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: 434YN

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 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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1923286.64413
FMO2-HF: Nuclear repulsion 1842837.695271
FMO2-HF: Total energy -80448.948859
FMO2-MP2: Total energy -80682.139226


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.
-14.804-11.2413.747-5.903-11.406-0.015
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 : 0.007 / q_NPA : 0.007
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].
3A25SER00.0090.0082.990-3.972-1.3510.030-1.185-1.4660.000
4A26ASN0-0.004-0.0132.376-2.608-2.4104.796-1.818-3.175-0.021
5A27LYS10.9660.9762.337-7.221-8.0066.785-2.129-3.8700.015
6A28ARG10.9080.9544.6811.1481.314-0.001-0.016-0.1490.000
7A29GLN00.0670.0337.206-0.003-0.0030.0000.0000.0000.000
8A30ILE0-0.042-0.0106.7770.2110.2110.0000.0000.0000.000
9A31ILE00.013-0.0029.3450.1400.1400.0000.0000.0000.000
10A32GLU-1-0.921-0.96411.378-0.858-0.8580.0000.0000.0000.000
11A33LYS10.9851.00012.5780.4600.4600.0000.0000.0000.000
12A34ALA0-0.0010.00014.0240.0720.0720.0000.0000.0000.000
13A35ILE00.0050.00015.3240.0470.0470.0000.0000.0000.000
14A36GLU-1-0.982-0.99016.892-0.417-0.4170.0000.0000.0000.000
15A37ARG10.7770.86318.4740.1500.1500.0000.0000.0000.000
16A38LYS10.8460.90420.0800.1480.1480.0000.0000.0000.000
17A39ASN0-0.031-0.02621.5120.0300.0300.0000.0000.0000.000
18A40GLU-1-0.941-0.95622.203-0.192-0.1920.0000.0000.0000.000
19A41ILE00.0120.01723.8030.0180.0180.0000.0000.0000.000
20A42GLU-1-0.894-0.94326.292-0.103-0.1030.0000.0000.0000.000
21A43THR0-0.137-0.07728.3000.0070.0070.0000.0000.0000.000
22A44LEU00.0130.02428.4020.0020.0020.0000.0000.0000.000
23A45PRO0-0.0080.00931.5740.0070.0070.0000.0000.0000.000
24A46PHE00.038-0.00631.4340.0050.0050.0000.0000.0000.000
25A47ASP-1-0.870-0.92436.581-0.044-0.0440.0000.0000.0000.000
26A48GLN00.015-0.00837.1050.0050.0050.0000.0000.0000.000
27A49ASN00.0060.01038.5690.0020.0020.0000.0000.0000.000
28A50LEU00.0610.02540.5190.0030.0030.0000.0000.0000.000
29A51ALA0-0.047-0.02242.8100.0030.0030.0000.0000.0000.000
30A52GLN0-0.046-0.00842.3070.0010.0010.0000.0000.0000.000
31A53LEU00.0450.01845.6960.0020.0020.0000.0000.0000.000
32A54SER0-0.101-0.07648.0180.0020.0020.0000.0000.0000.000
33A55LYS10.8810.94848.3020.0420.0420.0000.0000.0000.000
34A56LEU00.0110.02950.2890.0010.0010.0000.0000.0000.000
35A57ASN0-0.014-0.01553.350-0.001-0.0010.0000.0000.0000.000
36A58LEU00.0050.01549.2490.0010.0010.0000.0000.0000.000
37A59LYS10.7720.87453.4320.0180.0180.0000.0000.0000.000
38A60GLY00.0870.05154.9980.0000.0000.0000.0000.0000.000
39A61GLU-1-0.772-0.87753.283-0.012-0.0120.0000.0000.0000.000
40A62THR00.0190.00550.787-0.001-0.0010.0000.0000.0000.000
41A63LYS10.8120.88249.8600.0190.0190.0000.0000.0000.000
42A64THR0-0.030-0.01849.6610.0000.0000.0000.0000.0000.000
43A65LYS10.8620.92042.8990.0200.0200.0000.0000.0000.000
44A66TYR00.003-0.01345.543-0.001-0.0010.0000.0000.0000.000
45A67ASP-1-0.836-0.91144.882-0.022-0.0220.0000.0000.0000.000
46A68ALA0-0.040-0.01644.7150.0000.0000.0000.0000.0000.000
47A69MET00.0210.02540.8760.0010.0010.0000.0000.0000.000
48A70LYS10.8540.92940.1060.0360.0360.0000.0000.0000.000
49A71LYS10.8030.89539.9570.0100.0100.0000.0000.0000.000
50A72ASP-1-0.834-0.91638.215-0.015-0.0150.0000.0000.0000.000
51A73ASN00.0230.01535.7470.0000.0000.0000.0000.0000.000
52A74VAL00.0000.02435.008-0.003-0.0030.0000.0000.0000.000
53A75GLU-1-0.847-0.92535.086-0.009-0.0090.0000.0000.0000.000
54A76SER0-0.032-0.03532.4340.0030.0030.0000.0000.0000.000
55A77THR0-0.003-0.00930.990-0.003-0.0030.0000.0000.0000.000
56A78ASN0-0.063-0.04630.274-0.003-0.0030.0000.0000.0000.000
57A79LYS10.8610.94730.2640.0010.0010.0000.0000.0000.000
58A80TYR00.021-0.00527.3370.0100.0100.0000.0000.0000.000
59A81LEU00.0340.03125.255-0.004-0.0040.0000.0000.0000.000
60A82ALA0-0.014-0.01025.660-0.006-0.0060.0000.0000.0000.000
61A83PRO0-0.003-0.00624.720-0.004-0.0040.0000.0000.0000.000
62A84VAL00.0040.01320.3060.0040.0040.0000.0000.0000.000
63A85GLU-1-0.880-0.93820.267-0.099-0.0990.0000.0000.0000.000
64A86GLU-1-0.949-0.96819.9410.0050.0050.0000.0000.0000.000
65A87LYS10.7630.86118.085-0.063-0.0630.0000.0000.0000.000
66A88ILE00.018-0.00115.4180.0000.0000.0000.0000.0000.000
67A89HIS0-0.0050.01115.016-0.001-0.0010.0000.0000.0000.000
68A90ASN0-0.020-0.03215.5400.0070.0070.0000.0000.0000.000
69A91ALA00.0150.00911.8480.0450.0450.0000.0000.0000.000
70A92GLU-1-0.921-0.94710.721-0.264-0.2640.0000.0000.0000.000
71A93ALA0-0.007-0.00311.1410.0450.0450.0000.0000.0000.000
72A94LEU0-0.030-0.02211.2530.0770.0770.0000.0000.0000.000
73A95LEU0-0.044-0.0064.422-0.0770.042-0.001-0.020-0.0980.000
74A96ASP-1-0.796-0.8877.2920.4210.4210.0000.0000.0000.000
75A97LYS10.8780.9499.466-0.148-0.1480.0000.0000.0000.000
76A98PHE0-0.044-0.0414.9610.1580.1580.0000.0000.0000.000
77A99SER0-0.043-0.0057.3790.0710.0710.0000.0000.0000.000
78A100PHE00.004-0.0192.452-1.946-0.7012.138-0.735-2.648-0.009
79A101ASN00.0180.0036.8540.2100.2100.0000.0000.0000.000
80A102ALA00.0530.0329.997-0.094-0.0940.0000.0000.0000.000
81A103SER0-0.036-0.0398.460-0.094-0.0940.0000.0000.0000.000
82A104GLN0-0.056-0.0449.156-0.059-0.0590.0000.0000.0000.000
83A105SER00.0050.00510.815-0.052-0.0520.0000.0000.0000.000
84A106GLU-1-0.805-0.86913.7480.0460.0460.0000.0000.0000.000
85A107ILE0-0.006-0.01411.502-0.054-0.0540.0000.0000.0000.000
86A108ASP-1-0.857-0.91814.0590.1370.1370.0000.0000.0000.000
87A109ASP-1-0.803-0.88216.1390.0710.0710.0000.0000.0000.000
88A110ALA0-0.024-0.01517.168-0.015-0.0150.0000.0000.0000.000
89A111ASN0-0.035-0.04415.445-0.031-0.0310.0000.0000.0000.000
90A112GLU-1-0.908-0.92719.1250.0420.0420.0000.0000.0000.000
91A113LEU0-0.044-0.02421.852-0.004-0.0040.0000.0000.0000.000
92A114MET0-0.023-0.01518.578-0.007-0.0070.0000.0000.0000.000
93A115ASP-1-0.817-0.88122.271-0.061-0.0610.0000.0000.0000.000
94A116SER0-0.050-0.01624.6290.0040.0040.0000.0000.0000.000
95A117TYR0-0.022-0.01426.9460.0000.0000.0000.0000.0000.000
96A118GLU-1-0.812-0.89224.149-0.110-0.1100.0000.0000.0000.000
97A119GLN0-0.005-0.00328.356-0.002-0.0020.0000.0000.0000.000
98A120SER0-0.095-0.06930.5100.0030.0030.0000.0000.0000.000
99A121TYR00.0330.00631.5680.0000.0000.0000.0000.0000.000
100A122GLN0-0.011-0.00530.5720.0040.0040.0000.0000.0000.000
101A123GLN0-0.041-0.02134.1250.0030.0030.0000.0000.0000.000
102A124GLN00.0490.01436.4080.0000.0000.0000.0000.0000.000
103A125LEU0-0.0060.00135.1100.0010.0010.0000.0000.0000.000
104A126GLU-1-0.936-0.94538.567-0.025-0.0250.0000.0000.0000.000
105A127ASP-1-0.766-0.87440.303-0.020-0.0200.0000.0000.0000.000
106A128VAL0-0.056-0.03042.0100.0020.0020.0000.0000.0000.000
107A129ASN0-0.034-0.03541.1090.0010.0010.0000.0000.0000.000
108A130GLU-1-0.961-0.95944.431-0.017-0.0170.0000.0000.0000.000
109A131ILE0-0.008-0.00846.2870.0010.0010.0000.0000.0000.000
110A132ILE0-0.025-0.02245.5450.0010.0010.0000.0000.0000.000
111A133ALA0-0.0040.00348.3050.0010.0010.0000.0000.0000.000
112A134LEU00.0440.01650.1340.0010.0010.0000.0000.0000.000
113A135TYR0-0.047-0.03552.2800.0010.0010.0000.0000.0000.000
114A136LYS10.7880.88052.2710.0260.0260.0000.0000.0000.000
115A137ASP-1-0.849-0.92153.623-0.022-0.0220.0000.0000.0000.000
116A138ASN0-0.040-0.03255.8750.0020.0020.0000.0000.0000.000
117A139ASP-1-0.749-0.85157.887-0.020-0.0200.0000.0000.0000.000
118A140GLU-1-0.859-0.89756.544-0.023-0.0230.0000.0000.0000.000
119A141LEU0-0.042-0.02259.0810.0010.0010.0000.0000.0000.000
120A142TYR0-0.026-0.05262.0200.0010.0010.0000.0000.0000.000
121A143ASP-1-0.865-0.92463.438-0.019-0.0190.0000.0000.0000.000
122A144LYS10.8510.91964.4820.0130.0130.0000.0000.0000.000
123A145CYS0-0.044-0.02565.4840.0010.0010.0000.0000.0000.000
124A146LYS10.9020.93866.3430.0180.0180.0000.0000.0000.000
125A147VAL0-0.063-0.03269.0290.0000.0000.0000.0000.0000.000
126A148ASP-1-0.742-0.83869.592-0.012-0.0120.0000.0000.0000.000
127A149TYR0-0.044-0.05072.0840.0010.0010.0000.0000.0000.000
128A150ARG10.9180.95471.8360.0150.0150.0000.0000.0000.000
129A151GLU-1-0.968-0.97673.555-0.012-0.0120.0000.0000.0000.000
130A152MET0-0.007-0.00574.5880.0000.0000.0000.0000.0000.000
131A153LYS10.8270.90877.8690.0100.0100.0000.0000.0000.000
132A154ARG10.8710.93379.7860.0100.0100.0000.0000.0000.000
133A155ASP-1-0.824-0.92080.114-0.009-0.0090.0000.0000.0000.000
134A156VAL00.0040.00381.8710.0000.0000.0000.0000.0000.000
135A157LEU0-0.049-0.02083.6400.0000.0000.0000.0000.0000.000
136A158ALA0-0.069-0.03185.3730.0000.0000.0000.0000.0000.000
137A159ASN0-0.066-0.03884.1140.0000.0000.0000.0000.0000.000
138A160ARG10.9130.95687.3140.0070.0070.0000.0000.0000.000
139A161HIS00.005-0.00788.9230.0000.0000.0000.0000.0000.000
140A162GLN0-0.053-0.01884.4140.0000.0000.0000.0000.0000.000
141A163PHE0-0.0050.00982.3630.0000.0000.0000.0000.0000.000
142A164GLY0-0.044-0.01287.4280.0000.0000.0000.0000.0000.000
143A165GLU-1-0.928-0.97890.423-0.004-0.0040.0000.0000.0000.000
144A166ALA0-0.048-0.01785.1720.0000.0000.0000.0000.0000.000
145A167ALA00.0530.02885.4490.0000.0000.0000.0000.0000.000
146A168SER00.029-0.00786.1050.0000.0000.0000.0000.0000.000
147A169LEU0-0.0070.00684.0260.0000.0000.0000.0000.0000.000
148A170LEU00.0440.02080.8570.0000.0000.0000.0000.0000.000
149A171GLU-1-0.840-0.91181.454-0.007-0.0070.0000.0000.0000.000
150A172THR0-0.034-0.02182.3790.0000.0000.0000.0000.0000.000
151A173GLU-1-0.902-0.95477.912-0.006-0.0060.0000.0000.0000.000
152A174ILE00.0050.00377.2580.0000.0000.0000.0000.0000.000
153A175GLU-1-0.794-0.88577.156-0.009-0.0090.0000.0000.0000.000
154A176LYS10.8110.89676.2190.0050.0050.0000.0000.0000.000
155A177PHE0-0.005-0.01372.7940.0000.0000.0000.0000.0000.000
156A178GLU-1-0.836-0.87772.583-0.011-0.0110.0000.0000.0000.000
157A179PRO00.0280.02073.0450.0000.0000.0000.0000.0000.000
158A180ARG10.8520.92468.1770.0070.0070.0000.0000.0000.000
159A181LEU00.0200.01968.486-0.001-0.0010.0000.0000.0000.000
160A182GLU-1-0.883-0.93968.067-0.011-0.0110.0000.0000.0000.000
161A183GLN0-0.018-0.03767.7430.0000.0000.0000.0000.0000.000
162A184TYR0-0.009-0.01960.3160.0000.0000.0000.0000.0000.000
163A185GLU-1-0.843-0.88963.611-0.017-0.0170.0000.0000.0000.000
164A186VAL0-0.034-0.01564.023-0.001-0.0010.0000.0000.0000.000
165A187LEU00.0130.00861.3910.0000.0000.0000.0000.0000.000
166A188LYS10.8540.91759.0070.0200.0200.0000.0000.0000.000
167A189ALA0-0.0030.01859.101-0.001-0.0010.0000.0000.0000.000
168A190ASP-1-0.888-0.95260.346-0.015-0.0150.0000.0000.0000.000
169A191GLY0-0.0010.00156.2020.0000.0000.0000.0000.0000.000
170A192ASN0-0.0290.00355.3860.0000.0000.0000.0000.0000.000
171A193TYR00.0860.03049.2150.0010.0010.0000.0000.0000.000
172A194VAL00.0420.02652.7650.0000.0000.0000.0000.0000.000
173A195GLN0-0.092-0.05855.5120.0010.0010.0000.0000.0000.000
174A196ALA00.0110.00458.4120.0000.0000.0000.0000.0000.000
175A197HIS0-0.0030.00956.0410.0010.0010.0000.0000.0000.000
176A198ASN0-0.011-0.02556.9490.0000.0000.0000.0000.0000.000
177A199HIS0-0.108-0.04559.9620.0010.0010.0000.0000.0000.000
178A200ILE00.012-0.00360.7050.0010.0010.0000.0000.0000.000
179A201ALA00.0200.01759.9570.0000.0000.0000.0000.0000.000
180A202ALA0-0.024-0.00862.1160.0000.0000.0000.0000.0000.000
181A203LEU0-0.007-0.00664.9190.0000.0000.0000.0000.0000.000
182A204ASN00.0620.02263.0890.0000.0000.0000.0000.0000.000
183A205GLU-1-0.821-0.86764.893-0.008-0.0080.0000.0000.0000.000
184A206GLN00.0310.01466.7380.0000.0000.0000.0000.0000.000
185A207MET0-0.0200.00969.7500.0000.0000.0000.0000.0000.000
186A208LYS10.8290.89663.9170.0090.0090.0000.0000.0000.000
187A209GLN0-0.073-0.05268.0330.0010.0010.0000.0000.0000.000
188A210LEU00.0070.00472.1130.0000.0000.0000.0000.0000.000
189A211ARG10.8690.90470.2700.0110.0110.0000.0000.0000.000
190A212SER0-0.028-0.02172.0490.0000.0000.0000.0000.0000.000
191A213TYR0-0.021-0.00674.8790.0000.0000.0000.0000.0000.000
192A214MET0-0.063-0.02077.7200.0000.0000.0000.0000.0000.000
193A215HIS0-0.058-0.01075.707-0.001-0.0010.0000.0000.0000.000
194A216GLY00.0010.00480.1420.0000.0000.0000.0000.0000.000