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

tag_button

FMODB ID: 85V6Y

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 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. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2656597.099743
FMO2-HF: Nuclear repulsion 2570719.589059
FMO2-HF: Total energy -85877.510684
FMO2-MP2: Total energy -86124.762015


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.
-10.569-14.70936.578-15.85-16.587-0.07
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 : 0.034 / q_NPA : -0.001
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].
3A3VAL0-0.032-0.0093.044-2.2820.3670.012-1.172-1.4890.004
4A4ILE0-0.0270.0012.722-0.1331.2680.244-0.582-1.0620.002
5A5LYS10.8610.9024.8401.1981.224-0.001-0.011-0.0140.000
6A6PRO00.0590.0077.639-0.060-0.0600.0000.0000.0000.000
7A7GLU-1-0.858-0.9059.627-0.320-0.3200.0000.0000.0000.000
8A8MET0-0.0710.0148.112-0.200-0.2000.0000.0000.0000.000
9A9LYS10.9690.97712.4320.5080.5080.0000.0000.0000.000
10A10MET0-0.0110.01912.301-0.081-0.0810.0000.0000.0000.000
11A11LYS10.8500.91115.7860.4670.4670.0000.0000.0000.000
12A12TYR00.012-0.00216.453-0.057-0.0570.0000.0000.0000.000
13A13PHE00.0540.03520.2870.0280.0280.0000.0000.0000.000
14A14MET0-0.009-0.00122.416-0.017-0.0170.0000.0000.0000.000
15A15ASP-1-0.807-0.89924.790-0.196-0.1960.0000.0000.0000.000
16A16GLY00.014-0.00927.483-0.017-0.0170.0000.0000.0000.000
17A17SER00.0260.02629.8750.0140.0140.0000.0000.0000.000
18A18VAL0-0.015-0.00732.051-0.006-0.0060.0000.0000.0000.000
19A19ASN00.000-0.01034.6430.0040.0040.0000.0000.0000.000
20A20GLY0-0.0080.00237.3290.0070.0070.0000.0000.0000.000
21A21HIS0-0.059-0.02335.5650.0090.0090.0000.0000.0000.000
22A22GLU-1-0.830-0.91533.887-0.166-0.1660.0000.0000.0000.000
23A23PHE0-0.077-0.05328.6380.0030.0030.0000.0000.0000.000
24A24THR0-0.009-0.02128.484-0.003-0.0030.0000.0000.0000.000
25A25VAL0-0.054-0.02026.0770.0090.0090.0000.0000.0000.000
26A26GLU-1-0.851-0.90724.625-0.251-0.2510.0000.0000.0000.000
27A27GLY00.0330.00623.3580.0180.0180.0000.0000.0000.000
28A28GLU-1-0.897-0.93820.146-0.365-0.3650.0000.0000.0000.000
29A29GLY00.0650.03818.8890.0210.0210.0000.0000.0000.000
30A30THR0-0.086-0.04216.439-0.011-0.0110.0000.0000.0000.000
31A31GLY00.0500.00314.2450.0270.0270.0000.0000.0000.000
32A32LYS10.8440.92011.7660.3570.3570.0000.0000.0000.000
33A33PRO00.0250.0037.1220.0750.0750.0000.0000.0000.000
34A34TYR00.016-0.0163.149-1.998-0.6580.291-0.444-1.187-0.003
35A35GLU-1-0.862-0.9217.931-0.153-0.1530.0000.0000.0000.000
36A36GLY0-0.0120.01810.3720.0620.0620.0000.0000.0000.000
37A37LYS10.8630.92711.6720.4380.4380.0000.0000.0000.000
38A38HIS00.0170.00714.192-0.061-0.0610.0000.0000.0000.000
39A39LYS10.9280.96316.4170.3650.3650.0000.0000.0000.000
40A40ILE00.0070.00118.528-0.027-0.0270.0000.0000.0000.000
41A41THR0-0.050-0.01721.4480.0300.0300.0000.0000.0000.000
42A42LEU0-0.032-0.01922.562-0.017-0.0170.0000.0000.0000.000
43A43ASP-1-0.768-0.87326.222-0.180-0.1800.0000.0000.0000.000
44A44VAL0-0.036-0.01228.995-0.010-0.0100.0000.0000.0000.000
45A45THR0-0.059-0.05430.0460.0130.0130.0000.0000.0000.000
46A46LYS10.8690.94532.1350.1910.1910.0000.0000.0000.000
47A47GLY00.0410.02133.722-0.008-0.0080.0000.0000.0000.000
48A48GLY00.0120.02935.700-0.005-0.0050.0000.0000.0000.000
49A49PRO0-0.017-0.03336.1630.0070.0070.0000.0000.0000.000
50A50LEU0-0.007-0.00230.7330.0030.0030.0000.0000.0000.000
51A51PRO0-0.0210.00135.4690.0020.0020.0000.0000.0000.000
52A52PHE00.0270.01030.9310.0040.0040.0000.0000.0000.000
53A53ALA00.0230.01432.619-0.005-0.0050.0000.0000.0000.000
54A54PHE00.0450.01325.420-0.013-0.0130.0000.0000.0000.000
55A55ASP-1-0.809-0.88027.647-0.240-0.2400.0000.0000.0000.000
56A56LEU0-0.042-0.01426.973-0.017-0.0170.0000.0000.0000.000
57A57LEU00.0270.00525.958-0.015-0.0150.0000.0000.0000.000
58A58SER00.0110.02323.912-0.037-0.0370.0000.0000.0000.000
59A59THR0-0.002-0.01320.482-0.041-0.0410.0000.0000.0000.000
60A60VAL00.0180.01119.800-0.049-0.0490.0000.0000.0000.000
61A61PHE00.0390.01019.373-0.045-0.0450.0000.0000.0000.000
62A63GYS10.1980.24415.5650.2080.2080.0000.0000.0000.000
63A65ASN-1-0.049-0.13210.419-0.955-0.9550.0000.0000.0000.000
64A66ARG10.7730.81910.6580.7520.7520.0000.0000.0000.000
65A67CYS0-0.055-0.0017.180-0.298-0.2980.0000.0000.0000.000
66A68LEU0-0.101-0.0497.590-0.199-0.1990.0000.0000.0000.000
67A69THR0-0.002-0.0148.4080.2950.2950.0000.0000.0000.000
68A70LYS10.8390.9257.6390.0630.0630.0000.0000.0000.000
69A71TYR0-0.008-0.0415.572-0.076-0.0760.0000.0000.0000.000
70A72PRO0-0.0270.0087.6460.1200.1200.0000.0000.0000.000
71A73ASP-1-0.872-0.9577.4150.3100.3100.0000.0000.0000.000
72A74ASP-1-0.957-0.9698.114-0.083-0.0830.0000.0000.0000.000
73A75ILE0-0.048-0.0108.456-0.004-0.0040.0000.0000.0000.000
74A76PRO0-0.0040.0095.029-0.255-0.2550.0000.0000.0000.000
75A77ASP-1-0.735-0.8552.608-3.594-3.0270.689-0.317-0.939-0.002
76A78TYR00.005-0.0333.638-1.109-0.7100.019-0.149-0.268-0.001
77A79PHE00.0550.0136.037-0.157-0.1570.0000.0000.0000.000
78A80LYS10.8290.9052.2431.1781.8812.775-0.854-2.6240.000
79A81GLN0-0.050-0.0382.360-5.419-1.5754.473-3.519-4.799-0.024
80A82CYS0-0.065-0.0093.3770.9861.2090.0100.110-0.3430.000
81A83PHE0-0.0620.0043.427-0.0301.3680.004-0.744-0.6580.000
82A84PRO00.067-0.0071.6751.052-15.71228.063-8.166-3.133-0.046
83A85GLY00.003-0.0035.0530.1000.174-0.001-0.002-0.0710.000
84A86GLY00.0110.0297.4360.2250.2250.0000.0000.0000.000
85A87TYR0-0.049-0.0579.401-0.014-0.0140.0000.0000.0000.000
86A88SER00.0420.02911.4750.0410.0410.0000.0000.0000.000
87A89TRP0-0.095-0.04514.549-0.002-0.0020.0000.0000.0000.000
88A90GLU-1-0.784-0.86917.198-0.260-0.2600.0000.0000.0000.000
89A91ARG10.7910.88317.5890.4640.4640.0000.0000.0000.000
90A92LYS10.8410.92422.4920.2080.2080.0000.0000.0000.000
91A93PHE0-0.013-0.02423.713-0.014-0.0140.0000.0000.0000.000
92A94GLU-1-0.804-0.90327.581-0.172-0.1720.0000.0000.0000.000
93A95PHE0-0.010-0.02129.338-0.005-0.0050.0000.0000.0000.000
94A96GLU-1-0.818-0.91532.686-0.134-0.1340.0000.0000.0000.000
95A97ASP-1-0.812-0.89635.299-0.138-0.1380.0000.0000.0000.000
96A98GLY0-0.012-0.01136.4810.0060.0060.0000.0000.0000.000
97A99GLY0-0.0160.00635.110-0.001-0.0010.0000.0000.0000.000
98A100LEU0-0.034-0.01130.936-0.007-0.0070.0000.0000.0000.000
99A101ALA00.0300.00629.2250.0030.0030.0000.0000.0000.000
100A102ILE0-0.026-0.00326.043-0.009-0.0090.0000.0000.0000.000
101A103ALA00.0080.01123.3590.0070.0070.0000.0000.0000.000
102A104LYS10.8230.89421.3330.2540.2540.0000.0000.0000.000
103A105ALA00.0440.01617.5370.0160.0160.0000.0000.0000.000
104A106GLU-1-0.880-0.92515.366-0.489-0.4890.0000.0000.0000.000
105A107ILE0-0.054-0.01211.105-0.015-0.0150.0000.0000.0000.000
106A108SER0-0.041-0.04311.200-0.101-0.1010.0000.0000.0000.000
107A109LEU0-0.008-0.0046.473-0.067-0.0670.0000.0000.0000.000
108A110LYS10.9100.95610.4450.6630.6630.0000.0000.0000.000
109A111GLY00.0530.03011.6420.0110.0110.0000.0000.0000.000
110A112ASN0-0.021-0.03710.381-0.282-0.2820.0000.0000.0000.000
111A113CYS0-0.033-0.01212.059-0.009-0.0090.0000.0000.0000.000
112A114PHE00.0560.0187.398-0.030-0.0300.0000.0000.0000.000
113A115GLU-1-0.910-0.93212.464-0.381-0.3810.0000.0000.0000.000
114A116HIS00.003-0.00814.882-0.028-0.0280.0000.0000.0000.000
115A117LYS10.9270.97516.6960.3590.3590.0000.0000.0000.000
116A118SER00.013-0.01319.522-0.017-0.0170.0000.0000.0000.000
117A119THR0-0.010-0.00221.7550.0280.0280.0000.0000.0000.000
118A120ILE0-0.024-0.02124.726-0.022-0.0220.0000.0000.0000.000
119A121GLU-1-0.873-0.91827.274-0.175-0.1750.0000.0000.0000.000
120A122GLY0-0.010-0.02230.560-0.010-0.0100.0000.0000.0000.000
121A123THR0-0.0180.00232.7880.0090.0090.0000.0000.0000.000
122A124PHE0-0.004-0.02631.734-0.005-0.0050.0000.0000.0000.000
123A125PRO00.0490.04937.7500.0050.0050.0000.0000.0000.000
124A126ASP-1-0.828-0.93140.577-0.112-0.1120.0000.0000.0000.000
125A127SER0-0.054-0.02842.4190.0000.0000.0000.0000.0000.000
126A128SER0-0.047-0.02636.902-0.004-0.0040.0000.0000.0000.000
127A129PRO0-0.003-0.00835.7390.0010.0010.0000.0000.0000.000
128A130ILE00.0120.01231.508-0.004-0.0040.0000.0000.0000.000
129A131ALA00.0280.00735.156-0.002-0.0020.0000.0000.0000.000
130A132GLN0-0.013-0.00838.0390.0040.0040.0000.0000.0000.000
131A133ASN0-0.052-0.01635.660-0.003-0.0030.0000.0000.0000.000
132A134LYS10.9090.95537.0690.1200.1200.0000.0000.0000.000
133A135THR0-0.050-0.04231.9220.0060.0060.0000.0000.0000.000
134A136LEU0-0.041-0.02633.2060.0000.0000.0000.0000.0000.000
135A137GLY0-0.0100.00228.864-0.001-0.0010.0000.0000.0000.000
136A138TRP0-0.028-0.03525.0460.0100.0100.0000.0000.0000.000
137A139GLU-1-0.905-0.94826.525-0.173-0.1730.0000.0000.0000.000
138A140PRO0-0.056-0.03522.819-0.020-0.0200.0000.0000.0000.000
139A141SER0-0.012-0.01820.9800.0080.0080.0000.0000.0000.000
140A142THR0-0.022-0.02419.038-0.017-0.0170.0000.0000.0000.000
141A143GLU-1-0.795-0.84816.119-0.540-0.5400.0000.0000.0000.000
142A144LYS10.9170.96017.2230.2320.2320.0000.0000.0000.000
143A145MET0-0.0080.01012.726-0.008-0.0080.0000.0000.0000.000
144A146THR0-0.007-0.01715.7850.0470.0470.0000.0000.0000.000
145A147VAL00.0520.02012.827-0.057-0.0570.0000.0000.0000.000
146A148ARG10.9030.95115.5710.2450.2450.0000.0000.0000.000
147A149ASP-1-0.871-0.94717.679-0.197-0.1970.0000.0000.0000.000
148A150GLY0-0.0110.00514.1560.0010.0010.0000.0000.0000.000
149A151SER0-0.0300.02113.396-0.097-0.0970.0000.0000.0000.000
150A152MET00.0030.01910.7900.0430.0430.0000.0000.0000.000
151A153LYS10.8940.92513.9620.3300.3300.0000.0000.0000.000
152A154GLY00.0250.00716.802-0.021-0.0210.0000.0000.0000.000
153A155ASP-1-0.904-0.94817.955-0.263-0.2630.0000.0000.0000.000
154A156ASP-1-0.779-0.88420.535-0.338-0.3380.0000.0000.0000.000
155A157ALA0-0.0030.02222.4000.0120.0120.0000.0000.0000.000
156A158ALA00.0090.01224.3490.0020.0020.0000.0000.0000.000
157A159TYR00.0480.01226.0250.0140.0140.0000.0000.0000.000
158A160LEU0-0.043-0.01128.587-0.010-0.0100.0000.0000.0000.000
159A161LYS10.9150.95628.1290.2100.2100.0000.0000.0000.000
160A162LEU00.0060.00833.182-0.003-0.0030.0000.0000.0000.000
161A163VAL00.0380.01136.7380.0030.0030.0000.0000.0000.000
162A164GLY0-0.019-0.01239.8040.0030.0030.0000.0000.0000.000
163A165GLY0-0.043-0.01938.0800.0040.0040.0000.0000.0000.000
164A166GLY00.0060.01637.564-0.001-0.0010.0000.0000.0000.000
165A167ASN0-0.056-0.04832.5210.0000.0000.0000.0000.0000.000
166A168HIS0-0.0110.00433.1600.0100.0100.0000.0000.0000.000
167A169LYS10.8840.95230.4430.1340.1340.0000.0000.0000.000
168A170CYS0-0.073-0.03328.180-0.001-0.0010.0000.0000.0000.000
169A171TYR00.0210.01826.771-0.006-0.0060.0000.0000.0000.000
170A172PHE0-0.012-0.00921.402-0.012-0.0120.0000.0000.0000.000
171A173THR00.0390.02222.5690.0000.0000.0000.0000.0000.000
172A174THR0-0.021-0.00517.8230.0030.0030.0000.0000.0000.000
173A175THR0-0.0210.00817.8140.0200.0200.0000.0000.0000.000
174A176TYR0-0.033-0.05613.134-0.029-0.0290.0000.0000.0000.000
175A177THR00.003-0.01213.497-0.004-0.0040.0000.0000.0000.000
176A178ALA00.0330.0078.861-0.044-0.0440.0000.0000.0000.000
177A179LYS10.8710.93610.2050.6470.6470.0000.0000.0000.000
178A180LYS10.8880.9346.2310.1010.1010.0000.0000.0000.000
179A181LYS10.9820.9919.422-0.248-0.2480.0000.0000.0000.000
180A182ILE0-0.002-0.0036.2780.1410.1410.0000.0000.0000.000
181A183PRO0-0.055-0.0226.6510.0060.0060.0000.0000.0000.000
182A184ASN0-0.0030.0046.1290.0500.0500.0000.0000.0000.000
183A185LEU0-0.006-0.0047.349-0.349-0.3490.0000.0000.0000.000
184A186PRO00.0030.0108.4630.0880.0880.0000.0000.0000.000
185A187GLN00.0640.02810.0070.0030.0030.0000.0000.0000.000
186A188SER0-0.020-0.02912.759-0.073-0.0730.0000.0000.0000.000
187A189HIS0-0.029-0.00910.494-0.061-0.0610.0000.0000.0000.000
188A190PHE00.0270.02214.8580.0050.0050.0000.0000.0000.000
189A191ILE00.0320.01711.540-0.047-0.0470.0000.0000.0000.000
190A192GLY0-0.0200.01614.8320.0430.0430.0000.0000.0000.000
191A193HIS10.7750.85915.2870.4660.4660.0000.0000.0000.000
192A194ARG10.9180.93518.2520.3130.3130.0000.0000.0000.000
193A195ILE0-0.0200.00020.071-0.030-0.0300.0000.0000.0000.000
194A196SER0-0.050-0.01521.7870.0340.0340.0000.0000.0000.000
195A197SER00.022-0.00424.254-0.021-0.0210.0000.0000.0000.000
196A198VAL00.0130.00826.7820.0160.0160.0000.0000.0000.000
197A199VAL00.0370.02030.040-0.010-0.0100.0000.0000.0000.000
198A200ASN0-0.020-0.00832.4570.0150.0150.0000.0000.0000.000
199A201GLY00.0440.02335.0020.0000.0000.0000.0000.0000.000
200A202THR00.0250.01033.749-0.001-0.0010.0000.0000.0000.000
201A203LYS10.8190.91030.9750.1720.1720.0000.0000.0000.000
202A204ILE0-0.005-0.01027.4560.0070.0070.0000.0000.0000.000
203A205GLY0-0.0040.01625.996-0.013-0.0130.0000.0000.0000.000
204A206VAL00.004-0.01121.7150.0110.0110.0000.0000.0000.000
205A207MET0-0.023-0.01720.366-0.014-0.0140.0000.0000.0000.000
206A208GLU-1-0.752-0.85115.800-0.603-0.6030.0000.0000.0000.000
207A209ASP-1-0.819-0.86916.095-0.370-0.3700.0000.0000.0000.000
208A210ALA0-0.026-0.02413.0080.0270.0270.0000.0000.0000.000
209A211ILE00.009-0.00212.108-0.066-0.0660.0000.0000.0000.000
210A212ALA00.0130.0209.8980.0500.0500.0000.0000.0000.000
211A213HIS0-0.004-0.00311.9350.0660.0660.0000.0000.0000.000
212A214LEU00.0480.00414.234-0.022-0.0220.0000.0000.0000.000
213A215TYR00.0170.05316.6270.0400.0400.0000.0000.0000.000
214A216PRO0-0.030-0.03619.603-0.016-0.0160.0000.0000.0000.000
215A217PHE0-0.018-0.02621.4810.0140.0140.0000.0000.0000.000
216A218ASN0-0.0050.00817.569-0.006-0.0060.0000.0000.0000.000