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: MN6VZ

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2105987.840458
FMO2-HF: Nuclear repulsion 2029190.867413
FMO2-HF: Total energy -76796.973045
FMO2-MP2: Total energy -77018.207851


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.
-6.816-0.962.346-3.486-4.715-0.023
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 : 0.049 / q_NPA : 0.007
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].
3A4ILE00.0180.0183.689-1.0400.449-0.006-0.653-0.8310.001
4A5PRO0-0.023-0.0096.0200.3810.3810.0000.0000.0000.000
5A6LEU00.009-0.0168.539-0.127-0.1270.0000.0000.0000.000
6A7PHE00.023-0.00311.5550.1300.1300.0000.0000.0000.000
7A8PRO0-0.082-0.03614.967-0.017-0.0170.0000.0000.0000.000
8A9LEU00.0420.02616.7960.0380.0380.0000.0000.0000.000
9A10SER0-0.030-0.02719.610-0.003-0.0030.0000.0000.0000.000
10A11ASN0-0.044-0.02221.758-0.004-0.0040.0000.0000.0000.000
11A12ALA0-0.0200.00217.950-0.025-0.0250.0000.0000.0000.000
12A13LEU00.0270.01815.4250.0300.0300.0000.0000.0000.000
13A14PHE00.0330.00516.125-0.053-0.0530.0000.0000.0000.000
14A15PRO00.0660.04315.2920.0100.0100.0000.0000.0000.000
15A16ALA0-0.082-0.05717.4460.0420.0420.0000.0000.0000.000
16A17GLY0-0.0120.00719.5690.0310.0310.0000.0000.0000.000
17A18VAL0-0.011-0.01320.623-0.016-0.0160.0000.0000.0000.000
18A19LEU00.0070.00118.5150.0030.0030.0000.0000.0000.000
19A20ARG10.9110.96522.3220.1710.1710.0000.0000.0000.000
20A21LEU00.0100.01419.1360.0090.0090.0000.0000.0000.000
21A22ARG10.9220.96823.1680.1450.1450.0000.0000.0000.000
22A23VAL0-0.0080.00021.915-0.007-0.0070.0000.0000.0000.000
23A24PHE00.009-0.00524.0100.0150.0150.0000.0000.0000.000
24A25GLU-1-0.842-0.92423.264-0.140-0.1400.0000.0000.0000.000
25A26ILE00.0550.00423.340-0.013-0.0130.0000.0000.0000.000
26A27ARG10.8120.91220.0630.1750.1750.0000.0000.0000.000
27A28TYR00.0730.02616.419-0.011-0.0110.0000.0000.0000.000
28A29LEU0-0.0240.00418.542-0.015-0.0150.0000.0000.0000.000
29A30ASP-1-0.961-0.97717.450-0.084-0.0840.0000.0000.0000.000
30A31MET0-0.0090.01013.193-0.016-0.0160.0000.0000.0000.000
31A32VAL00.0490.01415.362-0.020-0.0200.0000.0000.0000.000
32A33ARG10.9410.97017.7370.1010.1010.0000.0000.0000.000
33A34ARG10.9680.99612.5750.0910.0910.0000.0000.0000.000
34A35CYS0-0.015-0.00912.670-0.006-0.0060.0000.0000.0000.000
35A36ILE0-0.057-0.02615.0850.0060.0060.0000.0000.0000.000
36A37ALA0-0.082-0.03617.5470.0130.0130.0000.0000.0000.000
37A38ASP-1-0.922-0.96713.883-0.192-0.1920.0000.0000.0000.000
38A39GLY0-0.0050.00414.888-0.015-0.0150.0000.0000.0000.000
39A40SER0-0.0190.01710.575-0.068-0.0680.0000.0000.0000.000
40A41GLU-1-0.874-0.94410.438-0.692-0.6920.0000.0000.0000.000
41A42PHE0-0.030-0.02810.253-0.075-0.0750.0000.0000.0000.000
42A43GLY00.0310.0199.423-0.005-0.0050.0000.0000.0000.000
43A44VAL00.0030.00610.2520.1230.1230.0000.0000.0000.000
44A45VAL0-0.021-0.00712.218-0.010-0.0100.0000.0000.0000.000
45A46VAL0-0.024-0.00614.0940.0490.0490.0000.0000.0000.000
46A47LEU0-0.027-0.02817.165-0.010-0.0100.0000.0000.0000.000
47A48GLU-1-0.900-0.96418.064-0.223-0.2230.0000.0000.0000.000
48A49GLN0-0.074-0.05120.6300.0180.0180.0000.0000.0000.000
49A50GLY00.0180.00422.1720.0090.0090.0000.0000.0000.000
50A51THR0-0.054-0.01623.143-0.004-0.0040.0000.0000.0000.000
51A52GLU-1-0.790-0.89521.683-0.224-0.2240.0000.0000.0000.000
52A53VAL0-0.0270.00522.473-0.005-0.0050.0000.0000.0000.000
53A54ARG10.9650.95622.7150.0970.0970.0000.0000.0000.000
54A55ARG10.9300.97525.4320.1020.1020.0000.0000.0000.000
55A56PRO0-0.018-0.00726.622-0.001-0.0010.0000.0000.0000.000
56A57ASP-1-0.919-0.96129.061-0.066-0.0660.0000.0000.0000.000
57A58GLY0-0.0090.00026.7780.0030.0030.0000.0000.0000.000
58A59ARG10.9090.95321.6030.0640.0640.0000.0000.0000.000
59A60GLU-1-0.860-0.93219.240-0.156-0.1560.0000.0000.0000.000
60A61VAL0-0.0200.00017.4970.0050.0050.0000.0000.0000.000
61A62LEU0-0.003-0.00512.185-0.006-0.0060.0000.0000.0000.000
62A63ALA00.0330.03515.1610.0260.0260.0000.0000.0000.000
63A64ARG10.9530.94612.3010.1950.1950.0000.0000.0000.000
64A65ALA0-0.0070.00210.712-0.063-0.0630.0000.0000.0000.000
65A66GLY0-0.0050.00510.9930.0950.0950.0000.0000.0000.000
66A67THR00.007-0.00111.263-0.066-0.0660.0000.0000.0000.000
67A68MET0-0.0350.0017.924-0.143-0.1430.0000.0000.0000.000
68A69ALA00.0090.01711.0850.1240.1240.0000.0000.0000.000
69A70ARG10.9570.98113.9040.2870.2870.0000.0000.0000.000
70A71ILE0-0.006-0.02416.2520.0340.0340.0000.0000.0000.000
71A72ASP-1-0.869-0.92019.094-0.246-0.2460.0000.0000.0000.000
72A73HIS0-0.055-0.04122.1880.0110.0110.0000.0000.0000.000
73A74TRP0-0.029-0.00322.908-0.001-0.0010.0000.0000.0000.000
74A75GLU-1-0.906-0.95524.792-0.111-0.1110.0000.0000.0000.000
75A76ALA00.007-0.01727.802-0.006-0.0060.0000.0000.0000.000
76A77PRO00.0010.03130.3970.0090.0090.0000.0000.0000.000
77A78MET0-0.001-0.00233.1260.0060.0060.0000.0000.0000.000
78A79PRO00.020-0.01532.808-0.004-0.0040.0000.0000.0000.000
79A80ALA0-0.032-0.01830.6480.0000.0000.0000.0000.0000.000
80A81LEU0-0.0280.00228.648-0.005-0.0050.0000.0000.0000.000
81A82LEU0-0.0170.00222.3450.0010.0010.0000.0000.0000.000
82A83GLU-1-0.898-0.96525.710-0.142-0.1420.0000.0000.0000.000
83A84LEU00.018-0.01120.4840.0040.0040.0000.0000.0000.000
84A85ALA0-0.0030.02023.317-0.010-0.0100.0000.0000.0000.000
85A86CYS0-0.065-0.03118.341-0.012-0.0120.0000.0000.0000.000
86A87THR00.009-0.00618.6700.0290.0290.0000.0000.0000.000
87A88GLY0-0.0080.00615.820-0.043-0.0430.0000.0000.0000.000
88A89THR0-0.044-0.03413.0050.0310.0310.0000.0000.0000.000
89A90GLY00.0840.05411.1050.0370.0370.0000.0000.0000.000
90A91ARG10.8840.94410.8970.3450.3450.0000.0000.0000.000
91A92PHE00.0000.0026.237-0.155-0.1550.0000.0000.0000.000
92A93ARG10.9750.9947.6250.6090.6090.0000.0000.0000.000
93A94LEU0-0.047-0.0276.374-0.300-0.3000.0000.0000.0000.000
94A95HIS0-0.0270.0044.8230.1880.1880.0000.0000.0000.000
95A96ALA00.007-0.0026.6130.1970.1970.0000.0000.0000.000
96A97CYS0-0.0230.0037.220-0.205-0.2050.0000.0000.0000.000
97A98THR0-0.009-0.0099.7300.1580.1580.0000.0000.0000.000
98A99GLN00.0070.01212.047-0.065-0.0650.0000.0000.0000.000
99A100GLY00.0200.01615.3110.0490.0490.0000.0000.0000.000
100A101LYS10.9740.97616.663-0.049-0.0490.0000.0000.0000.000
101A102TYR0-0.032-0.03518.891-0.013-0.0130.0000.0000.0000.000
102A103GLY00.0110.00419.629-0.011-0.0110.0000.0000.0000.000
103A104LEU0-0.020-0.00414.625-0.023-0.0230.0000.0000.0000.000
104A105TRP00.0250.01212.7520.0330.0330.0000.0000.0000.000
105A106THR0-0.035-0.0158.5260.0190.0190.0000.0000.0000.000
106A107GLY00.0370.0077.0790.3200.3200.0000.0000.0000.000
107A108GLN0-0.030-0.0093.104-1.467-0.7600.099-0.219-0.5860.000
108A109ALA00.002-0.0152.931-0.3381.0170.302-0.574-1.082-0.004
109A110GLU-1-0.914-0.9662.473-4.081-1.9431.948-1.983-2.103-0.020
110A111PRO0-0.026-0.0173.6020.0830.2500.003-0.057-0.1130.000
111A112VAL0-0.017-0.0126.5250.2070.2070.0000.0000.0000.000
112A113PRO0-0.006-0.01110.209-0.010-0.0100.0000.0000.0000.000
113A114ASP-1-0.919-0.95312.905-0.463-0.4630.0000.0000.0000.000
114A115ASP-1-0.889-0.95815.554-0.252-0.2520.0000.0000.0000.000
115A116ALA0-0.034-0.01418.5350.0040.0040.0000.0000.0000.000
116A117PRO0-0.028-0.00621.792-0.001-0.0010.0000.0000.0000.000
117A118LEU0-0.017-0.02924.6580.0100.0100.0000.0000.0000.000
118A119GLU-1-0.879-0.93727.625-0.098-0.0980.0000.0000.0000.000
119A120VAL0-0.066-0.03330.084-0.004-0.0040.0000.0000.0000.000
120A121PRO0-0.0260.00431.3060.0070.0070.0000.0000.0000.000
121A122PRO00.022-0.01134.369-0.001-0.0010.0000.0000.0000.000
122A123GLU-1-0.857-0.94035.071-0.084-0.0840.0000.0000.0000.000
123A124LEU0-0.031-0.00630.334-0.001-0.0010.0000.0000.0000.000
124A125ALA00.0600.03433.697-0.006-0.0060.0000.0000.0000.000
125A126ARG10.8930.95336.1330.0820.0820.0000.0000.0000.000
126A127SER00.0420.01031.688-0.001-0.0010.0000.0000.0000.000
127A128ALA00.0570.05232.567-0.005-0.0050.0000.0000.0000.000
128A129SER00.012-0.00533.4940.0010.0010.0000.0000.0000.000
129A130ALA0-0.038-0.03535.4610.0030.0030.0000.0000.0000.000
130A131LEU00.0220.02829.1690.0020.0020.0000.0000.0000.000
131A132GLY00.0490.00133.6650.0000.0000.0000.0000.0000.000
132A133ARG10.8760.95035.4180.0880.0880.0000.0000.0000.000
133A134LEU0-0.0050.01333.6460.0030.0030.0000.0000.0000.000
134A135ILE00.0400.01731.0030.0020.0020.0000.0000.0000.000
135A136ALA0-0.002-0.01134.9930.0030.0030.0000.0000.0000.000
136A137ARG10.8600.93838.3640.0810.0810.0000.0000.0000.000
137A138LEU00.0260.00233.6330.0030.0030.0000.0000.0000.000
138A139GLN00.0230.01235.840-0.001-0.0010.0000.0000.0000.000
139A140ARG10.8750.94638.8650.0760.0760.0000.0000.0000.000
140A141GLU-1-0.910-0.95241.147-0.071-0.0710.0000.0000.0000.000
141A142GLY0-0.057-0.01740.3580.0010.0010.0000.0000.0000.000
142A143VAL0-0.043-0.02335.9240.0010.0010.0000.0000.0000.000
143A144PRO00.0310.01036.096-0.003-0.0030.0000.0000.0000.000
144A145PRO00.0960.02632.191-0.005-0.0050.0000.0000.0000.000
145A146HIS0-0.021-0.00530.600-0.010-0.0100.0000.0000.0000.000
146A147ILE0-0.041-0.02131.480-0.002-0.0020.0000.0000.0000.000
147A148MET0-0.045-0.01231.611-0.001-0.0010.0000.0000.0000.000
148A149PRO0-0.019-0.01628.328-0.007-0.0070.0000.0000.0000.000
149A150MET00.0240.02926.508-0.011-0.0110.0000.0000.0000.000
150A151ALA00.0530.01525.1300.0110.0110.0000.0000.0000.000
151A152ALA0-0.011-0.01127.0380.0030.0030.0000.0000.0000.000
152A153PRO0-0.016-0.01725.6980.0070.0070.0000.0000.0000.000
153A154PHE00.0400.01327.331-0.009-0.0090.0000.0000.0000.000
154A155ARG10.9370.97124.4770.1910.1910.0000.0000.0000.000
155A156LEU0-0.021-0.01928.757-0.004-0.0040.0000.0000.0000.000
156A157ASP-1-0.862-0.93530.521-0.104-0.1040.0000.0000.0000.000
157A158ASP-1-0.867-0.93124.695-0.192-0.1920.0000.0000.0000.000
158A159CYS0-0.027-0.00226.166-0.006-0.0060.0000.0000.0000.000
159A160GLY00.0570.01222.401-0.005-0.0050.0000.0000.0000.000
160A161TRP00.0260.03223.064-0.006-0.0060.0000.0000.0000.000
161A162VAL0-0.042-0.03624.431-0.001-0.0010.0000.0000.0000.000
162A163ALA00.009-0.03324.0770.0010.0010.0000.0000.0000.000
163A164ASP-1-0.817-0.91120.340-0.291-0.2910.0000.0000.0000.000
164A165ARG10.8170.91721.4230.2390.2390.0000.0000.0000.000
165A166TRP0-0.021-0.03225.6850.0040.0040.0000.0000.0000.000
166A167ALA00.0030.00622.8360.0060.0060.0000.0000.0000.000
167A168GLU-1-0.855-0.92622.481-0.246-0.2460.0000.0000.0000.000
168A169MET0-0.067-0.03124.0340.0110.0110.0000.0000.0000.000
169A170LEU00.0110.01027.7090.0120.0120.0000.0000.0000.000
170A171SER0-0.019-0.01327.239-0.012-0.0120.0000.0000.0000.000
171A172LEU00.0090.00725.3290.0090.0090.0000.0000.0000.000
172A173PRO00.0190.02124.543-0.009-0.0090.0000.0000.0000.000
173A174PRO00.0860.03320.286-0.009-0.0090.0000.0000.0000.000
174A175ALA00.0410.00219.069-0.025-0.0250.0000.0000.0000.000
175A176ASP-1-0.835-0.90619.556-0.179-0.1790.0000.0000.0000.000
176A177LYS10.7780.91620.3380.1980.1980.0000.0000.0000.000
177A178ALA00.0250.01115.554-0.018-0.0180.0000.0000.0000.000
178A179ARG10.7700.86216.3870.1520.1520.0000.0000.0000.000
179A180LEU00.009-0.01918.284-0.007-0.0070.0000.0000.0000.000
180A181LEU0-0.0310.00213.8130.0050.0050.0000.0000.0000.000
181A182LEU0-0.025-0.03511.387-0.012-0.0120.0000.0000.0000.000
182A183LEU0-0.0630.00215.7350.0170.0170.0000.0000.0000.000
183A184PRO00.0280.01519.206-0.013-0.0130.0000.0000.0000.000
184A185PRO00.0380.01620.5190.0130.0130.0000.0000.0000.000
185A186LEU00.0080.00522.8790.0090.0090.0000.0000.0000.000
186A187ASP-1-0.886-0.96223.587-0.135-0.1350.0000.0000.0000.000
187A188ARG10.8310.95419.3360.2800.2800.0000.0000.0000.000
188A189LEU00.0120.00024.2270.0060.0060.0000.0000.0000.000
189A190ARG10.9400.95927.4460.1230.1230.0000.0000.0000.000
190A191GLU-1-0.834-0.89425.340-0.148-0.1480.0000.0000.0000.000
191A192ILE0-0.0320.00426.0020.0050.0050.0000.0000.0000.000
192A193ASP-1-0.889-0.94928.808-0.094-0.0940.0000.0000.0000.000
193A194ALA0-0.027-0.02031.4630.0070.0070.0000.0000.0000.000
194A195VAL0-0.039-0.01829.4140.0060.0060.0000.0000.0000.000
195A196LEU0-0.064-0.02131.9160.0050.0050.0000.0000.0000.000
196A197ALA0-0.081-0.01634.7960.0060.0060.0000.0000.0000.000
197A198ALA0-0.029-0.00936.0160.0030.0030.0000.0000.0000.000