FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: 8516Y

Calculation Name: 5DKM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DKM

Chain ID: A

ChEMBL ID:

UniProt ID: Q54137

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2559568.018517
FMO2-HF: Nuclear repulsion 2474993.096702
FMO2-HF: Total energy -84574.921816
FMO2-MP2: Total energy -84817.192055


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:ILE)


Summations of interaction energy for fragment #1(A:1:ILE)
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.
-28.932-15.8126.589-13.534-26.178-0.104
Interaction energy analysis for fragmet #1(A:1:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.050 / q_NPA : -0.036
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].
3A3GLY00.009-0.0043.086-0.8821.1830.187-1.004-1.248-0.002
4A4GLY0-0.022-0.0042.424-0.7820.2081.070-0.899-1.160-0.001
5A5GLU-1-0.895-0.9383.1220.8610.2280.0700.829-0.2660.000
6A6ASP-1-0.823-0.9025.6811.3841.3840.0000.0000.0000.000
7A7ALA0-0.034-0.0296.928-0.198-0.1980.0000.0000.0000.000
8A8ASN0-0.055-0.0358.6050.0420.0420.0000.0000.0000.000
9A9VAL00.0320.01210.298-0.019-0.0190.0000.0000.0000.000
10A10GLN0-0.024-0.02911.259-0.021-0.0210.0000.0000.0000.000
11A11ASP-1-0.845-0.90311.4150.3250.3250.0000.0000.0000.000
12A12HIS0-0.072-0.0398.1700.0360.0360.0000.0000.0000.000
13A13PRO00.0100.01511.223-0.012-0.0120.0000.0000.0000.000
14A14PHE00.0570.0199.231-0.012-0.0120.0000.0000.0000.000
15A15THR0-0.015-0.0026.884-0.046-0.0460.0000.0000.0000.000
16A16VAL0-0.043-0.0249.8700.0420.0420.0000.0000.0000.000
17A17ALA00.0280.0179.532-0.063-0.0630.0000.0000.0000.000
18A18LEU0-0.035-0.01910.7870.0230.0230.0000.0000.0000.000
19A19VAL00.022-0.00812.630-0.016-0.0160.0000.0000.0000.000
20A20THR00.013-0.01315.190-0.004-0.0040.0000.0000.0000.000
21A21PRO0-0.049-0.03418.2520.0200.0200.0000.0000.0000.000
22A22ASP-1-0.904-0.93120.049-0.001-0.0010.0000.0000.0000.000
23A23GLY0-0.027-0.00717.7420.0130.0130.0000.0000.0000.000
24A24GLN0-0.075-0.03112.1720.0550.0550.0000.0000.0000.000
25A25GLN0-0.012-0.0217.4430.0410.0410.0000.0000.0000.000
26A26PHE0-0.019-0.00910.592-0.022-0.0220.0000.0000.0000.000
27A27CYS0-0.079-0.0099.164-0.155-0.1550.0000.0000.0000.000
28A28GLY00.0390.0347.3570.1000.1000.0000.0000.0000.000
29A29GLY00.0370.0178.385-0.006-0.0060.0000.0000.0000.000
30A30THR0-0.006-0.0079.8080.0430.0430.0000.0000.0000.000
31A31LEU0-0.073-0.02012.010-0.014-0.0140.0000.0000.0000.000
32A32ALA00.0370.01015.4290.0090.0090.0000.0000.0000.000
33A33ALA0-0.008-0.01517.7820.0010.0010.0000.0000.0000.000
34A34PRO00.0270.01019.863-0.002-0.0020.0000.0000.0000.000
35A35ASN0-0.0060.01121.2040.0050.0050.0000.0000.0000.000
36A36LYS10.8110.92719.948-0.001-0.0010.0000.0000.0000.000
37A37VAL00.0330.01013.7360.0100.0100.0000.0000.0000.000
38A38VAL00.0180.01813.937-0.012-0.0120.0000.0000.0000.000
39A39THR0-0.003-0.01411.475-0.009-0.0090.0000.0000.0000.000
40A40ALA00.0650.02911.5080.0170.0170.0000.0000.0000.000
41A41ALA0-0.022-0.00613.3170.0090.0090.0000.0000.0000.000
42A42HIS0-0.006-0.00813.1130.0310.0310.0000.0000.0000.000
43A44THR0-0.005-0.03414.6440.0220.0220.0000.0000.0000.000
44A45VAL00.0240.00618.0920.0220.0220.0000.0000.0000.000
45A46GLY0-0.059-0.03020.790-0.004-0.0040.0000.0000.0000.000
46A47SER0-0.0130.01920.6120.0010.0010.0000.0000.0000.000
47A48GLN0-0.108-0.06022.8170.0090.0090.0000.0000.0000.000
48A49PRO0-0.008-0.03322.880-0.002-0.0020.0000.0000.0000.000
49A50ALA0-0.011-0.00622.7990.0030.0030.0000.0000.0000.000
50A51ASP-1-0.822-0.89521.480-0.053-0.0530.0000.0000.0000.000
51A52ILE0-0.018-0.00616.718-0.005-0.0050.0000.0000.0000.000
52A53ASN0-0.028-0.01618.2470.0170.0170.0000.0000.0000.000
53A54VAL00.0230.00914.277-0.012-0.0120.0000.0000.0000.000
54A55VAL0-0.013-0.00513.7420.0100.0100.0000.0000.0000.000
55A56SER00.021-0.00813.4080.0060.0060.0000.0000.0000.000
56A57GLY00.010-0.01414.6330.0000.0000.0000.0000.0000.000
57A58ARG10.7990.91413.899-0.198-0.1980.0000.0000.0000.000
58A59THR00.0530.03510.6230.0150.0150.0000.0000.0000.000
59A60VAL00.0290.02310.4540.1340.1340.0000.0000.0000.000
60A61MET0-0.0100.00510.150-0.154-0.1540.0000.0000.0000.000
61A62SER0-0.062-0.06312.801-0.093-0.0930.0000.0000.0000.000
62A63SER0-0.049-0.02515.679-0.058-0.0580.0000.0000.0000.000
63A64ASN0-0.021-0.05017.682-0.019-0.0190.0000.0000.0000.000
64A65GLU-1-0.928-0.95116.8250.2600.2600.0000.0000.0000.000
65A66GLY0-0.0080.00917.4530.0010.0010.0000.0000.0000.000
66A67THR0-0.067-0.05017.993-0.017-0.0170.0000.0000.0000.000
67A68VAL00.0190.01418.0510.0080.0080.0000.0000.0000.000
68A69SER0-0.065-0.02319.323-0.005-0.0050.0000.0000.0000.000
69A70LYS10.8830.92420.078-0.033-0.0330.0000.0000.0000.000
70A71VAL0-0.0060.00719.2530.0040.0040.0000.0000.0000.000
71A72THR0-0.067-0.03922.196-0.001-0.0010.0000.0000.0000.000
72A73ASN0-0.071-0.04823.827-0.004-0.0040.0000.0000.0000.000
73A74VAL00.0660.03420.1090.0030.0030.0000.0000.0000.000
74A75TRP00.0310.04819.884-0.004-0.0040.0000.0000.0000.000
75A76VAL00.0130.00519.786-0.009-0.0090.0000.0000.0000.000
76A77HIS00.0430.03220.6860.0080.0080.0000.0000.0000.000
77A78PRO0-0.034-0.01822.519-0.006-0.0060.0000.0000.0000.000
78A79GLU-1-0.937-0.97124.697-0.068-0.0680.0000.0000.0000.000
79A80TYR0-0.056-0.02416.718-0.004-0.0040.0000.0000.0000.000
80A81GLN0-0.064-0.04421.8670.0030.0030.0000.0000.0000.000
81A82ASP-1-0.818-0.91218.707-0.218-0.2180.0000.0000.0000.000
82A83ALA00.0610.05014.3160.0130.0130.0000.0000.0000.000
83A84ALA0-0.0020.00116.4330.0080.0080.0000.0000.0000.000
84A85LYS10.8050.88118.0500.1750.1750.0000.0000.0000.000
85A86GLY00.0200.02118.4100.0170.0170.0000.0000.0000.000
86A87PHE00.008-0.02119.382-0.005-0.0050.0000.0000.0000.000
87A88ASP-1-0.756-0.84213.934-0.253-0.2530.0000.0000.0000.000
88A89VAL0-0.045-0.02214.877-0.011-0.0110.0000.0000.0000.000
89A90SER0-0.027-0.02016.1990.0060.0060.0000.0000.0000.000
90A91VAL0-0.017-0.01716.6830.0030.0030.0000.0000.0000.000
91A92LEU00.0310.03415.7550.0040.0040.0000.0000.0000.000
92A93THR0-0.025-0.01119.2640.0110.0110.0000.0000.0000.000
93A94LEU00.0300.01418.237-0.003-0.0030.0000.0000.0000.000
94A95GLU-1-0.807-0.90122.3340.0280.0280.0000.0000.0000.000
95A96ALA0-0.019-0.01124.2430.0000.0000.0000.0000.0000.000
96A97PRO0-0.062-0.02923.454-0.001-0.0010.0000.0000.0000.000
97A98VAL00.0280.02018.2100.0040.0040.0000.0000.0000.000
98A99LYS10.7740.87219.999-0.130-0.1300.0000.0000.0000.000
99A100GLU-1-0.771-0.85216.2070.1300.1300.0000.0000.0000.000
100A101ALA00.0120.00218.178-0.014-0.0140.0000.0000.0000.000
101A102PRO0-0.0020.00616.4190.0090.0090.0000.0000.0000.000
102A103ILE0-0.041-0.01312.5120.0070.0070.0000.0000.0000.000
103A104GLU-1-0.805-0.89016.8780.0050.0050.0000.0000.0000.000
104A105LEU0-0.0030.00415.9350.0030.0030.0000.0000.0000.000
105A106ALA00.0060.01216.7700.0040.0040.0000.0000.0000.000
106A107LYS10.8730.93018.466-0.016-0.0160.0000.0000.0000.000
107A108ALA00.0310.00120.949-0.001-0.0010.0000.0000.0000.000
108A109ASP-1-0.954-0.97522.680-0.012-0.0120.0000.0000.0000.000
109A110ASP-1-0.827-0.88819.2290.0220.0220.0000.0000.0000.000
110A111ALA00.031-0.00220.225-0.004-0.0040.0000.0000.0000.000
111A112GLY0-0.040-0.01916.7240.0010.0010.0000.0000.0000.000
112A113TYR0-0.045-0.05115.296-0.001-0.0010.0000.0000.0000.000
113A114ALA0-0.028-0.00117.855-0.009-0.0090.0000.0000.0000.000
114A115PRO00.0160.00317.7010.0030.0030.0000.0000.0000.000
115A116ASP-1-0.939-0.96116.138-0.029-0.0290.0000.0000.0000.000
116A117THR0-0.082-0.05314.5680.0180.0180.0000.0000.0000.000
117A118ALA0-0.029-0.01012.263-0.006-0.0060.0000.0000.0000.000
118A119ALA00.0220.0119.8430.0120.0120.0000.0000.0000.000
119A120THR0-0.044-0.0157.1100.0110.0110.0000.0000.0000.000
120A121ILE0-0.0040.0022.827-1.253-0.1640.254-0.239-1.1050.001
121A122LEU0-0.012-0.0173.020-0.8610.2760.224-0.270-1.091-0.001
122A123GLY00.0010.0022.731-2.405-1.2591.877-0.881-2.142-0.010
123A124TRP0-0.008-0.0023.3911.1641.4030.0910.297-0.626-0.001
124A125GLY00.0260.0223.3950.3010.5890.006-0.088-0.2060.000
125A126ASN0-0.063-0.0453.3831.9253.1180.153-0.525-0.821-0.002
126A127THR00.0280.0151.998-5.949-7.5226.720-2.687-2.461-0.021
127A128SER0-0.002-0.0213.702-0.539-0.4460.0010.027-0.1210.000
128A129GLU-1-0.727-0.8386.060-0.623-0.6230.0000.0000.0000.000
129A130GLY0-0.044-0.0248.3030.1740.1740.0000.0000.0000.000
130A131GLY0-0.0360.0018.2230.1430.1430.0000.0000.0000.000
131A132GLN0-0.037-0.0317.5650.0110.0110.0000.0000.0000.000
132A133GLN0-0.007-0.0025.5820.0970.0970.0000.0000.0000.000
133A134ALA0-0.0110.0124.884-0.0710.011-0.001-0.009-0.0720.000
134A135ASP-1-0.773-0.8656.6430.2380.2380.0000.0000.0000.000
135A136HIS0-0.041-0.0288.471-0.327-0.3270.0000.0000.0000.000
136A137LEU0-0.0310.0105.2790.4900.4900.0000.0000.0000.000
137A138GLN0-0.025-0.0302.428-1.632-0.9562.148-0.788-2.0360.000
138A139LYS10.8040.8933.098-2.960-1.4260.219-0.658-1.095-0.006
139A140ALA00.0710.0332.499-0.456-0.0771.963-0.578-1.7650.000
140A141THR0-0.062-0.0483.714-0.305-0.2320.0050.056-0.1350.000
141A142VAL00.0090.0215.896-0.045-0.0450.0000.0000.0000.000
142A143PRO00.0040.0198.6120.0150.0150.0000.0000.0000.000
143A144VAL00.0350.00512.230-0.036-0.0360.0000.0000.0000.000
144A145ASN0-0.062-0.04513.327-0.009-0.0090.0000.0000.0000.000
145A146SER00.003-0.01315.9670.0030.0030.0000.0000.0000.000
146A147ASP-1-0.695-0.81119.119-0.093-0.0930.0000.0000.0000.000
147A148ASP-1-0.871-0.91820.613-0.079-0.0790.0000.0000.0000.000
148A149THR0-0.042-0.02317.709-0.005-0.0050.0000.0000.0000.000
149A150CYS0-0.037-0.00812.108-0.037-0.0370.0000.0000.0000.000
150A151LYS10.7870.88218.2500.1040.1040.0000.0000.0000.000
151A152GLN0-0.072-0.03021.2500.0010.0010.0000.0000.0000.000
152A153ALA0-0.0120.01016.668-0.004-0.0040.0000.0000.0000.000
153A154TYR0-0.047-0.03512.767-0.030-0.0300.0000.0000.0000.000
154A155GLY00.0280.02119.5770.0160.0160.0000.0000.0000.000
155A156GLU-1-0.892-0.96519.410-0.195-0.1950.0000.0000.0000.000
156A157TYR0-0.011-0.02216.0590.0030.0030.0000.0000.0000.000
157A158THR0-0.018-0.04119.7760.0140.0140.0000.0000.0000.000
158A159PRO00.0170.01220.198-0.006-0.0060.0000.0000.0000.000
159A160ASP-1-0.899-0.93920.954-0.074-0.0740.0000.0000.0000.000
160A161ALA0-0.026-0.00319.6700.0020.0020.0000.0000.0000.000
161A162MET0-0.0790.00715.912-0.016-0.0160.0000.0000.0000.000
162A163VAL00.0420.02312.5870.0220.0220.0000.0000.0000.000
163A165ALA00.0210.0109.0640.0420.0420.0000.0000.0000.000
164A166GLY00.0520.0238.848-0.070-0.0700.0000.0000.0000.000
165A167VAL0-0.0120.0119.7810.0370.0370.0000.0000.0000.000
166A168PRO00.0110.00412.082-0.044-0.0440.0000.0000.0000.000
167A169GLU-1-0.893-0.96113.036-0.136-0.1360.0000.0000.0000.000
168A170GLY0-0.0060.01010.874-0.017-0.0170.0000.0000.0000.000
169A171GLY0-0.045-0.0378.9780.0720.0720.0000.0000.0000.000
170A172VAL0-0.047-0.0324.442-0.203-0.139-0.001-0.008-0.0560.000
171A173ASP-1-0.780-0.8894.047-0.712-0.419-0.001-0.044-0.2490.000
172A174THR0-0.059-0.0232.130-3.525-1.3394.383-3.045-3.523-0.012
173A175CYS0-0.069-0.0363.1560.4250.2510.0320.866-0.7240.000
174A176GLN00.026-0.0174.737-0.0130.097-0.001-0.002-0.1060.000
175A177GLY00.0410.0285.805-0.225-0.2250.0000.0000.0000.000
176A178ASP-1-0.748-0.8752.086-12.888-11.1437.192-3.880-5.057-0.049
177A179SER0-0.016-0.0105.0770.3710.422-0.001-0.003-0.0470.000
178A180GLY00.019-0.0188.1300.0500.0500.0000.0000.0000.000
179A181GLY0-0.024-0.0045.3490.0930.0930.0000.0000.0000.000
180A182PRO0-0.045-0.0125.5070.0260.0260.0000.0000.0000.000
181A183MET00.0160.0195.8290.0760.0760.0000.0000.0000.000
182A184VAL0-0.053-0.0318.187-0.039-0.0390.0000.0000.0000.000
183A185VAL00.0550.02810.8300.0210.0210.0000.0000.0000.000
184A186ASN0-0.055-0.03213.788-0.001-0.0010.0000.0000.0000.000
185A187ASN0-0.028-0.01915.3090.0030.0030.0000.0000.0000.000
186A188LYS10.8450.91615.494-0.036-0.0360.0000.0000.0000.000
187A189LEU00.0200.01410.3860.0130.0130.0000.0000.0000.000
188A190ILE00.0290.00811.711-0.015-0.0150.0000.0000.0000.000
189A191GLY00.0050.02111.345-0.019-0.0190.0000.0000.0000.000
190A192VAL0-0.0140.0099.3870.0280.0280.0000.0000.0000.000
191A193THR00.0260.0114.7590.0210.090-0.001-0.001-0.0660.000
192A194SER0-0.032-0.0407.788-0.022-0.0220.0000.0000.0000.000
193A195TRP0-0.024-0.03510.666-0.069-0.0690.0000.0000.0000.000
194A196GLY00.0720.03310.376-0.003-0.0030.0000.0000.0000.000
195A197GLU-1-0.873-0.91811.937-0.304-0.3040.0000.0000.0000.000
196A198GLY0-0.037-0.01311.4100.0010.0010.0000.0000.0000.000
197A200ALA00.0070.0126.4460.0490.0490.0000.0000.0000.000
198A201ARG10.7920.8698.3380.5780.5780.0000.0000.0000.000
199A202PRO00.005-0.00812.1010.0330.0330.0000.0000.0000.000
200A203GLY0-0.062-0.02814.8890.0030.0030.0000.0000.0000.000
201A204LYS10.7720.88613.7810.2790.2790.0000.0000.0000.000
202A205PRO00.0130.02910.811-0.071-0.0710.0000.0000.0000.000
203A206GLY00.1050.0778.329-0.019-0.0190.0000.0000.0000.000
204A207VAL0-0.037-0.0399.4040.1120.1120.0000.0000.0000.000
205A208TYR00.0150.0005.8310.0090.0090.0000.0000.0000.000
206A209ALA00.0270.01311.2420.0230.0230.0000.0000.0000.000
207A210ARG10.7650.85013.7390.0920.0920.0000.0000.0000.000
208A211VAL00.0090.00313.9110.0060.0060.0000.0000.0000.000
209A212GLY00.0170.00816.6490.0040.0040.0000.0000.0000.000
210A213ALA0-0.045-0.02419.6490.0050.0050.0000.0000.0000.000
211A214TYR00.006-0.01218.277-0.006-0.0060.0000.0000.0000.000
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