Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

tag_button

FMODB ID: 2N7JR

Calculation Name: 1ZBO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZBO

Chain ID: A

ChEMBL ID:

UniProt ID: Q7WAM7

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2110466.757972
FMO2-HF: Nuclear repulsion 2033668.030546
FMO2-HF: Total energy -76798.727426
FMO2-MP2: Total energy -77019.844944


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:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-5.824-0.9412.104-2.988-3.999-0.019
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.000
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].
3A4ILE00.0010.0093.860-0.8710.522-0.007-0.654-0.7320.001
4A5PRO0-0.003-0.0066.2250.3890.3890.0000.0000.0000.000
5A6LEU0-0.010-0.0148.593-0.123-0.1230.0000.0000.0000.000
6A7PHE00.003-0.01411.7790.1350.1350.0000.0000.0000.000
7A8PRO0-0.035-0.01715.281-0.015-0.0150.0000.0000.0000.000
8A9LEU00.0000.00717.1480.0370.0370.0000.0000.0000.000
9A10SER0-0.025-0.05519.9220.0010.0010.0000.0000.0000.000
10A11ASN0-0.043-0.02121.6720.0110.0110.0000.0000.0000.000
11A12ALA0-0.0170.00818.185-0.025-0.0250.0000.0000.0000.000
12A13LEU00.0120.02015.8120.0320.0320.0000.0000.0000.000
13A14PHE00.0530.02916.555-0.048-0.0480.0000.0000.0000.000
14A15PRO00.0680.03315.3280.0160.0160.0000.0000.0000.000
15A16ALA0-0.082-0.04417.6500.0420.0420.0000.0000.0000.000
16A17GLY00.0430.04019.8940.0310.0310.0000.0000.0000.000
17A18VAL0-0.068-0.03820.822-0.018-0.0180.0000.0000.0000.000
18A19LEU00.0040.00818.9450.0040.0040.0000.0000.0000.000
19A20ARG10.8850.93422.5980.1780.1780.0000.0000.0000.000
20A21LEU00.0160.01919.8890.0040.0040.0000.0000.0000.000
21A22ARG10.8280.88023.9050.1450.1450.0000.0000.0000.000
22A23VAL0-0.012-0.00221.348-0.004-0.0040.0000.0000.0000.000
23A24PHE00.0360.00524.2630.0130.0130.0000.0000.0000.000
24A25GLU-1-0.789-0.86023.753-0.132-0.1320.0000.0000.0000.000
25A26ILE00.026-0.00123.261-0.014-0.0140.0000.0000.0000.000
26A27ARG10.7280.82919.7180.1830.1830.0000.0000.0000.000
27A28TYR00.0760.03317.440-0.011-0.0110.0000.0000.0000.000
28A29LEU0-0.021-0.00818.832-0.015-0.0150.0000.0000.0000.000
29A30ASP-1-0.873-0.89416.606-0.103-0.1030.0000.0000.0000.000
30A31MET00.0000.00713.339-0.012-0.0120.0000.0000.0000.000
31A32VAL00.0530.02015.674-0.018-0.0180.0000.0000.0000.000
32A33ARG10.9320.96018.0570.1050.1050.0000.0000.0000.000
33A34ARG10.8210.88913.1570.1410.1410.0000.0000.0000.000
34A35CYS00.0140.01112.9030.0000.0000.0000.0000.0000.000
35A36ILE0-0.059-0.02615.5020.0080.0080.0000.0000.0000.000
36A37ALA0-0.070-0.02618.3900.0140.0140.0000.0000.0000.000
37A38ASP-1-0.861-0.92113.970-0.224-0.2240.0000.0000.0000.000
38A39GLY0-0.0030.00915.473-0.002-0.0020.0000.0000.0000.000
39A40SER0-0.078-0.05310.680-0.061-0.0610.0000.0000.0000.000
40A41GLU-1-0.853-0.90810.867-0.628-0.6280.0000.0000.0000.000
41A42PHE0-0.018-0.02410.396-0.109-0.1090.0000.0000.0000.000
42A43GLY00.0470.0129.659-0.002-0.0020.0000.0000.0000.000
43A44VAL0-0.034-0.00410.4590.1060.1060.0000.0000.0000.000
44A45VAL0-0.001-0.00212.402-0.036-0.0360.0000.0000.0000.000
45A46VAL0-0.0180.00614.3880.0530.0530.0000.0000.0000.000
46A47LEU0-0.003-0.01017.186-0.015-0.0150.0000.0000.0000.000
47A48GLU-1-0.830-0.92417.849-0.237-0.2370.0000.0000.0000.000
48A49GLN0-0.052-0.03420.7440.0230.0230.0000.0000.0000.000
49A50GLY00.0270.01022.032-0.004-0.0040.0000.0000.0000.000
50A51THR0-0.090-0.04623.7030.0040.0040.0000.0000.0000.000
51A52GLU-1-0.785-0.86721.878-0.229-0.2290.0000.0000.0000.000
52A53VAL0-0.0250.00622.630-0.006-0.0060.0000.0000.0000.000
53A54ARG10.8730.92422.2010.1070.1070.0000.0000.0000.000
54A55ARG10.8580.92025.7450.0980.0980.0000.0000.0000.000
55A56PRO0-0.023-0.00427.000-0.001-0.0010.0000.0000.0000.000
56A57ASP-1-0.805-0.89629.603-0.070-0.0700.0000.0000.0000.000
57A58GLY0-0.024-0.01327.3470.0030.0030.0000.0000.0000.000
58A59ARG10.9010.93622.3320.0730.0730.0000.0000.0000.000
59A60GLU-1-0.809-0.90319.399-0.150-0.1500.0000.0000.0000.000
60A61VAL0-0.027-0.00317.8900.0050.0050.0000.0000.0000.000
61A62LEU0-0.001-0.00312.595-0.003-0.0030.0000.0000.0000.000
62A63ALA00.0290.02615.3630.0210.0210.0000.0000.0000.000
63A64ARG10.8530.89812.1290.1900.1900.0000.0000.0000.000
64A65ALA0-0.0050.00410.895-0.060-0.0600.0000.0000.0000.000
65A66GLY0-0.0060.00411.2280.0920.0920.0000.0000.0000.000
66A67THR0-0.020-0.02611.478-0.053-0.0530.0000.0000.0000.000
67A68MET0-0.0390.0008.283-0.133-0.1330.0000.0000.0000.000
68A69ALA00.0090.00511.4070.1170.1170.0000.0000.0000.000
69A70ARG10.9090.94714.6330.3040.3040.0000.0000.0000.000
70A71ILE00.020-0.01416.4310.0300.0300.0000.0000.0000.000
71A72ASP-1-0.845-0.87619.221-0.255-0.2550.0000.0000.0000.000
72A73HIS0-0.084-0.06222.2340.0100.0100.0000.0000.0000.000
73A74TRP0-0.014-0.01223.221-0.007-0.0070.0000.0000.0000.000
74A75GLU-1-0.876-0.92225.407-0.110-0.1100.0000.0000.0000.000
75A76ALA00.010-0.01528.203-0.006-0.0060.0000.0000.0000.000
76A77PRO00.0090.02630.7880.0090.0090.0000.0000.0000.000
77A78MET00.0030.00733.4400.0060.0060.0000.0000.0000.000
78A79PRO00.025-0.01233.202-0.004-0.0040.0000.0000.0000.000
79A80ALA0-0.030-0.02231.0180.0000.0000.0000.0000.0000.000
80A81LEU0-0.032-0.00128.918-0.006-0.0060.0000.0000.0000.000
81A82LEU0-0.0130.00522.8890.0000.0000.0000.0000.0000.000
82A83GLU-1-0.814-0.88226.123-0.147-0.1470.0000.0000.0000.000
83A84LEU0-0.005-0.01520.5910.0050.0050.0000.0000.0000.000
84A85ALA0-0.0040.02324.101-0.005-0.0050.0000.0000.0000.000
85A86CYS0-0.037-0.01518.783-0.018-0.0180.0000.0000.0000.000
86A87THR0-0.015-0.02819.0160.0290.0290.0000.0000.0000.000
87A88GLY00.0040.00616.165-0.039-0.0390.0000.0000.0000.000
88A89THR0-0.090-0.08613.5620.0370.0370.0000.0000.0000.000
89A90GLY00.0690.04611.0600.0310.0310.0000.0000.0000.000
90A91ARG10.8200.88510.8280.3230.3230.0000.0000.0000.000
91A92PHE0-0.028-0.0156.569-0.197-0.1970.0000.0000.0000.000
92A93ARG10.8990.9447.8710.6690.6690.0000.0000.0000.000
93A94LEU0-0.045-0.0296.515-0.389-0.3890.0000.0000.0000.000
94A95HIS0-0.046-0.0294.9640.3370.3370.0000.0000.0000.000
95A96ALA00.0000.0036.9440.2090.2090.0000.0000.0000.000
96A97CYS00.0120.0027.564-0.233-0.2330.0000.0000.0000.000
97A98THR0-0.051-0.02910.1220.1720.1720.0000.0000.0000.000
98A99GLN00.0290.03712.796-0.045-0.0450.0000.0000.0000.000
99A100GLY00.0440.01915.9650.0490.0490.0000.0000.0000.000
100A101LYS10.9500.96116.986-0.029-0.0290.0000.0000.0000.000
101A102TYR00.025-0.01019.510-0.010-0.0100.0000.0000.0000.000
102A103GLY00.0320.02219.859-0.004-0.0040.0000.0000.0000.000
103A104LEU0-0.0290.00915.420-0.024-0.0240.0000.0000.0000.000
104A105TRP00.0170.00413.3550.0450.0450.0000.0000.0000.000
105A106THR00.0170.0148.934-0.162-0.1620.0000.0000.0000.000
106A107GLY00.0430.0017.3800.3000.3000.0000.0000.0000.000
107A108GLN0-0.0300.0063.081-1.333-0.7130.074-0.196-0.4990.001
108A109ALA00.0240.0143.5530.3511.1530.033-0.266-0.569-0.001
109A110GLU-1-0.802-0.8772.615-4.068-2.2151.995-1.805-2.042-0.020
110A111PRO0-0.010-0.0073.3880.0540.2690.009-0.067-0.1570.000
111A112VAL0-0.032-0.0226.4110.2240.2240.0000.0000.0000.000
112A113PRO00.003-0.00610.0400.0060.0060.0000.0000.0000.000
113A114ASP-1-0.855-0.91812.757-0.495-0.4950.0000.0000.0000.000
114A115ASP-1-0.821-0.89815.423-0.280-0.2800.0000.0000.0000.000
115A116ALA0-0.014-0.00618.5630.0060.0060.0000.0000.0000.000
116A117PRO0-0.0210.00121.6430.0030.0030.0000.0000.0000.000
117A118LEU0-0.035-0.03624.3230.0110.0110.0000.0000.0000.000
118A119GLU-1-0.870-0.92727.616-0.100-0.1000.0000.0000.0000.000
119A120VAL0-0.041-0.02730.334-0.003-0.0030.0000.0000.0000.000
120A121PRO00.0010.02031.3340.0070.0070.0000.0000.0000.000
121A122PRO00.011-0.00734.361-0.001-0.0010.0000.0000.0000.000
122A123GLU-1-0.896-0.96634.377-0.089-0.0890.0000.0000.0000.000
123A124LEU0-0.005-0.00830.696-0.002-0.0020.0000.0000.0000.000
124A125ALA00.0360.01734.052-0.005-0.0050.0000.0000.0000.000
125A126ARG10.8240.91836.1500.0880.0880.0000.0000.0000.000
126A127SER00.061-0.00931.9560.0000.0000.0000.0000.0000.000
127A128ALA00.0430.03932.505-0.005-0.0050.0000.0000.0000.000
128A129SER00.004-0.00333.4360.0020.0020.0000.0000.0000.000
129A130ALA0-0.032-0.00135.3370.0040.0040.0000.0000.0000.000
130A131LEU00.0370.03129.0210.0020.0020.0000.0000.0000.000
131A132GLY00.0440.00933.488-0.001-0.0010.0000.0000.0000.000
132A133ARG10.8340.89535.5070.0880.0880.0000.0000.0000.000
133A134LEU0-0.0170.00133.9210.0040.0040.0000.0000.0000.000
134A135ILE00.0500.01830.6180.0020.0020.0000.0000.0000.000
135A136ALA00.0050.01135.0190.0030.0030.0000.0000.0000.000
136A137ARG10.7900.88338.6170.0800.0800.0000.0000.0000.000
137A138LEU00.0260.00533.5640.0030.0030.0000.0000.0000.000
138A139GLN0-0.005-0.00836.1750.0030.0030.0000.0000.0000.000
139A140ARG10.7920.89838.7580.0770.0770.0000.0000.0000.000
140A141GLU-1-0.786-0.87841.604-0.073-0.0730.0000.0000.0000.000
141A142GLY0-0.0060.01340.5110.0010.0010.0000.0000.0000.000
142A143VAL0-0.010-0.00935.5860.0000.0000.0000.0000.0000.000
143A144PRO00.0280.01135.955-0.004-0.0040.0000.0000.0000.000
144A145PRO00.0580.01931.877-0.005-0.0050.0000.0000.0000.000
145A146HIS0-0.0050.00430.592-0.013-0.0130.0000.0000.0000.000
146A147ILE0-0.043-0.02131.286-0.003-0.0030.0000.0000.0000.000
147A148MET0-0.029-0.00631.586-0.001-0.0010.0000.0000.0000.000
148A149PRO00.0100.00128.468-0.006-0.0060.0000.0000.0000.000
149A150MET00.0230.02426.303-0.011-0.0110.0000.0000.0000.000
150A151ALA00.0360.01224.7300.0120.0120.0000.0000.0000.000
151A152ALA00.021-0.00326.7840.0040.0040.0000.0000.0000.000
152A153PRO0-0.031-0.01025.4620.0090.0090.0000.0000.0000.000
153A154PHE00.0380.00827.262-0.009-0.0090.0000.0000.0000.000
154A155ARG10.9290.97824.3070.1940.1940.0000.0000.0000.000
155A156LEU0-0.009-0.02328.544-0.004-0.0040.0000.0000.0000.000
156A157ASP-1-0.878-0.93630.752-0.105-0.1050.0000.0000.0000.000
157A158ASP-1-0.850-0.93424.440-0.196-0.1960.0000.0000.0000.000
158A159CYS0-0.068-0.02626.152-0.003-0.0030.0000.0000.0000.000
159A160GLY00.0440.02122.472-0.005-0.0050.0000.0000.0000.000
160A161TRP00.0120.01823.217-0.002-0.0020.0000.0000.0000.000
161A162VAL0-0.010-0.01324.2110.0000.0000.0000.0000.0000.000
162A163ALA00.0080.00824.2380.0040.0040.0000.0000.0000.000
163A164ASP-1-0.784-0.87120.366-0.293-0.2930.0000.0000.0000.000
164A165ARG10.7700.85421.0040.2500.2500.0000.0000.0000.000
165A166TRP0-0.028-0.02625.7250.0090.0090.0000.0000.0000.000
166A167ALA00.0110.01122.7390.0060.0060.0000.0000.0000.000
167A168GLU-1-0.799-0.87222.365-0.252-0.2520.0000.0000.0000.000
168A169MET0-0.062-0.02323.7950.0100.0100.0000.0000.0000.000
169A170LEU00.0160.01527.6040.0110.0110.0000.0000.0000.000
170A171SER0-0.019-0.01227.340-0.014-0.0140.0000.0000.0000.000
171A172LEU0-0.010-0.00125.4250.0090.0090.0000.0000.0000.000
172A173PRO00.0240.00924.941-0.009-0.0090.0000.0000.0000.000
173A174PRO00.0370.01820.421-0.010-0.0100.0000.0000.0000.000
174A175ALA00.0410.01119.047-0.027-0.0270.0000.0000.0000.000
175A176ASP-1-0.808-0.89419.402-0.190-0.1900.0000.0000.0000.000
176A177LYS10.7830.90020.6010.2080.2080.0000.0000.0000.000
177A178ALA00.0100.00015.400-0.020-0.0200.0000.0000.0000.000
178A179ARG10.6970.80016.1460.1580.1580.0000.0000.0000.000
179A180LEU00.003-0.00718.254-0.005-0.0050.0000.0000.0000.000
180A181LEU0-0.0250.00213.9450.0080.0080.0000.0000.0000.000
181A182LEU00.000-0.01211.199-0.023-0.0230.0000.0000.0000.000
182A183LEU0-0.0340.01615.6740.0210.0210.0000.0000.0000.000
183A184PRO00.0410.01719.147-0.014-0.0140.0000.0000.0000.000
184A185PRO00.0330.02420.5340.0100.0100.0000.0000.0000.000
185A186LEU00.0120.00522.8040.0090.0090.0000.0000.0000.000
186A187ASP-1-0.837-0.90523.536-0.131-0.1310.0000.0000.0000.000
187A188ARG10.7250.82619.0670.2980.2980.0000.0000.0000.000
188A189LEU00.0100.00124.2140.0070.0070.0000.0000.0000.000
189A190ARG10.8620.89627.1270.1300.1300.0000.0000.0000.000
190A191GLU-1-0.819-0.86324.915-0.165-0.1650.0000.0000.0000.000
191A192ILE0-0.001-0.00726.1990.0070.0070.0000.0000.0000.000
192A193ASP-1-0.799-0.85929.005-0.096-0.0960.0000.0000.0000.000
193A194ALA0-0.0010.00131.5110.0080.0080.0000.0000.0000.000
194A195VAL0-0.021-0.00929.3770.0060.0060.0000.0000.0000.000
195A196LEU0-0.063-0.01931.7070.0050.0050.0000.0000.0000.000
196A197ALA0-0.056-0.01834.6930.0060.0060.0000.0000.0000.000
197A198ALA0-0.085-0.03835.6110.0050.0050.0000.0000.0000.000