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: K3633

Calculation Name: 4OK0-A-Xray372

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: 2023-06-20

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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2832916.921576
FMO2-HF: Nuclear repulsion 2741637.913268
FMO2-HF: Total energy -91279.008308
FMO2-MP2: Total energy -91543.973754


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:12:LEU)


Summations of interaction energy for fragment #1(A:12: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.
-7.082-6.13313.359-4.344-9.963-0.012
Interaction energy analysis for fragmet #1(A:12: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 : -0.012
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].
3A14GLU-1-0.855-0.9493.622-3.031-1.185-0.004-0.924-0.9180.004
4A15GLN0-0.082-0.0306.1760.0080.0080.0000.0000.0000.000
5A16ALA00.0670.0272.816-0.962-0.1810.446-0.269-0.958-0.001
6A17LEU00.0220.0222.1651.542-4.00311.621-1.608-4.4680.000
7A18ASN0-0.028-0.0263.648-0.186-0.0120.0140.024-0.2120.000
8A19HIS00.0100.0436.4760.0650.0650.0000.0000.0000.000
9A20GLU-1-0.803-0.8752.805-5.967-4.4340.381-0.749-1.164-0.009
10A21LYS10.8600.9305.8910.8790.8790.0000.0000.0000.000
11A22LEU0-0.014-0.0047.9560.1340.1340.0000.0000.0000.000
12A23MET0-0.0070.0016.8720.1410.1410.0000.0000.0000.000
13A24ARG10.9480.9786.8541.2941.2940.0000.0000.0000.000
14A25ALA0-0.035-0.00310.6390.0850.0850.0000.0000.0000.000
15A26ILE00.005-0.00213.3710.0690.0690.0000.0000.0000.000
16A27VAL00.015-0.00713.3990.0470.0470.0000.0000.0000.000
17A28LYS10.9400.96513.0340.5090.5090.0000.0000.0000.000
18A29ASN0-0.0220.00016.2410.0490.0490.0000.0000.0000.000
19A30LEU0-0.003-0.00218.4090.0320.0320.0000.0000.0000.000
20A31ALA00.0370.03719.1920.0210.0210.0000.0000.0000.000
21A32ASP-1-0.857-0.90420.960-0.179-0.1790.0000.0000.0000.000
22A33THR0-0.086-0.05623.0320.0230.0230.0000.0000.0000.000
23A34PRO0-0.009-0.03824.767-0.005-0.0050.0000.0000.0000.000
24A35MET0-0.043-0.00521.2670.0070.0070.0000.0000.0000.000
25A36VAL00.0110.01421.056-0.015-0.0150.0000.0000.0000.000
26A37LEU0-0.0120.00513.0350.0160.0160.0000.0000.0000.000
27A38LYS10.8570.90917.3420.1030.1030.0000.0000.0000.000
28A39GLY00.0600.02515.867-0.019-0.0190.0000.0000.0000.000
29A40GLU-1-0.848-0.93911.924-0.049-0.0490.0000.0000.0000.000
30A41THR00.044-0.0029.222-0.047-0.0470.0000.0000.0000.000
31A42ALA0-0.0240.01011.146-0.099-0.0990.0000.0000.0000.000
32A43LEU00.0050.01112.545-0.042-0.0420.0000.0000.0000.000
33A44TYR0-0.078-0.0773.223-1.119-0.0180.091-0.422-0.770-0.003
34A45LEU0-0.057-0.0447.795-0.146-0.1460.0000.0000.0000.000
35A46GLY0-0.052-0.01910.157-0.004-0.0040.0000.0000.0000.000
36A47TYR0-0.018-0.03712.5950.0370.0370.0000.0000.0000.000
37A48GLY00.0460.0389.9960.0620.0620.0000.0000.0000.000
38A49LEU0-0.041-0.0039.3420.0300.0300.0000.0000.0000.000
39A50ASN0-0.005-0.0087.721-0.176-0.1760.0000.0000.0000.000
40A51ARG10.8260.8846.6810.0950.0950.0000.0000.0000.000
41A52PHE0-0.0020.0082.614-1.335-0.2840.811-0.395-1.468-0.003
42A53SER0-0.012-0.0395.2710.2260.234-0.001-0.001-0.0050.000
43A54GLU-1-0.911-0.9637.0180.1280.1280.0000.0000.0000.000
44A55ASP-1-0.861-0.9109.309-0.049-0.0490.0000.0000.0000.000
45A56LEU0-0.042-0.01712.012-0.071-0.0710.0000.0000.0000.000
46A57ASP-1-0.846-0.91414.511-0.072-0.0720.0000.0000.0000.000
47A58PHE0-0.018-0.03616.561-0.026-0.0260.0000.0000.0000.000
48A59ASP-1-0.806-0.89320.169-0.083-0.0830.0000.0000.0000.000
49A60CYS0-0.034-0.03523.678-0.018-0.0180.0000.0000.0000.000
50A61HIS00.0390.02226.1710.0130.0130.0000.0000.0000.000
51A62LYS10.9530.98729.3300.1080.1080.0000.0000.0000.000
52A63LYS10.9220.96728.9980.0600.0600.0000.0000.0000.000
53A64ILE00.0210.01124.106-0.001-0.0010.0000.0000.0000.000
54A65ASN00.0160.00428.1050.0050.0050.0000.0000.0000.000
55A66LEU00.0480.02921.384-0.010-0.0100.0000.0000.0000.000
56A67LEU00.0470.01123.245-0.014-0.0140.0000.0000.0000.000
57A68GLY0-0.012-0.00123.968-0.007-0.0070.0000.0000.0000.000
58A69ARG10.8140.90221.8630.1780.1780.0000.0000.0000.000
59A70VAL00.0260.01118.272-0.018-0.0180.0000.0000.0000.000
60A71LYS10.9370.96219.4240.0940.0940.0000.0000.0000.000
61A72SER0-0.033-0.01921.074-0.004-0.0040.0000.0000.0000.000
62A73ALA0-0.027-0.00116.923-0.009-0.0090.0000.0000.0000.000
63A74ILE0-0.0310.00116.052-0.044-0.0440.0000.0000.0000.000
64A75PRO00.0090.02612.4090.0120.0120.0000.0000.0000.000
65A76ASN00.042-0.00815.3160.0270.0270.0000.0000.0000.000
66A77GLY0-0.047-0.03513.766-0.062-0.0620.0000.0000.0000.000
67A78ILE0-0.0150.01610.763-0.002-0.0020.0000.0000.0000.000
68A79ILE0-0.011-0.00614.8010.0190.0190.0000.0000.0000.000
69A80LEU0-0.0100.00017.5000.0050.0050.0000.0000.0000.000
70A81ASN0-0.031-0.01519.276-0.003-0.0030.0000.0000.0000.000
71A82ASP-1-0.874-0.94620.907-0.046-0.0460.0000.0000.0000.000
72A83ILE0-0.073-0.03321.044-0.015-0.0150.0000.0000.0000.000
73A84HIS00.0200.02022.7580.0080.0080.0000.0000.0000.000
74A85ILE00.015-0.00923.870-0.006-0.0060.0000.0000.0000.000
75A86LYS10.8860.96723.361-0.004-0.0040.0000.0000.0000.000
76A87LYS10.9070.93826.3760.0260.0260.0000.0000.0000.000
77A88ASP-1-0.869-0.92227.104-0.074-0.0740.0000.0000.0000.000
78A89THR0-0.024-0.01429.5730.0070.0070.0000.0000.0000.000
79A90ASP-1-0.882-0.94431.218-0.051-0.0510.0000.0000.0000.000
80A91SER0-0.054-0.02531.085-0.003-0.0030.0000.0000.0000.000
81A92VAL0-0.030-0.01725.598-0.002-0.0020.0000.0000.0000.000
82A93GLY00.0320.02625.2820.0030.0030.0000.0000.0000.000
83A94ARG10.7760.84222.1620.0250.0250.0000.0000.0000.000
84A95TYR00.012-0.00520.7900.0070.0070.0000.0000.0000.000
85A96MET00.0010.00119.2330.0030.0030.0000.0000.0000.000
86A97VAL00.0250.02116.8000.0060.0060.0000.0000.0000.000
87A98ARG10.9720.98316.9610.0010.0010.0000.0000.0000.000
88A99TYR0-0.046-0.05810.352-0.019-0.0190.0000.0000.0000.000
89A100ALA00.0790.04314.9800.0340.0340.0000.0000.0000.000
90A101THR0-0.0120.00111.057-0.079-0.0790.0000.0000.0000.000
91A102LYS10.9080.95012.4820.4430.4430.0000.0000.0000.000
92A103ASP-1-0.829-0.90910.972-0.368-0.3680.0000.0000.0000.000
93A104ASN0-0.013-0.01812.9080.0540.0540.0000.0000.0000.000
94A105LYS10.9830.98414.605-0.073-0.0730.0000.0000.0000.000
95A106GLU-1-0.957-0.96715.0670.2010.2010.0000.0000.0000.000
96A107GLU-1-0.932-0.95915.272-0.028-0.0280.0000.0000.0000.000
97A108GLN0-0.007-0.00411.5620.0730.0730.0000.0000.0000.000
98A109THR0-0.061-0.05013.975-0.015-0.0150.0000.0000.0000.000
99A110LEU00.0290.02111.6620.0030.0030.0000.0000.0000.000
100A111LYS10.9330.96814.304-0.038-0.0380.0000.0000.0000.000
101A112LEU00.0100.01215.564-0.028-0.0280.0000.0000.0000.000
102A113GLU-1-0.769-0.84317.899-0.019-0.0190.0000.0000.0000.000
103A114ILE0-0.008-0.00720.183-0.017-0.0170.0000.0000.0000.000
104A115SER0-0.0100.00222.8620.0200.0200.0000.0000.0000.000
105A116TYR00.005-0.02925.618-0.013-0.0130.0000.0000.0000.000
106A117ARG10.9370.96528.7220.0400.0400.0000.0000.0000.000
107A118ASP-1-0.879-0.93028.626-0.055-0.0550.0000.0000.0000.000
108A119ALA0-0.039-0.02027.191-0.005-0.0050.0000.0000.0000.000
109A120PRO00.0060.01124.3940.0060.0060.0000.0000.0000.000
110A121LYS10.9460.98827.6980.0930.0930.0000.0000.0000.000
111A122GLU-1-0.811-0.91927.873-0.146-0.1460.0000.0000.0000.000
112A123SER0-0.035-0.01828.363-0.006-0.0060.0000.0000.0000.000
113A124GLU-1-0.873-0.97027.037-0.093-0.0930.0000.0000.0000.000
114A125VAL0-0.027-0.00622.803-0.006-0.0060.0000.0000.0000.000
115A126ASN0-0.015-0.00420.5600.0200.0200.0000.0000.0000.000
116A127VAL0-0.015-0.01819.790-0.008-0.0080.0000.0000.0000.000
117A128ILE00.0140.01714.4750.0110.0110.0000.0000.0000.000
118A129GLU-1-0.912-0.95813.079-0.496-0.4960.0000.0000.0000.000
119A130GLY0-0.070-0.03715.271-0.027-0.0270.0000.0000.0000.000
120A131MET0-0.047-0.01511.5270.0000.0000.0000.0000.0000.000
121A132ARG10.8250.90616.9690.1930.1930.0000.0000.0000.000
122A133ILE0-0.019-0.00714.688-0.010-0.0100.0000.0000.0000.000
123A134ALA00.0200.01018.8000.0200.0200.0000.0000.0000.000
124A135LYS10.9140.99819.6680.1210.1210.0000.0000.0000.000
125A136ILE00.0550.02717.8520.0050.0050.0000.0000.0000.000
126A137GLU-1-0.798-0.88721.003-0.098-0.0980.0000.0000.0000.000
127A138ARG10.8850.96223.0640.1050.1050.0000.0000.0000.000
128A139ILE0-0.044-0.02217.0320.0080.0080.0000.0000.0000.000
129A140ILE00.0200.00620.5600.0140.0140.0000.0000.0000.000
130A141ASP-1-0.835-0.91222.339-0.025-0.0250.0000.0000.0000.000
131A142ASN0-0.007-0.01821.6210.0160.0160.0000.0000.0000.000
132A143LYS10.8170.91115.726-0.013-0.0130.0000.0000.0000.000
133A144LEU00.0370.02221.5510.0180.0180.0000.0000.0000.000
134A145CYS0-0.0040.01324.9450.0080.0080.0000.0000.0000.000
135A146ALA0-0.053-0.03321.9380.0080.0080.0000.0000.0000.000
136A147CYS0-0.094-0.04922.3440.0120.0120.0000.0000.0000.000
137A148PHE0-0.059-0.03024.3660.0110.0110.0000.0000.0000.000
138A149ASP-1-0.787-0.87627.8180.0080.0080.0000.0000.0000.000
139A150GLY00.0370.03028.677-0.006-0.0060.0000.0000.0000.000
140A151GLU-1-0.986-0.99529.6520.0070.0070.0000.0000.0000.000
141A152HIS0-0.079-0.04126.8030.0070.0070.0000.0000.0000.000
142A153THR0-0.0380.00926.5650.0020.0020.0000.0000.0000.000
143A154ARG10.7820.86418.458-0.040-0.0400.0000.0000.0000.000
144A155THR00.0310.01523.363-0.002-0.0020.0000.0000.0000.000
145A156LYS10.8790.93415.896-0.210-0.2100.0000.0000.0000.000
146A157ALA00.0770.03617.204-0.016-0.0160.0000.0000.0000.000
147A158ARG10.8270.88912.301-0.327-0.3270.0000.0000.0000.000
148A159ASP-1-0.769-0.84615.5970.0380.0380.0000.0000.0000.000
149A160LEU00.0340.03318.457-0.022-0.0220.0000.0000.0000.000
150A161PHE00.021-0.00410.965-0.009-0.0090.0000.0000.0000.000
151A162ASP-1-0.731-0.86213.4590.0200.0200.0000.0000.0000.000
152A163LEU00.0000.00415.781-0.037-0.0370.0000.0000.0000.000
153A164HIS0-0.057-0.02217.730-0.022-0.0220.0000.0000.0000.000
154A165PHE00.0300.01212.823-0.021-0.0210.0000.0000.0000.000
155A166LEU0-0.044-0.03916.370-0.031-0.0310.0000.0000.0000.000
156A167ALA0-0.025-0.01118.810-0.012-0.0120.0000.0000.0000.000
157A168LYS10.9490.97517.490-0.067-0.0670.0000.0000.0000.000
158A169HIS0-0.049-0.02715.411-0.020-0.0200.0000.0000.0000.000
159A170TYR0-0.049-0.03915.312-0.024-0.0240.0000.0000.0000.000
160A171GLU-1-0.906-0.95221.186-0.029-0.0290.0000.0000.0000.000
161A172GLU-1-0.901-0.95723.329-0.103-0.1030.0000.0000.0000.000
162A173HIS10.7460.85722.6010.1180.1180.0000.0000.0000.000
163A174PHE00.0110.02022.5560.0030.0030.0000.0000.0000.000
164A175ASN00.0370.02527.2470.0050.0050.0000.0000.0000.000
165A176LEU00.025-0.00730.7690.0040.0040.0000.0000.0000.000
166A177ASP-1-0.862-0.94431.552-0.015-0.0150.0000.0000.0000.000
167A178LEU00.0290.01226.0790.0050.0050.0000.0000.0000.000
168A179ALA00.0120.00828.4810.0070.0070.0000.0000.0000.000
169A180SER0-0.067-0.02929.6310.0100.0100.0000.0000.0000.000
170A181ARG10.7870.86828.2660.0180.0180.0000.0000.0000.000
171A182LEU00.0150.02123.5920.0080.0080.0000.0000.0000.000
172A183LYS10.9360.96427.615-0.009-0.0090.0000.0000.0000.000
173A184ASP-1-0.915-0.96730.1670.0400.0400.0000.0000.0000.000
174A185PHE0-0.016-0.01123.2430.0080.0080.0000.0000.0000.000
175A186SER0-0.059-0.04526.1000.0110.0110.0000.0000.0000.000
176A187LYS10.8620.94627.871-0.043-0.0430.0000.0000.0000.000
177A188ASP-1-0.921-0.96530.7230.0840.0840.0000.0000.0000.000
178A189PRO00.0300.00327.6290.0070.0070.0000.0000.0000.000
179A190ASP-1-0.854-0.92827.5980.1280.1280.0000.0000.0000.000
180A191LYS10.8710.94229.346-0.077-0.0770.0000.0000.0000.000
181A192LEU0-0.0110.00924.7060.0080.0080.0000.0000.0000.000
182A193VAL00.0260.00624.5390.0150.0150.0000.0000.0000.000
183A194SER0-0.042-0.03425.3560.0160.0160.0000.0000.0000.000
184A195ASP-1-0.917-0.95126.3820.1200.1200.0000.0000.0000.000
185A196TYR0-0.025-0.02221.1550.0080.0080.0000.0000.0000.000
186A197LEU00.0060.02021.4580.0340.0340.0000.0000.0000.000
187A198VAL0-0.016-0.02821.5890.0330.0330.0000.0000.0000.000
188A199ASP-1-0.799-0.91418.4490.2910.2910.0000.0000.0000.000
189A200VAL00.0360.01816.4650.0420.0420.0000.0000.0000.000
190A201LYS10.8760.93916.509-0.369-0.3690.0000.0000.0000.000
191A202LEU0-0.004-0.01617.3850.0490.0490.0000.0000.0000.000
192A203ASP-1-0.789-0.85312.5850.5270.5270.0000.0000.0000.000
193A204ALA0-0.002-0.00210.6710.0570.0570.0000.0000.0000.000
194A205LEU0-0.076-0.0416.8010.2740.2740.0000.0000.0000.000
195A206LEU00.003-0.0089.3850.0050.0050.0000.0000.0000.000
196A207ASN0-0.082-0.02912.1240.1660.1660.0000.0000.0000.000
197A208GLN0-0.0030.0039.706-0.238-0.2380.0000.0000.0000.000
198A209ILE0-0.054-0.0328.042-0.006-0.0060.0000.0000.0000.000
199A210MET0-0.040-0.00111.322-0.124-0.1240.0000.0000.0000.000
200A211ASP-1-0.813-0.88914.7480.3110.3110.0000.0000.0000.000
201A212LEU0-0.059-0.02518.131-0.037-0.0370.0000.0000.0000.000
202A213GLU-1-0.882-0.96020.5390.2480.2480.0000.0000.0000.000
203A214GLU-1-0.935-0.96219.3590.1940.1940.0000.0000.0000.000
204A215THR0-0.032-0.01718.252-0.025-0.0250.0000.0000.0000.000
205A216ALA0-0.011-0.01420.550-0.029-0.0290.0000.0000.0000.000
206A217LEU0-0.027-0.00123.684-0.022-0.0220.0000.0000.0000.000
207A218GLU-1-0.867-0.93821.0860.1000.1000.0000.0000.0000.000
208A219LEU00.0000.00021.746-0.019-0.0190.0000.0000.0000.000
209A220GLY00.0520.03923.819-0.015-0.0150.0000.0000.0000.000
210A221VAL0-0.051-0.03027.229-0.012-0.0120.0000.0000.0000.000
211A222MET0-0.012-0.00720.854-0.015-0.0150.0000.0000.0000.000
212A223ALA00.0370.03126.525-0.012-0.0120.0000.0000.0000.000
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