Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: VQJ41

Calculation Name: 4GJ1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GJ1

Chain ID: A

ChEMBL ID:

UniProt ID: Q9PM74

Base Structure: X-ray

Registration Date: 2023-09-23

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2888294.611888
FMO2-HF: Nuclear repulsion 2798243.23194
FMO2-HF: Total energy -90051.379948
FMO2-MP2: Total energy -90313.119561


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:2:THR)


Summations of interaction energy for fragment #1(A:2:THR)
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.
-31.112-32.06533.74-15.79-16.996-0.052
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.045
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].
3A4ILE00.0210.0113.481-1.7880.3660.021-0.935-1.2410.001
4A5ILE0-0.007-0.0065.1410.3830.417-0.001-0.001-0.0310.000
5A6PRO0-0.0070.0018.1010.0950.0950.0000.0000.0000.000
6A7ALA00.0140.00811.1120.0650.0650.0000.0000.0000.000
7A8LEU0-0.095-0.05113.7290.0390.0390.0000.0000.0000.000
8A9ASP-1-0.871-0.93317.505-0.417-0.4170.0000.0000.0000.000
9A10LEU0-0.018-0.02720.0160.0170.0170.0000.0000.0000.000
10A11ILE0-0.022-0.01823.4470.0020.0020.0000.0000.0000.000
11A12ASP-1-0.885-0.93126.972-0.142-0.1420.0000.0000.0000.000
12A13GLY0-0.025-0.01627.4230.0060.0060.0000.0000.0000.000
13A14GLU-1-0.973-0.98326.948-0.167-0.1670.0000.0000.0000.000
14A15VAL00.000-0.00720.867-0.016-0.0160.0000.0000.0000.000
15A16VAL0-0.012-0.00422.7560.0150.0150.0000.0000.0000.000
16A17ARG10.8770.93715.4890.4280.4280.0000.0000.0000.000
17A18LEU00.0020.01221.5060.0210.0210.0000.0000.0000.000
18A19VAL0-0.028-0.01721.264-0.033-0.0330.0000.0000.0000.000
19A20LYS10.8750.91219.2740.3730.3730.0000.0000.0000.000
20A21GLY00.0260.01023.332-0.007-0.0070.0000.0000.0000.000
21A22ASP-1-0.917-0.94324.893-0.159-0.1590.0000.0000.0000.000
22A23TYR0-0.021-0.01828.1600.0110.0110.0000.0000.0000.000
23A24GLU-1-0.955-0.96225.660-0.223-0.2230.0000.0000.0000.000
24A25GLN0-0.029-0.01726.3920.0230.0230.0000.0000.0000.000
25A26LYS10.9610.98725.7630.1560.1560.0000.0000.0000.000
26A27LYS10.8490.94622.7080.2690.2690.0000.0000.0000.000
27A28VAL00.0310.00524.998-0.020-0.0200.0000.0000.0000.000
28A29TYR0-0.073-0.05821.0620.0050.0050.0000.0000.0000.000
29A30LYS11.0161.00025.5710.1890.1890.0000.0000.0000.000
30A31TYR0-0.032-0.01621.8810.0150.0150.0000.0000.0000.000
31A32ASN00.0710.03124.940-0.003-0.0030.0000.0000.0000.000
32A33PRO00.0780.03222.202-0.010-0.0100.0000.0000.0000.000
33A34LEU00.0530.03221.526-0.019-0.0190.0000.0000.0000.000
34A35LYS10.9280.95522.3590.1400.1400.0000.0000.0000.000
35A36LYS10.8790.96018.1340.3280.3280.0000.0000.0000.000
36A37PHE00.0640.02015.432-0.024-0.0240.0000.0000.0000.000
37A38LYS10.8320.91017.7320.1480.1480.0000.0000.0000.000
38A39GLU-1-0.920-0.94918.390-0.286-0.2860.0000.0000.0000.000
39A40TYR00.030-0.01013.941-0.016-0.0160.0000.0000.0000.000
40A41GLU-1-0.782-0.89514.547-0.237-0.2370.0000.0000.0000.000
41A42LYS10.8990.94816.2160.1830.1830.0000.0000.0000.000
42A43ALA0-0.0150.00314.7190.0240.0240.0000.0000.0000.000
43A44GLY0-0.014-0.00713.240-0.027-0.0270.0000.0000.0000.000
44A45ALA0-0.044-0.02410.572-0.054-0.0540.0000.0000.0000.000
45A46LYS10.9740.9779.7910.2740.2740.0000.0000.0000.000
46A47GLU-1-0.754-0.8578.064-0.084-0.0840.0000.0000.0000.000
47A48LEU0-0.026-0.00910.828-0.141-0.1410.0000.0000.0000.000
48A49HIS00.0650.03311.9660.0440.0440.0000.0000.0000.000
49A50LEU00.0280.01113.9090.0070.0070.0000.0000.0000.000
50A51VAL00.0150.00716.8380.0160.0160.0000.0000.0000.000
51A52ASP-1-0.745-0.87019.297-0.177-0.1770.0000.0000.0000.000
52A53LEU00.002-0.01921.6170.0100.0100.0000.0000.0000.000
53A54THR00.0180.01324.5360.0060.0060.0000.0000.0000.000
54A55GLY00.0220.00826.7320.0120.0120.0000.0000.0000.000
55A56ALA0-0.107-0.04423.8770.0070.0070.0000.0000.0000.000
56A57LYS10.8930.95725.9280.1800.1800.0000.0000.0000.000
57A58ASP-1-0.829-0.91729.142-0.102-0.1020.0000.0000.0000.000
58A59PRO00.0180.01129.597-0.002-0.0020.0000.0000.0000.000
59A60SER0-0.079-0.03330.6050.0040.0040.0000.0000.0000.000
60A61LYS10.9140.95032.2820.1020.1020.0000.0000.0000.000
61A62ARG10.8420.92424.5590.1620.1620.0000.0000.0000.000
62A63GLN0-0.041-0.03625.9190.0150.0150.0000.0000.0000.000
63A64PHE00.0470.00227.169-0.009-0.0090.0000.0000.0000.000
64A65ALA00.0490.03328.170-0.002-0.0020.0000.0000.0000.000
65A66LEU0-0.026-0.00925.2570.0010.0010.0000.0000.0000.000
66A67ILE00.0150.00022.660-0.009-0.0090.0000.0000.0000.000
67A68GLU-1-0.904-0.95424.225-0.096-0.0960.0000.0000.0000.000
68A69LYS10.8150.90026.1840.1210.1210.0000.0000.0000.000
69A70LEU0-0.059-0.04121.445-0.002-0.0020.0000.0000.0000.000
70A71ALA00.012-0.00121.474-0.008-0.0080.0000.0000.0000.000
71A72LYS10.9490.98522.2860.0870.0870.0000.0000.0000.000
72A73GLU-1-0.864-0.90524.379-0.101-0.1010.0000.0000.0000.000
73A74VAL0-0.082-0.02417.810-0.004-0.0040.0000.0000.0000.000
74A75SER0-0.029-0.00719.8750.0230.0230.0000.0000.0000.000
75A76VAL0-0.088-0.02314.2510.0310.0310.0000.0000.0000.000
76A77ASN0-0.032-0.02911.8770.0170.0170.0000.0000.0000.000
77A78LEU00.0150.01614.314-0.079-0.0790.0000.0000.0000.000
78A79GLN0-0.005-0.01011.0300.0870.0870.0000.0000.0000.000
79A80VAL00.0300.01315.480-0.033-0.0330.0000.0000.0000.000
80A81GLY00.0360.02018.0320.0070.0070.0000.0000.0000.000
81A82GLY00.0210.00418.8350.0060.0060.0000.0000.0000.000
82A83GLY00.011-0.00121.8670.0230.0230.0000.0000.0000.000
83A84ILE0-0.056-0.00620.8660.0180.0180.0000.0000.0000.000
84A85ARG10.8950.93623.7690.1430.1430.0000.0000.0000.000
85A86SER00.0300.02326.4850.0130.0130.0000.0000.0000.000
86A87LYS10.9730.98127.0870.0440.0440.0000.0000.0000.000
87A88GLU-1-0.861-0.94028.264-0.071-0.0710.0000.0000.0000.000
88A89GLU-1-0.806-0.90826.197-0.143-0.1430.0000.0000.0000.000
89A90VAL0-0.008-0.00822.763-0.008-0.0080.0000.0000.0000.000
90A91LYS10.9520.97924.6680.0460.0460.0000.0000.0000.000
91A92ALA00.0200.01727.1500.0040.0040.0000.0000.0000.000
92A93LEU0-0.018-0.01922.200-0.004-0.0040.0000.0000.0000.000
93A94LEU0-0.030-0.01520.343-0.004-0.0040.0000.0000.0000.000
94A95ASP-1-0.882-0.92523.654-0.044-0.0440.0000.0000.0000.000
95A96CYS0-0.138-0.06725.0990.0030.0030.0000.0000.0000.000
96A97GLY0-0.006-0.00323.362-0.002-0.0020.0000.0000.0000.000
97A98VAL0-0.069-0.02418.879-0.010-0.0100.0000.0000.0000.000
98A99LYS10.9220.97914.833-0.004-0.0040.0000.0000.0000.000
99A100ARG10.7910.87610.6230.3510.3510.0000.0000.0000.000
100A101VAL00.0250.01616.608-0.039-0.0390.0000.0000.0000.000
101A102VAL0-0.036-0.02214.774-0.004-0.0040.0000.0000.0000.000
102A103ILE00.0320.01817.4330.0170.0170.0000.0000.0000.000
103A104GLY00.0900.02218.630-0.031-0.0310.0000.0000.0000.000
104A105SER0-0.0100.00820.6030.0060.0060.0000.0000.0000.000
105A106MET00.005-0.00423.6590.0070.0070.0000.0000.0000.000
106A107ALA00.0360.02321.4590.0130.0130.0000.0000.0000.000
107A108ILE00.0260.01923.4870.0120.0120.0000.0000.0000.000
108A109LYS10.8530.93226.3260.1610.1610.0000.0000.0000.000
109A110ASP-1-0.808-0.91827.942-0.071-0.0710.0000.0000.0000.000
110A111ALA00.0410.02526.359-0.004-0.0040.0000.0000.0000.000
111A112THR0-0.045-0.01726.9810.0050.0050.0000.0000.0000.000
112A113LEU00.0740.04627.5920.0040.0040.0000.0000.0000.000
113A114CYS0-0.029-0.00123.192-0.007-0.0070.0000.0000.0000.000
114A115LEU0-0.018-0.00824.1790.0050.0050.0000.0000.0000.000
115A116GLU-1-0.906-0.94225.677-0.038-0.0380.0000.0000.0000.000
116A117ILE0-0.0080.00122.8160.0060.0060.0000.0000.0000.000
117A118LEU0-0.010-0.01319.0540.0060.0060.0000.0000.0000.000
118A119LYS10.8710.93222.7850.0040.0040.0000.0000.0000.000
119A120GLU-1-0.974-0.96825.365-0.028-0.0280.0000.0000.0000.000
120A121PHE00.010-0.00922.5950.0050.0050.0000.0000.0000.000
121A122GLY00.0200.02321.1090.0110.0110.0000.0000.0000.000
122A123SER0-0.001-0.01616.887-0.017-0.0170.0000.0000.0000.000
123A124GLU-1-0.892-0.95012.8530.1620.1620.0000.0000.0000.000
124A125ALA00.0150.00515.158-0.030-0.0300.0000.0000.0000.000
125A126ILE0-0.0070.00617.241-0.039-0.0390.0000.0000.0000.000
126A127VAL0-0.028-0.01112.546-0.002-0.0020.0000.0000.0000.000
127A128LEU0-0.007-0.00615.1350.0140.0140.0000.0000.0000.000
128A129ALA0-0.026-0.02014.877-0.064-0.0640.0000.0000.0000.000
129A130LEU0-0.046-0.02915.3960.0640.0640.0000.0000.0000.000
130A131ASP-1-0.857-0.92215.831-0.436-0.4360.0000.0000.0000.000
131A132THR0-0.072-0.04315.8970.0450.0450.0000.0000.0000.000
132A133ILE00.0340.00518.504-0.024-0.0240.0000.0000.0000.000
133A134LEU0-0.0210.00220.1340.0090.0090.0000.0000.0000.000
134A135LYS10.9130.96721.8200.1240.1240.0000.0000.0000.000
135A136GLU-1-0.915-0.95425.529-0.100-0.1000.0000.0000.0000.000
136A137ASP-1-0.881-0.95423.319-0.086-0.0860.0000.0000.0000.000
137A138TYR00.013-0.00317.155-0.021-0.0210.0000.0000.0000.000
138A139VAL0-0.018-0.00521.0720.0140.0140.0000.0000.0000.000
139A140VAL0-0.006-0.00820.494-0.028-0.0280.0000.0000.0000.000
140A141ALA0-0.021-0.00821.5770.0170.0170.0000.0000.0000.000
141A150ASP-1-0.892-0.94826.356-0.111-0.1110.0000.0000.0000.000
142A151LYS10.8260.91625.1730.0890.0890.0000.0000.0000.000
143A152LYS10.9800.98623.2450.0520.0520.0000.0000.0000.000
144A153LEU00.0400.01015.7730.0060.0060.0000.0000.0000.000
145A154MET00.0460.01617.889-0.018-0.0180.0000.0000.0000.000
146A155GLU-1-0.820-0.91219.512-0.051-0.0510.0000.0000.0000.000
147A156VAL0-0.042-0.01820.4190.0130.0130.0000.0000.0000.000
148A157LEU0-0.023-0.02215.0690.0000.0000.0000.0000.0000.000
149A158ASP-1-0.885-0.94818.7680.0010.0010.0000.0000.0000.000
150A159PHE0-0.064-0.02220.7830.0190.0190.0000.0000.0000.000
151A160TYR0-0.030-0.05819.5900.0150.0150.0000.0000.0000.000
152A161SER00.0140.01917.5540.0160.0160.0000.0000.0000.000
153A162ASN0-0.025-0.00418.8850.0400.0400.0000.0000.0000.000
154A163LYS10.8470.91821.7510.0070.0070.0000.0000.0000.000
155A164GLY00.0040.01019.573-0.004-0.0040.0000.0000.0000.000
156A165LEU0-0.0060.00415.8340.0100.0100.0000.0000.0000.000
157A166LYS10.8930.95310.900-0.346-0.3460.0000.0000.0000.000
158A167HIS0-0.0020.0029.787-0.139-0.1390.0000.0000.0000.000
159A168ILE00.0260.01310.9490.0490.0490.0000.0000.0000.000
160A169LEU0-0.024-0.00710.229-0.185-0.1850.0000.0000.0000.000
161A170CYS0-0.029-0.00210.6750.1450.1450.0000.0000.0000.000
162A171THR00.0400.02411.483-0.173-0.1730.0000.0000.0000.000
163A172ASP-1-0.792-0.88614.006-0.268-0.2680.0000.0000.0000.000
164A173ILE0-0.006-0.00215.966-0.013-0.0130.0000.0000.0000.000
165A174SER00.0040.00418.2260.0470.0470.0000.0000.0000.000
166A175LYS10.8050.90714.8970.3520.3520.0000.0000.0000.000
167A176ASP-1-0.806-0.90015.720-0.391-0.3910.0000.0000.0000.000
168A177GLY00.0440.03515.671-0.056-0.0560.0000.0000.0000.000
169A178THR0-0.022-0.02118.2670.0090.0090.0000.0000.0000.000
170A179MET0-0.058-0.03017.4870.0250.0250.0000.0000.0000.000
171A180GLN00.0250.00116.808-0.018-0.0180.0000.0000.0000.000
172A181GLY00.0420.05813.6390.0120.0120.0000.0000.0000.000
173A182VAL00.0100.0038.4010.0210.0210.0000.0000.0000.000
174A183ASN0-0.060-0.05211.6400.1050.1050.0000.0000.0000.000
175A184VAL00.0310.0039.251-0.035-0.0350.0000.0000.0000.000
176A185ARG10.9300.96310.7440.0540.0540.0000.0000.0000.000
177A186LEU00.0420.03012.8360.0340.0340.0000.0000.0000.000
178A187TYR00.019-0.0278.113-0.041-0.0410.0000.0000.0000.000
179A188LYS10.9300.9509.499-0.150-0.1500.0000.0000.0000.000
180A189LEU00.0470.02910.4180.0820.0820.0000.0000.0000.000
181A190ILE00.0040.01011.1840.0240.0240.0000.0000.0000.000
182A191HIS0-0.024-0.0157.674-0.005-0.0050.0000.0000.0000.000
183A192GLU-1-0.986-0.98310.2920.1780.1780.0000.0000.0000.000
184A193ILE0-0.014-0.00113.1980.0440.0440.0000.0000.0000.000
185A194PHE0-0.033-0.01813.3300.0250.0250.0000.0000.0000.000
186A195PRO00.0240.01311.146-0.052-0.0520.0000.0000.0000.000
187A196ASN0-0.044-0.02810.5720.1470.1470.0000.0000.0000.000
188A197ILE0-0.0250.00310.6720.0220.0220.0000.0000.0000.000
189A198CYS0-0.069-0.0297.6640.1130.1130.0000.0000.0000.000
190A199ILE00.0370.0136.787-0.092-0.0920.0000.0000.0000.000
191A200GLN00.0120.0095.581-0.987-0.9870.0000.0000.0000.000
192A201ALA00.0470.0145.8080.3680.3680.0000.0000.0000.000
193A202SER0-0.021-0.0177.586-0.092-0.0920.0000.0000.0000.000
194A203GLY00.0250.01810.5020.0960.0960.0000.0000.0000.000
195A204GLY0-0.016-0.02112.120-0.033-0.0330.0000.0000.0000.000
196A205VAL0-0.050-0.0208.7080.0250.0250.0000.0000.0000.000
197A206ALA0-0.009-0.00511.3340.0310.0310.0000.0000.0000.000
198A207SER0-0.022-0.02312.0790.0610.0610.0000.0000.0000.000
199A208LEU00.0950.0319.871-0.091-0.0910.0000.0000.0000.000
200A209LYS10.8970.9569.0210.1040.1040.0000.0000.0000.000
201A210ASP-1-0.791-0.8968.997-0.454-0.4540.0000.0000.0000.000
202A211LEU0-0.007-0.0115.047-0.076-0.0760.0000.0000.0000.000
203A212GLU-1-0.922-0.9584.536-0.0200.062-0.001-0.005-0.0760.000
204A213ASN0-0.038-0.0276.7750.5570.5570.0000.0000.0000.000
205A214LEU0-0.019-0.0093.766-0.0910.1120.004-0.036-0.1710.000
206A215LYS10.8850.9502.675-3.017-0.5651.082-1.442-2.0930.006
207A216GLY0-0.055-0.0212.064-6.735-7.0594.186-1.567-2.2950.025
208A217ILE0-0.046-0.0063.813-2.233-1.8350.003-0.069-0.3320.000
209A218CYS0-0.0040.0143.152-0.8120.4760.059-0.563-0.7840.000
210A219SER0-0.0070.0171.583-14.278-24.26922.666-8.425-4.250-0.062
211A220GLY00.003-0.0062.622-1.5580.4411.572-1.774-1.797-0.019
212A221VAL00.0130.0092.667-0.2430.0660.950-0.156-1.102-0.001
213A222ILE00.0180.0105.0280.2290.234-0.001-0.003-0.0010.000
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215A224GLY0-0.034-0.02510.1400.0760.0760.0000.0000.0000.000
216A225LYS10.9360.95213.8870.3600.3600.0000.0000.0000.000
217A226ALA00.0320.02412.4830.0400.0400.0000.0000.0000.000
218A227LEU00.0240.02110.9040.0250.0250.0000.0000.0000.000
219A228LEU0-0.061-0.03014.6910.0590.0590.0000.0000.0000.000
220A229ASP-1-0.814-0.91417.906-0.280-0.2800.0000.0000.0000.000
221A230GLY0-0.017-0.00218.0020.0280.0280.0000.0000.0000.000
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223A232PHE00.0200.0119.723-0.009-0.0090.0000.0000.0000.000
224A233SER00.0100.01514.262-0.030-0.0300.0000.0000.0000.000
225A234VAL00.0340.00110.724-0.091-0.0910.0000.0000.0000.000
226A235GLU-1-0.894-0.95810.612-0.534-0.5340.0000.0000.0000.000
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228A237GLY00.0230.0038.381-0.013-0.0130.0000.0000.0000.000
229A238ILE0-0.011-0.0096.945-0.344-0.3440.0000.0000.0000.000
230A239ARG10.9250.9647.7640.2740.2740.0000.0000.0000.000
231A240CYS0-0.028-0.0067.3070.1090.1090.0000.0000.0000.000
232A241LEU0-0.0020.0052.059-0.282-0.3133.183-0.675-2.476-0.002
233A242ALA0-0.0260.0124.110-0.554-0.4230.000-0.056-0.0750.000
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