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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: 89MYY

Calculation Name: 4DKN-A-Xray372

Preferred Name:

Target Type:

Ligand Name: {(4z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1h-imidazol-1-yl}acetic acid

ligand 3-letter code: CR2

PDB ID: 4DKN

Chain ID: A

ChEMBL ID:

UniProt ID: C3YKQ3

Base Structure: X-ray

Registration Date: 2023-09-23

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2685556.710656
FMO2-HF: Nuclear repulsion 2599376.190773
FMO2-HF: Total energy -86180.519883
FMO2-MP2: Total energy -86430.455981


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:2:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
-4.7630.0333.6-2.901-5.497-0.009
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.018
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].
3A4PRO0-0.005-0.0043.108-3.127-0.5850.119-1.381-1.281-0.002
4A5ALA0-0.037-0.0205.6230.6460.6460.0000.0000.0000.000
5A6THR0-0.045-0.0557.5310.3550.3550.0000.0000.0000.000
6A7HIS00.0250.0398.839-0.393-0.3930.0000.0000.0000.000
7A8ASP-1-0.803-0.88811.456-0.601-0.6010.0000.0000.0000.000
8A9ILE00.009-0.00714.643-0.043-0.0430.0000.0000.0000.000
9A10HIS0-0.041-0.03517.3790.0300.0300.0000.0000.0000.000
10A11LEU0-0.019-0.00820.4730.0010.0010.0000.0000.0000.000
11A12HIS10.8230.89522.8400.3080.3080.0000.0000.0000.000
12A13GLY00.0340.02126.381-0.007-0.0070.0000.0000.0000.000
13A14SER00.006-0.00129.3730.0100.0100.0000.0000.0000.000
14A15ILE00.0100.01130.910-0.002-0.0020.0000.0000.0000.000
15A16ASN0-0.040-0.05934.4730.0020.0020.0000.0000.0000.000
16A17GLY0-0.0100.00537.0650.0060.0060.0000.0000.0000.000
17A18HIS0-0.026-0.00436.8730.0000.0000.0000.0000.0000.000
18A19GLU-1-0.889-0.96032.290-0.169-0.1690.0000.0000.0000.000
19A20PHE0-0.089-0.04426.6140.0070.0070.0000.0000.0000.000
20A21ASP-1-0.793-0.87726.385-0.258-0.2580.0000.0000.0000.000
21A22MET0-0.052-0.02224.6580.0140.0140.0000.0000.0000.000
22A23VAL00.0490.03221.555-0.022-0.0220.0000.0000.0000.000
23A24GLY00.003-0.00219.8250.0350.0350.0000.0000.0000.000
24A25GLY00.0280.02016.138-0.044-0.0440.0000.0000.0000.000
25A26GLY0-0.057-0.01414.5960.0820.0820.0000.0000.0000.000
26A27LYS10.9640.99011.9670.3750.3750.0000.0000.0000.000
27A28GLY00.0370.00911.1850.1100.1100.0000.0000.0000.000
28A29ASP-1-0.877-0.92310.403-0.512-0.5120.0000.0000.0000.000
29A30PRO0-0.012-0.0066.4720.1170.1170.0000.0000.0000.000
30A31ASN00.000-0.0019.5030.0910.0910.0000.0000.0000.000
31A32ALA0-0.084-0.04311.5260.0870.0870.0000.0000.0000.000
32A33GLY00.0090.00313.2300.0500.0500.0000.0000.0000.000
33A34SER0-0.087-0.02614.5590.0020.0020.0000.0000.0000.000
34A35LEU00.0380.01413.944-0.087-0.0870.0000.0000.0000.000
35A36VAL0-0.047-0.02015.5560.0840.0840.0000.0000.0000.000
36A37THR00.0250.00916.375-0.087-0.0870.0000.0000.0000.000
37A38THR0-0.0040.00618.4960.0410.0410.0000.0000.0000.000
38A39ALA0-0.0070.00420.531-0.027-0.0270.0000.0000.0000.000
39A40LYS10.9860.97722.8530.2310.2310.0000.0000.0000.000
40A41SER0-0.055-0.04925.900-0.010-0.0100.0000.0000.0000.000
41A42THR0-0.024-0.03626.3830.0120.0120.0000.0000.0000.000
42A43LYS10.8960.94929.3260.1710.1710.0000.0000.0000.000
43A44GLY00.0160.01732.6760.0100.0100.0000.0000.0000.000
44A45ALA0-0.032-0.01133.132-0.009-0.0090.0000.0000.0000.000
45A46LEU00.0040.00529.5830.0040.0040.0000.0000.0000.000
46A47LYS10.9200.95034.0010.1370.1370.0000.0000.0000.000
47A48PHE00.0440.03030.5550.0080.0080.0000.0000.0000.000
48A49SER00.004-0.00433.995-0.008-0.0080.0000.0000.0000.000
49A50PRO00.0200.00330.543-0.007-0.0070.0000.0000.0000.000
50A51TYR00.0290.01029.149-0.015-0.0150.0000.0000.0000.000
51A52LEU0-0.0110.01029.323-0.006-0.0060.0000.0000.0000.000
52A53MET0-0.029-0.02225.401-0.013-0.0130.0000.0000.0000.000
53A54ILE0-0.0540.00524.561-0.032-0.0320.0000.0000.0000.000
54A55PRO00.025-0.01022.9450.0190.0190.0000.0000.0000.000
55A56HIS00.005-0.01421.740-0.050-0.0500.0000.0000.0000.000
56A57LEU00.0100.01520.064-0.035-0.0350.0000.0000.0000.000
57A60CR210.1900.27915.6210.0820.0820.0000.0000.0000.000
58A61TYR-10.028-0.12712.001-0.651-0.6510.0000.0000.0000.000
59A62TYR0-0.100-0.08113.5280.0180.0180.0000.0000.0000.000
60A63GLN00.0380.0077.8940.1450.1450.0000.0000.0000.000
61A64TYR0-0.039-0.0558.974-0.350-0.3500.0000.0000.0000.000
62A65LEU0-0.0180.00811.0920.1530.1530.0000.0000.0000.000
63A66PRO00.0050.04511.9410.0150.0150.0000.0000.0000.000
64A67TYR0-0.005-0.04213.023-0.015-0.0150.0000.0000.0000.000
65A68PRO0-0.091-0.04915.8340.0180.0180.0000.0000.0000.000
66A69ASP-1-0.871-0.91517.4350.0790.0790.0000.0000.0000.000
67A70GLY00.0310.03313.3340.0630.0630.0000.0000.0000.000
68A71PRO00.0090.0138.911-0.089-0.0890.0000.0000.0000.000
69A72SER0-0.018-0.00810.9630.0450.0450.0000.0000.0000.000
70A73PRO00.013-0.01311.299-0.002-0.0020.0000.0000.0000.000
71A74PHE00.0160.00111.2540.0420.0420.0000.0000.0000.000
72A75GLN00.001-0.0097.5600.0050.0050.0000.0000.0000.000
73A76VAL0-0.0130.0016.606-0.098-0.0980.0000.0000.0000.000
74A77SER0-0.013-0.0057.6860.2490.2490.0000.0000.0000.000
75A78MET00.0200.0203.5210.5340.9830.004-0.116-0.3370.000
76A79LEU0-0.050-0.0162.326-0.640-1.0142.779-0.620-1.786-0.002
77A80GLU-1-0.942-0.9774.0942.5382.759-0.001-0.003-0.2170.000
78A81GLY0-0.0230.0035.516-0.087-0.0870.0000.0000.0000.000
79A82SER0-0.043-0.0106.853-0.070-0.0700.0000.0000.0000.000
80A83GLY00.033-0.0018.773-0.301-0.3010.0000.0000.0000.000
81A84TYR0-0.026-0.01710.6540.0950.0950.0000.0000.0000.000
82A85ALA00.0000.01714.100-0.073-0.0730.0000.0000.0000.000
83A86VAL0-0.023-0.01516.5210.0350.0350.0000.0000.0000.000
84A87TYR00.0070.01019.100-0.002-0.0020.0000.0000.0000.000
85A88ARG10.8570.92019.5560.3220.3220.0000.0000.0000.000
86A89VAL00.0170.01625.2730.0030.0030.0000.0000.0000.000
87A90PHE0-0.033-0.02025.7780.0000.0000.0000.0000.0000.000
88A91ASP-1-0.913-0.96930.779-0.098-0.0980.0000.0000.0000.000
89A92PHE0-0.015-0.02031.551-0.001-0.0010.0000.0000.0000.000
90A93GLU-1-0.824-0.91436.231-0.088-0.0880.0000.0000.0000.000
91A94ASP-1-0.843-0.90339.500-0.099-0.0990.0000.0000.0000.000
92A95GLY00.0040.00740.1040.0020.0020.0000.0000.0000.000
93A96GLY0-0.0160.01337.313-0.001-0.0010.0000.0000.0000.000
94A97LYS10.9000.95034.5320.1010.1010.0000.0000.0000.000
95A98LEU00.0140.00028.273-0.002-0.0020.0000.0000.0000.000
96A99SER0-0.0090.00828.6970.0010.0010.0000.0000.0000.000
97A100THR0-0.014-0.01923.610-0.002-0.0020.0000.0000.0000.000
98A101GLU-1-0.915-0.96822.363-0.211-0.2110.0000.0000.0000.000
99A102PHE0-0.015-0.00317.4500.0020.0020.0000.0000.0000.000
100A103LYS10.9810.98016.3180.3050.3050.0000.0000.0000.000
101A104TYR0-0.018-0.03011.501-0.008-0.0080.0000.0000.0000.000
102A105SER0-0.038-0.00311.1170.0890.0890.0000.0000.0000.000
103A106TYR00.014-0.0085.723-0.138-0.1380.0000.0000.0000.000
104A107GLU-1-0.875-0.9226.714-0.605-0.6050.0000.0000.0000.000
105A108GLY0-0.004-0.0013.027-0.2150.1840.105-0.157-0.3460.000
106A109SER0-0.025-0.0142.863-3.397-1.8590.553-0.749-1.343-0.005
107A110HIS0-0.0070.0123.3930.4570.4780.0410.125-0.1870.000
108A111ILE00.003-0.0046.953-0.164-0.1640.0000.0000.0000.000
109A112LYS10.8510.9299.1070.9280.9280.0000.0000.0000.000
110A113ALA00.006-0.00412.601-0.014-0.0140.0000.0000.0000.000
111A114ASP-1-0.860-0.90115.256-0.297-0.2970.0000.0000.0000.000
112A115MET0-0.015-0.02017.3410.0290.0290.0000.0000.0000.000
113A116LYS10.9080.97121.2440.2410.2410.0000.0000.0000.000
114A117LEU0-0.019-0.02523.9640.0030.0030.0000.0000.0000.000
115A118MET0-0.0060.01427.2780.0060.0060.0000.0000.0000.000
116A119GLY00.0310.00330.7740.0020.0020.0000.0000.0000.000
117A120SER0-0.047-0.02133.2850.0060.0060.0000.0000.0000.000
118A121GLY00.0570.02337.012-0.001-0.0010.0000.0000.0000.000
119A122PHE0-0.0180.00433.7380.0010.0010.0000.0000.0000.000
120A123PRO00.0550.03839.7050.0010.0010.0000.0000.0000.000
121A124ASP-1-0.922-0.96542.375-0.086-0.0860.0000.0000.0000.000
122A125ASP-1-0.896-0.94644.065-0.082-0.0820.0000.0000.0000.000
123A126GLY00.0120.00942.0630.0010.0010.0000.0000.0000.000
124A127PRO0-0.029-0.01638.585-0.003-0.0030.0000.0000.0000.000
125A128VAL00.0390.02235.041-0.005-0.0050.0000.0000.0000.000
126A129MET00.0150.00437.300-0.009-0.0090.0000.0000.0000.000
127A130THR0-0.0120.00239.4960.0010.0010.0000.0000.0000.000
128A131SER0-0.106-0.06337.345-0.002-0.0020.0000.0000.0000.000
129A132GLN00.0030.00838.2960.0020.0020.0000.0000.0000.000
130A133ILE0-0.063-0.02533.1280.0030.0030.0000.0000.0000.000
131A134VAL0-0.027-0.01235.117-0.002-0.0020.0000.0000.0000.000
132A135ASP-1-0.887-0.93231.144-0.156-0.1560.0000.0000.0000.000
133A136GLN0-0.011-0.00628.1420.0010.0010.0000.0000.0000.000
134A137ASP-1-0.730-0.80430.519-0.117-0.1170.0000.0000.0000.000
135A138GLY0-0.049-0.01228.021-0.013-0.0130.0000.0000.0000.000
136A139CYS0-0.047-0.02826.8210.0070.0070.0000.0000.0000.000
137A140VAL00.0330.01126.169-0.011-0.0110.0000.0000.0000.000
138A141SER0-0.029-0.00523.2820.0000.0000.0000.0000.0000.000
139A142LYS10.9330.97524.9020.0750.0750.0000.0000.0000.000
140A143LYN00.0100.02918.580-0.013-0.0130.0000.0000.0000.000
141A144THR0-0.035-0.02323.4670.0210.0210.0000.0000.0000.000
142A145TYR00.010-0.00418.033-0.009-0.0090.0000.0000.0000.000
143A146LEU00.0140.01023.2870.0080.0080.0000.0000.0000.000
144A147ASN0-0.022-0.01223.6500.0030.0030.0000.0000.0000.000
145A148ASN00.0490.00721.886-0.006-0.0060.0000.0000.0000.000
146A149ASN00.0250.02118.6370.0250.0250.0000.0000.0000.000
147A150THR00.0240.02719.022-0.039-0.0390.0000.0000.0000.000
148A151ILE0-0.0120.01516.9810.0230.0230.0000.0000.0000.000
149A152VAL00.0000.00120.787-0.022-0.0220.0000.0000.0000.000
150A153ASP-1-0.796-0.88022.255-0.208-0.2080.0000.0000.0000.000
151A154SER0-0.028-0.00924.7670.0070.0070.0000.0000.0000.000
152A155PHE0-0.014-0.03224.228-0.004-0.0040.0000.0000.0000.000
153A156ASP-1-0.846-0.91528.673-0.104-0.1040.0000.0000.0000.000
154A157TRP0-0.007-0.01026.050-0.007-0.0070.0000.0000.0000.000
155A158SER0-0.017-0.04730.9280.0090.0090.0000.0000.0000.000
156A159TYR0-0.0090.00429.2940.0000.0000.0000.0000.0000.000
157A160ASN0-0.041-0.03934.0100.0030.0030.0000.0000.0000.000
158A161LEU00.008-0.00536.477-0.006-0.0060.0000.0000.0000.000
159A162GLN00.0420.01939.2070.0060.0060.0000.0000.0000.000
160A163ASN0-0.028-0.01241.2320.0020.0020.0000.0000.0000.000
161A164GLY00.0300.01642.0640.0050.0050.0000.0000.0000.000
162A165LYS10.9010.95542.1550.0730.0730.0000.0000.0000.000
163A166ARG10.8130.87936.4400.0960.0960.0000.0000.0000.000
164A167TYR0-0.059-0.05635.7240.0020.0020.0000.0000.0000.000
165A168ARG10.8960.92535.2520.0820.0820.0000.0000.0000.000
166A169ALA00.0200.01831.9300.0020.0020.0000.0000.0000.000
167A170ARG10.9120.98232.4660.0990.0990.0000.0000.0000.000
168A171VAL0-0.014-0.01426.674-0.002-0.0020.0000.0000.0000.000
169A172SER0-0.032-0.00727.6920.0070.0070.0000.0000.0000.000
170A173SER00.015-0.00622.158-0.020-0.0200.0000.0000.0000.000
171A174HIS0-0.050-0.02922.6960.0290.0290.0000.0000.0000.000
172A175TYR0-0.023-0.03617.070-0.034-0.0340.0000.0000.0000.000
173A176ILE00.0040.00318.7050.0330.0330.0000.0000.0000.000
174A177PHE00.000-0.02012.523-0.051-0.0510.0000.0000.0000.000
175A178ASP-1-0.881-0.94113.733-0.249-0.2490.0000.0000.0000.000
176A179LYS10.8460.93711.747-0.222-0.2220.0000.0000.0000.000
177A180PRO0-0.044-0.04516.375-0.016-0.0160.0000.0000.0000.000
178A181PHE0-0.0040.01515.1550.0380.0380.0000.0000.0000.000
179A182SER0-0.045-0.02317.8640.0260.0260.0000.0000.0000.000
180A183ALA00.0410.02619.933-0.019-0.0190.0000.0000.0000.000
181A184ASP-1-0.829-0.89620.7440.0390.0390.0000.0000.0000.000
182A185LEU00.0080.01223.333-0.015-0.0150.0000.0000.0000.000
183A186MET0-0.023-0.02226.4400.0010.0010.0000.0000.0000.000
184A187LYS10.8020.88018.548-0.048-0.0480.0000.0000.0000.000
185A188LYS10.9430.96920.922-0.073-0.0730.0000.0000.0000.000
186A189GLN00.0300.04522.372-0.029-0.0290.0000.0000.0000.000
187A190PRO0-0.017-0.03324.9010.0080.0080.0000.0000.0000.000
188A191VAL00.0020.01719.5640.0110.0110.0000.0000.0000.000
189A192PHE0-0.016-0.00422.978-0.016-0.0160.0000.0000.0000.000
190A193VAL00.0200.00419.5770.0000.0000.0000.0000.0000.000
191A194TYR00.0030.01522.4650.0010.0010.0000.0000.0000.000
192A195ARG10.8440.89118.3010.2950.2950.0000.0000.0000.000
193A196LYS10.8820.94123.0950.1820.1820.0000.0000.0000.000
194A197CYS0-0.0090.00222.985-0.020-0.0200.0000.0000.0000.000
195A198HIS00.0000.00923.7990.0290.0290.0000.0000.0000.000
196A199VAL00.0310.00324.988-0.020-0.0200.0000.0000.0000.000
197A200LYS10.9450.98826.6920.2120.2120.0000.0000.0000.000
198A201ALA00.0130.00427.819-0.015-0.0150.0000.0000.0000.000
199A202THR00.0520.03530.1610.0150.0150.0000.0000.0000.000
200A203LYS10.9700.96731.6270.1220.1220.0000.0000.0000.000
201A204THR0-0.0020.00231.1650.0000.0000.0000.0000.0000.000
202A205GLU-1-0.930-0.94825.878-0.243-0.2430.0000.0000.0000.000
203A206VAL0-0.0110.00225.3520.0170.0170.0000.0000.0000.000
204A207THR00.0180.00922.240-0.027-0.0270.0000.0000.0000.000
205A208LEU0-0.032-0.01420.3190.0330.0330.0000.0000.0000.000
206A209ASP-1-0.838-0.88420.396-0.321-0.3210.0000.0000.0000.000
207A210GLU-1-0.818-0.94118.793-0.365-0.3650.0000.0000.0000.000
208A211ARG10.8140.88418.6630.2300.2300.0000.0000.0000.000
209A212GLU-1-0.772-0.88916.064-0.447-0.4470.0000.0000.0000.000
210A213LYS10.9600.98018.9310.1170.1170.0000.0000.0000.000
211A214ALA00.0320.02318.5510.0110.0110.0000.0000.0000.000
212A215PHE0-0.032-0.03620.3930.0180.0180.0000.0000.0000.000
213A216TYR0-0.024-0.03818.540-0.017-0.0170.0000.0000.0000.000
214A217GLU-1-0.947-0.98024.4390.0020.0020.0000.0000.0000.000
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