FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 2JJLR

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 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 183
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1981443.34501
FMO2-HF: Nuclear repulsion 1908552.464787
FMO2-HF: Total energy -72890.880223
FMO2-MP2: Total energy -73100.022732


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.
-46.956-48.99523.714-9.621-12.0490.014
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 : 0.031 / q_NPA : 0.006
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].
3A14LEU00.0300.0212.040-7.658-5.9195.395-3.361-3.772-0.034
4A15ARG10.8080.8981.843-25.073-30.28814.942-4.771-4.9550.054
5A16THR00.008-0.0095.868-0.529-0.5290.0000.0000.0000.000
6A17ASP-1-0.953-0.9959.0950.0940.0940.0000.0000.0000.000
7A18ASP-1-0.869-0.9194.800-3.477-3.425-0.001-0.002-0.0480.000
8A19GLU-1-0.849-0.8888.390-1.026-1.0260.0000.0000.0000.000
9A20VAL0-0.068-0.0467.502-0.639-0.6390.0000.0000.0000.000
10A21VAL00.0510.02810.1640.4430.4430.0000.0000.0000.000
11A22LEU00.005-0.00211.737-0.338-0.3380.0000.0000.0000.000
12A23GLN00.0130.00013.1710.2400.2400.0000.0000.0000.000
13A24CYS00.0110.01715.072-0.029-0.0290.0000.0000.0000.000
14A25THR0-0.0080.00117.587-0.026-0.0260.0000.0000.0000.000
15A26ALA00.0620.04319.9120.0560.0560.0000.0000.0000.000
16A27THR0-0.027-0.02323.701-0.007-0.0070.0000.0000.0000.000
17A28ILE00.0090.01126.4660.0240.0240.0000.0000.0000.000
18A29HIS00.0250.00730.2870.0020.0020.0000.0000.0000.000
19A30LYS10.8950.94529.5590.4550.4550.0000.0000.0000.000
20A31GLU-1-0.872-0.91528.148-0.560-0.5600.0000.0000.0000.000
21A32GLN0-0.069-0.05321.918-0.056-0.0560.0000.0000.0000.000
22A33GLN00.0230.02722.679-0.017-0.0170.0000.0000.0000.000
23A34LYS10.9090.95114.9051.5201.5200.0000.0000.0000.000
24A35LEU0-0.0120.01719.2480.0730.0730.0000.0000.0000.000
25A36CYS0-0.026-0.00517.001-0.209-0.2090.0000.0000.0000.000
26A37LEU00.0150.00817.2690.1230.1230.0000.0000.0000.000
27A38ALA00.0260.02118.396-0.066-0.0660.0000.0000.0000.000
28A39ALA00.004-0.00421.1140.0450.0450.0000.0000.0000.000
29A40GLU-1-0.880-0.94523.619-0.450-0.4500.0000.0000.0000.000
30A41GLY00.028-0.00326.1620.0100.0100.0000.0000.0000.000
31A42PHE0-0.058-0.02128.0550.0400.0400.0000.0000.0000.000
32A43GLY00.0030.00931.438-0.001-0.0010.0000.0000.0000.000
33A44ASN0-0.026-0.02131.469-0.001-0.0010.0000.0000.0000.000
34A45ARG10.8070.86728.6020.3050.3050.0000.0000.0000.000
35A46LEU0-0.039-0.01127.225-0.024-0.0240.0000.0000.0000.000
36A47CYS0-0.0410.02422.974-0.020-0.0200.0000.0000.0000.000
37A48PHE0-0.024-0.01523.9270.0360.0360.0000.0000.0000.000
38A49LEU0-0.017-0.01520.898-0.073-0.0730.0000.0000.0000.000
39A50GLU-1-0.767-0.88421.168-0.727-0.7270.0000.0000.0000.000
40A51SER0-0.008-0.02921.310-0.073-0.0730.0000.0000.0000.000
41A52THR0-0.060-0.04617.904-0.023-0.0230.0000.0000.0000.000
42A53SER0-0.074-0.04721.1630.0200.0200.0000.0000.0000.000
43A54ASN00.0140.02122.1190.0130.0130.0000.0000.0000.000
44A55SER00.0630.03520.1850.0280.0280.0000.0000.0000.000
45A56LYS10.8700.91415.4471.2711.2710.0000.0000.0000.000
46A57ASN0-0.035-0.03014.778-0.047-0.0470.0000.0000.0000.000
47A58VAL00.0240.02516.256-0.165-0.1650.0000.0000.0000.000
48A59PRO00.0560.03817.3080.0700.0700.0000.0000.0000.000
49A60PRO0-0.044-0.02520.3510.0120.0120.0000.0000.0000.000
50A61ASP-1-0.826-0.88622.572-0.582-0.5820.0000.0000.0000.000
51A62LEU0-0.002-0.01814.841-0.044-0.0440.0000.0000.0000.000
52A63SER0-0.082-0.05817.944-0.052-0.0520.0000.0000.0000.000
53A64ILE00.0170.01620.1510.0140.0140.0000.0000.0000.000
54A65CYS0-0.040-0.01416.883-0.026-0.0260.0000.0000.0000.000
55A66THR0-0.060-0.02713.793-0.139-0.1390.0000.0000.0000.000
56A67PHE00.018-0.00413.9560.1980.1980.0000.0000.0000.000
57A68VAL00.0030.01412.420-0.261-0.2610.0000.0000.0000.000
58A69LEU0-0.013-0.0017.8750.1320.1320.0000.0000.0000.000
59A70GLU-1-0.765-0.84711.831-0.172-0.1720.0000.0000.0000.000
60A71GLN0-0.034-0.03114.4860.1970.1970.0000.0000.0000.000
61A72SER0-0.001-0.00212.257-0.074-0.0740.0000.0000.0000.000
62A73LEU0-0.0020.00314.3450.1660.1660.0000.0000.0000.000
63A74SER00.0310.01017.387-0.069-0.0690.0000.0000.0000.000
64A75VAL00.1040.04419.2920.0020.0020.0000.0000.0000.000
65A76ARG10.8360.90722.081-0.026-0.0260.0000.0000.0000.000
66A77ALA00.005-0.00321.0650.0100.0100.0000.0000.0000.000
67A78LEU00.0420.02521.2910.0110.0110.0000.0000.0000.000
68A79GLN0-0.006-0.02923.2120.0270.0270.0000.0000.0000.000
69A80GLU-1-0.871-0.90026.1830.0670.0670.0000.0000.0000.000
70A81MET0-0.038-0.01221.534-0.002-0.0020.0000.0000.0000.000
71A82LEU00.0300.02926.1030.0010.0010.0000.0000.0000.000
72A83ALA00.0120.01428.9920.0010.0010.0000.0000.0000.000
73A84ASN0-0.090-0.06530.0230.0070.0070.0000.0000.0000.000
74A85THR0-0.081-0.03330.2250.0000.0000.0000.0000.0000.000
75A86VAL0-0.089-0.03432.834-0.002-0.0020.0000.0000.0000.000
76A110HIS00.0550.0258.618-0.241-0.2410.0000.0000.0000.000
77A111ARG10.8550.9288.5090.2370.2370.0000.0000.0000.000
78A112THR0-0.041-0.0286.324-0.020-0.0200.0000.0000.0000.000
79A113LEU00.0360.0407.3130.0600.0600.0000.0000.0000.000
80A114LEU0-0.065-0.0369.0100.1380.1380.0000.0000.0000.000
81A115TYR0-0.015-0.02810.010-0.163-0.1630.0000.0000.0000.000
82A116GLY00.0670.04014.1550.1740.1740.0000.0000.0000.000
83A117HIS0-0.109-0.04814.0250.1900.1900.0000.0000.0000.000
84A118ALA00.0450.03316.161-0.120-0.1200.0000.0000.0000.000
85A119ILE0-0.053-0.04312.3470.0550.0550.0000.0000.0000.000
86A120LEU00.0180.03015.235-0.001-0.0010.0000.0000.0000.000
87A121LEU0-0.008-0.01813.698-0.100-0.1000.0000.0000.0000.000
88A122ARG10.8880.94816.0920.4980.4980.0000.0000.0000.000
89A123HIS00.0110.01516.940-0.038-0.0380.0000.0000.0000.000
90A124SER0-0.055-0.06715.8240.0890.0890.0000.0000.0000.000
91A125TYR0-0.038-0.00618.6780.0940.0940.0000.0000.0000.000
92A126SER00.000-0.02922.1250.0630.0630.0000.0000.0000.000
93A127GLY0-0.039-0.00621.5740.0490.0490.0000.0000.0000.000
94A128MET0-0.044-0.00522.5720.0400.0400.0000.0000.0000.000
95A129TYR0-0.018-0.04819.198-0.060-0.0600.0000.0000.0000.000
96A130LEU00.0150.00717.9120.0320.0320.0000.0000.0000.000
97A131CYS0-0.0440.00121.0020.0170.0170.0000.0000.0000.000
98A132CYS00.0080.01323.896-0.014-0.0140.0000.0000.0000.000
99A133LEU00.0140.00526.1040.0390.0390.0000.0000.0000.000
100A134SER00.010-0.00929.7420.0000.0000.0000.0000.0000.000
101A135THR0-0.069-0.03232.6900.0240.0240.0000.0000.0000.000
102A136SER00.002-0.00232.743-0.010-0.0100.0000.0000.0000.000
103A137ARG10.8220.91033.0670.3250.3250.0000.0000.0000.000
104A138SER00.0480.00429.294-0.031-0.0310.0000.0000.0000.000
105A139SER0-0.087-0.04531.3890.0290.0290.0000.0000.0000.000
106A140THR0-0.045-0.02230.4310.0050.0050.0000.0000.0000.000
107A141ASP-1-0.754-0.86033.036-0.303-0.3030.0000.0000.0000.000
108A142LYS10.8290.89234.9750.2520.2520.0000.0000.0000.000
109A143LEU0-0.025-0.01234.7530.0170.0170.0000.0000.0000.000
110A144ALA00.0070.01929.8030.0040.0040.0000.0000.0000.000
111A145PHE0-0.059-0.03029.4180.0280.0280.0000.0000.0000.000
112A146ASP-1-0.697-0.82328.921-0.387-0.3870.0000.0000.0000.000
113A147VAL00.0110.00122.6720.0030.0030.0000.0000.0000.000
114A148GLY00.025-0.01725.352-0.002-0.0020.0000.0000.0000.000
115A149LEU0-0.0290.00421.992-0.032-0.0320.0000.0000.0000.000
116A150GLN0-0.015-0.02824.9830.0360.0360.0000.0000.0000.000
117A151GLU-1-0.755-0.85425.134-0.296-0.2960.0000.0000.0000.000
118A152ASP-1-0.870-0.90026.444-0.170-0.1700.0000.0000.0000.000
119A153THR00.0540.01821.744-0.029-0.0290.0000.0000.0000.000
120A154THR0-0.077-0.05024.1850.0070.0070.0000.0000.0000.000
121A155GLY00.0120.00426.893-0.017-0.0170.0000.0000.0000.000
122A156GLU-1-0.832-0.94024.743-0.187-0.1870.0000.0000.0000.000
123A157ALA00.0060.00724.507-0.032-0.0320.0000.0000.0000.000
124A158CYS0-0.063-0.02821.873-0.042-0.0420.0000.0000.0000.000
125A159TRP00.0020.00917.858-0.064-0.0640.0000.0000.0000.000
126A160TRP0-0.009-0.02017.5630.0110.0110.0000.0000.0000.000
127A161THR0-0.006-0.01317.223-0.039-0.0390.0000.0000.0000.000
128A162ILE0-0.0330.00010.794-0.095-0.0950.0000.0000.0000.000
129A163HIS0-0.017-0.02615.1080.1350.1350.0000.0000.0000.000
130A164PRO00.0230.01914.027-0.207-0.2070.0000.0000.0000.000
131A165ALA00.0320.01514.3380.0950.0950.0000.0000.0000.000
132A166SER0-0.047-0.03515.6530.1350.1350.0000.0000.0000.000
133A167LYS10.9470.96716.3660.1060.1060.0000.0000.0000.000
134A168GLN0-0.076-0.03413.2890.1530.1530.0000.0000.0000.000
135A169GLN00.004-0.0109.9950.2120.2120.0000.0000.0000.000
136A170SER00.0050.01512.800-0.086-0.0860.0000.0000.0000.000
137A171GLU-1-0.793-0.90314.979-0.334-0.3340.0000.0000.0000.000
138A172GLY0-0.020-0.00816.1480.0880.0880.0000.0000.0000.000
139A173GLU-1-0.892-0.94311.2050.5250.5250.0000.0000.0000.000
140A174LYS10.8950.9467.603-3.605-3.6050.0000.0000.0000.000
141A175VAL00.0430.0347.3890.0370.0370.0000.0000.0000.000
142A176ARG10.8580.9194.294-0.844-0.700-0.001-0.038-0.1050.000
143A177VAL0-0.005-0.0142.003-1.851-1.0413.379-1.348-2.840-0.006
144A178GLY0-0.005-0.0104.092-0.796-0.5200.000-0.077-0.1980.000
145A179ASP-1-0.820-0.8686.921-1.032-1.0320.0000.0000.0000.000
146A180ASP-1-0.851-0.9049.340-2.042-2.0420.0000.0000.0000.000
147A181LEU0-0.063-0.0369.5430.2130.2130.0000.0000.0000.000
148A182ILE00.0100.00713.8400.0830.0830.0000.0000.0000.000
149A183LEU00.0060.00313.940-0.014-0.0140.0000.0000.0000.000
150A184VAL00.0090.00417.9580.0290.0290.0000.0000.0000.000
151A185SER0-0.0150.00321.1470.0150.0150.0000.0000.0000.000
152A186VAL00.0490.00021.4670.0350.0350.0000.0000.0000.000
153A187SER0-0.025-0.00224.1860.0340.0340.0000.0000.0000.000
154A188SER0-0.053-0.03726.8150.0110.0110.0000.0000.0000.000
155A189GLU-1-0.923-0.95125.378-0.290-0.2900.0000.0000.0000.000
156A190ARG10.7690.88525.8620.3300.3300.0000.0000.0000.000
157A191TYR00.0200.00921.968-0.022-0.0220.0000.0000.0000.000
158A192LEU00.0240.01718.0060.0340.0340.0000.0000.0000.000
159A193HIS0-0.103-0.06121.189-0.057-0.0570.0000.0000.0000.000
160A194LEU00.006-0.00422.0080.0060.0060.0000.0000.0000.000
161A195SER0-0.027-0.01823.8160.0500.0500.0000.0000.0000.000
162A196TYR00.007-0.01627.528-0.025-0.0250.0000.0000.0000.000
163A197GLY00.0340.02930.2980.0250.0250.0000.0000.0000.000
164A198ASN0-0.057-0.04333.7420.0060.0060.0000.0000.0000.000
165A199SER0-0.033-0.01634.7890.0050.0050.0000.0000.0000.000
166A200SER00.0020.01030.616-0.013-0.0130.0000.0000.0000.000
167A201TRP00.0200.00525.7820.0040.0040.0000.0000.0000.000
168A202HIS0-0.036-0.02826.9620.0120.0120.0000.0000.0000.000
169A203VAL00.0360.01121.558-0.034-0.0340.0000.0000.0000.000
170A204ASP-1-0.791-0.85824.785-0.449-0.4490.0000.0000.0000.000
171A205ALA00.0650.03424.767-0.048-0.0480.0000.0000.0000.000
172A206ALA00.0060.01326.3030.0590.0590.0000.0000.0000.000
173A207PHE00.023-0.00827.247-0.009-0.0090.0000.0000.0000.000
174A208GLN0-0.023-0.00727.3280.0090.0090.0000.0000.0000.000
175A209GLN00.0460.02621.7530.0040.0040.0000.0000.0000.000
176A210THR0-0.043-0.02919.5000.0320.0320.0000.0000.0000.000
177A211LEU0-0.0360.00316.479-0.004-0.0040.0000.0000.0000.000
178A212TRP0-0.009-0.02514.651-0.001-0.0010.0000.0000.0000.000
179A213SER0-0.032-0.03511.855-0.126-0.1260.0000.0000.0000.000
180A214VAL0-0.061-0.0289.242-0.096-0.0960.0000.0000.0000.000
181A215ALA0-0.0060.0036.773-0.954-0.9540.0000.0000.0000.000
182A216PRO00.0000.0033.7770.4540.6090.000-0.024-0.1310.000
183A217ILE0-0.0030.0037.0810.0740.0740.0000.0000.0000.000