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: ZVRMN

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2499385.352656
FMO2-HF: Nuclear repulsion 2416614.767243
FMO2-HF: Total energy -82770.585414
FMO2-MP2: Total energy -83016.268219


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.
-17.859-7.8657.483-6.165-11.315-0.057
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 : -0.020 / q_NPA : -0.009
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].
3A3TYR0-0.081-0.0782.949-0.8071.1870.085-0.850-1.2300.002
4A4LYS10.9120.9492.649-1.3080.6590.871-1.025-1.814-0.012
5A5ALA00.0140.0104.6760.1190.253-0.001-0.006-0.1270.000
6A6VAL00.0050.0047.056-0.216-0.2160.0000.0000.0000.000
7A7LEU0-0.047-0.0209.7460.0720.0720.0000.0000.0000.000
8A8VAL00.002-0.00612.786-0.052-0.0520.0000.0000.0000.000
9A9ASP-1-0.751-0.85615.349-0.212-0.2120.0000.0000.0000.000
10A10PHE00.033-0.00118.825-0.021-0.0210.0000.0000.0000.000
11A11GLY00.0540.02821.096-0.010-0.0100.0000.0000.0000.000
12A12ASN0-0.073-0.05022.839-0.009-0.0090.0000.0000.0000.000
13A13THR0-0.039-0.00117.592-0.017-0.0170.0000.0000.0000.000
14A14LEU00.0010.00115.556-0.032-0.0320.0000.0000.0000.000
15A15VAL00.0020.00619.5800.0010.0010.0000.0000.0000.000
16A16GLY00.0160.01923.3630.0010.0010.0000.0000.0000.000
17A17PHE0-0.006-0.01926.3860.0060.0060.0000.0000.0000.000
18A18LYS10.8030.91830.0610.1310.1310.0000.0000.0000.000
19A19PRO00.0370.02233.4690.0010.0010.0000.0000.0000.000
20A20VAL00.0120.00537.124-0.003-0.0030.0000.0000.0000.000
21A21PHE00.0000.00138.484-0.001-0.0010.0000.0000.0000.000
22A22TYR0-0.005-0.01336.9230.0020.0020.0000.0000.0000.000
23A23GLU-1-0.854-0.92538.998-0.094-0.0940.0000.0000.0000.000
24A24LYS10.9120.97241.3650.0680.0680.0000.0000.0000.000
25A25VAL00.0210.00239.7150.0030.0030.0000.0000.0000.000
26A26TYR0-0.051-0.02839.7180.0020.0020.0000.0000.0000.000
27A27GLN0-0.041-0.03741.5270.0010.0010.0000.0000.0000.000
28A28VAL0-0.016-0.00445.1360.0030.0030.0000.0000.0000.000
29A29LEU00.0080.00640.0500.0030.0030.0000.0000.0000.000
30A30LYS10.8220.89844.3080.0770.0770.0000.0000.0000.000
31A31ASP-1-0.845-0.92245.856-0.059-0.0590.0000.0000.0000.000
32A32ASN0-0.133-0.08747.3620.0060.0060.0000.0000.0000.000
33A33GLY00.0020.01447.9040.0020.0020.0000.0000.0000.000
34A34TYR0-0.038-0.02442.523-0.001-0.0010.0000.0000.0000.000
35A35ASP-1-0.798-0.88042.619-0.080-0.0800.0000.0000.0000.000
36A36LEU0-0.0060.00337.587-0.002-0.0020.0000.0000.0000.000
37A37ASP-1-0.787-0.90634.054-0.129-0.1290.0000.0000.0000.000
38A38LEU00.0570.01834.599-0.003-0.0030.0000.0000.0000.000
39A39ARG10.8380.93426.9270.1700.1700.0000.0000.0000.000
40A40LYS10.8360.90930.9580.1290.1290.0000.0000.0000.000
41A41VAL00.0230.01833.1850.0010.0010.0000.0000.0000.000
42A42PHE00.024-0.01230.2920.0010.0010.0000.0000.0000.000
43A43ARG10.8710.95928.1480.1240.1240.0000.0000.0000.000
44A44ALA00.0220.00529.805-0.002-0.0020.0000.0000.0000.000
45A45TYR0-0.004-0.01632.7350.0010.0010.0000.0000.0000.000
46A46ALA00.0070.00227.8050.0030.0030.0000.0000.0000.000
47A47LYS10.8160.89625.7170.1670.1670.0000.0000.0000.000
48A48ALA00.0670.03530.7240.0050.0050.0000.0000.0000.000
49A49MET0-0.033-0.00930.8430.0050.0050.0000.0000.0000.000
50A50GLY0-0.075-0.03430.342-0.003-0.0030.0000.0000.0000.000
51A51MET0-0.085-0.02131.2000.0020.0020.0000.0000.0000.000
52A52ILE00.0230.02234.1700.0070.0070.0000.0000.0000.000
53A53ASN0-0.075-0.04435.5850.0010.0010.0000.0000.0000.000
54A54TYR0-0.049-0.03231.739-0.001-0.0010.0000.0000.0000.000
55A55PRO00.0030.03036.3550.0030.0030.0000.0000.0000.000
56A56ASP-1-0.935-0.98338.424-0.055-0.0550.0000.0000.0000.000
57A57GLU-1-0.968-0.98236.999-0.061-0.0610.0000.0000.0000.000
58A58ASP-1-0.855-0.92932.194-0.103-0.1030.0000.0000.0000.000
59A59GLY0-0.006-0.02134.601-0.002-0.0020.0000.0000.0000.000
60A60LEU0-0.030-0.01135.814-0.001-0.0010.0000.0000.0000.000
61A61GLU-1-0.855-0.92432.747-0.116-0.1160.0000.0000.0000.000
62A62HIS0-0.062-0.01935.7910.0010.0010.0000.0000.0000.000
63A63VAL00.0350.02935.3720.0040.0040.0000.0000.0000.000
64A64ASP-1-0.740-0.86838.323-0.061-0.0610.0000.0000.0000.000
65A65PRO0-0.021-0.02440.179-0.003-0.0030.0000.0000.0000.000
66A66LYS10.9200.96341.5800.0520.0520.0000.0000.0000.000
67A67ASP-1-0.847-0.91537.181-0.077-0.0770.0000.0000.0000.000
68A68PHE0-0.024-0.02636.055-0.004-0.0040.0000.0000.0000.000
69A69LEU0-0.015-0.01237.799-0.002-0.0020.0000.0000.0000.000
70A70TYR00.0060.00635.8660.0010.0010.0000.0000.0000.000
71A71ILE0-0.025-0.00232.627-0.002-0.0020.0000.0000.0000.000
72A72LEU0-0.056-0.01734.767-0.007-0.0070.0000.0000.0000.000
73A73GLY00.0020.01637.0240.0010.0010.0000.0000.0000.000
74A74ILE0-0.052-0.02139.2770.0040.0040.0000.0000.0000.000
75A75TYR0-0.009-0.02242.5000.0000.0000.0000.0000.0000.000
76A76PRO0-0.014-0.01443.9020.0000.0000.0000.0000.0000.000
77A77SER0-0.036-0.04246.3220.0020.0020.0000.0000.0000.000
78A78GLU-1-0.805-0.89449.453-0.048-0.0480.0000.0000.0000.000
79A79ARG10.8100.90651.8880.0520.0520.0000.0000.0000.000
80A80LEU00.0510.03745.355-0.001-0.0010.0000.0000.0000.000
81A81VAL0-0.004-0.01446.057-0.002-0.0020.0000.0000.0000.000
82A82LYS10.7980.89647.7100.0480.0480.0000.0000.0000.000
83A83GLU-1-0.783-0.89049.278-0.055-0.0550.0000.0000.0000.000
84A84LEU0-0.001-0.01142.489-0.002-0.0020.0000.0000.0000.000
85A85LYS10.8120.90444.9720.0570.0570.0000.0000.0000.000
86A86GLU-1-0.819-0.89047.046-0.052-0.0520.0000.0000.0000.000
87A87ALA0-0.082-0.03744.5750.0000.0000.0000.0000.0000.000
88A88ASP-1-0.868-0.94643.841-0.076-0.0760.0000.0000.0000.000
89A89ILE0-0.016-0.00939.310-0.004-0.0040.0000.0000.0000.000
90A90ARG10.8600.92639.4320.0660.0660.0000.0000.0000.000
91A91ASP-1-0.821-0.89239.144-0.083-0.0830.0000.0000.0000.000
92A92GLY00.0190.00935.566-0.001-0.0010.0000.0000.0000.000
93A93GLU-1-0.849-0.91432.964-0.126-0.1260.0000.0000.0000.000
94A94ALA00.0160.00727.971-0.006-0.0060.0000.0000.0000.000
95A95PHE0-0.020-0.02226.7480.0030.0030.0000.0000.0000.000
96A96LEU00.0180.00620.746-0.007-0.0070.0000.0000.0000.000
97A97TYR0-0.017-0.01920.7610.0130.0130.0000.0000.0000.000
98A98ASP-1-0.880-0.94820.952-0.277-0.2770.0000.0000.0000.000
99A99ASP-1-0.759-0.85416.973-0.420-0.4200.0000.0000.0000.000
100A100THR0-0.034-0.03016.049-0.076-0.0760.0000.0000.0000.000
101A101LEU00.0140.00315.471-0.046-0.0460.0000.0000.0000.000
102A102GLU-1-0.907-0.95314.502-0.519-0.5190.0000.0000.0000.000
103A103PHE0-0.001-0.00210.694-0.127-0.1270.0000.0000.0000.000
104A104LEU0-0.014-0.00310.326-0.170-0.1700.0000.0000.0000.000
105A105GLU-1-0.844-0.90110.296-0.548-0.5480.0000.0000.0000.000
106A106GLY00.0310.0449.387-0.075-0.0750.0000.0000.0000.000
107A107LEU0-0.001-0.0105.927-0.426-0.4260.0000.0000.0000.000
108A108LYS10.8220.9125.178-0.313-0.261-0.0010.001-0.0510.000
109A109SER0-0.079-0.0617.1300.0290.0290.0000.0000.0000.000
110A110ASN0-0.052-0.0313.7970.1690.3490.001-0.041-0.1400.000
111A111GLY0-0.0070.0042.475-4.633-3.6291.574-1.024-1.554-0.015
112A112TYR0-0.0200.0042.721-2.1580.4382.348-1.059-3.886-0.009
113A113LYS10.8440.9074.457-0.344-0.279-0.001-0.011-0.0540.000
114A114LEU00.0100.0098.204-0.123-0.1230.0000.0000.0000.000
115A115ALA0-0.030-0.02510.8430.0880.0880.0000.0000.0000.000
116A116LEU0-0.0010.01814.314-0.035-0.0350.0000.0000.0000.000
117A117VAL0-0.010-0.00817.3340.0370.0370.0000.0000.0000.000
118A118SER0-0.002-0.02219.811-0.007-0.0070.0000.0000.0000.000
119A119ASN00.0280.02923.3130.0090.0090.0000.0000.0000.000
120A120ALA00.0730.04627.0060.0080.0080.0000.0000.0000.000
121A121SER0-0.037-0.03226.934-0.002-0.0020.0000.0000.0000.000
122A122PRO00.0260.02927.671-0.007-0.0070.0000.0000.0000.000
123A123ARG10.9820.98029.2550.1150.1150.0000.0000.0000.000
124A124VAL0-0.061-0.03123.770-0.010-0.0100.0000.0000.0000.000
125A125LYS10.9200.96024.9800.0890.0890.0000.0000.0000.000
126A126THR00.007-0.01425.963-0.009-0.0090.0000.0000.0000.000
127A127LEU0-0.024-0.01825.972-0.005-0.0050.0000.0000.0000.000
128A128LEU0-0.034-0.02620.040-0.015-0.0150.0000.0000.0000.000
129A129GLU-1-0.801-0.87222.773-0.153-0.1530.0000.0000.0000.000
130A130LYS10.8390.94125.4430.1450.1450.0000.0000.0000.000
131A131PHE0-0.027-0.02422.6870.0020.0020.0000.0000.0000.000
132A132ASP-1-0.829-0.89321.271-0.249-0.2490.0000.0000.0000.000
133A133LEU00.0320.01318.125-0.028-0.0280.0000.0000.0000.000
134A134LYS10.7960.86217.4990.1240.1240.0000.0000.0000.000
135A135LYS10.8500.92716.3710.3010.3010.0000.0000.0000.000
136A136TYR0-0.006-0.03112.8090.0120.0120.0000.0000.0000.000
137A137PHE00.0010.00512.553-0.027-0.0270.0000.0000.0000.000
138A138ASP-1-0.799-0.87110.998-0.044-0.0440.0000.0000.0000.000
139A139ALA0-0.059-0.03514.1700.0460.0460.0000.0000.0000.000
140A140LEU00.0120.00716.749-0.034-0.0340.0000.0000.0000.000
141A141ALA0-0.038-0.01319.5600.0180.0180.0000.0000.0000.000
142A153PRO00.0790.02024.3330.0050.0050.0000.0000.0000.000
143A154LYS10.9820.98723.7390.0250.0250.0000.0000.0000.000
144A155ILE00.0130.01222.2980.0060.0060.0000.0000.0000.000
145A156PHE00.0600.03116.4730.0110.0110.0000.0000.0000.000
146A157GLY00.0150.01118.188-0.003-0.0030.0000.0000.0000.000
147A158PHE0-0.025-0.01118.1040.0120.0120.0000.0000.0000.000
148A159ALA00.0180.00717.1760.0140.0140.0000.0000.0000.000
149A160LEU00.0250.01212.2640.0120.0120.0000.0000.0000.000
150A161ALA0-0.035-0.02313.2040.0240.0240.0000.0000.0000.000
151A162LYS10.8420.92214.3160.0620.0620.0000.0000.0000.000
152A163VAL0-0.048-0.02110.9540.0390.0390.0000.0000.0000.000
153A164GLY00.0160.0269.7240.1370.1370.0000.0000.0000.000
154A165TYR0-0.003-0.0038.741-0.044-0.0440.0000.0000.0000.000
155A166PRO0-0.002-0.0276.9560.1320.1320.0000.0000.0000.000
156A167ALA0-0.0340.0076.756-0.046-0.0460.0000.0000.0000.000
157A168VAL00.0390.0297.7410.0060.0060.0000.0000.0000.000
158A169HIS10.7690.84010.3230.3080.3080.0000.0000.0000.000
159A170VAL00.0280.02212.1360.0190.0190.0000.0000.0000.000
160A171GLY00.0390.00114.9270.0210.0210.0000.0000.0000.000
161A172ASP-1-0.770-0.85518.711-0.195-0.1950.0000.0000.0000.000
162A173ILE0-0.049-0.02722.1710.0140.0140.0000.0000.0000.000
163A174TYR0-0.0010.00120.6870.0180.0180.0000.0000.0000.000
164A175GLU-1-0.980-0.98321.321-0.125-0.1250.0000.0000.0000.000
165A176LEU00.0130.00018.559-0.018-0.0180.0000.0000.0000.000
166A177ASP-1-0.820-0.87916.314-0.200-0.2000.0000.0000.0000.000
167A178TYR00.004-0.00918.9140.0110.0110.0000.0000.0000.000
168A179ILE0-0.043-0.01017.2320.0190.0190.0000.0000.0000.000
169A180GLY00.0380.00216.997-0.017-0.0170.0000.0000.0000.000
170A181ALA0-0.046-0.01018.1690.0100.0100.0000.0000.0000.000
171A182LYS10.9570.96718.575-0.105-0.1050.0000.0000.0000.000
172A183ARG10.9520.97614.458-0.084-0.0840.0000.0000.0000.000
173A184SER00.0820.04715.6900.0110.0110.0000.0000.0000.000
174A185TYR0-0.045-0.03112.8180.0170.0170.0000.0000.0000.000
175A186VAL0-0.006-0.01511.395-0.042-0.0420.0000.0000.0000.000
176A187ASP-1-0.765-0.82811.019-0.247-0.2470.0000.0000.0000.000
177A188PRO00.0090.00212.783-0.068-0.0680.0000.0000.0000.000
178A189ILE00.0160.00111.304-0.023-0.0230.0000.0000.0000.000
179A190LEU0-0.0110.01115.7300.0020.0020.0000.0000.0000.000
180A191LEU0-0.014-0.00817.314-0.019-0.0190.0000.0000.0000.000
181A192ASP-1-0.749-0.88719.415-0.163-0.1630.0000.0000.0000.000
182A193ARG10.8020.87819.0030.3530.3530.0000.0000.0000.000
183A194TYR0-0.021-0.01123.7160.0080.0080.0000.0000.0000.000
184A195ASP-1-0.933-0.95126.281-0.142-0.1420.0000.0000.0000.000
185A196PHE0-0.014-0.02927.3170.0160.0160.0000.0000.0000.000
186A197TYR00.005-0.00624.7950.0160.0160.0000.0000.0000.000
187A198PRO00.0250.01226.735-0.008-0.0080.0000.0000.0000.000
188A199ASP-1-0.883-0.94627.895-0.105-0.1050.0000.0000.0000.000
189A200VAL0-0.030-0.00522.8100.0040.0040.0000.0000.0000.000
190A201ARG10.9500.96920.8450.1110.1110.0000.0000.0000.000
191A202ASP-1-0.871-0.94116.609-0.265-0.2650.0000.0000.0000.000
192A203ARG10.7620.90217.9740.1390.1390.0000.0000.0000.000
193A204VAL00.0000.00615.4320.0040.0040.0000.0000.0000.000
194A205LYS10.8760.90818.7280.2860.2860.0000.0000.0000.000
195A206ASN0-0.064-0.05418.011-0.017-0.0170.0000.0000.0000.000
196A207LEU00.0360.00614.359-0.022-0.0220.0000.0000.0000.000
197A208ARG10.9660.99613.3410.3080.3080.0000.0000.0000.000
198A209GLU-1-0.752-0.84813.361-0.393-0.3930.0000.0000.0000.000
199A210ALA0-0.0080.00313.160-0.025-0.0250.0000.0000.0000.000
200A211LEU0-0.0120.0007.479-0.062-0.0620.0000.0000.0000.000
201A212GLN00.0200.0118.821-0.140-0.1400.0000.0000.0000.000
202A213LYS10.7640.87810.6500.3630.3630.0000.0000.0000.000
203A214ILE00.007-0.0125.5540.0790.0790.0000.0000.0000.000
204A215GLU-1-0.944-0.9845.819-1.925-1.9250.0000.0000.0000.000
205A216GLU-1-0.898-0.9307.059-0.089-0.0890.0000.0000.0000.000
206A217MET0-0.045-0.0188.6450.2020.2020.0000.0000.0000.000
207A218ASN0-0.048-0.0232.427-3.805-1.8032.607-2.150-2.459-0.023