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: 5JVJZ

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2403581.430883
FMO2-HF: Nuclear repulsion 2320712.372189
FMO2-HF: Total energy -82869.058694
FMO2-MP2: Total energy -83115.74399


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.
-7.9951.2425.44-4.244-10.429-0.036
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 : -0.025 / q_NPA : -0.025
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].
3A8ARG10.8740.9412.7670.4453.1410.440-1.012-2.1230.002
4A9ALA00.0300.0146.2290.3330.3330.0000.0000.0000.000
5A10VAL00.0050.0219.2840.0100.0100.0000.0000.0000.000
6A11ILE0-0.029-0.00312.6670.0600.0600.0000.0000.0000.000
7A12MET0-0.031-0.02115.486-0.011-0.0110.0000.0000.0000.000
8A13GLY00.0660.01819.0540.0220.0220.0000.0000.0000.000
9A14ALA00.0380.03122.447-0.008-0.0080.0000.0000.0000.000
10A15PRO0-0.020-0.00625.6120.0050.0050.0000.0000.0000.000
11A16GLY00.0830.03527.2500.0040.0040.0000.0000.0000.000
12A17SER0-0.044-0.02324.1820.0090.0090.0000.0000.0000.000
13A18GLY00.0340.01424.5270.0080.0080.0000.0000.0000.000
14A19LYS10.8780.94718.5800.1500.1500.0000.0000.0000.000
15A20GLY00.0440.03219.583-0.002-0.0020.0000.0000.0000.000
16A21THR0-0.013-0.01120.2320.0040.0040.0000.0000.0000.000
17A22VAL00.0190.00317.3510.0160.0160.0000.0000.0000.000
18A23SER00.0390.01115.7990.0240.0240.0000.0000.0000.000
19A24SER0-0.0120.01415.5860.0140.0140.0000.0000.0000.000
20A25ARG10.8480.91916.949-0.044-0.0440.0000.0000.0000.000
21A26ILE00.0100.00211.7600.0350.0350.0000.0000.0000.000
22A27THR0-0.005-0.02012.0800.0350.0350.0000.0000.0000.000
23A28THR0-0.061-0.01412.8190.0240.0240.0000.0000.0000.000
24A29HIS0-0.050-0.03114.4230.0360.0360.0000.0000.0000.000
25A30PHE0-0.058-0.0179.0410.0240.0240.0000.0000.0000.000
26A31GLU-1-0.918-0.9375.9880.3300.3300.0000.0000.0000.000
27A32LEU0-0.064-0.0475.5900.1810.1810.0000.0000.0000.000
28A33LYS10.9280.9706.8940.2210.2210.0000.0000.0000.000
29A34HIS0-0.050-0.0418.953-0.071-0.0710.0000.0000.0000.000
30A35LEU0-0.0060.0009.0760.0080.0080.0000.0000.0000.000
31A36SER00.0620.04012.906-0.011-0.0110.0000.0000.0000.000
32A37SER00.0230.00416.4930.0100.0100.0000.0000.0000.000
33A38GLY0-0.029-0.01618.5510.0120.0120.0000.0000.0000.000
34A39ASP-1-0.833-0.92918.754-0.107-0.1070.0000.0000.0000.000
35A40LEU00.0020.02316.6930.0160.0160.0000.0000.0000.000
36A41LEU0-0.036-0.03619.5190.0110.0110.0000.0000.0000.000
37A42ARG10.9140.92822.8230.1190.1190.0000.0000.0000.000
38A43ASP-1-0.821-0.89720.995-0.131-0.1310.0000.0000.0000.000
39A44ASN0-0.043-0.02220.6370.0090.0090.0000.0000.0000.000
40A45MET0-0.069-0.01724.2120.0100.0100.0000.0000.0000.000
41A46LEU0-0.041-0.00625.8160.0070.0070.0000.0000.0000.000
42A47ARG10.8500.91721.0110.1550.1550.0000.0000.0000.000
43A48GLY00.0070.02527.1660.0020.0020.0000.0000.0000.000
44A49THR0-0.036-0.02924.3130.0020.0020.0000.0000.0000.000
45A50GLU-1-0.857-0.94227.554-0.103-0.1030.0000.0000.0000.000
46A51ILE0-0.027-0.01223.4420.0020.0020.0000.0000.0000.000
47A52GLY00.0280.01926.4200.0000.0000.0000.0000.0000.000
48A53VAL00.0110.00327.3030.0060.0060.0000.0000.0000.000
49A54LEU00.0140.00627.6320.0040.0040.0000.0000.0000.000
50A55ALA0-0.013-0.02726.3860.0030.0030.0000.0000.0000.000
51A56LYS10.9070.93128.4570.0770.0770.0000.0000.0000.000
52A57ALA0-0.0150.00931.3910.0050.0050.0000.0000.0000.000
53A58PHE0-0.033-0.02330.2130.0040.0040.0000.0000.0000.000
54A59ILE00.004-0.01026.7760.0040.0040.0000.0000.0000.000
55A60ASP-1-0.830-0.89931.270-0.070-0.0700.0000.0000.0000.000
56A61GLN0-0.067-0.01834.5750.0070.0070.0000.0000.0000.000
57A62GLY0-0.025-0.00933.4460.0020.0020.0000.0000.0000.000
58A63LYS10.8480.92732.2900.0800.0800.0000.0000.0000.000
59A64LEU0-0.022-0.01226.572-0.003-0.0030.0000.0000.0000.000
60A65ILE00.0190.01224.8970.0040.0040.0000.0000.0000.000
61A66PRO00.0200.01826.457-0.007-0.0070.0000.0000.0000.000
62A67ASP-1-0.760-0.88024.354-0.190-0.1900.0000.0000.0000.000
63A68ASP-1-0.849-0.92823.403-0.184-0.1840.0000.0000.0000.000
64A69VAL0-0.037-0.02223.595-0.016-0.0160.0000.0000.0000.000
65A70MET0-0.0030.00420.407-0.012-0.0120.0000.0000.0000.000
66A71THR00.011-0.00518.527-0.029-0.0290.0000.0000.0000.000
67A72ARG10.8890.95418.4650.1630.1630.0000.0000.0000.000
68A73LEU0-0.0090.00118.714-0.017-0.0170.0000.0000.0000.000
69A74ALA00.0240.01315.543-0.014-0.0140.0000.0000.0000.000
70A75LEU00.025-0.00114.037-0.048-0.0480.0000.0000.0000.000
71A76HIS0-0.055-0.02513.745-0.044-0.0440.0000.0000.0000.000
72A77GLU-1-0.909-0.96512.467-0.352-0.3520.0000.0000.0000.000
73A78LEU00.004-0.0069.604-0.023-0.0230.0000.0000.0000.000
74A79LYS10.9310.9749.0000.2680.2680.0000.0000.0000.000
75A80ASN0-0.060-0.02110.096-0.030-0.0300.0000.0000.0000.000
76A81LEU00.0180.0107.4070.0490.0490.0000.0000.0000.000
77A82THR0-0.0020.0134.787-0.352-0.245-0.001-0.011-0.0940.000
78A83GLN00.0380.0222.993-1.835-0.4250.663-0.667-1.405-0.007
79A84TYR0-0.0020.0022.888-1.794-0.2971.614-0.854-2.257-0.009
80A85SER00.0590.0472.503-4.593-1.0592.677-2.129-4.081-0.022
81A86TRP0-0.067-0.0513.2430.3360.2770.0480.437-0.4260.000
82A87LEU00.0170.0096.374-0.045-0.0450.0000.0000.0000.000
83A88LEU00.002-0.0019.7390.0660.0660.0000.0000.0000.000
84A89ASP-1-0.792-0.89112.088-0.116-0.1160.0000.0000.0000.000
85A90GLY0-0.008-0.01415.6060.0140.0140.0000.0000.0000.000
86A91PHE0-0.0250.00314.9760.0250.0250.0000.0000.0000.000
87A92PRO00.0300.02315.309-0.032-0.0320.0000.0000.0000.000
88A93ARG10.8830.92418.2470.1560.1560.0000.0000.0000.000
89A94THR0-0.006-0.02721.7300.0140.0140.0000.0000.0000.000
90A95LEU00.0470.02121.966-0.020-0.0200.0000.0000.0000.000
91A96PRO00.0580.02722.152-0.021-0.0210.0000.0000.0000.000
92A97GLN0-0.040-0.01219.535-0.033-0.0330.0000.0000.0000.000
93A98ALA00.0200.00317.753-0.038-0.0380.0000.0000.0000.000
94A99GLU-1-0.928-0.96417.457-0.247-0.2470.0000.0000.0000.000
95A100ALA0-0.074-0.05118.558-0.021-0.0210.0000.0000.0000.000
96A101LEU0-0.015-0.01311.740-0.023-0.0230.0000.0000.0000.000
97A102ASP-1-0.934-0.96413.693-0.502-0.5020.0000.0000.0000.000
98A103ARG10.9210.97214.9030.2690.2690.0000.0000.0000.000
99A104ALA0-0.076-0.01913.4260.0140.0140.0000.0000.0000.000
100A105TYR0-0.023-0.0328.041-0.092-0.0920.0000.0000.0000.000
101A106GLN00.0420.0368.1810.1650.1650.0000.0000.0000.000
102A107ILE0-0.050-0.0308.036-0.330-0.3300.0000.0000.0000.000
103A108ASP-1-0.861-0.9345.931-1.451-1.4510.0000.0000.0000.000
104A109THR0-0.096-0.0519.1860.2810.2810.0000.0000.0000.000
105A110VAL00.0060.00611.289-0.077-0.0770.0000.0000.0000.000
106A111ILE00.0290.03212.9000.0580.0580.0000.0000.0000.000
107A112ASN00.021-0.00416.262-0.026-0.0260.0000.0000.0000.000
108A113LEU0-0.039-0.01619.4330.0250.0250.0000.0000.0000.000
109A114ASN0-0.032-0.02822.320-0.013-0.0130.0000.0000.0000.000
110A115VAL0-0.019-0.01025.6580.0120.0120.0000.0000.0000.000
111A116PRO00.0210.00828.448-0.006-0.0060.0000.0000.0000.000
112A117PHE00.0680.02031.9720.0000.0000.0000.0000.0000.000
113A118GLU-1-0.878-0.95033.446-0.023-0.0230.0000.0000.0000.000
114A119VAL0-0.0160.00332.1390.0020.0020.0000.0000.0000.000
115A120ILE0-0.021-0.01228.4820.0010.0010.0000.0000.0000.000
116A121LYS10.9800.99032.3040.0240.0240.0000.0000.0000.000
117A122GLN0-0.0390.00235.537-0.001-0.0010.0000.0000.0000.000
118A123ARG10.8860.93128.0740.0110.0110.0000.0000.0000.000
119A124LEU0-0.109-0.06930.576-0.001-0.0010.0000.0000.0000.000
120A125THR0-0.046-0.00434.563-0.001-0.0010.0000.0000.0000.000
121A126ALA00.0150.02337.3840.0020.0020.0000.0000.0000.000
122A127ARG10.8850.95936.4090.0220.0220.0000.0000.0000.000
123A128TRP00.0160.01239.778-0.002-0.0020.0000.0000.0000.000
124A129ILE0-0.029-0.02540.7060.0010.0010.0000.0000.0000.000
125A130HIS00.0700.04944.6900.0000.0000.0000.0000.0000.000
126A131PRO0-0.037-0.03047.3000.0000.0000.0000.0000.0000.000
127A132ALA00.0150.02048.2470.0000.0000.0000.0000.0000.000
128A133SER0-0.043-0.04548.6790.0000.0000.0000.0000.0000.000
129A134GLY00.0220.01844.9490.0000.0000.0000.0000.0000.000
130A135ARG10.8260.89643.5730.0050.0050.0000.0000.0000.000
131A136VAL0-0.031-0.01638.949-0.002-0.0020.0000.0000.0000.000
132A137TYR0-0.001-0.01542.4380.0030.0030.0000.0000.0000.000
133A138ASN00.0170.00336.538-0.001-0.0010.0000.0000.0000.000
134A139ILE00.004-0.01740.5280.0030.0030.0000.0000.0000.000
135A140GLU-1-0.867-0.94536.213-0.006-0.0060.0000.0000.0000.000
136A141PHE0-0.082-0.03933.9620.0030.0030.0000.0000.0000.000
137A142ASN0-0.057-0.03939.5280.0020.0020.0000.0000.0000.000
138A143PRO00.0390.03042.594-0.002-0.0020.0000.0000.0000.000
139A144PRO00.0030.01645.1010.0010.0010.0000.0000.0000.000
140A145LYS10.8990.93848.367-0.005-0.0050.0000.0000.0000.000
141A146THR00.0010.00851.3730.0010.0010.0000.0000.0000.000
142A147VAL00.019-0.00250.019-0.001-0.0010.0000.0000.0000.000
143A148GLY00.0030.00049.7140.0000.0000.0000.0000.0000.000
144A149ILE0-0.010-0.00250.829-0.001-0.0010.0000.0000.0000.000
145A150ASP-1-0.725-0.82949.992-0.005-0.0050.0000.0000.0000.000
146A151ASP-1-0.858-0.92949.5990.0010.0010.0000.0000.0000.000
147A152LEU0-0.084-0.03652.0430.0010.0010.0000.0000.0000.000
148A153THR0-0.015-0.03453.4830.0000.0000.0000.0000.0000.000
149A154GLY00.0110.02054.9520.0000.0000.0000.0000.0000.000
150A155GLU-1-0.917-0.94053.999-0.010-0.0100.0000.0000.0000.000
151A156PRO00.011-0.00652.9520.0000.0000.0000.0000.0000.000
152A157LEU0-0.049-0.00246.944-0.001-0.0010.0000.0000.0000.000
153A158ILE0-0.019-0.00544.947-0.001-0.0010.0000.0000.0000.000
154A159GLN0-0.001-0.00841.3300.0000.0000.0000.0000.0000.000
155A160ARG10.9040.94334.8370.0320.0320.0000.0000.0000.000
156A161GLU-1-0.773-0.89641.180-0.034-0.0340.0000.0000.0000.000
157A162ASP-1-0.954-0.97235.681-0.051-0.0510.0000.0000.0000.000
158A163ASP-1-0.895-0.95036.505-0.033-0.0330.0000.0000.0000.000
159A164LYS10.8580.93838.4790.0320.0320.0000.0000.0000.000
160A165PRO00.018-0.00739.699-0.003-0.0030.0000.0000.0000.000
161A166GLU-1-0.882-0.93739.806-0.034-0.0340.0000.0000.0000.000
162A167THR0-0.008-0.01436.870-0.004-0.0040.0000.0000.0000.000
163A168VAL00.0080.00134.577-0.005-0.0050.0000.0000.0000.000
164A169ILE0-0.021-0.01635.059-0.004-0.0040.0000.0000.0000.000
165A170LYS10.9840.99836.0400.0540.0540.0000.0000.0000.000
166A171ARG10.9490.97928.3240.0620.0620.0000.0000.0000.000
167A172LEU0-0.024-0.02430.607-0.008-0.0080.0000.0000.0000.000
168A173LYS10.9840.99331.5370.0450.0450.0000.0000.0000.000
169A174ALA00.0390.03531.653-0.004-0.0040.0000.0000.0000.000
170A175TYR00.000-0.00623.385-0.011-0.0110.0000.0000.0000.000
171A176GLU-1-0.950-0.97327.582-0.073-0.0730.0000.0000.0000.000
172A177ASP-1-0.912-0.95329.120-0.084-0.0840.0000.0000.0000.000
173A178GLN0-0.049-0.03226.213-0.012-0.0120.0000.0000.0000.000
174A179THR0-0.009-0.02623.497-0.010-0.0100.0000.0000.0000.000
175A180LYS10.9911.01724.5860.0700.0700.0000.0000.0000.000
176A181PRO00.007-0.01526.177-0.002-0.0020.0000.0000.0000.000
177A182VAL00.0180.02620.107-0.010-0.0100.0000.0000.0000.000
178A183LEU0-0.020-0.01721.080-0.015-0.0150.0000.0000.0000.000
179A184GLU-1-0.970-0.97822.166-0.131-0.1310.0000.0000.0000.000
180A185TYR00.0670.03217.833-0.011-0.0110.0000.0000.0000.000
181A186TYR00.031-0.01215.335-0.004-0.0040.0000.0000.0000.000
182A187GLN0-0.021-0.00918.4840.0090.0090.0000.0000.0000.000
183A188LYS10.9430.98120.8820.1380.1380.0000.0000.0000.000
184A189LYS10.8780.93716.6150.3060.3060.0000.0000.0000.000
185A190GLY0-0.0010.01716.866-0.014-0.0140.0000.0000.0000.000
186A191VAL0-0.0010.00512.8640.0230.0230.0000.0000.0000.000
187A192LEU0-0.097-0.04014.787-0.011-0.0110.0000.0000.0000.000
188A193GLU-1-0.894-0.93816.0890.0640.0640.0000.0000.0000.000
189A194THR0-0.036-0.02917.926-0.017-0.0170.0000.0000.0000.000
190A195PHE00.0310.01416.8080.0180.0180.0000.0000.0000.000
191A196SER00.0200.01522.207-0.015-0.0150.0000.0000.0000.000
192A197GLY00.001-0.00525.9260.0120.0120.0000.0000.0000.000
193A198THR00.0620.01528.049-0.006-0.0060.0000.0000.0000.000
194A199GLU-1-0.905-0.95528.9160.0270.0270.0000.0000.0000.000
195A200THR00.0470.01223.6560.0020.0020.0000.0000.0000.000
196A201ASN00.0380.00524.5290.0080.0080.0000.0000.0000.000
197A202LYS10.9330.98526.074-0.020-0.0200.0000.0000.0000.000
198A203ILE00.0090.02221.5840.0070.0070.0000.0000.0000.000
199A204TRP00.027-0.00216.075-0.004-0.0040.0000.0000.0000.000
200A205PRO00.0310.01919.6920.0170.0170.0000.0000.0000.000
201A206TYR00.0210.01419.7910.0240.0240.0000.0000.0000.000
202A207VAL0-0.0110.00815.6400.0150.0150.0000.0000.0000.000
203A208TYR0-0.013-0.01015.3300.0140.0140.0000.0000.0000.000
204A209ALA00.036-0.00215.1620.0590.0590.0000.0000.0000.000
205A210PHE00.0070.00012.9020.0640.0640.0000.0000.0000.000
206A211LEU00.002-0.0169.6690.0290.0290.0000.0000.0000.000
207A212GLN0-0.0130.01410.3480.2190.2190.0000.0000.0000.000
208A213THR0-0.035-0.01511.2650.1190.1190.0000.0000.0000.000
209A214LYS10.8950.9578.000-0.090-0.0900.0000.0000.0000.000
210A215VAL0-0.0080.0004.5860.4720.524-0.001-0.008-0.0430.000
211A216PRO00.0210.0195.110-0.356-0.3560.0000.0000.0000.000
212A217GLN00.0210.0188.097-0.150-0.1500.0000.0000.0000.000