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: 393NL

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 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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2009231.156014
FMO2-HF: Nuclear repulsion 1932867.122204
FMO2-HF: Total energy -76364.03381
FMO2-MP2: Total energy -76591.047554


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.
-9.583-2.1034.585-3.994-8.07-0.018
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 : 0.016 / q_NPA : -0.004
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-1-0.779-0.9083.037-1.1271.1730.176-1.198-1.277-0.002
4A38GLU-1-0.921-0.9475.752-0.323-0.3230.0000.0000.0000.000
5A39GLN00.0330.0142.377-3.183-0.7582.815-1.750-3.490-0.015
6A40LYS10.8040.8852.481-3.427-1.4841.262-0.855-2.351-0.001
7A41GLU-1-0.792-0.8874.2230.1250.2720.002-0.024-0.1250.000
8A42THR0-0.046-0.0145.8030.0650.0650.0000.0000.0000.000
9A43LEU0-0.004-0.0052.836-0.669-0.0040.330-0.167-0.8270.000
10A44LYS10.8290.8985.516-0.250-0.2500.0000.0000.0000.000
11A45LYS10.9540.9818.4090.0100.0100.0000.0000.0000.000
12A46LEU00.0450.0187.906-0.013-0.0130.0000.0000.0000.000
13A47LYS10.9160.9686.808-0.889-0.8890.0000.0000.0000.000
14A48LEU0-0.0100.00311.096-0.020-0.0200.0000.0000.0000.000
15A49TYR00.033-0.00313.063-0.021-0.0210.0000.0000.0000.000
16A50GLN00.0040.01713.124-0.024-0.0240.0000.0000.0000.000
17A51LYS10.8540.92815.091-0.141-0.1410.0000.0000.0000.000
18A52GLU-1-0.869-0.93517.1880.0550.0550.0000.0000.0000.000
19A53TYR0-0.082-0.05718.008-0.014-0.0140.0000.0000.0000.000
20A54TYR00.0330.01115.8680.0050.0050.0000.0000.0000.000
21A55ASP-1-0.881-0.91920.8090.1050.1050.0000.0000.0000.000
22A56TYR0-0.093-0.06222.438-0.008-0.0080.0000.0000.0000.000
23A57GLU-1-0.824-0.89122.0810.0660.0660.0000.0000.0000.000
24A58SER0-0.027-0.02624.281-0.002-0.0020.0000.0000.0000.000
25A59LYS10.8880.94426.130-0.073-0.0730.0000.0000.0000.000
26A60PHE00.0290.02327.804-0.005-0.0050.0000.0000.0000.000
27A61GLU-1-0.848-0.93727.7550.0440.0440.0000.0000.0000.000
28A62TYR0-0.060-0.02130.302-0.002-0.0020.0000.0000.0000.000
29A63GLU-1-0.935-0.98532.5690.0330.0330.0000.0000.0000.000
30A64LEU0-0.040-0.00232.141-0.004-0.0040.0000.0000.0000.000
31A65PHE0-0.018-0.01734.349-0.003-0.0030.0000.0000.0000.000
32A66LEU00.002-0.00536.159-0.002-0.0020.0000.0000.0000.000
33A67LEU0-0.035-0.00837.914-0.003-0.0030.0000.0000.0000.000
34A68ARG10.9640.96434.451-0.032-0.0320.0000.0000.0000.000
35A69GLN00.0220.01540.050-0.001-0.0010.0000.0000.0000.000
36A70LYS10.9320.98042.254-0.022-0.0220.0000.0000.0000.000
37A71TYR0-0.024-0.03642.860-0.002-0.0020.0000.0000.0000.000
38A72HIS0-0.0180.02344.252-0.002-0.0020.0000.0000.0000.000
39A73ASP-1-0.869-0.94346.0640.0250.0250.0000.0000.0000.000
40A74LEU0-0.109-0.05447.275-0.001-0.0010.0000.0000.0000.000
41A75TYR0-0.023-0.01845.268-0.001-0.0010.0000.0000.0000.000
42A76GLY00.0510.03750.471-0.001-0.0010.0000.0000.0000.000
43A77PRO00.0380.00852.249-0.001-0.0010.0000.0000.0000.000
44A78ILE0-0.055-0.02852.522-0.001-0.0010.0000.0000.0000.000
45A79TYR00.0260.01448.576-0.001-0.0010.0000.0000.0000.000
46A80ASP-1-0.802-0.87755.3980.0170.0170.0000.0000.0000.000
47A81LYS10.8910.94957.952-0.013-0.0130.0000.0000.0000.000
48A82ARG10.8660.94153.490-0.014-0.0140.0000.0000.0000.000
49A83ARG10.9430.97158.476-0.016-0.0160.0000.0000.0000.000
50A84GLU-1-0.879-0.92460.7620.0120.0120.0000.0000.0000.000
51A85ALA0-0.012-0.01063.3900.0000.0000.0000.0000.0000.000
52A86LEU0-0.027-0.00160.5570.0000.0000.0000.0000.0000.000
53A87VAL0-0.035-0.02263.1440.0000.0000.0000.0000.0000.000
54A88GLY00.0570.02266.0110.0000.0000.0000.0000.0000.000
55A89ASN0-0.118-0.08367.6920.0000.0000.0000.0000.0000.000
56A90GLY0-0.085-0.02669.3450.0000.0000.0000.0000.0000.000
57A91GLU-1-0.881-0.92766.2010.0140.0140.0000.0000.0000.000
58A92ALA0-0.010-0.01270.0310.0000.0000.0000.0000.0000.000
59A93LYS10.9070.95070.000-0.010-0.0100.0000.0000.0000.000
60A94ILE00.005-0.00468.3830.0000.0000.0000.0000.0000.000
61A95GLY00.0680.04665.0670.0000.0000.0000.0000.0000.000
62A96THR0-0.064-0.03862.3550.0000.0000.0000.0000.0000.000
63A97PRO0-0.036-0.00165.536-0.001-0.0010.0000.0000.0000.000
64A98ASN0-0.055-0.03367.769-0.001-0.0010.0000.0000.0000.000
65A99LEU0-0.099-0.04564.0240.0000.0000.0000.0000.0000.000
66A100PRO00.0440.01565.9430.0000.0000.0000.0000.0000.000
67A101GLU-1-0.827-0.90264.8030.0080.0080.0000.0000.0000.000
68A102PHE0-0.0010.00558.4330.0000.0000.0000.0000.0000.000
69A103TRP00.008-0.02254.8350.0000.0000.0000.0000.0000.000
70A104LEU00.0410.03458.2950.0000.0000.0000.0000.0000.000
71A105ARG10.8950.93259.480-0.008-0.0080.0000.0000.0000.000
72A106ALA0-0.022-0.00456.3790.0000.0000.0000.0000.0000.000
73A107LEU0-0.027-0.02853.5700.0000.0000.0000.0000.0000.000
74A108ARG10.8050.87655.159-0.009-0.0090.0000.0000.0000.000
75A109ASN0-0.055-0.02056.846-0.001-0.0010.0000.0000.0000.000
76A110ASN0-0.029-0.00849.2780.0000.0000.0000.0000.0000.000
77A111ASN00.0010.00450.0800.0010.0010.0000.0000.0000.000
78A112THR00.0110.00846.250-0.001-0.0010.0000.0000.0000.000
79A113VAL0-0.022-0.02549.2730.0010.0010.0000.0000.0000.000
80A114SER0-0.039-0.02951.6130.0000.0000.0000.0000.0000.000
81A115HIS0-0.024-0.00949.5570.0000.0000.0000.0000.0000.000
82A116VAL0-0.0130.00050.5450.0000.0000.0000.0000.0000.000
83A117ILE0-0.053-0.01053.7130.0010.0010.0000.0000.0000.000
84A118GLU-1-0.877-0.93557.1230.0090.0090.0000.0000.0000.000
85A119ASP-1-0.903-0.96260.2510.0080.0080.0000.0000.0000.000
86A120HIS0-0.049-0.04660.5300.0000.0000.0000.0000.0000.000
87A121ASP-1-0.714-0.83658.7320.0130.0130.0000.0000.0000.000
88A122GLU-1-0.831-0.90261.7720.0090.0090.0000.0000.0000.000
89A123GLU-1-0.944-0.97763.4950.0100.0100.0000.0000.0000.000
90A124ILE0-0.021-0.01962.0740.0000.0000.0000.0000.0000.000
91A125LEU0-0.002-0.01557.9450.0000.0000.0000.0000.0000.000
92A126VAL0-0.0140.00661.8810.0000.0000.0000.0000.0000.000
93A127TYR0-0.052-0.03064.4970.0000.0000.0000.0000.0000.000
94A128LEU0-0.0520.00557.2060.0010.0010.0000.0000.0000.000
95A129ASN00.032-0.01461.264-0.001-0.0010.0000.0000.0000.000
96A130ASP-1-0.832-0.93156.8410.0160.0160.0000.0000.0000.000
97A131ILE00.0060.02752.2390.0000.0000.0000.0000.0000.000
98A132ARG10.7780.86652.062-0.018-0.0180.0000.0000.0000.000
99A133CYS00.013-0.00645.7070.0000.0000.0000.0000.0000.000
100A134ASP-1-0.910-0.92946.8250.0240.0240.0000.0000.0000.000
101A135TYR0-0.0020.00040.7060.0010.0010.0000.0000.0000.000
102A145GLY00.0020.00438.4280.0010.0010.0000.0000.0000.000
103A146PHE0-0.058-0.04939.2140.0000.0000.0000.0000.0000.000
104A147ILE00.0170.01242.8650.0000.0000.0000.0000.0000.000
105A148LEU0-0.019-0.00946.473-0.001-0.0010.0000.0000.0000.000
106A149SER00.008-0.00548.9000.0000.0000.0000.0000.0000.000
107A150PHE00.0090.00950.993-0.001-0.0010.0000.0000.0000.000
108A151TYR0-0.001-0.00654.7790.0000.0000.0000.0000.0000.000
109A152PHE00.014-0.00757.698-0.001-0.0010.0000.0000.0000.000
110A153ALA00.0430.03161.9940.0000.0000.0000.0000.0000.000
111A154THR0-0.020-0.03565.6260.0000.0000.0000.0000.0000.000
112A155ASN00.0200.02364.149-0.001-0.0010.0000.0000.0000.000
113A156PRO0-0.025-0.01668.1800.0000.0000.0000.0000.0000.000
114A157PHE00.0090.00364.9850.0000.0000.0000.0000.0000.000
115A158PHE00.0380.02360.7060.0000.0000.0000.0000.0000.000
116A159SER0-0.027-0.00464.4330.0000.0000.0000.0000.0000.000
117A160ASN0-0.027-0.01259.5640.0000.0000.0000.0000.0000.000
118A161SER00.0440.02261.7080.0000.0000.0000.0000.0000.000
119A162VAL0-0.026-0.02655.4280.0000.0000.0000.0000.0000.000
120A163LEU0-0.0070.01955.2730.0000.0000.0000.0000.0000.000
121A164THR0-0.010-0.01950.7290.0000.0000.0000.0000.0000.000
122A165LYS10.8220.89045.990-0.024-0.0240.0000.0000.0000.000
123A166THR0-0.019-0.01543.536-0.001-0.0010.0000.0000.0000.000
124A167TYR0-0.006-0.03240.6780.0000.0000.0000.0000.0000.000
125A168HIS0-0.044-0.02238.6970.0020.0020.0000.0000.0000.000
126A169MET0-0.0200.01232.8030.0000.0000.0000.0000.0000.000
127A182HIS0-0.044-0.02438.7480.0020.0020.0000.0000.0000.000
128A183THR0-0.019-0.02440.3590.0000.0000.0000.0000.0000.000
129A184GLU-1-0.857-0.91943.5770.0360.0360.0000.0000.0000.000
130A185ALA00.0070.02446.803-0.001-0.0010.0000.0000.0000.000
131A186THR0-0.057-0.01650.1370.0000.0000.0000.0000.0000.000
132A187VAL00.0240.01353.6670.0000.0000.0000.0000.0000.000
133A188ILE0-0.003-0.00155.9700.0000.0000.0000.0000.0000.000
134A189ASP-1-0.888-0.92758.8640.0190.0190.0000.0000.0000.000
135A190TRP0-0.018-0.03259.229-0.001-0.0010.0000.0000.0000.000
136A191TYR0-0.026-0.01564.1670.0000.0000.0000.0000.0000.000
137A192ASP-1-0.863-0.94767.7880.0120.0120.0000.0000.0000.000
138A193ASN0-0.106-0.06069.723-0.001-0.0010.0000.0000.0000.000
139A194LYS10.8160.92967.665-0.012-0.0120.0000.0000.0000.000
140A195ASN00.0350.02161.4370.0000.0000.0000.0000.0000.000
141A196ILE0-0.0080.01161.1160.0000.0000.0000.0000.0000.000
142A197LEU0-0.0170.02157.494-0.001-0.0010.0000.0000.0000.000
143A222ARG10.8720.93759.953-0.011-0.0110.0000.0000.0000.000
144A223ASP-1-0.908-0.95255.3550.0130.0130.0000.0000.0000.000
145A224SER0-0.042-0.05356.1850.0000.0000.0000.0000.0000.000
146A225PHE00.0770.03252.5150.0010.0010.0000.0000.0000.000
147A226PHE0-0.032-0.04654.0350.0010.0010.0000.0000.0000.000
148A227HIS00.0010.00252.7880.0020.0020.0000.0000.0000.000
149A228PHE00.0020.02047.3190.0010.0010.0000.0000.0000.000
150A229PHE0-0.058-0.02149.8880.0010.0010.0000.0000.0000.000
151A230THR0-0.031-0.01149.2930.0000.0000.0000.0000.0000.000
152A231SER00.006-0.00447.1620.0000.0000.0000.0000.0000.000
153A232HIS00.0060.00942.5740.0010.0010.0000.0000.0000.000
154A252GLU-1-0.939-0.97936.1430.0260.0260.0000.0000.0000.000
155A253MET00.0320.01339.9410.0000.0000.0000.0000.0000.000
156A254ILE00.020-0.00842.653-0.001-0.0010.0000.0000.0000.000
157A255ILE0-0.008-0.01439.3840.0000.0000.0000.0000.0000.000
158A256GLU-1-0.925-0.95036.8080.0230.0230.0000.0000.0000.000
159A257GLY00.0200.01241.076-0.001-0.0010.0000.0000.0000.000
160A258ASP-1-0.815-0.87244.4460.0230.0230.0000.0000.0000.000
161A259TYR00.014-0.02437.5030.0000.0000.0000.0000.0000.000
162A260GLU-1-0.901-0.94242.2010.0130.0130.0000.0000.0000.000
163A261VAL00.0390.02143.185-0.001-0.0010.0000.0000.0000.000
164A262ALA0-0.0080.00544.128-0.001-0.0010.0000.0000.0000.000
165A263LEU0-0.0030.00139.6160.0000.0000.0000.0000.0000.000
166A264THR0-0.012-0.01043.429-0.001-0.0010.0000.0000.0000.000
167A265ILE00.015-0.00346.215-0.001-0.0010.0000.0000.0000.000
168A266LYS10.8530.92441.030-0.026-0.0260.0000.0000.0000.000
169A267GLU-1-0.907-0.95340.6040.0220.0220.0000.0000.0000.000
170A268ARG10.8870.94145.070-0.011-0.0110.0000.0000.0000.000
171A269ILE0-0.0020.00548.024-0.001-0.0010.0000.0000.0000.000
172A270ILE00.0180.01749.125-0.001-0.0010.0000.0000.0000.000
173A271PRO0-0.0010.00446.902-0.001-0.0010.0000.0000.0000.000
174A272TYR0-0.022-0.01145.881-0.001-0.0010.0000.0000.0000.000
175A273ALA0-0.0070.02252.418-0.001-0.0010.0000.0000.0000.000
176A274VAL00.044-0.00555.2050.0000.0000.0000.0000.0000.000
177A275ASP-1-0.865-0.92954.6550.0080.0080.0000.0000.0000.000
178A276TYR0-0.009-0.00349.9760.0000.0000.0000.0000.0000.000
179A277TYR0-0.024-0.00256.239-0.001-0.0010.0000.0000.0000.000
180A278LEU0-0.064-0.03959.6780.0000.0000.0000.0000.0000.000
181A279GLY00.0060.01958.324-0.001-0.0010.0000.0000.0000.000
182A280ILE0-0.094-0.04356.425-0.001-0.0010.0000.0000.0000.000
183A281ILE0-0.045-0.00750.9050.0000.0000.0000.0000.0000.000