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: 436QN

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 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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2550866.91539
FMO2-HF: Nuclear repulsion 2466071.755924
FMO2-HF: Total energy -84795.159466
FMO2-MP2: Total energy -85041.161528


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.
-0.2951.809-0.007-1.244-0.8530.004
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 : 0.052 / q_NPA : 0.032
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-1-0.834-0.8903.818-1.8440.260-0.007-1.244-0.8530.004
4A41ALA00.0080.0115.8170.0900.0900.0000.0000.0000.000
5A42VAL0-0.007-0.0046.586-0.035-0.0350.0000.0000.0000.000
6A43LYS10.8210.8829.7140.6180.6180.0000.0000.0000.000
7A44GLY0-0.002-0.00712.7140.0290.0290.0000.0000.0000.000
8A45VAL0-0.0020.01214.883-0.002-0.0020.0000.0000.0000.000
9A46VAL0-0.004-0.01317.616-0.004-0.0040.0000.0000.0000.000
10A47GLU-1-0.750-0.81120.404-0.008-0.0080.0000.0000.0000.000
11A48LEU0-0.023-0.00223.286-0.001-0.0010.0000.0000.0000.000
12A49PHE0-0.0060.00125.9480.0070.0070.0000.0000.0000.000
13A50THR0-0.005-0.07028.820-0.003-0.0030.0000.0000.0000.000
14A51SER00.0320.00531.4580.0050.0050.0000.0000.0000.000
15A52GLN0-0.018-0.00933.974-0.002-0.0020.0000.0000.0000.000
16A53GLY00.0020.00335.590-0.001-0.0010.0000.0000.0000.000
17A54CYS0-0.0580.02131.861-0.006-0.0060.0000.0000.0000.000
18A55ALA00.017-0.00236.006-0.004-0.0040.0000.0000.0000.000
19A56SER0-0.027-0.01736.158-0.002-0.0020.0000.0000.0000.000
20A58PRO00.0500.03631.020-0.006-0.0060.0000.0000.0000.000
21A59PRO0-0.010-0.01530.076-0.006-0.0060.0000.0000.0000.000
22A60ALA00.000-0.00327.616-0.009-0.0090.0000.0000.0000.000
23A61ASP-1-0.741-0.83726.224-0.059-0.0590.0000.0000.0000.000
24A62GLU-1-0.848-0.90025.671-0.107-0.1070.0000.0000.0000.000
25A63ALA0-0.020-0.01224.239-0.013-0.0130.0000.0000.0000.000
26A64LEU00.0270.01620.562-0.017-0.0170.0000.0000.0000.000
27A65ARG10.8840.95020.6950.0760.0760.0000.0000.0000.000
28A66LYS10.8360.89120.4620.1190.1190.0000.0000.0000.000
29A67MET0-0.0220.00617.735-0.024-0.0240.0000.0000.0000.000
30A68ILE0-0.030-0.01616.126-0.024-0.0240.0000.0000.0000.000
31A69GLN0-0.072-0.03215.9420.0090.0090.0000.0000.0000.000
32A70LYS10.7950.89214.0280.3330.3330.0000.0000.0000.000
33A71GLY00.0170.01611.794-0.064-0.0640.0000.0000.0000.000
34A72ASP-1-0.764-0.84810.415-0.375-0.3750.0000.0000.0000.000
35A73VAL0-0.021-0.01611.4900.0050.0050.0000.0000.0000.000
36A74VAL00.0260.01512.9920.0120.0120.0000.0000.0000.000
37A75GLY00.0040.01015.1560.0070.0070.0000.0000.0000.000
38A76LEU0-0.029-0.01618.3530.0130.0130.0000.0000.0000.000
39A77SER0-0.0010.00221.449-0.008-0.0080.0000.0000.0000.000
40A78TYR0-0.005-0.02323.5210.0110.0110.0000.0000.0000.000
41A79HIS00.0030.00428.030-0.006-0.0060.0000.0000.0000.000
42A80VAL0-0.005-0.00831.2590.0050.0050.0000.0000.0000.000
43A81ASP-1-0.788-0.87034.253-0.009-0.0090.0000.0000.0000.000
44A82TYR0-0.059-0.05635.041-0.002-0.0020.0000.0000.0000.000
45A83TRP0-0.004-0.00836.703-0.002-0.0020.0000.0000.0000.000
46A84ASN0-0.061-0.03337.8210.0010.0010.0000.0000.0000.000
47A85TYR00.015-0.00541.4540.0010.0010.0000.0000.0000.000
48A86LEU0-0.011-0.01245.1620.0010.0010.0000.0000.0000.000
49A87GLY0-0.0090.02145.2430.0010.0010.0000.0000.0000.000
50A88TRP0-0.060-0.03339.198-0.001-0.0010.0000.0000.0000.000
51A89THR00.001-0.01140.174-0.001-0.0010.0000.0000.0000.000
52A90ASP-1-0.704-0.82234.212-0.021-0.0210.0000.0000.0000.000
53A91SER00.0260.00835.6380.0020.0020.0000.0000.0000.000
54A92LEU0-0.132-0.07129.6290.0020.0020.0000.0000.0000.000
55A93ALA0-0.018-0.00332.0880.0010.0010.0000.0000.0000.000
56A94SER00.0110.00932.5230.0020.0020.0000.0000.0000.000
57A95LYS10.9000.94934.854-0.008-0.0080.0000.0000.0000.000
58A96GLU-1-0.857-0.94432.5990.0090.0090.0000.0000.0000.000
59A97ASN0-0.038-0.01929.6200.0030.0030.0000.0000.0000.000
60A98THR0-0.031-0.05631.463-0.004-0.0040.0000.0000.0000.000
61A99GLU-1-0.851-0.91734.3210.0050.0050.0000.0000.0000.000
62A100ARG10.8150.89323.735-0.004-0.0040.0000.0000.0000.000
63A101GLN00.0080.01830.6760.0000.0000.0000.0000.0000.000
64A102TYR0-0.015-0.02631.956-0.002-0.0020.0000.0000.0000.000
65A103GLY00.0240.01432.1800.0000.0000.0000.0000.0000.000
66A104TYR00.001-0.02823.9070.0000.0000.0000.0000.0000.000
67A105MET0-0.091-0.01330.761-0.004-0.0040.0000.0000.0000.000
68A106ARG10.8510.91234.170-0.003-0.0030.0000.0000.0000.000
69A107ALA0-0.019-0.00230.1900.0000.0000.0000.0000.0000.000
70A108LEU0-0.068-0.03028.223-0.002-0.0020.0000.0000.0000.000
71A109GLY0-0.0040.00532.301-0.003-0.0030.0000.0000.0000.000
72A110ARG10.8670.94033.3060.0330.0330.0000.0000.0000.000
73A111ASN00.000-0.00837.1610.0010.0010.0000.0000.0000.000
74A112GLY00.0470.00438.4340.0010.0010.0000.0000.0000.000
75A113VAL0-0.018-0.00334.750-0.002-0.0020.0000.0000.0000.000
76A114TYR0-0.059-0.04332.163-0.002-0.0020.0000.0000.0000.000
77A115THR00.0410.02933.0470.0000.0000.0000.0000.0000.000
78A116PRO00.0140.00230.1150.0010.0010.0000.0000.0000.000
79A117GLN0-0.032-0.01529.6380.0000.0000.0000.0000.0000.000
80A118ALA00.0240.01024.4820.0030.0030.0000.0000.0000.000
81A119ILE0-0.008-0.00124.766-0.004-0.0040.0000.0000.0000.000
82A120LEU0-0.003-0.00321.483-0.005-0.0050.0000.0000.0000.000
83A121ASN00.0420.01017.0480.0030.0030.0000.0000.0000.000
84A122GLY00.0510.03520.3830.0120.0120.0000.0000.0000.000
85A123ARG10.8350.92619.9870.0430.0430.0000.0000.0000.000
86A124ASP-1-0.783-0.86925.127-0.067-0.0670.0000.0000.0000.000
87A125HIS0-0.0160.00226.2310.0010.0010.0000.0000.0000.000
88A126VAL00.0360.02526.139-0.002-0.0020.0000.0000.0000.000
89A127LYS10.9530.97428.9960.0620.0620.0000.0000.0000.000
90A128GLY00.0260.00127.153-0.007-0.0070.0000.0000.0000.000
91A129ALA00.013-0.00326.563-0.006-0.0060.0000.0000.0000.000
92A130ASP-1-0.875-0.92627.675-0.121-0.1210.0000.0000.0000.000
93A131VAL0-0.014-0.03322.378-0.006-0.0060.0000.0000.0000.000
94A132ARG10.9060.97422.8830.1390.1390.0000.0000.0000.000
95A133GLY00.0990.05123.537-0.010-0.0100.0000.0000.0000.000
96A134ILE0-0.041-0.02421.2880.0000.0000.0000.0000.0000.000
97A135TYR0-0.034-0.05015.6320.0040.0040.0000.0000.0000.000
98A136ASP-1-0.888-0.94319.563-0.196-0.1960.0000.0000.0000.000
99A137ARG10.8150.88521.9400.0880.0880.0000.0000.0000.000
100A138LEU0-0.0200.00816.6520.0070.0070.0000.0000.0000.000
101A139ASP-1-0.822-0.89316.718-0.308-0.3080.0000.0000.0000.000
102A140ALA0-0.007-0.00718.2310.0010.0010.0000.0000.0000.000
103A141PHE0-0.013-0.02219.1890.0110.0110.0000.0000.0000.000
104A142LYS10.8820.93712.4380.3850.3850.0000.0000.0000.000
105A143ARG10.8180.90516.6520.2170.2170.0000.0000.0000.000
106A144GLU-1-0.942-0.96619.165-0.087-0.0870.0000.0000.0000.000
107A145GLY00.0100.01917.7440.0170.0170.0000.0000.0000.000
108A146GLN0-0.048-0.01918.8000.0300.0300.0000.0000.0000.000
109A147GLY00.0490.01515.211-0.005-0.0050.0000.0000.0000.000
110A148LEU0-0.063-0.02412.1050.0270.0270.0000.0000.0000.000
111A149ASN0-0.041-0.04412.173-0.007-0.0070.0000.0000.0000.000
112A150VAL0-0.0150.00913.3380.0270.0270.0000.0000.0000.000
113A151PRO0-0.0080.0019.466-0.018-0.0180.0000.0000.0000.000
114A152VAL00.0270.00310.951-0.002-0.0020.0000.0000.0000.000
115A153SER0-0.036-0.0199.3830.1080.1080.0000.0000.0000.000
116A154SER00.0100.01311.528-0.051-0.0510.0000.0000.0000.000
117A155LYS10.8610.92112.545-0.380-0.3800.0000.0000.0000.000
118A156PHE00.0710.02614.722-0.033-0.0330.0000.0000.0000.000
119A157ALA0-0.032-0.01617.0140.0420.0420.0000.0000.0000.000
120A158GLY00.0150.01019.497-0.001-0.0010.0000.0000.0000.000
121A159ASP-1-0.958-0.96422.5140.1260.1260.0000.0000.0000.000
122A160GLU-1-0.806-0.89322.3710.1780.1780.0000.0000.0000.000
123A161VAL0-0.051-0.03718.6790.0100.0100.0000.0000.0000.000
124A162GLU-1-0.840-0.91916.3490.3390.3390.0000.0000.0000.000
125A163ILE0-0.005-0.01215.8780.0150.0150.0000.0000.0000.000
126A164ASP-1-0.859-0.90513.1950.4400.4400.0000.0000.0000.000
127A165ILE0-0.001-0.00614.0530.0000.0000.0000.0000.0000.000
128A166GLY00.0440.02814.1040.0150.0150.0000.0000.0000.000
129A167ALA00.007-0.00214.951-0.038-0.0380.0000.0000.0000.000
130A168GLY0-0.008-0.02116.666-0.006-0.0060.0000.0000.0000.000
131A169ASN0-0.038-0.01619.286-0.001-0.0010.0000.0000.0000.000
132A170GLY00.0400.02822.669-0.008-0.0080.0000.0000.0000.000
133A171LYS10.8850.91825.237-0.065-0.0650.0000.0000.0000.000
134A172ALA0-0.0140.00622.095-0.010-0.0100.0000.0000.0000.000
135A173ASP-1-0.794-0.85824.1280.0680.0680.0000.0000.0000.000
136A174VAL0-0.013-0.01919.9090.0000.0000.0000.0000.0000.000
137A175VAL0-0.0080.00422.1670.0000.0000.0000.0000.0000.000
138A176VAL0-0.004-0.00620.4580.0090.0090.0000.0000.0000.000
139A177ALA00.0130.01621.402-0.008-0.0080.0000.0000.0000.000
140A178TYR00.002-0.02421.5450.0080.0080.0000.0000.0000.000
141A179PHE00.0240.00717.716-0.008-0.0080.0000.0000.0000.000
142A180THR0-0.007-0.00123.5090.0050.0050.0000.0000.0000.000
143A181ARG10.8680.92416.4130.0700.0700.0000.0000.0000.000
144A182GLU-1-0.775-0.88822.216-0.050-0.0500.0000.0000.0000.000
145A183GLN00.0370.02525.0630.0110.0110.0000.0000.0000.000
146A184THR0-0.061-0.01928.748-0.002-0.0020.0000.0000.0000.000
147A185VAL00.0080.01031.5030.0050.0050.0000.0000.0000.000
148A186ASP-1-0.849-0.90734.762-0.023-0.0230.0000.0000.0000.000
149A187VAL0-0.040-0.01437.3290.0010.0010.0000.0000.0000.000
150A195LYS11.0000.99738.8120.0360.0360.0000.0000.0000.000
151A196LYS10.8710.91534.7050.0230.0230.0000.0000.0000.000
152A197MET0-0.033-0.00632.844-0.003-0.0030.0000.0000.0000.000
153A198SER0-0.040-0.05327.7280.0010.0010.0000.0000.0000.000
154A199TYR0-0.039-0.02827.376-0.006-0.0060.0000.0000.0000.000
155A200TRP0-0.005-0.02020.520-0.001-0.0010.0000.0000.0000.000
156A201HIS00.0070.00516.509-0.003-0.0030.0000.0000.0000.000
157A202SER00.0060.00122.316-0.001-0.0010.0000.0000.0000.000
158A203VAL0-0.033-0.02123.5460.0070.0070.0000.0000.0000.000
159A204TYR0-0.019-0.01825.802-0.001-0.0010.0000.0000.0000.000
160A205ASP-1-0.839-0.92027.3920.0470.0470.0000.0000.0000.000
161A206VAL00.006-0.00125.5500.0000.0000.0000.0000.0000.000
162A207GLN00.0290.03326.0550.0030.0030.0000.0000.0000.000
163A208THR0-0.010-0.02525.5270.0050.0050.0000.0000.0000.000
164A209VAL0-0.057-0.02323.580-0.001-0.0010.0000.0000.0000.000
165A210GLY00.0190.00725.3720.0050.0050.0000.0000.0000.000
166A211MET0-0.038-0.00325.337-0.009-0.0090.0000.0000.0000.000
167A212TRP00.0500.02418.736-0.009-0.0090.0000.0000.0000.000
168A213ASP-1-0.873-0.95323.4140.1080.1080.0000.0000.0000.000
169A214GLY00.0020.01421.401-0.012-0.0120.0000.0000.0000.000
170A215SER0-0.019-0.03020.7510.0160.0160.0000.0000.0000.000
171A216PRO0-0.066-0.03217.1040.0000.0000.0000.0000.0000.000
172A217MET0-0.056-0.01718.032-0.027-0.0270.0000.0000.0000.000
173A218THR00.010-0.00917.2690.0130.0130.0000.0000.0000.000
174A219VAL0-0.055-0.02719.098-0.027-0.0270.0000.0000.0000.000
175A220LYS10.8190.90320.094-0.203-0.2030.0000.0000.0000.000
176A221LEU0-0.001-0.00222.065-0.019-0.0190.0000.0000.0000.000
177A222PRO00.0600.03424.1500.0070.0070.0000.0000.0000.000
178A223ALA00.1080.04926.233-0.003-0.0030.0000.0000.0000.000
179A224SER0-0.044-0.02827.589-0.003-0.0030.0000.0000.0000.000
180A225VAL00.0150.00123.257-0.009-0.0090.0000.0000.0000.000
181A226VAL00.0200.02322.702-0.004-0.0040.0000.0000.0000.000
182A227ALA0-0.006-0.00624.054-0.006-0.0060.0000.0000.0000.000
183A228LYS10.8000.89925.602-0.069-0.0690.0000.0000.0000.000
184A229VAL00.0170.01619.005-0.010-0.0100.0000.0000.0000.000
185A230LYS10.8070.89919.643-0.124-0.1240.0000.0000.0000.000
186A231LYS10.8560.95423.485-0.037-0.0370.0000.0000.0000.000
187A232GLY0-0.026-0.02422.480-0.012-0.0120.0000.0000.0000.000
188A233GLY00.0240.01619.111-0.002-0.0020.0000.0000.0000.000
189A234CYS0-0.062-0.00618.3420.0030.0030.0000.0000.0000.000
190A235ALA00.0300.00916.7930.0000.0000.0000.0000.0000.000
191A236VAL00.0020.00916.0630.0010.0010.0000.0000.0000.000
192A237LEU0-0.028-0.02716.643-0.007-0.0070.0000.0000.0000.000
193A238LEU00.0340.02617.3350.0020.0020.0000.0000.0000.000
194A239GLN0-0.021-0.02719.335-0.011-0.0110.0000.0000.0000.000
195A240THR0-0.027-0.02322.4270.0040.0040.0000.0000.0000.000
196A241ALA00.0390.00924.977-0.005-0.0050.0000.0000.0000.000
197A242ASN00.0070.00328.5870.0030.0030.0000.0000.0000.000
198A243ALA00.010-0.01031.5420.0030.0030.0000.0000.0000.000
199A244SER0-0.040-0.01334.9250.0020.0020.0000.0000.0000.000
200A245GLY00.0070.01632.7320.0010.0010.0000.0000.0000.000
201A246ASP-1-0.829-0.89431.9840.0050.0050.0000.0000.0000.000
202A247PRO0-0.039-0.01027.0390.0020.0020.0000.0000.0000.000
203A248ALA00.0290.00326.734-0.007-0.0070.0000.0000.0000.000
204A249ALA00.0100.01622.737-0.001-0.0010.0000.0000.0000.000
205A250ILE0-0.0040.01217.7860.0130.0130.0000.0000.0000.000
206A251VAL0-0.011-0.01217.931-0.017-0.0170.0000.0000.0000.000
207A252GLY00.0460.03114.2650.0070.0070.0000.0000.0000.000
208A253ALA0-0.026-0.02113.238-0.013-0.0130.0000.0000.0000.000
209A254SER00.0000.00011.8950.0300.0300.0000.0000.0000.000
210A255ILE0-0.008-0.01412.155-0.038-0.0380.0000.0000.0000.000
211A256LEU0-0.0290.01912.6470.0330.0330.0000.0000.0000.000
212A257LEU00.0330.00514.741-0.028-0.0280.0000.0000.0000.000
213A258GLY00.0350.01116.9210.0200.0200.0000.0000.0000.000
214A259ASN0-0.058-0.02318.4530.0250.0250.0000.0000.0000.000
215A260GLU-1-0.823-0.91815.0420.1850.1850.0000.0000.0000.000
216A261THR0-0.057-0.05215.8000.0150.0150.0000.0000.0000.000
217A262GLN0-0.022-0.01712.747-0.014-0.0140.0000.0000.0000.000
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