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: 17Q3Z

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 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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2557265.669286
FMO2-HF: Nuclear repulsion 2472691.19676
FMO2-HF: Total energy -84574.472526
FMO2-MP2: Total energy -84816.688184


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.
-27.784-26.26147.346-19.625-29.238-0.114
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 : -0.056
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].
3A3GLY00.0150.0023.309-0.4591.6350.116-0.881-1.3300.002
4A4GLY0-0.023-0.0072.515-0.5920.3130.923-0.731-1.0970.000
5A5GLU-1-0.992-0.9903.2690.4940.0790.0250.603-0.2120.000
6A6ASP-1-0.827-0.9055.4501.1041.1040.0000.0000.0000.000
7A7ALA0-0.058-0.0456.708-0.133-0.1330.0000.0000.0000.000
8A8ASN00.0220.0098.3970.0370.0370.0000.0000.0000.000
9A9VAL00.0480.01410.3680.0000.0000.0000.0000.0000.000
10A10GLN0-0.023-0.03311.254-0.004-0.0040.0000.0000.0000.000
11A11ASP-1-0.909-0.94311.8360.3250.3250.0000.0000.0000.000
12A12HIS0-0.072-0.0369.3100.0450.0450.0000.0000.0000.000
13A13PRO00.0050.00911.0930.0050.0050.0000.0000.0000.000
14A14PHE00.0440.0179.099-0.026-0.0260.0000.0000.0000.000
15A15THR00.0000.0046.873-0.026-0.0260.0000.0000.0000.000
16A16VAL0-0.041-0.0219.8910.0150.0150.0000.0000.0000.000
17A17ALA00.0260.0159.628-0.032-0.0320.0000.0000.0000.000
18A18LEU0-0.044-0.01910.9330.0110.0110.0000.0000.0000.000
19A19VAL00.0360.00412.568-0.021-0.0210.0000.0000.0000.000
20A20THR00.0440.02215.1260.0030.0030.0000.0000.0000.000
21A21PRO0-0.039-0.02418.0910.0180.0180.0000.0000.0000.000
22A22ASP-1-0.949-0.97120.766-0.024-0.0240.0000.0000.0000.000
23A23GLY0-0.039-0.01918.0270.0050.0050.0000.0000.0000.000
24A24GLN0-0.087-0.03312.1220.0390.0390.0000.0000.0000.000
25A25GLN00.0120.0017.3250.0480.0480.0000.0000.0000.000
26A26PHE0-0.001-0.00910.471-0.042-0.0420.0000.0000.0000.000
27A27CYS0-0.095-0.0308.864-0.160-0.1600.0000.0000.0000.000
28A28GLY00.0390.0317.3760.1080.1080.0000.0000.0000.000
29A29GLY00.0370.0148.412-0.030-0.0300.0000.0000.0000.000
30A30THR00.0010.0029.7690.0770.0770.0000.0000.0000.000
31A31LEU0-0.062-0.01611.810-0.031-0.0310.0000.0000.0000.000
32A32ALA00.0350.01215.2620.0150.0150.0000.0000.0000.000
33A33ALA0-0.011-0.01917.636-0.005-0.0050.0000.0000.0000.000
34A34PRO00.0260.01019.7370.0020.0020.0000.0000.0000.000
35A35ASN00.0320.01821.3940.0050.0050.0000.0000.0000.000
36A36LYS10.8430.93619.866-0.033-0.0330.0000.0000.0000.000
37A37VAL00.0280.01313.7170.0160.0160.0000.0000.0000.000
38A38VAL00.0000.00913.574-0.019-0.0190.0000.0000.0000.000
39A39THR00.009-0.01311.4970.0000.0000.0000.0000.0000.000
40A40ALA00.0420.02311.6760.0140.0140.0000.0000.0000.000
41A41ALA0-0.025-0.00913.4380.0020.0020.0000.0000.0000.000
42A42HIS0-0.007-0.00512.5880.0280.0280.0000.0000.0000.000
43A44THR0-0.016-0.02614.7530.0140.0140.0000.0000.0000.000
44A45VAL00.0110.00318.0920.0200.0200.0000.0000.0000.000
45A46GLY0-0.053-0.02320.803-0.008-0.0080.0000.0000.0000.000
46A47SER0-0.0090.01120.632-0.003-0.0030.0000.0000.0000.000
47A48GLN0-0.128-0.06222.8770.0120.0120.0000.0000.0000.000
48A49PRO00.003-0.01922.980-0.003-0.0030.0000.0000.0000.000
49A50ALA0-0.022-0.01322.8900.0030.0030.0000.0000.0000.000
50A51ASP-1-0.813-0.89421.305-0.059-0.0590.0000.0000.0000.000
51A52ILE0-0.022-0.00816.872-0.010-0.0100.0000.0000.0000.000
52A53ASN0-0.035-0.01418.1240.0090.0090.0000.0000.0000.000
53A54VAL00.0190.00414.757-0.010-0.0100.0000.0000.0000.000
54A55VAL0-0.0070.00113.8590.0050.0050.0000.0000.0000.000
55A56SER00.011-0.00613.5770.0200.0200.0000.0000.0000.000
56A57GLY00.0300.01014.553-0.009-0.0090.0000.0000.0000.000
57A58ARG10.8400.92313.901-0.166-0.1660.0000.0000.0000.000
58A59THR00.0370.02410.2140.0210.0210.0000.0000.0000.000
59A60VAL00.0350.03010.2600.1130.1130.0000.0000.0000.000
60A61MET00.0000.00110.148-0.119-0.1190.0000.0000.0000.000
61A62SER0-0.061-0.05012.790-0.065-0.0650.0000.0000.0000.000
62A63SER0-0.074-0.03415.739-0.038-0.0380.0000.0000.0000.000
63A64ASN0-0.028-0.04517.395-0.009-0.0090.0000.0000.0000.000
64A65GLU-1-0.945-0.95917.6880.1860.1860.0000.0000.0000.000
65A66GLY0-0.0090.00717.5240.0030.0030.0000.0000.0000.000
66A67THR0-0.045-0.02518.195-0.021-0.0210.0000.0000.0000.000
67A68VAL0-0.012-0.00118.2610.0070.0070.0000.0000.0000.000
68A69SER0-0.013-0.00919.337-0.004-0.0040.0000.0000.0000.000
69A70LYS10.9420.97420.463-0.022-0.0220.0000.0000.0000.000
70A71VAL00.0280.02519.2690.0080.0080.0000.0000.0000.000
71A72THR0-0.045-0.02622.398-0.005-0.0050.0000.0000.0000.000
72A73ASN0-0.053-0.05023.815-0.002-0.0020.0000.0000.0000.000
73A74VAL00.0520.03320.2230.0060.0060.0000.0000.0000.000
74A75TRP00.0120.03120.010-0.003-0.0030.0000.0000.0000.000
75A76VAL00.0340.01120.326-0.004-0.0040.0000.0000.0000.000
76A77HIS00.0320.03420.6720.0020.0020.0000.0000.0000.000
77A78PRO0-0.024-0.02022.464-0.008-0.0080.0000.0000.0000.000
78A79GLU-1-0.931-0.98024.844-0.040-0.0400.0000.0000.0000.000
79A80TYR0-0.038-0.00617.483-0.006-0.0060.0000.0000.0000.000
80A81GLN0-0.076-0.04122.3090.0020.0020.0000.0000.0000.000
81A82ASP-1-0.873-0.96819.320-0.215-0.2150.0000.0000.0000.000
82A83ALA00.0440.04214.6620.0150.0150.0000.0000.0000.000
83A84ALA00.0140.01316.7780.0160.0160.0000.0000.0000.000
84A85LYS10.8650.92418.0670.1490.1490.0000.0000.0000.000
85A86GLY00.0210.01918.6380.0170.0170.0000.0000.0000.000
86A87PHE00.020-0.00919.593-0.006-0.0060.0000.0000.0000.000
87A88ASP-1-0.776-0.86214.034-0.202-0.2020.0000.0000.0000.000
88A89VAL0-0.037-0.02114.7570.0000.0000.0000.0000.0000.000
89A90SER0-0.016-0.01216.172-0.005-0.0050.0000.0000.0000.000
90A91VAL0-0.011-0.01016.6710.0110.0110.0000.0000.0000.000
91A92LEU00.0100.02116.037-0.005-0.0050.0000.0000.0000.000
92A93THR0-0.0080.00219.4660.0150.0150.0000.0000.0000.000
93A94LEU00.0030.00518.413-0.005-0.0050.0000.0000.0000.000
94A95GLU-1-0.886-0.96422.4260.0320.0320.0000.0000.0000.000
95A96ALA0-0.024-0.01624.517-0.001-0.0010.0000.0000.0000.000
96A97PRO0-0.074-0.03423.4910.0030.0030.0000.0000.0000.000
97A98VAL00.0310.02618.415-0.001-0.0010.0000.0000.0000.000
98A99LYS10.9050.94620.707-0.135-0.1350.0000.0000.0000.000
99A100GLU-1-0.883-0.93916.0490.1560.1560.0000.0000.0000.000
100A101ALA00.0010.00018.133-0.013-0.0130.0000.0000.0000.000
101A102PRO0-0.021-0.00216.5280.0170.0170.0000.0000.0000.000
102A103ILE0-0.025-0.00612.3770.0030.0030.0000.0000.0000.000
103A104GLU-1-0.952-0.97716.7550.0780.0780.0000.0000.0000.000
104A105LEU0-0.012-0.00916.0200.0150.0150.0000.0000.0000.000
105A106ALA00.0280.02216.767-0.003-0.0030.0000.0000.0000.000
106A107LYS10.9870.98618.443-0.064-0.0640.0000.0000.0000.000
107A108ALA00.0480.01320.7950.0050.0050.0000.0000.0000.000
108A109ASP-1-0.988-0.98222.2650.0460.0460.0000.0000.0000.000
109A110ASP-1-0.844-0.91518.3090.1160.1160.0000.0000.0000.000
110A111ALA00.013-0.01720.404-0.001-0.0010.0000.0000.0000.000
111A112GLY0-0.026-0.01416.4610.0020.0020.0000.0000.0000.000
112A113TYR0-0.044-0.04315.2880.0090.0090.0000.0000.0000.000
113A114ALA0-0.0260.00617.642-0.014-0.0140.0000.0000.0000.000
114A115PRO0-0.006-0.01117.5740.0140.0140.0000.0000.0000.000
115A116ASP-1-0.918-0.95216.1770.0590.0590.0000.0000.0000.000
116A117THR0-0.091-0.05014.3080.0180.0180.0000.0000.0000.000
117A118ALA0-0.032-0.01012.1470.0120.0120.0000.0000.0000.000
118A119ALA00.0160.0039.318-0.011-0.0110.0000.0000.0000.000
119A120THR0-0.047-0.0236.7610.0580.0580.0000.0000.0000.000
120A121ILE00.0000.0102.553-1.533-0.4471.029-0.332-1.7830.003
121A122LEU0-0.008-0.0203.019-1.0170.2670.398-0.415-1.266-0.003
122A123GLY0-0.006-0.0012.589-2.175-1.1751.665-0.628-2.037-0.007
123A124TRP0-0.020-0.0183.1380.9251.5850.219-0.022-0.858-0.003
124A125GLY00.0170.0173.354-0.1280.2710.020-0.139-0.2810.000
125A126ASN0-0.014-0.0323.2151.3552.6740.265-0.651-0.933-0.002
126A127THR00.0340.0241.874-6.342-9.6659.508-3.492-2.693-0.024
127A128SER0-0.037-0.0293.8560.2470.3550.000-0.011-0.0960.000
128A129GLU-1-0.713-0.8376.348-0.760-0.7600.0000.0000.0000.000
129A130GLY0-0.041-0.0208.2090.1890.1890.0000.0000.0000.000
130A131GLY0-0.039-0.0068.0270.1810.1810.0000.0000.0000.000
131A132GLN0-0.049-0.0357.7790.1000.1000.0000.0000.0000.000
132A133GLN0-0.035-0.0145.701-0.182-0.1820.0000.0000.0000.000
133A134ALA00.0040.0175.145-0.055-0.0550.0000.0000.0000.000
134A135ASP-1-0.793-0.8816.9440.2050.2050.0000.0000.0000.000
135A136HIS0-0.051-0.0308.312-0.204-0.2040.0000.0000.0000.000
136A137LEU0-0.0330.0064.9280.3660.3660.0000.0000.0000.000
137A138GLN0-0.015-0.0162.217-1.482-1.2583.321-1.121-2.4230.001
138A139LYS10.8990.9522.800-3.219-1.3750.595-0.901-1.538-0.011
139A140ALA00.0500.0172.560-0.755-0.0311.328-0.449-1.602-0.001
140A141THR0-0.037-0.0183.848-0.364-0.2460.0040.018-0.1410.000
141A142VAL00.0100.0095.714-0.063-0.0630.0000.0000.0000.000
142A143PRO00.0040.0148.4150.0070.0070.0000.0000.0000.000
143A144VAL00.0320.00612.139-0.033-0.0330.0000.0000.0000.000
144A145ASN0-0.041-0.03613.520-0.042-0.0420.0000.0000.0000.000
145A146SER00.0280.01116.0010.0000.0000.0000.0000.0000.000
146A147ASP-1-0.751-0.88219.127-0.016-0.0160.0000.0000.0000.000
147A148ASP-1-0.954-0.98020.789-0.034-0.0340.0000.0000.0000.000
148A149THR0-0.056-0.02917.534-0.010-0.0100.0000.0000.0000.000
149A150CYS0-0.0220.00212.103-0.026-0.0260.0000.0000.0000.000
150A151LYS10.8620.93018.0410.0570.0570.0000.0000.0000.000
151A152GLN0-0.073-0.03021.268-0.006-0.0060.0000.0000.0000.000
152A153ALA0-0.0300.01516.765-0.009-0.0090.0000.0000.0000.000
153A154TYR00.018-0.01212.613-0.035-0.0350.0000.0000.0000.000
154A155GLY00.0220.01119.4010.0170.0170.0000.0000.0000.000
155A156GLU-1-0.905-0.96119.357-0.160-0.1600.0000.0000.0000.000
156A157TYR0-0.055-0.04016.3570.0060.0060.0000.0000.0000.000
157A158THR00.002-0.01619.5110.0120.0120.0000.0000.0000.000
158A159PRO00.0220.01819.805-0.003-0.0030.0000.0000.0000.000
159A160ASP-1-0.944-0.97220.884-0.019-0.0190.0000.0000.0000.000
160A161ALA0-0.038-0.01819.4360.0020.0020.0000.0000.0000.000
161A162MET0-0.075-0.01115.621-0.007-0.0070.0000.0000.0000.000
162A163VAL00.0030.00312.6680.0150.0150.0000.0000.0000.000
163A165ALA00.0310.0159.2310.0340.0340.0000.0000.0000.000
164A166GLY00.0370.0249.171-0.044-0.0440.0000.0000.0000.000
165A167VAL00.0040.01510.1410.0250.0250.0000.0000.0000.000
166A168PRO00.0120.00512.188-0.049-0.0490.0000.0000.0000.000
167A169GLU-1-0.905-0.96813.203-0.052-0.0520.0000.0000.0000.000
168A170GLY0-0.029-0.00210.962-0.035-0.0350.0000.0000.0000.000
169A171GLY0-0.035-0.0369.0600.0760.0760.0000.0000.0000.000
170A172VAL0-0.036-0.0294.575-0.156-0.076-0.001-0.008-0.0700.000
171A173ASP-1-0.804-0.8883.844-0.710-0.3860.000-0.071-0.2520.000
172A174THR0-0.046-0.0062.259-2.508-1.1125.680-3.128-3.948-0.015
173A175CYS0-0.075-0.0313.147-0.1060.5460.0560.163-0.8700.002
174A176GLN00.0640.0004.677-0.227-0.099-0.001-0.004-0.1220.000
175A177GLY00.0290.0265.472-0.343-0.3430.0000.0000.0000.000
176A178ASP-1-0.745-0.8631.704-10.470-19.61822.197-7.419-5.630-0.056
177A179SER0-0.011-0.0154.9510.4320.496-0.001-0.006-0.0560.000
178A180GLY00.005-0.0178.2650.0410.0410.0000.0000.0000.000
179A181GLY0-0.0130.0005.8260.0900.0900.0000.0000.0000.000
180A182PRO0-0.050-0.0145.698-0.002-0.0020.0000.0000.0000.000
181A183MET00.0470.0345.5950.1930.1930.0000.0000.0000.000
182A184VAL0-0.047-0.0277.983-0.106-0.1060.0000.0000.0000.000
183A185VAL00.0650.03010.6000.0410.0410.0000.0000.0000.000
184A186ASN0-0.054-0.03013.431-0.014-0.0140.0000.0000.0000.000
185A187ASN0-0.025-0.02214.6590.0000.0000.0000.0000.0000.000
186A188LYS10.8930.97215.229-0.128-0.1280.0000.0000.0000.000
187A189LEU0-0.0100.00010.3320.0300.0300.0000.0000.0000.000
188A190ILE00.0320.00611.856-0.033-0.0330.0000.0000.0000.000
189A191GLY00.0110.01310.960-0.038-0.0380.0000.0000.0000.000
190A192VAL0-0.0190.0089.4570.0480.0480.0000.0000.0000.000
191A193THR00.0220.0054.8280.0570.0570.0000.0000.0000.000
192A194SER0-0.032-0.0397.884-0.055-0.0550.0000.0000.0000.000
193A195TRP0-0.001-0.01610.720-0.073-0.0730.0000.0000.0000.000
194A196GLY00.0640.02910.7650.0350.0350.0000.0000.0000.000
195A197GLU-1-0.908-0.93911.943-0.320-0.3200.0000.0000.0000.000
196A198GLY0-0.046-0.02011.3610.0050.0050.0000.0000.0000.000
197A200ALA0-0.016-0.0046.5530.0230.0230.0000.0000.0000.000
198A201ARG10.7760.8638.2930.5840.5840.0000.0000.0000.000
199A202PRO00.002-0.01012.0250.0410.0410.0000.0000.0000.000
200A203GLY0-0.040-0.01314.709-0.006-0.0060.0000.0000.0000.000
201A204LYS10.7780.89513.1520.2340.2340.0000.0000.0000.000
202A205PRO00.0000.02011.082-0.061-0.0610.0000.0000.0000.000
203A206GLY00.1260.0868.241-0.067-0.0670.0000.0000.0000.000
204A207VAL0-0.033-0.0319.2830.1120.1120.0000.0000.0000.000
205A208TYR00.008-0.0035.131-0.069-0.0690.0000.0000.0000.000
206A209ALA00.0320.01211.2630.0070.0070.0000.0000.0000.000
207A210ARG10.8940.95313.4150.0180.0180.0000.0000.0000.000
208A211VAL00.0170.00613.615-0.008-0.0080.0000.0000.0000.000
209A212GLY00.002-0.00516.380-0.006-0.0060.0000.0000.0000.000
210A213ALA0-0.041-0.01919.210-0.002-0.0020.0000.0000.0000.000
211A214TYR0-0.006-0.00217.800-0.010-0.0100.0000.0000.0000.000
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