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: 6GN5Z

Calculation Name: 5AWE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5AWE

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SK23

Base Structure: X-ray

Registration Date: 2023-09-26

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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2004867.084707
FMO2-HF: Nuclear repulsion 1924687.713462
FMO2-HF: Total energy -80179.371245
FMO2-MP2: Total energy -80410.754223


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-22.904-16.04111.317-7.539-10.639-0.063
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : 0.000
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].
3A3VAL00.000-0.0093.857-0.1931.700-0.019-1.013-0.8600.004
4A4ARG10.7870.8406.4552.3762.3760.0000.0000.0000.000
5A5ASP-1-0.842-0.9021.932-14.883-15.8216.812-3.290-2.584-0.046
6A6TRP0-0.020-0.0162.881-0.3330.3870.054-0.166-0.6080.000
7A7MET0-0.094-0.0317.5640.2940.2940.0000.0000.0000.000
8A8THR00.0090.00910.5670.1180.1180.0000.0000.0000.000
9A9LYS10.8650.90712.9410.5630.5630.0000.0000.0000.000
10A10ASP-1-0.894-0.92715.214-0.435-0.4350.0000.0000.0000.000
11A11PRO00.0120.02017.5230.0450.0450.0000.0000.0000.000
12A12VAL0-0.0030.00020.0540.0140.0140.0000.0000.0000.000
13A13VAL0-0.004-0.00522.858-0.022-0.0220.0000.0000.0000.000
14A14VAL00.005-0.00325.2830.0260.0260.0000.0000.0000.000
15A15ALA00.0380.02728.590-0.019-0.0190.0000.0000.0000.000
16A16PRO00.0490.02730.9990.0110.0110.0000.0000.0000.000
17A17ASP-1-0.806-0.88233.001-0.175-0.1750.0000.0000.0000.000
18A18THR0-0.044-0.03432.5500.0100.0100.0000.0000.0000.000
19A19PRO00.0350.01934.841-0.003-0.0030.0000.0000.0000.000
20A20VAL00.0490.01934.103-0.005-0.0050.0000.0000.0000.000
21A21LEU0-0.005-0.01834.098-0.003-0.0030.0000.0000.0000.000
22A22GLU-1-0.925-0.97134.802-0.137-0.1370.0000.0000.0000.000
23A23ALA00.0170.01230.294-0.004-0.0040.0000.0000.0000.000
24A24ILE0-0.011-0.00330.247-0.003-0.0030.0000.0000.0000.000
25A25ARG10.9160.95930.9300.1010.1010.0000.0000.0000.000
26A26LEU00.0490.02928.2540.0030.0030.0000.0000.0000.000
27A27LEU0-0.006-0.00824.954-0.005-0.0050.0000.0000.0000.000
28A28LYS10.9020.95326.9040.0850.0850.0000.0000.0000.000
29A29GLU-1-0.890-0.92928.788-0.126-0.1260.0000.0000.0000.000
30A30LYS10.8610.91625.0780.1720.1720.0000.0000.0000.000
31A31GLY0-0.0100.01823.962-0.012-0.0120.0000.0000.0000.000
32A32PHE0-0.0170.00419.226-0.012-0.0120.0000.0000.0000.000
33A33ARG10.9530.95521.8250.1670.1670.0000.0000.0000.000
34A34ARG10.9130.98218.3620.3660.3660.0000.0000.0000.000
35A35LEU00.0240.01022.348-0.009-0.0090.0000.0000.0000.000
36A36PRO00.0150.01520.6320.0060.0060.0000.0000.0000.000
37A37VAL00.009-0.00123.2860.0210.0210.0000.0000.0000.000
38A38MET0-0.0180.00824.055-0.028-0.0280.0000.0000.0000.000
39A39GLU-1-0.800-0.90927.340-0.208-0.2080.0000.0000.0000.000
40A40GLY0-0.0020.01029.915-0.013-0.0130.0000.0000.0000.000
41A41GLY0-0.026-0.00827.730-0.005-0.0050.0000.0000.0000.000
42A42ARG10.8440.89225.7120.3530.3530.0000.0000.0000.000
43A43LEU00.0290.00420.7890.0230.0230.0000.0000.0000.000
44A44VAL0-0.057-0.02924.843-0.002-0.0020.0000.0000.0000.000
45A45GLY00.0450.00426.0030.0220.0220.0000.0000.0000.000
46A46LEU0-0.046-0.01121.343-0.024-0.0240.0000.0000.0000.000
47A47VAL00.0590.05724.8790.0180.0180.0000.0000.0000.000
48A48THR0-0.066-0.07323.164-0.011-0.0110.0000.0000.0000.000
49A49ASP-1-0.802-0.89425.618-0.132-0.1320.0000.0000.0000.000
50A50LYS10.8220.89027.1930.1640.1640.0000.0000.0000.000
51A51ASP-1-0.790-0.84927.019-0.234-0.2340.0000.0000.0000.000
52A52LEU0-0.025-0.01929.0270.0100.0100.0000.0000.0000.000
53A53LYS10.7710.86030.6610.1420.1420.0000.0000.0000.000
54A54ASP-1-0.850-0.91032.455-0.126-0.1260.0000.0000.0000.000
55A55ALA00.0040.01934.6500.0010.0010.0000.0000.0000.000
56A56MET0-0.002-0.01236.0710.0110.0110.0000.0000.0000.000
57A57PRO0-0.011-0.01339.471-0.002-0.0020.0000.0000.0000.000
58A58SER00.0100.03341.8040.0010.0010.0000.0000.0000.000
59A59LYS10.8560.90943.8960.0790.0790.0000.0000.0000.000
60A60ALA00.0210.01547.729-0.002-0.0020.0000.0000.0000.000
61A61THR00.026-0.01051.1430.0020.0020.0000.0000.0000.000
62A62THR0-0.054-0.04951.300-0.004-0.0040.0000.0000.0000.000
63A63LEU0-0.0160.01846.4910.0030.0030.0000.0000.0000.000
64A64SER00.016-0.01650.5680.0020.0020.0000.0000.0000.000
65A65VAL00.035-0.00847.881-0.004-0.0040.0000.0000.0000.000
66A66TRP00.0470.01047.950-0.003-0.0030.0000.0000.0000.000
67A67GLU-1-0.774-0.81248.927-0.072-0.0720.0000.0000.0000.000
68A68MET00.0290.01543.203-0.004-0.0040.0000.0000.0000.000
69A69ASN0-0.040-0.02744.372-0.005-0.0050.0000.0000.0000.000
70A70TYR00.018-0.00244.670-0.005-0.0050.0000.0000.0000.000
71A71LEU0-0.026-0.02844.084-0.004-0.0040.0000.0000.0000.000
72A72LEU00.0030.00539.094-0.006-0.0060.0000.0000.0000.000
73A73ALA0-0.050-0.02240.262-0.006-0.0060.0000.0000.0000.000
74A74LYS10.8780.93841.7380.1020.1020.0000.0000.0000.000
75A75LEU0-0.0110.03637.399-0.004-0.0040.0000.0000.0000.000
76A76THR0-0.035-0.03336.716-0.005-0.0050.0000.0000.0000.000
77A77VAL00.005-0.01830.258-0.003-0.0030.0000.0000.0000.000
78A78ARG10.7770.83232.4480.1900.1900.0000.0000.0000.000
79A79GLU-1-0.882-0.91834.015-0.153-0.1530.0000.0000.0000.000
80A80VAL0-0.020-0.01131.9160.0040.0040.0000.0000.0000.000
81A81MET0-0.090-0.01428.613-0.015-0.0150.0000.0000.0000.000
82A82ALA00.0010.00925.9450.0030.0030.0000.0000.0000.000
83A83ARG10.9110.95526.3130.2680.2680.0000.0000.0000.000
84A84PRO00.023-0.00824.8960.0230.0230.0000.0000.0000.000
85A85VAL0-0.015-0.00220.4960.0000.0000.0000.0000.0000.000
86A86VAL0-0.0190.00118.511-0.020-0.0200.0000.0000.0000.000
87A87THR0-0.019-0.02116.475-0.001-0.0010.0000.0000.0000.000
88A88VAL00.0340.02310.989-0.013-0.0130.0000.0000.0000.000
89A89GLU-1-0.775-0.87911.927-1.388-1.3880.0000.0000.0000.000
90A90ALA00.0380.00110.372-0.297-0.2970.0000.0000.0000.000
91A91ASP-1-0.858-0.9288.297-2.167-2.1670.0000.0000.0000.000
92A92ALA0-0.0240.0118.353-0.166-0.1660.0000.0000.0000.000
93A93PRO00.0510.0234.383-0.851-0.728-0.001-0.056-0.0660.000
94A94LEU0-0.0060.0032.8850.2451.8040.216-0.613-1.1610.002
95A95GLU-1-0.851-0.9662.747-10.107-7.5652.259-1.888-2.914-0.024
96A96LYS10.8250.9015.8532.1952.1950.0000.0000.0000.000
97A97ALA00.0230.0098.4290.4140.4140.0000.0000.0000.000
98A98ALA0-0.022-0.0118.4060.3010.3010.0000.0000.0000.000
99A99LEU00.0080.0139.7210.2120.2120.0000.0000.0000.000
100A100LEU00.0090.00511.8960.1550.1550.0000.0000.0000.000
101A101MET0-0.096-0.05011.7690.1540.1540.0000.0000.0000.000
102A102GLU-1-0.976-0.98214.085-0.262-0.2620.0000.0000.0000.000
103A103GLU-1-0.784-0.85515.767-0.498-0.4980.0000.0000.0000.000
104A104ARG10.7670.84517.7350.5940.5940.0000.0000.0000.000
105A105LYS10.9340.96819.2090.2410.2410.0000.0000.0000.000
106A106ILE0-0.0220.02318.2680.0350.0350.0000.0000.0000.000
107A107GLY00.0220.00017.479-0.008-0.0080.0000.0000.0000.000
108A108GLY0-0.039-0.07015.7440.0110.0110.0000.0000.0000.000
109A109LEU00.0260.01812.6030.0280.0280.0000.0000.0000.000
110A110PRO0-0.0190.00114.746-0.054-0.0540.0000.0000.0000.000
111A111VAL00.0040.00911.340-0.064-0.0640.0000.0000.0000.000
112A112MET0-0.011-0.00614.2980.1310.1310.0000.0000.0000.000
113A113GLU-1-0.839-0.90914.244-1.147-1.1470.0000.0000.0000.000
114A114GLY00.008-0.00316.3300.1060.1060.0000.0000.0000.000
115A115GLU-1-0.821-0.88619.049-0.464-0.4640.0000.0000.0000.000
116A116ARG10.9290.97418.9360.5730.5730.0000.0000.0000.000
117A117LEU00.0360.01118.195-0.068-0.0680.0000.0000.0000.000
118A118VAL0-0.047-0.02713.5990.0580.0580.0000.0000.0000.000
119A119GLY00.022-0.00814.4020.0240.0240.0000.0000.0000.000
120A120ILE0-0.066-0.01614.6910.0050.0050.0000.0000.0000.000
121A121ILE00.0470.0397.7810.0250.0250.0000.0000.0000.000
122A122THR0-0.058-0.05912.2320.0740.0740.0000.0000.0000.000
123A123VAL00.0920.02211.973-0.040-0.0400.0000.0000.0000.000
124A124THR0-0.065-0.02812.7390.0680.0680.0000.0000.0000.000
125A125ASP-1-0.767-0.8429.716-0.284-0.2840.0000.0000.0000.000
126A126VAL00.0380.0187.8940.1370.1370.0000.0000.0000.000
127A127LEU0-0.034-0.0128.3970.2240.2240.0000.0000.0000.000
128A128ARG10.8400.9149.7250.2980.2980.0000.0000.0000.000
129A129ALA00.0650.0424.5830.2520.327-0.001-0.006-0.0670.000
130A130PHE00.0110.0014.3880.7420.947-0.001-0.008-0.1960.000
131A131ILE0-0.064-0.0446.9630.3290.3290.0000.0000.0000.000
132A132GLU-1-0.946-0.9746.5592.3832.3830.0000.0000.0000.000
133A133VAL00.012-0.0012.219-1.460-0.7761.998-0.499-2.1830.001
134A134LEU0-0.018-0.0035.563-0.059-0.0590.0000.0000.0000.000
135A135GLY00.0710.0388.442-0.475-0.4750.0000.0000.0000.000
136A136LEU0-0.090-0.04810.952-0.352-0.3520.0000.0000.0000.000
137A137LYS10.9210.94912.981-0.820-0.8200.0000.0000.0000.000
138A138LEU00.0080.01611.394-0.076-0.0760.0000.0000.0000.000
139A139GLY0-0.0210.01215.652-0.063-0.0630.0000.0000.0000.000
140A140GLY00.0570.03017.7120.0760.0760.0000.0000.0000.000
141A141LEU0-0.0230.00119.053-0.074-0.0740.0000.0000.0000.000
142A142ARG10.8550.92016.719-0.393-0.3930.0000.0000.0000.000
143A143ILE00.007-0.01117.902-0.081-0.0810.0000.0000.0000.000
144A144THR0-0.044-0.03818.0750.0530.0530.0000.0000.0000.000
145A145VAL00.006-0.00818.680-0.034-0.0340.0000.0000.0000.000
146A146ASP-1-0.744-0.82019.8330.2590.2590.0000.0000.0000.000
147A147ILE00.0300.02318.0090.0010.0010.0000.0000.0000.000
148A148PRO00.0320.00922.116-0.018-0.0180.0000.0000.0000.000
149A149ASP-1-0.905-0.95721.0220.1680.1680.0000.0000.0000.000
150A150VAL0-0.019-0.00622.015-0.026-0.0260.0000.0000.0000.000
151A151PRO00.008-0.01719.8290.0300.0300.0000.0000.0000.000
152A152GLY00.0020.00519.5270.0310.0310.0000.0000.0000.000
153A153ALA00.0070.01120.9110.0260.0260.0000.0000.0000.000
154A154LEU00.0260.01513.8030.0220.0220.0000.0000.0000.000
155A155ALA00.0200.00018.2230.0490.0490.0000.0000.0000.000
156A156GLN0-0.0050.00619.2440.0270.0270.0000.0000.0000.000
157A157MET00.0250.02616.4520.0270.0270.0000.0000.0000.000
158A158ALA0-0.021-0.02417.4010.0220.0220.0000.0000.0000.000
159A159GLN0-0.058-0.03719.2620.0310.0310.0000.0000.0000.000
160A160ALA00.0050.01522.540-0.017-0.0170.0000.0000.0000.000
161A161VAL0-0.026-0.01718.223-0.008-0.0080.0000.0000.0000.000
162A162PRO00.0260.02420.595-0.002-0.0020.0000.0000.0000.000
163A163PRO0-0.006-0.00922.511-0.036-0.0360.0000.0000.0000.000
164A164ALA0-0.0380.01720.2680.0380.0380.0000.0000.0000.000
165A165ASN0-0.032-0.03515.4520.0100.0100.0000.0000.0000.000
166A166ILE00.0360.00712.462-0.027-0.0270.0000.0000.0000.000
167A167VAL0-0.038-0.0159.6780.0980.0980.0000.0000.0000.000
168A168SER0-0.035-0.0308.5880.4390.4390.0000.0000.0000.000
169A169ILE00.0190.0079.211-0.332-0.3320.0000.0000.0000.000
170A170ALA00.0090.0139.2720.0470.0470.0000.0000.0000.000
171A171THR0-0.0050.00611.133-0.044-0.0440.0000.0000.0000.000
172A172ALA0-0.041-0.01613.821-0.054-0.0540.0000.0000.0000.000
173A173ALA00.001-0.01116.380-0.051-0.0510.0000.0000.0000.000
174A174HIS00.0260.02315.3450.0270.0270.0000.0000.0000.000
175A175LEU0-0.040-0.02320.017-0.021-0.0210.0000.0000.0000.000
176A176PRO00.008-0.01123.5970.0010.0010.0000.0000.0000.000
177A177GLY00.0200.02825.9760.0060.0060.0000.0000.0000.000
178A178TYR0-0.019-0.01123.3350.0110.0110.0000.0000.0000.000
179A179GLN00.0040.00214.682-0.022-0.0220.0000.0000.0000.000
180A180ARG10.8110.87019.145-0.205-0.2050.0000.0000.0000.000
181A181LEU00.006-0.00414.2130.0070.0070.0000.0000.0000.000
182A182VAL0-0.045-0.02214.372-0.036-0.0360.0000.0000.0000.000
183A183MET00.0220.01413.4090.1010.1010.0000.0000.0000.000
184A184ARG10.8630.94212.680-1.083-1.0830.0000.0000.0000.000
185A185VAL00.0450.01814.2780.1480.1480.0000.0000.0000.000
186A186VAL00.011-0.01515.442-0.057-0.0570.0000.0000.0000.000
187A187GLY00.0260.01917.9840.0030.0030.0000.0000.0000.000
188A188GLU-1-0.919-0.96820.4520.4070.4070.0000.0000.0000.000
189A189ASP-1-0.775-0.88423.6260.4000.4000.0000.0000.0000.000
190A190VAL0-0.0120.00520.3780.0010.0010.0000.0000.0000.000
191A191GLU-1-0.899-0.96723.0850.4470.4470.0000.0000.0000.000
192A192GLY00.0070.00226.183-0.027-0.0270.0000.0000.0000.000
193A193VAL0-0.053-0.02120.995-0.015-0.0150.0000.0000.0000.000
194A194PRO00.004-0.00824.224-0.016-0.0160.0000.0000.0000.000
195A195LYS10.8600.92225.687-0.285-0.2850.0000.0000.0000.000
196A196ARG10.8270.90323.923-0.465-0.4650.0000.0000.0000.000
197A197LEU00.0030.00321.264-0.010-0.0100.0000.0000.0000.000
198A198GLU-1-0.846-0.90525.4170.2500.2500.0000.0000.0000.000
199A199ALA0-0.067-0.01628.306-0.021-0.0210.0000.0000.0000.000
200A200ALA0-0.063-0.02326.789-0.017-0.0170.0000.0000.0000.000
201A201GLY0-0.040-0.02928.230-0.001-0.0010.0000.0000.0000.000
202A202GLU-1-0.901-0.95622.6990.3280.3280.0000.0000.0000.000
203A203ARG10.8890.92525.174-0.235-0.2350.0000.0000.0000.000
204A204VAL00.006-0.00223.8380.0170.0170.0000.0000.0000.000
205A205VAL0-0.086-0.02222.999-0.024-0.0240.0000.0000.0000.000
206A206ASP-1-0.773-0.87822.3520.3420.3420.0000.0000.0000.000
207A207VAL00.0200.01422.8570.0380.0380.0000.0000.0000.000
208A208ARG10.8540.93821.287-0.372-0.3720.0000.0000.0000.000
209A209PRO00.0550.01921.7960.0460.0460.0000.0000.0000.000
210A210GLY0-0.034-0.00218.1200.0210.0210.0000.0000.0000.000