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: LJ299

Calculation Name: 4ZG0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ZG0

Chain ID: A

ChEMBL ID:

UniProt ID: Q8VHN8

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 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. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2166275.569381
FMO2-HF: Nuclear repulsion 2089154.685385
FMO2-HF: Total energy -77120.883996
FMO2-MP2: Total energy -77345.209858


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:8:GLU)


Summations of interaction energy for fragment #1(A:8:GLU)
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.
-123.288-116.2966.803-6.967-6.8270.063
Interaction energy analysis for fragmet #1(A:8:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.924 / q_NPA : -0.978
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].
3A10LYS10.9720.9933.558-29.648-27.815-0.002-0.841-0.9900.002
4A11GLN00.0230.0085.321-7.401-7.282-0.001-0.002-0.1150.000
5A12ILE0-0.062-0.0207.485-1.382-1.3820.0000.0000.0000.000
6A13SER00.0610.02711.0380.0100.0100.0000.0000.0000.000
7A14ARG10.9340.95313.817-16.532-16.5320.0000.0000.0000.000
8A15GLU-1-0.954-0.98516.42714.87114.8710.0000.0000.0000.000
9A16GLU-1-0.937-0.97414.68719.20119.2010.0000.0000.0000.000
10A17ALA00.0340.00614.950-0.546-0.5460.0000.0000.0000.000
11A18MET0-0.091-0.05016.654-0.678-0.6780.0000.0000.0000.000
12A19ARG10.9710.98618.629-16.175-16.1750.0000.0000.0000.000
13A20LEU0-0.061-0.00315.323-0.515-0.5150.0000.0000.0000.000
14A21GLY00.0280.01419.906-0.510-0.5100.0000.0000.0000.000
15A22PRO00.018-0.01722.0060.4880.4880.0000.0000.0000.000
16A23GLY0-0.045-0.00922.310-0.095-0.0950.0000.0000.0000.000
17A24TRP0-0.026-0.01013.7720.4150.4150.0000.0000.0000.000
18A25SER0-0.0110.00418.033-0.601-0.6010.0000.0000.0000.000
19A26HIS00.0850.03717.6511.4251.4250.0000.0000.0000.000
20A27SER00.0090.01215.054-0.604-0.6040.0000.0000.0000.000
21A28CYS0-0.055-0.01416.6270.9350.9350.0000.0000.0000.000
22A29HIS00.0110.01115.317-0.529-0.5290.0000.0000.0000.000
23A30ALA00.0270.01217.1260.5910.5910.0000.0000.0000.000
24A31MET0-0.011-0.00215.2970.3670.3670.0000.0000.0000.000
25A32LEU00.0190.00917.973-0.261-0.2610.0000.0000.0000.000
26A33TYR00.015-0.01219.2980.0740.0740.0000.0000.0000.000
27A34ALA00.0480.04122.038-0.460-0.4600.0000.0000.0000.000
28A35ALA00.0390.01924.1310.4030.4030.0000.0000.0000.000
29A36ASN0-0.036-0.04625.480-0.903-0.9030.0000.0000.0000.000
30A37PRO0-0.005-0.00127.2230.2430.2430.0000.0000.0000.000
31A38GLY00.0170.01329.630-0.320-0.3200.0000.0000.0000.000
32A39GLN00.0500.01129.3450.4930.4930.0000.0000.0000.000
33A40LEU00.0310.03427.636-0.380-0.3800.0000.0000.0000.000
34A41PHE00.013-0.00630.568-0.045-0.0450.0000.0000.0000.000
35A42GLY00.0250.00833.629-0.249-0.2490.0000.0000.0000.000
36A43ARG10.8490.92332.013-9.195-9.1950.0000.0000.0000.000
37A44ILE0-0.029-0.00626.0780.1460.1460.0000.0000.0000.000
38A45PRO00.0480.02025.8560.0290.0290.0000.0000.0000.000
39A46MET0-0.027-0.01825.0460.4950.4950.0000.0000.0000.000
40A47ARG10.8730.95519.063-15.284-15.2840.0000.0000.0000.000
41A48PHE00.0480.01920.342-0.095-0.0950.0000.0000.0000.000
42A49SER0-0.035-0.00422.186-0.206-0.2060.0000.0000.0000.000
43A50VAL00.0350.01817.127-0.162-0.1620.0000.0000.0000.000
44A51LEU00.0100.01320.533-0.230-0.2300.0000.0000.0000.000
45A52MET0-0.035-0.01114.2971.1611.1610.0000.0000.0000.000
46A53GLN00.0260.01419.468-1.036-1.0360.0000.0000.0000.000
47A54MET00.0160.02320.2010.9810.9810.0000.0000.0000.000
48A55ARG10.8130.89618.131-16.037-16.0370.0000.0000.0000.000
49A56PHE00.0630.02822.159-0.011-0.0110.0000.0000.0000.000
50A57ASP-1-0.845-0.90219.28214.98114.9810.0000.0000.0000.000
51A58GLY0-0.005-0.00121.2250.1650.1650.0000.0000.0000.000
52A59LEU0-0.051-0.01615.4120.5190.5190.0000.0000.0000.000
53A60LEU00.017-0.00616.687-0.443-0.4430.0000.0000.0000.000
54A61GLY0-0.011-0.02415.4861.3461.3460.0000.0000.0000.000
55A62PHE0-0.012-0.00612.551-0.540-0.5400.0000.0000.0000.000
56A63PRO00.0520.03017.386-0.174-0.1740.0000.0000.0000.000
57A64GLY00.016-0.00619.2820.7780.7780.0000.0000.0000.000
58A65GLY00.0200.01419.402-0.412-0.4120.0000.0000.0000.000
59A66PHE0-0.004-0.00817.6370.4090.4090.0000.0000.0000.000
60A67VAL0-0.043-0.01421.087-0.722-0.7220.0000.0000.0000.000
61A68ASP-1-0.773-0.87522.71111.85411.8540.0000.0000.0000.000
62A69ARG10.9440.96321.660-13.910-13.9100.0000.0000.0000.000
63A70ARG10.8090.90025.760-11.001-11.0010.0000.0000.0000.000
64A71PHE0-0.039-0.02228.685-0.369-0.3690.0000.0000.0000.000
65A72TRP00.0300.01926.827-0.193-0.1930.0000.0000.0000.000
66A73SER00.0570.03626.5020.5170.5170.0000.0000.0000.000
67A74LEU00.0450.00119.618-0.049-0.0490.0000.0000.0000.000
68A75GLU-1-0.746-0.85422.57614.24514.2450.0000.0000.0000.000
69A76ASP-1-0.914-0.96024.74810.83010.8300.0000.0000.0000.000
70A77GLY0-0.036-0.02725.182-0.251-0.2510.0000.0000.0000.000
71A78LEU00.0060.00520.560-0.053-0.0530.0000.0000.0000.000
72A79ASN0-0.031-0.03923.545-0.106-0.1060.0000.0000.0000.000
73A80ARG10.9040.98126.094-11.862-11.8620.0000.0000.0000.000
74A81VAL0-0.018-0.00523.204-0.304-0.3040.0000.0000.0000.000
75A82LEU0-0.005-0.02122.249-0.159-0.1590.0000.0000.0000.000
76A83GLY00.0030.02826.099-0.250-0.2500.0000.0000.0000.000
77A84LEU0-0.087-0.05829.749-0.181-0.1810.0000.0000.0000.000
78A85GLY00.0970.05627.828-0.334-0.3340.0000.0000.0000.000
79A86LEU0-0.095-0.05424.6460.2920.2920.0000.0000.0000.000
80A87GLY00.0500.04328.373-0.503-0.5030.0000.0000.0000.000
81A88GLY0-0.019-0.00627.7780.4650.4650.0000.0000.0000.000
82A89LEU0-0.035-0.03128.106-0.394-0.3940.0000.0000.0000.000
83A90ARG10.9200.97027.813-10.370-10.3700.0000.0000.0000.000
84A91LEU0-0.0140.00221.7820.0350.0350.0000.0000.0000.000
85A92THR0-0.023-0.02124.339-0.430-0.4300.0000.0000.0000.000
86A93GLU-1-0.910-0.96721.07415.45715.4570.0000.0000.0000.000
87A94ALA00.0570.03121.1510.6810.6810.0000.0000.0000.000
88A95ASP-1-0.803-0.88920.62414.31614.3160.0000.0000.0000.000
89A96TYR0-0.037-0.05714.2271.1411.1410.0000.0000.0000.000
90A97LEU0-0.020-0.01512.6660.3390.3390.0000.0000.0000.000
91A98SER0-0.032-0.0169.9262.1022.1020.0000.0000.0000.000
92A99SER00.0170.00611.179-2.083-2.0830.0000.0000.0000.000
93A100HIS00.0080.0165.5753.7493.7490.0000.0000.0000.000
94A101LEU0-0.025-0.0038.580-3.205-3.2050.0000.0000.0000.000
95A102THR00.002-0.0047.9692.6772.6770.0000.0000.0000.000
96A103GLU-1-0.968-0.9815.17531.14531.244-0.001-0.004-0.0940.000
97A104GLY00.0040.0208.323-1.288-1.2880.0000.0000.0000.000
98A105PRO00.005-0.01511.4190.3820.3820.0000.0000.0000.000
99A106HIS00.0330.00214.8540.3850.3850.0000.0000.0000.000
100A107ARG10.9460.98414.296-13.683-13.6830.0000.0000.0000.000
101A108VAL00.0080.01513.763-1.075-1.0750.0000.0000.0000.000
102A109VAL0-0.0050.01212.7531.5811.5810.0000.0000.0000.000
103A110ALA0-0.021-0.01911.055-1.441-1.4410.0000.0000.0000.000
104A111HIS00.0030.00612.2072.7352.7350.0000.0000.0000.000
105A112LEU0-0.060-0.02111.572-0.570-0.5700.0000.0000.0000.000
106A113TYR0-0.001-0.02014.5260.0340.0340.0000.0000.0000.000
107A114ALA0-0.012-0.00816.4280.3660.3660.0000.0000.0000.000
108A115ARG10.8620.93018.463-13.266-13.2660.0000.0000.0000.000
109A116GLN0-0.032-0.00921.836-0.309-0.3090.0000.0000.0000.000
110A117LEU0-0.025-0.01123.491-0.526-0.5260.0000.0000.0000.000
111A118THR00.0360.00026.9260.0740.0740.0000.0000.0000.000
112A119LEU00.028-0.00627.6310.1750.1750.0000.0000.0000.000
113A120GLU-1-0.922-0.95429.7859.0849.0840.0000.0000.0000.000
114A121GLN00.0410.01730.0420.2530.2530.0000.0000.0000.000
115A122LEU0-0.022-0.00724.1140.0690.0690.0000.0000.0000.000
116A123HIS0-0.009-0.00728.346-0.156-0.1560.0000.0000.0000.000
117A124ALA00.0150.01230.949-0.140-0.1400.0000.0000.0000.000
118A125VAL0-0.013-0.00426.129-0.108-0.1080.0000.0000.0000.000
119A126GLU-1-0.781-0.89627.44811.62011.6200.0000.0000.0000.000
120A127ILE0-0.022-0.00529.624-0.179-0.1790.0000.0000.0000.000
121A128SER0-0.078-0.04230.934-0.141-0.1410.0000.0000.0000.000
122A129ALA00.025-0.00128.329-0.117-0.1170.0000.0000.0000.000
123A130VAL0-0.0180.00130.2450.0170.0170.0000.0000.0000.000
124A131HIS0-0.048-0.01832.630-0.267-0.2670.0000.0000.0000.000
125A132SER0-0.056-0.02129.454-0.258-0.2580.0000.0000.0000.000
126A133ARG10.9360.95032.670-9.019-9.0190.0000.0000.0000.000
127A134ASP-1-0.810-0.89827.15011.21811.2180.0000.0000.0000.000
128A135HIS0-0.050-0.00929.4250.4520.4520.0000.0000.0000.000
129A136GLY0-0.036-0.02029.989-0.366-0.3660.0000.0000.0000.000
130A137LEU0-0.055-0.02430.160-0.232-0.2320.0000.0000.0000.000
131A138GLU-1-0.905-0.95725.36211.11611.1160.0000.0000.0000.000
132A139VAL0-0.034-0.02524.2360.7470.7470.0000.0000.0000.000
133A140LEU0-0.007-0.00925.399-0.491-0.4910.0000.0000.0000.000
134A141GLY00.0330.02026.069-0.373-0.3730.0000.0000.0000.000
135A142LEU0-0.017-0.00724.2100.6130.6130.0000.0000.0000.000
136A143VAL0-0.017-0.00821.154-0.349-0.3490.0000.0000.0000.000
137A144ARG10.8440.90522.368-11.327-11.3270.0000.0000.0000.000
138A145VAL0-0.024-0.01017.192-0.015-0.0150.0000.0000.0000.000
139A146PRO0-0.063-0.00220.008-0.392-0.3920.0000.0000.0000.000
140A147LEU00.063-0.00216.4440.7240.7240.0000.0000.0000.000
141A148TYR0-0.0220.00719.3710.3700.3700.0000.0000.0000.000
142A149THR00.005-0.00819.8030.6330.6330.0000.0000.0000.000
143A150GLN0-0.034-0.01222.175-0.303-0.3030.0000.0000.0000.000
144A151LYS10.9840.97124.842-10.133-10.1330.0000.0000.0000.000
145A152ASP-1-0.802-0.88625.51612.47512.4750.0000.0000.0000.000
146A153ARG10.9290.95921.889-13.070-13.0700.0000.0000.0000.000
147A154VAL00.0360.02020.4220.8390.8390.0000.0000.0000.000
148A155GLY00.0010.00721.3760.4410.4410.0000.0000.0000.000
149A156GLY0-0.012-0.01922.4290.1190.1190.0000.0000.0000.000
150A157PHE00.0380.00813.5150.3760.3760.0000.0000.0000.000
151A158PRO00.0160.01116.4700.8550.8550.0000.0000.0000.000
152A159ASN00.0530.00916.8970.6390.6390.0000.0000.0000.000
153A160PHE00.0230.02016.0620.1540.1540.0000.0000.0000.000
154A161LEU0-0.018-0.01012.1090.6740.6740.0000.0000.0000.000
155A162SER0-0.068-0.04113.6370.8580.8580.0000.0000.0000.000
156A163ASN0-0.059-0.01616.044-0.387-0.3870.0000.0000.0000.000
157A164ALA00.0420.02915.1091.0141.0140.0000.0000.0000.000
158A165PHE0-0.016-0.01012.081-0.070-0.0700.0000.0000.0000.000
159A166VAL00.0660.04112.3440.1840.1840.0000.0000.0000.000
160A167SER00.0300.0117.7370.5890.5890.0000.0000.0000.000
161A168THR00.0450.0088.1683.7093.7090.0000.0000.0000.000
162A169ALA00.0060.0189.0731.6521.6520.0000.0000.0000.000
163A170LYS10.9530.9899.084-26.065-26.0650.0000.0000.0000.000
164A171TYR0-0.016-0.0062.051-26.291-21.3506.807-6.120-5.6280.061
165A172GLN00.0360.0016.5891.0981.0980.0000.0000.0000.000
166A173LEU00.0110.0089.170-0.778-0.7780.0000.0000.0000.000
167A174LEU0-0.026-0.0167.407-1.446-1.4460.0000.0000.0000.000
168A175PHE00.0000.0005.556-0.822-0.8220.0000.0000.0000.000
169A176ALA00.0350.0067.996-2.217-2.2170.0000.0000.0000.000
170A177LEU0-0.001-0.01511.623-2.005-2.0050.0000.0000.0000.000
171A178LYS10.9290.9756.419-45.970-45.9700.0000.0000.0000.000
172A179VAL00.0090.01910.094-2.123-2.1230.0000.0000.0000.000
173A180LEU0-0.024-0.01111.814-1.981-1.9810.0000.0000.0000.000
174A181ASN0-0.044-0.01314.293-0.614-0.6140.0000.0000.0000.000
175A182MET0-0.0170.01015.473-1.220-1.2200.0000.0000.0000.000
176A183MET0-0.067-0.04014.087-1.844-1.8440.0000.0000.0000.000
177A184PRO00.0400.03013.7981.4451.4450.0000.0000.0000.000
178A185SER00.0640.0029.4212.1932.1930.0000.0000.0000.000
179A186GLU-1-0.912-0.94510.75722.12222.1220.0000.0000.0000.000
180A187LYS10.9940.99413.131-16.942-16.9420.0000.0000.0000.000
181A188LEU0-0.039-0.0119.524-0.402-0.4020.0000.0000.0000.000
182A189ALA0-0.0050.0049.8830.4520.4520.0000.0000.0000.000
183A190GLU-1-0.914-0.96110.90017.46017.4600.0000.0000.0000.000
184A191ALA0-0.0040.00313.832-0.986-0.9860.0000.0000.0000.000
185A192LEU00.0270.0117.339-0.966-0.9660.0000.0000.0000.000
186A193ALA00.0050.00612.071-0.648-0.6480.0000.0000.0000.000
187A194SER0-0.025-0.01613.530-1.332-1.3320.0000.0000.0000.000
188A195ALA0-0.013-0.01413.442-0.885-0.8850.0000.0000.0000.000
189A196THR0-0.029-0.02011.631-0.548-0.5480.0000.0000.0000.000
190A197GLU-1-0.934-0.96214.00314.80414.8040.0000.0000.0000.000
191A198LYS10.9260.96717.323-15.415-15.4150.0000.0000.0000.000
192A199GLN0-0.089-0.06713.647-0.003-0.0030.0000.0000.0000.000
193A200LYS10.9250.96813.819-18.615-18.6150.0000.0000.0000.000
194A201LYS10.9830.99318.607-12.719-12.7190.0000.0000.0000.000
195A202ALA0-0.083-0.03921.366-0.494-0.4940.0000.0000.0000.000
196A203LEU0-0.038-0.00118.696-0.361-0.3610.0000.0000.0000.000
197A204GLU-1-0.945-0.96022.33511.67211.6720.0000.0000.0000.000