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: LZM19

Calculation Name: 4QT4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4QT4

Chain ID: A

ChEMBL ID:

UniProt ID: B5XIP6

Base Structure: X-ray

Registration Date: 2023-06-21

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2153007.286227
FMO2-HF: Nuclear repulsion 2078359.918931
FMO2-HF: Total energy -74647.367296
FMO2-MP2: Total energy -74863.69159


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.
-17.503-10.7286.018-5.951-6.841-0.039
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 : 0.014 / q_NPA : 0.016
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].
3A3LYS10.8380.9233.2333.8086.666-0.018-1.470-1.3690.005
4A4MET0-0.0040.0046.2780.7330.7330.0000.0000.0000.000
5A5ILE00.0130.0019.5820.2350.2350.0000.0000.0000.000
6A6VAL00.002-0.00112.5490.1390.1390.0000.0000.0000.000
7A7GLY00.0280.01415.8660.0370.0370.0000.0000.0000.000
8A8LEU0-0.047-0.04119.3660.0340.0340.0000.0000.0000.000
9A9GLY00.027-0.00622.1750.0150.0150.0000.0000.0000.000
10A10ASN0-0.058-0.01825.6480.0020.0020.0000.0000.0000.000
11A11PRO00.0730.05126.830-0.001-0.0010.0000.0000.0000.000
12A12GLY00.0250.00128.5470.0160.0160.0000.0000.0000.000
13A13SER00.0600.01631.855-0.007-0.0070.0000.0000.0000.000
14A14LYS10.9370.97434.1710.1840.1840.0000.0000.0000.000
15A15TYR0-0.021-0.03031.3430.0110.0110.0000.0000.0000.000
16A16GLU-1-0.904-0.92030.686-0.236-0.2360.0000.0000.0000.000
17A17LYS10.9620.97331.0640.1920.1920.0000.0000.0000.000
18A18THR0-0.076-0.03031.7350.0000.0000.0000.0000.0000.000
19A19LYS10.9210.96030.9250.1870.1870.0000.0000.0000.000
20A20HIS10.7540.83928.4690.2710.2710.0000.0000.0000.000
21A21ASN0-0.009-0.00526.876-0.023-0.0230.0000.0000.0000.000
22A22ILE00.0550.03224.821-0.016-0.0160.0000.0000.0000.000
23A23GLY0-0.0030.00222.212-0.022-0.0220.0000.0000.0000.000
24A24PHE0-0.039-0.02521.671-0.038-0.0380.0000.0000.0000.000
25A25MET00.0200.02323.223-0.013-0.0130.0000.0000.0000.000
26A26ALA00.0050.00720.769-0.002-0.0020.0000.0000.0000.000
27A27ILE00.0090.01016.454-0.021-0.0210.0000.0000.0000.000
28A28ASP-1-0.792-0.88319.700-0.438-0.4380.0000.0000.0000.000
29A29ASN0-0.054-0.04122.3530.0280.0280.0000.0000.0000.000
30A30ILE0-0.005-0.00715.6930.0070.0070.0000.0000.0000.000
31A31VAL00.0080.00316.554-0.016-0.0160.0000.0000.0000.000
32A32LYS10.9270.98218.7180.3640.3640.0000.0000.0000.000
33A33ASN0-0.111-0.07620.3350.0530.0530.0000.0000.0000.000
34A34LEU0-0.080-0.03013.981-0.005-0.0050.0000.0000.0000.000
35A35ASP-1-0.922-0.93517.196-0.324-0.3240.0000.0000.0000.000
36A36VAL0-0.040-0.01414.407-0.024-0.0240.0000.0000.0000.000
37A37THR00.0230.00917.3250.0270.0270.0000.0000.0000.000
38A38PHE0-0.049-0.04017.721-0.036-0.0360.0000.0000.0000.000
39A39THR0-0.019-0.01217.4390.0540.0540.0000.0000.0000.000
40A40ASP-1-0.878-0.92919.165-0.371-0.3710.0000.0000.0000.000
41A41ASP-1-0.811-0.90615.727-0.425-0.4250.0000.0000.0000.000
42A42LYS10.9640.96318.8490.2020.2020.0000.0000.0000.000
43A43ASN0-0.0300.01014.9020.0620.0620.0000.0000.0000.000
44A44PHE0-0.029-0.02112.6880.0020.0020.0000.0000.0000.000
45A45LYS10.8670.94718.4450.3250.3250.0000.0000.0000.000
46A46ALA00.013-0.01218.031-0.018-0.0180.0000.0000.0000.000
47A47GLN0-0.077-0.03019.7760.0170.0170.0000.0000.0000.000
48A48ILE0-0.011-0.02013.443-0.068-0.0680.0000.0000.0000.000
49A49GLY00.0800.06215.1210.0920.0920.0000.0000.0000.000
50A50SER0-0.060-0.0379.664-0.135-0.1350.0000.0000.0000.000
51A51THR00.0350.0129.9020.2280.2280.0000.0000.0000.000
52A52PHE00.0180.0054.373-0.585-0.467-0.001-0.012-0.1040.000
53A53ILE0-0.027-0.0057.6530.2770.2770.0000.0000.0000.000
54A54ASN00.0150.0067.387-0.177-0.1770.0000.0000.0000.000
55A55HIS00.0220.0053.192-0.910-0.2180.031-0.165-0.5580.000
56A56GLU-1-0.860-0.9282.032-17.262-15.1336.002-3.868-4.264-0.045
57A57LYS10.8560.9563.4901.7662.6110.005-0.337-0.5130.001
58A58VAL00.0250.0065.258-1.031-1.122-0.001-0.0120.1040.000
59A59TYR00.019-0.0016.4850.6820.6820.0000.0000.0000.000
60A60PHE00.007-0.00610.635-0.072-0.0720.0000.0000.0000.000
61A61VAL00.037-0.00713.7070.1250.1250.0000.0000.0000.000
62A62LYS10.8230.92116.4340.4480.4480.0000.0000.0000.000
63A63PRO0-0.005-0.00418.8810.0400.0400.0000.0000.0000.000
64A64THR00.003-0.01821.1500.0250.0250.0000.0000.0000.000
65A65THR00.0410.02522.5460.0190.0190.0000.0000.0000.000
66A66PHE0-0.019-0.00325.2450.0270.0270.0000.0000.0000.000
67A67MET00.0700.05125.387-0.020-0.0200.0000.0000.0000.000
68A68ASN0-0.049-0.01925.525-0.029-0.0290.0000.0000.0000.000
69A69ASN0-0.006-0.00525.5840.0150.0150.0000.0000.0000.000
70A70SER0-0.015-0.02021.120-0.020-0.0200.0000.0000.0000.000
71A71GLY00.005-0.00519.970-0.051-0.0510.0000.0000.0000.000
72A72ILE0-0.0150.00919.643-0.029-0.0290.0000.0000.0000.000
73A73ALA00.0510.02118.860-0.015-0.0150.0000.0000.0000.000
74A74VAL0-0.006-0.00214.682-0.054-0.0540.0000.0000.0000.000
75A75LYS10.9510.97214.8940.2700.2700.0000.0000.0000.000
76A76ALA00.0100.02715.258-0.018-0.0180.0000.0000.0000.000
77A77LEU0-0.001-0.01212.568-0.009-0.0090.0000.0000.0000.000
78A78LEU0-0.032-0.02210.056-0.118-0.1180.0000.0000.0000.000
79A79THR0-0.012-0.01210.5830.0080.0080.0000.0000.0000.000
80A80TYR0-0.070-0.0349.9910.0680.0680.0000.0000.0000.000
81A81TYR0-0.013-0.0156.4170.1050.1050.0000.0000.0000.000
82A82ASN0-0.0310.0056.198-0.222-0.2220.0000.0000.0000.000
83A83ILE0-0.033-0.0095.948-0.009-0.0090.0000.0000.0000.000
84A84ASP-1-0.736-0.8587.077-0.422-0.4220.0000.0000.0000.000
85A85ILE0-0.025-0.0198.613-0.284-0.2840.0000.0000.0000.000
86A86THR0-0.085-0.0698.579-0.121-0.1210.0000.0000.0000.000
87A87ASP-1-0.863-0.9164.022-4.884-4.6600.000-0.087-0.1370.000
88A88LEU0-0.075-0.0187.102-0.177-0.1770.0000.0000.0000.000
89A89ILE0-0.025-0.01810.4660.1790.1790.0000.0000.0000.000
90A90VAL0-0.0260.00113.0600.0190.0190.0000.0000.0000.000
91A91ILE00.004-0.00716.1170.0590.0590.0000.0000.0000.000
92A92TYR0-0.016-0.04119.1230.0230.0230.0000.0000.0000.000
93A93ASP-1-0.683-0.80622.762-0.322-0.3220.0000.0000.0000.000
94A94ASP-1-0.872-0.94426.353-0.295-0.2950.0000.0000.0000.000
95A95LEU0-0.021-0.03227.4430.0120.0120.0000.0000.0000.000
96A96ASP-1-0.796-0.86230.470-0.175-0.1750.0000.0000.0000.000
97A97MET0-0.0540.02326.1040.0000.0000.0000.0000.0000.000
98A98GLU-1-0.837-0.92631.558-0.184-0.1840.0000.0000.0000.000
99A99VAL00.0210.00431.792-0.021-0.0210.0000.0000.0000.000
100A100SER0-0.0130.00329.3410.0060.0060.0000.0000.0000.000
101A101LYS10.9010.97728.1160.2300.2300.0000.0000.0000.000
102A102LEU00.0380.01421.680-0.011-0.0110.0000.0000.0000.000
103A103ARG10.8350.88223.6850.2890.2890.0000.0000.0000.000
104A104LEU00.0400.05616.971-0.016-0.0160.0000.0000.0000.000
105A105ARG10.8140.89519.4510.3890.3890.0000.0000.0000.000
106A106SER00.1610.07116.866-0.040-0.0400.0000.0000.0000.000
107A107LYS10.9961.01818.0970.2610.2610.0000.0000.0000.000
108A108GLY0-0.020-0.00220.800-0.002-0.0020.0000.0000.0000.000
109A109SER00.0310.01323.475-0.022-0.0220.0000.0000.0000.000
110A110ALA00.034-0.00425.837-0.003-0.0030.0000.0000.0000.000
111A111GLY00.0120.02326.701-0.002-0.0020.0000.0000.0000.000
112A112GLY0-0.012-0.01130.0230.0050.0050.0000.0000.0000.000
113A113HIS0-0.008-0.01025.1320.0090.0090.0000.0000.0000.000
114A114ASN00.0560.00927.181-0.021-0.0210.0000.0000.0000.000
115A115GLY00.0760.04024.5150.0000.0000.0000.0000.0000.000
116A116ILE00.0010.00021.141-0.016-0.0160.0000.0000.0000.000
117A117LYS10.9260.95423.0350.2140.2140.0000.0000.0000.000
118A118SER0-0.0060.00623.887-0.005-0.0050.0000.0000.0000.000
119A119ILE00.0550.02417.9630.0050.0050.0000.0000.0000.000
120A120ILE0-0.034-0.00720.022-0.005-0.0050.0000.0000.0000.000
121A121ALA0-0.036-0.01721.6490.0110.0110.0000.0000.0000.000
122A122HIS0-0.045-0.02120.2080.0330.0330.0000.0000.0000.000
123A123ILE0-0.023-0.01915.0510.0070.0070.0000.0000.0000.000
124A124GLY00.0170.02617.7160.0020.0020.0000.0000.0000.000
125A125THR00.0760.03516.5400.0340.0340.0000.0000.0000.000
126A126GLN0-0.029-0.02019.525-0.032-0.0320.0000.0000.0000.000
127A127GLU-1-0.953-0.98717.749-0.336-0.3360.0000.0000.0000.000
128A128PHE00.0860.04214.519-0.026-0.0260.0000.0000.0000.000
129A129ASN0-0.028-0.01411.3910.2280.2280.0000.0000.0000.000
130A130ARG10.7740.90315.1160.4240.4240.0000.0000.0000.000
131A131ILE00.0370.00615.3390.0350.0350.0000.0000.0000.000
132A132LYS10.8460.91719.1840.3560.3560.0000.0000.0000.000
133A133VAL00.0660.02822.8770.0120.0120.0000.0000.0000.000
134A134GLY0-0.025-0.00725.6020.0070.0070.0000.0000.0000.000
135A135ILE00.0000.00129.1280.0030.0030.0000.0000.0000.000
136A136GLY00.0540.02931.6600.0130.0130.0000.0000.0000.000
137A137ARG10.7800.85934.3050.1770.1770.0000.0000.0000.000
138A138PRO0-0.0240.01235.3280.0060.0060.0000.0000.0000.000
139A139LEU00.0590.01438.2290.0050.0050.0000.0000.0000.000
140A140LYS10.9860.98241.6140.1180.1180.0000.0000.0000.000
141A141GLY00.005-0.00242.8960.0040.0040.0000.0000.0000.000
142A142MET0-0.0340.01439.852-0.002-0.0020.0000.0000.0000.000
143A143THR0-0.037-0.02639.558-0.006-0.0060.0000.0000.0000.000
144A144VAL00.0630.00232.782-0.003-0.0030.0000.0000.0000.000
145A145ILE00.0270.01435.306-0.009-0.0090.0000.0000.0000.000
146A146ASN00.0460.02236.329-0.009-0.0090.0000.0000.0000.000
147A147HIS00.0290.03733.7880.0050.0050.0000.0000.0000.000
148A148VAL0-0.002-0.01231.260-0.005-0.0050.0000.0000.0000.000
149A149MET0-0.066-0.03732.112-0.010-0.0100.0000.0000.0000.000
150A150GLY00.0360.04435.4570.0060.0060.0000.0000.0000.000
151A151GLN00.003-0.01735.303-0.016-0.0160.0000.0000.0000.000
152A152PHE00.023-0.00229.8970.0000.0000.0000.0000.0000.000
153A153ASN0-0.0130.00135.8660.0100.0100.0000.0000.0000.000
154A154THR00.0370.00237.775-0.008-0.0080.0000.0000.0000.000
155A155GLU-1-0.904-0.94938.797-0.150-0.1500.0000.0000.0000.000
156A156ASP-1-0.845-0.92234.988-0.185-0.1850.0000.0000.0000.000
157A157ASN0-0.043-0.02134.097-0.024-0.0240.0000.0000.0000.000
158A158ILE00.0390.02332.884-0.016-0.0160.0000.0000.0000.000
159A159ALA00.0420.02732.228-0.011-0.0110.0000.0000.0000.000
160A160ILE00.012-0.00428.795-0.021-0.0210.0000.0000.0000.000
161A161SER0-0.021-0.02428.168-0.026-0.0260.0000.0000.0000.000
162A162LEU00.0130.01327.652-0.019-0.0190.0000.0000.0000.000
163A163THR0-0.078-0.06825.282-0.020-0.0200.0000.0000.0000.000
164A164LEU00.004-0.00323.620-0.037-0.0370.0000.0000.0000.000
165A165ASP-1-0.787-0.87022.697-0.371-0.3710.0000.0000.0000.000
166A166ARG10.8330.90922.2900.2970.2970.0000.0000.0000.000
167A167VAL0-0.029-0.01818.828-0.037-0.0370.0000.0000.0000.000
168A168VAL00.0340.02518.020-0.086-0.0860.0000.0000.0000.000
169A169ASN0-0.033-0.02217.209-0.073-0.0730.0000.0000.0000.000
170A170ALA00.0040.01117.071-0.028-0.0280.0000.0000.0000.000
171A171VAL00.0270.01112.535-0.075-0.0750.0000.0000.0000.000
172A172LYS10.9270.96612.4140.3830.3830.0000.0000.0000.000
173A173PHE0-0.016-0.01213.021-0.033-0.0330.0000.0000.0000.000
174A174TYR00.0650.0217.602-0.184-0.1840.0000.0000.0000.000
175A175LEU0-0.014-0.0197.759-0.133-0.1330.0000.0000.0000.000
176A176GLN0-0.108-0.0468.542-0.092-0.0920.0000.0000.0000.000
177A177GLU-1-0.846-0.92010.658-0.310-0.3100.0000.0000.0000.000
178A178ASN0-0.0010.0165.106-0.663-0.6630.0000.0000.0000.000
179A179ASP-1-0.773-0.8817.929-0.312-0.3120.0000.0000.0000.000
180A180PHE00.019-0.00610.9650.0580.0580.0000.0000.0000.000
181A181GLU-1-0.922-0.96013.007-0.285-0.2850.0000.0000.0000.000
182A182LYS10.8830.94112.7700.4210.4210.0000.0000.0000.000
183A183THR0-0.031-0.02613.6110.0210.0210.0000.0000.0000.000
184A184MET0-0.058-0.03816.2340.0390.0390.0000.0000.0000.000
185A185GLN0-0.038-0.01018.8980.0410.0410.0000.0000.0000.000
186A186LYS10.9270.98618.7270.3310.3310.0000.0000.0000.000
187A187PHE0-0.016-0.00618.2560.0180.0180.0000.0000.0000.000
188A188ASN0-0.044-0.01621.2020.0210.0210.0000.0000.0000.000
189A189GLY00.0070.01523.9410.0220.0220.0000.0000.0000.000