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: 722MK

Calculation Name: 4KEJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KEJ

Chain ID: A

ChEMBL ID:

UniProt ID: E9Q401

Base Structure: X-ray

Registration Date: 2023-06-21

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1975222.114901
FMO2-HF: Nuclear repulsion 1902331.891896
FMO2-HF: Total energy -72890.223005
FMO2-MP2: Total energy -73099.362034


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:GLN)


Summations of interaction energy for fragment #1(A:12:GLN)
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.
-48.937-50.89523.342-9.332-12.0520.019
Interaction energy analysis for fragmet #1(A:12:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.005
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].
3A14LEU00.0220.0192.117-8.444-5.8294.159-3.065-3.708-0.030
4A15ARG10.8040.8961.870-26.327-32.75816.571-4.908-5.2330.054
5A16THR0-0.014-0.0285.347-0.557-0.542-0.0010.000-0.0140.000
6A17ASP-1-0.962-0.9838.571-0.132-0.1320.0000.0000.0000.000
7A18ASP-1-0.919-0.9465.122-4.013-3.968-0.0010.000-0.0440.000
8A19GLU-1-0.837-0.8918.799-0.961-0.9610.0000.0000.0000.000
9A20VAL0-0.078-0.0547.284-0.711-0.7110.0000.0000.0000.000
10A21VAL00.0490.0159.9170.4770.4770.0000.0000.0000.000
11A22LEU0-0.0050.00411.749-0.283-0.2830.0000.0000.0000.000
12A23GLN00.0310.00913.4530.2810.2810.0000.0000.0000.000
13A24CYS00.0100.02415.499-0.031-0.0310.0000.0000.0000.000
14A25THR0-0.0120.00218.047-0.006-0.0060.0000.0000.0000.000
15A26ALA00.0480.03520.2510.0540.0540.0000.0000.0000.000
16A27THR0-0.006-0.01723.9890.0010.0010.0000.0000.0000.000
17A28ILE00.0160.01526.5590.0260.0260.0000.0000.0000.000
18A29HIS00.0450.02030.2830.0020.0020.0000.0000.0000.000
19A30LYS10.8620.93229.8350.4180.4180.0000.0000.0000.000
20A31GLU-1-0.891-0.93028.308-0.524-0.5240.0000.0000.0000.000
21A32GLN0-0.056-0.04021.604-0.065-0.0650.0000.0000.0000.000
22A33GLN00.0310.02522.795-0.026-0.0260.0000.0000.0000.000
23A34LYS10.8980.94515.4461.3571.3570.0000.0000.0000.000
24A35LEU0-0.0040.01519.7160.0510.0510.0000.0000.0000.000
25A36CYS0-0.0170.00217.159-0.184-0.1840.0000.0000.0000.000
26A37LEU00.0130.00017.4400.1220.1220.0000.0000.0000.000
27A38ALA00.0240.01718.449-0.077-0.0770.0000.0000.0000.000
28A39ALA00.010-0.00520.9290.0550.0550.0000.0000.0000.000
29A40GLU-1-0.882-0.94423.569-0.496-0.4960.0000.0000.0000.000
30A41GLY00.008-0.01326.0360.0160.0160.0000.0000.0000.000
31A42PHE0-0.050-0.02327.4530.0370.0370.0000.0000.0000.000
32A43GLY0-0.007-0.00131.027-0.009-0.0090.0000.0000.0000.000
33A44ASN0-0.027-0.02531.648-0.010-0.0100.0000.0000.0000.000
34A45ARG10.8960.93828.7370.3320.3320.0000.0000.0000.000
35A46LEU0-0.058-0.02127.174-0.029-0.0290.0000.0000.0000.000
36A47CYS0-0.0220.02322.832-0.017-0.0170.0000.0000.0000.000
37A48PHE0-0.037-0.01823.8960.0420.0420.0000.0000.0000.000
38A49LEU0-0.014-0.01621.158-0.070-0.0700.0000.0000.0000.000
39A50GLU-1-0.788-0.89021.516-0.758-0.7580.0000.0000.0000.000
40A51SER0-0.001-0.02621.753-0.058-0.0580.0000.0000.0000.000
41A52THR0-0.035-0.04418.116-0.034-0.0340.0000.0000.0000.000
42A53SER0-0.127-0.06420.9270.0310.0310.0000.0000.0000.000
43A54ASN00.0450.02922.0610.0220.0220.0000.0000.0000.000
44A55SER00.0630.02520.3540.0250.0250.0000.0000.0000.000
45A56LYS10.8710.92115.1201.2901.2900.0000.0000.0000.000
46A57ASN0-0.053-0.04014.710-0.032-0.0320.0000.0000.0000.000
47A58VAL00.0400.02416.036-0.181-0.1810.0000.0000.0000.000
48A59PRO00.0700.06217.4890.0790.0790.0000.0000.0000.000
49A60PRO0-0.054-0.02020.5370.0110.0110.0000.0000.0000.000
50A61ASP-1-0.816-0.89922.702-0.656-0.6560.0000.0000.0000.000
51A62LEU00.003-0.00915.211-0.068-0.0680.0000.0000.0000.000
52A63SER0-0.078-0.04417.870-0.066-0.0660.0000.0000.0000.000
53A64ILE0-0.0100.00619.389-0.030-0.0300.0000.0000.0000.000
54A65CYS0-0.031-0.01617.183-0.028-0.0280.0000.0000.0000.000
55A66THR0-0.068-0.02513.764-0.156-0.1560.0000.0000.0000.000
56A67PHE0-0.003-0.01413.6120.1950.1950.0000.0000.0000.000
57A68VAL00.0280.01112.422-0.262-0.2620.0000.0000.0000.000
58A69LEU0-0.067-0.0177.9480.1720.1720.0000.0000.0000.000
59A70GLU-1-0.741-0.84411.932-0.292-0.2920.0000.0000.0000.000
60A71GLN0-0.032-0.02014.6690.1900.1900.0000.0000.0000.000
61A72SER0-0.005-0.01312.209-0.087-0.0870.0000.0000.0000.000
62A73LEU0-0.0110.00314.3010.1650.1650.0000.0000.0000.000
63A74SER00.0280.01717.260-0.065-0.0650.0000.0000.0000.000
64A75VAL00.1360.05319.173-0.006-0.0060.0000.0000.0000.000
65A76ARG10.8310.90922.090-0.027-0.0270.0000.0000.0000.000
66A77ALA0-0.004-0.01220.9430.0040.0040.0000.0000.0000.000
67A78LEU00.0310.01621.0180.0070.0070.0000.0000.0000.000
68A79GLN00.000-0.02223.0380.0220.0220.0000.0000.0000.000
69A80GLU-1-0.887-0.90425.9980.0630.0630.0000.0000.0000.000
70A81MET0-0.032-0.02421.552-0.005-0.0050.0000.0000.0000.000
71A82LEU00.0270.02425.8100.0000.0000.0000.0000.0000.000
72A83ALA00.0150.01428.8580.0000.0000.0000.0000.0000.000
73A84ASN0-0.059-0.04729.6020.0030.0030.0000.0000.0000.000
74A85THR0-0.093-0.03430.3830.0010.0010.0000.0000.0000.000
75A86VAL0-0.072-0.01733.066-0.002-0.0020.0000.0000.0000.000
76A110HIS00.0460.0268.261-0.259-0.2590.0000.0000.0000.000
77A111ARG10.8930.9558.5790.4060.4060.0000.0000.0000.000
78A112THR0-0.034-0.0246.4370.2360.2360.0000.0000.0000.000
79A113LEU00.0450.0347.2610.0560.0560.0000.0000.0000.000
80A114LEU0-0.066-0.0439.1850.2800.2800.0000.0000.0000.000
81A115TYR00.004-0.01110.245-0.197-0.1970.0000.0000.0000.000
82A116GLY00.0630.03814.1740.1660.1660.0000.0000.0000.000
83A117HIS0-0.112-0.05613.9470.1540.1540.0000.0000.0000.000
84A118ALA00.0480.02515.949-0.120-0.1200.0000.0000.0000.000
85A119ILE0-0.067-0.04912.1570.0380.0380.0000.0000.0000.000
86A120LEU00.0210.03215.1030.0180.0180.0000.0000.0000.000
87A121LEU0-0.005-0.01613.703-0.108-0.1080.0000.0000.0000.000
88A122ARG10.9020.95516.1350.6460.6460.0000.0000.0000.000
89A123HIS00.0180.01516.877-0.072-0.0720.0000.0000.0000.000
90A124SER0-0.043-0.04015.8610.1040.1040.0000.0000.0000.000
91A125TYR0-0.036-0.00818.6830.0940.0940.0000.0000.0000.000
92A126SER00.015-0.01822.1030.0630.0630.0000.0000.0000.000
93A127GLY0-0.044-0.01121.7150.0530.0530.0000.0000.0000.000
94A128MET0-0.071-0.02322.7480.0440.0440.0000.0000.0000.000
95A129TYR0-0.031-0.05319.328-0.063-0.0630.0000.0000.0000.000
96A130LEU0-0.0090.00517.9720.0360.0360.0000.0000.0000.000
97A131CYS0-0.063-0.01821.1150.0250.0250.0000.0000.0000.000
98A132CYS00.0250.02423.766-0.021-0.0210.0000.0000.0000.000
99A133LEU0-0.0200.00226.0400.0410.0410.0000.0000.0000.000
100A134SER00.029-0.00129.6220.0050.0050.0000.0000.0000.000
101A135THR0-0.075-0.04832.3820.0280.0280.0000.0000.0000.000
102A136SER0-0.004-0.01032.577-0.010-0.0100.0000.0000.0000.000
103A137ARG10.7810.90133.6090.3330.3330.0000.0000.0000.000
104A138SER00.0850.03129.427-0.037-0.0370.0000.0000.0000.000
105A139SER0-0.108-0.06631.5490.0320.0320.0000.0000.0000.000
106A140THR0-0.013-0.00430.7970.0010.0010.0000.0000.0000.000
107A141ASP-1-0.666-0.83332.965-0.302-0.3020.0000.0000.0000.000
108A142LYS10.7700.86434.8600.2580.2580.0000.0000.0000.000
109A143LEU0-0.079-0.03335.1190.0150.0150.0000.0000.0000.000
110A144ALA00.0510.04830.086-0.001-0.0010.0000.0000.0000.000
111A145PHE0-0.023-0.01429.3640.0230.0230.0000.0000.0000.000
112A146ASP-1-0.707-0.81529.014-0.403-0.4030.0000.0000.0000.000
113A147VAL00.008-0.00422.6580.0080.0080.0000.0000.0000.000
114A148GLY00.0440.00225.553-0.010-0.0100.0000.0000.0000.000
115A149LEU0-0.0120.02222.096-0.023-0.0230.0000.0000.0000.000
116A150GLN0-0.004-0.03824.9930.0430.0430.0000.0000.0000.000
117A151GLU-1-0.769-0.86925.181-0.334-0.3340.0000.0000.0000.000
118A152ASP-1-0.877-0.91126.199-0.208-0.2080.0000.0000.0000.000
119A153THR00.0530.01522.659-0.029-0.0290.0000.0000.0000.000
120A154THR0-0.113-0.05524.3070.0090.0090.0000.0000.0000.000
121A155GLY00.0380.01826.970-0.013-0.0130.0000.0000.0000.000
122A156GLU-1-0.854-0.95325.044-0.208-0.2080.0000.0000.0000.000
123A157ALA0-0.008-0.00724.347-0.034-0.0340.0000.0000.0000.000
124A158CYS0-0.057-0.02422.079-0.039-0.0390.0000.0000.0000.000
125A159TRP00.0100.00817.589-0.061-0.0610.0000.0000.0000.000
126A160TRP00.001-0.00617.4450.0160.0160.0000.0000.0000.000
127A161THR00.0040.00316.980-0.055-0.0550.0000.0000.0000.000
128A162ILE0-0.0190.00311.011-0.087-0.0870.0000.0000.0000.000
129A163HIS0-0.007-0.01615.3960.1260.1260.0000.0000.0000.000
130A164PRO00.0290.02314.600-0.196-0.1960.0000.0000.0000.000
131A165ALA00.0170.01214.7570.0790.0790.0000.0000.0000.000
132A166SER0-0.039-0.03716.1880.1120.1120.0000.0000.0000.000
133A167LYS10.9570.98817.1370.0760.0760.0000.0000.0000.000
134A168GLN0-0.051-0.03513.7220.1170.1170.0000.0000.0000.000
135A169GLN0-0.003-0.01910.3280.1970.1970.0000.0000.0000.000
136A170SER00.0100.01013.616-0.079-0.0790.0000.0000.0000.000
137A171GLU-1-0.824-0.90415.705-0.284-0.2840.0000.0000.0000.000
138A172GLY0-0.033-0.01216.0730.0900.0900.0000.0000.0000.000
139A173GLU-1-0.950-0.97212.1320.6370.6370.0000.0000.0000.000
140A174LYS10.9140.9458.069-3.350-3.3500.0000.0000.0000.000
141A175VAL00.0360.0347.6590.0540.0540.0000.0000.0000.000
142A176ARG10.9290.9644.415-1.612-1.457-0.001-0.035-0.1200.000
143A177VAL00.022-0.0082.070-2.352-0.9502.617-1.290-2.729-0.005
144A178GLY0-0.018-0.0084.4340.1950.288-0.001-0.015-0.0760.000
145A179ASP-1-0.804-0.8687.194-0.735-0.7350.0000.0000.0000.000
146A180ASP-1-0.891-0.9499.450-1.881-1.8810.0000.0000.0000.000
147A181LEU0-0.064-0.0349.9190.2010.2010.0000.0000.0000.000
148A182ILE0-0.0040.00114.2330.0400.0400.0000.0000.0000.000
149A183LEU0-0.008-0.00814.212-0.002-0.0020.0000.0000.0000.000
150A184VAL00.0180.01118.2480.0310.0310.0000.0000.0000.000
151A185SER0-0.038-0.00820.885-0.004-0.0040.0000.0000.0000.000
152A186VAL00.0400.00121.3670.0370.0370.0000.0000.0000.000
153A187SER0-0.0140.01524.0640.0360.0360.0000.0000.0000.000
154A188SER0-0.056-0.05726.9790.0150.0150.0000.0000.0000.000
155A189GLU-1-0.901-0.94825.341-0.271-0.2710.0000.0000.0000.000
156A190ARG10.7600.87626.4610.3280.3280.0000.0000.0000.000
157A191TYR00.0190.00222.157-0.020-0.0200.0000.0000.0000.000
158A192LEU00.0150.02018.0660.0300.0300.0000.0000.0000.000
159A193HIS0-0.107-0.06721.449-0.048-0.0480.0000.0000.0000.000
160A194LEU00.0010.00022.4920.0020.0020.0000.0000.0000.000
161A195SER0-0.039-0.02524.2500.0500.0500.0000.0000.0000.000
162A196TYR0-0.016-0.02227.989-0.025-0.0250.0000.0000.0000.000
163A197GLY00.0330.02230.5720.0260.0260.0000.0000.0000.000
164A198ASN0-0.061-0.03533.6060.0160.0160.0000.0000.0000.000
165A199SER0-0.003-0.01134.8130.0010.0010.0000.0000.0000.000
166A200SER0-0.0090.00230.294-0.018-0.0180.0000.0000.0000.000
167A201TRP00.0260.01526.0560.0080.0080.0000.0000.0000.000
168A202HIS0-0.028-0.02127.0320.0070.0070.0000.0000.0000.000
169A203VAL00.0330.01521.756-0.028-0.0280.0000.0000.0000.000
170A204ASP-1-0.784-0.87425.033-0.456-0.4560.0000.0000.0000.000
171A205ALA00.0590.02724.976-0.042-0.0420.0000.0000.0000.000
172A206ALA0-0.015-0.00226.3590.0570.0570.0000.0000.0000.000
173A207PHE00.028-0.00827.496-0.006-0.0060.0000.0000.0000.000
174A208GLN0-0.027-0.00227.6130.0000.0000.0000.0000.0000.000
175A209GLN00.0630.03322.2170.0000.0000.0000.0000.0000.000
176A210THR0-0.042-0.02619.8200.0290.0290.0000.0000.0000.000
177A211LEU0-0.041-0.00116.646-0.004-0.0040.0000.0000.0000.000
178A212TRP0-0.012-0.02514.801-0.023-0.0230.0000.0000.0000.000
179A213SER0-0.028-0.02611.818-0.106-0.1060.0000.0000.0000.000
180A214VAL0-0.034-0.0118.797-0.039-0.0390.0000.0000.0000.000
181A215ALA0-0.024-0.0116.671-0.909-0.9090.0000.0000.0000.000
182A216PRO00.0200.0163.8340.4790.627-0.001-0.019-0.1280.000
183A217ILE0-0.0140.0037.0910.1740.1740.0000.0000.0000.000