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: N9G7Q

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 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. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2657385.631275
FMO2-HF: Nuclear repulsion 2571507.36121
FMO2-HF: Total energy -85878.270065
FMO2-MP2: Total energy -86125.403096


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.
-14.305-6.43316.392-9.822-14.441-0.053
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 : 0.042 / q_NPA : 0.010
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].
3A3VAL0-0.0090.0053.574-1.6030.703-0.013-1.070-1.2230.002
4A4ILE0-0.0040.0093.2420.2851.3130.037-0.360-0.7050.001
5A5LYS10.8310.8904.6421.0881.128-0.001-0.011-0.0280.000
6A6PRO00.0520.0037.395-0.041-0.0410.0000.0000.0000.000
7A7GLU-1-0.867-0.9159.670-0.240-0.2400.0000.0000.0000.000
8A8MET0-0.0670.0098.368-0.196-0.1960.0000.0000.0000.000
9A9LYS10.9760.98412.5430.4290.4290.0000.0000.0000.000
10A10MET0-0.0100.00612.894-0.085-0.0850.0000.0000.0000.000
11A11LYS10.8110.89016.0840.4150.4150.0000.0000.0000.000
12A12TYR00.009-0.00516.864-0.064-0.0640.0000.0000.0000.000
13A13PHE00.0520.02920.4190.0280.0280.0000.0000.0000.000
14A14MET00.0050.01522.358-0.021-0.0210.0000.0000.0000.000
15A15ASP-1-0.789-0.88324.942-0.193-0.1930.0000.0000.0000.000
16A16GLY00.033-0.00127.554-0.019-0.0190.0000.0000.0000.000
17A17SER00.0090.02330.1690.0130.0130.0000.0000.0000.000
18A18VAL00.003-0.00332.401-0.007-0.0070.0000.0000.0000.000
19A19ASN0-0.019-0.02135.0290.0010.0010.0000.0000.0000.000
20A20GLY00.0010.01337.5190.0070.0070.0000.0000.0000.000
21A21HIS0-0.066-0.03035.7440.0080.0080.0000.0000.0000.000
22A22GLU-1-0.844-0.91633.981-0.164-0.1640.0000.0000.0000.000
23A23PHE0-0.054-0.04028.7940.0040.0040.0000.0000.0000.000
24A24THR0-0.023-0.03928.616-0.003-0.0030.0000.0000.0000.000
25A25VAL0-0.065-0.02726.5580.0100.0100.0000.0000.0000.000
26A26GLU-1-0.841-0.89424.990-0.246-0.2460.0000.0000.0000.000
27A27GLY00.0300.00523.9040.0190.0190.0000.0000.0000.000
28A28GLU-1-0.870-0.92820.549-0.332-0.3320.0000.0000.0000.000
29A29GLY00.0600.03318.9740.0220.0220.0000.0000.0000.000
30A30THR0-0.077-0.04116.675-0.010-0.0100.0000.0000.0000.000
31A31GLY00.0460.00814.2000.0210.0210.0000.0000.0000.000
32A32LYS10.8710.93511.8400.2170.2170.0000.0000.0000.000
33A33PRO00.0130.0037.0510.0680.0680.0000.0000.0000.000
34A34TYR00.012-0.0103.064-2.107-0.6660.401-0.494-1.348-0.002
35A35GLU-1-0.866-0.9228.0430.0410.0410.0000.0000.0000.000
36A36GLY0-0.0140.00910.4190.0260.0260.0000.0000.0000.000
37A37LYS10.8730.94011.6900.2820.2820.0000.0000.0000.000
38A38HIS00.000-0.00114.364-0.043-0.0430.0000.0000.0000.000
39A39LYS10.9480.97316.3660.2980.2980.0000.0000.0000.000
40A40ILE00.0060.00118.822-0.024-0.0240.0000.0000.0000.000
41A41THR0-0.047-0.01821.5940.0290.0290.0000.0000.0000.000
42A42LEU0-0.027-0.01222.840-0.016-0.0160.0000.0000.0000.000
43A43ASP-1-0.741-0.85726.657-0.154-0.1540.0000.0000.0000.000
44A44VAL0-0.031-0.00829.324-0.011-0.0110.0000.0000.0000.000
45A45THR0-0.065-0.05329.9880.0130.0130.0000.0000.0000.000
46A46LYS10.8450.92232.0820.1880.1880.0000.0000.0000.000
47A47GLY00.0500.03033.803-0.007-0.0070.0000.0000.0000.000
48A48GLY00.0180.01835.767-0.005-0.0050.0000.0000.0000.000
49A49PRO0-0.030-0.03236.1530.0060.0060.0000.0000.0000.000
50A50LEU00.0040.00530.9630.0020.0020.0000.0000.0000.000
51A51PRO0-0.014-0.00235.6940.0020.0020.0000.0000.0000.000
52A52PHE00.0070.00131.1280.0040.0040.0000.0000.0000.000
53A53ALA00.0220.01732.471-0.005-0.0050.0000.0000.0000.000
54A54PHE00.0460.01525.635-0.013-0.0130.0000.0000.0000.000
55A55ASP-1-0.795-0.88027.485-0.218-0.2180.0000.0000.0000.000
56A56LEU0-0.034-0.00826.734-0.016-0.0160.0000.0000.0000.000
57A57LEU00.0290.00925.819-0.014-0.0140.0000.0000.0000.000
58A58SER00.0170.02323.920-0.036-0.0360.0000.0000.0000.000
59A59THR0-0.036-0.03120.640-0.035-0.0350.0000.0000.0000.000
60A60VAL00.0160.02119.926-0.039-0.0390.0000.0000.0000.000
61A61PHE00.0550.02319.468-0.042-0.0420.0000.0000.0000.000
62A63GYS1-0.099-0.07316.7930.2890.2890.0000.0000.0000.000
63A65ASN-10.1600.06310.760-0.754-0.7540.0000.0000.0000.000
64A66ARG10.7780.87610.7460.6640.6640.0000.0000.0000.000
65A67CYS0-0.0220.0247.196-0.262-0.2620.0000.0000.0000.000
66A68LEU0-0.079-0.0307.539-0.098-0.0980.0000.0000.0000.000
67A69THR00.004-0.0198.5300.2400.2400.0000.0000.0000.000
68A70LYS10.8170.9057.670-0.080-0.0800.0000.0000.0000.000
69A71TYR00.003-0.0335.548-0.097-0.0970.0000.0000.0000.000
70A72PRO0-0.0230.0077.3740.1440.1440.0000.0000.0000.000
71A73ASP-1-0.888-0.9557.1590.2880.2880.0000.0000.0000.000
72A74ASP-1-0.914-0.9518.172-0.105-0.1050.0000.0000.0000.000
73A75ILE0-0.059-0.0138.334-0.016-0.0160.0000.0000.0000.000
74A76PRO00.0030.0004.965-0.273-0.2730.0000.0000.0000.000
75A77ASP-1-0.746-0.8652.387-3.120-2.8081.208-0.400-1.120-0.003
76A78TYR00.010-0.0133.687-1.006-0.6230.016-0.143-0.256-0.001
77A79PHE00.0290.0086.285-0.130-0.1300.0000.0000.0000.000
78A80LYS10.8370.8952.2570.3831.3992.475-0.886-2.605-0.001
79A81GLN0-0.044-0.0412.213-4.539-0.9364.205-3.459-4.349-0.017
80A82CYS0-0.0500.0043.2940.6510.7500.0050.210-0.3140.000
81A83PHE0-0.061-0.0023.7080.5241.0780.001-0.219-0.3350.000
82A84PRO00.043-0.0061.894-5.474-8.3848.058-2.990-2.158-0.032
83A85GLY00.0010.0015.4010.1070.1070.0000.0000.0000.000
84A86GLY00.0160.0327.4730.2200.2200.0000.0000.0000.000
85A87TYR0-0.037-0.0559.373-0.001-0.0010.0000.0000.0000.000
86A88SER00.0330.02811.6590.0530.0530.0000.0000.0000.000
87A89TRP0-0.070-0.03214.632-0.007-0.0070.0000.0000.0000.000
88A90GLU-1-0.776-0.86417.203-0.260-0.2600.0000.0000.0000.000
89A91ARG10.7850.87917.6940.4230.4230.0000.0000.0000.000
90A92LYS10.8470.92422.5000.2020.2020.0000.0000.0000.000
91A93PHE00.003-0.01423.474-0.015-0.0150.0000.0000.0000.000
92A94GLU-1-0.791-0.89027.582-0.166-0.1660.0000.0000.0000.000
93A95PHE00.006-0.00929.216-0.004-0.0040.0000.0000.0000.000
94A96GLU-1-0.795-0.88332.675-0.124-0.1240.0000.0000.0000.000
95A97ASP-1-0.794-0.89135.447-0.131-0.1310.0000.0000.0000.000
96A98GLY0-0.013-0.00736.6780.0060.0060.0000.0000.0000.000
97A99GLY0-0.0240.00035.0730.0000.0000.0000.0000.0000.000
98A100LEU0-0.026-0.00931.091-0.007-0.0070.0000.0000.0000.000
99A101ALA00.0200.00429.2130.0030.0030.0000.0000.0000.000
100A102ILE0-0.028-0.01526.041-0.007-0.0070.0000.0000.0000.000
101A103ALA00.0050.01723.3020.0070.0070.0000.0000.0000.000
102A104LYS10.8270.89121.4680.2540.2540.0000.0000.0000.000
103A105ALA00.0320.01117.8740.0200.0200.0000.0000.0000.000
104A106GLU-1-0.831-0.89815.083-0.539-0.5390.0000.0000.0000.000
105A107ILE0-0.063-0.01111.2740.0030.0030.0000.0000.0000.000
106A108SER0-0.013-0.04311.656-0.159-0.1590.0000.0000.0000.000
107A109LEU0-0.020-0.0247.123-0.089-0.0890.0000.0000.0000.000
108A110LYS10.8790.94111.0810.5980.5980.0000.0000.0000.000
109A111GLY00.0620.02712.2900.0230.0230.0000.0000.0000.000
110A112ASN0-0.037-0.02710.944-0.249-0.2490.0000.0000.0000.000
111A113CYS0-0.036-0.00212.3060.0280.0280.0000.0000.0000.000
112A114PHE00.0640.0187.870-0.025-0.0250.0000.0000.0000.000
113A115GLU-1-0.821-0.87612.792-0.383-0.3830.0000.0000.0000.000
114A116HIS00.0130.00915.274-0.033-0.0330.0000.0000.0000.000
115A117LYS10.8800.94916.7870.3540.3540.0000.0000.0000.000
116A118SER0-0.025-0.01719.579-0.019-0.0190.0000.0000.0000.000
117A119THR0-0.014-0.00621.7680.0290.0290.0000.0000.0000.000
118A120ILE0-0.022-0.02324.628-0.022-0.0220.0000.0000.0000.000
119A121GLU-1-0.849-0.90827.227-0.174-0.1740.0000.0000.0000.000
120A122GLY0-0.006-0.01930.522-0.009-0.0090.0000.0000.0000.000
121A123THR0-0.028-0.00533.0000.0080.0080.0000.0000.0000.000
122A124PHE00.021-0.00431.857-0.003-0.0030.0000.0000.0000.000
123A125PRO00.0510.04937.8810.0050.0050.0000.0000.0000.000
124A126ASP-1-0.836-0.93640.680-0.108-0.1080.0000.0000.0000.000
125A127SER0-0.036-0.01742.9590.0000.0000.0000.0000.0000.000
126A128SER0-0.022-0.02836.998-0.002-0.0020.0000.0000.0000.000
127A129PRO0-0.006-0.02535.5060.0020.0020.0000.0000.0000.000
128A130ILE00.0020.01031.579-0.003-0.0030.0000.0000.0000.000
129A131ALA00.0340.00835.135-0.001-0.0010.0000.0000.0000.000
130A132GLN0-0.0040.00838.2330.0040.0040.0000.0000.0000.000
131A133ASN0-0.067-0.02835.500-0.001-0.0010.0000.0000.0000.000
132A134LYS10.8710.95536.9710.1110.1110.0000.0000.0000.000
133A135THR0-0.048-0.04531.7270.0060.0060.0000.0000.0000.000
134A136LEU0-0.032-0.01533.2950.0020.0020.0000.0000.0000.000
135A137GLY00.0250.02429.0150.0000.0000.0000.0000.0000.000
136A138TRP0-0.020-0.03325.1210.0080.0080.0000.0000.0000.000
137A139GLU-1-0.859-0.91827.009-0.143-0.1430.0000.0000.0000.000
138A140PRO0-0.074-0.04423.101-0.018-0.0180.0000.0000.0000.000
139A141SER0-0.011-0.00421.1400.0070.0070.0000.0000.0000.000
140A142THR0-0.086-0.06818.844-0.006-0.0060.0000.0000.0000.000
141A143GLU-1-0.767-0.81616.136-0.500-0.5000.0000.0000.0000.000
142A144LYS10.8280.90817.1580.2420.2420.0000.0000.0000.000
143A145MET0-0.0150.01112.470-0.009-0.0090.0000.0000.0000.000
144A146THR0-0.018-0.02415.8290.0470.0470.0000.0000.0000.000
145A147VAL00.0550.03112.606-0.051-0.0510.0000.0000.0000.000
146A148ARG10.8890.94215.3400.2700.2700.0000.0000.0000.000
147A149ASP-1-0.847-0.93117.424-0.248-0.2480.0000.0000.0000.000
148A150GLY0-0.0180.00014.4260.0000.0000.0000.0000.0000.000
149A151SER0-0.0330.00913.208-0.111-0.1110.0000.0000.0000.000
150A152MET0-0.0230.00411.1630.0330.0330.0000.0000.0000.000
151A153LYS10.9060.93314.2770.3480.3480.0000.0000.0000.000
152A154GLY00.0420.01016.430-0.031-0.0310.0000.0000.0000.000
153A155ASP-1-0.869-0.91217.712-0.277-0.2770.0000.0000.0000.000
154A156ASP-1-0.765-0.88120.438-0.293-0.2930.0000.0000.0000.000
155A157ALA00.0040.02322.3420.0070.0070.0000.0000.0000.000
156A158ALA00.0050.00824.0740.0100.0100.0000.0000.0000.000
157A159TYR00.0480.02125.8450.0110.0110.0000.0000.0000.000
158A160LEU0-0.038-0.00528.347-0.010-0.0100.0000.0000.0000.000
159A161LYS10.8610.92028.7030.1760.1760.0000.0000.0000.000
160A162LEU00.0180.01233.292-0.004-0.0040.0000.0000.0000.000
161A163VAL00.013-0.00436.7840.0040.0040.0000.0000.0000.000
162A164GLY00.0030.00439.9210.0020.0020.0000.0000.0000.000
163A165GLY0-0.051-0.02038.0910.0040.0040.0000.0000.0000.000
164A166GLY00.0120.01737.600-0.001-0.0010.0000.0000.0000.000
165A167ASN0-0.090-0.07232.2180.0010.0010.0000.0000.0000.000
166A168HIS0-0.027-0.00833.2790.0100.0100.0000.0000.0000.000
167A169LYS10.8380.90830.0610.1270.1270.0000.0000.0000.000
168A170CYS0-0.077-0.03927.794-0.003-0.0030.0000.0000.0000.000
169A171TYR00.0010.00626.942-0.006-0.0060.0000.0000.0000.000
170A172PHE0-0.007-0.00521.446-0.012-0.0120.0000.0000.0000.000
171A173THR00.019-0.00122.5760.0050.0050.0000.0000.0000.000
172A174THR0-0.036-0.01217.8000.0030.0030.0000.0000.0000.000
173A175THR0-0.031-0.00718.1370.0220.0220.0000.0000.0000.000
174A176TYR0-0.020-0.05113.560-0.027-0.0270.0000.0000.0000.000
175A177THR00.006-0.00913.922-0.001-0.0010.0000.0000.0000.000
176A178ALA00.0300.0079.042-0.039-0.0390.0000.0000.0000.000
177A179LYS10.7950.88810.6930.6740.6740.0000.0000.0000.000
178A180LYS10.8920.9255.6320.9020.9020.0000.0000.0000.000
179A181LYS10.9730.9929.638-0.099-0.0990.0000.0000.0000.000
180A182ILE00.0190.0136.1380.0760.0760.0000.0000.0000.000
181A183PRO0-0.057-0.0186.1630.0840.0840.0000.0000.0000.000
182A184ASN0-0.016-0.0125.7630.1210.1210.0000.0000.0000.000
183A185LEU00.0080.0017.205-0.350-0.3500.0000.0000.0000.000
184A186PRO0-0.0090.0118.4020.1100.1100.0000.0000.0000.000
185A187GLN00.0730.01710.181-0.015-0.0150.0000.0000.0000.000
186A188SER0-0.012-0.01612.954-0.077-0.0770.0000.0000.0000.000
187A189HIS00.0360.03710.700-0.028-0.0280.0000.0000.0000.000
188A190PHE00.0310.01714.5660.0200.0200.0000.0000.0000.000
189A191ILE00.0150.00111.429-0.044-0.0440.0000.0000.0000.000
190A192GLY00.0100.03214.7870.0320.0320.0000.0000.0000.000
191A193HIS10.7530.84715.3450.4030.4030.0000.0000.0000.000
192A194ARG10.9060.91918.4090.2410.2410.0000.0000.0000.000
193A195ILE0-0.0060.01220.283-0.017-0.0170.0000.0000.0000.000
194A196SER0-0.034-0.00821.6890.0290.0290.0000.0000.0000.000
195A197SER00.006-0.01524.129-0.020-0.0200.0000.0000.0000.000
196A198VAL00.0080.01026.7810.0140.0140.0000.0000.0000.000
197A199VAL00.0430.01929.961-0.011-0.0110.0000.0000.0000.000
198A200ASN0-0.028-0.01432.6030.0140.0140.0000.0000.0000.000
199A201GLY00.0430.02135.3630.0000.0000.0000.0000.0000.000
200A202THR00.0120.00133.851-0.001-0.0010.0000.0000.0000.000
201A203LYS10.8130.90431.5100.1470.1470.0000.0000.0000.000
202A204ILE00.001-0.00227.3830.0050.0050.0000.0000.0000.000
203A205GLY0-0.0080.00726.032-0.009-0.0090.0000.0000.0000.000
204A206VAL0-0.001-0.01221.7920.0100.0100.0000.0000.0000.000
205A207MET0-0.019-0.01420.310-0.005-0.0050.0000.0000.0000.000
206A208GLU-1-0.742-0.84815.962-0.513-0.5130.0000.0000.0000.000
207A209ASP-1-0.808-0.86016.184-0.280-0.2800.0000.0000.0000.000
208A210ALA0-0.028-0.01513.0890.0130.0130.0000.0000.0000.000
209A211ILE00.002-0.00812.118-0.045-0.0450.0000.0000.0000.000
210A212ALA00.0140.0169.8340.0350.0350.0000.0000.0000.000
211A213HIS0-0.010-0.01011.8680.0630.0630.0000.0000.0000.000
212A214LEU00.0540.00714.119-0.031-0.0310.0000.0000.0000.000
213A215TYR00.0280.05816.6120.0340.0340.0000.0000.0000.000
214A216PRO0-0.030-0.03019.473-0.014-0.0140.0000.0000.0000.000
215A217PHE0-0.012-0.02221.4480.0140.0140.0000.0000.0000.000
216A218ASN0-0.0100.00317.288-0.007-0.0070.0000.0000.0000.000