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: N921Q

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1994974.172209
FMO2-HF: Nuclear repulsion 1919279.835964
FMO2-HF: Total energy -75694.336245
FMO2-MP2: Total energy -75913.857136


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.
88.58893.2781.117-2.431-3.3740.015
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 : -0.911 / q_NPA : -0.954
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].
3A10ALA00.0220.0083.657-7.778-5.528-0.013-1.055-1.1810.004
4A11LEU0-0.059-0.0302.398-10.504-8.2511.131-1.314-2.0700.011
5A12ALA00.0580.0274.624-5.828-5.641-0.001-0.062-0.1230.000
6A13GLU-1-0.749-0.8536.52320.82120.8210.0000.0000.0000.000
7A14ARG10.9600.9708.407-28.477-28.4770.0000.0000.0000.000
8A15GLN0-0.034-0.0057.550-0.879-0.8790.0000.0000.0000.000
9A16ALA00.0590.01410.572-2.029-2.0290.0000.0000.0000.000
10A17GLN0-0.035-0.02212.496-1.555-1.5550.0000.0000.0000.000
11A18ALA0-0.049-0.01413.928-1.344-1.3440.0000.0000.0000.000
12A19LEU0-0.023-0.01514.075-1.164-1.1640.0000.0000.0000.000
13A20LEU0-0.0030.00916.896-0.942-0.9420.0000.0000.0000.000
14A21ALA0-0.038-0.00618.767-0.752-0.7520.0000.0000.0000.000
15A22HIS00.0010.01419.982-1.208-1.2080.0000.0000.0000.000
16A23PRO00.0310.00522.6690.2350.2350.0000.0000.0000.000
17A24ALA0-0.026-0.01024.5990.0310.0310.0000.0000.0000.000
18A25THR0-0.010-0.02919.163-0.040-0.0400.0000.0000.0000.000
19A26ALA0-0.0150.00619.5540.6970.6970.0000.0000.0000.000
20A27SER00.018-0.02419.9460.4180.4180.0000.0000.0000.000
21A28GLY00.0210.01618.2200.1860.1860.0000.0000.0000.000
22A29ALA0-0.0080.00015.4751.0181.0180.0000.0000.0000.000
23A30ARG10.9440.98015.328-13.167-13.1670.0000.0000.0000.000
24A31PHE00.0180.02214.7520.4430.4430.0000.0000.0000.000
25A32MET00.0130.00910.7091.1101.1100.0000.0000.0000.000
26A33LEU0-0.021-0.01911.6341.4431.4430.0000.0000.0000.000
27A34GLY00.0250.02313.0310.4190.4190.0000.0000.0000.000
28A35TYR00.0350.00411.0560.0770.0770.0000.0000.0000.000
29A36VAL0-0.037-0.0157.5021.4181.4180.0000.0000.0000.000
30A37TYR0-0.078-0.0759.0821.1211.1210.0000.0000.0000.000
31A38ALA00.0040.01011.627-0.435-0.4350.0000.0000.0000.000
32A39PHE0-0.016-0.0037.2360.1090.1090.0000.0000.0000.000
33A40MET0-0.117-0.0477.0611.5691.5690.0000.0000.0000.000
34A41ASP-1-0.880-0.9449.08518.98118.9810.0000.0000.0000.000
35A42ARG10.7240.83910.334-23.431-23.4310.0000.0000.0000.000
36A43PHE00.0650.00514.420-0.250-0.2500.0000.0000.0000.000
37A44ASP-1-0.900-0.93917.07113.35413.3540.0000.0000.0000.000
38A45GLU-1-0.833-0.89715.42017.91617.9160.0000.0000.0000.000
39A46ALA0-0.0010.01014.908-0.165-0.1650.0000.0000.0000.000
40A47ARG10.8610.92516.609-13.349-13.3490.0000.0000.0000.000
41A48ALA00.0200.00820.299-0.411-0.4110.0000.0000.0000.000
42A49SER0-0.054-0.03117.025-0.474-0.4740.0000.0000.0000.000
43A50PHE00.005-0.00315.471-0.351-0.3510.0000.0000.0000.000
44A51GLN00.0260.01020.431-0.403-0.4030.0000.0000.0000.000
45A52ALA0-0.057-0.01922.458-0.525-0.5250.0000.0000.0000.000
46A53LEU0-0.015-0.01320.081-0.353-0.3530.0000.0000.0000.000
47A54GLN00.0660.03823.747-0.086-0.0860.0000.0000.0000.000
48A55GLN0-0.018-0.01426.380-0.471-0.4710.0000.0000.0000.000
49A56GLN0-0.067-0.02724.997-0.032-0.0320.0000.0000.0000.000
50A57ALA00.0360.02427.386-0.246-0.2460.0000.0000.0000.000
51A58GLN0-0.028-0.01029.208-0.263-0.2630.0000.0000.0000.000
52A59LYS10.8560.94129.703-10.320-10.3200.0000.0000.0000.000
53A60SER0-0.034-0.03531.2530.0570.0570.0000.0000.0000.000
54A61GLY0-0.032-0.00433.600-0.186-0.1860.0000.0000.0000.000
55A62ASP-1-0.850-0.92129.30310.33310.3330.0000.0000.0000.000
56A63HIS00.0590.01330.7360.0470.0470.0000.0000.0000.000
57A64THR0-0.025-0.01227.4810.0860.0860.0000.0000.0000.000
58A65ALA0-0.028-0.02425.7390.4280.4280.0000.0000.0000.000
59A66GLU-1-0.849-0.91725.5659.9039.9030.0000.0000.0000.000
60A67HIS0-0.016-0.01826.0820.2610.2610.0000.0000.0000.000
61A68ARG10.9590.99321.314-12.031-12.0310.0000.0000.0000.000
62A69ALA0-0.017-0.01322.3310.5600.5600.0000.0000.0000.000
63A70LEU0-0.012-0.00223.1950.3540.3540.0000.0000.0000.000
64A71HIS0-0.054-0.02421.3220.6180.6180.0000.0000.0000.000
65A72GLN0-0.004-0.00718.4460.3270.3270.0000.0000.0000.000
66A73VAL0-0.020-0.01620.0800.4420.4420.0000.0000.0000.000
67A74GLY00.0280.00122.2320.0880.0880.0000.0000.0000.000
68A75MET0-0.0130.00315.4340.1790.1790.0000.0000.0000.000
69A76VAL0-0.012-0.02416.6790.3790.3790.0000.0000.0000.000
70A77GLU-1-0.803-0.88019.13312.27612.2760.0000.0000.0000.000
71A78ARG10.7880.85719.279-14.379-14.3790.0000.0000.0000.000
72A79MET0-0.082-0.02514.9970.0120.0120.0000.0000.0000.000
73A80ALA0-0.0150.00219.0900.1480.1480.0000.0000.0000.000
74A81GLY0-0.0130.00420.680-0.370-0.3700.0000.0000.0000.000
75A82ASN0-0.074-0.04123.705-0.867-0.8670.0000.0000.0000.000
76A83TRP00.043-0.01124.464-0.123-0.1230.0000.0000.0000.000
77A84ASP-1-0.852-0.90227.7718.9728.9720.0000.0000.0000.000
78A85ALA00.0280.01426.899-0.198-0.1980.0000.0000.0000.000
79A86ALA00.0380.02725.337-0.039-0.0390.0000.0000.0000.000
80A87ARG10.8710.90926.960-9.031-9.0310.0000.0000.0000.000
81A88ARG10.8890.94630.437-9.045-9.0450.0000.0000.0000.000
82A89CYS00.0040.01126.684-0.130-0.1300.0000.0000.0000.000
83A90PHE00.0490.02023.265-0.091-0.0910.0000.0000.0000.000
84A91LEU0-0.018-0.00729.031-0.171-0.1710.0000.0000.0000.000
85A92GLU-1-0.907-0.96631.1139.2889.2880.0000.0000.0000.000
86A93GLU-1-0.777-0.86826.81811.12011.1200.0000.0000.0000.000
87A94ARG10.7590.85230.301-9.332-9.3320.0000.0000.0000.000
88A95GLU-1-0.948-0.96832.8577.8997.8990.0000.0000.0000.000
89A96LEU0-0.016-0.00830.506-0.111-0.1110.0000.0000.0000.000
90A97LEU00.004-0.00429.095-0.131-0.1310.0000.0000.0000.000
91A98ALA0-0.0280.00933.393-0.118-0.1180.0000.0000.0000.000
92A99SER0-0.122-0.06336.180-0.247-0.2470.0000.0000.0000.000
93A100LEU0-0.057-0.01931.436-0.080-0.0800.0000.0000.0000.000
94A101PRO0-0.029-0.02834.503-0.133-0.1330.0000.0000.0000.000
95A102GLU-1-0.964-0.97234.1848.4018.4010.0000.0000.0000.000
96A103ASP-1-0.808-0.91728.42710.78910.7890.0000.0000.0000.000
97A104PRO00.001-0.00530.7010.1390.1390.0000.0000.0000.000
98A105LEU00.0400.03023.1680.1090.1090.0000.0000.0000.000
99A106ALA0-0.030-0.01626.3250.2920.2920.0000.0000.0000.000
100A107ALA00.004-0.00127.3620.0890.0890.0000.0000.0000.000
101A108SER0-0.006-0.01327.1060.0490.0490.0000.0000.0000.000
102A109ALA00.0330.02523.4730.0340.0340.0000.0000.0000.000
103A110ASN0-0.010-0.01825.249-0.199-0.1990.0000.0000.0000.000
104A111ALA0-0.007-0.01027.694-0.072-0.0720.0000.0000.0000.000
105A112TYR0-0.002-0.00422.873-0.114-0.1140.0000.0000.0000.000
106A113GLU-1-0.761-0.84821.97213.36213.3620.0000.0000.0000.000
107A114VAL0-0.047-0.02126.251-0.127-0.1270.0000.0000.0000.000
108A115ALA0-0.012-0.00829.277-0.265-0.2650.0000.0000.0000.000
109A116THR00.0060.01024.493-0.045-0.0450.0000.0000.0000.000
110A117VAL0-0.037-0.02427.378-0.111-0.1110.0000.0000.0000.000
111A118ALA0-0.0130.00229.316-0.196-0.1960.0000.0000.0000.000
112A119LEU00.0340.02029.365-0.250-0.2500.0000.0000.0000.000
113A120HIS10.8410.94228.284-10.452-10.4520.0000.0000.0000.000
114A121PHE0-0.086-0.07130.397-0.054-0.0540.0000.0000.0000.000
115A122GLY00.0390.02733.734-0.272-0.2720.0000.0000.0000.000
116A123ASP-1-0.918-0.95535.7057.8577.8570.0000.0000.0000.000
117A124LEU00.001-0.00235.8480.1150.1150.0000.0000.0000.000
118A125ALA00.0040.00037.0660.0780.0780.0000.0000.0000.000
119A126GLY00.0270.01837.3600.0090.0090.0000.0000.0000.000
120A127ALA0-0.028-0.01932.6780.1530.1530.0000.0000.0000.000
121A128ARG10.7770.83333.644-7.993-7.9930.0000.0000.0000.000
122A129GLN0-0.009-0.00335.6080.1100.1100.0000.0000.0000.000
123A130GLU-1-0.758-0.84432.0639.0409.0400.0000.0000.0000.000
124A131TYR00.0500.01427.1990.1250.1250.0000.0000.0000.000
125A132GLU-1-0.911-0.95631.6928.8148.8140.0000.0000.0000.000
126A133LYS10.7970.89933.674-8.458-8.4580.0000.0000.0000.000
127A134SER0-0.030-0.01127.8570.1290.1290.0000.0000.0000.000
128A135LEU00.0410.03529.6990.2750.2750.0000.0000.0000.000
129A136VAL0-0.012-0.01131.2250.0410.0410.0000.0000.0000.000
130A137TYR0-0.052-0.04430.931-0.061-0.0610.0000.0000.0000.000
131A138ALA00.0360.02327.5100.1090.1090.0000.0000.0000.000
132A139GLN0-0.055-0.02529.0720.1210.1210.0000.0000.0000.000
133A140GLN0-0.048-0.02331.683-0.018-0.0180.0000.0000.0000.000
134A141ALA0-0.055-0.02927.737-0.084-0.0840.0000.0000.0000.000
135A142ASP-1-0.916-0.94827.77210.73310.7330.0000.0000.0000.000
136A143ASP-1-0.865-0.92322.57213.95513.9550.0000.0000.0000.000
137A144GLN0-0.004-0.03324.400-0.055-0.0550.0000.0000.0000.000
138A145VAL00.0560.03318.946-0.094-0.0940.0000.0000.0000.000
139A146ALA00.0080.02522.3580.0270.0270.0000.0000.0000.000
140A147ILE0-0.003-0.00424.278-0.365-0.3650.0000.0000.0000.000
141A148ALA0-0.023-0.00923.758-0.289-0.2890.0000.0000.0000.000
142A149CYS0-0.063-0.04621.8430.0460.0460.0000.0000.0000.000
143A150ALA00.0120.02324.565-0.180-0.1800.0000.0000.0000.000
144A151PHE00.0080.00528.037-0.325-0.3250.0000.0000.0000.000
145A152ARG10.9340.95520.330-14.416-14.4160.0000.0000.0000.000
146A153GLY00.0180.02827.678-0.098-0.0980.0000.0000.0000.000
147A154LEU00.019-0.00328.573-0.271-0.2710.0000.0000.0000.000
148A155GLY00.0010.00131.411-0.302-0.3020.0000.0000.0000.000
149A156ASP-1-0.798-0.86327.12111.18911.1890.0000.0000.0000.000
150A157LEU0-0.0230.00330.881-0.180-0.1800.0000.0000.0000.000
151A158ALA00.0120.00433.517-0.270-0.2700.0000.0000.0000.000
152A159GLN0-0.008-0.01031.587-0.081-0.0810.0000.0000.0000.000
153A160GLN0-0.045-0.02032.141-0.364-0.3640.0000.0000.0000.000
154A161GLU-1-0.867-0.91035.5787.8887.8880.0000.0000.0000.000
155A162LYS10.8560.91637.494-8.479-8.4790.0000.0000.0000.000
156A163ASN00.0050.01739.002-0.264-0.2640.0000.0000.0000.000
157A164LEU00.0430.00836.7080.1670.1670.0000.0000.0000.000
158A165LEU00.0330.01737.9600.1370.1370.0000.0000.0000.000
159A166GLU-1-0.786-0.84037.0658.2578.2570.0000.0000.0000.000
160A167ALA0-0.0040.00134.0500.1770.1770.0000.0000.0000.000
161A168GLN00.0190.00133.7230.1000.1000.0000.0000.0000.000
162A169GLN0-0.077-0.04934.2610.1060.1060.0000.0000.0000.000
163A170HIS00.005-0.01332.3670.2810.2810.0000.0000.0000.000
164A171TRP0-0.009-0.02729.5930.2330.2330.0000.0000.0000.000
165A172LEU0-0.003-0.00829.3420.3630.3630.0000.0000.0000.000
166A173ARG10.8750.96729.901-10.149-10.1490.0000.0000.0000.000
167A174ALA00.0260.00526.4880.2030.2030.0000.0000.0000.000
168A175ARG10.8380.89825.737-10.170-10.1700.0000.0000.0000.000
169A176ASP-1-0.872-0.94325.87110.61310.6130.0000.0000.0000.000
170A177ILE0-0.0080.01524.8740.1290.1290.0000.0000.0000.000
171A178PHE00.029-0.01620.4200.2700.2700.0000.0000.0000.000
172A179ALA0-0.008-0.00221.6040.6400.6400.0000.0000.0000.000
173A180GLU-1-0.931-0.95623.36411.09911.0990.0000.0000.0000.000
174A181LEU0-0.070-0.04220.0960.1470.1470.0000.0000.0000.000
175A182GLU-1-0.998-0.98519.15115.68215.6820.0000.0000.0000.000
176A183ASP-1-0.862-0.91317.09418.87718.8770.0000.0000.0000.000
177A184SER00.008-0.02916.973-0.546-0.5460.0000.0000.0000.000
178A185GLU-1-0.933-0.97314.53517.97917.9790.0000.0000.0000.000
179A186ALA00.0280.02417.592-0.804-0.8040.0000.0000.0000.000
180A187VAL0-0.051-0.02420.062-0.876-0.8760.0000.0000.0000.000
181A188ASN0-0.050-0.02619.539-1.389-1.3890.0000.0000.0000.000
182A189GLU-1-0.814-0.88820.76213.75213.7520.0000.0000.0000.000
183A190LEU0-0.017-0.02222.783-0.647-0.6470.0000.0000.0000.000
184A191MET0-0.0130.01725.386-0.709-0.7090.0000.0000.0000.000
185A192THR0-0.039-0.00524.803-0.380-0.3800.0000.0000.0000.000
186A193ARG10.7030.81323.616-12.803-12.8030.0000.0000.0000.000
187A194LEU0-0.026-0.01729.179-0.427-0.4270.0000.0000.0000.000
188A195ASN00.0370.01830.576-0.285-0.2850.0000.0000.0000.000
189A196GLY0-0.049-0.00831.447-0.247-0.2470.0000.0000.0000.000
190A197LEU0-0.087-0.03732.930-0.225-0.2250.0000.0000.0000.000
191A198GLU-1-0.934-0.96235.6808.5728.5720.0000.0000.0000.000
192A199HIS0-0.072-0.03437.9140.0890.0890.0000.0000.0000.000