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: VQG51

Calculation Name: 1ZD8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZD8

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UIJ7

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2411337.461452
FMO2-HF: Nuclear repulsion 2328467.056229
FMO2-HF: Total energy -82870.405222
FMO2-MP2: Total energy -83117.074741


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:6:LEU)


Summations of interaction energy for fragment #1(A:6:LEU)
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.
-8.143-0.0397.76-4.526-11.337-0.04
Interaction energy analysis for fragmet #1(A:6:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : 0.007
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].
3A8ARG10.8290.9202.6891.0214.0050.728-1.360-2.3510.003
4A9ALA00.0350.0216.5670.4130.4130.0000.0000.0000.000
5A10VAL00.0030.0109.4310.0930.0930.0000.0000.0000.000
6A11ILE0-0.0140.00012.7790.0300.0300.0000.0000.0000.000
7A12MET0-0.019-0.01015.9250.0310.0310.0000.0000.0000.000
8A13GLY00.0720.01719.5610.0100.0100.0000.0000.0000.000
9A14ALA00.0270.02523.0300.0010.0010.0000.0000.0000.000
10A15PRO0-0.027-0.01025.9790.0030.0030.0000.0000.0000.000
11A16GLY00.0870.04527.5470.0040.0040.0000.0000.0000.000
12A17SER0-0.027-0.02224.6170.0050.0050.0000.0000.0000.000
13A18GLY00.0380.01024.8290.0050.0050.0000.0000.0000.000
14A19LYS10.7910.89318.9050.2680.2680.0000.0000.0000.000
15A20GLY00.0550.03419.842-0.007-0.0070.0000.0000.0000.000
16A21THR0-0.002-0.00720.3420.0060.0060.0000.0000.0000.000
17A22VAL0-0.0030.00117.0790.0160.0160.0000.0000.0000.000
18A23SER00.032-0.01715.6270.0000.0000.0000.0000.0000.000
19A24SER0-0.0250.02215.5550.0160.0160.0000.0000.0000.000
20A25ARG10.8600.92917.1460.0770.0770.0000.0000.0000.000
21A26ILE00.0270.00311.5800.0290.0290.0000.0000.0000.000
22A27THR0-0.003-0.02412.4550.0280.0280.0000.0000.0000.000
23A28THR0-0.080-0.03713.4420.0510.0510.0000.0000.0000.000
24A29HIS00.0070.01214.2980.0410.0410.0000.0000.0000.000
25A30PHE0-0.0410.0098.9550.0000.0000.0000.0000.0000.000
26A31GLU-1-0.807-0.8695.5170.7750.7750.0000.0000.0000.000
27A32LEU0-0.032-0.0265.7110.2670.2670.0000.0000.0000.000
28A33LYS10.7720.8766.738-0.360-0.3600.0000.0000.0000.000
29A34HIS0-0.047-0.0368.769-0.141-0.1410.0000.0000.0000.000
30A35LEU0-0.0040.0039.3740.0390.0390.0000.0000.0000.000
31A36SER0-0.028-0.03113.223-0.037-0.0370.0000.0000.0000.000
32A37SER00.008-0.01516.8740.0310.0310.0000.0000.0000.000
33A38GLY00.003-0.00518.4890.0200.0200.0000.0000.0000.000
34A39ASP-1-0.795-0.86519.080-0.100-0.1000.0000.0000.0000.000
35A40LEU00.0470.04616.4790.0210.0210.0000.0000.0000.000
36A41LEU0-0.027-0.01519.5530.0160.0160.0000.0000.0000.000
37A42ARG10.8430.89422.5290.1210.1210.0000.0000.0000.000
38A43ASP-1-0.785-0.85720.707-0.060-0.0600.0000.0000.0000.000
39A44ASN0-0.001-0.01120.6090.0180.0180.0000.0000.0000.000
40A45MET0-0.063-0.01724.3140.0070.0070.0000.0000.0000.000
41A46LEU0-0.048-0.00825.6650.0060.0060.0000.0000.0000.000
42A47ARG10.7800.85221.2020.0730.0730.0000.0000.0000.000
43A48GLY00.0010.01227.1940.0020.0020.0000.0000.0000.000
44A49THR0-0.013-0.01224.4880.0000.0000.0000.0000.0000.000
45A50GLU-1-0.862-0.93627.742-0.064-0.0640.0000.0000.0000.000
46A51ILE0-0.022-0.01423.187-0.004-0.0040.0000.0000.0000.000
47A52GLY00.0380.02426.426-0.007-0.0070.0000.0000.0000.000
48A53VAL00.0140.00227.6110.0000.0000.0000.0000.0000.000
49A54LEU0-0.020-0.00427.753-0.001-0.0010.0000.0000.0000.000
50A55ALA00.007-0.01926.383-0.002-0.0020.0000.0000.0000.000
51A56LYS10.8610.89528.4100.0600.0600.0000.0000.0000.000
52A57ALA0-0.0010.01531.4070.0020.0020.0000.0000.0000.000
53A58PHE0-0.025-0.01330.2230.0000.0000.0000.0000.0000.000
54A59ILE0-0.004-0.01027.0160.0000.0000.0000.0000.0000.000
55A60ASP-1-0.811-0.88431.493-0.062-0.0620.0000.0000.0000.000
56A61GLN0-0.047-0.01634.5670.0050.0050.0000.0000.0000.000
57A62GLY0-0.0120.00533.5580.0000.0000.0000.0000.0000.000
58A63LYS10.7970.89132.1530.0830.0830.0000.0000.0000.000
59A64LEU0-0.013-0.00426.600-0.002-0.0020.0000.0000.0000.000
60A65ILE00.0330.01824.3430.0070.0070.0000.0000.0000.000
61A66PRO00.0310.02026.237-0.011-0.0110.0000.0000.0000.000
62A67ASP-1-0.748-0.84424.197-0.207-0.2070.0000.0000.0000.000
63A68ASP-1-0.785-0.86722.972-0.169-0.1690.0000.0000.0000.000
64A69VAL0-0.017-0.00723.255-0.008-0.0080.0000.0000.0000.000
65A70MET0-0.019-0.00320.486-0.001-0.0010.0000.0000.0000.000
66A71THR00.003-0.01718.668-0.028-0.0280.0000.0000.0000.000
67A72ARG10.8130.88318.3070.1340.1340.0000.0000.0000.000
68A73LEU0-0.020-0.00218.684-0.002-0.0020.0000.0000.0000.000
69A74ALA00.0280.01315.285-0.001-0.0010.0000.0000.0000.000
70A75LEU00.0270.00013.902-0.032-0.0320.0000.0000.0000.000
71A76HIS0-0.0170.00213.928-0.019-0.0190.0000.0000.0000.000
72A77GLU-1-0.861-0.94212.382-0.269-0.2690.0000.0000.0000.000
73A78LEU00.0260.0009.1350.0200.0200.0000.0000.0000.000
74A79LYS10.8730.9398.6800.1640.1640.0000.0000.0000.000
75A80ASN0-0.047-0.0179.1910.0370.0370.0000.0000.0000.000
76A81LEU00.0230.0147.2020.0970.0970.0000.0000.0000.000
77A82THR0-0.0190.0024.918-0.197-0.1970.0000.0000.0000.000
78A83GLN0-0.0020.0042.741-1.996-0.6861.076-0.742-1.644-0.009
79A84TYR00.0310.0162.541-1.0230.2682.046-0.734-2.604-0.008
80A85SER00.0450.0372.537-4.423-2.0653.876-1.910-4.323-0.026
81A86TRP0-0.061-0.0533.4330.1200.2810.0340.220-0.4150.000
82A87LEU00.0120.0086.557-0.104-0.1040.0000.0000.0000.000
83A88LEU00.0230.0209.5050.1390.1390.0000.0000.0000.000
84A89ASP-1-0.745-0.84112.234-0.238-0.2380.0000.0000.0000.000
85A90GLY0-0.017-0.01215.8590.0340.0340.0000.0000.0000.000
86A91PHE00.0150.02314.7150.0400.0400.0000.0000.0000.000
87A92PRO00.0370.03215.322-0.043-0.0430.0000.0000.0000.000
88A93ARG10.8180.88218.1450.1840.1840.0000.0000.0000.000
89A94THR00.006-0.02521.7280.0120.0120.0000.0000.0000.000
90A95LEU00.0470.01921.960-0.024-0.0240.0000.0000.0000.000
91A96PRO00.0570.02422.257-0.023-0.0230.0000.0000.0000.000
92A97GLN0-0.015-0.01519.479-0.033-0.0330.0000.0000.0000.000
93A98ALA00.0170.00117.848-0.037-0.0370.0000.0000.0000.000
94A99GLU-1-0.854-0.91317.651-0.294-0.2940.0000.0000.0000.000
95A100ALA0-0.055-0.03518.427-0.019-0.0190.0000.0000.0000.000
96A101LEU0-0.0020.00511.625-0.005-0.0050.0000.0000.0000.000
97A102ASP-1-0.850-0.91813.724-0.614-0.6140.0000.0000.0000.000
98A103ARG10.8000.88614.7330.2690.2690.0000.0000.0000.000
99A104ALA0-0.053-0.01113.7760.0440.0440.0000.0000.0000.000
100A105TYR0-0.019-0.0268.622-0.019-0.0190.0000.0000.0000.000
101A106GLN00.0070.0168.5730.1730.1730.0000.0000.0000.000
102A107ILE0-0.012-0.0148.544-0.260-0.2600.0000.0000.0000.000
103A108ASP-1-0.791-0.8956.178-2.818-2.8180.0000.0000.0000.000
104A109THR0-0.072-0.0499.7090.2240.2240.0000.0000.0000.000
105A110VAL0-0.0110.00411.842-0.050-0.0500.0000.0000.0000.000
106A111ILE00.0320.02612.6440.0720.0720.0000.0000.0000.000
107A112ASN00.006-0.01516.1050.0190.0190.0000.0000.0000.000
108A113LEU0-0.030-0.00919.5060.0190.0190.0000.0000.0000.000
109A114ASN0-0.021-0.01422.4510.0140.0140.0000.0000.0000.000
110A115VAL00.0050.00025.8480.0120.0120.0000.0000.0000.000
111A116PRO00.0250.00528.640-0.002-0.0020.0000.0000.0000.000
112A117PHE00.0360.01332.2640.0030.0030.0000.0000.0000.000
113A118GLU-1-0.754-0.87433.567-0.071-0.0710.0000.0000.0000.000
114A119VAL00.0120.01732.2840.0040.0040.0000.0000.0000.000
115A120ILE0-0.046-0.02128.8370.0020.0020.0000.0000.0000.000
116A121LYS10.8680.90432.3560.0730.0730.0000.0000.0000.000
117A122GLN0-0.067-0.01635.7120.0040.0040.0000.0000.0000.000
118A123ARG10.8450.90227.7790.0940.0940.0000.0000.0000.000
119A124LEU0-0.087-0.04831.2410.0020.0020.0000.0000.0000.000
120A125THR0-0.038-0.02435.1010.0030.0030.0000.0000.0000.000
121A126ALA00.0180.02337.7430.0040.0040.0000.0000.0000.000
122A127ARG10.8910.96236.5380.0470.0470.0000.0000.0000.000
123A128TRP00.0130.01139.9560.0000.0000.0000.0000.0000.000
124A129ILE0-0.033-0.02240.7670.0010.0010.0000.0000.0000.000
125A130HIS00.0620.04544.8660.0000.0000.0000.0000.0000.000
126A131PRO0-0.018-0.02147.8250.0010.0010.0000.0000.0000.000
127A132ALA00.0100.01148.8480.0000.0000.0000.0000.0000.000
128A133SER0-0.052-0.05648.7770.0020.0020.0000.0000.0000.000
129A134GLY00.0080.01544.7070.0010.0010.0000.0000.0000.000
130A135ARG10.8260.88343.5630.0160.0160.0000.0000.0000.000
131A136VAL0-0.025-0.01039.043-0.002-0.0020.0000.0000.0000.000
132A137TYR00.008-0.01242.4920.0020.0020.0000.0000.0000.000
133A138ASN00.000-0.00136.788-0.002-0.0020.0000.0000.0000.000
134A139ILE00.012-0.00940.5020.0020.0020.0000.0000.0000.000
135A140GLU-1-0.824-0.90536.418-0.057-0.0570.0000.0000.0000.000
136A141PHE0-0.083-0.03734.1530.0010.0010.0000.0000.0000.000
137A142ASN0-0.066-0.04539.4170.0010.0010.0000.0000.0000.000
138A143PRO00.0670.04442.3030.0000.0000.0000.0000.0000.000
139A144PRO00.0130.01745.1560.0020.0020.0000.0000.0000.000
140A145LYS10.7780.87147.8940.0190.0190.0000.0000.0000.000
141A146THR0-0.022-0.01551.5400.0010.0010.0000.0000.0000.000
142A147VAL00.0150.00349.610-0.001-0.0010.0000.0000.0000.000
143A148GLY00.0210.01549.7660.0000.0000.0000.0000.0000.000
144A149ILE0-0.0060.00650.9030.0000.0000.0000.0000.0000.000
145A150ASP-1-0.715-0.80150.078-0.019-0.0190.0000.0000.0000.000
146A151ASP-1-0.802-0.90049.529-0.018-0.0180.0000.0000.0000.000
147A152LEU0-0.079-0.02752.0170.0010.0010.0000.0000.0000.000
148A153THR0-0.026-0.03953.6230.0010.0010.0000.0000.0000.000
149A154GLY00.0060.01655.1200.0000.0000.0000.0000.0000.000
150A155GLU-1-0.875-0.91954.063-0.020-0.0200.0000.0000.0000.000
151A156PRO0-0.012-0.01953.244-0.001-0.0010.0000.0000.0000.000
152A157LEU0-0.041-0.00447.0160.0000.0000.0000.0000.0000.000
153A158ILE0-0.032-0.01745.037-0.001-0.0010.0000.0000.0000.000
154A159GLN0-0.005-0.02641.547-0.001-0.0010.0000.0000.0000.000
155A160ARG10.7720.85534.7120.0570.0570.0000.0000.0000.000
156A161GLU-1-0.759-0.89040.740-0.051-0.0510.0000.0000.0000.000
157A162ASP-1-0.910-0.94335.713-0.065-0.0650.0000.0000.0000.000
158A163ASP-1-0.803-0.87736.552-0.061-0.0610.0000.0000.0000.000
159A164LYS10.8500.94038.4480.0480.0480.0000.0000.0000.000
160A165PRO00.0230.00039.817-0.005-0.0050.0000.0000.0000.000
161A166GLU-1-0.859-0.93240.038-0.060-0.0600.0000.0000.0000.000
162A167THR0-0.045-0.03536.802-0.005-0.0050.0000.0000.0000.000
163A168VAL0-0.0080.00034.966-0.008-0.0080.0000.0000.0000.000
164A169ILE0-0.001-0.00535.269-0.008-0.0080.0000.0000.0000.000
165A170LYS10.9800.99836.1800.0720.0720.0000.0000.0000.000
166A171ARG10.9420.97029.1260.0920.0920.0000.0000.0000.000
167A172LEU0-0.032-0.01930.679-0.011-0.0110.0000.0000.0000.000
168A173LYS10.8900.93531.4910.0990.0990.0000.0000.0000.000
169A174ALA00.0460.03131.937-0.007-0.0070.0000.0000.0000.000
170A175TYR00.012-0.00323.416-0.009-0.0090.0000.0000.0000.000
171A176GLU-1-0.803-0.86727.576-0.142-0.1420.0000.0000.0000.000
172A177ASP-1-0.912-0.96128.957-0.135-0.1350.0000.0000.0000.000
173A178GLN0-0.0040.01026.373-0.013-0.0130.0000.0000.0000.000
174A179THR0-0.016-0.02823.445-0.016-0.0160.0000.0000.0000.000
175A180LYS10.8880.93624.6260.1280.1280.0000.0000.0000.000
176A181PRO00.0240.00026.109-0.007-0.0070.0000.0000.0000.000
177A182VAL0-0.0010.01420.127-0.013-0.0130.0000.0000.0000.000
178A183LEU0-0.006-0.00521.261-0.030-0.0300.0000.0000.0000.000
179A184GLU-1-0.837-0.90322.343-0.242-0.2420.0000.0000.0000.000
180A185TYR00.0330.01618.1480.0020.0020.0000.0000.0000.000
181A186TYR00.0680.00415.589-0.009-0.0090.0000.0000.0000.000
182A187GLN0-0.027-0.00118.810-0.025-0.0250.0000.0000.0000.000
183A188LYS10.8100.89421.3390.2260.2260.0000.0000.0000.000
184A189LYS10.7940.89516.5610.4950.4950.0000.0000.0000.000
185A190GLY00.0020.01517.298-0.040-0.0400.0000.0000.0000.000
186A191VAL00.0010.00113.334-0.020-0.0200.0000.0000.0000.000
187A192LEU0-0.099-0.03815.089-0.040-0.0400.0000.0000.0000.000
188A193GLU-1-0.863-0.92916.175-0.288-0.2880.0000.0000.0000.000
189A194THR0-0.037-0.02418.0340.0050.0050.0000.0000.0000.000
190A195PHE00.0650.03616.5750.0340.0340.0000.0000.0000.000
191A196SER00.007-0.00422.1640.0010.0010.0000.0000.0000.000
192A197GLY0-0.024-0.01125.8830.0090.0090.0000.0000.0000.000
193A198THR00.008-0.03228.331-0.004-0.0040.0000.0000.0000.000
194A199GLU-1-0.731-0.82129.469-0.060-0.0600.0000.0000.0000.000
195A200THR00.0380.00923.479-0.002-0.0020.0000.0000.0000.000
196A201ASN00.0290.01124.411-0.008-0.0080.0000.0000.0000.000
197A202LYS10.8510.92325.8720.0700.0700.0000.0000.0000.000
198A203ILE00.0030.01921.796-0.002-0.0020.0000.0000.0000.000
199A204TRP00.0440.00716.165-0.020-0.0200.0000.0000.0000.000
200A205PRO00.0180.00919.559-0.009-0.0090.0000.0000.0000.000
201A206TYR00.0280.02119.9630.0040.0040.0000.0000.0000.000
202A207VAL0-0.019-0.00215.277-0.018-0.0180.0000.0000.0000.000
203A208TYR0-0.036-0.02915.235-0.032-0.0320.0000.0000.0000.000
204A209ALA00.0350.01315.3700.0180.0180.0000.0000.0000.000
205A210PHE0-0.012-0.01213.078-0.012-0.0120.0000.0000.0000.000
206A211LEU00.007-0.0019.775-0.078-0.0780.0000.0000.0000.000
207A212GLN0-0.0110.00610.2790.0590.0590.0000.0000.0000.000
208A213THR0-0.034-0.01010.5680.0600.0600.0000.0000.0000.000
209A214LYS10.8580.9347.0140.6740.6740.0000.0000.0000.000
210A215VAL0-0.006-0.0055.091-0.541-0.5410.0000.0000.0000.000
211A216PRO00.0150.0175.412-0.032-0.0320.0000.0000.0000.000
212A217GLN0-0.047-0.0478.2830.0260.0260.0000.0000.0000.000