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: 437KN

Calculation Name: 4AXZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4AXZ

Chain ID: A

ChEMBL ID:

UniProt ID: O50962

Base Structure: X-ray

Registration Date: 2023-06-20

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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2655811.364719
FMO2-HF: Nuclear repulsion 2567040.325646
FMO2-HF: Total energy -88771.039072
FMO2-MP2: Total energy -89032.704347


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:72:ASN)


Summations of interaction energy for fragment #1(A:72:ASN)
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.
-26.75-20.8872.757-3.368-5.253-0.031
Interaction energy analysis for fragmet #1(A:72:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : -0.001
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].
3A74LYS10.9750.9793.119-6.654-4.9500.095-0.657-1.1430.001
4A75GLU-1-0.843-0.9082.259-25.191-21.4842.662-2.588-3.781-0.032
5A76LYS10.8320.8933.959-1.613-1.1610.000-0.123-0.3290.000
6A77ILE0-0.009-0.0035.9660.4050.4050.0000.0000.0000.000
7A78ILE00.0210.0097.3740.0140.0140.0000.0000.0000.000
8A79LYS10.8790.9295.8335.7035.7030.0000.0000.0000.000
9A80LYS10.9780.9939.5771.0301.0300.0000.0000.0000.000
10A81ILE00.0180.01911.5030.1360.1360.0000.0000.0000.000
11A82ALA0-0.011-0.00312.5760.0860.0860.0000.0000.0000.000
12A83GLN0-0.071-0.03713.768-0.038-0.0380.0000.0000.0000.000
13A84GLU-1-0.835-0.91915.540-0.148-0.1480.0000.0000.0000.000
14A85PHE0-0.025-0.01317.1100.0520.0520.0000.0000.0000.000
15A86ASP-1-0.836-0.91318.306-0.620-0.6200.0000.0000.0000.000
16A87GLU-1-0.854-0.92518.728-0.510-0.5100.0000.0000.0000.000
17A88ASN0-0.015-0.01821.5110.0550.0550.0000.0000.0000.000
18A89GLU-1-0.839-0.90423.057-0.375-0.3750.0000.0000.0000.000
19A90LYS10.7670.87222.2420.5750.5750.0000.0000.0000.000
20A91LEU0-0.039-0.01725.1040.0310.0310.0000.0000.0000.000
21A92ILE00.0170.00227.4690.0290.0290.0000.0000.0000.000
22A93ASN0-0.025-0.02428.1440.0420.0420.0000.0000.0000.000
23A94LYS10.7380.87730.1370.2060.2060.0000.0000.0000.000
24A95ILE0-0.028-0.01332.3220.0170.0170.0000.0000.0000.000
25A96GLY00.0430.03233.3960.0130.0130.0000.0000.0000.000
26A97PRO00.026-0.00234.1770.0130.0130.0000.0000.0000.000
27A98ASN0-0.018-0.00137.3740.0030.0030.0000.0000.0000.000
28A99ILE00.0230.01035.2800.0110.0110.0000.0000.0000.000
29A100GLU-1-0.822-0.87937.700-0.142-0.1420.0000.0000.0000.000
30A101MET00.0230.01140.1070.0070.0070.0000.0000.0000.000
31A102PHE0-0.013-0.01241.0480.0080.0080.0000.0000.0000.000
32A103ALA00.0440.02041.9090.0080.0080.0000.0000.0000.000
33A104GLN0-0.0070.00143.9150.0030.0030.0000.0000.0000.000
34A105THR0-0.025-0.01346.1250.0050.0050.0000.0000.0000.000
35A106ILE0-0.006-0.00544.9910.0050.0050.0000.0000.0000.000
36A107ASN0-0.037-0.01647.4610.0040.0040.0000.0000.0000.000
37A108THR00.015-0.00849.3340.0040.0040.0000.0000.0000.000
38A109ASP-1-0.750-0.85651.890-0.058-0.0580.0000.0000.0000.000
39A110ILE0-0.104-0.04749.8300.0040.0040.0000.0000.0000.000
40A111GLN0-0.066-0.03152.1640.0050.0050.0000.0000.0000.000
41A112LYS10.8060.92355.5450.0600.0600.0000.0000.0000.000
42A113ILE0-0.007-0.00358.5280.0030.0030.0000.0000.0000.000
43A114GLU-1-0.766-0.82961.819-0.030-0.0300.0000.0000.0000.000
44A115PRO00.0100.02263.1080.0010.0010.0000.0000.0000.000
45A116ASN00.022-0.01366.6050.0000.0000.0000.0000.0000.000
46A117ASP-1-0.846-0.92868.429-0.031-0.0310.0000.0000.0000.000
47A118GLN0-0.079-0.04765.3610.0020.0020.0000.0000.0000.000
48A119PHE00.0460.02261.6190.0000.0000.0000.0000.0000.000
49A120GLY00.0200.00266.204-0.001-0.0010.0000.0000.0000.000
50A121ILE0-0.0120.00062.5610.0020.0020.0000.0000.0000.000
51A122ASN00.0260.02566.6820.0020.0020.0000.0000.0000.000
52A123LYS10.9230.93369.4860.0110.0110.0000.0000.0000.000
53A124THR0-0.105-0.06672.3000.0010.0010.0000.0000.0000.000
54A125LEU0-0.042-0.00871.4450.0000.0000.0000.0000.0000.000
55A126PHE0-0.0030.00367.5140.0000.0000.0000.0000.0000.000
56A127THR0-0.009-0.00871.0610.0000.0000.0000.0000.0000.000
57A128GLU-1-0.772-0.88170.516-0.009-0.0090.0000.0000.0000.000
58A129LYS10.8120.88670.0050.0060.0060.0000.0000.0000.000
59A130LYS10.8080.91970.7320.0090.0090.0000.0000.0000.000
60A131ASP-1-0.739-0.87964.164-0.009-0.0090.0000.0000.0000.000
61A132ASN0-0.0200.00162.8660.0000.0000.0000.0000.0000.000
62A133ASN0-0.029-0.01959.7030.0000.0000.0000.0000.0000.000
63A134ILE00.0100.01462.006-0.002-0.0020.0000.0000.0000.000
64A135ASP-1-0.779-0.89365.054-0.008-0.0080.0000.0000.0000.000
65A136PHE0-0.084-0.03659.7870.0000.0000.0000.0000.0000.000
66A137MET00.0120.02960.095-0.001-0.0010.0000.0000.0000.000
67A138LEU0-0.052-0.01462.541-0.001-0.0010.0000.0000.0000.000
68A139LYS10.8370.91262.5390.0070.0070.0000.0000.0000.000
69A140ASP-1-0.790-0.87758.327-0.017-0.0170.0000.0000.0000.000
70A141ASN00.0770.02560.0110.0000.0000.0000.0000.0000.000
71A142ARG10.8400.91554.7690.0160.0160.0000.0000.0000.000
72A143LEU0-0.0010.00954.896-0.002-0.0020.0000.0000.0000.000
73A144ARG10.8000.86656.8880.0220.0220.0000.0000.0000.000
74A145ARG10.8010.85950.6600.0440.0440.0000.0000.0000.000
75A146LEU0-0.022-0.00250.515-0.004-0.0040.0000.0000.0000.000
76A147PHE00.0180.00153.740-0.003-0.0030.0000.0000.0000.000
77A148TYR0-0.020-0.02256.163-0.002-0.0020.0000.0000.0000.000
78A149SER00.029-0.02551.435-0.002-0.0020.0000.0000.0000.000
79A150SER0-0.077-0.03051.605-0.005-0.0050.0000.0000.0000.000
80A151LEU0-0.029-0.01852.633-0.002-0.0020.0000.0000.0000.000
81A152ASN0-0.027-0.01550.811-0.002-0.0020.0000.0000.0000.000
82A153TYR0-0.0040.00253.132-0.001-0.0010.0000.0000.0000.000
83A154ASP-1-0.815-0.90456.191-0.057-0.0570.0000.0000.0000.000
84A155GLU-1-0.863-0.95358.468-0.047-0.0470.0000.0000.0000.000
85A156ASN0-0.036-0.00961.6920.0050.0050.0000.0000.0000.000
86A157LYS10.8160.89356.4530.0620.0620.0000.0000.0000.000
87A158ILE0-0.0140.01158.1880.0030.0030.0000.0000.0000.000
88A159LYS10.9420.99662.0460.0350.0350.0000.0000.0000.000
89A160LYS10.7870.88865.1060.0450.0450.0000.0000.0000.000
90A161LEU00.0340.01360.6490.0020.0020.0000.0000.0000.000
91A162ALA00.0070.00764.7000.0020.0020.0000.0000.0000.000
92A163THR0-0.038-0.05166.4180.0020.0020.0000.0000.0000.000
93A164ILE0-0.0070.01366.5650.0010.0010.0000.0000.0000.000
94A165LEU00.0190.00263.3550.0020.0020.0000.0000.0000.000
95A166ALA0-0.0050.01168.0630.0020.0020.0000.0000.0000.000
96A167GLN0-0.039-0.00571.1390.0010.0010.0000.0000.0000.000
97A168THR0-0.048-0.02468.5720.0010.0010.0000.0000.0000.000
98A169SER0-0.023-0.02872.0180.0010.0010.0000.0000.0000.000
99A170SER00.015-0.02172.5530.0000.0000.0000.0000.0000.000
100A171SER0-0.044-0.03474.7020.0000.0000.0000.0000.0000.000
101A172ASN00.0250.00971.6710.0000.0000.0000.0000.0000.000
102A173ASP-1-0.748-0.86972.589-0.007-0.0070.0000.0000.0000.000
103A174TYR0-0.039-0.03264.0170.0000.0000.0000.0000.0000.000
104A175HIS00.0650.07067.9840.0000.0000.0000.0000.0000.000
105A176TYR00.001-0.01067.863-0.001-0.0010.0000.0000.0000.000
106A177THR00.0270.01364.0770.0000.0000.0000.0000.0000.000
107A178LEU00.0050.01262.797-0.001-0.0010.0000.0000.0000.000
108A179ILE0-0.014-0.00862.973-0.002-0.0020.0000.0000.0000.000
109A180GLY00.0120.00662.682-0.002-0.0020.0000.0000.0000.000
110A181LEU00.011-0.00258.782-0.001-0.0010.0000.0000.0000.000
111A182ILE00.0010.01658.207-0.002-0.0020.0000.0000.0000.000
112A183PHE00.004-0.02158.112-0.002-0.0020.0000.0000.0000.000
113A184TRP00.0580.01453.308-0.001-0.0010.0000.0000.0000.000
114A185THR0-0.045-0.03253.426-0.001-0.0010.0000.0000.0000.000
115A186GLY00.0580.01852.966-0.002-0.0020.0000.0000.0000.000
116A187PHE0-0.004-0.01752.805-0.002-0.0020.0000.0000.0000.000
117A188LYS10.8020.88650.7900.0120.0120.0000.0000.0000.000
118A189ILE0-0.0010.00748.006-0.001-0.0010.0000.0000.0000.000
119A190GLN0-0.023-0.01547.631-0.005-0.0050.0000.0000.0000.000
120A191GLU-1-0.813-0.88747.773-0.019-0.0190.0000.0000.0000.000
121A192ALA00.0210.02044.5730.0000.0000.0000.0000.0000.000
122A193PHE0-0.014-0.01243.459-0.003-0.0030.0000.0000.0000.000
123A194GLU-1-0.694-0.82143.132-0.055-0.0550.0000.0000.0000.000
124A195SER0-0.021-0.00742.831-0.001-0.0010.0000.0000.0000.000
125A196ALA00.0180.00539.185-0.001-0.0010.0000.0000.0000.000
126A197VAL0-0.042-0.02238.658-0.007-0.0070.0000.0000.0000.000
127A198ASN0-0.079-0.05039.438-0.007-0.0070.0000.0000.0000.000
128A199ILE00.0100.02635.5690.0000.0000.0000.0000.0000.000
129A200LEU0-0.0110.00833.431-0.004-0.0040.0000.0000.0000.000
130A201THR00.0330.01535.054-0.018-0.0180.0000.0000.0000.000
131A202LYS10.8840.90433.4380.1440.1440.0000.0000.0000.000
132A203ASP-1-0.875-0.93231.071-0.146-0.1460.0000.0000.0000.000
133A204GLU-1-0.774-0.86530.003-0.059-0.0590.0000.0000.0000.000
134A205GLN0-0.051-0.03429.573-0.022-0.0220.0000.0000.0000.000
135A206LYS10.8670.92027.0400.1420.1420.0000.0000.0000.000
136A207ARG10.7980.88125.5400.0050.0050.0000.0000.0000.000
137A208LEU0-0.036-0.02424.9390.0000.0000.0000.0000.0000.000
138A209ILE0-0.009-0.00722.491-0.012-0.0120.0000.0000.0000.000
139A210PHE0-0.006-0.00620.213-0.038-0.0380.0000.0000.0000.000
140A211ASN0-0.073-0.04020.2420.0250.0250.0000.0000.0000.000
141A212PHE0-0.0130.01121.8880.0500.0500.0000.0000.0000.000
142A213ARG10.9290.96920.029-0.044-0.0440.0000.0000.0000.000
143A214THR00.0660.00520.6140.0180.0180.0000.0000.0000.000
144A215LYS10.7830.88422.4360.0510.0510.0000.0000.0000.000
145A216THR0-0.010-0.02924.6930.0180.0180.0000.0000.0000.000
146A217VAL00.0160.03324.4760.0130.0130.0000.0000.0000.000
147A218LYS10.8640.92326.5640.1690.1690.0000.0000.0000.000
148A219GLU-1-0.829-0.88628.457-0.029-0.0290.0000.0000.0000.000
149A220ILE00.0430.03129.2730.0090.0090.0000.0000.0000.000
150A221GLN00.007-0.00930.382-0.004-0.0040.0000.0000.0000.000
151A222GLU-1-0.823-0.90831.319-0.146-0.1460.0000.0000.0000.000
152A223ASN0-0.078-0.04234.1860.0150.0150.0000.0000.0000.000
153A224PHE00.0690.02735.6540.0050.0050.0000.0000.0000.000
154A225GLU-1-0.743-0.86834.499-0.162-0.1620.0000.0000.0000.000
155A226LYS10.8800.94135.8770.0910.0910.0000.0000.0000.000
156A227LEU00.0170.02140.1670.0040.0040.0000.0000.0000.000
157A228MET0-0.0190.00139.8740.0010.0010.0000.0000.0000.000
158A229GLN0-0.0120.00042.536-0.002-0.0020.0000.0000.0000.000
159A230GLU-1-0.792-0.87144.344-0.041-0.0410.0000.0000.0000.000
160A231ARG10.8400.90446.1040.0720.0720.0000.0000.0000.000
161A232ASN0-0.015-0.01545.2890.0040.0040.0000.0000.0000.000
162A233SER0-0.051-0.02947.763-0.001-0.0010.0000.0000.0000.000
163A234TRP00.0360.01550.2930.0040.0040.0000.0000.0000.000
164A235ILE0-0.0050.00450.8070.0020.0020.0000.0000.0000.000
165A236LYS10.8860.94149.7710.0760.0760.0000.0000.0000.000
166A237ILE00.0180.03453.4070.0010.0010.0000.0000.0000.000
167A238VAL00.0230.01656.6440.0020.0020.0000.0000.0000.000
168A239ASP-1-0.814-0.89556.807-0.056-0.0560.0000.0000.0000.000
169A240ASN0-0.083-0.04757.3580.0010.0010.0000.0000.0000.000
170A241ILE00.0150.01460.1980.0020.0020.0000.0000.0000.000
171A242ILE0-0.042-0.02461.4910.0020.0020.0000.0000.0000.000
172A243GLY00.0450.01763.0740.0010.0010.0000.0000.0000.000
173A244GLU-1-0.807-0.85264.028-0.037-0.0370.0000.0000.0000.000
174A245TYR00.0370.00966.8070.0000.0000.0000.0000.0000.000
175A246ASP-1-0.812-0.89266.674-0.042-0.0420.0000.0000.0000.000
176A247LYS10.8270.89664.1530.0410.0410.0000.0000.0000.000
177A248ASN0-0.0100.00269.5380.0020.0020.0000.0000.0000.000
178A249THR00.013-0.01967.7120.0010.0010.0000.0000.0000.000
179A250GLY00.0230.00870.9560.0010.0010.0000.0000.0000.000
180A251GLY0-0.0030.00473.8950.0010.0010.0000.0000.0000.000
181A252CYS0-0.088-0.03171.4310.0000.0000.0000.0000.0000.000
182A253LYS10.8460.91771.9590.0350.0350.0000.0000.0000.000
183A254ALA0-0.043-0.01475.1030.0000.0000.0000.0000.0000.000
184A255ASP-1-0.842-0.90776.768-0.017-0.0170.0000.0000.0000.000
185A256GLY00.1050.04374.423-0.001-0.0010.0000.0000.0000.000
186A257LYS10.8570.91873.4770.0120.0120.0000.0000.0000.000
187A258ILE0-0.030-0.00273.3200.0000.0000.0000.0000.0000.000
188A259LEU0-0.020-0.01269.412-0.001-0.0010.0000.0000.0000.000
189A260GLY00.0210.00969.375-0.001-0.0010.0000.0000.0000.000
190A261GLU-1-0.803-0.87268.446-0.015-0.0150.0000.0000.0000.000
191A262VAL0-0.033-0.01167.516-0.001-0.0010.0000.0000.0000.000
192A263ILE0-0.001-0.00663.932-0.001-0.0010.0000.0000.0000.000
193A264ARG10.7610.85263.8000.0130.0130.0000.0000.0000.000
194A265VAL0-0.009-0.01163.6090.0000.0000.0000.0000.0000.000
195A266GLY0-0.0030.01463.265-0.001-0.0010.0000.0000.0000.000
196A267TYR0-0.033-0.06258.749-0.002-0.0020.0000.0000.0000.000
197A268GLU-1-0.816-0.88759.113-0.013-0.0130.0000.0000.0000.000
198A269HIS10.7460.84557.3710.0280.0280.0000.0000.0000.000
199A270GLU-1-0.828-0.89754.324-0.033-0.0330.0000.0000.0000.000
200A271LEU0-0.086-0.02754.176-0.003-0.0030.0000.0000.0000.000
201A272ASP-1-0.778-0.88449.420-0.020-0.0200.0000.0000.0000.000
202A273SER00.0140.01149.950-0.003-0.0030.0000.0000.0000.000
203A274ASN0-0.044-0.02948.5750.0020.0020.0000.0000.0000.000
204A275LYS10.8220.90044.7080.0390.0390.0000.0000.0000.000
205A276SER00.003-0.01744.127-0.003-0.0030.0000.0000.0000.000
206A277MET00.0000.00243.801-0.001-0.0010.0000.0000.0000.000
207A278GLN0-0.0110.00239.7350.0060.0060.0000.0000.0000.000
208A279ILE0-0.042-0.02839.2090.0010.0010.0000.0000.0000.000
209A280LEU0-0.0060.01538.948-0.006-0.0060.0000.0000.0000.000
210A281ASN00.0270.01038.7260.0030.0030.0000.0000.0000.000
211A282ASN0-0.045-0.01136.1550.0150.0150.0000.0000.0000.000
212A283ILE0-0.036-0.00634.548-0.004-0.0040.0000.0000.0000.000
213A284GLU-1-0.854-0.94934.054-0.011-0.0110.0000.0000.0000.000
214A285THR0-0.104-0.07334.5620.0100.0100.0000.0000.0000.000
215A286PRO0-0.0130.00329.6510.0160.0160.0000.0000.0000.000
216A287LEU00.0640.04029.8860.0080.0080.0000.0000.0000.000
217A288LYS10.9370.99531.204-0.054-0.0540.0000.0000.0000.000
218A289THR0-0.104-0.05426.1300.0150.0150.0000.0000.0000.000