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: 98ZK2

Calculation Name: 1G2Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1G2Q

Chain ID: A

ChEMBL ID:

UniProt ID: P49435

Base Structure: X-ray

Registration Date: 2023-09-23

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 OptAll
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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1826496.696072
FMO2-HF: Nuclear repulsion 1759080.13181
FMO2-HF: Total energy -67416.564261
FMO2-MP2: Total energy -67617.178497


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.
-0.4374.6652.446-2.318-5.23-0.001
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 : 0.081 / q_NPA : 0.038
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].
3A3ILE00.1020.0572.572-2.1970.3911.659-1.359-2.8890.000
4A4ALA00.0410.0202.461-0.8100.5290.780-0.612-1.508-0.001
5A5SER0-0.078-0.0413.2360.2931.1130.010-0.328-0.5020.000
6A6TYR00.027-0.0015.3500.4610.608-0.001-0.008-0.1380.000
7A7ALA00.0390.0267.3170.2180.2180.0000.0000.0000.000
8A8GLN0-0.080-0.0475.6550.3720.3720.0000.0000.0000.000
9A9GLU-1-0.831-0.8979.445-0.671-0.6710.0000.0000.0000.000
10A10LEU0-0.009-0.00811.1950.1110.1110.0000.0000.0000.000
11A11LYS10.9660.98512.6580.1560.1560.0000.0000.0000.000
12A12LEU0-0.059-0.03112.4840.0460.0460.0000.0000.0000.000
13A13ALA0-0.037-0.00215.5610.0190.0190.0000.0000.0000.000
14A14LEU0-0.0080.00816.8630.0210.0210.0000.0000.0000.000
15A15HIS0-0.035-0.02119.782-0.005-0.0050.0000.0000.0000.000
16A16GLN0-0.025-0.01321.4920.0120.0120.0000.0000.0000.000
17A17TYR0-0.056-0.03024.9980.0000.0000.0000.0000.0000.000
18A18PRO00.026-0.00228.5130.0040.0040.0000.0000.0000.000
19A19ASN0-0.0320.00430.2390.0010.0010.0000.0000.0000.000
20A20PHE00.0230.03529.4470.0000.0000.0000.0000.0000.000
21A21PRO0-0.023-0.01829.7950.0000.0000.0000.0000.0000.000
22A22SER00.011-0.00932.6600.0010.0010.0000.0000.0000.000
23A23GLU-1-0.932-0.97533.340-0.010-0.0100.0000.0000.0000.000
24A24GLY0-0.018-0.01233.1020.0020.0020.0000.0000.0000.000
25A25ILE0-0.047-0.00228.3240.0020.0020.0000.0000.0000.000
26A26LEU0-0.021-0.00824.589-0.003-0.0030.0000.0000.0000.000
27A27PHE0-0.010-0.00525.5100.0020.0020.0000.0000.0000.000
28A28GLU-1-0.787-0.91520.646-0.070-0.0700.0000.0000.0000.000
29A29ASP-1-0.848-0.92922.939-0.078-0.0780.0000.0000.0000.000
30A30PHE00.0690.01719.438-0.014-0.0140.0000.0000.0000.000
31A31LEU0-0.005-0.01620.906-0.015-0.0150.0000.0000.0000.000
32A32PRO0-0.078-0.03621.197-0.004-0.0040.0000.0000.0000.000
33A33ILE00.0130.01416.445-0.015-0.0150.0000.0000.0000.000
34A34PHE0-0.001-0.00719.524-0.013-0.0130.0000.0000.0000.000
35A35ARG10.8120.92222.0020.1030.1030.0000.0000.0000.000
36A36ASN00.0180.01119.415-0.007-0.0070.0000.0000.0000.000
37A37PRO00.0470.02120.023-0.015-0.0150.0000.0000.0000.000
38A38GLY00.0230.01717.590-0.008-0.0080.0000.0000.0000.000
39A39LEU0-0.025-0.01015.028-0.050-0.0500.0000.0000.0000.000
40A40PHE00.0260.00615.491-0.008-0.0080.0000.0000.0000.000
41A41GLN0-0.032-0.02714.3310.0440.0440.0000.0000.0000.000
42A42LYS10.8400.89810.9480.7570.7570.0000.0000.0000.000
43A43LEU00.0010.00311.295-0.017-0.0170.0000.0000.0000.000
44A44ILE0-0.030-0.01413.0620.0550.0550.0000.0000.0000.000
45A45ASP-1-0.825-0.91410.108-0.286-0.2860.0000.0000.0000.000
46A46ALA0-0.049-0.0228.1590.0250.0250.0000.0000.0000.000
47A47PHE0-0.007-0.0119.1270.1790.1790.0000.0000.0000.000
48A48LYS10.8520.93911.7450.1390.1390.0000.0000.0000.000
49A49LEU00.0060.0134.225-0.141-0.028-0.001-0.010-0.1010.000
50A50HIS10.7970.8728.477-0.258-0.2580.0000.0000.0000.000
51A51LEU0-0.001-0.0099.309-0.034-0.0340.0000.0000.0000.000
52A52GLU-1-0.926-0.98110.737-0.036-0.0360.0000.0000.0000.000
53A53GLU-1-0.930-0.9545.9491.1521.247-0.001-0.001-0.0920.000
54A54ALA0-0.050-0.0219.854-0.070-0.0700.0000.0000.0000.000
55A55PHE0-0.033-0.02512.452-0.038-0.0380.0000.0000.0000.000
56A56PRO0-0.0090.00812.930-0.020-0.0200.0000.0000.0000.000
57A57GLU-1-0.949-0.97415.7840.0170.0170.0000.0000.0000.000
58A58VAL0-0.074-0.03818.755-0.007-0.0070.0000.0000.0000.000
59A59LYS10.8570.91619.6540.0000.0000.0000.0000.0000.000
60A60ILE00.0650.03917.2010.0000.0000.0000.0000.0000.000
61A61ASP-1-0.837-0.89921.6940.0020.0020.0000.0000.0000.000
62A62TYR00.008-0.00824.311-0.007-0.0070.0000.0000.0000.000
63A63ILE00.0100.02119.2050.0070.0070.0000.0000.0000.000
64A64VAL00.006-0.00622.834-0.007-0.0070.0000.0000.0000.000
65A65GLY00.0370.02024.2050.0040.0040.0000.0000.0000.000
66A66LEU0-0.021-0.00725.1070.0000.0000.0000.0000.0000.000
67A67GLU-1-0.784-0.86127.234-0.021-0.0210.0000.0000.0000.000
68A68SER0-0.014-0.03128.8230.0030.0030.0000.0000.0000.000
69A69ARG10.8340.93024.1540.0270.0270.0000.0000.0000.000
70A70GLY00.0820.05622.643-0.006-0.0060.0000.0000.0000.000
71A71PHE0-0.064-0.04123.368-0.002-0.0020.0000.0000.0000.000
72A72LEU0-0.027-0.00423.360-0.003-0.0030.0000.0000.0000.000
73A73PHE00.0180.00117.744-0.015-0.0150.0000.0000.0000.000
74A74GLY00.0490.03720.070-0.001-0.0010.0000.0000.0000.000
75A75PRO0-0.016-0.01021.6080.0030.0030.0000.0000.0000.000
76A76THR0-0.013-0.00319.8500.0050.0050.0000.0000.0000.000
77A77LEU00.0170.01315.132-0.009-0.0090.0000.0000.0000.000
78A78ALA00.005-0.00218.5670.0040.0040.0000.0000.0000.000
79A79LEU00.0010.00221.3260.0020.0020.0000.0000.0000.000
80A80ALA0-0.022-0.00917.144-0.001-0.0010.0000.0000.0000.000
81A81LEU0-0.010-0.00515.101-0.005-0.0050.0000.0000.0000.000
82A82GLY0-0.0330.00618.7460.0070.0070.0000.0000.0000.000
83A83VAL0-0.068-0.02521.1120.0060.0060.0000.0000.0000.000
84A84GLY00.0190.01423.619-0.006-0.0060.0000.0000.0000.000
85A85PHE0-0.006-0.01923.9710.0010.0010.0000.0000.0000.000
86A86VAL00.0030.00526.412-0.001-0.0010.0000.0000.0000.000
87A87PRO0-0.044-0.00827.9830.0020.0020.0000.0000.0000.000
88A88VAL00.0620.03629.0500.0010.0010.0000.0000.0000.000
89A89ARG10.7900.85230.8130.0150.0150.0000.0000.0000.000
90A90LYS10.9130.95931.7840.0170.0170.0000.0000.0000.000
91A91ALA00.010-0.00635.840-0.002-0.0020.0000.0000.0000.000
92A92GLY0-0.028-0.01139.086-0.001-0.0010.0000.0000.0000.000
93A93LYS10.8130.90537.1730.0110.0110.0000.0000.0000.000
94A94LEU00.0020.00934.615-0.002-0.0020.0000.0000.0000.000
95A95PRO0-0.0100.01138.5550.0010.0010.0000.0000.0000.000
96A96GLY00.0430.01240.4680.0000.0000.0000.0000.0000.000
97A97GLU-1-0.836-0.90342.050-0.003-0.0030.0000.0000.0000.000
98A98CYS0-0.045-0.00938.5430.0000.0000.0000.0000.0000.000
99A99PHE00.0310.02435.9030.0000.0000.0000.0000.0000.000
100A100LYS10.8270.87937.6090.0020.0020.0000.0000.0000.000
101A101ALA00.0500.06134.1800.0010.0010.0000.0000.0000.000
102A102THR0-0.013-0.01736.003-0.002-0.0020.0000.0000.0000.000
103A103TYR00.0260.05832.4520.0020.0020.0000.0000.0000.000
104A104GLU-1-0.904-0.95534.8710.0050.0050.0000.0000.0000.000
105A105LYS10.7670.87435.2510.0030.0030.0000.0000.0000.000
106A106GLU-1-0.806-0.87337.4390.0040.0040.0000.0000.0000.000
107A107TYR0-0.047-0.04039.8850.0000.0000.0000.0000.0000.000
108A108GLY00.0100.00841.381-0.001-0.0010.0000.0000.0000.000
109A109SER0-0.009-0.01238.5280.0010.0010.0000.0000.0000.000
110A110ASP-1-0.894-0.92335.025-0.004-0.0040.0000.0000.0000.000
111A111LEU00.0060.00936.6580.0010.0010.0000.0000.0000.000
112A112PHE0-0.010-0.02031.831-0.002-0.0020.0000.0000.0000.000
113A113GLU-1-0.778-0.88834.873-0.004-0.0040.0000.0000.0000.000
114A114ILE00.0550.02230.269-0.001-0.0010.0000.0000.0000.000
115A115GLN0-0.004-0.02234.5490.0000.0000.0000.0000.0000.000
116A116LYS10.8340.91135.5690.0020.0020.0000.0000.0000.000
117A117ASN0-0.024-0.02036.8750.0010.0010.0000.0000.0000.000
118A118ALA0-0.037-0.01132.840-0.001-0.0010.0000.0000.0000.000
119A119ILE00.0080.00828.243-0.001-0.0010.0000.0000.0000.000
120A120PRO0-0.025-0.00231.8000.0010.0010.0000.0000.0000.000
121A121ALA00.0750.05932.1270.0010.0010.0000.0000.0000.000
122A122GLY0-0.042-0.02731.083-0.001-0.0010.0000.0000.0000.000
123A123SER0-0.071-0.04628.2320.0010.0010.0000.0000.0000.000
124A124ASN0-0.009-0.00723.1120.0020.0020.0000.0000.0000.000
125A125VAL0-0.017-0.01523.798-0.004-0.0040.0000.0000.0000.000
126A126ILE00.0150.02517.5310.0070.0070.0000.0000.0000.000
127A127ILE00.0020.00620.971-0.011-0.0110.0000.0000.0000.000
128A128VAL0-0.015-0.00818.6280.0090.0090.0000.0000.0000.000
129A129ASP-1-0.799-0.94020.518-0.020-0.0200.0000.0000.0000.000
130A130ASP-1-0.827-0.92820.132-0.033-0.0330.0000.0000.0000.000
131A131ILE0-0.009-0.00919.9280.0050.0050.0000.0000.0000.000
132A132ILE0-0.0330.01919.313-0.001-0.0010.0000.0000.0000.000
133A133ALA00.0990.01322.155-0.001-0.0010.0000.0000.0000.000
134A134THR0-0.006-0.01125.0360.0040.0040.0000.0000.0000.000
135A135GLY00.0460.01825.9070.0020.0020.0000.0000.0000.000
136A136GLY00.0250.00526.6360.0010.0010.0000.0000.0000.000
137A137SER0-0.005-0.00427.2880.0010.0010.0000.0000.0000.000
138A138ALA00.0420.02224.5160.0000.0000.0000.0000.0000.000
139A139ALA00.0270.02126.3960.0020.0020.0000.0000.0000.000
140A140ALA00.0130.01228.9140.0000.0000.0000.0000.0000.000
141A141ALA00.004-0.01727.188-0.001-0.0010.0000.0000.0000.000
142A142GLY00.0310.01927.7240.0000.0000.0000.0000.0000.000
143A143GLU-1-0.827-0.93128.4540.0090.0090.0000.0000.0000.000
144A144LEU0-0.087-0.03531.235-0.002-0.0020.0000.0000.0000.000
145A145VAL0-0.018-0.01526.765-0.002-0.0020.0000.0000.0000.000
146A146GLU-1-0.935-0.96230.0000.0170.0170.0000.0000.0000.000
147A147GLN0-0.041-0.05531.830-0.002-0.0020.0000.0000.0000.000
148A148LEU0-0.100-0.04031.316-0.002-0.0020.0000.0000.0000.000
149A149GLU-1-0.924-0.95533.3870.0100.0100.0000.0000.0000.000
150A150ALA0-0.028-0.00128.8630.0000.0000.0000.0000.0000.000
151A151ASN0-0.015-0.01225.5180.0020.0020.0000.0000.0000.000
152A152LEU0-0.015-0.01822.8770.0020.0020.0000.0000.0000.000
153A153LEU0-0.0240.00319.4200.0020.0020.0000.0000.0000.000
154A154GLU-1-0.795-0.88314.2510.2000.2000.0000.0000.0000.000
155A155TYR0-0.053-0.02918.845-0.014-0.0140.0000.0000.0000.000
156A156ASN0-0.043-0.04914.2620.0430.0430.0000.0000.0000.000
157A157PHE00.015-0.00216.301-0.026-0.0260.0000.0000.0000.000
158A158VAL00.0000.01115.4340.0200.0200.0000.0000.0000.000
159A159MET0-0.018-0.01315.4780.0050.0050.0000.0000.0000.000
160A160GLU-1-0.844-0.92217.5700.0750.0750.0000.0000.0000.000
161A161LEU0-0.031-0.01219.676-0.005-0.0050.0000.0000.0000.000
162A162ASP-1-0.844-0.92923.0250.0170.0170.0000.0000.0000.000
163A163PHE0-0.019-0.03226.025-0.006-0.0060.0000.0000.0000.000
164A164LEU0-0.0310.00029.277-0.001-0.0010.0000.0000.0000.000
165A165LYS10.8190.88530.562-0.005-0.0050.0000.0000.0000.000
166A166GLY0-0.0010.02028.6570.0010.0010.0000.0000.0000.000
167A167ARG10.8710.92819.463-0.063-0.0630.0000.0000.0000.000
168A168SER0-0.037-0.02127.3580.0020.0020.0000.0000.0000.000
169A169LYS10.8500.91626.563-0.026-0.0260.0000.0000.0000.000
170A170LEU00.0230.01722.713-0.003-0.0030.0000.0000.0000.000
171A171ASN00.0060.00924.5680.0050.0050.0000.0000.0000.000
172A172ALA00.0390.02621.835-0.002-0.0020.0000.0000.0000.000
173A173PRO0-0.0060.00816.7500.0000.0000.0000.0000.0000.000
174A174VAL0-0.029-0.02917.108-0.008-0.0080.0000.0000.0000.000
175A175PHE00.0100.0238.7410.0140.0140.0000.0000.0000.000
176A176THR0-0.010-0.01312.991-0.047-0.0470.0000.0000.0000.000
177A177LEU0-0.0230.0099.2330.0480.0480.0000.0000.0000.000
178A178LEU0-0.069-0.03010.8750.0170.0170.0000.0000.0000.000