Manual

About

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: 85N2Y

Calculation Name: 3GW4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GW4

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RRX4

Base Structure: X-ray

Registration Date: 2023-06-22

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1992835.344407
FMO2-HF: Nuclear repulsion 1917142.061754
FMO2-HF: Total energy -75693.282652
FMO2-MP2: Total energy -75912.828709


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:8:ASP)


Summations of interaction energy for fragment #1(A:8: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.
91.88895.923.302-3.299-4.0350.016
Interaction energy analysis for fragmet #1(A:8:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.905 / q_NPA : -0.958
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].
3A10ALA00.0200.0073.691-8.190-5.854-0.010-1.103-1.2230.003
4A11LEU0-0.069-0.0302.156-10.516-8.9943.313-2.134-2.7010.013
5A12ALA00.0730.0334.625-5.890-5.716-0.001-0.062-0.1110.000
6A13GLU-1-0.829-0.9146.52420.80220.8020.0000.0000.0000.000
7A14ARG10.9550.9738.309-28.908-28.9080.0000.0000.0000.000
8A15GLN0-0.042-0.0107.261-0.508-0.5080.0000.0000.0000.000
9A16ALA00.0570.01410.575-1.984-1.9840.0000.0000.0000.000
10A17GLN0-0.020-0.01312.501-1.810-1.8100.0000.0000.0000.000
11A18ALA0-0.051-0.01313.932-1.328-1.3280.0000.0000.0000.000
12A19LEU0-0.031-0.01914.578-1.155-1.1550.0000.0000.0000.000
13A20LEU0-0.0070.01016.890-0.940-0.9400.0000.0000.0000.000
14A21ALA0-0.035-0.00418.770-0.742-0.7420.0000.0000.0000.000
15A22HIS0-0.0050.00920.022-1.240-1.2400.0000.0000.0000.000
16A23PRO00.0290.00422.6700.2250.2250.0000.0000.0000.000
17A24ALA0-0.022-0.00824.6070.0320.0320.0000.0000.0000.000
18A25THR0-0.008-0.02619.124-0.065-0.0650.0000.0000.0000.000
19A26ALA0-0.0090.00419.5510.6740.6740.0000.0000.0000.000
20A27SER00.004-0.04319.9460.4670.4670.0000.0000.0000.000
21A28GLY00.0310.01718.2600.1860.1860.0000.0000.0000.000
22A29ALA0-0.013-0.00215.4720.9920.9920.0000.0000.0000.000
23A30ARG10.9550.98315.360-12.903-12.9030.0000.0000.0000.000
24A31PHE00.0210.02214.7610.4930.4930.0000.0000.0000.000
25A32MET00.0010.00810.7661.1251.1250.0000.0000.0000.000
26A33LEU0-0.009-0.01611.7161.5041.5040.0000.0000.0000.000
27A34GLY00.0230.02612.8760.4670.4670.0000.0000.0000.000
28A35TYR00.0280.00211.1340.1050.1050.0000.0000.0000.000
29A36VAL0-0.029-0.0117.5011.4131.4130.0000.0000.0000.000
30A37TYR0-0.050-0.0618.8171.3321.3320.0000.0000.0000.000
31A38ALA0-0.0050.00211.384-0.393-0.3930.0000.0000.0000.000
32A39PHE0-0.0200.0016.9230.0990.0990.0000.0000.0000.000
33A40MET0-0.116-0.0456.8371.7851.7850.0000.0000.0000.000
34A41ASP-1-0.864-0.9338.93720.16720.1670.0000.0000.0000.000
35A42ARG10.7750.90110.684-23.507-23.5070.0000.0000.0000.000
36A43PHE00.0720.00914.273-0.263-0.2630.0000.0000.0000.000
37A44ASP-1-0.941-0.97516.87613.54213.5420.0000.0000.0000.000
38A45GLU-1-0.866-0.93815.92717.30217.3020.0000.0000.0000.000
39A46ALA00.0020.01714.627-0.196-0.1960.0000.0000.0000.000
40A47ARG10.9500.99816.348-13.502-13.5020.0000.0000.0000.000
41A48ALA00.0130.00720.035-0.428-0.4280.0000.0000.0000.000
42A49SER0-0.060-0.03116.975-0.469-0.4690.0000.0000.0000.000
43A50PHE00.007-0.00915.814-0.345-0.3450.0000.0000.0000.000
44A51GLN00.0330.01120.412-0.349-0.3490.0000.0000.0000.000
45A52ALA0-0.054-0.01622.446-0.514-0.5140.0000.0000.0000.000
46A53LEU0-0.028-0.02019.949-0.368-0.3680.0000.0000.0000.000
47A54GLN00.0570.03523.893-0.132-0.1320.0000.0000.0000.000
48A55GLN0-0.010-0.01126.528-0.386-0.3860.0000.0000.0000.000
49A56GLN0-0.044-0.00425.267-0.052-0.0520.0000.0000.0000.000
50A57ALA00.0360.02527.549-0.239-0.2390.0000.0000.0000.000
51A58GLN00.0040.02229.334-0.263-0.2630.0000.0000.0000.000
52A59LYS10.8420.93729.698-10.280-10.2800.0000.0000.0000.000
53A60SER0-0.001-0.03831.2360.0460.0460.0000.0000.0000.000
54A61GLY0-0.053-0.00433.706-0.191-0.1910.0000.0000.0000.000
55A62ASP-1-0.884-0.93029.56410.08910.0890.0000.0000.0000.000
56A63HIS00.0550.01330.8480.0810.0810.0000.0000.0000.000
57A64THR0-0.008-0.00527.4530.1340.1340.0000.0000.0000.000
58A65ALA0-0.001-0.01425.8400.3970.3970.0000.0000.0000.000
59A66GLU-1-0.889-0.95925.6919.9409.9400.0000.0000.0000.000
60A67HIS0-0.024-0.01226.4050.2580.2580.0000.0000.0000.000
61A68ARG10.9801.00021.589-11.937-11.9370.0000.0000.0000.000
62A69ALA0-0.027-0.02722.4950.5770.5770.0000.0000.0000.000
63A70LEU0-0.005-0.00223.2770.3690.3690.0000.0000.0000.000
64A71HIS0-0.038-0.00621.4690.6080.6080.0000.0000.0000.000
65A72GLN00.0090.00418.3170.5950.5950.0000.0000.0000.000
66A73VAL0-0.015-0.00719.9790.4590.4590.0000.0000.0000.000
67A74GLY00.0460.00321.9730.1070.1070.0000.0000.0000.000
68A75MET0-0.021-0.00115.4850.1450.1450.0000.0000.0000.000
69A76VAL0-0.010-0.02517.0300.4230.4230.0000.0000.0000.000
70A77GLU-1-0.830-0.91418.87712.32412.3240.0000.0000.0000.000
71A78ARG10.8370.92518.716-14.609-14.6090.0000.0000.0000.000
72A79MET0-0.093-0.03214.8230.0250.0250.0000.0000.0000.000
73A80ALA0-0.021-0.00118.8870.1890.1890.0000.0000.0000.000
74A81GLY0-0.0150.00420.508-0.358-0.3580.0000.0000.0000.000
75A82ASN0-0.073-0.03923.544-0.835-0.8350.0000.0000.0000.000
76A83TRP00.043-0.00924.201-0.151-0.1510.0000.0000.0000.000
77A84ASP-1-0.854-0.90627.5659.0109.0100.0000.0000.0000.000
78A85ALA00.0260.00926.674-0.206-0.2060.0000.0000.0000.000
79A86ALA00.0360.02725.095-0.047-0.0470.0000.0000.0000.000
80A87ARG10.8730.91826.706-9.103-9.1030.0000.0000.0000.000
81A88ARG10.8830.94130.179-9.003-9.0030.0000.0000.0000.000
82A89CYS00.0170.02126.603-0.119-0.1190.0000.0000.0000.000
83A90PHE00.0410.02123.221-0.122-0.1220.0000.0000.0000.000
84A91LEU0-0.024-0.01328.999-0.179-0.1790.0000.0000.0000.000
85A92GLU-1-0.915-0.96631.1479.2699.2690.0000.0000.0000.000
86A93GLU-1-0.782-0.89326.81111.08711.0870.0000.0000.0000.000
87A94ARG10.7420.84530.462-9.301-9.3010.0000.0000.0000.000
88A95GLU-1-0.953-0.97333.0137.9057.9050.0000.0000.0000.000
89A96LEU0-0.020-0.01330.507-0.126-0.1260.0000.0000.0000.000
90A97LEU00.001-0.00629.292-0.129-0.1290.0000.0000.0000.000
91A98ALA0-0.0290.00933.518-0.120-0.1200.0000.0000.0000.000
92A99SER0-0.124-0.05836.274-0.252-0.2520.0000.0000.0000.000
93A100LEU0-0.054-0.02131.568-0.085-0.0850.0000.0000.0000.000
94A101PRO0-0.025-0.02534.688-0.132-0.1320.0000.0000.0000.000
95A102GLU-1-0.960-0.96734.2648.2758.2750.0000.0000.0000.000
96A103ASP-1-0.825-0.93428.66010.69510.6950.0000.0000.0000.000
97A104PRO00.004-0.00330.7840.1180.1180.0000.0000.0000.000
98A105LEU00.0380.02723.1700.0970.0970.0000.0000.0000.000
99A106ALA0-0.026-0.00726.4280.2940.2940.0000.0000.0000.000
100A107ALA00.0100.00227.4600.0950.0950.0000.0000.0000.000
101A108SER0-0.018-0.01127.3300.0720.0720.0000.0000.0000.000
102A109ALA00.0430.02823.5850.0450.0450.0000.0000.0000.000
103A110ASN0-0.015-0.01525.371-0.228-0.2280.0000.0000.0000.000
104A111ALA0-0.006-0.00327.840-0.066-0.0660.0000.0000.0000.000
105A112TYR0-0.010-0.01522.737-0.101-0.1010.0000.0000.0000.000
106A113GLU-1-0.823-0.91622.01213.31913.3190.0000.0000.0000.000
107A114VAL0-0.042-0.02026.242-0.096-0.0960.0000.0000.0000.000
108A115ALA0-0.004-0.00529.310-0.252-0.2520.0000.0000.0000.000
109A116THR0-0.0100.01024.3420.0000.0000.0000.0000.0000.000
110A117VAL0-0.047-0.03327.203-0.099-0.0990.0000.0000.0000.000
111A118ALA0-0.0020.00729.091-0.188-0.1880.0000.0000.0000.000
112A119LEU00.0300.01628.798-0.236-0.2360.0000.0000.0000.000
113A120HIS10.8510.94328.057-10.616-10.6160.0000.0000.0000.000
114A121PHE0-0.090-0.06830.220-0.058-0.0580.0000.0000.0000.000
115A122GLY00.0330.02533.550-0.275-0.2750.0000.0000.0000.000
116A123ASP-1-0.916-0.95435.4947.9017.9010.0000.0000.0000.000
117A124LEU00.0100.00135.6740.1200.1200.0000.0000.0000.000
118A125ALA00.0060.00036.9000.0770.0770.0000.0000.0000.000
119A126GLY00.0340.02137.2180.0050.0050.0000.0000.0000.000
120A127ALA0-0.029-0.01832.4670.1490.1490.0000.0000.0000.000
121A128ARG10.7970.86433.634-8.034-8.0340.0000.0000.0000.000
122A129GLN0-0.035-0.02035.7030.1060.1060.0000.0000.0000.000
123A130GLU-1-0.764-0.85932.1169.1359.1350.0000.0000.0000.000
124A131TYR00.0450.01527.2370.1490.1490.0000.0000.0000.000
125A132GLU-1-0.923-0.96831.8248.8058.8050.0000.0000.0000.000
126A133LYS10.8950.97033.761-8.473-8.4730.0000.0000.0000.000
127A134SER0-0.019-0.01027.8970.1030.1030.0000.0000.0000.000
128A135LEU00.0300.02029.7900.2860.2860.0000.0000.0000.000
129A136VAL00.000-0.00431.3120.0470.0470.0000.0000.0000.000
130A137TYR0-0.058-0.04331.011-0.071-0.0710.0000.0000.0000.000
131A138ALA00.0270.01627.5830.1080.1080.0000.0000.0000.000
132A139GLN0-0.059-0.03329.1100.1580.1580.0000.0000.0000.000
133A140GLN0-0.052-0.01931.720-0.109-0.1090.0000.0000.0000.000
134A141ALA0-0.043-0.02127.741-0.084-0.0840.0000.0000.0000.000
135A142ASP-1-0.951-0.95627.78510.26310.2630.0000.0000.0000.000
136A143ASP-1-0.890-0.94322.49413.88013.8800.0000.0000.0000.000
137A144GLN00.016-0.02124.378-0.092-0.0920.0000.0000.0000.000
138A145VAL00.0740.04319.071-0.132-0.1320.0000.0000.0000.000
139A146ALA00.0280.03722.3990.0600.0600.0000.0000.0000.000
140A147ILE00.0140.00224.350-0.337-0.3370.0000.0000.0000.000
141A148ALA0-0.029-0.01123.827-0.279-0.2790.0000.0000.0000.000
142A149CYS0-0.074-0.06122.0000.0550.0550.0000.0000.0000.000
143A150ALA00.0200.02324.661-0.158-0.1580.0000.0000.0000.000
144A151PHE00.0120.00628.141-0.323-0.3230.0000.0000.0000.000
145A152ARG10.9870.99120.637-14.262-14.2620.0000.0000.0000.000
146A153GLY00.0120.02227.753-0.082-0.0820.0000.0000.0000.000
147A154LEU00.019-0.00228.545-0.270-0.2700.0000.0000.0000.000
148A155GLY00.0080.00431.418-0.302-0.3020.0000.0000.0000.000
149A156ASP-1-0.800-0.88727.11211.17211.1720.0000.0000.0000.000
150A157LEU0-0.0310.00330.741-0.175-0.1750.0000.0000.0000.000
151A158ALA00.0200.00633.354-0.274-0.2740.0000.0000.0000.000
152A159GLN0-0.015-0.01531.243-0.045-0.0450.0000.0000.0000.000
153A160GLN0-0.056-0.02331.673-0.353-0.3530.0000.0000.0000.000
154A161GLU-1-0.905-0.94835.4567.8737.8730.0000.0000.0000.000
155A162LYS10.8630.92237.685-8.497-8.4970.0000.0000.0000.000
156A163ASN00.0170.02238.868-0.226-0.2260.0000.0000.0000.000
157A164LEU00.0440.00336.5730.1670.1670.0000.0000.0000.000
158A165LEU00.0540.02737.7800.1340.1340.0000.0000.0000.000
159A166GLU-1-0.828-0.87237.0358.2698.2690.0000.0000.0000.000
160A167ALA0-0.0010.00233.9330.1760.1760.0000.0000.0000.000
161A168GLN00.0230.00433.5840.1120.1120.0000.0000.0000.000
162A169GLN0-0.081-0.04534.1380.1250.1250.0000.0000.0000.000
163A170HIS00.0210.00632.4000.2830.2830.0000.0000.0000.000
164A171TRP0-0.017-0.03729.2610.2460.2460.0000.0000.0000.000
165A172LEU0-0.023-0.02029.2380.3700.3700.0000.0000.0000.000
166A173ARG10.9601.00830.738-9.841-9.8410.0000.0000.0000.000
167A174ALA00.0270.00426.3990.1890.1890.0000.0000.0000.000
168A175ARG10.8590.92525.672-10.108-10.1080.0000.0000.0000.000
169A176ASP-1-0.904-0.97525.83110.54810.5480.0000.0000.0000.000
170A177ILE0-0.0110.00225.1590.1290.1290.0000.0000.0000.000
171A178PHE00.025-0.01120.5090.2560.2560.0000.0000.0000.000
172A179ALA0-0.0070.00121.6260.6330.6330.0000.0000.0000.000
173A180GLU-1-1.002-0.98923.41211.04211.0420.0000.0000.0000.000
174A181LEU0-0.079-0.04420.1340.1260.1260.0000.0000.0000.000
175A182GLU-1-0.992-0.98618.92315.53115.5310.0000.0000.0000.000
176A183ASP-1-0.888-0.92916.82519.18319.1830.0000.0000.0000.000
177A184SER0-0.028-0.04517.043-0.497-0.4970.0000.0000.0000.000
178A185GLU-1-0.902-0.95314.26019.20319.2030.0000.0000.0000.000
179A186ALA00.0400.02917.416-0.837-0.8370.0000.0000.0000.000
180A187VAL0-0.055-0.02319.935-0.890-0.8900.0000.0000.0000.000
181A188ASN0-0.022-0.01620.197-1.211-1.2110.0000.0000.0000.000
182A189GLU-1-0.925-0.96519.44715.28715.2870.0000.0000.0000.000
183A190LEU0-0.068-0.03422.543-0.659-0.6590.0000.0000.0000.000
184A191MET0-0.0010.02525.170-0.745-0.7450.0000.0000.0000.000
185A192THR0-0.027-0.00124.479-0.332-0.3320.0000.0000.0000.000
186A193ARG10.7970.89823.498-12.835-12.8350.0000.0000.0000.000
187A194LEU0-0.032-0.02028.922-0.407-0.4070.0000.0000.0000.000
188A195ASN00.0470.02330.241-0.491-0.4910.0000.0000.0000.000
189A196GLY0-0.054-0.01031.159-0.243-0.2430.0000.0000.0000.000
190A197LEU0-0.090-0.03632.618-0.215-0.2150.0000.0000.0000.000
191A198GLU-1-0.928-0.95935.4048.5618.5610.0000.0000.0000.000
192A199HIS0-0.082-0.03837.6080.0810.0810.0000.0000.0000.000