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

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FMODB ID: 7632K

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2106009.09574
FMO2-HF: Nuclear repulsion 2029210.959185
FMO2-HF: Total energy -76798.136555
FMO2-MP2: Total energy -77019.279937


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.
-6.458-0.7212.22-3.368-4.587-0.022
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 : 0.041 / q_NPA : 0.002
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].
3A4ILE00.0040.0133.746-1.0490.431-0.007-0.638-0.8350.001
4A5PRO0-0.002-0.0056.0170.3860.3860.0000.0000.0000.000
5A6LEU0-0.013-0.0218.348-0.122-0.1220.0000.0000.0000.000
6A7PHE00.024-0.00711.5560.1330.1330.0000.0000.0000.000
7A8PRO0-0.061-0.02414.968-0.019-0.0190.0000.0000.0000.000
8A9LEU00.0240.01816.8040.0380.0380.0000.0000.0000.000
9A10SER0-0.023-0.04919.618-0.001-0.0010.0000.0000.0000.000
10A11ASN0-0.039-0.02121.7990.0070.0070.0000.0000.0000.000
11A12ALA0-0.0170.00018.025-0.024-0.0240.0000.0000.0000.000
12A13LEU00.0240.02115.3030.0320.0320.0000.0000.0000.000
13A14PHE00.0500.02616.132-0.054-0.0540.0000.0000.0000.000
14A15PRO00.0580.03815.1900.0140.0140.0000.0000.0000.000
15A16ALA0-0.081-0.05617.4450.0430.0430.0000.0000.0000.000
16A17GLY00.0030.01619.5600.0310.0310.0000.0000.0000.000
17A18VAL0-0.034-0.02320.617-0.017-0.0170.0000.0000.0000.000
18A19LEU00.0120.00718.4740.0030.0030.0000.0000.0000.000
19A20ARG10.8900.95022.3160.1730.1730.0000.0000.0000.000
20A21LEU00.0080.01319.1840.0090.0090.0000.0000.0000.000
21A22ARG10.8400.90123.1600.1470.1470.0000.0000.0000.000
22A23VAL0-0.015-0.01021.342-0.007-0.0070.0000.0000.0000.000
23A24PHE00.0170.00224.0000.0150.0150.0000.0000.0000.000
24A25GLU-1-0.821-0.89323.277-0.142-0.1420.0000.0000.0000.000
25A26ILE00.0480.00723.336-0.013-0.0130.0000.0000.0000.000
26A27ARG10.7800.87619.4460.1840.1840.0000.0000.0000.000
27A28TYR00.0780.02916.739-0.011-0.0110.0000.0000.0000.000
28A29LEU0-0.0180.00318.539-0.017-0.0170.0000.0000.0000.000
29A30ASP-1-0.861-0.89916.619-0.104-0.1040.0000.0000.0000.000
30A31MET0-0.0080.00913.211-0.015-0.0150.0000.0000.0000.000
31A32VAL00.0560.01515.402-0.019-0.0190.0000.0000.0000.000
32A33ARG10.9330.96717.7350.1090.1090.0000.0000.0000.000
33A34ARG10.8450.90513.0470.1330.1330.0000.0000.0000.000
34A35CYS0-0.0010.00412.489-0.006-0.0060.0000.0000.0000.000
35A36ILE0-0.052-0.02615.0840.0070.0070.0000.0000.0000.000
36A37ALA0-0.077-0.03717.6640.0130.0130.0000.0000.0000.000
37A38ASP-1-0.902-0.93313.675-0.217-0.2170.0000.0000.0000.000
38A39GLY0-0.0060.00414.889-0.016-0.0160.0000.0000.0000.000
39A40SER0-0.041-0.02210.581-0.067-0.0670.0000.0000.0000.000
40A41GLU-1-0.859-0.91610.370-0.699-0.6990.0000.0000.0000.000
41A42PHE0-0.027-0.02610.253-0.080-0.0800.0000.0000.0000.000
42A43GLY00.0370.0229.428-0.001-0.0010.0000.0000.0000.000
43A44VAL0-0.016-0.00410.2490.1250.1250.0000.0000.0000.000
44A45VAL0-0.013-0.00212.204-0.006-0.0060.0000.0000.0000.000
45A46VAL0-0.021-0.00514.1080.0480.0480.0000.0000.0000.000
46A47LEU0-0.021-0.02117.193-0.010-0.0100.0000.0000.0000.000
47A48GLU-1-0.837-0.92417.767-0.217-0.2170.0000.0000.0000.000
48A49GLN0-0.074-0.05320.6640.0190.0190.0000.0000.0000.000
49A50GLY00.0300.01122.2820.0090.0090.0000.0000.0000.000
50A51THR0-0.093-0.03423.192-0.002-0.0020.0000.0000.0000.000
51A52GLU-1-0.800-0.87521.755-0.223-0.2230.0000.0000.0000.000
52A53VAL0-0.0130.00322.479-0.005-0.0050.0000.0000.0000.000
53A54ARG10.9160.94022.5510.1030.1030.0000.0000.0000.000
54A55ARG10.8740.93625.4750.0990.0990.0000.0000.0000.000
55A56PRO0-0.031-0.00726.688-0.001-0.0010.0000.0000.0000.000
56A57ASP-1-0.835-0.91429.129-0.068-0.0680.0000.0000.0000.000
57A58GLY0-0.024-0.00926.8400.0030.0030.0000.0000.0000.000
58A59ARG10.9130.95221.7230.0620.0620.0000.0000.0000.000
59A60GLU-1-0.810-0.90419.030-0.151-0.1510.0000.0000.0000.000
60A61VAL0-0.034-0.01017.7040.0050.0050.0000.0000.0000.000
61A62LEU00.0080.00112.201-0.007-0.0070.0000.0000.0000.000
62A63ALA00.0280.02715.2720.0270.0270.0000.0000.0000.000
63A64ARG10.8750.90612.3020.1840.1840.0000.0000.0000.000
64A65ALA0-0.0050.00210.710-0.061-0.0610.0000.0000.0000.000
65A66GLY0-0.0070.00611.0120.0920.0920.0000.0000.0000.000
66A67THR0-0.003-0.01911.275-0.062-0.0620.0000.0000.0000.000
67A68MET0-0.0350.0037.960-0.146-0.1460.0000.0000.0000.000
68A69ALA00.0040.01011.1030.1280.1280.0000.0000.0000.000
69A70ARG10.9140.94513.8850.2910.2910.0000.0000.0000.000
70A71ILE00.006-0.02316.2320.0370.0370.0000.0000.0000.000
71A72ASP-1-0.833-0.87519.095-0.256-0.2560.0000.0000.0000.000
72A73HIS0-0.059-0.04922.1910.0110.0110.0000.0000.0000.000
73A74TRP0-0.046-0.01522.8300.0000.0000.0000.0000.0000.000
74A75GLU-1-0.879-0.92724.793-0.114-0.1140.0000.0000.0000.000
75A76ALA00.014-0.01527.801-0.006-0.0060.0000.0000.0000.000
76A77PRO00.0010.02430.3960.0090.0090.0000.0000.0000.000
77A78MET00.0060.00733.1520.0060.0060.0000.0000.0000.000
78A79PRO00.019-0.01732.807-0.004-0.0040.0000.0000.0000.000
79A80ALA0-0.042-0.02230.6290.0000.0000.0000.0000.0000.000
80A81LEU0-0.0170.00928.764-0.005-0.0050.0000.0000.0000.000
81A82LEU0-0.018-0.00522.5220.0010.0010.0000.0000.0000.000
82A83GLU-1-0.818-0.89125.709-0.147-0.1470.0000.0000.0000.000
83A84LEU00.006-0.01120.3030.0040.0040.0000.0000.0000.000
84A85ALA0-0.0040.02123.303-0.010-0.0100.0000.0000.0000.000
85A86CYS0-0.058-0.02518.301-0.013-0.0130.0000.0000.0000.000
86A87THR0-0.004-0.03218.6400.0310.0310.0000.0000.0000.000
87A88GLY0-0.0030.01315.817-0.043-0.0430.0000.0000.0000.000
88A89THR0-0.062-0.06313.1990.0370.0370.0000.0000.0000.000
89A90GLY00.0840.05511.0980.0370.0370.0000.0000.0000.000
90A91ARG10.8380.89910.8950.3270.3270.0000.0000.0000.000
91A92PHE0-0.013-0.0096.225-0.171-0.1710.0000.0000.0000.000
92A93ARG10.9200.9617.5900.5980.5980.0000.0000.0000.000
93A94LEU0-0.071-0.0376.359-0.295-0.2950.0000.0000.0000.000
94A95HIS0-0.044-0.0224.5970.1960.254-0.001-0.003-0.0540.000
95A96ALA00.0040.0006.6520.1800.1800.0000.0000.0000.000
96A97CYS0-0.0030.0087.282-0.215-0.2150.0000.0000.0000.000
97A98THR0-0.019-0.0129.7970.1570.1570.0000.0000.0000.000
98A99GLN00.0010.01012.124-0.064-0.0640.0000.0000.0000.000
99A100GLY00.0280.02015.3870.0490.0490.0000.0000.0000.000
100A101LYS10.9610.97016.734-0.034-0.0340.0000.0000.0000.000
101A102TYR00.004-0.02118.891-0.012-0.0120.0000.0000.0000.000
102A103GLY00.0470.01919.701-0.012-0.0120.0000.0000.0000.000
103A104LEU0-0.035-0.00115.075-0.023-0.0230.0000.0000.0000.000
104A105TRP00.0240.00612.9190.0350.0350.0000.0000.0000.000
105A106THR00.0070.0048.782-0.158-0.1580.0000.0000.0000.000
106A107GLY00.0370.0137.1480.3270.3270.0000.0000.0000.000
107A108GLN0-0.034-0.0103.105-1.264-0.7020.083-0.187-0.4570.000
108A109ALA00.011-0.0112.961-0.3101.0610.268-0.578-1.061-0.004
109A110GLU-1-0.818-0.8962.500-3.767-1.6641.874-1.909-2.068-0.019
110A111PRO0-0.018-0.0143.6260.0620.2250.003-0.053-0.1120.000
111A112VAL0-0.022-0.0206.5330.2170.2170.0000.0000.0000.000
112A113PRO0-0.004-0.00710.220-0.010-0.0100.0000.0000.0000.000
113A114ASP-1-0.883-0.93012.907-0.474-0.4740.0000.0000.0000.000
114A115ASP-1-0.853-0.91115.554-0.267-0.2670.0000.0000.0000.000
115A116ALA0-0.013-0.00518.5410.0030.0030.0000.0000.0000.000
116A117PRO0-0.021-0.00521.7950.0000.0000.0000.0000.0000.000
117A118LEU0-0.025-0.03224.6610.0100.0100.0000.0000.0000.000
118A119GLU-1-0.878-0.93227.631-0.097-0.0970.0000.0000.0000.000
119A120VAL0-0.046-0.03330.111-0.003-0.0030.0000.0000.0000.000
120A121PRO0-0.0170.00831.4000.0060.0060.0000.0000.0000.000
121A122PRO00.020-0.01434.381-0.001-0.0010.0000.0000.0000.000
122A123GLU-1-0.885-0.94934.484-0.086-0.0860.0000.0000.0000.000
123A124LEU0-0.038-0.01330.484-0.001-0.0010.0000.0000.0000.000
124A125ALA00.0620.03333.710-0.006-0.0060.0000.0000.0000.000
125A126ARG10.8360.91536.1440.0830.0830.0000.0000.0000.000
126A127SER00.046-0.02331.651-0.001-0.0010.0000.0000.0000.000
127A128ALA00.0520.05032.576-0.005-0.0050.0000.0000.0000.000
128A129SER00.0290.01333.5020.0010.0010.0000.0000.0000.000
129A130ALA0-0.026-0.01235.5360.0030.0030.0000.0000.0000.000
130A131LEU00.0350.03129.1820.0020.0020.0000.0000.0000.000
131A132GLY00.0420.00233.6710.0000.0000.0000.0000.0000.000
132A133ARG10.8430.91935.4210.0870.0870.0000.0000.0000.000
133A134LEU0-0.0050.01433.5220.0030.0030.0000.0000.0000.000
134A135ILE00.0500.01530.7790.0020.0020.0000.0000.0000.000
135A136ALA0-0.002-0.00334.9930.0030.0030.0000.0000.0000.000
136A137ARG10.7810.88238.3740.0810.0810.0000.0000.0000.000
137A138LEU00.0230.00233.6840.0030.0030.0000.0000.0000.000
138A139GLN00.006-0.00236.2990.0020.0020.0000.0000.0000.000
139A140ARG10.8820.95538.8600.0760.0760.0000.0000.0000.000
140A141GLU-1-0.849-0.91141.123-0.073-0.0730.0000.0000.0000.000
141A142GLY0-0.032-0.00440.3500.0010.0010.0000.0000.0000.000
142A143VAL0-0.040-0.02035.7470.0010.0010.0000.0000.0000.000
143A144PRO00.0260.00936.084-0.003-0.0030.0000.0000.0000.000
144A145PRO00.0910.02732.162-0.005-0.0050.0000.0000.0000.000
145A146HIS0-0.028-0.01230.589-0.011-0.0110.0000.0000.0000.000
146A147ILE0-0.033-0.02231.471-0.002-0.0020.0000.0000.0000.000
147A148MET0-0.0240.00531.462-0.001-0.0010.0000.0000.0000.000
148A149PRO0-0.001-0.00728.325-0.007-0.0070.0000.0000.0000.000
149A150MET00.0100.01726.477-0.011-0.0110.0000.0000.0000.000
150A151ALA00.0470.01325.0510.0120.0120.0000.0000.0000.000
151A152ALA0-0.019-0.01527.0300.0030.0030.0000.0000.0000.000
152A153PRO0-0.005-0.01425.6020.0070.0070.0000.0000.0000.000
153A154PHE00.0290.01827.325-0.008-0.0080.0000.0000.0000.000
154A155ARG10.9420.97624.4200.1920.1920.0000.0000.0000.000
155A156LEU0-0.021-0.02228.759-0.004-0.0040.0000.0000.0000.000
156A157ASP-1-0.854-0.92630.524-0.102-0.1020.0000.0000.0000.000
157A158ASP-1-0.868-0.93724.627-0.192-0.1920.0000.0000.0000.000
158A159CYS0-0.049-0.01026.077-0.006-0.0060.0000.0000.0000.000
159A160GLY00.0500.02722.431-0.004-0.0040.0000.0000.0000.000
160A161TRP00.0120.02123.072-0.005-0.0050.0000.0000.0000.000
161A162VAL0-0.026-0.03024.435-0.001-0.0010.0000.0000.0000.000
162A163ALA0-0.003-0.01324.1230.0020.0020.0000.0000.0000.000
163A164ASP-1-0.781-0.87120.243-0.288-0.2880.0000.0000.0000.000
164A165ARG10.7720.87021.0580.2470.2470.0000.0000.0000.000
165A166TRP0-0.029-0.03825.6920.0050.0050.0000.0000.0000.000
166A167ALA00.0100.01122.8580.0060.0060.0000.0000.0000.000
167A168GLU-1-0.826-0.88322.396-0.248-0.2480.0000.0000.0000.000
168A169MET0-0.059-0.02624.0450.0100.0100.0000.0000.0000.000
169A170LEU00.0010.00527.7280.0110.0110.0000.0000.0000.000
170A171SER0-0.024-0.02227.255-0.015-0.0150.0000.0000.0000.000
171A172LEU00.0150.01725.4290.0090.0090.0000.0000.0000.000
172A173PRO00.0100.00624.528-0.009-0.0090.0000.0000.0000.000
173A174PRO00.0750.03420.295-0.009-0.0090.0000.0000.0000.000
174A175ALA00.023-0.00519.078-0.025-0.0250.0000.0000.0000.000
175A176ASP-1-0.813-0.89719.557-0.175-0.1750.0000.0000.0000.000
176A177LYS10.7810.92220.4710.2000.2000.0000.0000.0000.000
177A178ALA00.0200.00515.549-0.018-0.0180.0000.0000.0000.000
178A179ARG10.7440.83216.3720.1480.1480.0000.0000.0000.000
179A180LEU00.006-0.01718.269-0.007-0.0070.0000.0000.0000.000
180A181LEU0-0.041-0.00813.8030.0040.0040.0000.0000.0000.000
181A182LEU0-0.018-0.03011.349-0.016-0.0160.0000.0000.0000.000
182A183LEU0-0.0650.00515.6990.0190.0190.0000.0000.0000.000
183A184PRO00.0560.02419.166-0.012-0.0120.0000.0000.0000.000
184A185PRO00.0270.00920.4060.0120.0120.0000.0000.0000.000
185A186LEU00.0010.00722.8940.0080.0080.0000.0000.0000.000
186A187ASP-1-0.817-0.91123.611-0.126-0.1260.0000.0000.0000.000
187A188ARG10.7630.87319.1800.2870.2870.0000.0000.0000.000
188A189LEU00.014-0.00124.2470.0060.0060.0000.0000.0000.000
189A190ARG10.8650.90627.4070.1230.1230.0000.0000.0000.000
190A191GLU-1-0.823-0.87825.178-0.152-0.1520.0000.0000.0000.000
191A192ILE0-0.013-0.00726.0340.0050.0050.0000.0000.0000.000
192A193ASP-1-0.813-0.87728.827-0.093-0.0930.0000.0000.0000.000
193A194ALA0-0.038-0.02631.4280.0070.0070.0000.0000.0000.000
194A195VAL0-0.026-0.01229.4670.0060.0060.0000.0000.0000.000
195A196LEU0-0.056-0.01731.8980.0050.0050.0000.0000.0000.000
196A197ALA0-0.088-0.02334.8150.0060.0060.0000.0000.0000.000
197A198ALA0-0.020-0.00236.0830.0030.0030.0000.0000.0000.000