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: KG873

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 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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2901495.019717
FMO2-HF: Nuclear repulsion 2811760.889295
FMO2-HF: Total energy -89734.130423
FMO2-MP2: Total energy -89999.720793


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.
-22.258-13.029.925-6.369-12.795-0.038
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 : -0.027 / q_NPA : -0.002
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].
3A3LYS10.8230.8933.8551.9203.687-0.009-0.805-0.9530.004
4A4ILE00.0180.0115.6380.2620.2620.0000.0000.0000.000
5A5GLY0-0.001-0.0077.9350.1140.1140.0000.0000.0000.000
6A6ILE0-0.032-0.01811.7360.0210.0210.0000.0000.0000.000
7A7ILE00.0260.00714.5620.0150.0150.0000.0000.0000.000
8A8GLY00.0580.01518.2050.0280.0280.0000.0000.0000.000
9A9GLY00.009-0.00319.977-0.023-0.0230.0000.0000.0000.000
10A10THR0-0.065-0.03023.104-0.009-0.0090.0000.0000.0000.000
11A11THR00.0050.00924.9810.0030.0030.0000.0000.0000.000
12A12PRO0-0.013-0.02123.6570.0130.0130.0000.0000.0000.000
13A13GLU-1-0.825-0.91323.1890.1140.1140.0000.0000.0000.000
14A14SER00.019-0.00121.8540.0290.0290.0000.0000.0000.000
15A15THR0-0.018-0.01418.6390.0130.0130.0000.0000.0000.000
16A16LEU0-0.022-0.00518.6060.0450.0450.0000.0000.0000.000
17A17TYR0-0.043-0.05019.6250.0590.0590.0000.0000.0000.000
18A18TYR00.034-0.01815.1950.0520.0520.0000.0000.0000.000
19A19TYR00.0240.01212.9120.0740.0740.0000.0000.0000.000
20A20LYS10.8510.91315.113-0.258-0.2580.0000.0000.0000.000
21A21LYS10.8420.92315.648-0.310-0.3100.0000.0000.0000.000
22A22TYR00.014-0.0158.073-0.129-0.1290.0000.0000.0000.000
23A23ILE0-0.047-0.01311.1340.2460.2460.0000.0000.0000.000
24A24GLU-1-0.844-0.90912.5570.4790.4790.0000.0000.0000.000
25A25ILE00.0470.0159.4490.0320.0320.0000.0000.0000.000
26A26SER0-0.024-0.0327.6940.3210.3210.0000.0000.0000.000
27A27ARG10.8390.9068.194-0.770-0.7700.0000.0000.0000.000
28A28GLU-1-0.916-0.92610.9450.4620.4620.0000.0000.0000.000
29A29LYS10.7960.9075.328-1.187-1.1870.0000.0000.0000.000
30A30PHE0-0.003-0.0022.584-1.1410.0670.815-0.538-1.486-0.007
31A31GLU-1-0.899-0.9416.1580.7970.7970.0000.0000.0000.000
32A32LYS10.8950.9358.353-0.372-0.3720.0000.0000.0000.000
33A33TYR0-0.025-0.03510.910-0.070-0.0700.0000.0000.0000.000
34A34PHE00.0140.0272.872-2.476-2.9353.965-0.818-2.6880.003
35A35TYR00.0300.0127.112-0.514-0.5140.0000.0000.0000.000
36A36PRO00.0280.0433.122-0.975-0.0430.757-0.450-1.2390.003
37A37GLU-1-0.821-0.8904.271-2.800-2.6440.002-0.042-0.1160.000
38A38LEU0-0.0070.0066.257-0.428-0.4280.0000.0000.0000.000
39A39ILE0-0.0150.0049.2590.0320.0320.0000.0000.0000.000
40A40ILE00.000-0.01112.382-0.014-0.0140.0000.0000.0000.000
41A41TYR0-0.012-0.00115.651-0.012-0.0120.0000.0000.0000.000
42A42SER0-0.004-0.00618.8300.0050.0050.0000.0000.0000.000
43A43ILE0-0.0240.00321.718-0.004-0.0040.0000.0000.0000.000
44A44ASN00.000-0.02624.6640.0250.0250.0000.0000.0000.000
45A45PHE00.0760.03028.049-0.009-0.0090.0000.0000.0000.000
46A46LYS10.9490.98228.963-0.007-0.0070.0000.0000.0000.000
47A47GLU-1-0.865-0.92030.523-0.034-0.0340.0000.0000.0000.000
48A48PHE00.0610.03326.407-0.007-0.0070.0000.0000.0000.000
49A49PHE00.0000.00130.060-0.004-0.0040.0000.0000.0000.000
50A50GLN0-0.020-0.02132.213-0.002-0.0020.0000.0000.0000.000
51A51ASN00.0030.01032.247-0.004-0.0040.0000.0000.0000.000
52A52PRO00.0160.00534.7940.0000.0000.0000.0000.0000.000
53A53GLU-1-0.825-0.88735.035-0.075-0.0750.0000.0000.0000.000
54A54GLY00.0130.00635.187-0.004-0.0040.0000.0000.0000.000
55A55TRP00.020-0.02327.761-0.003-0.0030.0000.0000.0000.000
56A56GLU-1-0.820-0.89030.959-0.111-0.1110.0000.0000.0000.000
57A57GLY00.0280.01131.387-0.009-0.0090.0000.0000.0000.000
58A58ARG10.7940.88828.5660.0310.0310.0000.0000.0000.000
59A59LYS10.8500.92426.8450.1070.1070.0000.0000.0000.000
60A60LYS10.8420.91226.2730.0730.0730.0000.0000.0000.000
61A61ILE0-0.027-0.00625.461-0.012-0.0120.0000.0000.0000.000
62A62LEU0-0.021-0.01022.378-0.006-0.0060.0000.0000.0000.000
63A63ILE00.0550.03121.665-0.023-0.0230.0000.0000.0000.000
64A64ASN0-0.060-0.02222.289-0.023-0.0230.0000.0000.0000.000
65A65ALA00.019-0.00320.203-0.016-0.0160.0000.0000.0000.000
66A66ALA00.0140.01417.687-0.022-0.0220.0000.0000.0000.000
67A67LYS10.9070.94417.5330.2200.2200.0000.0000.0000.000
68A68ALA0-0.094-0.02919.391-0.020-0.0200.0000.0000.0000.000
69A69LEU0-0.013-0.00513.891-0.017-0.0170.0000.0000.0000.000
70A70GLU-1-0.791-0.90014.230-0.542-0.5420.0000.0000.0000.000
71A71ARG10.8240.90014.9440.1980.1980.0000.0000.0000.000
72A72ALA0-0.054-0.01414.6210.0080.0080.0000.0000.0000.000
73A73GLY0-0.0020.00611.3840.0010.0010.0000.0000.0000.000
74A74ALA0-0.036-0.0189.705-0.329-0.3290.0000.0000.0000.000
75A75GLU-1-0.812-0.9176.044-4.477-4.4770.0000.0000.0000.000
76A76LEU0-0.032-0.0047.826-0.004-0.0040.0000.0000.0000.000
77A77ILE0-0.0050.00610.1000.1410.1410.0000.0000.0000.000
78A78ALA00.0280.01513.1690.0250.0250.0000.0000.0000.000
79A79PHE00.0340.01015.4230.0090.0090.0000.0000.0000.000
80A80ALA00.0400.02317.4970.0200.0200.0000.0000.0000.000
81A81ALA00.0020.00118.8510.0170.0170.0000.0000.0000.000
82A82ASN00.0700.04522.200-0.023-0.0230.0000.0000.0000.000
83A83THR00.0380.00524.365-0.014-0.0140.0000.0000.0000.000
84A84PRO0-0.007-0.00822.809-0.008-0.0080.0000.0000.0000.000
85A85HIS00.0060.01019.848-0.032-0.0320.0000.0000.0000.000
86A86LEU0-0.057-0.00824.087-0.009-0.0090.0000.0000.0000.000
87A87VAL0-0.001-0.00325.635-0.002-0.0020.0000.0000.0000.000
88A88PHE00.0100.00217.784-0.010-0.0100.0000.0000.0000.000
89A89ASP-1-0.792-0.88122.535-0.166-0.1660.0000.0000.0000.000
90A90ASP-1-0.806-0.90524.701-0.159-0.1590.0000.0000.0000.000
91A91VAL0-0.039-0.01820.903-0.008-0.0080.0000.0000.0000.000
92A92GLN00.019-0.00917.810-0.048-0.0480.0000.0000.0000.000
93A93ARG10.7330.85421.5320.1350.1350.0000.0000.0000.000
94A94GLU-1-0.828-0.90023.428-0.238-0.2380.0000.0000.0000.000
95A95VAL0-0.036-0.01117.221-0.003-0.0030.0000.0000.0000.000
96A96ASN0-0.111-0.05517.8050.0090.0090.0000.0000.0000.000
97A97VAL0-0.019-0.01112.453-0.094-0.0940.0000.0000.0000.000
98A98PRO0-0.0080.00111.9380.0970.0970.0000.0000.0000.000
99A99MET0-0.0010.01513.113-0.043-0.0430.0000.0000.0000.000
100A100VAL00.0120.00012.1540.0030.0030.0000.0000.0000.000
101A101SER0-0.026-0.02115.1210.0570.0570.0000.0000.0000.000
102A102ILE00.012-0.00518.1160.0090.0090.0000.0000.0000.000
103A103ILE00.0110.01219.3640.0170.0170.0000.0000.0000.000
104A104ASP-1-0.801-0.87819.093-0.122-0.1220.0000.0000.0000.000
105A105ALA00.0050.01316.4350.0050.0050.0000.0000.0000.000
106A106VAL0-0.011-0.01518.0160.0240.0240.0000.0000.0000.000
107A107ALA00.0340.02221.2340.0060.0060.0000.0000.0000.000
108A108GLU-1-0.868-0.90015.769-0.071-0.0710.0000.0000.0000.000
109A109GLU-1-0.816-0.91317.5300.1560.1560.0000.0000.0000.000
110A110ILE00.000-0.00320.2270.0050.0050.0000.0000.0000.000
111A111LEU0-0.014-0.01023.3890.0000.0000.0000.0000.0000.000
112A112LYS10.8410.91715.505-0.116-0.1160.0000.0000.0000.000
113A113ARG10.7530.85520.423-0.128-0.1280.0000.0000.0000.000
114A114GLY0-0.043-0.00623.7400.0040.0040.0000.0000.0000.000
115A115VAL0-0.012-0.00626.574-0.007-0.0070.0000.0000.0000.000
116A116ARG10.7780.88326.483-0.007-0.0070.0000.0000.0000.000
117A117LYS10.7950.90330.878-0.016-0.0160.0000.0000.0000.000
118A118VAL0-0.020-0.01928.2920.0090.0090.0000.0000.0000.000
119A119LEU00.0140.01631.742-0.005-0.0050.0000.0000.0000.000
120A120LEU0-0.026-0.00528.6230.0090.0090.0000.0000.0000.000
121A121LEU00.013-0.00630.566-0.003-0.0030.0000.0000.0000.000
122A122GLY00.006-0.01629.9660.0050.0050.0000.0000.0000.000
123A123THR00.0310.00830.859-0.004-0.0040.0000.0000.0000.000
124A124LYS10.8820.91633.095-0.025-0.0250.0000.0000.0000.000
125A125THR0-0.0160.01132.363-0.004-0.0040.0000.0000.0000.000
126A126THR0-0.054-0.03528.007-0.006-0.0060.0000.0000.0000.000
127A127MET0-0.0590.01131.095-0.003-0.0030.0000.0000.0000.000
128A128THR00.004-0.02833.922-0.004-0.0040.0000.0000.0000.000
129A129ALA0-0.0140.01230.388-0.006-0.0060.0000.0000.0000.000
130A130ASP-1-0.868-0.93331.766-0.022-0.0220.0000.0000.0000.000
131A131PHE0-0.010-0.02126.286-0.001-0.0010.0000.0000.0000.000
132A132TYR0-0.036-0.01623.935-0.006-0.0060.0000.0000.0000.000
133A133ILE00.0420.02128.5550.0000.0000.0000.0000.0000.000
134A134LYS10.8460.90930.9500.0650.0650.0000.0000.0000.000
135A135THR0-0.050-0.04025.848-0.007-0.0070.0000.0000.0000.000
136A136LEU0-0.007-0.00825.273-0.008-0.0080.0000.0000.0000.000
137A137GLU-1-0.833-0.90927.692-0.017-0.0170.0000.0000.0000.000
138A138GLU-1-0.829-0.90529.630-0.074-0.0740.0000.0000.0000.000
139A139LYS10.7540.87923.1250.0960.0960.0000.0000.0000.000
140A140GLY0-0.057-0.01627.466-0.003-0.0030.0000.0000.0000.000
141A141LEU0-0.067-0.03826.4030.0070.0070.0000.0000.0000.000
142A142GLU-1-0.841-0.90130.982-0.003-0.0030.0000.0000.0000.000
143A143VAL0-0.042-0.04230.4620.0080.0080.0000.0000.0000.000
144A144VAL00.0400.04433.313-0.002-0.0020.0000.0000.0000.000
145A145VAL0-0.008-0.02534.3500.0050.0050.0000.0000.0000.000
146A146PRO00.0030.01336.123-0.002-0.0020.0000.0000.0000.000
147A147ASN00.0450.01739.284-0.005-0.0050.0000.0000.0000.000
148A148ASP-1-0.851-0.94441.5840.0140.0140.0000.0000.0000.000
149A149GLU-1-0.947-0.95642.8640.0310.0310.0000.0000.0000.000
150A150GLU-1-0.671-0.80540.7290.0330.0330.0000.0000.0000.000
151A151LYS10.7930.87337.861-0.010-0.0100.0000.0000.0000.000
152A152GLU-1-0.854-0.91138.5600.0290.0290.0000.0000.0000.000
153A153GLU-1-0.764-0.86540.4340.0510.0510.0000.0000.0000.000
154A154LEU0-0.012-0.00333.6920.0050.0050.0000.0000.0000.000
155A155ASN00.008-0.01035.8300.0080.0080.0000.0000.0000.000
156A156ARG10.7390.83336.774-0.048-0.0480.0000.0000.0000.000
157A157ILE0-0.0120.00036.0110.0050.0050.0000.0000.0000.000
158A158ILE0-0.031-0.01531.8850.0080.0080.0000.0000.0000.000
159A159PHE0-0.033-0.02133.1360.0070.0070.0000.0000.0000.000
160A160GLU-1-0.847-0.90535.9180.0510.0510.0000.0000.0000.000
161A161GLU-1-0.832-0.89136.8840.0700.0700.0000.0000.0000.000
162A162LEU0-0.029-0.01331.5740.0070.0070.0000.0000.0000.000
163A163ALA00.0240.02331.3650.0120.0120.0000.0000.0000.000
164A164PHE0-0.072-0.02932.4560.0020.0020.0000.0000.0000.000
165A165GLY0-0.020-0.00631.6020.0030.0030.0000.0000.0000.000
166A166ASN0-0.037-0.01632.4520.0030.0030.0000.0000.0000.000
167A167LEU00.014-0.00530.997-0.006-0.0060.0000.0000.0000.000
168A168LYS10.8380.92135.158-0.068-0.0680.0000.0000.0000.000
169A169ASN00.006-0.01638.521-0.004-0.0040.0000.0000.0000.000
170A170LYS10.8120.89830.961-0.127-0.1270.0000.0000.0000.000
171A171GLU-1-0.817-0.90236.1220.0670.0670.0000.0000.0000.000
172A172TRP0-0.027-0.00938.686-0.002-0.0020.0000.0000.0000.000
173A173ILE00.0180.00533.347-0.003-0.0030.0000.0000.0000.000
174A174VAL00.0080.00634.065-0.002-0.0020.0000.0000.0000.000
175A175ARG10.8760.91736.072-0.059-0.0590.0000.0000.0000.000
176A176LEU0-0.0270.00436.862-0.004-0.0040.0000.0000.0000.000
177A177ILE00.018-0.00332.014-0.004-0.0040.0000.0000.0000.000
178A178GLU-1-0.790-0.87135.4040.0610.0610.0000.0000.0000.000
179A179LYS10.8140.90538.124-0.034-0.0340.0000.0000.0000.000
180A180TYR0-0.027-0.04737.665-0.005-0.0050.0000.0000.0000.000
181A181ARG10.8640.95334.707-0.056-0.0560.0000.0000.0000.000
182A182GLU-1-1.007-1.01037.9660.0270.0270.0000.0000.0000.000
183A183SER0-0.013-0.00841.631-0.003-0.0030.0000.0000.0000.000
184A184GLU-1-0.902-0.96239.6450.0110.0110.0000.0000.0000.000
185A185GLY0-0.0160.01438.511-0.003-0.0030.0000.0000.0000.000
186A186ILE0-0.040-0.01333.690-0.002-0.0020.0000.0000.0000.000
187A187GLU-1-0.771-0.89631.0600.0270.0270.0000.0000.0000.000
188A188GLY0-0.001-0.01128.9700.0080.0080.0000.0000.0000.000
189A189VAL0-0.007-0.00428.647-0.007-0.0070.0000.0000.0000.000
190A190ILE00.0120.00825.2570.0130.0130.0000.0000.0000.000
191A191LEU0-0.0080.00125.125-0.006-0.0060.0000.0000.0000.000
192A192GLY00.0510.01525.3110.0090.0090.0000.0000.0000.000
193A193CYS0-0.134-0.07026.176-0.011-0.0110.0000.0000.0000.000
194A194THR00.029-0.01122.2730.0030.0030.0000.0000.0000.000
195A195GLU-1-0.837-0.89724.9200.1480.1480.0000.0000.0000.000
196A196LEU00.0290.00828.2690.0030.0030.0000.0000.0000.000
197A197PRO00.0310.02323.998-0.003-0.0030.0000.0000.0000.000
198A198LEU0-0.0250.00625.7290.0130.0130.0000.0000.0000.000
199A199ALA00.0020.01527.9230.0000.0000.0000.0000.0000.000
200A200ILE0-0.018-0.01428.4410.0030.0030.0000.0000.0000.000
201A201LYS10.8020.87924.740-0.156-0.1560.0000.0000.0000.000
202A202GLN00.045-0.01023.477-0.010-0.0100.0000.0000.0000.000
203A203GLY00.0060.01325.903-0.006-0.0060.0000.0000.0000.000
204A204ASP-1-0.841-0.90128.7200.1290.1290.0000.0000.0000.000
205A205VAL0-0.005-0.00630.354-0.007-0.0070.0000.0000.0000.000
206A206SER0-0.106-0.08431.4040.0040.0040.0000.0000.0000.000
207A207VAL0-0.038-0.00931.017-0.007-0.0070.0000.0000.0000.000
208A208GLU-1-0.777-0.85424.5750.1190.1190.0000.0000.0000.000
209A209VAL0-0.017-0.00424.978-0.007-0.0070.0000.0000.0000.000
210A210PHE0-0.007-0.00122.2580.0180.0180.0000.0000.0000.000
211A211ASP-1-0.750-0.86520.8760.2150.2150.0000.0000.0000.000
212A212SER00.0290.00820.5080.0180.0180.0000.0000.0000.000
213A213ALA00.0160.01118.948-0.003-0.0030.0000.0000.0000.000
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