Manual

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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: G6241

Calculation Name: 2ZO6-A-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: 2ZO6

Chain ID: A

ChEMBL ID:

UniProt ID:

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 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. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2654451.687393
FMO2-HF: Nuclear repulsion 2568575.080124
FMO2-HF: Total energy -85876.607269
FMO2-MP2: Total energy -86123.79101


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:1:MET)


Summations of interaction energy for fragment #1(A:1: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.
-11.488-15.50135.913-15.718-16.18-0.069
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.005
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].
3A3VAL0-0.063-0.0303.039-2.1930.4640.013-1.195-1.4750.004
4A4ILE0-0.029-0.0092.853-0.3001.1420.156-0.575-1.0220.002
5A5LYS10.9330.9624.6780.8900.932-0.001-0.011-0.0300.000
6A6PRO00.0550.0077.405-0.054-0.0540.0000.0000.0000.000
7A7GLU-1-0.939-0.9529.425-0.300-0.3000.0000.0000.0000.000
8A8MET0-0.0680.0018.176-0.209-0.2090.0000.0000.0000.000
9A9LYS10.9580.96712.4480.5110.5110.0000.0000.0000.000
10A10MET0-0.0220.01612.357-0.078-0.0780.0000.0000.0000.000
11A11LYS10.9210.95215.8120.4850.4850.0000.0000.0000.000
12A12TYR00.0170.00616.441-0.050-0.0500.0000.0000.0000.000
13A13PHE00.0300.02620.3170.0270.0270.0000.0000.0000.000
14A14MET0-0.018-0.00422.448-0.018-0.0180.0000.0000.0000.000
15A15ASP-1-0.838-0.90924.818-0.195-0.1950.0000.0000.0000.000
16A16GLY00.001-0.02527.509-0.016-0.0160.0000.0000.0000.000
17A17SER00.0160.02129.8980.0130.0130.0000.0000.0000.000
18A18VAL0-0.001-0.00132.245-0.006-0.0060.0000.0000.0000.000
19A19ASN00.000-0.00634.6580.0030.0030.0000.0000.0000.000
20A20GLY0-0.0020.00237.3460.0070.0070.0000.0000.0000.000
21A21HIS0-0.059-0.01935.5570.0090.0090.0000.0000.0000.000
22A22GLU-1-0.920-0.96534.405-0.152-0.1520.0000.0000.0000.000
23A23PHE0-0.099-0.06128.6420.0030.0030.0000.0000.0000.000
24A24THR00.0160.00028.458-0.002-0.0020.0000.0000.0000.000
25A25VAL0-0.063-0.02126.1130.0090.0090.0000.0000.0000.000
26A26GLU-1-0.827-0.91424.648-0.242-0.2420.0000.0000.0000.000
27A27GLY00.0200.00723.3950.0170.0170.0000.0000.0000.000
28A28GLU-1-0.981-0.99020.169-0.333-0.3330.0000.0000.0000.000
29A29GLY00.0710.03618.9040.0190.0190.0000.0000.0000.000
30A30THR0-0.083-0.03916.453-0.015-0.0150.0000.0000.0000.000
31A31GLY00.041-0.00614.2270.0300.0300.0000.0000.0000.000
32A32LYS10.9260.97511.8110.3600.3600.0000.0000.0000.000
33A33PRO00.0300.0037.1800.0690.0690.0000.0000.0000.000
34A34TYR00.015-0.0193.005-2.153-0.7910.303-0.470-1.196-0.003
35A35GLU-1-0.937-0.9668.301-0.138-0.1380.0000.0000.0000.000
36A36GLY0-0.0330.00310.7250.0570.0570.0000.0000.0000.000
37A37LYS10.8320.90112.0190.4100.4100.0000.0000.0000.000
38A38HIS00.0130.00714.192-0.056-0.0560.0000.0000.0000.000
39A39LYS10.9190.95216.4050.3630.3630.0000.0000.0000.000
40A40ILE00.0070.01118.550-0.027-0.0270.0000.0000.0000.000
41A41THR0-0.047-0.02121.4560.0280.0280.0000.0000.0000.000
42A42LEU0-0.034-0.01822.711-0.017-0.0170.0000.0000.0000.000
43A43ASP-1-0.826-0.91726.240-0.184-0.1840.0000.0000.0000.000
44A44VAL0-0.046-0.01729.020-0.009-0.0090.0000.0000.0000.000
45A45THR0-0.060-0.05430.1480.0120.0120.0000.0000.0000.000
46A46LYS10.9750.99532.5560.1750.1750.0000.0000.0000.000
47A47GLY00.0330.02133.748-0.008-0.0080.0000.0000.0000.000
48A48GLY00.0190.02735.723-0.004-0.0040.0000.0000.0000.000
49A49PRO0-0.023-0.03836.1830.0060.0060.0000.0000.0000.000
50A50LEU0-0.005-0.00230.7770.0030.0030.0000.0000.0000.000
51A51PRO0-0.0220.00435.4830.0020.0020.0000.0000.0000.000
52A52PHE00.0260.01430.9530.0040.0040.0000.0000.0000.000
53A53ALA00.0250.01332.742-0.005-0.0050.0000.0000.0000.000
54A54PHE00.0410.01425.451-0.012-0.0120.0000.0000.0000.000
55A55ASP-1-0.813-0.88427.824-0.226-0.2260.0000.0000.0000.000
56A56LEU0-0.032-0.01327.126-0.015-0.0150.0000.0000.0000.000
57A57LEU00.0240.00325.964-0.015-0.0150.0000.0000.0000.000
58A58SER00.0150.02224.034-0.035-0.0350.0000.0000.0000.000
59A59THR00.002-0.00520.570-0.041-0.0410.0000.0000.0000.000
60A60VAL00.0280.01419.905-0.047-0.0470.0000.0000.0000.000
61A61PHE00.0400.00919.383-0.043-0.0430.0000.0000.0000.000
62A63GYS10.1990.24015.5740.1880.1880.0000.0000.0000.000
63A65ASN-1-0.045-0.13210.517-0.909-0.9090.0000.0000.0000.000
64A66ARG10.8100.85110.6270.7240.7240.0000.0000.0000.000
65A67CYS0-0.073-0.0157.261-0.232-0.2320.0000.0000.0000.000
66A68LEU0-0.107-0.0507.792-0.184-0.1840.0000.0000.0000.000
67A69THR00.003-0.0068.6080.2760.2760.0000.0000.0000.000
68A70LYS10.9590.9917.9830.0390.0390.0000.0000.0000.000
69A71TYR0-0.014-0.0475.914-0.084-0.0840.0000.0000.0000.000
70A72PRO0-0.045-0.0018.0290.1300.1300.0000.0000.0000.000
71A73ASP-1-0.846-0.9477.6210.4400.4400.0000.0000.0000.000
72A74ASP-1-0.967-0.9698.289-0.054-0.0540.0000.0000.0000.000
73A75ILE0-0.055-0.0168.725-0.013-0.0130.0000.0000.0000.000
74A76PRO0-0.0170.0005.215-0.202-0.2020.0000.0000.0000.000
75A77ASP-1-0.757-0.8852.646-3.388-2.7320.412-0.265-0.804-0.001
76A78TYR00.002-0.0393.920-0.952-0.6810.008-0.087-0.1910.000
77A79PHE00.0590.0096.183-0.179-0.1790.0000.0000.0000.000
78A80LYS10.8570.9472.2040.9721.6692.630-0.855-2.471-0.001
79A81GLN0-0.063-0.0462.363-5.231-1.5154.333-3.364-4.685-0.024
80A82CYS0-0.055-0.0023.3790.8151.0830.0080.066-0.3430.000
81A83PHE0-0.0500.0113.405-0.0211.3680.005-0.742-0.6520.000
82A84PRO00.035-0.0221.6740.531-16.05728.047-8.218-3.240-0.046
83A85GLY00.000-0.0035.0500.0600.135-0.001-0.002-0.0710.000
84A86GLY00.0020.0117.4440.2210.2210.0000.0000.0000.000
85A87TYR0-0.051-0.0519.4010.0120.0120.0000.0000.0000.000
86A88SER0-0.0190.01111.4710.0650.0650.0000.0000.0000.000
87A89TRP0-0.051-0.03114.604-0.008-0.0080.0000.0000.0000.000
88A90GLU-1-0.868-0.93417.196-0.254-0.2540.0000.0000.0000.000
89A91ARG10.7850.87417.7070.4380.4380.0000.0000.0000.000
90A92LYS10.9460.98922.4970.1970.1970.0000.0000.0000.000
91A93PHE0-0.027-0.02823.918-0.012-0.0120.0000.0000.0000.000
92A94GLU-1-0.910-0.97227.636-0.168-0.1680.0000.0000.0000.000
93A95PHE0-0.021-0.03129.525-0.004-0.0040.0000.0000.0000.000
94A96GLU-1-0.855-0.92232.789-0.124-0.1240.0000.0000.0000.000
95A97ASP-1-0.858-0.93335.418-0.128-0.1280.0000.0000.0000.000
96A98GLY0-0.021-0.01436.5640.0060.0060.0000.0000.0000.000
97A99GLY0-0.0140.00235.193-0.002-0.0020.0000.0000.0000.000
98A100LEU0-0.040-0.01330.793-0.007-0.0070.0000.0000.0000.000
99A101ALA00.0280.00729.1530.0030.0030.0000.0000.0000.000
100A102ILE0-0.0170.00026.013-0.008-0.0080.0000.0000.0000.000
101A103ALA00.0030.00823.3510.0070.0070.0000.0000.0000.000
102A104LYS10.9250.96621.3450.2360.2360.0000.0000.0000.000
103A105ALA00.0420.01617.4990.0160.0160.0000.0000.0000.000
104A106GLU-1-0.903-0.95015.211-0.477-0.4770.0000.0000.0000.000
105A107ILE0-0.0370.00410.976-0.014-0.0140.0000.0000.0000.000
106A108SER0-0.005-0.00811.187-0.074-0.0740.0000.0000.0000.000
107A109LEU0-0.013-0.0076.507-0.051-0.0510.0000.0000.0000.000
108A110LYS10.9380.96510.4470.6050.6050.0000.0000.0000.000
109A111GLY00.0360.02211.6320.0120.0120.0000.0000.0000.000
110A112ASN0-0.034-0.03210.385-0.244-0.2440.0000.0000.0000.000
111A113CYS0-0.026-0.00612.099-0.002-0.0020.0000.0000.0000.000
112A114PHE00.0570.0147.319-0.034-0.0340.0000.0000.0000.000
113A115GLU-1-0.976-0.98312.501-0.336-0.3360.0000.0000.0000.000
114A116HIS0-0.025-0.02214.921-0.029-0.0290.0000.0000.0000.000
115A117LYS10.9881.00516.7290.3540.3540.0000.0000.0000.000
116A118SER0-0.010-0.02319.553-0.018-0.0180.0000.0000.0000.000
117A119THR0-0.009-0.00221.7820.0280.0280.0000.0000.0000.000
118A120ILE0-0.015-0.01924.746-0.022-0.0220.0000.0000.0000.000
119A121GLU-1-0.881-0.92427.292-0.170-0.1700.0000.0000.0000.000
120A122GLY0-0.014-0.02330.572-0.009-0.0090.0000.0000.0000.000
121A123THR0-0.024-0.00432.7980.0080.0080.0000.0000.0000.000
122A124PHE0-0.005-0.02531.903-0.005-0.0050.0000.0000.0000.000
123A125PRO00.0530.04437.8160.0050.0050.0000.0000.0000.000
124A126ASP-1-0.833-0.93140.674-0.107-0.1070.0000.0000.0000.000
125A127SER0-0.084-0.04642.824-0.001-0.0010.0000.0000.0000.000
126A128SER00.0380.04436.532-0.003-0.0030.0000.0000.0000.000
127A129PRO0-0.001-0.01135.9050.0010.0010.0000.0000.0000.000
128A130ILE00.0060.00831.609-0.004-0.0040.0000.0000.0000.000
129A131ALA00.0260.00435.296-0.002-0.0020.0000.0000.0000.000
130A132GLN0-0.001-0.00138.1560.0030.0030.0000.0000.0000.000
131A133ASN0-0.041-0.01535.869-0.004-0.0040.0000.0000.0000.000
132A134LYS10.8980.95337.2480.1130.1130.0000.0000.0000.000
133A135THR0-0.055-0.04532.1290.0050.0050.0000.0000.0000.000
134A136LEU0-0.044-0.02933.4500.0000.0000.0000.0000.0000.000
135A137GLY0-0.0130.00029.1070.0000.0000.0000.0000.0000.000
136A138TRP0-0.043-0.03525.2320.0090.0090.0000.0000.0000.000
137A139GLU-1-0.973-0.98326.793-0.163-0.1630.0000.0000.0000.000
138A140PRO0-0.083-0.05223.179-0.019-0.0190.0000.0000.0000.000
139A141SER0-0.006-0.00321.1140.0070.0070.0000.0000.0000.000
140A142THR0-0.015-0.02419.229-0.014-0.0140.0000.0000.0000.000
141A143GLU-1-0.805-0.85816.487-0.496-0.4960.0000.0000.0000.000
142A144LYS10.9360.96617.3960.2120.2120.0000.0000.0000.000
143A145MET00.0010.01212.877-0.010-0.0100.0000.0000.0000.000
144A146THR0-0.001-0.01715.9270.0440.0440.0000.0000.0000.000
145A147VAL00.0500.02113.068-0.054-0.0540.0000.0000.0000.000
146A148ARG10.9240.95215.7360.2380.2380.0000.0000.0000.000
147A149ASP-1-0.892-0.94517.765-0.184-0.1840.0000.0000.0000.000
148A150GLY0-0.016-0.00114.1410.0000.0000.0000.0000.0000.000
149A151SER0-0.0130.03613.413-0.098-0.0980.0000.0000.0000.000
150A152MET0-0.0130.01011.1060.0440.0440.0000.0000.0000.000
151A153LYS10.9160.95114.1830.3120.3120.0000.0000.0000.000
152A154GLY00.0150.00416.895-0.019-0.0190.0000.0000.0000.000
153A155ASP-1-0.915-0.94818.001-0.251-0.2510.0000.0000.0000.000
154A156ASP-1-0.783-0.89020.773-0.315-0.3150.0000.0000.0000.000
155A157ALA0-0.0140.01522.5410.0110.0110.0000.0000.0000.000
156A158ALA00.0180.01724.6180.0030.0030.0000.0000.0000.000
157A159TYR00.0490.01126.2100.0170.0170.0000.0000.0000.000
158A160LEU0-0.033-0.00928.816-0.009-0.0090.0000.0000.0000.000
159A161LYS10.9630.98029.3810.1880.1880.0000.0000.0000.000
160A162LEU00.0090.01233.430-0.003-0.0030.0000.0000.0000.000
161A163VAL00.0400.01136.9750.0030.0030.0000.0000.0000.000
162A164GLY0-0.021-0.01340.0530.0020.0020.0000.0000.0000.000
163A165GLY0-0.042-0.01838.3590.0040.0040.0000.0000.0000.000
164A166GLY00.0080.01637.834-0.001-0.0010.0000.0000.0000.000
165A167ASN0-0.032-0.02933.333-0.006-0.0060.0000.0000.0000.000
166A168HIS00.0410.02133.1590.0100.0100.0000.0000.0000.000
167A169LYS10.9150.95430.3600.1290.1290.0000.0000.0000.000
168A170CYS0-0.067-0.02428.254-0.002-0.0020.0000.0000.0000.000
169A171TYR00.0290.02326.895-0.005-0.0050.0000.0000.0000.000
170A172PHE0-0.011-0.01321.402-0.011-0.0110.0000.0000.0000.000
171A173THR00.0530.02822.665-0.003-0.0030.0000.0000.0000.000
172A174THR0-0.026-0.00417.8140.0020.0020.0000.0000.0000.000
173A175THR0-0.030-0.01217.9340.0190.0190.0000.0000.0000.000
174A176TYR0-0.041-0.05513.294-0.032-0.0320.0000.0000.0000.000
175A177THR00.005-0.01713.515-0.005-0.0050.0000.0000.0000.000
176A178ALA00.0350.0068.876-0.043-0.0430.0000.0000.0000.000
177A179LYS10.8670.94310.1910.6550.6550.0000.0000.0000.000
178A180LYS10.9570.9727.583-0.286-0.2860.0000.0000.0000.000
179A181LYS10.9700.9879.418-0.211-0.2110.0000.0000.0000.000
180A182ILE0-0.009-0.0046.2700.1370.1370.0000.0000.0000.000
181A183PRO0-0.059-0.0296.6490.0230.0230.0000.0000.0000.000
182A184ASN00.0260.0315.635-0.028-0.0280.0000.0000.0000.000
183A185LEU0-0.002-0.0047.351-0.329-0.3290.0000.0000.0000.000
184A186PRO0-0.0010.0108.6790.0820.0820.0000.0000.0000.000
185A187GLN00.0760.03810.1680.0040.0040.0000.0000.0000.000
186A188SER0-0.041-0.04012.998-0.063-0.0630.0000.0000.0000.000
187A189HIS0-0.029-0.00310.857-0.055-0.0550.0000.0000.0000.000
188A190PHE00.0140.02415.1690.0000.0000.0000.0000.0000.000
189A191ILE00.0300.01411.616-0.040-0.0400.0000.0000.0000.000
190A192GLY0-0.0280.01115.0750.0370.0370.0000.0000.0000.000
191A193HIS10.7790.86415.7650.4330.4330.0000.0000.0000.000
192A194ARG10.9380.95918.5370.2900.2900.0000.0000.0000.000
193A195ILE0-0.0220.00220.370-0.028-0.0280.0000.0000.0000.000
194A196SER0-0.045-0.01622.0550.0230.0230.0000.0000.0000.000
195A197SER00.0280.00124.506-0.020-0.0200.0000.0000.0000.000
196A198VAL00.0080.00227.0200.0160.0160.0000.0000.0000.000
197A199VAL00.0430.02530.008-0.010-0.0100.0000.0000.0000.000
198A200ASN0-0.020-0.00832.4500.0140.0140.0000.0000.0000.000
199A201GLY00.0330.01635.0130.0000.0000.0000.0000.0000.000
200A202THR00.0130.00633.773-0.002-0.0020.0000.0000.0000.000
201A203LYS10.9230.98231.0020.1610.1610.0000.0000.0000.000
202A204ILE0-0.004-0.00627.2240.0070.0070.0000.0000.0000.000
203A205GLY0-0.0040.01325.968-0.012-0.0120.0000.0000.0000.000
204A206VAL00.021-0.00321.5730.0120.0120.0000.0000.0000.000
205A207MET0-0.039-0.01920.505-0.012-0.0120.0000.0000.0000.000
206A208GLU-1-0.769-0.87615.813-0.569-0.5690.0000.0000.0000.000
207A209ASP-1-0.810-0.86916.410-0.363-0.3630.0000.0000.0000.000
208A210ALA0-0.022-0.02213.2490.0250.0250.0000.0000.0000.000
209A211ILE00.000-0.00512.471-0.056-0.0560.0000.0000.0000.000
210A212ALA00.0160.02010.2010.0410.0410.0000.0000.0000.000
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