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: LZML9

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 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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2014319.191076
FMO2-HF: Nuclear repulsion 1937954.852652
FMO2-HF: Total energy -76364.338424
FMO2-MP2: Total energy -76591.362968


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.
-9.009-2.4526.498-4.46-8.594-0.019
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 : 0.029 / q_NPA : 0.002
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-1-0.798-0.9023.280-0.8310.9930.062-0.958-0.9280.000
4A38GLU-1-0.908-0.9395.957-0.445-0.4450.0000.0000.0000.000
5A39GLN00.0420.0302.327-3.092-1.2514.165-2.161-3.845-0.016
6A40LYS10.8030.8832.437-3.045-1.0811.914-1.131-2.747-0.003
7A41GLU-1-0.785-0.8904.1170.0000.1830.005-0.029-0.1590.000
8A42THR0-0.051-0.0305.5660.0790.0790.0000.0000.0000.000
9A43LEU00.001-0.0022.847-0.719-0.0040.353-0.181-0.8870.000
10A44LYS10.8230.8925.311-0.235-0.205-0.0010.000-0.0280.000
11A45LYS10.9220.9738.3800.0410.0410.0000.0000.0000.000
12A46LEU00.0420.0167.402-0.009-0.0090.0000.0000.0000.000
13A47LYS10.9260.9656.688-0.841-0.8410.0000.0000.0000.000
14A48LEU0-0.0090.01210.874-0.016-0.0160.0000.0000.0000.000
15A49TYR00.0410.00512.827-0.018-0.0180.0000.0000.0000.000
16A50GLN00.0120.01812.851-0.023-0.0230.0000.0000.0000.000
17A51LYS10.8010.89214.846-0.130-0.1300.0000.0000.0000.000
18A52GLU-1-0.870-0.92616.9380.0450.0450.0000.0000.0000.000
19A53TYR0-0.062-0.05117.752-0.013-0.0130.0000.0000.0000.000
20A54TYR00.0270.01215.8580.0040.0040.0000.0000.0000.000
21A55ASP-1-0.867-0.90420.7610.0960.0960.0000.0000.0000.000
22A56TYR0-0.091-0.06221.713-0.007-0.0070.0000.0000.0000.000
23A57GLU-1-0.827-0.89521.8930.0590.0590.0000.0000.0000.000
24A58SER0-0.012-0.02924.052-0.002-0.0020.0000.0000.0000.000
25A59LYS10.8340.92626.242-0.062-0.0620.0000.0000.0000.000
26A60PHE00.0440.02727.719-0.004-0.0040.0000.0000.0000.000
27A61GLU-1-0.844-0.94027.8680.0360.0360.0000.0000.0000.000
28A62TYR0-0.045-0.00930.292-0.002-0.0020.0000.0000.0000.000
29A63GLU-1-0.925-0.98232.2290.0290.0290.0000.0000.0000.000
30A64LEU0-0.0310.00031.998-0.004-0.0040.0000.0000.0000.000
31A65PHE0-0.007-0.00834.310-0.002-0.0020.0000.0000.0000.000
32A66LEU0-0.003-0.00336.100-0.002-0.0020.0000.0000.0000.000
33A67LEU0-0.044-0.02037.452-0.002-0.0020.0000.0000.0000.000
34A68ARG10.9560.96533.905-0.028-0.0280.0000.0000.0000.000
35A69GLN00.0150.01340.013-0.001-0.0010.0000.0000.0000.000
36A70LYS10.9280.97542.194-0.018-0.0180.0000.0000.0000.000
37A71TYR0-0.024-0.02642.591-0.002-0.0020.0000.0000.0000.000
38A72HIS0-0.0300.00244.005-0.001-0.0010.0000.0000.0000.000
39A73ASP-1-0.869-0.94745.8480.0230.0230.0000.0000.0000.000
40A74LEU0-0.102-0.05147.294-0.001-0.0010.0000.0000.0000.000
41A75TYR0-0.013-0.01344.982-0.001-0.0010.0000.0000.0000.000
42A76GLY00.0600.04650.257-0.001-0.0010.0000.0000.0000.000
43A77PRO00.023-0.00252.065-0.001-0.0010.0000.0000.0000.000
44A78ILE0-0.072-0.03552.033-0.001-0.0010.0000.0000.0000.000
45A79TYR00.0360.01748.417-0.001-0.0010.0000.0000.0000.000
46A80ASP-1-0.757-0.85955.2520.0150.0150.0000.0000.0000.000
47A81LYS10.8990.95857.331-0.011-0.0110.0000.0000.0000.000
48A82ARG10.8290.92753.128-0.012-0.0120.0000.0000.0000.000
49A83ARG10.9230.95858.397-0.015-0.0150.0000.0000.0000.000
50A84GLU-1-0.864-0.92860.8090.0110.0110.0000.0000.0000.000
51A85ALA0-0.013-0.01463.0060.0000.0000.0000.0000.0000.000
52A86LEU0-0.030-0.00660.1200.0000.0000.0000.0000.0000.000
53A87VAL0-0.054-0.02863.0760.0000.0000.0000.0000.0000.000
54A88GLY00.0230.02465.4340.0000.0000.0000.0000.0000.000
55A89ASN0-0.081-0.06467.1710.0000.0000.0000.0000.0000.000
56A90GLY0-0.082-0.04069.2960.0000.0000.0000.0000.0000.000
57A91GLU-1-0.881-0.92065.6600.0130.0130.0000.0000.0000.000
58A92ALA00.006-0.00269.4310.0000.0000.0000.0000.0000.000
59A93LYS10.9060.94969.518-0.010-0.0100.0000.0000.0000.000
60A94ILE0-0.008-0.01368.1600.0000.0000.0000.0000.0000.000
61A95GLY00.0470.03564.7220.0000.0000.0000.0000.0000.000
62A96THR0-0.079-0.04662.1040.0000.0000.0000.0000.0000.000
63A97PRO0-0.0150.00165.293-0.001-0.0010.0000.0000.0000.000
64A98ASN0-0.050-0.02467.493-0.001-0.0010.0000.0000.0000.000
65A99LEU0-0.086-0.04063.722-0.001-0.0010.0000.0000.0000.000
66A100PRO00.0500.02365.6770.0000.0000.0000.0000.0000.000
67A101GLU-1-0.823-0.89964.6270.0060.0060.0000.0000.0000.000
68A102PHE0-0.0150.00258.1350.0000.0000.0000.0000.0000.000
69A103TRP00.011-0.02254.7070.0000.0000.0000.0000.0000.000
70A104LEU00.0210.02858.1520.0000.0000.0000.0000.0000.000
71A105ARG10.8770.91959.309-0.007-0.0070.0000.0000.0000.000
72A106ALA0-0.031-0.01456.0570.0000.0000.0000.0000.0000.000
73A107LEU0-0.023-0.02253.4130.0000.0000.0000.0000.0000.000
74A108ARG10.8090.88055.026-0.008-0.0080.0000.0000.0000.000
75A109ASN0-0.060-0.02556.811-0.001-0.0010.0000.0000.0000.000
76A110ASN0-0.030-0.01449.2710.0000.0000.0000.0000.0000.000
77A111ASN0-0.002-0.00649.7080.0010.0010.0000.0000.0000.000
78A112THR00.0150.00346.1260.0000.0000.0000.0000.0000.000
79A113VAL0-0.006-0.01549.0810.0010.0010.0000.0000.0000.000
80A114SER0-0.076-0.04051.5450.0000.0000.0000.0000.0000.000
81A115HIS0-0.018-0.01549.1770.0000.0000.0000.0000.0000.000
82A116VAL0-0.032-0.00250.3270.0000.0000.0000.0000.0000.000
83A117ILE0-0.015-0.00653.6270.0010.0010.0000.0000.0000.000
84A118GLU-1-0.868-0.92857.1400.0080.0080.0000.0000.0000.000
85A119ASP-1-0.889-0.95260.3240.0070.0070.0000.0000.0000.000
86A120HIS0-0.055-0.05460.4820.0000.0000.0000.0000.0000.000
87A121ASP-1-0.722-0.82958.6810.0120.0120.0000.0000.0000.000
88A122GLU-1-0.812-0.89661.5220.0080.0080.0000.0000.0000.000
89A123GLU-1-0.932-0.97563.2690.0090.0090.0000.0000.0000.000
90A124ILE0-0.013-0.01262.0860.0000.0000.0000.0000.0000.000
91A125LEU00.008-0.00357.7310.0000.0000.0000.0000.0000.000
92A126VAL0-0.025-0.00261.7160.0000.0000.0000.0000.0000.000
93A127TYR0-0.025-0.02364.2430.0000.0000.0000.0000.0000.000
94A128LEU0-0.0360.00256.7300.0010.0010.0000.0000.0000.000
95A129ASN0-0.012-0.02560.438-0.001-0.0010.0000.0000.0000.000
96A130ASP-1-0.820-0.91556.6320.0140.0140.0000.0000.0000.000
97A131ILE00.0050.01552.0920.0000.0000.0000.0000.0000.000
98A132ARG10.7370.84851.527-0.016-0.0160.0000.0000.0000.000
99A133CYS00.0220.00145.3070.0000.0000.0000.0000.0000.000
100A134ASP-1-0.902-0.91946.1760.0220.0220.0000.0000.0000.000
101A135TYR00.0210.01040.3350.0000.0000.0000.0000.0000.000
102A145GLY00.0390.01537.4750.0010.0010.0000.0000.0000.000
103A146PHE0-0.085-0.05838.856-0.001-0.0010.0000.0000.0000.000
104A147ILE00.0080.00742.3350.0010.0010.0000.0000.0000.000
105A148LEU0-0.0070.00445.974-0.001-0.0010.0000.0000.0000.000
106A149SER00.006-0.01048.5450.0010.0010.0000.0000.0000.000
107A150PHE00.0160.01050.725-0.001-0.0010.0000.0000.0000.000
108A151TYR0-0.002-0.00454.4090.0000.0000.0000.0000.0000.000
109A152PHE00.033-0.00757.466-0.001-0.0010.0000.0000.0000.000
110A153ALA00.0370.03261.8550.0000.0000.0000.0000.0000.000
111A154THR0-0.033-0.03865.5540.0000.0000.0000.0000.0000.000
112A155ASN00.0480.03664.169-0.001-0.0010.0000.0000.0000.000
113A156PRO0-0.049-0.01468.1080.0000.0000.0000.0000.0000.000
114A157PHE00.0280.01364.8680.0000.0000.0000.0000.0000.000
115A158PHE00.0430.02060.5780.0000.0000.0000.0000.0000.000
116A159SER0-0.045-0.01264.4510.0000.0000.0000.0000.0000.000
117A160ASN0-0.031-0.02359.5190.0000.0000.0000.0000.0000.000
118A161SER00.0360.01861.6790.0000.0000.0000.0000.0000.000
119A162VAL0-0.031-0.02255.5690.0000.0000.0000.0000.0000.000
120A163LEU0-0.0070.02455.2420.0000.0000.0000.0000.0000.000
121A164THR0-0.024-0.03750.7980.0000.0000.0000.0000.0000.000
122A165LYS10.8220.88546.154-0.022-0.0220.0000.0000.0000.000
123A166THR0-0.0170.00043.238-0.001-0.0010.0000.0000.0000.000
124A167TYR0-0.015-0.04240.5350.0000.0000.0000.0000.0000.000
125A168HIS0-0.042-0.01538.5740.0020.0020.0000.0000.0000.000
126A169MET0-0.0240.01532.5440.0000.0000.0000.0000.0000.000
127A182HIS0-0.040-0.02338.4310.0020.0020.0000.0000.0000.000
128A183THR0-0.013-0.01839.9630.0000.0000.0000.0000.0000.000
129A184GLU-1-0.847-0.91343.2950.0340.0340.0000.0000.0000.000
130A185ALA00.0300.01946.720-0.001-0.0010.0000.0000.0000.000
131A186THR0-0.080-0.01450.1940.0000.0000.0000.0000.0000.000
132A187VAL00.0250.01553.706-0.001-0.0010.0000.0000.0000.000
133A188ILE00.0190.01155.7710.0000.0000.0000.0000.0000.000
134A189ASP-1-0.880-0.91558.7730.0180.0180.0000.0000.0000.000
135A190TRP0-0.010-0.02859.243-0.001-0.0010.0000.0000.0000.000
136A191TYR0-0.049-0.01864.0750.0000.0000.0000.0000.0000.000
137A192ASP-1-0.821-0.92267.5800.0120.0120.0000.0000.0000.000
138A193ASN0-0.134-0.08469.773-0.001-0.0010.0000.0000.0000.000
139A194LYS10.7950.90867.820-0.011-0.0110.0000.0000.0000.000
140A195ASN00.0480.02561.3510.0000.0000.0000.0000.0000.000
141A196ILE0-0.0240.00960.7450.0000.0000.0000.0000.0000.000
142A197LEU0-0.0050.02257.332-0.001-0.0010.0000.0000.0000.000
143A222ARG10.8600.92959.615-0.010-0.0100.0000.0000.0000.000
144A223ASP-1-0.897-0.94455.2430.0120.0120.0000.0000.0000.000
145A224SER0-0.028-0.05256.1430.0000.0000.0000.0000.0000.000
146A225PHE00.0530.02352.6430.0010.0010.0000.0000.0000.000
147A226PHE0-0.032-0.03553.9990.0010.0010.0000.0000.0000.000
148A227HIS0-0.019-0.01252.7880.0020.0020.0000.0000.0000.000
149A228PHE00.0050.02347.1590.0010.0010.0000.0000.0000.000
150A229PHE0-0.041-0.01450.0400.0010.0010.0000.0000.0000.000
151A230THR0-0.027-0.02149.0990.0000.0000.0000.0000.0000.000
152A231SER0-0.012-0.01447.0970.0000.0000.0000.0000.0000.000
153A232HIS0-0.0020.01042.5000.0010.0010.0000.0000.0000.000
154A252GLU-1-0.950-0.97835.9850.0250.0250.0000.0000.0000.000
155A253MET00.0480.01739.6430.0000.0000.0000.0000.0000.000
156A254ILE00.0260.00542.095-0.001-0.0010.0000.0000.0000.000
157A255ILE0-0.005-0.00439.4850.0000.0000.0000.0000.0000.000
158A256GLU-1-0.930-0.96236.9570.0190.0190.0000.0000.0000.000
159A257GLY00.0210.01240.752-0.001-0.0010.0000.0000.0000.000
160A258ASP-1-0.818-0.87344.2480.0210.0210.0000.0000.0000.000
161A259TYR00.022-0.02637.3230.0000.0000.0000.0000.0000.000
162A260GLU-1-0.887-0.91742.2310.0110.0110.0000.0000.0000.000
163A261VAL00.0370.02543.116-0.001-0.0010.0000.0000.0000.000
164A262ALA0-0.0040.00543.7640.0000.0000.0000.0000.0000.000
165A263LEU0-0.004-0.00439.2420.0000.0000.0000.0000.0000.000
166A264THR0-0.015-0.01743.111-0.001-0.0010.0000.0000.0000.000
167A265ILE00.011-0.01045.976-0.001-0.0010.0000.0000.0000.000
168A266LYS10.8250.90540.778-0.023-0.0230.0000.0000.0000.000
169A267GLU-1-0.905-0.94840.5710.0190.0190.0000.0000.0000.000
170A268ARG10.8780.94044.957-0.009-0.0090.0000.0000.0000.000
171A269ILE00.0090.00847.914-0.001-0.0010.0000.0000.0000.000
172A270ILE00.0060.01548.643-0.001-0.0010.0000.0000.0000.000
173A271PRO00.0030.00746.8480.0000.0000.0000.0000.0000.000
174A272TYR0-0.018-0.00845.875-0.001-0.0010.0000.0000.0000.000
175A273ALA00.0220.02752.332-0.001-0.0010.0000.0000.0000.000
176A274VAL00.017-0.00255.1020.0000.0000.0000.0000.0000.000
177A275ASP-1-0.868-0.94154.2350.0060.0060.0000.0000.0000.000
178A276TYR00.008-0.00149.7690.0000.0000.0000.0000.0000.000
179A277TYR0-0.0220.00455.9380.0000.0000.0000.0000.0000.000
180A278LEU0-0.067-0.04459.4210.0000.0000.0000.0000.0000.000
181A279GLY00.0110.01758.074-0.001-0.0010.0000.0000.0000.000
182A280ILE0-0.090-0.03456.057-0.001-0.0010.0000.0000.0000.000
183A281ILE0-0.045-0.00850.5520.0000.0000.0000.0000.0000.000