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: K36V3

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 OptH
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 -1921316.324091
FMO2-HF: Nuclear repulsion 1840868.957851
FMO2-HF: Total energy -80447.36624
FMO2-MP2: Total energy -80680.494391


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.
-7.694-3.4439.871-4.814-9.307-0.012
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 : 0.021 / q_NPA : 0.006
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].
3A25SER0-0.025-0.0113.168-3.960-1.6120.011-1.069-1.2910.003
4A26ASN00.0070.0012.432-2.981-2.7474.449-1.616-3.067-0.018
5A27LYS10.9950.9961.8081.1381.0035.009-1.591-3.2830.007
6A28ARG10.9950.9934.5600.6460.8530.000-0.027-0.1780.000
7A29GLN00.0710.0387.164-0.028-0.0280.0000.0000.0000.000
8A30ILE0-0.049-0.0146.2710.1900.1900.0000.0000.0000.000
9A31ILE00.0170.0039.2140.1650.1650.0000.0000.0000.000
10A32GLU-1-0.935-0.96411.290-0.567-0.5670.0000.0000.0000.000
11A33LYS10.9900.99912.4600.6130.6130.0000.0000.0000.000
12A34ALA0-0.0030.00113.7110.0800.0800.0000.0000.0000.000
13A35ILE00.0040.00015.3510.0620.0620.0000.0000.0000.000
14A36GLU-1-0.974-0.99116.787-0.429-0.4290.0000.0000.0000.000
15A37ARG10.8170.89618.2130.2940.2940.0000.0000.0000.000
16A38LYS10.9500.97019.7430.2020.2020.0000.0000.0000.000
17A39ASN0-0.027-0.02221.5690.0360.0360.0000.0000.0000.000
18A40GLU-1-0.938-0.95622.281-0.233-0.2330.0000.0000.0000.000
19A41ILE00.0120.02823.3970.0210.0210.0000.0000.0000.000
20A42GLU-1-0.935-0.98125.656-0.140-0.1400.0000.0000.0000.000
21A43THR0-0.145-0.08627.9700.0140.0140.0000.0000.0000.000
22A44LEU00.0070.01627.8590.0050.0050.0000.0000.0000.000
23A45PRO0-0.0010.01731.2040.0070.0070.0000.0000.0000.000
24A46PHE00.038-0.00531.0530.0070.0070.0000.0000.0000.000
25A47ASP-1-0.935-0.96736.117-0.072-0.0720.0000.0000.0000.000
26A48GLN00.016-0.00736.6370.0050.0050.0000.0000.0000.000
27A49ASN00.0030.01038.0620.0050.0050.0000.0000.0000.000
28A50LEU00.0550.01740.0680.0050.0050.0000.0000.0000.000
29A51ALA0-0.051-0.02442.3140.0040.0040.0000.0000.0000.000
30A52GLN0-0.044-0.00242.0780.0050.0050.0000.0000.0000.000
31A53LEU00.0530.02145.1790.0030.0030.0000.0000.0000.000
32A54SER0-0.113-0.08847.5600.0030.0030.0000.0000.0000.000
33A55LYS10.8880.95148.3450.0560.0560.0000.0000.0000.000
34A56LEU00.0140.02949.5020.0010.0010.0000.0000.0000.000
35A57ASN0-0.012-0.01152.8620.0010.0010.0000.0000.0000.000
36A58LEU00.0080.02048.7950.0000.0000.0000.0000.0000.000
37A59LYS10.8640.91752.9010.0350.0350.0000.0000.0000.000
38A60GLY00.0920.05854.376-0.001-0.0010.0000.0000.0000.000
39A61GLU-1-0.779-0.90952.558-0.036-0.0360.0000.0000.0000.000
40A62THR00.0150.00150.236-0.002-0.0020.0000.0000.0000.000
41A63LYS10.8570.93349.2270.0390.0390.0000.0000.0000.000
42A64THR0-0.014-0.00649.027-0.001-0.0010.0000.0000.0000.000
43A65LYS10.8740.94841.9820.0580.0580.0000.0000.0000.000
44A66TYR0-0.005-0.01944.906-0.002-0.0020.0000.0000.0000.000
45A67ASP-1-0.878-0.95344.269-0.046-0.0460.0000.0000.0000.000
46A68ALA0-0.057-0.02944.062-0.001-0.0010.0000.0000.0000.000
47A69MET00.0250.02540.145-0.001-0.0010.0000.0000.0000.000
48A70LYS10.9070.96939.4590.0590.0590.0000.0000.0000.000
49A71LYS10.8910.94239.3450.0460.0460.0000.0000.0000.000
50A72ASP-1-0.830-0.90037.232-0.063-0.0630.0000.0000.0000.000
51A73ASN00.0220.01235.104-0.006-0.0060.0000.0000.0000.000
52A74VAL0-0.0250.02334.389-0.005-0.0050.0000.0000.0000.000
53A75GLU-1-0.929-0.97934.429-0.057-0.0570.0000.0000.0000.000
54A76SER0-0.018-0.02331.622-0.003-0.0030.0000.0000.0000.000
55A77THR0-0.019-0.03030.304-0.009-0.0090.0000.0000.0000.000
56A78ASN0-0.032-0.03029.651-0.007-0.0070.0000.0000.0000.000
57A79LYS10.8900.97029.7380.0750.0750.0000.0000.0000.000
58A80TYR00.005-0.02526.5480.0010.0010.0000.0000.0000.000
59A81LEU00.0350.03224.727-0.012-0.0120.0000.0000.0000.000
60A82ALA0-0.019-0.01425.093-0.008-0.0080.0000.0000.0000.000
61A83PRO0-0.003-0.00324.128-0.003-0.0030.0000.0000.0000.000
62A84VAL00.0080.01319.614-0.008-0.0080.0000.0000.0000.000
63A85GLU-1-0.952-0.97519.890-0.137-0.1370.0000.0000.0000.000
64A86GLU-1-0.932-0.95819.948-0.081-0.0810.0000.0000.0000.000
65A87LYS10.8460.93817.6450.1320.1320.0000.0000.0000.000
66A88ILE00.0170.00115.029-0.034-0.0340.0000.0000.0000.000
67A89HIS00.0150.01815.198-0.007-0.0070.0000.0000.0000.000
68A90ASN0-0.005-0.02315.8300.0280.0280.0000.0000.0000.000
69A91ALA00.0110.00811.7550.0160.0160.0000.0000.0000.000
70A92GLU-1-0.925-0.96210.981-0.342-0.3420.0000.0000.0000.000
71A93ALA0-0.019-0.00111.4970.0800.0800.0000.0000.0000.000
72A94LEU0-0.008-0.01711.5080.0870.0870.0000.0000.0000.000
73A95LEU0-0.054-0.0124.681-0.122-0.013-0.001-0.018-0.0900.000
74A96ASP-1-0.938-0.9617.7390.7330.7330.0000.0000.0000.000
75A97LYS10.9230.9649.414-0.012-0.0120.0000.0000.0000.000
76A98PHE0-0.072-0.0495.4450.2020.2020.0000.0000.0000.000
77A99SER0-0.030-0.0027.690-0.035-0.0350.0000.0000.0000.000
78A100PHE0-0.013-0.0262.902-1.835-0.3470.403-0.493-1.398-0.004
79A101ASN00.0190.0057.060-0.075-0.0750.0000.0000.0000.000
80A102ALA00.0470.02910.008-0.035-0.0350.0000.0000.0000.000
81A103SER0-0.029-0.0288.670-0.078-0.0780.0000.0000.0000.000
82A104GLN0-0.029-0.0168.051-0.179-0.1790.0000.0000.0000.000
83A105SER00.0150.00710.0450.0240.0240.0000.0000.0000.000
84A106GLU-1-0.881-0.93213.490-0.135-0.1350.0000.0000.0000.000
85A107ILE0-0.014-0.01710.908-0.008-0.0080.0000.0000.0000.000
86A108ASP-1-0.908-0.95713.356-0.325-0.3250.0000.0000.0000.000
87A109ASP-1-0.830-0.91215.137-0.134-0.1340.0000.0000.0000.000
88A110ALA0-0.031-0.02116.4690.0150.0150.0000.0000.0000.000
89A111ASN0-0.020-0.02514.5510.0250.0250.0000.0000.0000.000
90A112GLU-1-0.895-0.92118.319-0.123-0.1230.0000.0000.0000.000
91A113LEU0-0.054-0.03020.9240.0180.0180.0000.0000.0000.000
92A114MET0-0.027-0.01718.1590.0140.0140.0000.0000.0000.000
93A115ASP-1-0.828-0.88621.400-0.208-0.2080.0000.0000.0000.000
94A116SER0-0.052-0.01423.8340.0170.0170.0000.0000.0000.000
95A117TYR0-0.024-0.01126.1810.0100.0100.0000.0000.0000.000
96A118GLU-1-0.866-0.94724.059-0.192-0.1920.0000.0000.0000.000
97A119GLN0-0.011-0.00327.6970.0030.0030.0000.0000.0000.000
98A120SER0-0.091-0.05629.7480.0110.0110.0000.0000.0000.000
99A121TYR00.0470.01431.0250.0090.0090.0000.0000.0000.000
100A122GLN0-0.012-0.00830.3010.0130.0130.0000.0000.0000.000
101A123GLN0-0.0050.00433.4600.0020.0020.0000.0000.0000.000
102A124GLN00.044-0.00335.7310.0060.0060.0000.0000.0000.000
103A125LEU0-0.034-0.01334.7620.0050.0050.0000.0000.0000.000
104A126GLU-1-0.974-0.97137.889-0.073-0.0730.0000.0000.0000.000
105A127ASP-1-0.768-0.89439.625-0.062-0.0620.0000.0000.0000.000
106A128VAL0-0.071-0.03741.3660.0050.0050.0000.0000.0000.000
107A129ASN00.009-0.00340.2280.0040.0040.0000.0000.0000.000
108A130GLU-1-0.954-0.95643.801-0.051-0.0510.0000.0000.0000.000
109A131ILE0-0.019-0.01645.7140.0030.0030.0000.0000.0000.000
110A132ILE0-0.030-0.02445.0750.0030.0030.0000.0000.0000.000
111A133ALA0-0.011-0.00147.6770.0020.0020.0000.0000.0000.000
112A134LEU00.0530.01849.5130.0020.0020.0000.0000.0000.000
113A135TYR0-0.063-0.04351.7270.0030.0030.0000.0000.0000.000
114A136LYS10.9120.96451.3650.0480.0480.0000.0000.0000.000
115A137ASP-1-0.879-0.94053.358-0.043-0.0430.0000.0000.0000.000
116A138ASN0-0.055-0.03955.2400.0020.0020.0000.0000.0000.000
117A139ASP-1-0.805-0.89357.287-0.035-0.0350.0000.0000.0000.000
118A140GLU-1-0.923-0.94556.045-0.040-0.0400.0000.0000.0000.000
119A141LEU0-0.050-0.03058.5100.0020.0020.0000.0000.0000.000
120A142TYR00.0260.01261.3630.0020.0020.0000.0000.0000.000
121A143ASP-1-0.920-0.95962.385-0.032-0.0320.0000.0000.0000.000
122A144LYS10.8580.93763.8990.0300.0300.0000.0000.0000.000
123A145CYS0-0.006-0.00664.8650.0010.0010.0000.0000.0000.000
124A146LYS10.9480.97166.4920.0300.0300.0000.0000.0000.000
125A147VAL0-0.062-0.03068.2850.0010.0010.0000.0000.0000.000
126A148ASP-1-0.810-0.91068.469-0.026-0.0260.0000.0000.0000.000
127A149TYR0-0.015-0.00871.4580.0010.0010.0000.0000.0000.000
128A150ARG10.9280.95771.3910.0260.0260.0000.0000.0000.000
129A151GLU-1-0.953-0.97672.907-0.024-0.0240.0000.0000.0000.000
130A152MET00.0100.01273.9850.0000.0000.0000.0000.0000.000
131A153LYS10.9720.99777.2290.0200.0200.0000.0000.0000.000
132A154ARG10.9380.96479.1490.0200.0200.0000.0000.0000.000
133A155ASP-1-0.903-0.95579.511-0.019-0.0190.0000.0000.0000.000
134A156VAL00.0400.01681.4070.0010.0010.0000.0000.0000.000
135A157LEU0-0.069-0.03282.8850.0000.0000.0000.0000.0000.000
136A158ALA0-0.074-0.03484.7930.0000.0000.0000.0000.0000.000
137A159ASN0-0.079-0.03583.7600.0010.0010.0000.0000.0000.000
138A160ARG10.9841.00186.7280.0160.0160.0000.0000.0000.000
139A161HIS00.007-0.00888.2900.0000.0000.0000.0000.0000.000
140A162GLN0-0.047-0.01083.9500.0000.0000.0000.0000.0000.000
141A163PHE00.0080.01181.6320.0000.0000.0000.0000.0000.000
142A164GLY0-0.051-0.01686.8220.0000.0000.0000.0000.0000.000
143A165GLU-1-0.932-0.98289.744-0.013-0.0130.0000.0000.0000.000
144A166ALA0-0.042-0.01284.4250.0000.0000.0000.0000.0000.000
145A167ALA00.0530.02684.7200.0000.0000.0000.0000.0000.000
146A168SER00.020-0.01685.3500.0000.0000.0000.0000.0000.000
147A169LEU0-0.018-0.00383.2630.0000.0000.0000.0000.0000.000
148A170LEU00.0460.02280.2460.0000.0000.0000.0000.0000.000
149A171GLU-1-0.891-0.94980.703-0.017-0.0170.0000.0000.0000.000
150A172THR0-0.049-0.02381.6550.0000.0000.0000.0000.0000.000
151A173GLU-1-0.951-0.98977.184-0.019-0.0190.0000.0000.0000.000
152A174ILE0-0.013-0.00776.490-0.001-0.0010.0000.0000.0000.000
153A175GLU-1-0.869-0.92776.443-0.020-0.0200.0000.0000.0000.000
154A176LYS10.8770.93275.3950.0180.0180.0000.0000.0000.000
155A177PHE0-0.020-0.02472.080-0.001-0.0010.0000.0000.0000.000
156A178GLU-1-0.927-0.95071.885-0.022-0.0220.0000.0000.0000.000
157A179PRO00.0220.01572.378-0.001-0.0010.0000.0000.0000.000
158A180ARG10.8430.91467.5100.0230.0230.0000.0000.0000.000
159A181LEU00.0360.02067.701-0.001-0.0010.0000.0000.0000.000
160A182GLU-1-0.880-0.93967.418-0.023-0.0230.0000.0000.0000.000
161A183GLN0-0.039-0.03966.866-0.001-0.0010.0000.0000.0000.000
162A184TYR0-0.020-0.02959.725-0.001-0.0010.0000.0000.0000.000
163A185GLU-1-0.937-0.97262.967-0.030-0.0300.0000.0000.0000.000
164A186VAL0-0.022-0.00563.426-0.001-0.0010.0000.0000.0000.000
165A187LEU00.0290.01860.677-0.001-0.0010.0000.0000.0000.000
166A188LYS10.9130.96358.1140.0350.0350.0000.0000.0000.000
167A189ALA0-0.0270.00358.504-0.001-0.0010.0000.0000.0000.000
168A190ASP-1-0.967-0.98959.732-0.030-0.0300.0000.0000.0000.000
169A191GLY0-0.024-0.01655.592-0.001-0.0010.0000.0000.0000.000
170A192ASN0-0.0090.01954.730-0.002-0.0020.0000.0000.0000.000
171A193TYR00.0710.02648.5720.0010.0010.0000.0000.0000.000
172A194VAL00.0500.03251.8710.0000.0000.0000.0000.0000.000
173A195GLN0-0.083-0.04454.7550.0020.0020.0000.0000.0000.000
174A196ALA00.0130.00957.6620.0010.0010.0000.0000.0000.000
175A197HIS00.0050.00955.5760.0010.0010.0000.0000.0000.000
176A198ASN0-0.013-0.02456.0360.0010.0010.0000.0000.0000.000
177A199HIS0-0.103-0.03359.1640.0010.0010.0000.0000.0000.000
178A200ILE00.017-0.00460.0090.0010.0010.0000.0000.0000.000
179A201ALA00.0250.01959.2090.0010.0010.0000.0000.0000.000
180A202ALA0-0.015-0.00461.3450.0010.0010.0000.0000.0000.000
181A203LEU0-0.005-0.00464.1110.0010.0010.0000.0000.0000.000
182A204ASN00.0520.00662.7240.0010.0010.0000.0000.0000.000
183A205GLU-1-0.931-0.94264.062-0.026-0.0260.0000.0000.0000.000
184A206GLN00.0210.00665.9980.0010.0010.0000.0000.0000.000
185A207MET0-0.0190.01569.0380.0010.0010.0000.0000.0000.000
186A208LYS10.9080.95963.8670.0290.0290.0000.0000.0000.000
187A209GLN0-0.061-0.04567.5080.0010.0010.0000.0000.0000.000
188A210LEU00.0130.01071.4470.0010.0010.0000.0000.0000.000
189A211ARG10.9450.96168.8980.0250.0250.0000.0000.0000.000
190A212SER0-0.057-0.02771.7680.0000.0000.0000.0000.0000.000
191A213TYR0-0.028-0.01174.3040.0010.0010.0000.0000.0000.000
192A214MET0-0.048-0.01377.1220.0000.0000.0000.0000.0000.000
193A215HIS0-0.054-0.00675.8010.0000.0000.0000.0000.0000.000
194A216GLY00.0010.00479.5690.0000.0000.0000.0000.0000.000