Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 53K5Z

Calculation Name: 4UY3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4UY3

Chain ID: A

ChEMBL ID:

UniProt ID: A7X3E7

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1929434.790622
FMO2-HF: Nuclear repulsion 1848985.481925
FMO2-HF: Total energy -80449.308698
FMO2-MP2: Total energy -80682.602125


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:23:MET)


Summations of interaction energy for fragment #1(A:23:MET)
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.
-17.486-22.24126.979-9.289-12.9350.005
Interaction energy analysis for fragmet #1(A:23:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : 0.029
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].
3A25SER00.0170.0183.220-2.687-0.4500.000-0.984-1.2530.000
4A26ASN00.021-0.0022.360-0.842-0.5923.788-1.409-2.629-0.018
5A27LYS10.9270.9322.227-11.712-20.88720.430-5.869-5.3860.036
6A28ARG10.8850.9415.1791.0111.149-0.001-0.010-0.1270.000
7A29GLN00.0570.0287.7090.0190.0190.0000.0000.0000.000
8A30ILE0-0.046-0.0137.4840.1740.1740.0000.0000.0000.000
9A31ILE00.0230.0169.1530.0680.0680.0000.0000.0000.000
10A32GLU-1-0.919-0.97411.243-0.788-0.7880.0000.0000.0000.000
11A33LYS10.9921.00013.1710.1620.1620.0000.0000.0000.000
12A34ALA0-0.0040.00314.5890.0430.0430.0000.0000.0000.000
13A35ILE00.008-0.00215.5310.0190.0190.0000.0000.0000.000
14A36GLU-1-0.978-0.98817.053-0.241-0.2410.0000.0000.0000.000
15A37ARG10.7510.83119.018-0.014-0.0140.0000.0000.0000.000
16A38LYS10.8330.88920.4220.0690.0690.0000.0000.0000.000
17A39ASN0-0.035-0.02821.6710.0160.0160.0000.0000.0000.000
18A40GLU-1-0.945-0.96422.512-0.070-0.0700.0000.0000.0000.000
19A41ILE00.0140.01424.1720.0090.0090.0000.0000.0000.000
20A42GLU-1-0.863-0.91226.304-0.045-0.0450.0000.0000.0000.000
21A43THR0-0.132-0.07628.667-0.001-0.0010.0000.0000.0000.000
22A44LEU00.0070.01828.9970.0010.0010.0000.0000.0000.000
23A45PRO0-0.0160.00532.1160.0020.0020.0000.0000.0000.000
24A46PHE00.0370.00231.9630.0030.0030.0000.0000.0000.000
25A47ASP-1-0.854-0.92137.223-0.010-0.0100.0000.0000.0000.000
26A48GLN0-0.003-0.01237.7830.0030.0030.0000.0000.0000.000
27A49ASN00.0200.00439.3470.0000.0000.0000.0000.0000.000
28A50LEU00.0410.02140.9710.0010.0010.0000.0000.0000.000
29A51ALA0-0.046-0.02343.4730.0010.0010.0000.0000.0000.000
30A52GLN0-0.0330.00242.883-0.001-0.0010.0000.0000.0000.000
31A53LEU00.0550.02646.5070.0000.0000.0000.0000.0000.000
32A54SER0-0.109-0.07848.7530.0000.0000.0000.0000.0000.000
33A55LYS10.8540.92848.8040.0130.0130.0000.0000.0000.000
34A56LEU00.0310.03850.7730.0000.0000.0000.0000.0000.000
35A57ASN00.003-0.00453.971-0.001-0.0010.0000.0000.0000.000
36A58LEU0-0.0180.01250.0490.0010.0010.0000.0000.0000.000
37A59LYS10.7780.86253.9650.0000.0000.0000.0000.0000.000
38A60GLY00.0870.04655.0350.0000.0000.0000.0000.0000.000
39A61GLU-1-0.778-0.86953.5020.0090.0090.0000.0000.0000.000
40A62THR00.0320.02151.0760.0010.0010.0000.0000.0000.000
41A63LYS10.8070.88150.1420.0000.0000.0000.0000.0000.000
42A64THR0-0.033-0.02649.8090.0000.0000.0000.0000.0000.000
43A65LYS10.8750.92143.262-0.013-0.0130.0000.0000.0000.000
44A66TYR00.0100.00045.8450.0000.0000.0000.0000.0000.000
45A67ASP-1-0.835-0.90945.0620.0010.0010.0000.0000.0000.000
46A68ALA0-0.0170.00044.8620.0000.0000.0000.0000.0000.000
47A69MET00.0100.03141.2570.0010.0010.0000.0000.0000.000
48A70LYS10.8380.92040.3590.0070.0070.0000.0000.0000.000
49A71LYS10.7800.87740.111-0.018-0.0180.0000.0000.0000.000
50A72ASP-1-0.833-0.92338.6640.0170.0170.0000.0000.0000.000
51A73ASN00.0290.01735.8680.0040.0040.0000.0000.0000.000
52A74VAL0-0.0180.01634.970-0.001-0.0010.0000.0000.0000.000
53A75GLU-1-0.829-0.90734.8070.0200.0200.0000.0000.0000.000
54A76SER0-0.020-0.02332.6160.0050.0050.0000.0000.0000.000
55A77THR00.012-0.00530.7640.0010.0010.0000.0000.0000.000
56A78ASN0-0.073-0.05529.757-0.001-0.0010.0000.0000.0000.000
57A79LYS10.8710.94029.803-0.047-0.0470.0000.0000.0000.000
58A80TYR0-0.005-0.00426.9240.0110.0110.0000.0000.0000.000
59A81LEU00.0460.03624.9790.0020.0020.0000.0000.0000.000
60A82ALA0-0.007-0.00525.100-0.003-0.0030.0000.0000.0000.000
61A83PRO0-0.009-0.01024.058-0.004-0.0040.0000.0000.0000.000
62A84VAL00.0000.00820.2720.0060.0060.0000.0000.0000.000
63A85GLU-1-0.883-0.93919.721-0.054-0.0540.0000.0000.0000.000
64A86GLU-1-0.958-0.97519.6800.0230.0230.0000.0000.0000.000
65A87LYS10.7610.85517.908-0.128-0.1280.0000.0000.0000.000
66A88ILE00.0330.00915.3410.0070.0070.0000.0000.0000.000
67A89HIS0-0.056-0.02514.551-0.008-0.0080.0000.0000.0000.000
68A90ASN0-0.014-0.02515.094-0.020-0.0200.0000.0000.0000.000
69A91ALA00.0240.01911.3100.0160.0160.0000.0000.0000.000
70A92GLU-1-0.882-0.92010.394-0.247-0.2470.0000.0000.0000.000
71A93ALA00.0040.00410.834-0.017-0.0170.0000.0000.0000.000
72A94LEU0-0.026-0.02110.9330.0300.0300.0000.0000.0000.000
73A95LEU0-0.046-0.0034.207-0.209-0.070-0.001-0.025-0.1120.000
74A96ASP-1-0.756-0.8586.972-0.102-0.1020.0000.0000.0000.000
75A97LYS10.8620.9449.165-0.009-0.0090.0000.0000.0000.000
76A98PHE0-0.011-0.0204.5220.0540.185-0.001-0.006-0.1240.000
77A99SER0-0.0240.0096.7880.0070.0070.0000.0000.0000.000
78A100PHE0-0.005-0.0262.647-3.024-1.4992.764-0.986-3.304-0.013
79A101ASN00.0240.0096.4410.2810.2810.0000.0000.0000.000
80A102ALA00.0380.0389.442-0.044-0.0440.0000.0000.0000.000
81A103SER0-0.048-0.0478.040-0.043-0.0430.0000.0000.0000.000
82A104GLN0-0.064-0.0518.7020.1380.1380.0000.0000.0000.000
83A105SER00.021-0.00110.356-0.075-0.0750.0000.0000.0000.000
84A106GLU-1-0.821-0.88213.5160.0970.0970.0000.0000.0000.000
85A107ILE0-0.003-0.00811.529-0.055-0.0550.0000.0000.0000.000
86A108ASP-1-0.853-0.91314.0480.4440.4440.0000.0000.0000.000
87A109ASP-1-0.800-0.88716.0660.1390.1390.0000.0000.0000.000
88A110ALA0-0.026-0.01617.048-0.024-0.0240.0000.0000.0000.000
89A111ASN0-0.044-0.02916.161-0.046-0.0460.0000.0000.0000.000
90A112GLU-1-0.891-0.92319.5080.1230.1230.0000.0000.0000.000
91A113LEU0-0.053-0.01621.562-0.016-0.0160.0000.0000.0000.000
92A114MET00.0020.00518.671-0.019-0.0190.0000.0000.0000.000
93A115ASP-1-0.816-0.89022.6810.0770.0770.0000.0000.0000.000
94A116SER0-0.060-0.03925.148-0.006-0.0060.0000.0000.0000.000
95A117TYR0-0.038-0.02527.019-0.006-0.0060.0000.0000.0000.000
96A118GLU-1-0.793-0.86724.7220.0020.0020.0000.0000.0000.000
97A119GLN0-0.004-0.00329.018-0.003-0.0030.0000.0000.0000.000
98A120SER0-0.076-0.05531.140-0.003-0.0030.0000.0000.0000.000
99A121TYR00.0230.00132.165-0.004-0.0040.0000.0000.0000.000
100A122GLN0-0.015-0.01431.169-0.003-0.0030.0000.0000.0000.000
101A123GLN0-0.057-0.03134.6930.0020.0020.0000.0000.0000.000
102A124GLN00.0310.00036.990-0.005-0.0050.0000.0000.0000.000
103A125LEU0-0.0010.01735.545-0.003-0.0030.0000.0000.0000.000
104A126GLU-1-0.920-0.93639.0560.0200.0200.0000.0000.0000.000
105A127ASP-1-0.777-0.88040.9060.0160.0160.0000.0000.0000.000
106A128VAL0-0.043-0.02942.670-0.001-0.0010.0000.0000.0000.000
107A129ASN0-0.058-0.04442.040-0.002-0.0020.0000.0000.0000.000
108A130GLU-1-0.942-0.95345.1220.0130.0130.0000.0000.0000.000
109A131ILE0-0.010-0.00246.917-0.001-0.0010.0000.0000.0000.000
110A132ILE0-0.010-0.01346.123-0.001-0.0010.0000.0000.0000.000
111A133ALA0-0.0070.00448.947-0.001-0.0010.0000.0000.0000.000
112A134LEU00.0160.00550.7560.0000.0000.0000.0000.0000.000
113A135TYR0-0.027-0.03952.853-0.001-0.0010.0000.0000.0000.000
114A136LYS10.7700.88353.038-0.002-0.0020.0000.0000.0000.000
115A137ASP-1-0.840-0.92454.2590.0040.0040.0000.0000.0000.000
116A138ASN0-0.030-0.02256.6090.0010.0010.0000.0000.0000.000
117A139ASP-1-0.717-0.83758.7530.0000.0000.0000.0000.0000.000
118A140GLU-1-0.853-0.90157.1640.0000.0000.0000.0000.0000.000
119A141LEU0-0.033-0.01559.5100.0000.0000.0000.0000.0000.000
120A142TYR0-0.026-0.03862.5710.0000.0000.0000.0000.0000.000
121A143ASP-1-0.868-0.93663.916-0.001-0.0010.0000.0000.0000.000
122A144LYS10.8380.91264.981-0.004-0.0040.0000.0000.0000.000
123A145CYS0-0.055-0.02166.1260.0000.0000.0000.0000.0000.000
124A146LYS10.9040.94466.7900.0000.0000.0000.0000.0000.000
125A147VAL0-0.0410.00269.398-0.001-0.0010.0000.0000.0000.000
126A148ASP-1-0.759-0.86570.0470.0040.0040.0000.0000.0000.000
127A149TYR0-0.030-0.04972.4420.0000.0000.0000.0000.0000.000
128A150ARG10.8720.91872.4170.0000.0000.0000.0000.0000.000
129A151GLU-1-0.898-0.93373.8470.0020.0020.0000.0000.0000.000
130A152MET0-0.010-0.00475.0310.0000.0000.0000.0000.0000.000
131A153LYS10.8190.89878.319-0.002-0.0020.0000.0000.0000.000
132A154ARG10.8550.92080.168-0.001-0.0010.0000.0000.0000.000
133A155ASP-1-0.829-0.91180.6160.0020.0020.0000.0000.0000.000
134A156VAL00.0350.01182.1790.0000.0000.0000.0000.0000.000
135A157LEU0-0.042-0.02284.1340.0000.0000.0000.0000.0000.000
136A158ALA0-0.065-0.02685.8330.0000.0000.0000.0000.0000.000
137A159ASN0-0.047-0.03184.2630.0000.0000.0000.0000.0000.000
138A160ARG10.8610.91687.672-0.003-0.0030.0000.0000.0000.000
139A161HIS0-0.009-0.00989.2900.0000.0000.0000.0000.0000.000
140A162GLN0-0.030-0.01284.7790.0000.0000.0000.0000.0000.000
141A163PHE0-0.0020.00982.5320.0000.0000.0000.0000.0000.000
142A164GLY0-0.0120.00187.7350.0000.0000.0000.0000.0000.000
143A165GLU-1-0.945-0.98790.6130.0050.0050.0000.0000.0000.000
144A166ALA0-0.0070.00085.8300.0000.0000.0000.0000.0000.000
145A167ALA00.0220.02086.2350.0000.0000.0000.0000.0000.000
146A168SER00.0420.01086.3790.0000.0000.0000.0000.0000.000
147A169LEU0-0.0140.01784.4840.0000.0000.0000.0000.0000.000
148A170LEU00.0370.01581.3450.0000.0000.0000.0000.0000.000
149A171GLU-1-0.847-0.90781.7320.0030.0030.0000.0000.0000.000
150A172THR0-0.018-0.02682.7340.0000.0000.0000.0000.0000.000
151A173GLU-1-0.871-0.90078.4680.0060.0060.0000.0000.0000.000
152A174ILE00.008-0.00577.8540.0000.0000.0000.0000.0000.000
153A175GLU-1-0.808-0.89077.7320.0020.0020.0000.0000.0000.000
154A176LYS10.7470.84176.666-0.005-0.0050.0000.0000.0000.000
155A177PHE0-0.011-0.01973.3910.0000.0000.0000.0000.0000.000
156A178GLU-1-0.803-0.85173.2360.0010.0010.0000.0000.0000.000
157A179PRO00.0380.02073.6840.0000.0000.0000.0000.0000.000
158A180ARG10.8410.92268.755-0.006-0.0060.0000.0000.0000.000
159A181LEU00.0080.01469.1180.0000.0000.0000.0000.0000.000
160A182GLU-1-0.901-0.95568.7970.0010.0010.0000.0000.0000.000
161A183GLN0-0.004-0.02568.2490.0000.0000.0000.0000.0000.000
162A184TYR0-0.028-0.03360.9770.0010.0010.0000.0000.0000.000
163A185GLU-1-0.749-0.85164.065-0.001-0.0010.0000.0000.0000.000
164A186VAL0-0.028-0.00564.5090.0000.0000.0000.0000.0000.000
165A187LEU0-0.016-0.00761.8230.0000.0000.0000.0000.0000.000
166A188LYS10.8160.90159.8710.0010.0010.0000.0000.0000.000
167A189ALA0-0.0010.01559.698-0.001-0.0010.0000.0000.0000.000
168A190ASP-1-0.900-0.95360.5960.0010.0010.0000.0000.0000.000
169A191GLY00.0020.00556.6400.0000.0000.0000.0000.0000.000
170A192ASN0-0.031-0.00655.7870.0010.0010.0000.0000.0000.000
171A193TYR00.0800.02449.8230.0000.0000.0000.0000.0000.000
172A194VAL00.0400.03153.0830.0000.0000.0000.0000.0000.000
173A195GLN0-0.091-0.06656.0270.0000.0000.0000.0000.0000.000
174A196ALA00.000-0.00359.2580.0000.0000.0000.0000.0000.000
175A197HIS0-0.0060.00956.5080.0010.0010.0000.0000.0000.000
176A198ASN00.000-0.01157.6600.0000.0000.0000.0000.0000.000
177A199HIS0-0.089-0.04260.7620.0010.0010.0000.0000.0000.000
178A200ILE00.001-0.00161.3790.0000.0000.0000.0000.0000.000
179A201ALA00.0260.01860.6640.0000.0000.0000.0000.0000.000
180A202ALA0-0.021-0.01462.8190.0000.0000.0000.0000.0000.000
181A203LEU0-0.025-0.01465.7340.0000.0000.0000.0000.0000.000
182A204ASN00.0860.02663.793-0.001-0.0010.0000.0000.0000.000
183A205GLU-1-0.825-0.86965.2290.0090.0090.0000.0000.0000.000
184A206GLN00.0390.01967.2830.0000.0000.0000.0000.0000.000
185A207MET0-0.0380.00270.3100.0000.0000.0000.0000.0000.000
186A208LYS10.8300.90465.172-0.009-0.0090.0000.0000.0000.000
187A209GLN0-0.055-0.04568.3980.0000.0000.0000.0000.0000.000
188A210LEU00.0130.00972.4970.0000.0000.0000.0000.0000.000
189A211ARG10.8110.86371.329-0.004-0.0040.0000.0000.0000.000
190A212SER0-0.021-0.01672.4720.0000.0000.0000.0000.0000.000
191A213TYR0-0.030-0.01075.3350.0000.0000.0000.0000.0000.000
192A214MET0-0.067-0.01978.3430.0000.0000.0000.0000.0000.000
193A215HIS0-0.057-0.01575.783-0.001-0.0010.0000.0000.0000.000
194A216GLY0-0.020-0.01080.3820.0000.0000.0000.0000.0000.000