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: 6YLJZ

Calculation Name: 2ZG6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZG6

Chain ID: A

ChEMBL ID:

UniProt ID: Q96X90

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2493360.086053
FMO2-HF: Nuclear repulsion 2410590.64656
FMO2-HF: Total energy -82769.439493
FMO2-MP2: Total energy -83015.136031


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-18.802-9.4617.1-5.723-10.718-0.054
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / 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].
3A3TYR0-0.102-0.0943.229-0.9020.8760.033-0.708-1.1030.003
4A4LYS10.9250.9612.973-1.2420.4350.257-0.721-1.213-0.007
5A5ALA00.0080.0134.6300.1970.332-0.001-0.005-0.1280.000
6A6VAL00.0190.0106.855-0.174-0.1740.0000.0000.0000.000
7A7LEU0-0.075-0.0389.6030.1210.1210.0000.0000.0000.000
8A8VAL00.0170.01012.659-0.040-0.0400.0000.0000.0000.000
9A9ASP-1-0.727-0.83915.192-0.279-0.2790.0000.0000.0000.000
10A10PHE00.028-0.00518.484-0.021-0.0210.0000.0000.0000.000
11A11GLY00.0490.01821.119-0.013-0.0130.0000.0000.0000.000
12A12ASN0-0.071-0.03922.937-0.005-0.0050.0000.0000.0000.000
13A13THR0-0.034-0.00317.216-0.024-0.0240.0000.0000.0000.000
14A14LEU00.0160.01215.457-0.024-0.0240.0000.0000.0000.000
15A15VAL0-0.0030.00319.4330.0050.0050.0000.0000.0000.000
16A16GLY00.0170.02523.1710.0010.0010.0000.0000.0000.000
17A17PHE00.009-0.02426.2050.0060.0060.0000.0000.0000.000
18A18LYS10.8320.95029.8150.1520.1520.0000.0000.0000.000
19A19PRO00.0440.02933.0260.0020.0020.0000.0000.0000.000
20A20VAL00.0210.00236.608-0.004-0.0040.0000.0000.0000.000
21A21PHE0-0.011-0.00238.037-0.001-0.0010.0000.0000.0000.000
22A22TYR00.014-0.00736.5450.0020.0020.0000.0000.0000.000
23A23GLU-1-0.866-0.93138.623-0.108-0.1080.0000.0000.0000.000
24A24LYS10.9540.98441.0520.0810.0810.0000.0000.0000.000
25A25VAL00.025-0.00339.2810.0030.0030.0000.0000.0000.000
26A26TYR0-0.064-0.02639.4880.0030.0030.0000.0000.0000.000
27A27GLN0-0.051-0.04441.2480.0000.0000.0000.0000.0000.000
28A28VAL0-0.0090.00244.6790.0040.0040.0000.0000.0000.000
29A29LEU0-0.003-0.00139.8530.0030.0030.0000.0000.0000.000
30A30LYS10.8560.92344.0860.0910.0910.0000.0000.0000.000
31A31ASP-1-0.883-0.92945.422-0.070-0.0700.0000.0000.0000.000
32A32ASN0-0.183-0.11247.2020.0060.0060.0000.0000.0000.000
33A33GLY00.0190.01347.7200.0010.0010.0000.0000.0000.000
34A34TYR0-0.032-0.02342.260-0.001-0.0010.0000.0000.0000.000
35A35ASP-1-0.798-0.87542.642-0.094-0.0940.0000.0000.0000.000
36A36LEU0-0.033-0.00637.106-0.003-0.0030.0000.0000.0000.000
37A37ASP-1-0.756-0.90433.923-0.149-0.1490.0000.0000.0000.000
38A38LEU00.0550.01234.403-0.003-0.0030.0000.0000.0000.000
39A39ARG10.8550.94726.9160.2010.2010.0000.0000.0000.000
40A40LYS10.8320.92130.6980.1550.1550.0000.0000.0000.000
41A41VAL00.0170.01633.2720.0000.0000.0000.0000.0000.000
42A42PHE00.019-0.01429.8770.0010.0010.0000.0000.0000.000
43A43ARG10.9000.98128.1540.1510.1510.0000.0000.0000.000
44A44ALA00.018-0.00129.861-0.004-0.0040.0000.0000.0000.000
45A45TYR00.0170.00532.5780.0010.0010.0000.0000.0000.000
46A46ALA0-0.0040.00027.6800.0030.0030.0000.0000.0000.000
47A47LYS10.7900.88425.4510.2140.2140.0000.0000.0000.000
48A48ALA00.0670.03530.4700.0050.0050.0000.0000.0000.000
49A49MET0-0.064-0.02430.8680.0070.0070.0000.0000.0000.000
50A50GLY0-0.090-0.03930.597-0.003-0.0030.0000.0000.0000.000
51A51MET0-0.054-0.01131.3340.0020.0020.0000.0000.0000.000
52A52ILE00.0130.03334.3210.0080.0080.0000.0000.0000.000
53A53ASN0-0.087-0.03535.8950.0020.0020.0000.0000.0000.000
54A54TYR00.031-0.01232.177-0.002-0.0020.0000.0000.0000.000
55A55PRO0-0.070-0.00936.9000.0050.0050.0000.0000.0000.000
56A56ASP-1-0.930-0.97838.517-0.070-0.0700.0000.0000.0000.000
57A57GLU-1-0.979-0.99337.403-0.076-0.0760.0000.0000.0000.000
58A58ASP-1-0.877-0.97132.703-0.123-0.1230.0000.0000.0000.000
59A59GLY00.013-0.00634.288-0.005-0.0050.0000.0000.0000.000
60A60LEU0-0.057-0.02535.294-0.001-0.0010.0000.0000.0000.000
61A61GLU-1-0.910-0.95933.217-0.136-0.1360.0000.0000.0000.000
62A62HIS0-0.035-0.02535.8310.0050.0050.0000.0000.0000.000
63A63VAL00.0260.03434.9940.0040.0040.0000.0000.0000.000
64A64ASP-1-0.770-0.88737.828-0.079-0.0790.0000.0000.0000.000
65A65PRO0-0.043-0.03339.759-0.003-0.0030.0000.0000.0000.000
66A66LYS10.9310.95641.7100.0670.0670.0000.0000.0000.000
67A67ASP-1-0.829-0.91837.121-0.097-0.0970.0000.0000.0000.000
68A68PHE0-0.053-0.03235.657-0.005-0.0050.0000.0000.0000.000
69A69LEU00.001-0.00837.694-0.003-0.0030.0000.0000.0000.000
70A70TYR00.0120.01635.8450.0020.0020.0000.0000.0000.000
71A71ILE0-0.036-0.00632.635-0.003-0.0030.0000.0000.0000.000
72A72LEU0-0.067-0.03835.244-0.006-0.0060.0000.0000.0000.000
73A73GLY00.0010.01737.2600.0010.0010.0000.0000.0000.000
74A74ILE0-0.053-0.02339.3780.0050.0050.0000.0000.0000.000
75A75TYR0-0.020-0.01842.4960.0000.0000.0000.0000.0000.000
76A76PRO0-0.012-0.01544.2520.0010.0010.0000.0000.0000.000
77A77SER0-0.031-0.01746.6150.0030.0030.0000.0000.0000.000
78A78GLU-1-0.849-0.93649.472-0.059-0.0590.0000.0000.0000.000
79A79ARG10.8370.91851.3880.0630.0630.0000.0000.0000.000
80A80LEU00.0660.03945.118-0.001-0.0010.0000.0000.0000.000
81A81VAL00.0070.00045.826-0.003-0.0030.0000.0000.0000.000
82A82LYS10.7570.88047.4630.0580.0580.0000.0000.0000.000
83A83GLU-1-0.758-0.87948.834-0.067-0.0670.0000.0000.0000.000
84A84LEU00.0020.00142.240-0.002-0.0020.0000.0000.0000.000
85A85LYS10.9260.95844.7460.0650.0650.0000.0000.0000.000
86A86GLU-1-0.841-0.90146.688-0.063-0.0630.0000.0000.0000.000
87A87ALA0-0.083-0.03544.2700.0000.0000.0000.0000.0000.000
88A88ASP-1-0.880-0.94743.751-0.092-0.0920.0000.0000.0000.000
89A89ILE0-0.022-0.00939.026-0.004-0.0040.0000.0000.0000.000
90A90ARG10.8690.92939.2750.0820.0820.0000.0000.0000.000
91A91ASP-1-0.841-0.90939.029-0.100-0.1000.0000.0000.0000.000
92A92GLY00.0170.02235.159-0.002-0.0020.0000.0000.0000.000
93A93GLU-1-0.873-0.94832.915-0.144-0.1440.0000.0000.0000.000
94A94ALA0-0.029-0.02027.670-0.007-0.0070.0000.0000.0000.000
95A95PHE0-0.022-0.01926.5080.0050.0050.0000.0000.0000.000
96A96LEU0-0.007-0.00320.552-0.010-0.0100.0000.0000.0000.000
97A97TYR0-0.034-0.03520.5080.0130.0130.0000.0000.0000.000
98A98ASP-1-0.874-0.95121.045-0.298-0.2980.0000.0000.0000.000
99A99ASP-1-0.764-0.84516.872-0.473-0.4730.0000.0000.0000.000
100A100THR0-0.038-0.03316.044-0.080-0.0800.0000.0000.0000.000
101A101LEU00.0280.00515.271-0.060-0.0600.0000.0000.0000.000
102A102GLU-1-0.905-0.94714.497-0.548-0.5480.0000.0000.0000.000
103A103PHE00.003-0.00110.640-0.121-0.1210.0000.0000.0000.000
104A104LEU0-0.035-0.01410.291-0.184-0.1840.0000.0000.0000.000
105A105GLU-1-0.860-0.92010.176-0.606-0.6060.0000.0000.0000.000
106A106GLY00.0280.0439.144-0.053-0.0530.0000.0000.0000.000
107A107LEU00.0410.0175.762-0.431-0.4310.0000.0000.0000.000
108A108LYS10.8810.9405.318-0.105-0.1050.0000.0000.0000.000
109A109SER0-0.102-0.0637.3820.0970.0970.0000.0000.0000.000
110A110ASN0-0.052-0.0413.5250.1940.4280.006-0.051-0.1890.000
111A111GLY0-0.021-0.0022.401-4.592-3.9472.079-1.061-1.664-0.015
112A112TYR0-0.0150.0122.704-2.0030.2482.310-1.037-3.523-0.011
113A113LYS10.8380.9085.019-0.0290.013-0.001-0.004-0.0370.000
114A114LEU0-0.005-0.0038.445-0.142-0.1420.0000.0000.0000.000
115A115ALA0-0.027-0.02411.0060.0990.0990.0000.0000.0000.000
116A116LEU00.0070.01614.453-0.045-0.0450.0000.0000.0000.000
117A117VAL0-0.022-0.00917.2110.0460.0460.0000.0000.0000.000
118A118SER0-0.019-0.02119.682-0.007-0.0070.0000.0000.0000.000
119A119ASN00.0150.01023.1050.0130.0130.0000.0000.0000.000
120A120ALA00.0470.02926.9280.0030.0030.0000.0000.0000.000
121A121SER0-0.012-0.01027.248-0.002-0.0020.0000.0000.0000.000
122A122PRO00.0220.03528.145-0.010-0.0100.0000.0000.0000.000
123A123ARG11.0371.02829.0720.1480.1480.0000.0000.0000.000
124A124VAL0-0.048-0.02523.886-0.010-0.0100.0000.0000.0000.000
125A125LYS10.9160.94925.3210.1200.1200.0000.0000.0000.000
126A126THR00.0380.02926.325-0.008-0.0080.0000.0000.0000.000
127A127LEU0-0.039-0.00925.855-0.006-0.0060.0000.0000.0000.000
128A128LEU0-0.003-0.01520.739-0.016-0.0160.0000.0000.0000.000
129A129GLU-1-0.797-0.87323.088-0.175-0.1750.0000.0000.0000.000
130A130LYS10.9040.96625.6000.1650.1650.0000.0000.0000.000
131A131PHE0-0.045-0.04122.6980.0020.0020.0000.0000.0000.000
132A132ASP-1-0.820-0.88021.685-0.269-0.2690.0000.0000.0000.000
133A133LEU00.007-0.00818.170-0.030-0.0300.0000.0000.0000.000
134A134LYS10.8050.86617.6720.1470.1470.0000.0000.0000.000
135A135LYS10.8480.92916.8330.3040.3040.0000.0000.0000.000
136A136TYR0-0.057-0.05612.9550.0170.0170.0000.0000.0000.000
137A137PHE0-0.0010.00512.876-0.041-0.0410.0000.0000.0000.000
138A138ASP-1-0.791-0.86811.432-0.142-0.1420.0000.0000.0000.000
139A139ALA0-0.064-0.04214.6040.0570.0570.0000.0000.0000.000
140A140LEU00.0070.01616.769-0.038-0.0380.0000.0000.0000.000
141A141ALA00.002-0.01119.4590.0250.0250.0000.0000.0000.000
142A153PRO00.0820.02624.9320.0050.0050.0000.0000.0000.000
143A154LYS10.9570.97324.4300.0580.0580.0000.0000.0000.000
144A155ILE0-0.0030.00122.3580.0060.0060.0000.0000.0000.000
145A156PHE00.0460.02717.0350.0070.0070.0000.0000.0000.000
146A157GLY00.0650.02518.490-0.014-0.0140.0000.0000.0000.000
147A158PHE0-0.038-0.00518.5980.0130.0130.0000.0000.0000.000
148A159ALA00.0160.00017.3300.0100.0100.0000.0000.0000.000
149A160LEU00.0090.01512.6250.0020.0020.0000.0000.0000.000
150A161ALA0-0.024-0.01213.4950.0060.0060.0000.0000.0000.000
151A162LYS10.8420.91414.3010.1210.1210.0000.0000.0000.000
152A163VAL0-0.047-0.02211.0370.0430.0430.0000.0000.0000.000
153A164GLY00.0200.0299.6880.0590.0590.0000.0000.0000.000
154A165TYR0-0.017-0.0099.041-0.067-0.0670.0000.0000.0000.000
155A166PRO00.014-0.0266.9520.1230.1230.0000.0000.0000.000
156A167ALA0-0.0270.0067.128-0.135-0.1350.0000.0000.0000.000
157A168VAL00.0240.0278.0440.0630.0630.0000.0000.0000.000
158A169HIS10.7620.85110.6440.3610.3610.0000.0000.0000.000
159A170VAL00.0240.01012.0990.0140.0140.0000.0000.0000.000
160A171GLY00.0590.00414.8720.0240.0240.0000.0000.0000.000
161A172ASP-1-0.789-0.86918.595-0.251-0.2510.0000.0000.0000.000
162A173ILE0-0.059-0.04221.7800.0210.0210.0000.0000.0000.000
163A174TYR0-0.016-0.00420.4520.0190.0190.0000.0000.0000.000
164A175GLU-1-0.966-0.96821.062-0.167-0.1670.0000.0000.0000.000
165A176LEU00.011-0.00118.809-0.024-0.0240.0000.0000.0000.000
166A177ASP-1-0.821-0.88217.048-0.267-0.2670.0000.0000.0000.000
167A178TYR00.009-0.01219.1890.0130.0130.0000.0000.0000.000
168A179ILE0-0.037-0.00617.7420.0230.0230.0000.0000.0000.000
169A180GLY00.028-0.00117.602-0.019-0.0190.0000.0000.0000.000
170A181ALA0-0.030-0.00418.3870.0090.0090.0000.0000.0000.000
171A182LYS10.9280.94718.679-0.121-0.1210.0000.0000.0000.000
172A183ARG10.9880.98714.851-0.093-0.0930.0000.0000.0000.000
173A184SER00.0560.04416.4250.0050.0050.0000.0000.0000.000
174A185TYR0-0.042-0.03013.1730.0170.0170.0000.0000.0000.000
175A186VAL00.013-0.00611.924-0.058-0.0580.0000.0000.0000.000
176A187ASP-1-0.828-0.85511.500-0.296-0.2960.0000.0000.0000.000
177A188PRO00.0090.00513.081-0.087-0.0870.0000.0000.0000.000
178A189ILE00.0040.00210.932-0.017-0.0170.0000.0000.0000.000
179A190LEU0-0.0080.00515.4080.0130.0130.0000.0000.0000.000
180A191LEU0-0.021-0.01317.106-0.015-0.0150.0000.0000.0000.000
181A192ASP-1-0.751-0.87619.012-0.203-0.2030.0000.0000.0000.000
182A193ARG10.8010.87618.7130.4100.4100.0000.0000.0000.000
183A194TYR0-0.006-0.01123.6340.0080.0080.0000.0000.0000.000
184A195ASP-1-0.928-0.95526.066-0.170-0.1700.0000.0000.0000.000
185A196PHE0-0.019-0.04127.0730.0190.0190.0000.0000.0000.000
186A197TYR00.0100.00824.7420.0180.0180.0000.0000.0000.000
187A198PRO00.0150.00226.164-0.013-0.0130.0000.0000.0000.000
188A199ASP-1-0.917-0.95827.913-0.126-0.1260.0000.0000.0000.000
189A200VAL0-0.0220.00222.3470.0050.0050.0000.0000.0000.000
190A201ARG10.9390.95521.6820.1550.1550.0000.0000.0000.000
191A202ASP-1-0.862-0.91616.714-0.346-0.3460.0000.0000.0000.000
192A203ARG10.7770.91117.7090.1790.1790.0000.0000.0000.000
193A204VAL00.0010.00314.887-0.006-0.0060.0000.0000.0000.000
194A205LYS10.8790.90118.3030.3370.3370.0000.0000.0000.000
195A206ASN0-0.073-0.04717.967-0.019-0.0190.0000.0000.0000.000
196A207LEU00.0420.00014.054-0.025-0.0250.0000.0000.0000.000
197A208ARG10.9761.00413.3130.3310.3310.0000.0000.0000.000
198A209GLU-1-0.742-0.84613.384-0.457-0.4570.0000.0000.0000.000
199A210ALA0-0.0100.00413.114-0.047-0.0470.0000.0000.0000.000
200A211LEU00.0070.0047.346-0.082-0.0820.0000.0000.0000.000
201A212GLN00.0080.0038.688-0.176-0.1760.0000.0000.0000.000
202A213LYS10.7920.88310.1160.4450.4450.0000.0000.0000.000
203A214ILE0-0.006-0.0165.4010.0430.0430.0000.0000.0000.000
204A215GLU-1-0.962-0.9885.307-2.341-2.3410.0000.0000.0000.000
205A216GLU-1-0.892-0.9256.528-0.278-0.2780.0000.0000.0000.000
206A217MET0-0.042-0.0218.5260.2090.2090.0000.0000.0000.000
207A218ASN0-0.052-0.0242.529-4.469-1.8902.417-2.136-2.861-0.024