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: JL6M9

Calculation Name: 3GYW-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3GYW

Chain ID: A

ChEMBL ID:
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UniProt ID: Q8I608

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 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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2007085.257047
FMO2-HF: Nuclear repulsion 1930721.969909
FMO2-HF: Total energy -76363.287138
FMO2-MP2: Total energy -76590.161325


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:35:LEU)


Summations of interaction energy for fragment #1(A:35:LEU)
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.
-7.1830.7334.18-3.848-8.248-0.013
Interaction energy analysis for fragmet #1(A:35:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.021
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].
3A37GLU-1-0.835-0.9513.046-3.590-1.3220.188-1.157-1.298-0.002
4A38GLU-1-0.913-0.9505.773-0.350-0.3500.0000.0000.0000.000
5A39GLN00.0230.0042.402-3.209-0.4881.576-1.389-2.908-0.012
6A40LYS10.8940.9552.461-0.3122.2451.041-0.988-2.6100.000
7A41GLU-1-0.905-0.9543.981-0.326-0.1810.004-0.007-0.1430.000
8A42THR0-0.048-0.0135.6760.2030.2030.0000.0000.0000.000
9A43LEU0-0.008-0.0112.324-0.359-0.1341.371-0.307-1.2890.001
10A44LYS10.9490.9765.4150.3350.3350.0000.0000.0000.000
11A45LYS10.9550.9798.2390.3850.3850.0000.0000.0000.000
12A46LEU00.0410.0167.8150.0360.0360.0000.0000.0000.000
13A47LYS10.9160.9696.2640.0230.0230.0000.0000.0000.000
14A48LEU0-0.024-0.00310.9510.0160.0160.0000.0000.0000.000
15A49TYR00.0490.00112.972-0.002-0.0020.0000.0000.0000.000
16A50GLN00.0000.01613.0180.0190.0190.0000.0000.0000.000
17A51LYS10.9200.96414.9250.0770.0770.0000.0000.0000.000
18A52GLU-1-0.886-0.94916.946-0.093-0.0930.0000.0000.0000.000
19A53TYR0-0.045-0.01317.9770.0050.0050.0000.0000.0000.000
20A54TYR00.003-0.00615.7360.0040.0040.0000.0000.0000.000
21A55ASP-1-0.923-0.95220.639-0.063-0.0630.0000.0000.0000.000
22A56TYR0-0.074-0.04622.6770.0090.0090.0000.0000.0000.000
23A57GLU-1-0.877-0.94422.251-0.043-0.0430.0000.0000.0000.000
24A58SER0-0.003-0.00224.5180.0060.0060.0000.0000.0000.000
25A59LYS10.9100.95326.4300.0530.0530.0000.0000.0000.000
26A60PHE00.0390.02627.7320.0030.0030.0000.0000.0000.000
27A61GLU-1-0.866-0.94227.365-0.027-0.0270.0000.0000.0000.000
28A62TYR0-0.060-0.02330.1900.0030.0030.0000.0000.0000.000
29A63GLU-1-0.948-0.99032.423-0.033-0.0330.0000.0000.0000.000
30A64LEU0-0.0310.00131.9920.0020.0020.0000.0000.0000.000
31A65PHE0-0.022-0.01734.2390.0020.0020.0000.0000.0000.000
32A66LEU00.003-0.00736.0470.0020.0020.0000.0000.0000.000
33A67LEU0-0.033-0.00637.8060.0010.0010.0000.0000.0000.000
34A68ARG10.9710.96934.6140.0200.0200.0000.0000.0000.000
35A69GLN00.0230.01639.8640.0020.0020.0000.0000.0000.000
36A70LYS10.9470.98742.1460.0210.0210.0000.0000.0000.000
37A71TYR0-0.045-0.04442.9430.0000.0000.0000.0000.0000.000
38A72HIS0-0.0170.02044.2220.0010.0010.0000.0000.0000.000
39A73ASP-1-0.852-0.93445.989-0.013-0.0130.0000.0000.0000.000
40A74LEU0-0.120-0.05947.3500.0000.0000.0000.0000.0000.000
41A75TYR0-0.024-0.01545.1920.0000.0000.0000.0000.0000.000
42A76GLY00.0510.03650.3930.0010.0010.0000.0000.0000.000
43A77PRO00.0370.01352.1750.0010.0010.0000.0000.0000.000
44A78ILE0-0.042-0.02252.6080.0010.0010.0000.0000.0000.000
45A79TYR00.0320.01548.5780.0010.0010.0000.0000.0000.000
46A80ASP-1-0.855-0.91155.359-0.008-0.0080.0000.0000.0000.000
47A81LYS10.9070.95057.9770.0100.0100.0000.0000.0000.000
48A82ARG10.8840.94853.6160.0070.0070.0000.0000.0000.000
49A83ARG10.9800.99558.4270.0070.0070.0000.0000.0000.000
50A84GLU-1-0.876-0.92560.732-0.006-0.0060.0000.0000.0000.000
51A85ALA0-0.009-0.01163.3630.0000.0000.0000.0000.0000.000
52A86LEU0-0.0270.00360.5930.0000.0000.0000.0000.0000.000
53A87VAL0-0.031-0.02263.1480.0000.0000.0000.0000.0000.000
54A88GLY00.0670.02365.9890.0000.0000.0000.0000.0000.000
55A89ASN0-0.133-0.08267.7870.0000.0000.0000.0000.0000.000
56A90GLY0-0.078-0.02369.3340.0000.0000.0000.0000.0000.000
57A91GLU-1-0.884-0.93466.081-0.004-0.0040.0000.0000.0000.000
58A92ALA0-0.012-0.01569.9780.0000.0000.0000.0000.0000.000
59A93LYS10.9080.95069.9820.0020.0020.0000.0000.0000.000
60A94ILE00.005-0.00268.7070.0000.0000.0000.0000.0000.000
61A95GLY00.0740.04665.0820.0000.0000.0000.0000.0000.000
62A96THR0-0.066-0.04062.4150.0000.0000.0000.0000.0000.000
63A97PRO0-0.0370.00365.5430.0000.0000.0000.0000.0000.000
64A98ASN0-0.061-0.03967.7090.0000.0000.0000.0000.0000.000
65A99LEU0-0.102-0.05064.0790.0000.0000.0000.0000.0000.000
66A100PRO00.0440.01865.9780.0000.0000.0000.0000.0000.000
67A101GLU-1-0.836-0.91564.855-0.002-0.0020.0000.0000.0000.000
68A102PHE0-0.0120.00658.4200.0000.0000.0000.0000.0000.000
69A103TRP00.022-0.01954.9090.0000.0000.0000.0000.0000.000
70A104LEU00.0430.04158.3580.0000.0000.0000.0000.0000.000
71A105ARG10.9080.94059.5660.0020.0020.0000.0000.0000.000
72A106ALA0-0.023-0.00456.4030.0000.0000.0000.0000.0000.000
73A107LEU0-0.025-0.02753.6720.0000.0000.0000.0000.0000.000
74A108ARG10.8320.90955.2620.0000.0000.0000.0000.0000.000
75A109ASN0-0.051-0.02156.9650.0010.0010.0000.0000.0000.000
76A110ASN0-0.021-0.00549.3120.0000.0000.0000.0000.0000.000
77A111ASN00.0110.01250.2640.0000.0000.0000.0000.0000.000
78A112THR00.0270.01646.2320.0000.0000.0000.0000.0000.000
79A113VAL0-0.006-0.01349.4090.0000.0000.0000.0000.0000.000
80A114SER0-0.047-0.04151.7240.0000.0000.0000.0000.0000.000
81A115HIS0-0.030-0.01149.9750.0000.0000.0000.0000.0000.000
82A116VAL0-0.0080.00750.6310.0000.0000.0000.0000.0000.000
83A117ILE0-0.057-0.01453.8350.0000.0000.0000.0000.0000.000
84A118GLU-1-0.876-0.94657.2350.0020.0020.0000.0000.0000.000
85A119ASP-1-0.911-0.96960.3730.0010.0010.0000.0000.0000.000
86A120HIS0-0.054-0.04260.7180.0000.0000.0000.0000.0000.000
87A121ASP-1-0.706-0.83658.8430.0010.0010.0000.0000.0000.000
88A122GLU-1-0.856-0.93061.858-0.001-0.0010.0000.0000.0000.000
89A123GLU-1-0.955-0.97863.5800.0000.0000.0000.0000.0000.000
90A124ILE0-0.017-0.02062.0980.0000.0000.0000.0000.0000.000
91A125LEU0-0.009-0.02158.0930.0000.0000.0000.0000.0000.000
92A126VAL0-0.0140.00861.9330.0000.0000.0000.0000.0000.000
93A127TYR0-0.056-0.02964.5340.0000.0000.0000.0000.0000.000
94A128LEU0-0.0400.00557.1490.0000.0000.0000.0000.0000.000
95A129ASN00.028-0.00661.2580.0000.0000.0000.0000.0000.000
96A130ASP-1-0.858-0.94357.030-0.006-0.0060.0000.0000.0000.000
97A131ILE0-0.0010.02652.1200.0000.0000.0000.0000.0000.000
98A132ARG10.7850.86952.0060.0070.0070.0000.0000.0000.000
99A133CYS0-0.021-0.01245.8820.0000.0000.0000.0000.0000.000
100A134ASP-1-0.890-0.91946.802-0.009-0.0090.0000.0000.0000.000
101A135TYR0-0.009-0.00840.8740.0010.0010.0000.0000.0000.000
102A145GLY00.008-0.00138.3610.0000.0000.0000.0000.0000.000
103A146PHE0-0.053-0.04839.161-0.001-0.0010.0000.0000.0000.000
104A147ILE00.0310.02342.8180.0010.0010.0000.0000.0000.000
105A148LEU0-0.049-0.02346.429-0.001-0.0010.0000.0000.0000.000
106A149SER00.0230.00348.8830.0010.0010.0000.0000.0000.000
107A150PHE0-0.0020.00551.1340.0000.0000.0000.0000.0000.000
108A151TYR0-0.004-0.01054.7720.0000.0000.0000.0000.0000.000
109A152PHE00.010-0.00557.8500.0000.0000.0000.0000.0000.000
110A153ALA00.0410.02961.9840.0000.0000.0000.0000.0000.000
111A154THR0-0.018-0.03565.6110.0000.0000.0000.0000.0000.000
112A155ASN00.0220.03364.1980.0000.0000.0000.0000.0000.000
113A156PRO0-0.041-0.02768.1850.0000.0000.0000.0000.0000.000
114A157PHE0-0.027-0.01664.9720.0000.0000.0000.0000.0000.000
115A158PHE00.0360.01560.7770.0000.0000.0000.0000.0000.000
116A159SER0-0.0140.00464.4480.0000.0000.0000.0000.0000.000
117A160ASN0-0.0020.01559.1340.0000.0000.0000.0000.0000.000
118A161SER00.0460.02361.6700.0000.0000.0000.0000.0000.000
119A162VAL0-0.017-0.01855.3400.0000.0000.0000.0000.0000.000
120A163LEU0-0.0140.01155.2090.0000.0000.0000.0000.0000.000
121A164THR0-0.019-0.02850.7070.0000.0000.0000.0000.0000.000
122A165LYS10.8720.92745.9380.0010.0010.0000.0000.0000.000
123A166THR0-0.020-0.01543.442-0.001-0.0010.0000.0000.0000.000
124A167TYR0-0.016-0.04440.6700.0010.0010.0000.0000.0000.000
125A168HIS0-0.0070.00538.602-0.002-0.0020.0000.0000.0000.000
126A169MET0-0.0180.00232.8100.0000.0000.0000.0000.0000.000
127A182HIS0-0.017-0.00438.7810.0010.0010.0000.0000.0000.000
128A183THR0-0.027-0.02240.350-0.001-0.0010.0000.0000.0000.000
129A184GLU-1-0.913-0.96943.571-0.002-0.0020.0000.0000.0000.000
130A185ALA00.0070.02146.776-0.001-0.0010.0000.0000.0000.000
131A186THR0-0.0420.00650.1250.0000.0000.0000.0000.0000.000
132A187VAL00.0210.01453.6420.0000.0000.0000.0000.0000.000
133A188ILE0-0.017-0.00755.9580.0000.0000.0000.0000.0000.000
134A189ASP-1-0.908-0.95158.8660.0000.0000.0000.0000.0000.000
135A190TRP0-0.026-0.03359.3020.0000.0000.0000.0000.0000.000
136A191TYR0-0.030-0.01964.1820.0000.0000.0000.0000.0000.000
137A192ASP-1-0.906-0.96667.8150.0020.0020.0000.0000.0000.000
138A193ASN0-0.084-0.04469.7650.0000.0000.0000.0000.0000.000
139A194LYS10.9070.95867.1600.0000.0000.0000.0000.0000.000
140A195ASN00.0230.01661.3910.0000.0000.0000.0000.0000.000
141A196ILE0-0.0210.01161.4070.0000.0000.0000.0000.0000.000
142A197LEU00.0040.02257.4340.0000.0000.0000.0000.0000.000
143A222ARG10.8740.93760.142-0.002-0.0020.0000.0000.0000.000
144A223ASP-1-0.904-0.95655.3360.0040.0040.0000.0000.0000.000
145A224SER0-0.042-0.04656.2860.0000.0000.0000.0000.0000.000
146A225PHE00.0770.03552.4400.0000.0000.0000.0000.0000.000
147A226PHE0-0.028-0.04354.1060.0000.0000.0000.0000.0000.000
148A227HIS00.0140.01552.8270.0000.0000.0000.0000.0000.000
149A228PHE0-0.0030.02347.5940.0000.0000.0000.0000.0000.000
150A229PHE0-0.070-0.03149.9300.0000.0000.0000.0000.0000.000
151A230THR0-0.029-0.01349.5510.0000.0000.0000.0000.0000.000
152A231SER0-0.013-0.01447.171-0.001-0.0010.0000.0000.0000.000
153A232HIS00.0170.01442.4640.0010.0010.0000.0000.0000.000
154A252GLU-1-0.936-0.97836.2350.0100.0100.0000.0000.0000.000
155A253MET00.0300.01640.063-0.001-0.0010.0000.0000.0000.000
156A254ILE00.014-0.01042.797-0.001-0.0010.0000.0000.0000.000
157A255ILE0-0.007-0.01739.505-0.001-0.0010.0000.0000.0000.000
158A256GLU-1-0.916-0.95037.1500.0040.0040.0000.0000.0000.000
159A257GLY00.0230.01641.188-0.001-0.0010.0000.0000.0000.000
160A258ASP-1-0.836-0.88544.410-0.001-0.0010.0000.0000.0000.000
161A259TYR00.009-0.01237.789-0.001-0.0010.0000.0000.0000.000
162A260GLU-1-0.930-0.95742.269-0.001-0.0010.0000.0000.0000.000
163A261VAL00.0310.03043.284-0.001-0.0010.0000.0000.0000.000
164A262ALA00.0000.00344.199-0.001-0.0010.0000.0000.0000.000
165A263LEU0-0.008-0.00239.512-0.001-0.0010.0000.0000.0000.000
166A264THR0-0.018-0.02243.486-0.001-0.0010.0000.0000.0000.000
167A265ILE00.005-0.00746.291-0.001-0.0010.0000.0000.0000.000
168A266LYS10.9310.96540.9020.0090.0090.0000.0000.0000.000
169A267GLU-1-0.978-0.99740.604-0.011-0.0110.0000.0000.0000.000
170A268ARG10.8860.94445.1110.0060.0060.0000.0000.0000.000
171A269ILE0-0.0050.00448.0870.0000.0000.0000.0000.0000.000
172A270ILE00.0200.01648.9440.0000.0000.0000.0000.0000.000
173A271PRO0-0.0230.00646.9860.0000.0000.0000.0000.0000.000
174A272TYR0-0.014-0.01245.8680.0000.0000.0000.0000.0000.000
175A273ALA0-0.0100.02052.4640.0000.0000.0000.0000.0000.000
176A274VAL00.035-0.01055.2490.0000.0000.0000.0000.0000.000
177A275ASP-1-0.843-0.91854.788-0.007-0.0070.0000.0000.0000.000
178A276TYR0-0.027-0.00850.0150.0000.0000.0000.0000.0000.000
179A277TYR0-0.028-0.00156.3270.0010.0010.0000.0000.0000.000
180A278LEU0-0.064-0.04259.7630.0000.0000.0000.0000.0000.000
181A279GLY00.0070.02258.4400.0000.0000.0000.0000.0000.000
182A280ILE0-0.089-0.04056.7780.0000.0000.0000.0000.0000.000
183A281ILE0-0.051-0.01250.9740.0000.0000.0000.0000.0000.000