.3310.1410.1410.0000.0000.0000.000
122A160GLU-1-0.834-0.91622.5310.1860.1860.0000.0000.0000.000
123A161VAL0-0.060-0.02918.5220.0150.0150.0000.0000.0000.000
124A162GLU-1-0.854-0.91316.3590.3670.3670.0000.0000.0000.000
125A163ILE0-0.008-0.01315.8350.0260.0260.0000.0000.0000.000
126A164ASP-1-0.831-0.89512.9120.4510.4510.0000.0000.0000.000
127A165ILE0-0.034-0.01913.6650.0140.0140.0000.0000.0000.000
128A166GLY00.0360.02113.9530.0130.0130.0000.0000.0000.000
129A167ALA0-0.008-0.01014.778-0.038-0.0380.0000.0000.0000.000
130A168GLY0-0.021-0.03516.381-0.002-0.0020.0000.0000.0000.000
131A169ASN0-0.033-0.01318.950-0.005-0.0050.0000.0000.0000.000
132A170GLY00.0090.00922.436-0.006-0.0060.0000.0000.0000.000
133A171LYS10.9370.96024.591-0.061-0.0610.0000.0000.0000.000
134A172ALA0-0.024-0.01022.146-0.010-0.0100.0000.0000.0000.000
135A173ASP-1-0.815-0.88624.2180.0820.0820.0000.0000.0000.000
136A174VAL0-0.025-0.01919.7620.0020.0020.0000.0000.0000.000
137A175VAL0-0.016-0.00721.576-0.003-0.0030.0000.0000.0000.000
138A176VAL00.0000.00220.3710.0080.0080.0000.0000.0000.000
139A177ALA00.0140.01621.153-0.009-0.0090.0000.0000.0000.000
140A178TYR00.005-0.02621.5350.0090.0090.0000.0000.0000.000
141A179PHE00.0200.00517.760-0.011-0.0110.0000.0000.0000.000
142A180THR00.0040.00923.5520.0070.0070.0000.0000.0000.000
143A181ARG10.9160.94117.1590.0410.0410.0000.0000.0000.000
144A182GLU-1-0.846-0.90922.703-0.036-0.0360.0000.0000.0000.000
145A183GLN00.0390.03125.5090.0090.0090.0000.0000.0000.000
146A184THR00.000-0.00129.155-0.004-0.0040.0000.0000.0000.000
147A185VAL0-0.0030.00332.1480.0040.0040.0000.0000.0000.000
148A186ASP-1-0.862-0.91835.286-0.015-0.0150.0000.0000.0000.000
149A187VAL0-0.044-0.01437.2690.0010.0010.0000.0000.0000.000
150A195LYS10.9900.98839.0750.0310.0310.0000.0000.0000.000
151A196LYS10.8920.91335.2080.0150.0150.0000.0000.0000.000
152A197MET0-0.037-0.00333.253-0.004-0.0040.0000.0000.0000.000
153A198SER0-0.060-0.05728.0110.0010.0010.0000.0000.0000.000
154A199TYR0-0.009-0.00127.719-0.005-0.0050.0000.0000.0000.000
155A200TRP0-0.007-0.02420.9170.0000.0000.0000.0000.0000.000
156A201HIS00.0030.00316.852-0.004-0.0040.0000.0000.0000.000
157A202SER00.0110.01322.591-0.001-0.0010.0000.0000.0000.000
158A203VAL0-0.026-0.02423.6020.0070.0070.0000.0000.0000.000
159A204TYR0-0.015-0.01125.967-0.001-0.0010.0000.0000.0000.000
160A205ASP-1-0.854-0.93127.3300.0590.0590.0000.0000.0000.000
161A206VAL00.0060.01325.1460.0030.0030.0000.0000.0000.000
162A207GLN00.0390.03525.7600.0040.0040.0000.0000.0000.000
163A208THR00.0040.00225.2480.0060.0060.0000.0000.0000.000
164A209VAL0-0.064-0.03923.514-0.002-0.0020.0000.0000.0000.000
165A210GLY00.0400.02425.0490.0080.0080.0000.0000.0000.000
166A211MET0-0.032-0.01325.335-0.010-0.0100.0000.0000.0000.000
167A212TRP00.0400.01718.373-0.008-0.0080.0000.0000.0000.000
168A213ASP-1-0.872-0.94423.2090.1190.1190.0000.0000.0000.000
169A214GLY00.0060.02021.266-0.009-0.0090.0000.0000.0000.000
170A215SER0-0.016-0.02720.5280.0150.0150.0000.0000.0000.000
171A216PRO0-0.068-0.02916.8250.0010.0010.0000.0000.0000.000
172A217MET0-0.044-0.00717.922-0.024-0.0240.0000.0000.0000.000
173A218THR00.012-0.01417.1590.0130.0130.0000.0000.0000.000
174A219VAL0-0.067-0.02919.144-0.026-0.0260.0000.0000.0000.000
175A220LYS10.8500.92220.351-0.217-0.2170.0000.0000.0000.000
176A221LEU0-0.020-0.01021.767-0.021-0.0210.0000.0000.0000.000
177A222PRO00.0730.02824.2070.0070.0070.0000.0000.0000.000
178A223ALA00.1210.05426.0550.0000.0000.0000.0000.0000.000
179A224SER0-0.046-0.02927.645-0.001-0.0010.0000.0000.0000.000
180A225VAL00.0260.00723.053-0.008-0.0080.0000.0000.0000.000
181A226VAL00.0150.03022.621-0.004-0.0040.0000.0000.0000.000
182A227ALA0-0.013-0.01624.231-0.005-0.0050.0000.0000.0000.000
183A228LYS10.8120.90725.817-0.084-0.0840.0000.0000.0000.000
184A229VAL00.0100.00619.253-0.010-0.0100.0000.0000.0000.000
185A230LYS10.8480.92620.257-0.150-0.1500.0000.0000.0000.000
186A231LYS10.8460.95423.684-0.053-0.0530.0000.0000.0000.000
187A232GLY0-0.036-0.04222.889-0.014-0.0140.0000.0000.0000.000
188A233GLY00.0090.02219.2940.0050.0050.0000.0000.0000.000
189A234CYS0-0.058-0.00618.3590.0000.0000.0000.0000.0000.000
190A235ALA00.0350.01316.7010.0060.0060.0000.0000.0000.000
191A236VAL0-0.0010.00015.733-0.004-0.0040.0000.0000.0000.000
192A237LEU0-0.027-0.03216.347-0.004-0.0040.0000.0000.0000.000
193A238LEU00.0250.02417.3670.0020.0020.0000.0000.0000.000
194A239GLN0-0.053-0.04519.247-0.010-0.0100.0000.0000.0000.000
195A240THR0-0.011-0.00622.3100.0020.0020.0000.0000.0000.000
196A241ALA00.0450.01424.965-0.005-0.0050.0000.0000.0000.000
197A242ASN00.0140.01028.5550.0030.0030.0000.0000.0000.000
198A243ALA00.015-0.00831.4430.0030.0030.0000.0000.0000.000
199A244SER0-0.039-0.01834.8610.0010.0010.0000.0000.0000.000
200A245GLY00.0080.01632.4980.0010.0010.0000.0000.0000.000
201A246ASP-1-0.813-0.87131.8270.0160.0160.0000.0000.0000.000
202A247PRO0-0.046-0.01926.9570.0020.0020.0000.0000.0000.000
203A248ALA00.0310.01026.531-0.007-0.0070.0000.0000.0000.000
204A249ALA0-0.0050.00722.3370.0010.0010.0000.0000.0000.000
205A250ILE0-0.0040.01517.7580.0120.0120.0000.0000.0000.000
206A251VAL0-0.005-0.01317.878-0.016-0.0160.0000.0000.0000.000
207A252GLY00.0520.02514.2600.0090.0090.0000.0000.0000.000
208A253ALA0-0.026-0.02113.107-0.018-0.0180.0000.0000.0000.000
209A254SER0-0.0050.00811.7260.0250.0250.0000.0000.0000.000
210A255ILE0-0.0030.00311.992-0.034-0.0340.0000.0000.0000.000
211A256LEU0-0.0350.01512.6140.0300.0300.0000.0000.0000.000
212A257LEU00.001-0.01514.874-0.035-0.0350.0000.0000.0000.000
213A258GLY00.0600.02116.8490.0220.0220.0000.0000.0000.000
214A259ASN0-0.043-0.01118.8150.0250.0250.0000.0000.0000.000
215A260GLU-1-0.853-0.93114.9580.2520.2520.0000.0000.0000.000
216A261THR0-0.055-0.04416.5230.0190.0190.0000.0000.0000.000
217A262GLN00.0000.00312.302-0.045-0.0450.0000.0000.0000.000
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