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: JL239

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2003713.749008
FMO2-HF: Nuclear repulsion 1928019.03639
FMO2-HF: Total energy -75694.712617
FMO2-MP2: Total energy -75914.300019


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.
84.66489.7940.536-2.317-3.3490.015
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 : -0.886 / q_NPA : -0.944
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].
3A10ALA00.0390.0162.936-8.957-6.5770.081-1.095-1.3660.006
4A11LEU0-0.076-0.0392.692-10.303-7.8740.456-1.066-1.8190.008
5A12ALA00.0500.0204.305-6.659-6.338-0.001-0.156-0.1640.001
6A13GLU-1-0.741-0.8316.29121.40121.4010.0000.0000.0000.000
7A14ARG10.9500.9708.101-29.638-29.6380.0000.0000.0000.000
8A15GLN0-0.012-0.0047.215-0.638-0.6380.0000.0000.0000.000
9A16ALA00.0500.02010.270-2.127-2.1270.0000.0000.0000.000
10A17GLN0-0.026-0.02312.222-1.555-1.5550.0000.0000.0000.000
11A18ALA0-0.043-0.01913.478-1.397-1.3970.0000.0000.0000.000
12A19LEU0-0.005-0.00713.493-1.247-1.2470.0000.0000.0000.000
13A20LEU0-0.0110.00416.333-1.038-1.0380.0000.0000.0000.000
14A21ALA0-0.052-0.01018.245-0.810-0.8100.0000.0000.0000.000
15A22HIS00.0160.01819.637-1.202-1.2020.0000.0000.0000.000
16A23PRO00.020-0.00222.0910.2980.2980.0000.0000.0000.000
17A24ALA0-0.030-0.01324.011-0.077-0.0770.0000.0000.0000.000
18A25THR0-0.013-0.03018.736-0.022-0.0220.0000.0000.0000.000
19A26ALA0-0.0100.00919.3310.6600.6600.0000.0000.0000.000
20A27SER00.020-0.02019.8310.3280.3280.0000.0000.0000.000
21A28GLY00.0300.01718.2720.2420.2420.0000.0000.0000.000
22A29ALA0-0.0080.00215.3181.0021.0020.0000.0000.0000.000
23A30ARG10.9210.97115.350-13.296-13.2960.0000.0000.0000.000
24A31PHE00.0400.03714.6320.2940.2940.0000.0000.0000.000
25A32MET0-0.005-0.00310.7801.0751.0750.0000.0000.0000.000
26A33LEU0-0.016-0.01411.5181.5181.5180.0000.0000.0000.000
27A34GLY00.0320.02012.8370.5590.5590.0000.0000.0000.000
28A35TYR00.0240.00611.068-0.100-0.1000.0000.0000.0000.000
29A36VAL0-0.042-0.0267.3381.3671.3670.0000.0000.0000.000
30A37TYR0-0.081-0.0718.8801.0241.0240.0000.0000.0000.000
31A38ALA00.0170.01211.607-0.348-0.3480.0000.0000.0000.000
32A39PHE0-0.051-0.0247.172-0.105-0.1050.0000.0000.0000.000
33A40MET0-0.062-0.0257.0653.3203.3200.0000.0000.0000.000
34A41ASP-1-0.858-0.9279.40219.37019.3700.0000.0000.0000.000
35A42ARG10.7030.8219.696-24.191-24.1910.0000.0000.0000.000
36A43PHE00.046-0.00414.347-0.252-0.2520.0000.0000.0000.000
37A44ASP-1-0.846-0.90416.76113.45513.4550.0000.0000.0000.000
38A45GLU-1-0.829-0.88414.87418.35218.3520.0000.0000.0000.000
39A46ALA0-0.008-0.00114.741-0.178-0.1780.0000.0000.0000.000
40A47ARG10.8130.89016.362-13.427-13.4270.0000.0000.0000.000
41A48ALA00.0200.00920.068-0.511-0.5110.0000.0000.0000.000
42A49SER0-0.059-0.04917.156-0.495-0.4950.0000.0000.0000.000
43A50PHE00.0120.01515.351-0.391-0.3910.0000.0000.0000.000
44A51GLN00.0450.01420.512-0.366-0.3660.0000.0000.0000.000
45A52ALA0-0.065-0.02822.312-0.548-0.5480.0000.0000.0000.000
46A53LEU0-0.014-0.00320.105-0.355-0.3550.0000.0000.0000.000
47A54GLN00.0450.01723.565-0.086-0.0860.0000.0000.0000.000
48A55GLN0-0.001-0.00526.294-0.542-0.5420.0000.0000.0000.000
49A56GLN0-0.037-0.00224.6930.0380.0380.0000.0000.0000.000
50A57ALA00.0450.03127.394-0.269-0.2690.0000.0000.0000.000
51A58GLN0-0.029-0.02429.126-0.260-0.2600.0000.0000.0000.000
52A59LYS10.7960.90829.373-10.442-10.4420.0000.0000.0000.000
53A60SER0-0.080-0.04830.936-0.042-0.0420.0000.0000.0000.000
54A61GLY00.0100.00532.949-0.264-0.2640.0000.0000.0000.000
55A62ASP-1-0.857-0.91529.00310.21010.2100.0000.0000.0000.000
56A63HIS00.041-0.00830.2640.1690.1690.0000.0000.0000.000
57A64THR00.0220.01627.9570.1400.1400.0000.0000.0000.000
58A65ALA0-0.019-0.01325.7300.4460.4460.0000.0000.0000.000
59A66GLU-1-0.842-0.90525.6589.8929.8920.0000.0000.0000.000
60A67HIS0-0.022-0.01926.2440.2470.2470.0000.0000.0000.000
61A68ARG10.9290.98021.280-12.053-12.0530.0000.0000.0000.000
62A69ALA0-0.012-0.00422.3520.5450.5450.0000.0000.0000.000
63A70LEU00.0080.00123.0140.3930.3930.0000.0000.0000.000
64A71HIS0-0.053-0.02921.2990.5870.5870.0000.0000.0000.000
65A72GLN0-0.020-0.02118.2420.0630.0630.0000.0000.0000.000
66A73VAL0-0.022-0.02119.8090.5310.5310.0000.0000.0000.000
67A74GLY00.0280.00422.2270.0650.0650.0000.0000.0000.000
68A75MET0-0.0190.00115.5930.1710.1710.0000.0000.0000.000
69A76VAL00.000-0.01616.4710.3230.3230.0000.0000.0000.000
70A77GLU-1-0.812-0.88719.00312.34712.3470.0000.0000.0000.000
71A78ARG10.7780.84819.442-14.231-14.2310.0000.0000.0000.000
72A79MET0-0.096-0.02815.1070.0500.0500.0000.0000.0000.000
73A80ALA00.0020.00819.1710.0690.0690.0000.0000.0000.000
74A81GLY00.0070.01720.692-0.417-0.4170.0000.0000.0000.000
75A82ASN0-0.047-0.02423.841-0.898-0.8980.0000.0000.0000.000
76A83TRP00.021-0.02524.593-0.184-0.1840.0000.0000.0000.000
77A84ASP-1-0.851-0.89527.4738.9778.9770.0000.0000.0000.000
78A85ALA00.0330.02326.873-0.202-0.2020.0000.0000.0000.000
79A86ALA00.0300.02425.090-0.020-0.0200.0000.0000.0000.000
80A87ARG10.8420.89426.758-9.058-9.0580.0000.0000.0000.000
81A88ARG10.8390.91830.317-9.257-9.2570.0000.0000.0000.000
82A89CYS0-0.024-0.00426.476-0.111-0.1110.0000.0000.0000.000
83A90PHE00.0620.02423.068-0.120-0.1200.0000.0000.0000.000
84A91LEU0-0.0080.00928.812-0.186-0.1860.0000.0000.0000.000
85A92GLU-1-0.876-0.95430.8819.2639.2630.0000.0000.0000.000
86A93GLU-1-0.752-0.85226.69311.17011.1700.0000.0000.0000.000
87A94ARG10.7700.86930.239-9.355-9.3550.0000.0000.0000.000
88A95GLU-1-0.929-0.96432.8867.9067.9060.0000.0000.0000.000
89A96LEU0-0.031-0.00930.653-0.111-0.1110.0000.0000.0000.000
90A97LEU0-0.009-0.00828.978-0.120-0.1200.0000.0000.0000.000
91A98ALA0-0.027-0.00133.187-0.124-0.1240.0000.0000.0000.000
92A99SER0-0.108-0.05835.879-0.263-0.2630.0000.0000.0000.000
93A100LEU0-0.048-0.01731.435-0.046-0.0460.0000.0000.0000.000
94A101PRO0-0.041-0.03634.496-0.145-0.1450.0000.0000.0000.000
95A102GLU-1-0.955-0.96634.0278.4568.4560.0000.0000.0000.000
96A103ASP-1-0.822-0.91827.95610.90810.9080.0000.0000.0000.000
97A104PRO00.002-0.00730.4850.1360.1360.0000.0000.0000.000
98A105LEU00.0500.03822.9690.1040.1040.0000.0000.0000.000
99A106ALA0-0.009-0.00726.0900.2660.2660.0000.0000.0000.000
100A107ALA0-0.010-0.00327.1050.0510.0510.0000.0000.0000.000
101A108SER0-0.028-0.02227.2100.0670.0670.0000.0000.0000.000
102A109ALA00.0540.03623.6150.0380.0380.0000.0000.0000.000
103A110ASN0-0.031-0.03725.447-0.259-0.2590.0000.0000.0000.000
104A111ALA0-0.008-0.00627.836-0.106-0.1060.0000.0000.0000.000
105A112TYR00.0160.01423.132-0.123-0.1230.0000.0000.0000.000
106A113GLU-1-0.752-0.83322.06613.26113.2610.0000.0000.0000.000
107A114VAL0-0.027-0.01426.290-0.153-0.1530.0000.0000.0000.000
108A115ALA00.0010.00529.570-0.250-0.2500.0000.0000.0000.000
109A116THR00.0100.00424.576-0.090-0.0900.0000.0000.0000.000
110A117VAL0-0.067-0.04427.363-0.068-0.0680.0000.0000.0000.000
111A118ALA0-0.026-0.01229.367-0.186-0.1860.0000.0000.0000.000
112A119LEU00.0220.00529.482-0.235-0.2350.0000.0000.0000.000
113A120HIS10.8500.94428.315-10.414-10.4140.0000.0000.0000.000
114A121PHE0-0.070-0.05130.445-0.020-0.0200.0000.0000.0000.000
115A122GLY00.0340.03033.760-0.264-0.2640.0000.0000.0000.000
116A123ASP-1-0.888-0.93235.8167.8667.8660.0000.0000.0000.000
117A124LEU00.012-0.00435.5440.1620.1620.0000.0000.0000.000
118A125ALA0-0.0030.00936.9570.0450.0450.0000.0000.0000.000
119A126GLY00.0120.00137.226-0.006-0.0060.0000.0000.0000.000
120A127ALA0-0.021-0.01832.8050.1400.1400.0000.0000.0000.000
121A128ARG10.7700.83833.595-7.995-7.9950.0000.0000.0000.000
122A129GLN0-0.010-0.00235.6870.0910.0910.0000.0000.0000.000
123A130GLU-1-0.795-0.86532.3928.9368.9360.0000.0000.0000.000
124A131TYR00.0490.00227.2970.1600.1600.0000.0000.0000.000
125A132GLU-1-0.911-0.95431.8718.7908.7900.0000.0000.0000.000
126A133LYS10.7830.88633.894-8.339-8.3390.0000.0000.0000.000
127A134SER0-0.033-0.02027.9530.1310.1310.0000.0000.0000.000
128A135LEU00.0660.04430.0190.2310.2310.0000.0000.0000.000
129A136VAL0-0.039-0.01331.5280.0080.0080.0000.0000.0000.000
130A137TYR0-0.034-0.02131.018-0.048-0.0480.0000.0000.0000.000
131A138ALA00.0310.01727.6860.1170.1170.0000.0000.0000.000
132A139GLN0-0.052-0.03729.1240.0060.0060.0000.0000.0000.000
133A140GLN0-0.058-0.03331.776-0.070-0.0700.0000.0000.0000.000
134A141ALA0-0.065-0.02827.432-0.066-0.0660.0000.0000.0000.000
135A142ASP-1-0.896-0.93327.74410.74810.7480.0000.0000.0000.000
136A143ASP-1-0.840-0.90822.95313.68513.6850.0000.0000.0000.000
137A144GLN0-0.011-0.04424.727-0.071-0.0710.0000.0000.0000.000
138A145VAL00.0210.01919.1330.0460.0460.0000.0000.0000.000
139A146ALA00.0090.01822.537-0.029-0.0290.0000.0000.0000.000
140A147ILE0-0.005-0.00324.474-0.344-0.3440.0000.0000.0000.000
141A148ALA00.0030.00924.009-0.315-0.3150.0000.0000.0000.000
142A149CYS0-0.073-0.03722.0670.1450.1450.0000.0000.0000.000
143A150ALA00.0160.01224.758-0.204-0.2040.0000.0000.0000.000
144A151PHE0-0.006-0.00128.295-0.319-0.3190.0000.0000.0000.000
145A152ARG10.9120.93620.503-14.215-14.2150.0000.0000.0000.000
146A153GLY00.0080.01827.713-0.126-0.1260.0000.0000.0000.000
147A154LEU00.005-0.01328.922-0.253-0.2530.0000.0000.0000.000
148A155GLY00.0130.00531.262-0.318-0.3180.0000.0000.0000.000
149A156ASP-1-0.795-0.86026.98211.13211.1320.0000.0000.0000.000
150A157LEU0-0.032-0.00630.720-0.195-0.1950.0000.0000.0000.000
151A158ALA00.0180.01433.456-0.260-0.2600.0000.0000.0000.000
152A159GLN0-0.018-0.01831.601-0.080-0.0800.0000.0000.0000.000
153A160GLN0-0.056-0.03132.378-0.378-0.3780.0000.0000.0000.000
154A161GLU-1-0.843-0.91935.5947.9127.9120.0000.0000.0000.000
155A162LYS10.8740.94037.370-8.462-8.4620.0000.0000.0000.000
156A163ASN00.0040.02239.437-0.262-0.2620.0000.0000.0000.000
157A164LEU00.017-0.01337.0240.1530.1530.0000.0000.0000.000
158A165LEU00.0230.01438.1130.1400.1400.0000.0000.0000.000
159A166GLU-1-0.778-0.82937.2518.1998.1990.0000.0000.0000.000
160A167ALA00.0090.00334.2800.1810.1810.0000.0000.0000.000
161A168GLN00.0170.01033.8680.1160.1160.0000.0000.0000.000
162A169GLN0-0.059-0.04434.4840.1300.1300.0000.0000.0000.000
163A170HIS0-0.005-0.01032.3570.2880.2880.0000.0000.0000.000
164A171TRP00.005-0.02829.6480.2040.2040.0000.0000.0000.000
165A172LEU0-0.025-0.00529.7290.3370.3370.0000.0000.0000.000
166A173ARG10.8600.91830.434-9.965-9.9650.0000.0000.0000.000
167A174ALA00.0200.00926.9730.2410.2410.0000.0000.0000.000
168A175ARG10.8500.89226.049-10.139-10.1390.0000.0000.0000.000
169A176ASP-1-0.890-0.93826.21610.52210.5220.0000.0000.0000.000
170A177ILE00.0070.01425.2160.1700.1700.0000.0000.0000.000
171A178PHE00.026-0.01420.8860.3680.3680.0000.0000.0000.000
172A179ALA0-0.031-0.01722.2330.5700.5700.0000.0000.0000.000
173A180GLU-1-0.897-0.92723.96910.85910.8590.0000.0000.0000.000
174A181LEU0-0.059-0.02720.6530.1030.1030.0000.0000.0000.000
175A182GLU-1-0.991-0.98419.34215.70815.7080.0000.0000.0000.000
176A183ASP-1-0.847-0.91017.77918.10218.1020.0000.0000.0000.000
177A184SER0-0.002-0.03017.488-0.518-0.5180.0000.0000.0000.000
178A185GLU-1-0.902-0.93815.41417.24517.2450.0000.0000.0000.000
179A186ALA00.0110.01018.473-0.751-0.7510.0000.0000.0000.000
180A187VAL0-0.014-0.01120.901-0.858-0.8580.0000.0000.0000.000
181A188ASN0-0.065-0.03719.983-1.407-1.4070.0000.0000.0000.000
182A189GLU-1-0.804-0.87420.92413.27813.2780.0000.0000.0000.000
183A190LEU0-0.016-0.00723.044-0.625-0.6250.0000.0000.0000.000
184A191MET0-0.0240.01326.033-0.681-0.6810.0000.0000.0000.000
185A192THR0-0.032-0.01624.955-0.442-0.4420.0000.0000.0000.000
186A193ARG10.6970.80923.818-12.624-12.6240.0000.0000.0000.000
187A194LEU0-0.043-0.02129.331-0.445-0.4450.0000.0000.0000.000
188A195ASN0-0.043-0.03931.187-0.061-0.0610.0000.0000.0000.000
189A196GLY0-0.0290.00031.833-0.166-0.1660.0000.0000.0000.000
190A197LEU0-0.076-0.03732.943-0.197-0.1970.0000.0000.0000.000
191A198GLU-1-0.902-0.93335.9428.6198.6190.0000.0000.0000.000
192A199HIS0-0.069-0.03038.0910.0670.0670.0000.0000.0000.000