FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 8NJKY

Calculation Name: 1O20-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1O20

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WYC9

Base Structure: X-ray

Registration Date: 2023-09-26

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 414
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7021072.344804
FMO2-HF: Nuclear repulsion 6860981.916011
FMO2-HF: Total energy -160090.428792
FMO2-MP2: Total energy -160565.671422


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:ASP)


Summations of interaction energy for fragment #1(A:2:ASP)
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.
-72.373-58.0218.451-10.535-12.2660.083
Interaction energy analysis for fragmet #1(A:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.860 / q_NPA : -0.952
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].
3A4LEU00.0140.0082.739-15.054-10.6950.711-2.255-2.8150.023
4A5LEU00.0200.0132.076-38.009-31.5476.839-6.046-7.2540.083
5A6GLU-1-0.975-0.9842.45817.34920.7660.902-2.230-2.089-0.023
6A7LYS10.8140.8815.379-36.148-36.034-0.001-0.004-0.1080.000
7A8ALA00.0270.0176.756-4.627-4.6270.0000.0000.0000.000
8A9LYS10.9230.9635.615-41.577-41.5770.0000.0000.0000.000
9A10LYS10.9620.9908.408-28.116-28.1160.0000.0000.0000.000
10A11VAL00.0310.02511.405-2.087-2.0870.0000.0000.0000.000
11A12ARG10.9170.98012.647-20.409-20.4090.0000.0000.0000.000
12A13GLU-1-0.966-0.98612.70820.06220.0620.0000.0000.0000.000
13A14ALA0-0.0120.00015.479-1.296-1.2960.0000.0000.0000.000
14A15TRP0-0.015-0.01617.246-0.965-0.9650.0000.0000.0000.000
15A16ASP-1-0.933-0.96418.95113.06113.0610.0000.0000.0000.000
16A17VAL00.0160.01420.814-0.754-0.7540.0000.0000.0000.000
17A18LEU0-0.023-0.00520.953-0.630-0.6300.0000.0000.0000.000
18A19ARG10.7920.91022.330-13.824-13.8240.0000.0000.0000.000
19A20ASN0-0.058-0.04124.547-0.785-0.7850.0000.0000.0000.000
20A21ALA00.0290.04426.672-0.436-0.4360.0000.0000.0000.000
21A22THR00.019-0.00428.454-0.183-0.1830.0000.0000.0000.000
22A23THR00.011-0.05630.7780.1110.1110.0000.0000.0000.000
23A24ARG10.9030.96532.246-8.279-8.2790.0000.0000.0000.000
24A25GLU-1-0.796-0.90128.72210.27510.2750.0000.0000.0000.000
25A26LYS10.8450.91726.897-10.941-10.9410.0000.0000.0000.000
26A27ASN00.0530.01328.7410.3630.3630.0000.0000.0000.000
27A28LYS10.9200.97931.004-9.843-9.8430.0000.0000.0000.000
28A29ALA00.0420.02125.961-0.032-0.0320.0000.0000.0000.000
29A30ILE00.0080.00427.0110.1310.1310.0000.0000.0000.000
30A31LYS10.9300.96728.688-8.878-8.8780.0000.0000.0000.000
31A32LYS10.8850.92328.606-10.180-10.1800.0000.0000.0000.000
32A33ILE00.0000.00724.2290.1220.1220.0000.0000.0000.000
33A34ALA0-0.021-0.01727.6280.0380.0380.0000.0000.0000.000
34A35GLU-1-0.918-0.96530.7789.2409.2400.0000.0000.0000.000
35A36LYS10.9080.97326.526-10.792-10.7920.0000.0000.0000.000
36A37LEU0-0.042-0.03025.6850.1280.1280.0000.0000.0000.000
37A38ASP-1-0.905-0.95828.9198.8688.8680.0000.0000.0000.000
38A39GLU-1-0.911-0.96630.3729.7459.7450.0000.0000.0000.000
39A40ARG10.7710.88125.982-11.264-11.2640.0000.0000.0000.000
40A41ARG10.7650.87228.401-8.882-8.8820.0000.0000.0000.000
41A42LYS10.9600.97130.293-8.722-8.7220.0000.0000.0000.000
42A43GLU-1-0.845-0.92525.45610.79110.7910.0000.0000.0000.000
43A44ILE0-0.016-0.00925.2770.3960.3960.0000.0000.0000.000
44A45LEU0-0.036-0.02326.6870.1680.1680.0000.0000.0000.000
45A46GLU-1-0.844-0.90626.99810.62510.6250.0000.0000.0000.000
46A47ALA0-0.005-0.00822.9670.1600.1600.0000.0000.0000.000
47A48ASN0-0.035-0.04524.700-0.183-0.1830.0000.0000.0000.000
48A49ARG10.8320.91826.424-10.453-10.4530.0000.0000.0000.000
49A50ILE0-0.0110.00323.447-0.057-0.0570.0000.0000.0000.000
50A51ASP-1-0.734-0.83022.11114.40014.4000.0000.0000.0000.000
51A52VAL0-0.043-0.02224.730-0.078-0.0780.0000.0000.0000.000
52A53GLU-1-0.877-0.94528.3659.7529.7520.0000.0000.0000.000
53A54LYS10.9840.99220.418-14.481-14.4810.0000.0000.0000.000
54A55ALA0-0.037-0.01926.5610.0030.0030.0000.0000.0000.000
55A56ARG10.8440.90427.532-9.708-9.7080.0000.0000.0000.000
56A57GLU-1-0.917-0.95128.22610.70110.7010.0000.0000.0000.000
57A58ARG10.8090.90623.777-13.195-13.1950.0000.0000.0000.000
58A59GLY0-0.0030.00429.1380.0000.0000.0000.0000.0000.000
59A60VAL0-0.043-0.01027.378-0.052-0.0520.0000.0000.0000.000
60A61LYS10.9530.97430.657-9.708-9.7080.0000.0000.0000.000
61A62GLU-1-0.690-0.87732.6029.6309.6300.0000.0000.0000.000
62A63SER0-0.0010.01433.6760.0180.0180.0000.0000.0000.000
63A64LEU0-0.095-0.05728.6300.1080.1080.0000.0000.0000.000
64A65VAL00.0510.03829.0970.3970.3970.0000.0000.0000.000
65A66ASP-1-0.837-0.91830.0199.7439.7430.0000.0000.0000.000
66A67ARG10.8770.94727.858-10.965-10.9650.0000.0000.0000.000
67A68LEU0-0.0150.00424.1900.2990.2990.0000.0000.0000.000
68A69ALA0-0.0010.01527.1630.2070.2070.0000.0000.0000.000
69A70LEU0-0.014-0.01026.043-0.036-0.0360.0000.0000.0000.000
70A71ASN00.014-0.00730.454-0.242-0.2420.0000.0000.0000.000
71A72ASP-1-0.771-0.90033.0849.0879.0870.0000.0000.0000.000
72A73LYS10.9760.99235.049-7.896-7.8960.0000.0000.0000.000
73A74ARG10.8200.90431.174-9.789-9.7890.0000.0000.0000.000
74A75ILE00.0120.01429.6480.2410.2410.0000.0000.0000.000
75A76ASP-1-0.845-0.91931.6328.8368.8360.0000.0000.0000.000
76A77GLU-1-0.989-0.98632.4959.4639.4630.0000.0000.0000.000
77A78MET0-0.029-0.01327.0230.2710.2710.0000.0000.0000.000
78A79ILE00.0330.02730.1770.1820.1820.0000.0000.0000.000
79A80LYS11.0031.00432.392-8.476-8.4760.0000.0000.0000.000
80A81ALA0-0.020-0.00829.969-0.109-0.1090.0000.0000.0000.000
81A82CYS0-0.018-0.01529.2370.1620.1620.0000.0000.0000.000
82A83GLU-1-0.975-0.98630.9848.5968.5960.0000.0000.0000.000
83A84THR0-0.049-0.02533.600-0.253-0.2530.0000.0000.0000.000
84A85VAL00.0190.00828.619-0.146-0.1460.0000.0000.0000.000
85A86ILE0-0.037-0.01531.953-0.068-0.0680.0000.0000.0000.000
86A87GLY0-0.040-0.02033.553-0.141-0.1410.0000.0000.0000.000
87A88LEU0-0.0140.01732.138-0.204-0.2040.0000.0000.0000.000
88A89LYS10.8230.89034.946-8.724-8.7240.0000.0000.0000.000
89A90ASP-1-0.720-0.83230.94510.63010.6300.0000.0000.0000.000
90A91PRO0-0.0170.00529.936-0.306-0.3060.0000.0000.0000.000
91A92VAL00.022-0.00528.042-0.094-0.0940.0000.0000.0000.000
92A93GLY0-0.006-0.00431.161-0.232-0.2320.0000.0000.0000.000
93A94GLU-1-0.891-0.93133.8638.5928.5920.0000.0000.0000.000
94A95VAL0-0.010-0.00635.6590.1940.1940.0000.0000.0000.000
95A96ILE0-0.083-0.03533.923-0.076-0.0760.0000.0000.0000.000
96A97ASP-1-0.758-0.87038.3197.9177.9170.0000.0000.0000.000
97A98SER0-0.013-0.04340.3910.1330.1330.0000.0000.0000.000
98A99TRP0-0.044-0.01140.750-0.132-0.1320.0000.0000.0000.000
99A100VAL0-0.001-0.00345.3950.1430.1430.0000.0000.0000.000
100A101ARG10.7780.87945.389-7.035-7.0350.0000.0000.0000.000
101A102GLU-1-0.904-0.96148.8666.0986.0980.0000.0000.0000.000
102A103ASP-1-0.693-0.82349.1316.6336.6330.0000.0000.0000.000
103A104GLY00.0100.00450.5010.0060.0060.0000.0000.0000.000
104A105LEU0-0.056-0.00643.4040.1190.1190.0000.0000.0000.000
105A106ARG10.9540.97943.026-7.116-7.1160.0000.0000.0000.000
106A107ILE0-0.017-0.00639.9790.2300.2300.0000.0000.0000.000
107A108ALA00.0250.02438.959-0.168-0.1680.0000.0000.0000.000
108A109ARG10.8240.92035.913-8.266-8.2660.0000.0000.0000.000
109A110VAL0-0.003-0.00933.512-0.174-0.1740.0000.0000.0000.000
110A111ARG10.9310.97731.193-9.149-9.1490.0000.0000.0000.000
111A112VAL0-0.052-0.02526.846-0.182-0.1820.0000.0000.0000.000
112A113PRO00.0510.02723.636-0.042-0.0420.0000.0000.0000.000
113A114ILE0-0.0130.00021.176-0.024-0.0240.0000.0000.0000.000
114A115GLY0-0.012-0.01519.3500.2790.2790.0000.0000.0000.000
115A116PRO0-0.027-0.00214.628-0.308-0.3080.0000.0000.0000.000
116A117ILE00.0140.00316.4080.2210.2210.0000.0000.0000.000
117A118GLY00.0240.01013.6670.8050.8050.0000.0000.0000.000
118A119ILE0-0.020-0.00714.364-1.204-1.2040.0000.0000.0000.000
119A120ILE0-0.002-0.00113.0761.0671.0670.0000.0000.0000.000
120A121TYR0-0.010-0.02715.786-0.901-0.9010.0000.0000.0000.000
121A122GLU-1-0.883-0.95717.62616.33116.3310.0000.0000.0000.000
122A123SER0-0.004-0.00819.9550.3320.3320.0000.0000.0000.000
123A124ARG10.9750.99222.509-11.702-11.7020.0000.0000.0000.000
124A125PRO00.0470.03122.5610.3910.3910.0000.0000.0000.000
125A126ASN0-0.005-0.03923.4300.4590.4590.0000.0000.0000.000
126A127VAL00.0120.01121.013-0.043-0.0430.0000.0000.0000.000
127A128THR0-0.0070.01719.1790.5350.5350.0000.0000.0000.000
128A129VAL00.0550.03421.1900.3140.3140.0000.0000.0000.000
129A130GLU-1-0.868-0.90823.97211.58611.5860.0000.0000.0000.000
130A131THR0-0.024-0.02820.6540.1390.1390.0000.0000.0000.000
131A132THR00.0230.00720.1570.2900.2900.0000.0000.0000.000
132A133ILE0-0.013-0.00821.637-0.085-0.0850.0000.0000.0000.000
133A134LEU00.0260.01424.904-0.350-0.3500.0000.0000.0000.000
134A135ALA00.0040.01420.683-0.253-0.2530.0000.0000.0000.000
135A136LEU00.0220.01020.785-0.219-0.2190.0000.0000.0000.000
136A137LYS10.8170.91823.724-10.111-10.1110.0000.0000.0000.000
137A138SER0-0.046-0.03025.249-0.259-0.2590.0000.0000.0000.000
138A139GLY0-0.001-0.00524.741-0.049-0.0490.0000.0000.0000.000
139A140ASN0-0.036-0.02720.3090.4780.4780.0000.0000.0000.000
140A141THR00.021-0.00316.180-0.183-0.1830.0000.0000.0000.000
141A142ILE0-0.020-0.00516.117-0.016-0.0160.0000.0000.0000.000
142A143LEU00.0080.0108.4720.5070.5070.0000.0000.0000.000
143A144LEU0-0.011-0.00212.918-0.308-0.3080.0000.0000.0000.000
144A145ARG10.9450.96410.752-21.299-21.2990.0000.0000.0000.000
145A146GLY00.0240.02613.121-1.093-1.0930.0000.0000.0000.000
146A147GLY0-0.017-0.02815.3531.0141.0140.0000.0000.0000.000
147A148SER00.012-0.01116.637-0.025-0.0250.0000.0000.0000.000
148A149ASP-1-0.951-0.96617.62813.92813.9280.0000.0000.0000.000
149A150ALA00.0070.02220.301-0.513-0.5130.0000.0000.0000.000
150A151LEU00.0170.01614.264-0.007-0.0070.0000.0000.0000.000
151A152ASN0-0.073-0.06218.0830.6400.6400.0000.0000.0000.000
152A153SER00.011-0.01320.200-0.401-0.4010.0000.0000.0000.000
153A154ASN00.018-0.00218.115-0.896-0.8960.0000.0000.0000.000
154A155LYS10.9590.99314.788-18.471-18.4710.0000.0000.0000.000
155A156ALA00.0270.02618.171-0.054-0.0540.0000.0000.0000.000
156A157ILE00.0040.00121.624-0.340-0.3400.0000.0000.0000.000
157A158VAL0-0.007-0.01616.103-0.247-0.2470.0000.0000.0000.000
158A159SER0-0.021-0.01219.0510.0940.0940.0000.0000.0000.000
159A160ALA00.0240.01419.879-0.268-0.2680.0000.0000.0000.000
160A161ILE0-0.010-0.00520.838-0.341-0.3410.0000.0000.0000.000
161A162ARG10.8650.92714.067-19.121-19.1210.0000.0000.0000.000
162A163GLU-1-0.799-0.87920.44811.61511.6150.0000.0000.0000.000
163A164ALA0-0.0130.00723.148-0.419-0.4190.0000.0000.0000.000
164A165LEU0-0.054-0.02220.056-0.317-0.3170.0000.0000.0000.000
165A166LYS10.9790.99320.723-13.461-13.4610.0000.0000.0000.000
166A167GLU-1-0.910-0.91923.37810.10110.1010.0000.0000.0000.000
167A168THR0-0.138-0.08625.380-0.504-0.5040.0000.0000.0000.000
168A169GLU-1-0.947-0.96925.70510.57410.5740.0000.0000.0000.000
169A170ILE0-0.069-0.02422.3740.3260.3260.0000.0000.0000.000
170A171PRO00.0300.01018.9730.1140.1140.0000.0000.0000.000
171A172GLU-1-0.841-0.93717.56815.95215.9520.0000.0000.0000.000
172A173SER00.005-0.00514.209-0.083-0.0830.0000.0000.0000.000
173A174SER0-0.042-0.03615.2650.9920.9920.0000.0000.0000.000
174A175VAL00.0020.00016.3990.0370.0370.0000.0000.0000.000
175A176GLU-1-0.864-0.92811.14323.82623.8260.0000.0000.0000.000
176A177PHE0-0.001-0.00812.372-0.283-0.2830.0000.0000.0000.000
177A178ILE0-0.038-0.0176.9601.2851.2850.0000.0000.0000.000
178A179GLU-1-0.939-0.9819.74220.25120.2510.0000.0000.0000.000
179A180ASN0-0.039-0.0106.390-4.685-4.6850.0000.0000.0000.000
180A181THR00.0540.0009.514-0.013-0.0130.0000.0000.0000.000
181A182ASP-1-0.854-0.88510.03225.50825.5080.0000.0000.0000.000
182A183ARG10.9530.97010.695-16.685-16.6850.0000.0000.0000.000
183A184SER0-0.041-0.04210.0090.9200.9200.0000.0000.0000.000
184A185LEU00.0590.0195.4641.9741.9740.0000.0000.0000.000
185A186VAL0-0.017-0.0048.1090.8260.8260.0000.0000.0000.000
186A187LEU0-0.028-0.01110.967-0.836-0.8360.0000.0000.0000.000
187A188GLU-1-0.895-0.9466.15142.94542.9450.0000.0000.0000.000
188A189MET0-0.038-0.0078.133-0.277-0.2770.0000.0000.0000.000
189A190ILE0-0.049-0.0218.857-1.867-1.8670.0000.0000.0000.000
190A191ARG10.9580.98510.623-26.388-26.3880.0000.0000.0000.000
191A192LEU00.0050.0176.105-0.452-0.4520.0000.0000.0000.000
192A193ARG10.9480.96710.380-19.898-19.8980.0000.0000.0000.000
193A194GLU-1-0.942-0.96111.32925.10325.1030.0000.0000.0000.000
194A195TYR0-0.065-0.0468.4270.2970.2970.0000.0000.0000.000
195A196LEU0-0.002-0.00310.531-1.273-1.2730.0000.0000.0000.000
196A197SER0-0.0020.00013.814-0.065-0.0650.0000.0000.0000.000
197A198LEU0-0.044-0.02416.685-1.014-1.0140.0000.0000.0000.000
198A199VAL0-0.0130.00313.7761.1441.1440.0000.0000.0000.000
199A200ILE00.006-0.01216.897-1.107-1.1070.0000.0000.0000.000
200A201PRO0-0.0190.01118.4030.4600.4600.0000.0000.0000.000
201A202ARG10.9340.95719.325-13.602-13.6020.0000.0000.0000.000
202A203GLY00.014-0.00820.9730.5620.5620.0000.0000.0000.000
203A204GLY00.0130.00823.417-0.444-0.4440.0000.0000.0000.000
204A205TYR00.055-0.00623.5630.7330.7330.0000.0000.0000.000
205A206GLY00.0110.04523.5620.2250.2250.0000.0000.0000.000
206A207LEU0-0.056-0.03016.6340.6210.6210.0000.0000.0000.000
207A208ILE00.0070.01119.3770.8740.8740.0000.0000.0000.000
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