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: QVM7Y

Calculation Name: 2ZSK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZSK

Chain ID: A

ChEMBL ID:

UniProt ID: O59384

Base Structure: X-ray

Registration Date: 2023-09-22

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2892190.114622
FMO2-HF: Nuclear repulsion 2802456.517734
FMO2-HF: Total energy -89733.596889
FMO2-MP2: Total energy -89999.21678


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.
-19.58-10.9498.177-5.488-11.319-0.032
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 : -0.026 / q_NPA : 0.000
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].
3A3LYS10.8300.8973.7021.8143.827-0.005-0.938-1.0700.005
4A4ILE00.0240.0155.7080.2690.2690.0000.0000.0000.000
5A5GLY00.0090.0037.9330.1390.1390.0000.0000.0000.000
6A6ILE0-0.023-0.01011.6330.0230.0230.0000.0000.0000.000
7A7ILE00.0120.00514.4530.0130.0130.0000.0000.0000.000
8A8GLY00.0720.01918.1020.0230.0230.0000.0000.0000.000
9A9GLY00.0100.00220.203-0.020-0.0200.0000.0000.0000.000
10A10THR0-0.086-0.01923.078-0.002-0.0020.0000.0000.0000.000
11A11THR0-0.011-0.01524.9380.0050.0050.0000.0000.0000.000
12A12PRO00.020-0.01223.6050.0070.0070.0000.0000.0000.000
13A13GLU-1-0.826-0.91323.3220.0710.0710.0000.0000.0000.000
14A14SER00.0130.00621.9950.0250.0250.0000.0000.0000.000
15A15THR0-0.004-0.01918.4020.0060.0060.0000.0000.0000.000
16A16LEU0-0.040-0.01818.8410.0380.0380.0000.0000.0000.000
17A17TYR0-0.050-0.05519.9520.0500.0500.0000.0000.0000.000
18A18TYR00.018-0.02215.2170.0420.0420.0000.0000.0000.000
19A19TYR00.0310.01413.1360.0670.0670.0000.0000.0000.000
20A20LYS10.8700.93015.406-0.204-0.2040.0000.0000.0000.000
21A21LYS10.8770.94015.989-0.223-0.2230.0000.0000.0000.000
22A22TYR0-0.004-0.0258.303-0.091-0.0910.0000.0000.0000.000
23A23ILE0-0.054-0.01311.4330.2120.2120.0000.0000.0000.000
24A24GLU-1-0.871-0.93012.6350.4090.4090.0000.0000.0000.000
25A25ILE00.0580.0239.5730.0280.0280.0000.0000.0000.000
26A26SER0-0.007-0.0168.0710.2170.2170.0000.0000.0000.000
27A27ARG10.8270.9018.659-0.631-0.6310.0000.0000.0000.000
28A28GLU-1-0.912-0.93011.3170.3710.3710.0000.0000.0000.000
29A29LYS10.8240.9335.493-0.568-0.5680.0000.0000.0000.000
30A30PHE0-0.017-0.0182.628-0.8150.1750.411-0.376-1.025-0.004
31A31GLU-1-0.907-0.9456.6660.8920.8920.0000.0000.0000.000
32A32LYS10.9120.9468.868-0.424-0.4240.0000.0000.0000.000
33A33TYR0-0.045-0.04610.872-0.023-0.0230.0000.0000.0000.000
34A34PHE00.0090.0212.852-2.245-2.3763.251-0.734-2.3860.004
35A35TYR00.0320.0187.544-0.374-0.3740.0000.0000.0000.000
36A36PRO00.0350.0433.338-0.926-0.0880.381-0.308-0.9100.002
37A37GLU-1-0.825-0.8884.796-2.731-2.6560.000-0.029-0.0460.000
38A38LEU0-0.016-0.0036.402-0.395-0.3950.0000.0000.0000.000
39A39ILE0-0.023-0.0109.1380.0430.0430.0000.0000.0000.000
40A40ILE00.007-0.00812.158-0.016-0.0160.0000.0000.0000.000
41A41TYR00.0120.01115.407-0.002-0.0020.0000.0000.0000.000
42A42SER00.0010.00318.6130.0090.0090.0000.0000.0000.000
43A43ILE0-0.040-0.00821.474-0.002-0.0020.0000.0000.0000.000
44A44ASN00.012-0.02124.4560.0240.0240.0000.0000.0000.000
45A45PHE00.0840.03227.809-0.008-0.0080.0000.0000.0000.000
46A46LYS10.9720.99828.9200.0140.0140.0000.0000.0000.000
47A47GLU-1-0.910-0.94030.653-0.056-0.0560.0000.0000.0000.000
48A48PHE00.0270.01226.680-0.008-0.0080.0000.0000.0000.000
49A49PHE00.0120.00230.247-0.003-0.0030.0000.0000.0000.000
50A50GLN0-0.020-0.00732.2250.0000.0000.0000.0000.0000.000
51A51ASN00.0200.01232.258-0.001-0.0010.0000.0000.0000.000
52A52PRO00.0140.00135.0970.0010.0010.0000.0000.0000.000
53A53GLU-1-0.823-0.89134.913-0.089-0.0890.0000.0000.0000.000
54A54GLY00.0330.01835.473-0.005-0.0050.0000.0000.0000.000
55A55TRP00.034-0.02027.732-0.004-0.0040.0000.0000.0000.000
56A56GLU-1-0.844-0.90531.163-0.126-0.1260.0000.0000.0000.000
57A57GLY00.0320.02032.002-0.009-0.0090.0000.0000.0000.000
58A58ARG10.7600.86928.5740.0530.0530.0000.0000.0000.000
59A59LYS10.8650.93326.8830.1200.1200.0000.0000.0000.000
60A60LYS10.8460.91726.3530.0870.0870.0000.0000.0000.000
61A61ILE0-0.019-0.00525.465-0.014-0.0140.0000.0000.0000.000
62A62LEU0-0.014-0.00322.402-0.010-0.0100.0000.0000.0000.000
63A63ILE00.0550.03121.716-0.025-0.0250.0000.0000.0000.000
64A64ASN0-0.071-0.02321.973-0.029-0.0290.0000.0000.0000.000
65A65ALA00.0220.00720.208-0.019-0.0190.0000.0000.0000.000
66A66ALA00.0110.01017.681-0.029-0.0290.0000.0000.0000.000
67A67LYS10.9430.96017.3280.2400.2400.0000.0000.0000.000
68A68ALA0-0.094-0.04418.569-0.036-0.0360.0000.0000.0000.000
69A69LEU0-0.007-0.01113.810-0.029-0.0290.0000.0000.0000.000
70A70GLU-1-0.808-0.91414.014-0.611-0.6110.0000.0000.0000.000
71A71ARG10.8490.93214.3930.2350.2350.0000.0000.0000.000
72A72ALA0-0.065-0.02114.3900.0080.0080.0000.0000.0000.000
73A73GLY00.0020.00110.718-0.011-0.0110.0000.0000.0000.000
74A74ALA0-0.057-0.0199.519-0.375-0.3750.0000.0000.0000.000
75A75GLU-1-0.798-0.9105.895-4.698-4.6980.0000.0000.0000.000
76A76LEU0-0.030-0.0067.9220.0960.0960.0000.0000.0000.000
77A77ILE00.0230.0179.9950.1330.1330.0000.0000.0000.000
78A78ALA00.0330.01413.0380.0240.0240.0000.0000.0000.000
79A79PHE00.0170.01015.2030.0160.0160.0000.0000.0000.000
80A80ALA00.0510.02517.2230.0180.0180.0000.0000.0000.000
81A81ALA00.002-0.01318.8210.0160.0160.0000.0000.0000.000
82A82ASN00.0620.03122.192-0.022-0.0220.0000.0000.0000.000
83A83THR00.0450.01824.724-0.013-0.0130.0000.0000.0000.000
84A84PRO00.0260.01423.056-0.007-0.0070.0000.0000.0000.000
85A85HIS00.006-0.00119.948-0.035-0.0350.0000.0000.0000.000
86A86LEU0-0.074-0.01624.397-0.005-0.0050.0000.0000.0000.000
87A87VAL0-0.028-0.01725.9350.0000.0000.0000.0000.0000.000
88A88PHE00.0200.00118.097-0.011-0.0110.0000.0000.0000.000
89A89ASP-1-0.794-0.88122.877-0.181-0.1810.0000.0000.0000.000
90A90ASP-1-0.819-0.91924.805-0.168-0.1680.0000.0000.0000.000
91A91VAL0-0.043-0.02820.898-0.012-0.0120.0000.0000.0000.000
92A92GLN00.0480.00417.878-0.050-0.0500.0000.0000.0000.000
93A93ARG10.7370.86321.0440.1540.1540.0000.0000.0000.000
94A94GLU-1-0.904-0.93823.299-0.253-0.2530.0000.0000.0000.000
95A95VAL0-0.045-0.01216.915-0.012-0.0120.0000.0000.0000.000
96A96ASN0-0.091-0.02917.7140.0190.0190.0000.0000.0000.000
97A97VAL0-0.028-0.01812.143-0.100-0.1000.0000.0000.0000.000
98A98PRO0-0.017-0.00411.9440.0820.0820.0000.0000.0000.000
99A99MET00.0100.02213.351-0.043-0.0430.0000.0000.0000.000
100A100VAL00.0170.00012.0990.0200.0200.0000.0000.0000.000
101A101SER0-0.031-0.01215.1070.0510.0510.0000.0000.0000.000
102A102ILE00.007-0.00418.3280.0080.0080.0000.0000.0000.000
103A103ILE00.0250.00719.4210.0170.0170.0000.0000.0000.000
104A104ASP-1-0.851-0.91819.228-0.152-0.1520.0000.0000.0000.000
105A105ALA00.0110.01116.7230.0070.0070.0000.0000.0000.000
106A106VAL0-0.013-0.01118.3780.0210.0210.0000.0000.0000.000
107A107ALA00.0400.01921.5440.0090.0090.0000.0000.0000.000
108A108GLU-1-0.870-0.89116.235-0.118-0.1180.0000.0000.0000.000
109A109GLU-1-0.803-0.91217.7550.0850.0850.0000.0000.0000.000
110A110ILE0-0.017-0.01620.3510.0070.0070.0000.0000.0000.000
111A111LEU0-0.012-0.01023.6320.0040.0040.0000.0000.0000.000
112A112LYS10.8540.92815.802-0.045-0.0450.0000.0000.0000.000
113A113ARG10.7380.84620.566-0.079-0.0790.0000.0000.0000.000
114A114GLY0-0.047-0.01723.9150.0040.0040.0000.0000.0000.000
115A115VAL0-0.0120.01526.721-0.001-0.0010.0000.0000.0000.000
116A116ARG10.8000.88326.6900.0140.0140.0000.0000.0000.000
117A117LYS10.8220.91830.8820.0000.0000.0000.0000.0000.000
118A118VAL0-0.018-0.01028.4620.0070.0070.0000.0000.0000.000
119A119LEU00.0240.02031.912-0.004-0.0040.0000.0000.0000.000
120A120LEU0-0.022-0.00729.0450.0060.0060.0000.0000.0000.000
121A121LEU00.011-0.00430.885-0.001-0.0010.0000.0000.0000.000
122A122GLY00.019-0.00830.2230.0030.0030.0000.0000.0000.000
123A123THR00.0220.01331.439-0.003-0.0030.0000.0000.0000.000
124A124LYS10.9260.93333.568-0.007-0.0070.0000.0000.0000.000
125A125THR0-0.0120.01032.732-0.003-0.0030.0000.0000.0000.000
126A126THR0-0.030-0.01728.583-0.004-0.0040.0000.0000.0000.000
127A127MET0-0.0630.00431.474-0.003-0.0030.0000.0000.0000.000
128A128THR0-0.001-0.03334.089-0.002-0.0020.0000.0000.0000.000
129A129ALA0-0.0240.00930.949-0.005-0.0050.0000.0000.0000.000
130A130ASP-1-0.855-0.92432.388-0.040-0.0400.0000.0000.0000.000
131A131PHE00.007-0.01026.5250.0000.0000.0000.0000.0000.000
132A132TYR0-0.0300.00824.238-0.004-0.0040.0000.0000.0000.000
133A133ILE00.0520.01429.203-0.002-0.0020.0000.0000.0000.000
134A134LYS10.8380.90731.7850.0790.0790.0000.0000.0000.000
135A135THR0-0.068-0.05826.145-0.008-0.0080.0000.0000.0000.000
136A136LEU0-0.029-0.01725.836-0.006-0.0060.0000.0000.0000.000
137A137GLU-1-0.816-0.90128.296-0.034-0.0340.0000.0000.0000.000
138A138GLU-1-0.860-0.90430.076-0.087-0.0870.0000.0000.0000.000
139A139LYS10.7880.89623.1240.1250.1250.0000.0000.0000.000
140A140GLY0-0.057-0.02228.051-0.002-0.0020.0000.0000.0000.000
141A141LEU0-0.069-0.03126.4910.0070.0070.0000.0000.0000.000
142A142GLU-1-0.841-0.89631.061-0.018-0.0180.0000.0000.0000.000
143A143VAL0-0.054-0.05230.9530.0070.0070.0000.0000.0000.000
144A144VAL00.0440.03633.789-0.001-0.0010.0000.0000.0000.000
145A145VAL0-0.021-0.02834.9110.0040.0040.0000.0000.0000.000
146A146PRO00.0150.01836.507-0.001-0.0010.0000.0000.0000.000
147A147ASN00.0800.03939.690-0.003-0.0030.0000.0000.0000.000
148A148ASP-1-0.856-0.95042.237-0.003-0.0030.0000.0000.0000.000
149A149GLU-1-0.987-0.98243.3920.0150.0150.0000.0000.0000.000
150A150GLU-1-0.691-0.81840.9450.0170.0170.0000.0000.0000.000
151A151LYS10.7990.88738.3440.0060.0060.0000.0000.0000.000
152A152GLU-1-0.841-0.91039.0710.0090.0090.0000.0000.0000.000
153A153GLU-1-0.775-0.86441.0800.0320.0320.0000.0000.0000.000
154A154LEU0-0.011-0.00934.1620.0040.0040.0000.0000.0000.000
155A155ASN00.002-0.01436.2900.0050.0050.0000.0000.0000.000
156A156ARG10.7890.88537.204-0.030-0.0300.0000.0000.0000.000
157A157ILE0-0.0110.00636.4050.0040.0040.0000.0000.0000.000
158A158ILE0-0.029-0.00932.1800.0060.0060.0000.0000.0000.000
159A159PHE0-0.037-0.02833.8040.0050.0050.0000.0000.0000.000
160A160GLU-1-0.880-0.94336.1460.0340.0340.0000.0000.0000.000
161A161GLU-1-0.847-0.90537.3560.0500.0500.0000.0000.0000.000
162A162LEU0-0.012-0.00331.9340.0060.0060.0000.0000.0000.000
163A163ALA00.0210.03531.8650.0090.0090.0000.0000.0000.000
164A164PHE0-0.083-0.04632.8120.0030.0030.0000.0000.0000.000
165A165GLY0-0.034-0.00732.1930.0050.0050.0000.0000.0000.000
166A166ASN0-0.054-0.02733.0910.0040.0040.0000.0000.0000.000
167A167LEU00.031-0.00131.554-0.003-0.0030.0000.0000.0000.000
168A168LYS10.8480.92335.821-0.049-0.0490.0000.0000.0000.000
169A169ASN0-0.039-0.03538.720-0.004-0.0040.0000.0000.0000.000
170A170LYS10.8580.92331.549-0.095-0.0950.0000.0000.0000.000
171A171GLU-1-0.827-0.91036.6020.0480.0480.0000.0000.0000.000
172A172TRP0-0.009-0.00538.862-0.002-0.0020.0000.0000.0000.000
173A173ILE00.0230.00333.729-0.003-0.0030.0000.0000.0000.000
174A174VAL00.0060.00634.426-0.002-0.0020.0000.0000.0000.000
175A175ARG10.8870.92636.518-0.042-0.0420.0000.0000.0000.000
176A176LEU0-0.0360.00736.851-0.004-0.0040.0000.0000.0000.000
177A177ILE00.025-0.00832.375-0.004-0.0040.0000.0000.0000.000
178A178GLU-1-0.803-0.86735.7060.0430.0430.0000.0000.0000.000
179A179LYS10.8360.91838.347-0.018-0.0180.0000.0000.0000.000
180A180TYR0-0.039-0.06737.876-0.004-0.0040.0000.0000.0000.000
181A181ARG10.9240.99335.411-0.037-0.0370.0000.0000.0000.000
182A182GLU-1-1.000-1.00238.1720.0160.0160.0000.0000.0000.000
183A183SER0-0.067-0.02241.689-0.003-0.0030.0000.0000.0000.000
184A184GLU-1-0.905-0.96739.809-0.005-0.0050.0000.0000.0000.000
185A185GLY0-0.0110.00738.881-0.002-0.0020.0000.0000.0000.000
186A186ILE0-0.054-0.01433.926-0.002-0.0020.0000.0000.0000.000
187A187GLU-1-0.793-0.91131.5700.0070.0070.0000.0000.0000.000
188A188GLY00.017-0.01429.3410.0060.0060.0000.0000.0000.000
189A189VAL0-0.023-0.00329.081-0.006-0.0060.0000.0000.0000.000
190A190ILE00.0220.00625.6900.0080.0080.0000.0000.0000.000
191A191LEU0-0.024-0.00625.546-0.004-0.0040.0000.0000.0000.000
192A192GLY00.0240.00025.5510.0060.0060.0000.0000.0000.000
193A193CYS0-0.105-0.05226.235-0.007-0.0070.0000.0000.0000.000
194A194THR00.013-0.01222.5000.0030.0030.0000.0000.0000.000
195A195GLU-1-0.852-0.91525.1560.1020.1020.0000.0000.0000.000
196A196LEU00.0440.00028.5980.0040.0040.0000.0000.0000.000
197A197PRO00.0190.02724.1130.0010.0010.0000.0000.0000.000
198A198LEU0-0.038-0.01825.8210.0140.0140.0000.0000.0000.000
199A199ALA0-0.035-0.02328.0190.0010.0010.0000.0000.0000.000
200A200ILE0-0.025-0.01528.829-0.003-0.0030.0000.0000.0000.000
201A201LYS10.8530.92325.322-0.132-0.1320.0000.0000.0000.000
202A202GLN00.0810.01324.183-0.008-0.0080.0000.0000.0000.000
203A203GLY0-0.0210.00026.306-0.008-0.0080.0000.0000.0000.000
204A204ASP-1-0.808-0.88428.9760.0990.0990.0000.0000.0000.000
205A205VAL0-0.037-0.01830.700-0.006-0.0060.0000.0000.0000.000
206A206SER0-0.122-0.09031.7820.0020.0020.0000.0000.0000.000
207A207VAL0-0.048-0.00730.914-0.003-0.0030.0000.0000.0000.000
208A208GLU-1-0.794-0.87224.8730.0840.0840.0000.0000.0000.000
209A209VAL0-0.017-0.00425.289-0.007-0.0070.0000.0000.0000.000
210A210PHE0-0.0040.00522.4070.0120.0120.0000.0000.0000.000
211A211ASP-1-0.766-0.87621.0660.1500.1500.0000.0000.0000.000
212A212SER00.0370.01520.6020.0140.0140.0000.0000.0000.000
213A213ALA00.0290.00919.220-0.003-0.0030.0000.0000.0000.000
214A214GLU-1-0.921-0.95016.6000.2940.2940.0000.0000.0000.000
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