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: ZY2LN

Calculation Name: 4OK0-A-Xray322

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OK0

Chain ID: A

ChEMBL ID:

UniProt ID: Q9ZKK2

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 227
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2842719.216283
FMO2-HF: Nuclear repulsion 2751269.366668
FMO2-HF: Total energy -91449.849616
FMO2-MP2: Total energy -91715.336246


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:11:ACE )


Summations of interaction energy for fragment #1(A:11:ACE )
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.
1.0031.883-0.005-0.407-0.467-0.001
Interaction energy analysis for fragmet #1(A:11:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / 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].
3A13SER 00.0210.0253.8511.0461.926-0.005-0.407-0.467-0.001
4A14GLU -1-0.851-0.9486.476-0.341-0.3410.0000.0000.0000.000
5A15GLN 0-0.087-0.03110.074-0.111-0.1110.0000.0000.0000.000
6A16ALA 00.0720.0297.2940.0490.0490.0000.0000.0000.000
7A17LEU 00.0280.0247.4230.0880.0880.0000.0000.0000.000
8A18ASN 0-0.031-0.0279.9060.1490.1490.0000.0000.0000.000
9A19HIS 00.0070.04112.1720.0780.0780.0000.0000.0000.000
10A20GLU -1-0.799-0.8739.769-0.836-0.8360.0000.0000.0000.000
11A21LYS 10.8620.93112.8900.3650.3650.0000.0000.0000.000
12A22LEU 0-0.016-0.00515.3480.0610.0610.0000.0000.0000.000
13A23MET 0-0.012-0.00113.2910.0620.0620.0000.0000.0000.000
14A24ARG 10.9520.97913.5690.4390.4390.0000.0000.0000.000
15A25ALA 0-0.035-0.00317.9780.0370.0370.0000.0000.0000.000
16A26ILE 00.005-0.00320.7390.0300.0300.0000.0000.0000.000
17A27VAL 00.013-0.00819.7910.0230.0230.0000.0000.0000.000
18A28LYS 10.9410.96520.2410.1990.1990.0000.0000.0000.000
19A29ASN 0-0.0170.00223.5360.0200.0200.0000.0000.0000.000
20A30LEU 0-0.008-0.00525.1120.0140.0140.0000.0000.0000.000
21A31ALA 00.0370.03826.1970.0080.0080.0000.0000.0000.000
22A32ASP -1-0.856-0.90427.910-0.092-0.0920.0000.0000.0000.000
23A33THR 0-0.085-0.05729.8260.0070.0070.0000.0000.0000.000
24A34PRO 0-0.014-0.04031.299-0.001-0.0010.0000.0000.0000.000
25A35MET 0-0.040-0.00327.4650.0000.0000.0000.0000.0000.000
26A36VAL 00.0090.01326.243-0.002-0.0020.0000.0000.0000.000
27A37LEU 0-0.0130.00518.6700.0010.0010.0000.0000.0000.000
28A38LYS 10.8670.91222.6570.1250.1250.0000.0000.0000.000
29A39GLY 00.0540.02320.743-0.015-0.0150.0000.0000.0000.000
30A40GLU -1-0.849-0.94015.620-0.199-0.1990.0000.0000.0000.000
31A41THR 00.037-0.00514.940-0.046-0.0460.0000.0000.0000.000
32A42ALA 0-0.0140.01416.172-0.014-0.0140.0000.0000.0000.000
33A43LEU 00.0010.00915.6950.0020.0020.0000.0000.0000.000
34A44TYR 0-0.081-0.0778.108-0.040-0.0400.0000.0000.0000.000
35A45LEU 0-0.051-0.04212.960-0.017-0.0170.0000.0000.0000.000
36A46GLY 0-0.050-0.01915.1560.0220.0220.0000.0000.0000.000
37A47TYR 0-0.020-0.03916.0970.0320.0320.0000.0000.0000.000
38A48GLY 00.0460.03812.6520.0320.0320.0000.0000.0000.000
39A49LEU 0-0.043-0.00311.3210.0140.0140.0000.0000.0000.000
40A50ASN 00.001-0.0058.194-0.143-0.1430.0000.0000.0000.000
41A51ARG 10.8210.8817.1310.3770.3770.0000.0000.0000.000
42A52PHE 00.0090.0136.853-0.072-0.0720.0000.0000.0000.000
43A53SER 0-0.019-0.0418.5200.2190.2190.0000.0000.0000.000
44A54GLU -1-0.914-0.96412.307-0.528-0.5280.0000.0000.0000.000
45A55ASP -1-0.861-0.91014.571-0.221-0.2210.0000.0000.0000.000
46A56LEU 0-0.041-0.01617.921-0.015-0.0150.0000.0000.0000.000
47A57ASP -1-0.844-0.91320.446-0.165-0.1650.0000.0000.0000.000
48A58PHE 0-0.015-0.03522.964-0.004-0.0040.0000.0000.0000.000
49A59ASP -1-0.808-0.89325.868-0.096-0.0960.0000.0000.0000.000
50A60CYS 0-0.035-0.03629.193-0.003-0.0030.0000.0000.0000.000
51A61HIS 00.0330.02032.0140.0060.0060.0000.0000.0000.000
52A62LYS 10.9600.99035.3650.0710.0710.0000.0000.0000.000
53A63LYS 10.9210.96635.2120.0680.0680.0000.0000.0000.000
54A64ILE 00.0220.01130.8220.0030.0030.0000.0000.0000.000
55A65ASN 00.0160.00434.971-0.003-0.0030.0000.0000.0000.000
56A66LEU 00.0460.02927.872-0.003-0.0030.0000.0000.0000.000
57A67LEU 00.0480.01230.047-0.007-0.0070.0000.0000.0000.000
58A68GLY 0-0.0090.00030.793-0.004-0.0040.0000.0000.0000.000
59A69ARG 10.8110.90129.0560.1020.1020.0000.0000.0000.000
60A70VAL 00.0280.01124.991-0.007-0.0070.0000.0000.0000.000
61A71LYS 10.9350.96126.4850.0920.0920.0000.0000.0000.000
62A72SER 0-0.032-0.01828.1740.0000.0000.0000.0000.0000.000
63A73ALA 0-0.027-0.00124.3210.0000.0000.0000.0000.0000.000
64A74ILE 0-0.0320.00122.891-0.018-0.0180.0000.0000.0000.000
65A75PRO 00.0120.02619.7360.0120.0120.0000.0000.0000.000
66A76ASN 00.041-0.00822.3890.0010.0010.0000.0000.0000.000
67A77GLY 0-0.048-0.03519.763-0.021-0.0210.0000.0000.0000.000
68A78ILE 0-0.0170.01617.098-0.016-0.0160.0000.0000.0000.000
69A79ILE 0-0.011-0.00720.9480.0220.0220.0000.0000.0000.000
70A80LEU 0-0.0060.00123.391-0.010-0.0100.0000.0000.0000.000
71A81ASN 0-0.031-0.01524.3900.0150.0150.0000.0000.0000.000
72A82ASP -1-0.874-0.94626.598-0.095-0.0950.0000.0000.0000.000
73A83ILE 0-0.076-0.03426.772-0.014-0.0140.0000.0000.0000.000
74A84HIS 00.0220.02028.3660.0050.0050.0000.0000.0000.000
75A85ILE 00.014-0.00929.561-0.007-0.0070.0000.0000.0000.000
76A86LYS 10.8880.96928.0770.1120.1120.0000.0000.0000.000
77A87LYS 10.9070.93831.8820.0790.0790.0000.0000.0000.000
78A88ASP -1-0.869-0.92232.908-0.084-0.0840.0000.0000.0000.000
79A89THR 0-0.024-0.01535.4860.0060.0060.0000.0000.0000.000
80A90ASP -1-0.884-0.94537.111-0.059-0.0590.0000.0000.0000.000
81A91SER 0-0.055-0.02536.474-0.002-0.0020.0000.0000.0000.000
82A92VAL 0-0.030-0.01730.977-0.003-0.0030.0000.0000.0000.000
83A93GLY 00.0350.02631.2660.0050.0050.0000.0000.0000.000
84A94ARG 10.7730.84227.4900.0990.0990.0000.0000.0000.000
85A95TYR 00.011-0.00526.8600.0100.0100.0000.0000.0000.000
86A96MET 0-0.001-0.00124.766-0.014-0.0140.0000.0000.0000.000
87A97VAL 00.0270.02222.7470.0140.0140.0000.0000.0000.000
88A98ARG 10.9720.98322.4520.1130.1130.0000.0000.0000.000
89A99TYR 0-0.043-0.05715.8070.0140.0140.0000.0000.0000.000
90A100ALA 00.0790.04220.158-0.006-0.0060.0000.0000.0000.000
91A101THR 0-0.0160.00016.113-0.026-0.0260.0000.0000.0000.000
92A102LYS 10.9090.95117.4280.2310.2310.0000.0000.0000.000
93A103ASP -1-0.828-0.90915.710-0.229-0.2290.0000.0000.0000.000
94A104ASN 0-0.014-0.02016.3920.0200.0200.0000.0000.0000.000
95A105LYS 10.9840.98418.4800.0830.0830.0000.0000.0000.000
96A106GLU -1-0.957-0.96717.963-0.168-0.1680.0000.0000.0000.000
97A107GLU -1-0.930-0.95819.448-0.159-0.1590.0000.0000.0000.000
98A108GLN 0-0.009-0.00515.737-0.047-0.0470.0000.0000.0000.000
99A109THR 0-0.058-0.04918.5930.0300.0300.0000.0000.0000.000
100A110LEU 00.0280.02017.759-0.028-0.0280.0000.0000.0000.000
101A111LYS 10.9290.96719.9560.2140.2140.0000.0000.0000.000
102A112LEU 00.0130.01321.375-0.014-0.0140.0000.0000.0000.000
103A113GLU -1-0.768-0.84323.893-0.103-0.1030.0000.0000.0000.000
104A114ILE 0-0.009-0.00825.934-0.005-0.0050.0000.0000.0000.000
105A115SER 0-0.0100.00128.6590.0090.0090.0000.0000.0000.000
106A116TYR 00.005-0.02931.069-0.002-0.0020.0000.0000.0000.000
107A117ARG 10.9380.96534.0910.0650.0650.0000.0000.0000.000
108A118ASP -1-0.879-0.93133.694-0.065-0.0650.0000.0000.0000.000
109A119ALA 0-0.038-0.01932.369-0.003-0.0030.0000.0000.0000.000
110A120PRO 00.0080.01229.4060.0050.0050.0000.0000.0000.000
111A121LYS 10.9440.98732.5940.0560.0560.0000.0000.0000.000
112A122GLU -1-0.812-0.91933.511-0.081-0.0810.0000.0000.0000.000
113A123SER 0-0.031-0.01633.326-0.001-0.0010.0000.0000.0000.000
114A124GLU -1-0.879-0.97331.289-0.064-0.0640.0000.0000.0000.000
115A125VAL 0-0.027-0.00527.962-0.006-0.0060.0000.0000.0000.000
116A126ASN 0-0.017-0.00524.4030.0150.0150.0000.0000.0000.000
117A127VAL 0-0.013-0.01725.341-0.007-0.0070.0000.0000.0000.000
118A128ILE 00.0120.01619.4260.0090.0090.0000.0000.0000.000
119A129GLU -1-0.909-0.95718.449-0.163-0.1630.0000.0000.0000.000
120A130GLY 0-0.069-0.03621.662-0.012-0.0120.0000.0000.0000.000
121A131MET 0-0.045-0.01517.674-0.007-0.0070.0000.0000.0000.000
122A132ARG 10.8250.90623.3020.1050.1050.0000.0000.0000.000
123A133ILE 0-0.015-0.00519.699-0.011-0.0110.0000.0000.0000.000
124A134ALA 00.0180.00923.8630.0150.0150.0000.0000.0000.000
125A135LYS 10.9130.99823.7930.0670.0670.0000.0000.0000.000
126A136ILE 00.0530.02620.425-0.004-0.0040.0000.0000.0000.000
127A137GLU -1-0.798-0.88623.915-0.067-0.0670.0000.0000.0000.000
128A138ARG 10.8880.96327.0080.0830.0830.0000.0000.0000.000
129A139ILE 0-0.044-0.02120.428-0.003-0.0030.0000.0000.0000.000
130A140ILE 00.0150.00523.469-0.003-0.0030.0000.0000.0000.000
131A141ASP -1-0.832-0.91124.689-0.060-0.0600.0000.0000.0000.000
132A142ASN 0-0.004-0.01725.1360.0070.0070.0000.0000.0000.000
133A143LYS 10.8200.91218.0700.1540.1540.0000.0000.0000.000
134A144LEU 00.0300.02024.0330.0030.0030.0000.0000.0000.000
135A145CYS 0-0.0010.01426.8870.0050.0050.0000.0000.0000.000
136A146ALA 0-0.053-0.03124.5450.0020.0020.0000.0000.0000.000
137A147CYS 0-0.097-0.05023.8820.0030.0030.0000.0000.0000.000
138A148PHE 0-0.054-0.02825.9990.0070.0070.0000.0000.0000.000
139A149ASP -1-0.793-0.87729.211-0.044-0.0440.0000.0000.0000.000
140A150GLY 00.0410.02931.0300.0010.0010.0000.0000.0000.000
141A151GLU -1-0.989-0.99532.297-0.043-0.0430.0000.0000.0000.000
142A152HIS 0-0.079-0.04130.3270.0050.0050.0000.0000.0000.000
143A153THR 0-0.0380.01028.878-0.006-0.0060.0000.0000.0000.000
144A154ARG 10.7830.86421.4370.1190.1190.0000.0000.0000.000
145A155THR 00.0290.01524.1210.0040.0040.0000.0000.0000.000
146A156LYS 10.8810.93518.1320.1470.1470.0000.0000.0000.000
147A157ALA 00.0830.03717.498-0.001-0.0010.0000.0000.0000.000
148A158ARG 10.8200.88714.4630.2580.2580.0000.0000.0000.000
149A159ASP -1-0.764-0.84516.626-0.126-0.1260.0000.0000.0000.000
150A160LEU 00.0240.02919.0800.0040.0040.0000.0000.0000.000
151A161PHE 00.027-0.00210.255-0.005-0.0050.0000.0000.0000.000
152A162ASP -1-0.733-0.86214.802-0.215-0.2150.0000.0000.0000.000
153A163LEU 0-0.0020.00316.7460.0050.0050.0000.0000.0000.000
154A164HIS 0-0.055-0.02116.293-0.007-0.0070.0000.0000.0000.000
155A165PHE 00.0230.01113.3870.0040.0040.0000.0000.0000.000
156A166LEU 0-0.038-0.03816.5560.0060.0060.0000.0000.0000.000
157A167ALA 0-0.024-0.01019.6850.0070.0070.0000.0000.0000.000
158A168LYS 10.9450.97315.674-0.056-0.0560.0000.0000.0000.000
159A169HIS 0-0.048-0.02514.6550.0090.0090.0000.0000.0000.000
160A170TYR 0-0.051-0.04117.276-0.003-0.0030.0000.0000.0000.000
161A171GLU -1-0.903-0.95022.157-0.009-0.0090.0000.0000.0000.000
162A172GLU -1-0.901-0.95724.738-0.041-0.0410.0000.0000.0000.000
163A173HIS 10.7470.85724.2200.0590.0590.0000.0000.0000.000
164A174PHE 00.0090.01923.474-0.003-0.0030.0000.0000.0000.000
165A175ASN 00.0390.02528.5320.0050.0050.0000.0000.0000.000
166A176LEU 00.025-0.00631.9620.0000.0000.0000.0000.0000.000
167A177ASP -1-0.860-0.94233.644-0.038-0.0380.0000.0000.0000.000
168A178LEU 00.0250.01128.1280.0000.0000.0000.0000.0000.000
169A179ALA 00.0120.00729.3500.0000.0000.0000.0000.0000.000
170A180SER 0-0.060-0.02630.4160.0040.0040.0000.0000.0000.000
171A181ARG 10.7810.86530.7430.0510.0510.0000.0000.0000.000
172A182LEU 00.0160.02224.0310.0000.0000.0000.0000.0000.000
173A183LYS 10.9360.96428.0910.0110.0110.0000.0000.0000.000
174A184ASP -1-0.916-0.96730.218-0.017-0.0170.0000.0000.0000.000
175A185PHE 0-0.015-0.01123.4190.0010.0010.0000.0000.0000.000
176A186SER 0-0.067-0.04825.9070.0030.0030.0000.0000.0000.000
177A187LYS 10.8690.94927.5360.0210.0210.0000.0000.0000.000
178A188ASP -1-0.918-0.96430.0760.0040.0040.0000.0000.0000.000
179A189PRO 00.0270.00126.085-0.002-0.0020.0000.0000.0000.000
180A190ASP -1-0.853-0.92826.2010.0210.0210.0000.0000.0000.000
181A191LYS 10.8710.94227.9000.0170.0170.0000.0000.0000.000
182A192LEU 0-0.0120.00923.944-0.004-0.0040.0000.0000.0000.000
183A193VAL 00.0260.00622.770-0.005-0.0050.0000.0000.0000.000
184A194SER 0-0.041-0.03424.1540.0000.0000.0000.0000.0000.000
185A195ASP -1-0.919-0.95226.070-0.022-0.0220.0000.0000.0000.000
186A196TYR 0-0.022-0.02220.761-0.012-0.0120.0000.0000.0000.000
187A197LEU 00.0040.01920.613-0.004-0.0040.0000.0000.0000.000
188A198VAL 0-0.014-0.02720.7750.0020.0020.0000.0000.0000.000
189A199ASP -1-0.799-0.91319.405-0.100-0.1000.0000.0000.0000.000
190A200VAL 00.0360.01715.456-0.014-0.0140.0000.0000.0000.000
191A201LYS 10.8750.94015.964-0.048-0.0480.0000.0000.0000.000
192A202LEU 0-0.006-0.01716.8410.0020.0020.0000.0000.0000.000
193A203ASP -1-0.789-0.85413.986-0.245-0.2450.0000.0000.0000.000
194A204ALA 00.000-0.00111.4460.0180.0180.0000.0000.0000.000
195A205LEU 0-0.077-0.0409.384-0.027-0.0270.0000.0000.0000.000
196A206LEU 0-0.005-0.0119.494-0.013-0.0130.0000.0000.0000.000
197A207ASN 0-0.077-0.02611.4970.0800.0800.0000.0000.0000.000
198A208GLN 0-0.0030.0028.1010.0230.0230.0000.0000.0000.000
199A209ILE 0-0.055-0.0326.0180.1010.1010.0000.0000.0000.000
200A210MET 0-0.038-0.0019.216-0.013-0.0130.0000.0000.0000.000
201A211ASP -1-0.812-0.89012.7590.1160.1160.0000.0000.0000.000
202A212LEU 0-0.058-0.02415.941-0.019-0.0190.0000.0000.0000.000
203A213GLU -1-0.887-0.96218.5980.0540.0540.0000.0000.0000.000
204A214GLU -1-0.931-0.96016.9360.1200.1200.0000.0000.0000.000
205A215THR 0-0.033-0.01716.544-0.014-0.0140.0000.0000.0000.000
206A216ALA 0-0.011-0.01418.861-0.012-0.0120.0000.0000.0000.000
207A217LEU 0-0.026-0.00122.310-0.005-0.0050.0000.0000.0000.000
208A218GLU -1-0.865-0.93819.1600.0600.0600.0000.0000.0000.000
209A219LEU 0-0.005-0.00221.454-0.006-0.0060.0000.0000.0000.000
210A220GLY 00.0570.04122.963-0.004-0.0040.0000.0000.0000.000
211A221VAL 0-0.051-0.03125.783-0.002-0.0020.0000.0000.0000.000
212A222MET 0-0.017-0.00920.037-0.002-0.0020.0000.0000.0000.000
213A223ALA 00.0400.03225.729-0.003-0.0030.0000.0000.0000.000
214A224GLN 0-0.019-0.01227.597-0.001-0.0010.0000.0000.0000.000
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