Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: K95M3

Calculation Name: 5J3N-B-Xray372

Preferred Name:

Target Type:

Ligand Name: [(4z)-2-(1-amino-2-hydroxyethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic acid

ligand 3-letter code: GYS

PDB ID: 5J3N

Chain ID: B

ChEMBL ID:

UniProt ID: P42212

Base Structure: X-ray

Registration Date: 2023-09-19

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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2997342.574564
FMO2-HF: Nuclear repulsion 2906125.79041
FMO2-HF: Total energy -91216.784154
FMO2-MP2: Total energy -91485.058279


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(B:7:HIS)


Summations of interaction energy for fragment #1(B:7:HIS)
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.
-46.987-36.70519.033-11.436-17.876-0.089
Interaction energy analysis for fragmet #1(B:7:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.068 / q_NPA : -0.042
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].
3B9LYS10.8300.8843.892-1.5480.618-0.022-1.222-0.9220.001
4B10GLY00.0550.0436.8570.0720.0720.0000.0000.0000.000
5B11GLU-1-0.841-0.9391.884-32.069-30.57812.551-7.159-6.883-0.099
6B12GLU-1-0.899-0.9625.729-0.971-0.9710.0000.0000.0000.000
7B13LEU0-0.055-0.0127.7380.1790.1790.0000.0000.0000.000
8B14PHE00.003-0.0109.4740.1730.1730.0000.0000.0000.000
9B15THR0-0.057-0.0358.781-0.105-0.1050.0000.0000.0000.000
10B16GLY00.0090.00311.1070.1080.1080.0000.0000.0000.000
11B17VAL0-0.066-0.02614.835-0.026-0.0260.0000.0000.0000.000
12B18VAL00.0010.01914.6690.0450.0450.0000.0000.0000.000
13B19PRO00.0020.00017.9280.0030.0030.0000.0000.0000.000
14B20ILE0-0.014-0.01418.927-0.014-0.0140.0000.0000.0000.000
15B21LEU0-0.012-0.00321.8780.0350.0350.0000.0000.0000.000
16B22VAL0-0.025-0.01423.100-0.015-0.0150.0000.0000.0000.000
17B23GLU-1-0.879-0.91425.487-0.164-0.1640.0000.0000.0000.000
18B24LEU0-0.014-0.00427.7770.0010.0010.0000.0000.0000.000
19B25ASP-1-0.839-0.88430.066-0.107-0.1070.0000.0000.0000.000
20B26GLY00.007-0.01932.449-0.001-0.0010.0000.0000.0000.000
21B27ASP-1-0.921-0.96734.638-0.057-0.0570.0000.0000.0000.000
22B28VAL00.0380.02036.1140.0000.0000.0000.0000.0000.000
23B29ASN0-0.023-0.02238.6970.0000.0000.0000.0000.0000.000
24B30GLY00.0110.01941.2990.0030.0030.0000.0000.0000.000
25B31HIS0-0.028-0.01841.414-0.002-0.0020.0000.0000.0000.000
26B32LYS10.8880.93939.2360.0520.0520.0000.0000.0000.000
27B33PHE0-0.062-0.03933.546-0.002-0.0020.0000.0000.0000.000
28B34SER00.031-0.00234.8360.0040.0040.0000.0000.0000.000
29B35VAL0-0.081-0.04631.151-0.002-0.0020.0000.0000.0000.000
30B36SER00.0160.00530.5340.0020.0020.0000.0000.0000.000
31B37GLY0-0.005-0.02428.7320.0040.0040.0000.0000.0000.000
32B38GLU-1-0.960-0.96026.509-0.247-0.2470.0000.0000.0000.000
33B39GLY00.0210.00225.3500.0020.0020.0000.0000.0000.000
34B40GLU-1-0.847-0.91421.189-0.593-0.5930.0000.0000.0000.000
35B41GLY00.0770.02918.5050.0280.0280.0000.0000.0000.000
36B42ASP-1-0.809-0.89614.710-1.221-1.2210.0000.0000.0000.000
37B43ALA00.0470.02410.9070.0230.0230.0000.0000.0000.000
38B44THR0-0.041-0.02411.680-0.283-0.2830.0000.0000.0000.000
39B45TYR0-0.086-0.05312.665-0.025-0.0250.0000.0000.0000.000
40B46GLY0-0.0100.01914.1770.0870.0870.0000.0000.0000.000
41B47LYS10.7910.89515.2330.7200.7200.0000.0000.0000.000
42B48LEU00.0360.01517.853-0.038-0.0380.0000.0000.0000.000
43B49THR0-0.034-0.01520.7220.0290.0290.0000.0000.0000.000
44B50LEU00.0160.01722.2260.0010.0010.0000.0000.0000.000
45B51LYS10.8180.89926.1860.2280.2280.0000.0000.0000.000
46B52PHE00.0440.01625.438-0.002-0.0020.0000.0000.0000.000
47B53ILE0-0.001-0.01731.1040.0090.0090.0000.0000.0000.000
48B54CYS0-0.033-0.00234.5810.0050.0050.0000.0000.0000.000
49B55THR00.002-0.00435.5240.0080.0080.0000.0000.0000.000
50B56THR00.0340.02437.9550.0050.0050.0000.0000.0000.000
51B57GLY0-0.029-0.00940.2570.0070.0070.0000.0000.0000.000
52B58LYS10.8160.90641.2020.1060.1060.0000.0000.0000.000
53B59LEU00.0290.03034.6880.0060.0060.0000.0000.0000.000
54B60PRO00.0020.00538.1010.0010.0010.0000.0000.0000.000
55B61VAL00.0330.02635.0510.0060.0060.0000.0000.0000.000
56B62PRO00.0360.02136.085-0.007-0.0070.0000.0000.0000.000
57B63TRP00.0310.00232.154-0.008-0.0080.0000.0000.0000.000
58B64PRO00.0670.02631.298-0.011-0.0110.0000.0000.0000.000
59B65THR0-0.074-0.03630.183-0.008-0.0080.0000.0000.0000.000
60B66LEU00.0290.01729.2810.0050.0050.0000.0000.0000.000
61B67VAL00.0320.03725.434-0.015-0.0150.0000.0000.0000.000
62B68THR0-0.075-0.06623.609-0.027-0.0270.0000.0000.0000.000
63B69THR0-0.037-0.00123.049-0.003-0.0030.0000.0000.0000.000
64B70PHE00.0510.01623.835-0.005-0.0050.0000.0000.0000.000
65B72GYS1-0.0280.00519.9270.3150.3150.0000.0000.0000.000
66B74VAL-10.1310.06617.529-0.386-0.3860.0000.0000.0000.000
67B75GLN0-0.029-0.03414.633-0.047-0.0470.0000.0000.0000.000
68B76CYS0-0.0020.02911.454-0.099-0.0990.0000.0000.0000.000
69B77PHE00.0550.01611.305-0.310-0.3100.0000.0000.0000.000
70B78SER0-0.053-0.04111.3600.0010.0010.0000.0000.0000.000
71B79ARG10.8940.92610.7851.1101.1100.0000.0000.0000.000
72B80TYR0-0.011-0.0327.0270.2360.2360.0000.0000.0000.000
73B81PRO00.0060.0087.613-0.717-0.7170.0000.0000.0000.000
74B82ASP-1-0.798-0.9084.186-5.714-5.535-0.001-0.007-0.1700.000
75B83HIS0-0.099-0.0533.115-4.382-3.5330.063-0.427-0.484-0.004
76B84MET0-0.067-0.0325.3351.4181.4180.0000.0000.0000.000
77B85LYS10.8710.9442.5066.5457.2323.309-1.085-2.9100.005
78B86ARG10.8750.9422.835-7.011-2.5472.139-1.933-4.6700.006
79B87HIS0-0.027-0.0213.543-1.352-1.5980.1460.749-0.6490.004
80B88ASP-1-0.744-0.8524.834-2.559-2.5590.0000.0000.0000.000
81B89PHE00.001-0.0066.303-0.355-0.3550.0000.0000.0000.000
82B90PHE00.0070.0128.609-0.026-0.0260.0000.0000.0000.000
83B91LYS10.8210.9036.5862.4722.4720.0000.0000.0000.000
84B92SER0-0.043-0.0205.6160.3890.3890.0000.0000.0000.000
85B93ALA00.006-0.0077.1810.3210.3210.0000.0000.0000.000
86B94MET0-0.0630.02810.2240.1810.1810.0000.0000.0000.000
87B95PRO00.019-0.00910.739-0.024-0.0240.0000.0000.0000.000
88B96GLU-1-0.846-0.91513.506-0.084-0.0840.0000.0000.0000.000
89B97GLY00.0670.01214.4000.0150.0150.0000.0000.0000.000
90B98TYR0-0.056-0.03313.1940.0330.0330.0000.0000.0000.000
91B99VAL00.0180.02416.309-0.023-0.0230.0000.0000.0000.000
92B100GLN00.0210.00417.676-0.021-0.0210.0000.0000.0000.000
93B101GLU-1-0.874-0.92320.203-0.020-0.0200.0000.0000.0000.000
94B102ARG10.7870.84420.3900.2260.2260.0000.0000.0000.000
95B103THR0-0.044-0.01025.4470.0110.0110.0000.0000.0000.000
96B104ILE0-0.018-0.00726.637-0.003-0.0030.0000.0000.0000.000
97B105PHE0-0.004-0.00729.7560.0050.0050.0000.0000.0000.000
98B106PHE0-0.0090.00031.973-0.009-0.0090.0000.0000.0000.000
99B107LYS10.8370.90235.1270.0630.0630.0000.0000.0000.000
100B108ASP-1-0.819-0.88337.097-0.057-0.0570.0000.0000.0000.000
101B109ASP-1-0.774-0.90438.749-0.073-0.0730.0000.0000.0000.000
102B110GLY00.0450.03538.5580.0050.0050.0000.0000.0000.000
103B111ASN0-0.093-0.04633.721-0.003-0.0030.0000.0000.0000.000
104B112TYR00.050-0.00530.6870.0070.0070.0000.0000.0000.000
105B113LYS10.8820.93730.0040.0390.0390.0000.0000.0000.000
106B114THR00.004-0.00726.2370.0000.0000.0000.0000.0000.000
107B115ARG10.8530.91723.8600.0620.0620.0000.0000.0000.000
108B116ALA00.0140.01422.367-0.005-0.0050.0000.0000.0000.000
109B117GLU-1-0.849-0.90620.700-0.082-0.0820.0000.0000.0000.000
110B118VAL0-0.0100.00516.704-0.014-0.0140.0000.0000.0000.000
111B119LYS10.9060.94416.7820.1530.1530.0000.0000.0000.000
112B120PHE00.0190.01513.208-0.017-0.0170.0000.0000.0000.000
113B121GLU-1-0.872-0.91918.166-0.140-0.1400.0000.0000.0000.000
114B122GLY0-0.011-0.01220.3520.0270.0270.0000.0000.0000.000
115B123ASP-1-0.886-0.94018.911-0.348-0.3480.0000.0000.0000.000
116B124THR0-0.046-0.02518.591-0.066-0.0660.0000.0000.0000.000
117B125LEU0-0.0290.00215.8030.0260.0260.0000.0000.0000.000
118B126VAL0-0.010-0.02418.8030.0170.0170.0000.0000.0000.000
119B127ASN00.013-0.00120.4170.0150.0150.0000.0000.0000.000
120B128ARG10.7950.87822.0780.2030.2030.0000.0000.0000.000
121B129ILE0-0.016-0.01824.6490.0080.0080.0000.0000.0000.000
122B130GLU-1-0.844-0.90826.836-0.053-0.0530.0000.0000.0000.000
123B131LEU0-0.025-0.02429.123-0.002-0.0020.0000.0000.0000.000
124B132LYS10.8550.91631.5140.0560.0560.0000.0000.0000.000
125B133GLY0-0.002-0.00133.9240.0010.0010.0000.0000.0000.000
126B134ILE0-0.034-0.01536.0360.0030.0030.0000.0000.0000.000
127B135ASP-1-0.847-0.93738.624-0.038-0.0380.0000.0000.0000.000
128B136PHE0-0.0250.00735.423-0.001-0.0010.0000.0000.0000.000
129B137LYS10.8920.94441.4290.0580.0580.0000.0000.0000.000
130B138ASP-1-0.888-0.94943.935-0.060-0.0600.0000.0000.0000.000
131B139ASP-1-0.886-0.93745.847-0.073-0.0730.0000.0000.0000.000
132B140GLY00.0060.00142.9920.0000.0000.0000.0000.0000.000
133B141ASN0-0.018-0.02739.842-0.003-0.0030.0000.0000.0000.000
134B142ILE0-0.018-0.00336.522-0.007-0.0070.0000.0000.0000.000
135B143LEU0-0.011-0.00939.388-0.004-0.0040.0000.0000.0000.000
136B144GLY00.0350.02742.2800.0010.0010.0000.0000.0000.000
137B145HIS0-0.176-0.10139.681-0.006-0.0060.0000.0000.0000.000
138B146LYS10.8520.93141.6230.0750.0750.0000.0000.0000.000
139B147LEU0-0.045-0.01535.5180.0000.0000.0000.0000.0000.000
140B148GLU-1-0.785-0.86337.050-0.175-0.1750.0000.0000.0000.000
141B149TYR0-0.080-0.06634.378-0.006-0.0060.0000.0000.0000.000
142B150ASN0-0.038-0.03333.399-0.025-0.0250.0000.0000.0000.000
143B151TYR0-0.047-0.04726.2340.0090.0090.0000.0000.0000.000
144B152ASN0-0.031-0.00629.547-0.006-0.0060.0000.0000.0000.000
145B153GLU-1-0.838-0.90324.547-0.408-0.4080.0000.0000.0000.000
146B154HIS00.0100.00323.7730.0540.0540.0000.0000.0000.000
147B155LEU0-0.019-0.00120.637-0.044-0.0440.0000.0000.0000.000
148B156VAL0-0.029-0.01218.0060.0490.0490.0000.0000.0000.000
149B157TYR00.012-0.00217.683-0.026-0.0260.0000.0000.0000.000
150B158ILE00.0030.00113.0980.0160.0160.0000.0000.0000.000
151B159MET0-0.031-0.02015.7850.0640.0640.0000.0000.0000.000
152B160ALA00.0390.01312.829-0.030-0.0300.0000.0000.0000.000
153B161ASP-1-0.794-0.87814.6810.2570.2570.0000.0000.0000.000
154B162LYS10.9210.94511.724-1.008-1.0080.0000.0000.0000.000
155B163GLN0-0.0100.01516.153-0.009-0.0090.0000.0000.0000.000
156B164LYS10.8170.88818.384-0.214-0.2140.0000.0000.0000.000
157B165ASN00.0130.01313.1800.0560.0560.0000.0000.0000.000
158B166GLY00.0840.03314.031-0.043-0.0430.0000.0000.0000.000
159B167THR0-0.102-0.04211.9970.0920.0920.0000.0000.0000.000
160B168LYS10.8780.93115.144-0.095-0.0950.0000.0000.0000.000
161B169ALA00.0330.02417.3780.0020.0020.0000.0000.0000.000
162B170ILE0-0.019-0.01519.6410.0170.0170.0000.0000.0000.000
163B171PHE0-0.012-0.00521.607-0.014-0.0140.0000.0000.0000.000
164B172GLN0-0.007-0.01424.4190.0030.0030.0000.0000.0000.000
165B173VAL0-0.050-0.01426.136-0.017-0.0170.0000.0000.0000.000
166B174HIS0-0.001-0.01528.5150.0170.0170.0000.0000.0000.000
167B175HIS00.0190.01630.047-0.017-0.0170.0000.0000.0000.000
168B176ASN00.020-0.00233.6410.0130.0130.0000.0000.0000.000
169B177ILE0-0.058-0.03136.734-0.001-0.0010.0000.0000.0000.000
170B178GLU-1-0.882-0.95640.150-0.138-0.1380.0000.0000.0000.000
171B179ASP-1-0.974-0.98842.187-0.092-0.0920.0000.0000.0000.000
172B180GLY0-0.0130.00243.1570.0040.0040.0000.0000.0000.000
173B181GLY0-0.022-0.01341.1580.0070.0070.0000.0000.0000.000
174B182VAL0-0.024-0.01534.581-0.008-0.0080.0000.0000.0000.000
175B183GLN0-0.038-0.01135.4580.0120.0120.0000.0000.0000.000
176B184LEU0-0.022-0.00533.111-0.009-0.0090.0000.0000.0000.000
177B185ALA00.0500.01730.7090.0090.0090.0000.0000.0000.000
178B186ASP-1-0.853-0.89629.103-0.093-0.0930.0000.0000.0000.000
179B187HIS0-0.0090.00824.603-0.009-0.0090.0000.0000.0000.000
180B188TYR00.000-0.01324.7180.0150.0150.0000.0000.0000.000
181B189GLN00.0110.00618.0130.0000.0000.0000.0000.0000.000
182B190GLN0-0.055-0.04319.8850.0380.0380.0000.0000.0000.000
183B191ASN00.0220.02015.494-0.037-0.0370.0000.0000.0000.000
184B192THR00.0070.00516.2350.0560.0560.0000.0000.0000.000
185B193PRO00.0220.01913.548-0.069-0.0690.0000.0000.0000.000
186B194ILE0-0.035-0.01715.5890.0420.0420.0000.0000.0000.000
187B195GLY00.0030.00916.6260.0150.0150.0000.0000.0000.000
188B196ASP-1-0.947-0.98015.9740.2180.2180.0000.0000.0000.000
189B197GLY0-0.0140.00913.1410.0820.0820.0000.0000.0000.000
190B198PRO0-0.064-0.0368.9900.0170.0170.0000.0000.0000.000
191B199VAL00.0150.0067.978-0.193-0.1930.0000.0000.0000.000
192B200LEU0-0.041-0.0112.644-0.2810.4110.848-0.352-1.188-0.002
193B201LEU0-0.010-0.0066.460-0.319-0.3190.0000.0000.0000.000
194B202PRO0-0.036-0.0078.5980.2810.2810.0000.0000.0000.000
195B203ASP-1-0.817-0.9169.5591.3901.3900.0000.0000.0000.000
196B204ASN0-0.028-0.02311.974-0.109-0.1090.0000.0000.0000.000
197B205HIS0-0.0240.00410.970-0.169-0.1690.0000.0000.0000.000
198B206TYR00.0120.00914.7850.0290.0290.0000.0000.0000.000
199B207LEU00.0180.01812.761-0.088-0.0880.0000.0000.0000.000
200B208HIS0-0.027-0.02116.4050.0810.0810.0000.0000.0000.000
201B209THR0-0.039-0.02118.435-0.095-0.0950.0000.0000.0000.000
202B210GLN0-0.048-0.02720.7140.0430.0430.0000.0000.0000.000
203B211SER0-0.001-0.04023.267-0.027-0.0270.0000.0000.0000.000
204B212ALA00.0130.01025.6800.0260.0260.0000.0000.0000.000
205B213LEU00.0020.00728.720-0.009-0.0090.0000.0000.0000.000
206B214SER00.0000.00131.2400.0070.0070.0000.0000.0000.000
207B215LYS10.8750.94033.8390.1780.1780.0000.0000.0000.000
208B216ASP-1-0.734-0.86535.417-0.208-0.2080.0000.0000.0000.000
209B217PRO0-0.008-0.00537.0970.0110.0110.0000.0000.0000.000
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