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: 9G9L2

Calculation Name: 1ZQ7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZQ7

Chain ID: A

ChEMBL ID:

UniProt ID: Q8PZK8

Base Structure: X-ray

Registration Date: 2023-06-20

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2237031.315509
FMO2-HF: Nuclear repulsion 2157452.538623
FMO2-HF: Total energy -79578.776886
FMO2-MP2: Total energy -79809.570338


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.
-29.797-30.37625.759-10.79-14.39-0.011
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 : -0.005
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].
3A3THR0-0.023-0.0443.692-0.8520.773-0.003-0.768-0.8540.000
4A4GLU-1-0.855-0.9415.9580.2280.2280.0000.0000.0000.000
5A5THR0-0.052-0.0318.5280.1150.1150.0000.0000.0000.000
6A6GLU-1-0.752-0.8157.099-0.196-0.1960.0000.0000.0000.000
7A7GLY00.0570.0228.0970.2280.2280.0000.0000.0000.000
8A8ARG10.9260.9558.713-0.182-0.1820.0000.0000.0000.000
9A9ALA0-0.005-0.00711.906-0.002-0.0020.0000.0000.0000.000
10A10ALA00.0520.0229.4520.0030.0030.0000.0000.0000.000
11A11VAL00.0160.00611.565-0.026-0.0260.0000.0000.0000.000
12A12LYS10.7960.90513.940-0.382-0.3820.0000.0000.0000.000
13A13LEU00.0030.01914.024-0.053-0.0530.0000.0000.0000.000
14A14ALA00.0170.02114.892-0.037-0.0370.0000.0000.0000.000
15A15ARG10.7410.85416.786-0.333-0.3330.0000.0000.0000.000
16A16LYS10.8900.94219.545-0.307-0.3070.0000.0000.0000.000
17A17THR0-0.042-0.03118.851-0.033-0.0330.0000.0000.0000.000
18A18ILE0-0.0100.00119.930-0.028-0.0280.0000.0000.0000.000
19A19GLU-1-0.827-0.92423.0870.2420.2420.0000.0000.0000.000
20A20ILE0-0.022-0.01323.769-0.027-0.0270.0000.0000.0000.000
21A21PHE0-0.042-0.00825.282-0.022-0.0220.0000.0000.0000.000
22A22LEU0-0.0080.00326.414-0.016-0.0160.0000.0000.0000.000
23A23SER0-0.075-0.00628.864-0.021-0.0210.0000.0000.0000.000
24A24LYS10.8490.91729.484-0.229-0.2290.0000.0000.0000.000
25A25GLY00.0290.01730.706-0.004-0.0040.0000.0000.0000.000
26A26LYS10.7720.87228.193-0.256-0.2560.0000.0000.0000.000
27A27SER00.0720.01324.048-0.006-0.0060.0000.0000.0000.000
28A28PRO0-0.085-0.01023.861-0.004-0.0040.0000.0000.0000.000
29A29ARG00.1500.13919.5610.0460.0460.0000.0000.0000.000
30A30PRO00.002-0.01222.635-0.027-0.0270.0000.0000.0000.000
31A31ASP-1-0.842-0.93625.1150.2260.2260.0000.0000.0000.000
32A32ALA0-0.014-0.01325.913-0.003-0.0030.0000.0000.0000.000
33A33SER00.0390.01019.7760.0020.0020.0000.0000.0000.000
34A34GLY0-0.024-0.00122.342-0.007-0.0070.0000.0000.0000.000
35A35VAL0-0.054-0.02116.034-0.022-0.0220.0000.0000.0000.000
36A36GLU-1-0.936-0.96417.0090.2350.2350.0000.0000.0000.000
37A37LEU0-0.036-0.01313.3930.0290.0290.0000.0000.0000.000
38A38SER0-0.033-0.0539.6140.0310.0310.0000.0000.0000.000
39A39PRO00.0670.00010.7100.1000.1000.0000.0000.0000.000
40A40VAL00.0340.0365.2120.1310.1310.0000.0000.0000.000
41A41PHE0-0.035-0.0298.1060.5570.5570.0000.0000.0000.000
42A42GLU-1-0.879-0.94010.6550.6430.6430.0000.0000.0000.000
43A43GLU-1-0.900-0.9255.1833.3143.326-0.001-0.001-0.0100.000
44A44TYR0-0.053-0.0209.4390.0640.0640.0000.0000.0000.000
45A45ARG10.8050.8601.911-19.557-26.43114.866-4.203-3.7900.025
46A46GLY00.0100.0378.992-0.326-0.3260.0000.0000.0000.000
47A47VAL0-0.004-0.0238.9770.6080.6080.0000.0000.0000.000
48A48PHE0-0.0060.00010.926-0.329-0.3290.0000.0000.0000.000
49A49VAL00.0000.01212.6980.0990.0990.0000.0000.0000.000
50A50THR0-0.020-0.03015.321-0.061-0.0610.0000.0000.0000.000
51A51LEU00.0190.02717.4770.0030.0030.0000.0000.0000.000
52A52THR00.0270.00619.996-0.032-0.0320.0000.0000.0000.000
53A53GLU-1-0.801-0.91022.6440.1820.1820.0000.0000.0000.000
54A54GLY0-0.009-0.00126.080-0.011-0.0110.0000.0000.0000.000
55A55GLY0-0.036-0.01824.231-0.014-0.0140.0000.0000.0000.000
56A56LEU0-0.028-0.00724.654-0.007-0.0070.0000.0000.0000.000
57A57LEU0-0.028-0.00920.4610.0150.0150.0000.0000.0000.000
58A58ARG10.7640.85723.315-0.229-0.2290.0000.0000.0000.000
59A59GLY00.0410.02422.869-0.011-0.0110.0000.0000.0000.000
60A60CYS0-0.102-0.05517.0620.0280.0280.0000.0000.0000.000
61A61ILE0-0.009-0.00218.430-0.042-0.0420.0000.0000.0000.000
62A62GLY00.0390.00815.5200.0660.0660.0000.0000.0000.000
63A63HIS0-0.067-0.01814.619-0.047-0.0470.0000.0000.0000.000
64A64PRO0-0.005-0.00513.3980.1910.1910.0000.0000.0000.000
65A65TYR00.0350.01512.4740.1300.1300.0000.0000.0000.000
66A66PRO00.0010.02410.4840.0720.0720.0000.0000.0000.000
67A67ASP-1-0.888-0.96212.3640.6440.6440.0000.0000.0000.000
68A68SER0-0.069-0.03914.416-0.143-0.1430.0000.0000.0000.000
69A69THR00.0280.01512.3470.2030.2030.0000.0000.0000.000
70A70LEU00.0420.0207.170-0.118-0.1180.0000.0000.0000.000
71A71LYN0-0.033-0.02711.075-0.148-0.1480.0000.0000.0000.000
72A72GLH0-0.082-0.09913.972-0.098-0.0980.0000.0000.0000.000
73A73ALA00.0400.02812.863-0.089-0.0890.0000.0000.0000.000
74A74ILE00.0050.01310.305-0.084-0.0840.0000.0000.0000.000
75A75LEU0-0.039-0.02114.456-0.114-0.1140.0000.0000.0000.000
76A76ASP-1-0.861-0.93418.1010.4920.4920.0000.0000.0000.000
77A77SER00.0120.00415.751-0.067-0.0670.0000.0000.0000.000
78A78ALA00.002-0.00517.205-0.062-0.0620.0000.0000.0000.000
79A79ILE00.0090.00318.714-0.059-0.0590.0000.0000.0000.000
80A80SER0-0.024-0.01421.041-0.064-0.0640.0000.0000.0000.000
81A81ALA0-0.034-0.00419.432-0.041-0.0410.0000.0000.0000.000
82A82ALA00.0260.02121.590-0.034-0.0340.0000.0000.0000.000
83A83THR0-0.056-0.05224.383-0.035-0.0350.0000.0000.0000.000
84A84ARG10.8620.92623.359-0.394-0.3940.0000.0000.0000.000
85A85ASP-1-0.691-0.80523.7000.3110.3110.0000.0000.0000.000
86A86PRO0-0.023-0.02025.916-0.019-0.0190.0000.0000.0000.000
87A87ARG10.7780.86421.417-0.315-0.3150.0000.0000.0000.000
88A88PHE0-0.031-0.01524.504-0.017-0.0170.0000.0000.0000.000
89A89PRO0-0.0070.01629.5150.0040.0040.0000.0000.0000.000
90A90THR00.021-0.00329.2740.0130.0130.0000.0000.0000.000
91A91VAL0-0.0290.00125.691-0.011-0.0110.0000.0000.0000.000
92A92GLU-1-0.905-0.95928.9830.1750.1750.0000.0000.0000.000
93A93GLN0-0.021-0.03229.8010.0090.0090.0000.0000.0000.000
94A94ASP-1-0.989-0.99629.8550.1530.1530.0000.0000.0000.000
95A95GLU-1-0.689-0.83528.7830.1880.1880.0000.0000.0000.000
96A96MET00.0650.04522.0660.0050.0050.0000.0000.0000.000
97A97LYS10.7910.91825.485-0.130-0.1300.0000.0000.0000.000
98A98ASN0-0.063-0.04327.545-0.021-0.0210.0000.0000.0000.000
99A99ILE00.0110.02922.284-0.001-0.0010.0000.0000.0000.000
100A100LEU0-0.050-0.02119.9920.0020.0020.0000.0000.0000.000
101A101VAL0-0.002-0.01016.0570.0200.0200.0000.0000.0000.000
102A102GLU-1-0.830-0.91914.2690.4000.4000.0000.0000.0000.000
103A103VAL0-0.0080.0009.955-0.011-0.0110.0000.0000.0000.000
104A104THR0-0.0070.0038.7450.0250.0250.0000.0000.0000.000
105A105ILE0-0.024-0.0125.100-0.181-0.1810.0000.0000.0000.000
106A106LEU00.0000.0065.2980.8900.8900.0000.0000.0000.000
107A107THR00.010-0.0012.1160.8760.2995.515-1.434-3.5040.004
108A108GLN0-0.038-0.0344.185-2.838-2.6870.003-0.077-0.0770.000
109A109PRO0-0.043-0.0216.761-0.597-0.5970.0000.0000.0000.000
110A110GLU-1-0.911-0.9496.887-1.052-1.0520.0000.0000.0000.000
111A111LYS10.8120.90010.266-0.141-0.1410.0000.0000.0000.000
112A112ILE00.0490.02712.378-0.086-0.0860.0000.0000.0000.000
113A113ASN0-0.070-0.04714.4720.0980.0980.0000.0000.0000.000
114A114ALA00.0150.00817.469-0.034-0.0340.0000.0000.0000.000
115A115SER0-0.056-0.03419.5480.0380.0380.0000.0000.0000.000
116A116PRO00.0570.00021.551-0.020-0.0200.0000.0000.0000.000
117A117LYS10.8600.91722.4980.1010.1010.0000.0000.0000.000
118A118GLU-1-0.723-0.83619.787-0.255-0.2550.0000.0000.0000.000
119A119LEU0-0.0240.00617.053-0.036-0.0360.0000.0000.0000.000
120A120PRO00.012-0.00116.933-0.040-0.0400.0000.0000.0000.000
121A121ASP-1-0.907-0.95217.533-0.324-0.3240.0000.0000.0000.000
122A122LYS10.7720.87613.9090.3160.3160.0000.0000.0000.000
123A123VAL0-0.0200.00412.461-0.094-0.0940.0000.0000.0000.000
124A124GLU-1-0.817-0.9009.359-1.451-1.4510.0000.0000.0000.000
125A125ILE00.002-0.00410.688-0.079-0.0790.0000.0000.0000.000
126A126GLY00.0180.00910.888-0.043-0.0430.0000.0000.0000.000
127A127LYS10.7840.9055.1852.2242.2240.0000.0000.0000.000
128A128HIS00.0160.0056.4080.1990.1990.0000.0000.0000.000
129A129GLY00.0340.0368.4820.1550.1550.0000.0000.0000.000
130A130LEU0-0.037-0.03110.208-0.048-0.0480.0000.0000.0000.000
131A131ILE00.0310.00412.2970.0850.0850.0000.0000.0000.000
132A132VAL0-0.038-0.00815.067-0.056-0.0560.0000.0000.0000.000
133A133LYS10.8920.92618.342-0.194-0.1940.0000.0000.0000.000
134A134GLN00.003-0.00920.375-0.045-0.0450.0000.0000.0000.000
135A135GLY0-0.015-0.00224.022-0.002-0.0020.0000.0000.0000.000
136A136TYR0-0.022-0.02723.6470.0210.0210.0000.0000.0000.000
137A137CYS0-0.0350.00324.4580.0120.0120.0000.0000.0000.000
138A138GLN00.0630.01017.5970.0160.0160.0000.0000.0000.000
139A139GLY0-0.015-0.00819.295-0.004-0.0040.0000.0000.0000.000
140A140LEU0-0.0120.00213.649-0.013-0.0130.0000.0000.0000.000
141A141LEU0-0.033-0.00614.9350.0040.0040.0000.0000.0000.000
142A142LEU00.0130.00011.6110.0050.0050.0000.0000.0000.000
143A143PRO00.0710.0227.5640.0050.0050.0000.0000.0000.000
144A144GLN00.0340.03210.332-0.091-0.0910.0000.0000.0000.000
145A145VAL0-0.050-0.02812.7470.0020.0020.0000.0000.0000.000
146A146ALA00.0400.01314.254-0.001-0.0010.0000.0000.0000.000
147A147PRO00.0090.01512.5410.0070.0070.0000.0000.0000.000
148A148GLU-1-0.829-0.91415.5500.0260.0260.0000.0000.0000.000
149A149ASN0-0.146-0.09017.7860.0380.0380.0000.0000.0000.000
150A150ASP-1-0.975-0.97119.720-0.141-0.1410.0000.0000.0000.000
151A151MET0-0.0540.00018.2100.0250.0250.0000.0000.0000.000
152A152ASP-1-0.804-0.90518.003-0.229-0.2290.0000.0000.0000.000
153A153SER00.024-0.01616.8580.0150.0150.0000.0000.0000.000
154A154ILE0-0.040-0.01918.0900.0280.0280.0000.0000.0000.000
155A155ASP-1-0.848-0.90520.689-0.083-0.0830.0000.0000.0000.000
156A156PHE00.0090.00912.4520.0450.0450.0000.0000.0000.000
157A157LEU00.0090.01616.9570.0490.0490.0000.0000.0000.000
158A158SER0-0.012-0.01219.1130.0420.0420.0000.0000.0000.000
159A159HIS00.027-0.00120.3140.0230.0230.0000.0000.0000.000
160A160THR0-0.004-0.01816.5090.0410.0410.0000.0000.0000.000
161A161CYS0-0.095-0.02519.4970.0340.0340.0000.0000.0000.000
162A162MET00.0120.01622.3220.0170.0170.0000.0000.0000.000
163A163LYS10.8790.95319.424-0.205-0.2050.0000.0000.0000.000
164A164ALA0-0.030-0.01121.2800.0300.0300.0000.0000.0000.000
165A165GLY0-0.040-0.01322.9630.0050.0050.0000.0000.0000.000
166A166LEU0-0.083-0.03823.477-0.012-0.0120.0000.0000.0000.000
167A167SER0-0.018-0.03826.856-0.004-0.0040.0000.0000.0000.000
168A168PRO00.0750.02225.501-0.001-0.0010.0000.0000.0000.000
169A169ASP-1-0.848-0.90625.017-0.014-0.0140.0000.0000.0000.000
170A170ALA00.004-0.00624.570-0.007-0.0070.0000.0000.0000.000
171A171TRP00.0620.00421.001-0.008-0.0080.0000.0000.0000.000
172A172VAL0-0.063-0.02422.858-0.017-0.0170.0000.0000.0000.000
173A173LYS10.8350.91125.5530.0000.0000.0000.0000.0000.000
174A174GLY0-0.0070.00224.2170.0070.0070.0000.0000.0000.000
175A175ALA0-0.0330.00622.6500.0100.0100.0000.0000.0000.000
176A176GLU-1-0.819-0.87818.8500.1290.1290.0000.0000.0000.000
177A177VAL00.0290.01314.7430.0330.0330.0000.0000.0000.000
178A178TYR0-0.069-0.05112.428-0.038-0.0380.0000.0000.0000.000
179A179CYS00.0340.0298.5190.0210.0210.0000.0000.0000.000
180A180PHE0-0.031-0.0086.4500.1000.1000.0000.0000.0000.000
181A181GLU-1-0.798-0.9172.472-9.569-8.2362.255-1.382-2.207-0.015
182A182GLY00.022-0.0093.5422.0462.4620.009-0.110-0.3140.000
183A183GLN0-0.0160.0092.389-5.192-1.8993.116-2.806-3.603-0.025
184A184ILE00.0150.0075.3910.1270.169-0.001-0.009-0.0310.000
185A185PHE00.0390.0455.545-0.168-0.1680.0000.0000.0000.000
186A186LYS10.8550.90110.584-0.326-0.3260.0000.0000.0000.000
187A187GLU-1-0.755-0.86614.3500.2780.2780.0000.0000.0000.000
188A188LYS10.9110.96217.568-0.100-0.1000.0000.0000.0000.000
189A189GLU-1-0.941-0.98519.9330.0900.0900.0000.0000.0000.000
190A190PRO00.0280.02321.2940.0260.0260.0000.0000.0000.000
191A191ASP-1-0.880-0.94421.0260.2390.2390.0000.0000.0000.000
192A192GLY0-0.043-0.01621.393-0.018-0.0180.0000.0000.0000.000
193A193GLU-1-0.980-1.01317.5970.1230.1230.0000.0000.0000.000
194A194VAL0-0.050-0.02112.8470.0190.0190.0000.0000.0000.000
195A195ILE00.0110.01813.596-0.034-0.0340.0000.0000.0000.000
196A196GLU-1-0.832-0.9196.1051.2721.2720.0000.0000.0000.000
197A197GLU-1-0.926-0.94110.525-0.161-0.1610.0000.0000.0000.000
198A198LYS10.8510.8887.3270.3270.3270.0000.0000.0000.000
199A199PHE0-0.047-0.0107.289-0.329-0.3290.0000.0000.0000.000
200A200LEU0-0.017-0.0106.3530.2290.2290.0000.0000.0000.000
201A201GLU-1-0.912-0.9619.725-0.385-0.3850.0000.0000.0000.000
202A202HIS0-0.069-0.02312.687-0.030-0.0300.0000.0000.0000.000
203A203HIS0-0.079-0.04316.001-0.017-0.0170.0000.0000.0000.000
204A204HIS0-0.013-0.00313.0430.0520.0520.0000.0000.0000.000