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: JQG59

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 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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2688287.609428
FMO2-HF: Nuclear repulsion 2602106.098795
FMO2-HF: Total energy -86181.510633
FMO2-MP2: Total energy -86431.596564


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.
-7.736-1.7926.759-4.6-8.101-0.027
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 : 0.002 / q_NPA : -0.009
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].
3A4PRO0-0.010-0.0042.910-3.244-0.1980.307-1.714-1.639-0.006
4A5ALA0-0.025-0.0165.2370.5760.654-0.001-0.004-0.0720.000
5A6THR0-0.039-0.0467.4830.3110.3110.0000.0000.0000.000
6A7HIS00.0260.0248.571-0.388-0.3880.0000.0000.0000.000
7A8ASP-1-0.809-0.88311.156-0.589-0.5890.0000.0000.0000.000
8A9ILE00.0090.01114.217-0.057-0.0570.0000.0000.0000.000
9A10HIS0-0.053-0.04417.0620.0340.0340.0000.0000.0000.000
10A11LEU00.0120.01420.2400.0020.0020.0000.0000.0000.000
11A12HIS10.7850.87522.2380.3500.3500.0000.0000.0000.000
12A13GLY00.0880.04226.032-0.010-0.0100.0000.0000.0000.000
13A14SER0-0.001-0.03429.1860.0080.0080.0000.0000.0000.000
14A15ILE0-0.025-0.00130.333-0.003-0.0030.0000.0000.0000.000
15A16ASN0-0.018-0.04134.2190.0040.0040.0000.0000.0000.000
16A17GLY0-0.0010.01036.6560.0070.0070.0000.0000.0000.000
17A18HIS0-0.026-0.01336.642-0.002-0.0020.0000.0000.0000.000
18A19GLU-1-0.802-0.87731.721-0.194-0.1940.0000.0000.0000.000
19A20PHE0-0.038-0.02626.2500.0090.0090.0000.0000.0000.000
20A21ASP-1-0.798-0.88226.078-0.269-0.2690.0000.0000.0000.000
21A22MET0-0.043-0.00824.3930.0180.0180.0000.0000.0000.000
22A23VAL00.0530.04021.160-0.025-0.0250.0000.0000.0000.000
23A24GLY0-0.001-0.00519.4910.0350.0350.0000.0000.0000.000
24A25GLY00.0280.01415.853-0.046-0.0460.0000.0000.0000.000
25A26GLY0-0.042-0.01614.3570.0790.0790.0000.0000.0000.000
26A27LYS10.9550.99111.7830.3320.3320.0000.0000.0000.000
27A28GLY00.0300.00711.1970.0960.0960.0000.0000.0000.000
28A29ASP-1-0.838-0.90410.347-0.485-0.4850.0000.0000.0000.000
29A30PRO0-0.020-0.0036.4350.0900.0900.0000.0000.0000.000
30A31ASN0-0.066-0.0499.0680.1770.1770.0000.0000.0000.000
31A32ALA0-0.025-0.01011.7230.0750.0750.0000.0000.0000.000
32A33GLY00.0160.01913.4730.0350.0350.0000.0000.0000.000
33A34SER0-0.067-0.02614.3460.0580.0580.0000.0000.0000.000
34A35LEU00.0160.00413.999-0.065-0.0650.0000.0000.0000.000
35A36VAL0-0.044-0.02115.5930.0810.0810.0000.0000.0000.000
36A37THR00.0230.00616.108-0.085-0.0850.0000.0000.0000.000
37A38THR00.0050.01418.1620.0480.0480.0000.0000.0000.000
38A39ALA00.0120.01620.057-0.032-0.0320.0000.0000.0000.000
39A40LYS10.9020.93222.4900.2340.2340.0000.0000.0000.000
40A41SER0-0.046-0.04125.594-0.012-0.0120.0000.0000.0000.000
41A42THR0-0.025-0.03226.2340.0140.0140.0000.0000.0000.000
42A43LYS10.7880.88529.1250.2060.2060.0000.0000.0000.000
43A44GLY00.0060.00832.4140.0090.0090.0000.0000.0000.000
44A45ALA0-0.0020.00632.917-0.009-0.0090.0000.0000.0000.000
45A46LEU00.0160.00029.2960.0040.0040.0000.0000.0000.000
46A47LYS10.8810.94033.7040.1530.1530.0000.0000.0000.000
47A48PHE00.0620.03530.5320.0070.0070.0000.0000.0000.000
48A49SER00.013-0.00533.690-0.004-0.0040.0000.0000.0000.000
49A50PRO00.007-0.00230.365-0.009-0.0090.0000.0000.0000.000
50A51TYR0-0.017-0.01828.799-0.017-0.0170.0000.0000.0000.000
51A52LEU00.0140.02028.668-0.009-0.0090.0000.0000.0000.000
52A53MET0-0.044-0.02624.844-0.015-0.0150.0000.0000.0000.000
53A54ILE0-0.0240.00723.974-0.035-0.0350.0000.0000.0000.000
54A55PRO00.0420.01222.4880.0230.0230.0000.0000.0000.000
55A56HIS0-0.024-0.00721.318-0.056-0.0560.0000.0000.0000.000
56A57LEU00.0140.01119.424-0.042-0.0420.0000.0000.0000.000
57A60CR210.1500.21115.5860.1150.1150.0000.0000.0000.000
58A61TYR-10.004-0.12911.712-0.708-0.7080.0000.0000.0000.000
59A62TYR0-0.080-0.06612.934-0.024-0.0240.0000.0000.0000.000
60A63GLN00.028-0.0038.0900.1860.1860.0000.0000.0000.000
61A64TYR0-0.038-0.0489.134-0.331-0.3310.0000.0000.0000.000
62A65LEU0-0.035-0.00311.1840.1490.1490.0000.0000.0000.000
63A66PRO00.0040.04112.494-0.036-0.0360.0000.0000.0000.000
64A67TYR0-0.011-0.04113.395-0.002-0.0020.0000.0000.0000.000
65A68PRO0-0.089-0.04515.9600.0240.0240.0000.0000.0000.000
66A69ASP-1-0.798-0.86917.6510.0010.0010.0000.0000.0000.000
67A70GLY00.0170.02413.7570.0630.0630.0000.0000.0000.000
68A71PRO00.0240.0199.079-0.074-0.0740.0000.0000.0000.000
69A72SER0-0.019-0.01211.0670.0390.0390.0000.0000.0000.000
70A73PRO00.008-0.01210.952-0.058-0.0580.0000.0000.0000.000
71A74PHE00.011-0.00110.7490.0190.0190.0000.0000.0000.000
72A75GLN00.0260.0147.380-0.108-0.1080.0000.0000.0000.000
73A76VAL0-0.036-0.0166.129-0.411-0.4110.0000.0000.0000.000
74A77SER00.0160.0177.0910.1140.1140.0000.0000.0000.000
75A78MET00.0100.0143.0040.3981.1610.048-0.193-0.618-0.001
76A79LEU0-0.049-0.0212.226-2.144-1.6683.149-1.529-2.095-0.004
77A80GLU-1-0.858-0.9193.7332.1362.350-0.0010.027-0.2400.000
78A81GLY0-0.032-0.0015.0860.1550.1550.0000.0000.0000.000
79A82SER0-0.103-0.0596.5030.0460.0460.0000.0000.0000.000
80A83GLY00.009-0.0208.117-0.426-0.4260.0000.0000.0000.000
81A84TYR0-0.009-0.01210.5580.1330.1330.0000.0000.0000.000
82A85ALA0-0.0240.00313.830-0.069-0.0690.0000.0000.0000.000
83A86VAL0-0.025-0.01216.5930.0420.0420.0000.0000.0000.000
84A87TYR00.0210.00718.9960.0130.0130.0000.0000.0000.000
85A88ARG10.8370.91819.2830.3950.3950.0000.0000.0000.000
86A89VAL00.0130.01125.2550.0050.0050.0000.0000.0000.000
87A90PHE0-0.018-0.00825.071-0.002-0.0020.0000.0000.0000.000
88A91ASP-1-0.854-0.93230.674-0.122-0.1220.0000.0000.0000.000
89A92PHE0-0.005-0.01031.493-0.001-0.0010.0000.0000.0000.000
90A93GLU-1-0.820-0.89536.584-0.105-0.1050.0000.0000.0000.000
91A94ASP-1-0.819-0.89339.185-0.118-0.1180.0000.0000.0000.000
92A95GLY00.0200.01840.4600.0040.0040.0000.0000.0000.000
93A96GLY0-0.019-0.00537.347-0.002-0.0020.0000.0000.0000.000
94A97LYS10.8040.89934.5520.1240.1240.0000.0000.0000.000
95A98LEU00.003-0.00528.036-0.001-0.0010.0000.0000.0000.000
96A99SER00.0070.00828.6090.0000.0000.0000.0000.0000.000
97A100THR0-0.035-0.02723.848-0.003-0.0030.0000.0000.0000.000
98A101GLU-1-0.836-0.89822.205-0.260-0.2600.0000.0000.0000.000
99A102PHE00.005-0.00417.5220.0150.0150.0000.0000.0000.000
100A103LYS10.8900.93316.3310.3340.3340.0000.0000.0000.000
101A104TYR0-0.012-0.01611.259-0.006-0.0060.0000.0000.0000.000
102A105SER0-0.032-0.00810.3590.1150.1150.0000.0000.0000.000
103A106TYR00.014-0.0025.177-0.145-0.1450.0000.0000.0000.000
104A107GLU-1-0.891-0.9416.321-0.556-0.5560.0000.0000.0000.000
105A108GLY00.0310.0203.079-0.390-0.0180.123-0.114-0.3810.000
106A109SER0-0.013-0.0022.406-4.390-2.8113.046-1.787-2.838-0.016
107A110HIS0-0.051-0.0113.1381.0020.4180.0880.714-0.2180.000
108A111ILE00.0070.0016.528-0.275-0.2750.0000.0000.0000.000
109A112LYS10.8480.9058.7200.9690.9690.0000.0000.0000.000
110A113ALA00.0130.00012.208-0.037-0.0370.0000.0000.0000.000
111A114ASP-1-0.854-0.90214.903-0.311-0.3110.0000.0000.0000.000
112A115MET00.016-0.00416.7770.0070.0070.0000.0000.0000.000
113A116LYS10.8700.93320.8620.2790.2790.0000.0000.0000.000
114A117LEU0-0.033-0.01423.246-0.001-0.0010.0000.0000.0000.000
115A118MET0-0.0090.01126.7400.0070.0070.0000.0000.0000.000
116A119GLY00.0290.00930.400-0.001-0.0010.0000.0000.0000.000
117A120SER0-0.053-0.02233.1920.0080.0080.0000.0000.0000.000
118A121GLY00.0640.02837.000-0.002-0.0020.0000.0000.0000.000
119A122PHE0-0.0140.00533.5390.0030.0030.0000.0000.0000.000
120A123PRO00.0380.03539.4740.0010.0010.0000.0000.0000.000
121A124ASP-1-0.944-0.97541.815-0.098-0.0980.0000.0000.0000.000
122A125ASP-1-0.849-0.94043.493-0.092-0.0920.0000.0000.0000.000
123A126GLY00.0590.04441.764-0.001-0.0010.0000.0000.0000.000
124A127PRO0-0.047-0.02238.476-0.003-0.0030.0000.0000.0000.000
125A128VAL00.0270.01434.453-0.005-0.0050.0000.0000.0000.000
126A129MET00.0020.01436.699-0.009-0.0090.0000.0000.0000.000
127A130THR0-0.004-0.01339.146-0.002-0.0020.0000.0000.0000.000
128A131SER0-0.086-0.04136.918-0.002-0.0020.0000.0000.0000.000
129A132GLN00.0000.00037.9410.0020.0020.0000.0000.0000.000
130A133ILE0-0.043-0.01232.8000.0040.0040.0000.0000.0000.000
131A134VAL0-0.013-0.00334.711-0.001-0.0010.0000.0000.0000.000
132A135ASP-1-0.809-0.87430.140-0.184-0.1840.0000.0000.0000.000
133A136GLN00.006-0.00927.532-0.004-0.0040.0000.0000.0000.000
134A137ASP-1-0.722-0.78330.124-0.137-0.1370.0000.0000.0000.000
135A138GLY0-0.0200.00528.195-0.015-0.0150.0000.0000.0000.000
136A139CYS0-0.0220.00026.8370.0110.0110.0000.0000.0000.000
137A140VAL00.010-0.00526.333-0.009-0.0090.0000.0000.0000.000
138A141SER0-0.031-0.00423.197-0.001-0.0010.0000.0000.0000.000
139A142LYS10.9490.98124.8020.1150.1150.0000.0000.0000.000
140A143LYN00.0100.02718.399-0.012-0.0120.0000.0000.0000.000
141A144THR0-0.020-0.02123.1760.0260.0260.0000.0000.0000.000
142A145TYR00.0220.01217.906-0.030-0.0300.0000.0000.0000.000
143A146LEU00.0160.00822.6770.0150.0150.0000.0000.0000.000
144A147ASN0-0.019-0.01823.0750.0000.0000.0000.0000.0000.000
145A148ASN00.0300.00722.225-0.004-0.0040.0000.0000.0000.000
146A149ASN00.0440.03518.2510.0280.0280.0000.0000.0000.000
147A150THR00.0080.01418.281-0.050-0.0500.0000.0000.0000.000
148A151ILE0-0.0270.00116.3150.0280.0280.0000.0000.0000.000
149A152VAL00.0180.00420.416-0.019-0.0190.0000.0000.0000.000
150A153ASP-1-0.776-0.85922.122-0.278-0.2780.0000.0000.0000.000
151A154SER0-0.0140.00124.4830.0140.0140.0000.0000.0000.000
152A155PHE00.001-0.01724.220-0.006-0.0060.0000.0000.0000.000
153A156ASP-1-0.824-0.89328.685-0.134-0.1340.0000.0000.0000.000
154A157TRP00.0000.00825.675-0.005-0.0050.0000.0000.0000.000
155A158SER0-0.006-0.04330.9250.0090.0090.0000.0000.0000.000
156A159TYR0-0.0040.00028.6960.0010.0010.0000.0000.0000.000
157A160ASN0-0.035-0.04533.4900.0050.0050.0000.0000.0000.000
158A161LEU00.013-0.00335.984-0.005-0.0050.0000.0000.0000.000
159A162GLN00.0380.01238.7840.0060.0060.0000.0000.0000.000
160A163ASN0-0.049-0.02340.8750.0050.0050.0000.0000.0000.000
161A164GLY00.0260.01542.0510.0050.0050.0000.0000.0000.000
162A165LYS10.9100.96341.9620.0830.0830.0000.0000.0000.000
163A166ARG10.8080.86835.9300.1130.1130.0000.0000.0000.000
164A167TYR0-0.058-0.05735.3100.0030.0030.0000.0000.0000.000
165A168ARG10.8760.91034.9760.0980.0980.0000.0000.0000.000
166A169ALA00.0000.00231.8860.0030.0030.0000.0000.0000.000
167A170ARG10.8780.93931.4440.1330.1330.0000.0000.0000.000
168A171VAL0-0.019-0.01326.794-0.004-0.0040.0000.0000.0000.000
169A172SER0-0.053-0.03327.2640.0100.0100.0000.0000.0000.000
170A173SER0-0.001-0.02522.113-0.016-0.0160.0000.0000.0000.000
171A174HIS0-0.062-0.03522.3860.0350.0350.0000.0000.0000.000
172A175TYR0-0.026-0.03916.758-0.034-0.0340.0000.0000.0000.000
173A176ILE0-0.0020.00218.2890.0300.0300.0000.0000.0000.000
174A177PHE00.0280.00311.854-0.048-0.0480.0000.0000.0000.000
175A178ASP-1-0.822-0.88012.600-0.399-0.3990.0000.0000.0000.000
176A179LYS10.8130.90311.0380.0360.0360.0000.0000.0000.000
177A180PRO0-0.038-0.04016.040-0.028-0.0280.0000.0000.0000.000
178A181PHE00.0050.00615.2770.0270.0270.0000.0000.0000.000
179A182SER0-0.031-0.01417.3470.0400.0400.0000.0000.0000.000
180A183ALA00.0160.00919.7180.0100.0100.0000.0000.0000.000
181A184ASP-1-0.838-0.89120.417-0.062-0.0620.0000.0000.0000.000
182A185LEU00.0110.01623.014-0.009-0.0090.0000.0000.0000.000
183A186MET0-0.005-0.01226.2210.0040.0040.0000.0000.0000.000
184A187LYS10.7950.87518.1840.0670.0670.0000.0000.0000.000
185A188LYS10.9000.93820.249-0.012-0.0120.0000.0000.0000.000
186A189GLN0-0.0140.00022.306-0.038-0.0380.0000.0000.0000.000
187A190PRO0-0.007-0.01824.8060.0120.0120.0000.0000.0000.000
188A191VAL0-0.0190.00019.7190.0140.0140.0000.0000.0000.000
189A192PHE0-0.0100.01223.001-0.020-0.0200.0000.0000.0000.000
190A193VAL00.016-0.00219.608-0.004-0.0040.0000.0000.0000.000
191A194TYR00.0120.02022.6340.0020.0020.0000.0000.0000.000
192A195ARG10.8290.87818.1920.3560.3560.0000.0000.0000.000
193A196LYS10.7810.87823.1870.2150.2150.0000.0000.0000.000
194A197CYS0-0.018-0.00522.719-0.015-0.0150.0000.0000.0000.000
195A198HIS00.0180.01124.1720.0300.0300.0000.0000.0000.000
196A199VAL00.013-0.00324.695-0.021-0.0210.0000.0000.0000.000
197A200LYS10.9340.97225.9900.2220.2220.0000.0000.0000.000
198A201ALA00.0360.01827.359-0.016-0.0160.0000.0000.0000.000
199A202THR00.0330.01929.7380.0160.0160.0000.0000.0000.000
200A203LYS10.8800.93231.2370.1350.1350.0000.0000.0000.000
201A204THR00.0080.00831.1590.0050.0050.0000.0000.0000.000
202A205GLU-1-0.893-0.93225.810-0.237-0.2370.0000.0000.0000.000
203A206VAL0-0.0100.00125.1810.0180.0180.0000.0000.0000.000
204A207THR0-0.002-0.01322.213-0.015-0.0150.0000.0000.0000.000
205A208LEU0-0.031-0.00919.8240.0300.0300.0000.0000.0000.000
206A209ASP-1-0.857-0.89620.354-0.309-0.3090.0000.0000.0000.000
207A210GLU-1-0.780-0.88818.803-0.391-0.3910.0000.0000.0000.000
208A211ARG10.8320.88118.6100.2420.2420.0000.0000.0000.000
209A212GLU-1-0.775-0.87615.958-0.514-0.5140.0000.0000.0000.000
210A213LYS10.9440.96618.8780.1550.1550.0000.0000.0000.000
211A214ALA00.0390.02518.5620.0170.0170.0000.0000.0000.000
212A215PHE0-0.050-0.04220.4050.0210.0210.0000.0000.0000.000
213A216TYR0-0.020-0.04418.785-0.017-0.0170.0000.0000.0000.000
214A217GLU-1-0.899-0.92924.703-0.032-0.0320.0000.0000.0000.000
215A218LEU0-0.034-0.02626.808-0.003-0.0030.0000.0000.0000.000
216A219ALA0-0.046-0.02329.7430.0030.0030.0000.0000.0000.000