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: G6M41

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 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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2559013.516936
FMO2-HF: Nuclear repulsion 2474438.678929
FMO2-HF: Total energy -84574.838007
FMO2-MP2: Total energy -84817.112923


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.
-28.071-20.37138.049-17.01-28.743-0.112
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 : -0.049 / q_NPA : -0.048
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].
3A3GLY00.0170.0023.325-0.4761.5840.097-0.874-1.2840.002
4A4GLY0-0.019-0.0062.515-0.6690.2480.828-0.700-1.0460.000
5A5GLU-1-0.907-0.9433.2810.4550.0930.0250.548-0.2100.000
6A6ASP-1-0.819-0.9015.4801.1521.1520.0000.0000.0000.000
7A7ALA0-0.055-0.0366.727-0.150-0.1500.0000.0000.0000.000
8A8ASN0-0.030-0.0268.4360.0280.0280.0000.0000.0000.000
9A9VAL00.0430.01610.382-0.013-0.0130.0000.0000.0000.000
10A10GLN0-0.026-0.03311.271-0.011-0.0110.0000.0000.0000.000
11A11ASP-1-0.869-0.92011.7220.3130.3130.0000.0000.0000.000
12A12HIS0-0.060-0.0308.6990.0470.0470.0000.0000.0000.000
13A13PRO00.0140.01811.069-0.003-0.0030.0000.0000.0000.000
14A14PHE00.0460.0159.064-0.021-0.0210.0000.0000.0000.000
15A15THR0-0.013-0.0056.894-0.039-0.0390.0000.0000.0000.000
16A16VAL0-0.040-0.0229.9020.0300.0300.0000.0000.0000.000
17A17ALA00.0240.0149.642-0.048-0.0480.0000.0000.0000.000
18A18LEU0-0.036-0.01410.9260.0190.0190.0000.0000.0000.000
19A19VAL00.028-0.00512.571-0.017-0.0170.0000.0000.0000.000
20A20THR00.0550.03115.135-0.002-0.0020.0000.0000.0000.000
21A21PRO0-0.033-0.02518.0870.0200.0200.0000.0000.0000.000
22A22ASP-1-0.964-0.98120.544-0.026-0.0260.0000.0000.0000.000
23A23GLY0-0.031-0.01318.0530.0080.0080.0000.0000.0000.000
24A24GLN0-0.085-0.03112.1300.0470.0470.0000.0000.0000.000
25A25GLN00.014-0.0107.3790.0530.0530.0000.0000.0000.000
26A26PHE0-0.011-0.00810.481-0.032-0.0320.0000.0000.0000.000
27A27CYS0-0.090-0.0258.870-0.163-0.1630.0000.0000.0000.000
28A28GLY00.0380.0387.3690.1170.1170.0000.0000.0000.000
29A29GLY00.0340.0138.407-0.018-0.0180.0000.0000.0000.000
30A30THR0-0.0020.0039.7540.0580.0580.0000.0000.0000.000
31A31LEU0-0.064-0.01811.780-0.021-0.0210.0000.0000.0000.000
32A32ALA00.0360.01015.2410.0130.0130.0000.0000.0000.000
33A33ALA0-0.009-0.01917.599-0.001-0.0010.0000.0000.0000.000
34A34PRO00.0260.01019.7200.0010.0010.0000.0000.0000.000
35A35ASN00.0190.00821.3910.0040.0040.0000.0000.0000.000
36A36LYS10.8420.94419.839-0.010-0.0100.0000.0000.0000.000
37A37VAL00.0260.01113.6810.0130.0130.0000.0000.0000.000
38A38VAL00.0030.01013.698-0.014-0.0140.0000.0000.0000.000
39A39THR00.004-0.01511.470-0.008-0.0080.0000.0000.0000.000
40A40ALA00.0420.02311.5620.0170.0170.0000.0000.0000.000
41A41ALA0-0.023-0.00613.3740.0050.0050.0000.0000.0000.000
42A42HIS0-0.012-0.00713.0460.0260.0260.0000.0000.0000.000
43A44THR0-0.002-0.02114.7600.0180.0180.0000.0000.0000.000
44A45VAL00.0070.00418.0570.0230.0230.0000.0000.0000.000
45A46GLY0-0.053-0.02320.798-0.007-0.0070.0000.0000.0000.000
46A47SER0-0.0080.00920.557-0.002-0.0020.0000.0000.0000.000
47A48GLN0-0.120-0.06222.8820.0120.0120.0000.0000.0000.000
48A49PRO00.006-0.01822.966-0.003-0.0030.0000.0000.0000.000
49A50ALA0-0.023-0.01222.8880.0020.0020.0000.0000.0000.000
50A51ASP-1-0.823-0.89621.382-0.065-0.0650.0000.0000.0000.000
51A52ILE0-0.020-0.00816.825-0.010-0.0100.0000.0000.0000.000
52A53ASN0-0.036-0.01218.1360.0130.0130.0000.0000.0000.000
53A54VAL00.0270.01014.749-0.011-0.0110.0000.0000.0000.000
54A55VAL0-0.007-0.00313.8750.0090.0090.0000.0000.0000.000
55A56SER00.003-0.01713.5710.0130.0130.0000.0000.0000.000
56A57GLY00.0250.00414.531-0.004-0.0040.0000.0000.0000.000
57A58ARG10.8250.92413.910-0.161-0.1610.0000.0000.0000.000
58A59THR00.0400.02710.2410.0130.0130.0000.0000.0000.000
59A60VAL00.0360.03210.3270.1180.1180.0000.0000.0000.000
60A61MET00.0030.01110.126-0.130-0.1300.0000.0000.0000.000
61A62SER0-0.073-0.06212.835-0.074-0.0740.0000.0000.0000.000
62A63SER0-0.073-0.03915.789-0.044-0.0440.0000.0000.0000.000
63A64ASN0-0.012-0.05217.435-0.011-0.0110.0000.0000.0000.000
64A65GLU-1-0.939-0.95117.6160.1940.1940.0000.0000.0000.000
65A66GLY0-0.0180.00217.5570.0020.0020.0000.0000.0000.000
66A67THR0-0.055-0.03118.220-0.016-0.0160.0000.0000.0000.000
67A68VAL00.0030.00518.2620.0040.0040.0000.0000.0000.000
68A69SER0-0.041-0.01719.331-0.004-0.0040.0000.0000.0000.000
69A70LYS10.9310.96420.477-0.024-0.0240.0000.0000.0000.000
70A71VAL00.0090.01719.2620.0060.0060.0000.0000.0000.000
71A72THR0-0.039-0.02922.395-0.003-0.0030.0000.0000.0000.000
72A73ASN0-0.054-0.04623.796-0.002-0.0020.0000.0000.0000.000
73A74VAL00.0480.03120.1370.0040.0040.0000.0000.0000.000
74A75TRP00.0060.03219.922-0.002-0.0020.0000.0000.0000.000
75A76VAL00.0340.01520.076-0.007-0.0070.0000.0000.0000.000
76A77HIS00.0390.03020.6020.0050.0050.0000.0000.0000.000
77A78PRO0-0.027-0.02022.390-0.007-0.0070.0000.0000.0000.000
78A79GLU-1-0.930-0.97424.698-0.056-0.0560.0000.0000.0000.000
79A80TYR0-0.035-0.00717.170-0.004-0.0040.0000.0000.0000.000
80A81GLN0-0.062-0.03222.2310.0010.0010.0000.0000.0000.000
81A82ASP-1-0.819-0.93418.955-0.219-0.2190.0000.0000.0000.000
82A83ALA00.0500.04814.5710.0140.0140.0000.0000.0000.000
83A84ALA00.0140.01016.6980.0140.0140.0000.0000.0000.000
84A85LYS10.8040.88417.9850.1730.1730.0000.0000.0000.000
85A86GLY00.0120.01618.5540.0180.0180.0000.0000.0000.000
86A87PHE00.013-0.01219.510-0.006-0.0060.0000.0000.0000.000
87A88ASP-1-0.778-0.85713.896-0.248-0.2480.0000.0000.0000.000
88A89VAL0-0.041-0.02314.677-0.007-0.0070.0000.0000.0000.000
89A90SER0-0.015-0.01416.1140.0010.0010.0000.0000.0000.000
90A91VAL0-0.015-0.01316.6150.0060.0060.0000.0000.0000.000
91A92LEU00.0110.02215.992-0.001-0.0010.0000.0000.0000.000
92A93THR0-0.005-0.00419.4360.0130.0130.0000.0000.0000.000
93A94LEU00.0120.00818.348-0.004-0.0040.0000.0000.0000.000
94A95GLU-1-0.864-0.94722.4200.0210.0210.0000.0000.0000.000
95A96ALA0-0.028-0.02024.5150.0000.0000.0000.0000.0000.000
96A97PRO0-0.066-0.03023.4830.0010.0010.0000.0000.0000.000
97A98VAL00.0310.02518.3890.0020.0020.0000.0000.0000.000
98A99LYS10.8870.94220.363-0.124-0.1240.0000.0000.0000.000
99A100GLU-1-0.861-0.92016.0380.1310.1310.0000.0000.0000.000
100A101ALA00.0030.00218.157-0.013-0.0130.0000.0000.0000.000
101A102PRO0-0.017-0.00116.5080.0120.0120.0000.0000.0000.000
102A103ILE0-0.025-0.00512.2850.0050.0050.0000.0000.0000.000
103A104GLU-1-0.895-0.94316.7210.0420.0420.0000.0000.0000.000
104A105LEU00.001-0.00215.7960.0090.0090.0000.0000.0000.000
105A106ALA00.0230.01316.6850.0010.0010.0000.0000.0000.000
106A107LYS10.9200.95418.364-0.047-0.0470.0000.0000.0000.000
107A108ALA00.0420.00820.7060.0030.0030.0000.0000.0000.000
108A109ASP-1-0.974-0.97922.1700.0210.0210.0000.0000.0000.000
109A110ASP-1-0.845-0.90318.7800.0760.0760.0000.0000.0000.000
110A111ALA00.027-0.00720.319-0.002-0.0020.0000.0000.0000.000
111A112GLY0-0.031-0.02416.3840.0020.0020.0000.0000.0000.000
112A113TYR0-0.050-0.04515.2350.0060.0060.0000.0000.0000.000
113A114ALA0-0.0300.00717.547-0.012-0.0120.0000.0000.0000.000
114A115PRO00.005-0.00517.4850.0110.0110.0000.0000.0000.000
115A116ASP-1-0.932-0.96316.0810.0390.0390.0000.0000.0000.000
116A117THR0-0.087-0.04514.3900.0190.0190.0000.0000.0000.000
117A118ALA0-0.032-0.00912.0890.0070.0070.0000.0000.0000.000
118A119ALA00.0210.0029.331-0.009-0.0090.0000.0000.0000.000
119A120THR0-0.045-0.0216.7050.0660.0660.0000.0000.0000.000
120A121ILE00.0040.0122.551-1.542-0.4451.076-0.342-1.8310.003
121A122LEU0-0.010-0.0202.961-1.1270.1940.418-0.431-1.308-0.003
122A123GLY0-0.0040.0002.591-2.196-1.1511.647-0.650-2.042-0.007
123A124TRP0-0.018-0.0173.1730.9961.6020.1820.021-0.809-0.003
124A125GLY00.0240.0203.339-0.0630.3390.019-0.139-0.2820.000
125A126ASN0-0.033-0.0383.2501.7202.9770.262-0.615-0.903-0.002
126A127THR00.0410.0291.886-5.923-9.2319.156-3.296-2.552-0.024
127A128SER0-0.033-0.0323.9020.0970.2030.000-0.013-0.0940.000
128A129GLU-1-0.727-0.8346.361-0.715-0.7150.0000.0000.0000.000
129A130GLY0-0.031-0.0168.1940.1900.1900.0000.0000.0000.000
130A131GLY0-0.042-0.0048.0200.1710.1710.0000.0000.0000.000
131A132GLN0-0.047-0.0377.8070.0680.0680.0000.0000.0000.000
132A133GLN0-0.020-0.0105.736-0.098-0.0980.0000.0000.0000.000
133A134ALA0-0.0020.0145.207-0.083-0.0830.0000.0000.0000.000
134A135ASP-1-0.794-0.8756.9970.2100.2100.0000.0000.0000.000
135A136HIS0-0.047-0.0258.378-0.245-0.2450.0000.0000.0000.000
136A137LEU0-0.0290.0134.8910.4100.4100.0000.0000.0000.000
137A138GLN0-0.018-0.0292.218-1.446-1.0692.872-1.009-2.2400.000
138A139LYS10.8130.9052.818-3.433-1.5210.543-0.929-1.527-0.011
139A140ALA00.0500.0162.540-0.5030.0201.744-0.517-1.7510.000
140A141THR0-0.040-0.0213.807-0.367-0.2540.0050.026-0.1450.000
141A142VAL00.0220.0145.639-0.039-0.0390.0000.0000.0000.000
142A143PRO00.0080.0158.3490.0000.0000.0000.0000.0000.000
143A144VAL00.0290.00612.070-0.033-0.0330.0000.0000.0000.000
144A145ASN0-0.059-0.04813.431-0.030-0.0300.0000.0000.0000.000
145A146SER00.017-0.00115.8950.0000.0000.0000.0000.0000.000
146A147ASP-1-0.725-0.86519.060-0.042-0.0420.0000.0000.0000.000
147A148ASP-1-0.922-0.95420.721-0.048-0.0480.0000.0000.0000.000
148A149THR0-0.047-0.02017.752-0.003-0.0030.0000.0000.0000.000
149A150CYS0-0.0200.00612.031-0.030-0.0300.0000.0000.0000.000
150A151LYS10.8170.89917.9730.0730.0730.0000.0000.0000.000
151A152GLN0-0.076-0.03221.197-0.003-0.0030.0000.0000.0000.000
152A153ALA0-0.0300.00916.759-0.006-0.0060.0000.0000.0000.000
153A154TYR0-0.015-0.02212.544-0.032-0.0320.0000.0000.0000.000
154A155GLY00.0320.01919.3290.0160.0160.0000.0000.0000.000
155A156GLU-1-0.889-0.95919.271-0.174-0.1740.0000.0000.0000.000
156A157TYR0-0.037-0.03815.8790.0030.0030.0000.0000.0000.000
157A158THR0-0.007-0.04119.4300.0120.0120.0000.0000.0000.000
158A159PRO00.0110.01219.731-0.004-0.0040.0000.0000.0000.000
159A160ASP-1-0.912-0.94320.806-0.045-0.0450.0000.0000.0000.000
160A161ALA0-0.020-0.00719.4510.0010.0010.0000.0000.0000.000
161A162MET0-0.0640.00215.528-0.013-0.0130.0000.0000.0000.000
162A163VAL00.0250.01512.5930.0190.0190.0000.0000.0000.000
163A165ALA00.0290.0159.1340.0350.0350.0000.0000.0000.000
164A166GLY00.0400.0239.129-0.048-0.0480.0000.0000.0000.000
165A167VAL00.0020.0189.9690.0230.0230.0000.0000.0000.000
166A168PRO00.0090.00312.164-0.046-0.0460.0000.0000.0000.000
167A169GLU-1-0.902-0.96613.302-0.046-0.0460.0000.0000.0000.000
168A170GLY0-0.026-0.00210.972-0.030-0.0300.0000.0000.0000.000
169A171GLY0-0.038-0.0369.0750.0750.0750.0000.0000.0000.000
170A172VAL0-0.041-0.0314.573-0.134-0.053-0.001-0.009-0.0720.000
171A173ASP-1-0.795-0.8823.858-0.847-0.5080.000-0.071-0.2680.000
172A174THR0-0.0260.0092.207-2.509-0.7665.257-3.181-3.820-0.016
173A175CYS0-0.095-0.0463.0800.2310.6640.0630.374-0.8700.001
174A176GLN00.056-0.0034.618-0.207-0.077-0.001-0.004-0.1240.000
175A177GLY00.0380.0285.446-0.300-0.3000.0000.0000.0000.000
176A178ASP-1-0.750-0.8641.855-11.674-14.89313.859-5.193-5.446-0.052
177A179SER0-0.024-0.0244.9520.4100.472-0.001-0.005-0.0560.000
178A180GLY00.022-0.0128.2150.0500.0500.0000.0000.0000.000
179A181GLY0-0.0160.0005.7860.1040.1040.0000.0000.0000.000
180A182PRO0-0.040-0.0115.5520.0130.0130.0000.0000.0000.000
181A183MET00.0430.0325.5220.1350.1350.0000.0000.0000.000
182A184VAL0-0.047-0.0277.901-0.077-0.0770.0000.0000.0000.000
183A185VAL00.0530.03110.5530.0380.0380.0000.0000.0000.000
184A186ASN0-0.048-0.02713.382-0.010-0.0100.0000.0000.0000.000
185A187ASN0-0.035-0.02514.6320.0000.0000.0000.0000.0000.000
186A188LYS10.8710.94715.191-0.087-0.0870.0000.0000.0000.000
187A189LEU0-0.0080.00310.1910.0230.0230.0000.0000.0000.000
188A190ILE00.0320.00611.648-0.025-0.0250.0000.0000.0000.000
189A191GLY00.0170.01910.862-0.027-0.0270.0000.0000.0000.000
190A192VAL0-0.0210.0069.3700.0340.0340.0000.0000.0000.000
191A193THR00.0110.0054.7990.0400.105-0.001-0.001-0.0630.000
192A194SER0-0.025-0.0447.793-0.041-0.0410.0000.0000.0000.000
193A195TRP0-0.023-0.03110.629-0.067-0.0670.0000.0000.0000.000
194A196GLY00.0680.03210.6860.0270.0270.0000.0000.0000.000
195A197GLU-1-0.891-0.93511.921-0.304-0.3040.0000.0000.0000.000
196A198GLY0-0.038-0.01711.3220.0070.0070.0000.0000.0000.000
197A200ALA0-0.016-0.0046.4330.0440.0440.0000.0000.0000.000
198A201ARG10.7910.8698.2860.5740.5740.0000.0000.0000.000
199A202PRO00.002-0.01012.0150.0350.0350.0000.0000.0000.000
200A203GLY0-0.046-0.01514.708-0.006-0.0060.0000.0000.0000.000
201A204LYS10.7790.89513.3030.2430.2430.0000.0000.0000.000
202A205PRO0-0.0030.01711.071-0.060-0.0600.0000.0000.0000.000
203A206GLY00.1150.0838.169-0.064-0.0640.0000.0000.0000.000
204A207VAL0-0.028-0.0299.2120.1110.1110.0000.0000.0000.000
205A208TYR0-0.005-0.0255.3450.0110.0110.0000.0000.0000.000
206A209ALA00.0300.01611.1820.0190.0190.0000.0000.0000.000
207A210ARG10.8230.91713.3170.0480.0480.0000.0000.0000.000
208A211VAL00.0130.00213.559-0.003-0.0030.0000.0000.0000.000
209A212GLY00.000-0.00616.289-0.001-0.0010.0000.0000.0000.000
210A213ALA0-0.037-0.01719.1210.0010.0010.0000.0000.0000.000
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