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: NNQYQ

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 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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2687936.502302
FMO2-HF: Nuclear repulsion 2601755.337493
FMO2-HF: Total energy -86181.16481
FMO2-MP2: Total energy -86431.164788


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.
-6.114-0.2734.125-3.814-6.152-0.011
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].
3A4PRO0-0.003-0.0023.228-3.218-0.3920.102-1.545-1.3830.000
4A5ALA0-0.032-0.0185.3880.5770.663-0.001-0.004-0.0800.000
5A6THR0-0.040-0.0517.4220.3550.3550.0000.0000.0000.000
6A7HIS00.0330.0358.659-0.401-0.4010.0000.0000.0000.000
7A8ASP-1-0.807-0.87511.288-0.590-0.5900.0000.0000.0000.000
8A9ILE0-0.003-0.00414.507-0.048-0.0480.0000.0000.0000.000
9A10HIS0-0.051-0.03717.2470.0320.0320.0000.0000.0000.000
10A11LEU0-0.010-0.00120.367-0.002-0.0020.0000.0000.0000.000
11A12HIS10.8350.89922.2150.3340.3340.0000.0000.0000.000
12A13GLY00.0420.01826.282-0.009-0.0090.0000.0000.0000.000
13A14SER00.019-0.02429.2540.0080.0080.0000.0000.0000.000
14A15ILE0-0.0350.00330.584-0.002-0.0020.0000.0000.0000.000
15A16ASN0-0.029-0.05434.3480.0030.0030.0000.0000.0000.000
16A17GLY0-0.0100.00336.9920.0060.0060.0000.0000.0000.000
17A18HIS0-0.0260.00136.7620.0000.0000.0000.0000.0000.000
18A19GLU-1-0.879-0.93531.840-0.182-0.1820.0000.0000.0000.000
19A20PHE0-0.087-0.04626.4930.0080.0080.0000.0000.0000.000
20A21ASP-1-0.786-0.87726.340-0.267-0.2670.0000.0000.0000.000
21A22MET0-0.050-0.01624.5060.0160.0160.0000.0000.0000.000
22A23VAL00.0530.03221.395-0.024-0.0240.0000.0000.0000.000
23A24GLY00.0050.00119.6900.0360.0360.0000.0000.0000.000
24A25GLY00.0290.02215.971-0.046-0.0460.0000.0000.0000.000
25A26GLY0-0.065-0.02014.4070.0850.0850.0000.0000.0000.000
26A27LYS10.9680.99511.7300.3620.3620.0000.0000.0000.000
27A28GLY00.0360.00811.1570.1060.1060.0000.0000.0000.000
28A29ASP-1-0.853-0.91310.487-0.497-0.4970.0000.0000.0000.000
29A30PRO0-0.020-0.0016.5080.1080.1080.0000.0000.0000.000
30A31ASN0-0.059-0.0388.7650.1800.1800.0000.0000.0000.000
31A32ALA0-0.040-0.02211.5460.0810.0810.0000.0000.0000.000
32A33GLY00.0130.00813.2830.0450.0450.0000.0000.0000.000
33A34SER0-0.089-0.02814.6950.0360.0360.0000.0000.0000.000
34A35LEU00.0160.00013.948-0.084-0.0840.0000.0000.0000.000
35A36VAL0-0.044-0.02215.5710.0840.0840.0000.0000.0000.000
36A37THR00.0130.00316.149-0.086-0.0860.0000.0000.0000.000
37A38THR00.0160.01918.2820.0490.0490.0000.0000.0000.000
38A39ALA00.0040.01720.349-0.028-0.0280.0000.0000.0000.000
39A40LYS10.9080.92522.6780.2410.2410.0000.0000.0000.000
40A41SER0-0.048-0.04425.751-0.011-0.0110.0000.0000.0000.000
41A42THR0-0.022-0.03626.2420.0130.0130.0000.0000.0000.000
42A43LYS10.8930.95429.2060.1830.1830.0000.0000.0000.000
43A44GLY00.0160.01832.5570.0100.0100.0000.0000.0000.000
44A45ALA0-0.027-0.01132.984-0.009-0.0090.0000.0000.0000.000
45A46LEU00.0060.00329.4060.0040.0040.0000.0000.0000.000
46A47LYS10.9230.95033.8420.1450.1450.0000.0000.0000.000
47A48PHE00.0410.02730.5040.0080.0080.0000.0000.0000.000
48A49SER00.001-0.00833.959-0.006-0.0060.0000.0000.0000.000
49A50PRO00.0240.00630.359-0.008-0.0080.0000.0000.0000.000
50A51TYR0-0.010-0.01128.959-0.017-0.0170.0000.0000.0000.000
51A52LEU0-0.0050.01229.130-0.007-0.0070.0000.0000.0000.000
52A53MET0-0.048-0.03325.239-0.013-0.0130.0000.0000.0000.000
53A54ILE0-0.0350.01224.409-0.034-0.0340.0000.0000.0000.000
54A55PRO00.0290.00222.7980.0210.0210.0000.0000.0000.000
55A56HIS00.002-0.01121.553-0.053-0.0530.0000.0000.0000.000
56A57LEU00.0010.01219.881-0.038-0.0380.0000.0000.0000.000
57A60CR210.1880.27315.6110.0870.0870.0000.0000.0000.000
58A61TYR-10.026-0.13711.825-0.699-0.6990.0000.0000.0000.000
59A62TYR0-0.097-0.08113.5120.0110.0110.0000.0000.0000.000
60A63GLN00.031-0.0017.9460.1670.1670.0000.0000.0000.000
61A64TYR0-0.042-0.0538.974-0.357-0.3570.0000.0000.0000.000
62A65LEU0-0.0380.00111.1640.1660.1660.0000.0000.0000.000
63A66PRO0-0.0020.04011.961-0.002-0.0020.0000.0000.0000.000
64A67TYR0-0.003-0.04213.036-0.008-0.0080.0000.0000.0000.000
65A68PRO0-0.078-0.04115.8440.0220.0220.0000.0000.0000.000
66A69ASP-1-0.810-0.87117.4270.0430.0430.0000.0000.0000.000
67A70GLY00.0300.03413.3440.0640.0640.0000.0000.0000.000
68A71PRO00.0160.0148.885-0.079-0.0790.0000.0000.0000.000
69A72SER0-0.020-0.00610.9710.0450.0450.0000.0000.0000.000
70A73PRO00.027-0.00511.261-0.030-0.0300.0000.0000.0000.000
71A74PHE00.014-0.00111.1350.0190.0190.0000.0000.0000.000
72A75GLN00.0160.0037.636-0.035-0.0350.0000.0000.0000.000
73A76VAL0-0.036-0.0156.482-0.240-0.2400.0000.0000.0000.000
74A77SER00.0100.0137.5100.1200.1200.0000.0000.0000.000
75A78MET00.0120.0123.6400.5620.9900.003-0.104-0.3270.000
76A79LEU0-0.045-0.0152.237-1.286-1.2592.966-1.202-1.791-0.003
77A80GLU-1-0.878-0.9263.9012.3482.574-0.0010.000-0.2250.000
78A81GLY0-0.0170.0055.3770.0860.0860.0000.0000.0000.000
79A82SER0-0.072-0.0306.7500.0130.0130.0000.0000.0000.000
80A83GLY00.0600.0148.719-0.327-0.3270.0000.0000.0000.000
81A84TYR0-0.016-0.00410.5980.1170.1170.0000.0000.0000.000
82A85ALA0-0.0100.01114.060-0.069-0.0690.0000.0000.0000.000
83A86VAL0-0.026-0.01516.5800.0350.0350.0000.0000.0000.000
84A87TYR00.0050.00619.1040.0040.0040.0000.0000.0000.000
85A88ARG10.8540.91919.4150.3630.3630.0000.0000.0000.000
86A89VAL00.0190.01525.2840.0040.0040.0000.0000.0000.000
87A90PHE0-0.029-0.01825.5200.0000.0000.0000.0000.0000.000
88A91ASP-1-0.860-0.93330.806-0.110-0.1100.0000.0000.0000.000
89A92PHE0-0.015-0.01931.561-0.001-0.0010.0000.0000.0000.000
90A93GLU-1-0.803-0.88836.267-0.097-0.0970.0000.0000.0000.000
91A94ASP-1-0.852-0.91239.431-0.110-0.1100.0000.0000.0000.000
92A95GLY00.0230.01240.1460.0030.0030.0000.0000.0000.000
93A96GLY00.0000.02537.371-0.001-0.0010.0000.0000.0000.000
94A97LYS10.8110.90134.5720.1140.1140.0000.0000.0000.000
95A98LEU00.009-0.00528.428-0.002-0.0020.0000.0000.0000.000
96A99SER00.0020.01528.7340.0000.0000.0000.0000.0000.000
97A100THR0-0.010-0.01923.435-0.001-0.0010.0000.0000.0000.000
98A101GLU-1-0.842-0.90822.401-0.240-0.2400.0000.0000.0000.000
99A102PHE0-0.005-0.00717.5950.0080.0080.0000.0000.0000.000
100A103LYS10.9180.95416.3510.3230.3230.0000.0000.0000.000
101A104TYR0-0.008-0.02211.424-0.017-0.0170.0000.0000.0000.000
102A105SER0-0.023-0.00210.7890.0940.0940.0000.0000.0000.000
103A106TYR00.003-0.0055.374-0.151-0.1510.0000.0000.0000.000
104A107GLU-1-0.899-0.9396.565-0.556-0.5560.0000.0000.0000.000
105A108GLY00.0320.0223.039-0.2790.1210.127-0.157-0.3710.000
106A109SER0-0.009-0.0092.691-4.071-2.0760.863-1.090-1.769-0.008
107A110HIS0-0.043-0.0093.2410.6570.5100.0660.288-0.2060.000
108A111ILE00.0060.0016.843-0.169-0.1690.0000.0000.0000.000
109A112LYS10.8530.9119.0040.9420.9420.0000.0000.0000.000
110A113ALA00.0100.00212.530-0.018-0.0180.0000.0000.0000.000
111A114ASP-1-0.868-0.90415.166-0.310-0.3100.0000.0000.0000.000
112A115MET0-0.004-0.01417.1440.0280.0280.0000.0000.0000.000
113A116LYS10.8540.92221.1630.2580.2580.0000.0000.0000.000
114A117LEU0-0.026-0.02523.8140.0010.0010.0000.0000.0000.000
115A118MET00.0060.01427.3460.0060.0060.0000.0000.0000.000
116A119GLY00.0280.00330.8450.0010.0010.0000.0000.0000.000
117A120SER0-0.054-0.02733.3560.0070.0070.0000.0000.0000.000
118A121GLY00.0710.03137.079-0.001-0.0010.0000.0000.0000.000
119A122PHE0-0.0230.00033.8500.0010.0010.0000.0000.0000.000
120A123PRO00.0630.04439.6760.0010.0010.0000.0000.0000.000
121A124ASP-1-0.933-0.96642.213-0.093-0.0930.0000.0000.0000.000
122A125ASP-1-0.896-0.95243.907-0.087-0.0870.0000.0000.0000.000
123A126GLY00.0200.01441.8910.0010.0010.0000.0000.0000.000
124A127PRO0-0.023-0.01438.358-0.002-0.0020.0000.0000.0000.000
125A128VAL00.0290.01834.687-0.005-0.0050.0000.0000.0000.000
126A129MET00.0150.00537.122-0.009-0.0090.0000.0000.0000.000
127A130THR0-0.0020.00539.3260.0010.0010.0000.0000.0000.000
128A131SER0-0.085-0.04837.054-0.002-0.0020.0000.0000.0000.000
129A132GLN00.0090.00938.1020.0030.0030.0000.0000.0000.000
130A133ILE0-0.064-0.02532.9340.0030.0030.0000.0000.0000.000
131A134VAL00.0000.00134.876-0.002-0.0020.0000.0000.0000.000
132A135ASP-1-0.835-0.89930.630-0.171-0.1710.0000.0000.0000.000
133A136GLN0-0.008-0.00927.893-0.004-0.0040.0000.0000.0000.000
134A137ASP-1-0.729-0.78530.472-0.128-0.1280.0000.0000.0000.000
135A138GLY0-0.0170.00728.114-0.013-0.0130.0000.0000.0000.000
136A139CYS00.002-0.00726.6590.0100.0100.0000.0000.0000.000
137A140VAL0-0.005-0.00126.169-0.012-0.0120.0000.0000.0000.000
138A141SER0-0.029-0.00223.2390.0010.0010.0000.0000.0000.000
139A142LYS10.9410.97724.8580.0960.0960.0000.0000.0000.000
140A143LYN0-0.0030.01618.793-0.012-0.0120.0000.0000.0000.000
141A144THR0-0.008-0.01323.3910.0220.0220.0000.0000.0000.000
142A145TYR00.0060.00118.292-0.024-0.0240.0000.0000.0000.000
143A146LEU00.0050.01023.1710.0120.0120.0000.0000.0000.000
144A147ASN0-0.017-0.01423.5300.0010.0010.0000.0000.0000.000
145A148ASN00.0430.00722.301-0.009-0.0090.0000.0000.0000.000
146A149ASN00.0240.01918.5470.0240.0240.0000.0000.0000.000
147A150THR00.0110.01718.918-0.043-0.0430.0000.0000.0000.000
148A151ILE0-0.0060.02116.6700.0250.0250.0000.0000.0000.000
149A152VAL00.0050.00020.697-0.021-0.0210.0000.0000.0000.000
150A153ASP-1-0.770-0.85322.082-0.247-0.2470.0000.0000.0000.000
151A154SER0-0.031-0.01424.7160.0090.0090.0000.0000.0000.000
152A155PHE0-0.001-0.02324.328-0.005-0.0050.0000.0000.0000.000
153A156ASP-1-0.825-0.88828.660-0.121-0.1210.0000.0000.0000.000
154A157TRP00.0020.00026.078-0.007-0.0070.0000.0000.0000.000
155A158SER0-0.017-0.04930.9550.0100.0100.0000.0000.0000.000
156A159TYR0-0.012-0.00429.0080.0010.0010.0000.0000.0000.000
157A160ASN0-0.036-0.04633.8030.0050.0050.0000.0000.0000.000
158A161LEU00.013-0.00436.259-0.006-0.0060.0000.0000.0000.000
159A162GLN00.0370.01838.9920.0050.0050.0000.0000.0000.000
160A163ASN0-0.040-0.02541.0100.0040.0040.0000.0000.0000.000
161A164GLY00.0290.01941.9150.0050.0050.0000.0000.0000.000
162A165LYS10.9100.96542.0200.0790.0790.0000.0000.0000.000
163A166ARG10.8180.87236.2800.1060.1060.0000.0000.0000.000
164A167TYR0-0.065-0.05835.5140.0020.0020.0000.0000.0000.000
165A168ARG10.8840.90735.2950.0900.0900.0000.0000.0000.000
166A169ALA00.0090.01332.0330.0020.0020.0000.0000.0000.000
167A170ARG10.8670.93932.1810.1160.1160.0000.0000.0000.000
168A171VAL0-0.020-0.01626.773-0.002-0.0020.0000.0000.0000.000
169A172SER0-0.029-0.00527.6410.0080.0080.0000.0000.0000.000
170A173SER00.009-0.02822.159-0.018-0.0180.0000.0000.0000.000
171A174HIS0-0.058-0.03122.6550.0320.0320.0000.0000.0000.000
172A175TYR0-0.023-0.03717.013-0.032-0.0320.0000.0000.0000.000
173A176ILE0-0.009-0.00318.6650.0320.0320.0000.0000.0000.000
174A177PHE00.016-0.01212.304-0.052-0.0520.0000.0000.0000.000
175A178ASP-1-0.878-0.93213.349-0.323-0.3230.0000.0000.0000.000
176A179LYS10.7840.88311.399-0.109-0.1090.0000.0000.0000.000
177A180PRO0-0.029-0.03316.233-0.020-0.0200.0000.0000.0000.000
178A181PHE00.0020.01315.4130.0320.0320.0000.0000.0000.000
179A182SER0-0.052-0.01817.6930.0270.0270.0000.0000.0000.000
180A183ALA00.0290.00519.937-0.004-0.0040.0000.0000.0000.000
181A184ASP-1-0.828-0.88920.546-0.016-0.0160.0000.0000.0000.000
182A185LEU00.0080.01423.129-0.011-0.0110.0000.0000.0000.000
183A186MET0-0.016-0.01726.3550.0030.0030.0000.0000.0000.000
184A187LYS10.7980.87118.3110.0140.0140.0000.0000.0000.000
185A188LYS10.8860.93020.460-0.043-0.0430.0000.0000.0000.000
186A189GLN0-0.0050.02322.374-0.034-0.0340.0000.0000.0000.000
187A190PRO0-0.004-0.02624.9040.0110.0110.0000.0000.0000.000
188A191VAL0-0.0220.00419.6060.0120.0120.0000.0000.0000.000
189A192PHE0-0.017-0.00322.984-0.017-0.0170.0000.0000.0000.000
190A193VAL00.0160.00119.4890.0000.0000.0000.0000.0000.000
191A194TYR0-0.0010.01622.4760.0010.0010.0000.0000.0000.000
192A195ARG10.8230.87618.1440.3310.3310.0000.0000.0000.000
193A196LYS10.8370.91723.1860.2000.2000.0000.0000.0000.000
194A197CYS0-0.037-0.01122.911-0.017-0.0170.0000.0000.0000.000
195A198HIS00.0050.00323.9790.0300.0300.0000.0000.0000.000
196A199VAL00.014-0.00424.817-0.020-0.0200.0000.0000.0000.000
197A200LYS10.9500.98826.4180.2180.2180.0000.0000.0000.000
198A201ALA00.0110.00727.599-0.016-0.0160.0000.0000.0000.000
199A202THR00.0390.02629.9470.0150.0150.0000.0000.0000.000
200A203LYS10.9300.94731.4340.1310.1310.0000.0000.0000.000
201A204THR00.0170.01530.9780.0040.0040.0000.0000.0000.000
202A205GLU-1-0.895-0.92125.834-0.242-0.2420.0000.0000.0000.000
203A206VAL0-0.0040.00525.2460.0180.0180.0000.0000.0000.000
204A207THR0-0.004-0.01522.046-0.015-0.0150.0000.0000.0000.000
205A208LEU0-0.028-0.01420.2560.0320.0320.0000.0000.0000.000
206A209ASP-1-0.827-0.86620.318-0.319-0.3190.0000.0000.0000.000
207A210GLU-1-0.807-0.91318.649-0.371-0.3710.0000.0000.0000.000
208A211ARG10.8120.85818.7540.2370.2370.0000.0000.0000.000
209A212GLU-1-0.726-0.86016.164-0.472-0.4720.0000.0000.0000.000
210A213LYS10.9650.98118.9910.1310.1310.0000.0000.0000.000
211A214ALA00.0320.02418.5060.0120.0120.0000.0000.0000.000
212A215PHE0-0.038-0.04020.4050.0200.0200.0000.0000.0000.000
213A216TYR0-0.017-0.04218.537-0.019-0.0190.0000.0000.0000.000
214A217GLU-1-0.946-0.97724.447-0.015-0.0150.0000.0000.0000.000
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