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: 2N7ZR

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2491907.3544
FMO2-HF: Nuclear repulsion 2409139.611907
FMO2-HF: Total energy -82767.742493
FMO2-MP2: Total energy -83013.484513


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.
-18.202-7.5364.68-5.522-9.824-0.051
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 : -0.016 / q_NPA : -0.011
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].
3A3TYR0-0.091-0.0903.204-1.0080.7680.037-0.663-1.1510.003
4A4LYS10.9410.9822.864-1.4750.2810.318-0.798-1.276-0.009
5A5ALA00.0070.0084.6410.3730.505-0.001-0.005-0.1250.000
6A6VAL00.0310.0187.458-0.152-0.1520.0000.0000.0000.000
7A7LEU0-0.080-0.04710.0270.1020.1020.0000.0000.0000.000
8A8VAL00.0260.01913.084-0.031-0.0310.0000.0000.0000.000
9A9ASP-1-0.701-0.82015.652-0.253-0.2530.0000.0000.0000.000
10A10PHE00.036-0.00718.880-0.016-0.0160.0000.0000.0000.000
11A11GLY00.0360.01221.516-0.009-0.0090.0000.0000.0000.000
12A12ASN0-0.043-0.02423.265-0.006-0.0060.0000.0000.0000.000
13A13THR0-0.0200.00217.538-0.020-0.0200.0000.0000.0000.000
14A14LEU0-0.0050.00215.754-0.020-0.0200.0000.0000.0000.000
15A15VAL0-0.0080.00019.6790.0050.0050.0000.0000.0000.000
16A16GLY00.0270.02523.4140.0010.0010.0000.0000.0000.000
17A17PHE00.001-0.02426.4510.0030.0030.0000.0000.0000.000
18A18LYS10.8530.95030.0530.1400.1400.0000.0000.0000.000
19A19PRO00.0470.03433.2250.0010.0010.0000.0000.0000.000
20A20VAL00.0480.01636.779-0.003-0.0030.0000.0000.0000.000
21A21PHE0-0.005-0.00138.2210.0000.0000.0000.0000.0000.000
22A22TYR0-0.001-0.01836.6820.0020.0020.0000.0000.0000.000
23A23GLU-1-0.905-0.94838.757-0.091-0.0910.0000.0000.0000.000
24A24LYS10.9690.99241.1350.0720.0720.0000.0000.0000.000
25A25VAL00.018-0.00439.3880.0030.0030.0000.0000.0000.000
26A26TYR0-0.053-0.01939.5100.0020.0020.0000.0000.0000.000
27A27GLN0-0.068-0.05541.3610.0000.0000.0000.0000.0000.000
28A28VAL00.0070.01744.8420.0030.0030.0000.0000.0000.000
29A29LEU0-0.025-0.00740.0690.0030.0030.0000.0000.0000.000
30A30LYS11.0001.01544.1370.0750.0750.0000.0000.0000.000
31A31ASP-1-0.875-0.91945.461-0.061-0.0610.0000.0000.0000.000
32A32ASN0-0.226-0.13847.3700.0060.0060.0000.0000.0000.000
33A33GLY00.0120.00647.6850.0010.0010.0000.0000.0000.000
34A34TYR0-0.035-0.02542.196-0.001-0.0010.0000.0000.0000.000
35A35ASP-1-0.894-0.95442.458-0.082-0.0820.0000.0000.0000.000
36A36LEU0-0.026-0.00537.051-0.003-0.0030.0000.0000.0000.000
37A37ASP-1-0.805-0.91234.373-0.124-0.1240.0000.0000.0000.000
38A38LEU00.067-0.00534.305-0.003-0.0030.0000.0000.0000.000
39A39ARG10.8800.96126.6020.1710.1710.0000.0000.0000.000
40A40LYS10.8780.95230.7860.1290.1290.0000.0000.0000.000
41A41VAL00.0270.02333.3000.0000.0000.0000.0000.0000.000
42A42PHE00.022-0.01430.1340.0000.0000.0000.0000.0000.000
43A43ARG10.9260.98828.0980.1360.1360.0000.0000.0000.000
44A44ALA00.0230.01030.066-0.005-0.0050.0000.0000.0000.000
45A45TYR00.004-0.01132.9550.0000.0000.0000.0000.0000.000
46A46ALA0-0.0010.00028.0280.0010.0010.0000.0000.0000.000
47A47LYS10.7810.89026.0340.1840.1840.0000.0000.0000.000
48A48ALA00.0770.03630.8220.0040.0040.0000.0000.0000.000
49A49MET0-0.053-0.02131.1990.0060.0060.0000.0000.0000.000
50A50GLY0-0.110-0.04831.043-0.004-0.0040.0000.0000.0000.000
51A51MET0-0.050-0.01131.7810.0010.0010.0000.0000.0000.000
52A52ILE00.0130.03334.7430.0070.0070.0000.0000.0000.000
53A53ASN0-0.086-0.03336.3820.0010.0010.0000.0000.0000.000
54A54TYR00.037-0.01332.741-0.002-0.0020.0000.0000.0000.000
55A55PRO0-0.070-0.01137.3090.0040.0040.0000.0000.0000.000
56A56ASP-1-0.935-0.97639.006-0.069-0.0690.0000.0000.0000.000
57A57GLU-1-0.964-0.99138.020-0.076-0.0760.0000.0000.0000.000
58A58ASP-1-0.870-0.96333.209-0.116-0.1160.0000.0000.0000.000
59A59GLY0-0.009-0.01734.802-0.004-0.0040.0000.0000.0000.000
60A60LEU0-0.069-0.02135.7860.0000.0000.0000.0000.0000.000
61A61GLU-1-0.913-0.97034.128-0.120-0.1200.0000.0000.0000.000
62A62HIS00.001-0.01036.2300.0050.0050.0000.0000.0000.000
63A63VAL00.0190.03035.2640.0030.0030.0000.0000.0000.000
64A64ASP-1-0.776-0.89338.193-0.073-0.0730.0000.0000.0000.000
65A65PRO0-0.034-0.03140.116-0.003-0.0030.0000.0000.0000.000
66A66LYS10.9280.96142.0300.0620.0620.0000.0000.0000.000
67A67ASP-1-0.820-0.91737.531-0.088-0.0880.0000.0000.0000.000
68A68PHE0-0.040-0.03135.999-0.004-0.0040.0000.0000.0000.000
69A69LEU0-0.008-0.00737.950-0.002-0.0020.0000.0000.0000.000
70A70TYR00.0000.01636.0150.0020.0020.0000.0000.0000.000
71A71ILE0-0.050-0.02132.901-0.002-0.0020.0000.0000.0000.000
72A72LEU0-0.059-0.04035.324-0.005-0.0050.0000.0000.0000.000
73A73GLY0-0.0150.01637.3210.0010.0010.0000.0000.0000.000
74A74ILE0-0.050-0.02139.4500.0040.0040.0000.0000.0000.000
75A75TYR0-0.007-0.00642.559-0.001-0.0010.0000.0000.0000.000
76A76PRO00.006-0.00444.7160.0000.0000.0000.0000.0000.000
77A77SER00.0050.00846.8380.0030.0030.0000.0000.0000.000
78A78GLU-1-0.928-0.97149.761-0.052-0.0520.0000.0000.0000.000
79A79ARG10.8750.94151.6880.0550.0550.0000.0000.0000.000
80A80LEU00.0840.03145.046-0.001-0.0010.0000.0000.0000.000
81A81VAL00.0210.01146.033-0.002-0.0020.0000.0000.0000.000
82A82LYS10.8750.95047.7580.0490.0490.0000.0000.0000.000
83A83GLU-1-0.773-0.89748.882-0.060-0.0600.0000.0000.0000.000
84A84LEU0-0.003-0.00142.917-0.002-0.0020.0000.0000.0000.000
85A85LYS10.9180.95645.0020.0590.0590.0000.0000.0000.000
86A86GLU-1-0.959-0.97246.973-0.057-0.0570.0000.0000.0000.000
87A87ALA0-0.094-0.04244.4700.0000.0000.0000.0000.0000.000
88A88ASP-1-0.866-0.93943.812-0.083-0.0830.0000.0000.0000.000
89A89ILE0-0.028-0.00439.224-0.004-0.0040.0000.0000.0000.000
90A90ARG10.9100.95639.5600.0750.0750.0000.0000.0000.000
91A91ASP-1-0.883-0.91839.389-0.090-0.0900.0000.0000.0000.000
92A92GLY0-0.020-0.00635.440-0.002-0.0020.0000.0000.0000.000
93A93GLU-1-0.877-0.93932.831-0.123-0.1230.0000.0000.0000.000
94A94ALA0-0.050-0.03727.871-0.006-0.0060.0000.0000.0000.000
95A95PHE0-0.034-0.02326.5600.0050.0050.0000.0000.0000.000
96A96LEU00.0050.00120.681-0.008-0.0080.0000.0000.0000.000
97A97TYR0-0.049-0.05420.5610.0130.0130.0000.0000.0000.000
98A98ASP-1-0.847-0.93621.086-0.263-0.2630.0000.0000.0000.000
99A99ASP-1-0.787-0.87916.751-0.407-0.4070.0000.0000.0000.000
100A100THR0-0.047-0.03716.018-0.067-0.0670.0000.0000.0000.000
101A101LEU00.0260.00415.370-0.051-0.0510.0000.0000.0000.000
102A102GLU-1-0.892-0.94514.527-0.461-0.4610.0000.0000.0000.000
103A103PHE0-0.007-0.00110.880-0.108-0.1080.0000.0000.0000.000
104A104LEU0-0.034-0.01610.348-0.152-0.1520.0000.0000.0000.000
105A105GLU-1-0.946-0.98210.354-0.564-0.5640.0000.0000.0000.000
106A106GLY00.0290.0219.023-0.046-0.0460.0000.0000.0000.000
107A107LEU00.0320.0125.822-0.391-0.3910.0000.0000.0000.000
108A108LYS10.9140.9685.5510.0440.0440.0000.0000.0000.000
109A109SER0-0.115-0.0537.5950.1010.1010.0000.0000.0000.000
110A110ASN0-0.016-0.0143.0540.1220.4520.032-0.077-0.2860.000
111A111GLY0-0.023-0.0072.387-5.069-3.8911.786-1.209-1.755-0.018
112A112TYR0-0.0130.0102.606-1.4170.8881.684-0.994-2.994-0.010
113A113LYS10.9230.9605.652-0.011-0.0110.0000.0000.0000.000
114A114LEU0-0.012-0.0088.552-0.115-0.1150.0000.0000.0000.000
115A115ALA0-0.030-0.02211.6010.0750.0750.0000.0000.0000.000
116A116LEU00.0020.01015.071-0.032-0.0320.0000.0000.0000.000
117A117VAL0-0.022-0.00717.4120.0350.0350.0000.0000.0000.000
118A118SER0-0.017-0.02020.131-0.002-0.0020.0000.0000.0000.000
119A119ASN00.0250.01523.6410.0110.0110.0000.0000.0000.000
120A120ALA00.0280.01727.4710.0020.0020.0000.0000.0000.000
121A121SER0-0.017-0.01227.675-0.001-0.0010.0000.0000.0000.000
122A122PRO00.0460.04928.657-0.009-0.0090.0000.0000.0000.000
123A123ARG11.0851.05028.4720.1400.1400.0000.0000.0000.000
124A124VAL0-0.053-0.02924.354-0.009-0.0090.0000.0000.0000.000
125A125LYS10.9240.95125.7350.1260.1260.0000.0000.0000.000
126A126THR00.0350.03226.747-0.007-0.0070.0000.0000.0000.000
127A127LEU0-0.047-0.01726.233-0.004-0.0040.0000.0000.0000.000
128A128LEU0-0.023-0.02521.110-0.013-0.0130.0000.0000.0000.000
129A129GLU-1-0.904-0.94523.424-0.161-0.1610.0000.0000.0000.000
130A130LYS10.9110.96025.8880.1470.1470.0000.0000.0000.000
131A131PHE0-0.051-0.03922.9300.0030.0030.0000.0000.0000.000
132A132ASP-1-0.870-0.92322.026-0.241-0.2410.0000.0000.0000.000
133A133LEU0-0.013-0.02618.220-0.027-0.0270.0000.0000.0000.000
134A134LYS10.9090.94918.0330.1540.1540.0000.0000.0000.000
135A135LYS10.9240.97616.9950.2740.2740.0000.0000.0000.000
136A136TYR0-0.037-0.02313.2680.0130.0130.0000.0000.0000.000
137A137PHE0-0.0020.00913.327-0.031-0.0310.0000.0000.0000.000
138A138ASP-1-0.828-0.90812.098-0.222-0.2220.0000.0000.0000.000
139A139ALA0-0.113-0.07115.2090.0420.0420.0000.0000.0000.000
140A140LEU00.0020.01217.382-0.028-0.0280.0000.0000.0000.000
141A141ALA0-0.003-0.01519.4990.0220.0220.0000.0000.0000.000
142A153PRO00.1060.04224.7900.0050.0050.0000.0000.0000.000
143A154LYS10.9480.96624.4080.0740.0740.0000.0000.0000.000
144A155ILE0-0.017-0.00222.2060.0020.0020.0000.0000.0000.000
145A156PHE00.0620.03016.8670.0020.0020.0000.0000.0000.000
146A157GLY00.0620.02218.469-0.018-0.0180.0000.0000.0000.000
147A158PHE0-0.038-0.00618.6270.0040.0040.0000.0000.0000.000
148A159ALA00.010-0.00317.2110.0020.0020.0000.0000.0000.000
149A160LEU00.0060.01412.667-0.007-0.0070.0000.0000.0000.000
150A161ALA0-0.018-0.00613.523-0.014-0.0140.0000.0000.0000.000
151A162LYS10.9030.95514.3710.1480.1480.0000.0000.0000.000
152A163VAL0-0.050-0.02611.0630.0280.0280.0000.0000.0000.000
153A164GLY00.0010.0179.7130.0040.0040.0000.0000.0000.000
154A165TYR0-0.021-0.0069.069-0.039-0.0390.0000.0000.0000.000
155A166PRO0-0.002-0.0426.9330.0890.0890.0000.0000.0000.000
156A167ALA0-0.0300.0037.131-0.214-0.2140.0000.0000.0000.000
157A168VAL00.0310.0337.9300.0760.0760.0000.0000.0000.000
158A169HIS10.7420.83210.5160.3450.3450.0000.0000.0000.000
159A170VAL00.0220.01012.3240.0170.0170.0000.0000.0000.000
160A171GLY00.030-0.00315.0100.0180.0180.0000.0000.0000.000
161A172ASP-1-0.810-0.88418.759-0.233-0.2330.0000.0000.0000.000
162A173ILE0-0.074-0.05621.8660.0190.0190.0000.0000.0000.000
163A174TYR0-0.017-0.00320.4230.0170.0170.0000.0000.0000.000
164A175GLU-1-0.954-0.96421.094-0.157-0.1570.0000.0000.0000.000
165A176LEU00.0210.00318.872-0.020-0.0200.0000.0000.0000.000
166A177ASP-1-0.817-0.88217.356-0.252-0.2520.0000.0000.0000.000
167A178TYR00.009-0.01619.1540.0090.0090.0000.0000.0000.000
168A179ILE0-0.040-0.00617.7490.0210.0210.0000.0000.0000.000
169A180GLY00.019-0.00217.626-0.022-0.0220.0000.0000.0000.000
170A181ALA0-0.023-0.00118.4730.0130.0130.0000.0000.0000.000
171A182LYS10.9190.94318.739-0.084-0.0840.0000.0000.0000.000
172A183ARG10.9900.98614.612-0.036-0.0360.0000.0000.0000.000
173A184SER00.0460.04216.278-0.004-0.0040.0000.0000.0000.000
174A185TYR0-0.040-0.03113.1790.0150.0150.0000.0000.0000.000
175A186VAL00.008-0.00411.924-0.076-0.0760.0000.0000.0000.000
176A187ASP-1-0.834-0.86311.416-0.255-0.2550.0000.0000.0000.000
177A188PRO00.0090.00312.964-0.079-0.0790.0000.0000.0000.000
178A189ILE00.0010.00410.953-0.008-0.0080.0000.0000.0000.000
179A190LEU0-0.0030.00715.4670.0090.0090.0000.0000.0000.000
180A191LEU0-0.031-0.01617.184-0.010-0.0100.0000.0000.0000.000
181A192ASP-1-0.754-0.87919.002-0.174-0.1740.0000.0000.0000.000
182A193ARG10.8120.89818.6770.3520.3520.0000.0000.0000.000
183A194TYR0-0.028-0.01523.5730.0070.0070.0000.0000.0000.000
184A195ASP-1-0.951-0.97425.977-0.139-0.1390.0000.0000.0000.000
185A196PHE0-0.028-0.03727.0100.0160.0160.0000.0000.0000.000
186A197TYR00.0110.00725.0520.0140.0140.0000.0000.0000.000
187A198PRO00.0100.00526.098-0.010-0.0100.0000.0000.0000.000
188A199ASP-1-0.914-0.95427.804-0.099-0.0990.0000.0000.0000.000
189A200VAL0-0.0190.00522.2180.0050.0050.0000.0000.0000.000
190A201ARG10.9480.95121.7020.1070.1070.0000.0000.0000.000
191A202ASP-1-0.853-0.92316.547-0.273-0.2730.0000.0000.0000.000
192A203ARG10.8150.93517.6220.1450.1450.0000.0000.0000.000
193A204VAL00.0010.00614.743-0.001-0.0010.0000.0000.0000.000
194A205LYS10.9200.94018.1720.2710.2710.0000.0000.0000.000
195A206ASN0-0.041-0.02317.560-0.026-0.0260.0000.0000.0000.000
196A207LEU00.0500.00514.126-0.017-0.0170.0000.0000.0000.000
197A208ARG10.9650.99913.2230.2700.2700.0000.0000.0000.000
198A209GLU-1-0.809-0.90413.127-0.390-0.3900.0000.0000.0000.000
199A210ALA0-0.023-0.00312.991-0.037-0.0370.0000.0000.0000.000
200A211LEU00.0110.0076.951-0.055-0.0550.0000.0000.0000.000
201A212GLN00.0230.0108.441-0.155-0.1550.0000.0000.0000.000
202A213LYS10.8450.9299.8190.3590.3590.0000.0000.0000.000
203A214ILE0-0.019-0.0185.3010.0680.0680.0000.0000.0000.000
204A215GLU-1-0.974-0.9934.883-2.059-2.0590.0000.0000.0000.000
205A216GLU-1-0.952-0.9676.222-0.117-0.1170.0000.0000.0000.000
206A217MET0-0.046-0.0178.2570.2110.2110.0000.0000.0000.000
207A218ASN0-0.048-0.0212.913-4.616-1.4270.824-1.776-2.237-0.017