FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 9G5N2

Calculation Name: 5LW6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LW6

Chain ID: A

ChEMBL ID:

UniProt ID: Q54B72

Base Structure: X-ray

Registration Date: 2023-06-20

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 220
LigandCharge DGL=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2884566.946853
FMO2-HF: Nuclear repulsion 2795870.526962
FMO2-HF: Total energy -88696.41989
FMO2-MP2: Total energy -88957.491031


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:SER)


Summations of interaction energy for fragment #1(A:1:SER)
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.
-28.284-25.45516.281-9.325-9.783-0.047
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.029
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].
3A3ILE00.0600.0383.850-1.965-0.9550.001-0.438-0.5730.002
4A4ILE0-0.091-0.0435.7711.0621.0620.0000.0000.0000.000
5A5GLY00.0650.0398.7340.3630.3630.0000.0000.0000.000
6A6PRO00.0160.02511.0200.0500.0500.0000.0000.0000.000
7A7LYS10.7630.85511.9770.8340.8340.0000.0000.0000.000
8A8TYR0-0.037-0.02914.8980.0440.0440.0000.0000.0000.000
9A9ARG10.8660.92218.2930.2610.2610.0000.0000.0000.000
10A10LYS10.8570.93721.1390.2800.2800.0000.0000.0000.000
11A11LYS10.8530.91521.5650.2640.2640.0000.0000.0000.000
12A12ARG10.8920.93527.0560.1650.1650.0000.0000.0000.000
13A13LEU00.0020.01330.2970.0070.0070.0000.0000.0000.000
14A14THR0-0.008-0.01127.299-0.002-0.0020.0000.0000.0000.000
15A15ASP-1-0.799-0.88529.065-0.095-0.0950.0000.0000.0000.000
16A16ALA00.0650.03029.520-0.012-0.0120.0000.0000.0000.000
17A17LEU0-0.039-0.03230.197-0.007-0.0070.0000.0000.0000.000
18A18LYS10.8150.88925.3620.1010.1010.0000.0000.0000.000
19A19GLU-1-0.768-0.81425.770-0.204-0.2040.0000.0000.0000.000
20A20ARG10.7140.81522.1570.2740.2740.0000.0000.0000.000
21A21SER0-0.024-0.03923.796-0.026-0.0260.0000.0000.0000.000
22A22LEU00.003-0.01017.5570.0000.0000.0000.0000.0000.000
23A23ALA00.0280.02122.014-0.004-0.0040.0000.0000.0000.000
24A24PHE00.004-0.01817.314-0.025-0.0250.0000.0000.0000.000
25A25PRO00.0180.02915.7020.0320.0320.0000.0000.0000.000
26A26PHE00.014-0.00517.449-0.071-0.0710.0000.0000.0000.000
27A27ILE0-0.034-0.01211.514-0.004-0.0040.0000.0000.0000.000
28A28SER00.002-0.02811.441-0.079-0.0790.0000.0000.0000.000
29A29THR0-0.064-0.02914.3590.0840.0840.0000.0000.0000.000
30A30SER00.019-0.00217.9780.0350.0350.0000.0000.0000.000
31A31THR0-0.059-0.03317.6740.0310.0310.0000.0000.0000.000
32A32PHE0-0.037-0.02410.8770.0860.0860.0000.0000.0000.000
33A33GLY00.0280.02215.352-0.026-0.0260.0000.0000.0000.000
34A34PHE00.002-0.00911.776-0.019-0.0190.0000.0000.0000.000
35A35ASN00.0540.02916.1590.0280.0280.0000.0000.0000.000
36A36ILE00.0950.03518.679-0.053-0.0530.0000.0000.0000.000
37A37ASP-1-0.896-0.91920.955-0.384-0.3840.0000.0000.0000.000
38A38ASP-1-0.803-0.89917.029-0.651-0.6510.0000.0000.0000.000
39A39ALA0-0.009-0.00916.665-0.079-0.0790.0000.0000.0000.000
40A40THR0-0.060-0.05217.631-0.009-0.0090.0000.0000.0000.000
41A41GLU-1-0.871-0.90818.429-0.651-0.6510.0000.0000.0000.000
42A42ILE0-0.0190.00213.470-0.020-0.0200.0000.0000.0000.000
43A43SER0-0.009-0.00617.010-0.007-0.0070.0000.0000.0000.000
44A44ALA00.0220.01018.0640.0200.0200.0000.0000.0000.000
45A45ASN0-0.012-0.02019.2390.0700.0700.0000.0000.0000.000
46A46ALA00.0040.00515.6070.0210.0210.0000.0000.0000.000
47A47ILE0-0.012-0.00817.5680.0270.0270.0000.0000.0000.000
48A48SER00.0210.00220.0990.0530.0530.0000.0000.0000.000
49A49GLU-1-0.858-0.88916.630-0.764-0.7640.0000.0000.0000.000
50A50TYR0-0.031-0.04618.2520.0500.0500.0000.0000.0000.000
51A51LEU0-0.010-0.00820.2190.0450.0450.0000.0000.0000.000
52A52HIS00.0300.01723.8520.0420.0420.0000.0000.0000.000
53A53PHE0-0.025-0.01121.7010.0330.0330.0000.0000.0000.000
54A54HIS10.7170.85820.4400.3900.3900.0000.0000.0000.000
55A55GLU-1-0.717-0.83025.320-0.187-0.1870.0000.0000.0000.000
56A56LYS10.8070.87328.8220.1920.1920.0000.0000.0000.000
57A57GLU-1-0.716-0.82025.634-0.256-0.2560.0000.0000.0000.000
58A58ASP-1-0.828-0.92027.999-0.207-0.2070.0000.0000.0000.000
59A59ASP-1-0.771-0.84926.428-0.231-0.2310.0000.0000.0000.000
60A60ILE0-0.064-0.01323.476-0.009-0.0090.0000.0000.0000.000
61A61LYS10.8350.89525.0070.2120.2120.0000.0000.0000.000
62A62LEU0-0.018-0.00320.864-0.013-0.0130.0000.0000.0000.000
63A63LYS10.8280.89223.4030.2400.2400.0000.0000.0000.000
64A64MET0-0.0050.02520.134-0.038-0.0380.0000.0000.0000.000
65A65MET0-0.0110.00320.4980.0490.0490.0000.0000.0000.000
66A66VAL0-0.022-0.01721.636-0.042-0.0420.0000.0000.0000.000
67A67GLU-1-0.771-0.86521.787-0.257-0.2570.0000.0000.0000.000
68A68LYS10.8290.88425.2560.1440.1440.0000.0000.0000.000
69A69SER0-0.026-0.00725.5920.0020.0020.0000.0000.0000.000
70A70ILE00.0000.00422.2670.0000.0000.0000.0000.0000.000
71A71TYR0-0.009-0.01225.579-0.009-0.0090.0000.0000.0000.000
72A72SER00.0390.01527.8410.0190.0190.0000.0000.0000.000
73A73ASP-1-0.836-0.92630.136-0.207-0.2070.0000.0000.0000.000
74A74ASN0-0.017-0.00430.3000.0040.0040.0000.0000.0000.000
75A75LEU00.0100.02523.640-0.012-0.0120.0000.0000.0000.000
76A76ILE00.0230.00427.519-0.019-0.0190.0000.0000.0000.000
77A77GLN0-0.015-0.02229.6980.0000.0000.0000.0000.0000.000
78A78SER00.0030.00925.809-0.005-0.0050.0000.0000.0000.000
79A79PHE00.0180.00421.564-0.018-0.0180.0000.0000.0000.000
80A80LYS10.8930.93926.7170.2130.2130.0000.0000.0000.000
81A81LYS10.9710.99227.9800.3130.3130.0000.0000.0000.000
82A82HIS0-0.026-0.01324.054-0.010-0.0100.0000.0000.0000.000
83A83PHE0-0.010-0.00123.931-0.002-0.0020.0000.0000.0000.000
84A84ASN0-0.096-0.04927.9670.0350.0350.0000.0000.0000.000
85A85ASP-1-0.855-0.94131.027-0.207-0.2070.0000.0000.0000.000
86A86LYS10.8560.94831.5430.2520.2520.0000.0000.0000.000
87A87TRP0-0.041-0.03028.212-0.019-0.0190.0000.0000.0000.000
88A88ASP-1-0.769-0.87227.666-0.258-0.2580.0000.0000.0000.000
89A89LYS10.8920.92329.4690.1830.1830.0000.0000.0000.000
90A90ARG10.7200.84426.7210.2880.2880.0000.0000.0000.000
91A91PHE0-0.0060.00222.810-0.025-0.0250.0000.0000.0000.000
92A92GLU-1-0.788-0.86626.256-0.211-0.2110.0000.0000.0000.000
93A93ILE0-0.014-0.00325.005-0.026-0.0260.0000.0000.0000.000
94A94ILE0-0.011-0.00626.0050.0250.0250.0000.0000.0000.000
95A95LYS10.9460.97626.3970.1680.1680.0000.0000.0000.000
96A96ILE0-0.0190.00223.8250.0130.0130.0000.0000.0000.000
97A97GLU-1-0.823-0.90328.054-0.157-0.1570.0000.0000.0000.000
98A98ASN0-0.016-0.03325.960-0.002-0.0020.0000.0000.0000.000
99A99SER00.001-0.01920.9850.0110.0110.0000.0000.0000.000
100A100ASN0-0.046-0.02722.8580.0010.0010.0000.0000.0000.000
101A101SER0-0.080-0.05525.1140.0230.0230.0000.0000.0000.000
102A102LEU00.0600.00227.358-0.014-0.0140.0000.0000.0000.000
103A103GLU-1-0.810-0.86129.021-0.176-0.1760.0000.0000.0000.000
104A104GLN0-0.048-0.04622.863-0.030-0.0300.0000.0000.0000.000
105A105PHE0-0.023-0.01723.272-0.013-0.0130.0000.0000.0000.000
106A106ASN00.0230.01227.1680.0050.0050.0000.0000.0000.000
107A107LEU0-0.0040.00625.7130.0030.0030.0000.0000.0000.000
108A108GLY00.0380.02929.081-0.006-0.0060.0000.0000.0000.000
109A109CYS0-0.083-0.04724.346-0.002-0.0020.0000.0000.0000.000
110A110LYS10.9240.97825.2810.1490.1490.0000.0000.0000.000
111A111LEU0-0.027-0.00419.0300.0040.0040.0000.0000.0000.000
112A112PHE00.0450.01520.327-0.014-0.0140.0000.0000.0000.000
113A113ALA0-0.006-0.00315.5500.0000.0000.0000.0000.0000.000
114A114THR00.0080.00615.6450.0420.0420.0000.0000.0000.000
115A115GLU-1-0.787-0.89112.607-0.720-0.7200.0000.0000.0000.000
116A116SER0-0.048-0.03311.5810.1750.1750.0000.0000.0000.000
117A117THR00.0510.0179.354-0.098-0.0980.0000.0000.0000.000
118A118TRP00.0570.0117.336-0.010-0.0100.0000.0000.0000.000
119A119ARG10.9310.9688.482-0.315-0.3150.0000.0000.0000.000
120A120LEU0-0.053-0.0109.5830.0090.0090.0000.0000.0000.000
121A121LYS10.8280.93012.673-0.248-0.2480.0000.0000.0000.000
122A122LYS10.8570.92115.824-0.054-0.0540.0000.0000.0000.000
123A123THR0-0.020-0.01615.3150.0220.0220.0000.0000.0000.000
124A124PRO0-0.005-0.02418.571-0.007-0.0070.0000.0000.0000.000
125A125GLN00.0740.05118.4910.0170.0170.0000.0000.0000.000
126A126ASN00.0810.05316.3280.0290.0290.0000.0000.0000.000
127A127LYS10.8710.91520.7100.0580.0580.0000.0000.0000.000
128A128GLN00.0290.01723.2520.0180.0180.0000.0000.0000.000
129A129LEU00.0350.02119.7820.0090.0090.0000.0000.0000.000
130A130TYR00.030-0.00515.8910.0350.0350.0000.0000.0000.000
131A131GLU-1-0.810-0.86822.828-0.011-0.0110.0000.0000.0000.000
132A132MET0-0.0150.01626.4010.0080.0080.0000.0000.0000.000
133A133LEU0-0.0180.00521.667-0.002-0.0020.0000.0000.0000.000
134A134ASP-1-0.767-0.84925.7390.0490.0490.0000.0000.0000.000
135A135THR00.0180.00521.9040.0010.0010.0000.0000.0000.000
136A136GLY00.0120.01822.6940.0150.0150.0000.0000.0000.000
137A137THR0-0.042-0.05823.8890.0260.0260.0000.0000.0000.000
138A138PHE00.0370.01717.4770.0200.0200.0000.0000.0000.000
139A139GLU-1-0.808-0.90918.4460.1170.1170.0000.0000.0000.000
140A140LYS10.8680.93718.775-0.057-0.0570.0000.0000.0000.000
141A141VAL00.000-0.00319.5870.0280.0280.0000.0000.0000.000
142A142THR00.006-0.01314.4600.0060.0060.0000.0000.0000.000
143A143LYS10.8170.91115.150-0.461-0.4610.0000.0000.0000.000
144A144ASN0-0.011-0.01316.4610.0910.0910.0000.0000.0000.000
145A145LEU0-0.0180.00215.2080.0250.0250.0000.0000.0000.000
146A146TYR0-0.013-0.03110.7880.0200.0200.0000.0000.0000.000
147A147PRO0-0.0140.01512.4130.0860.0860.0000.0000.0000.000
148A148ASN00.0540.0109.659-0.155-0.1550.0000.0000.0000.000
149A149CYS0-0.038-0.0159.0940.2940.2940.0000.0000.0000.000
150A150GLY00.0360.0287.3600.1750.1750.0000.0000.0000.000
151A151LYS10.7860.8762.214-3.875-2.3682.118-1.443-2.1820.015
152A152ILE00.0710.0392.518-4.885-3.2231.440-1.075-2.0270.005
153A153GLY00.0640.0521.764-19.616-22.03312.648-6.111-4.119-0.068
154A154LYS10.7490.8573.0985.0895.8910.066-0.203-0.664-0.001
155A155VAL00.0030.0005.7820.3790.3790.0000.0000.0000.000
156A156TYR00.0030.0035.4750.0680.0680.0000.0000.0000.000
157A157PRO00.0240.02311.4100.0450.0450.0000.0000.0000.000
158A158ILE00.0020.01214.9370.0820.0820.0000.0000.0000.000
159A159SER0-0.0250.00017.882-0.015-0.0150.0000.0000.0000.000
160A160LEU00.009-0.01421.1230.0260.0260.0000.0000.0000.000
161A161GLN0-0.031-0.01424.3970.0220.0220.0000.0000.0000.000
162A162ASN0-0.008-0.00623.1440.0250.0250.0000.0000.0000.000
163A163ASN00.007-0.00520.2760.0120.0120.0000.0000.0000.000
164A164LYS10.8890.94424.626-0.020-0.0200.0000.0000.0000.000
165A165GLN00.0520.03026.8320.0100.0100.0000.0000.0000.000
166A166LEU00.0070.00322.279-0.004-0.0040.0000.0000.0000.000
167A167VAL00.0190.03626.827-0.013-0.0130.0000.0000.0000.000
168A168ASN00.005-0.00829.037-0.011-0.0110.0000.0000.0000.000
169A169SER0-0.005-0.00627.740-0.003-0.0030.0000.0000.0000.000
170A170ILE00.0600.03229.744-0.005-0.0050.0000.0000.0000.000
171A171LEU0-0.024-0.01124.430-0.008-0.0080.0000.0000.0000.000
172A172HIS0-0.072-0.02927.6950.0000.0000.0000.0000.0000.000
173A173LYS10.8270.90629.2040.0420.0420.0000.0000.0000.000
174A174GLU-1-0.862-0.93832.641-0.064-0.0640.0000.0000.0000.000
175A175TYR0-0.053-0.03429.120-0.004-0.0040.0000.0000.0000.000
176A176GLY0-0.0070.01829.741-0.014-0.0140.0000.0000.0000.000
177A177ILE0-0.027-0.00723.457-0.011-0.0110.0000.0000.0000.000
178A178ASP-1-0.777-0.90224.780-0.104-0.1040.0000.0000.0000.000
179A179ILE0-0.053-0.03218.1190.0220.0220.0000.0000.0000.000
180A180VAL00.0530.04318.030-0.027-0.0270.0000.0000.0000.000
181A181ILE0-0.033-0.02813.4070.0110.0110.0000.0000.0000.000
182A182LEU0-0.0060.00712.386-0.028-0.0280.0000.0000.0000.000
183A183VAL00.017-0.00210.314-0.122-0.1220.0000.0000.0000.000
184A184LEU0-0.060-0.0135.8790.2730.2730.0000.0000.0000.000
185A185GLY00.0770.0326.216-1.015-1.0150.0000.0000.0000.000
186A186VAL0-0.038-0.0087.2030.0570.0570.0000.0000.0000.000
187A187ASN00.0050.0058.8340.1700.1700.0000.0000.0000.000
188A188MET00.0260.03211.398-0.091-0.0910.0000.0000.0000.000
189A189ASN00.0180.02114.2030.1260.1260.0000.0000.0000.000
190A190PRO00.0390.00115.8880.0270.0270.0000.0000.0000.000
191A191ASN0-0.087-0.03017.5290.0690.0690.0000.0000.0000.000
192A192LYS10.8620.92614.7030.1500.1500.0000.0000.0000.000
193A193PRO0-0.002-0.01111.6280.0040.0040.0000.0000.0000.000
194A194ASP-1-0.859-0.9347.9220.4940.4940.0000.0000.0000.000
195A195ALA0-0.0210.0129.560-0.192-0.1920.0000.0000.0000.000
196A196PHE0-0.031-0.0275.6730.0150.0150.0000.0000.0000.000
197A197LYS10.9620.96811.8510.0990.0990.0000.0000.0000.000
198A198DGL-1-0.897-0.96414.507-0.488-0.4880.0000.0000.0000.000
199A199ASN00.0290.02016.424-0.034-0.0340.0000.0000.0000.000
200A200SER0-0.053-0.01610.364-0.026-0.0260.0000.0000.0000.000
201A201GLU-1-0.857-0.93412.497-0.626-0.6260.0000.0000.0000.000
202A202LEU0-0.024-0.0175.912-0.139-0.1390.0000.0000.0000.000
203A203ALA0-0.0090.0018.377-0.483-0.4830.0000.0000.0000.000
204A204LYS10.8540.89210.2940.4480.4480.0000.0000.0000.000
205A205PRO0-0.001-0.0048.734-0.142-0.1420.0000.0000.0000.000
206A206LEU00.0110.0023.632-0.682-0.4170.008-0.055-0.2180.000
207A207LEU00.0260.0377.177-0.361-0.3610.0000.0000.0000.000
208A208LEU00.0330.01910.1030.1050.1050.0000.0000.0000.000
209A209GLU-1-0.716-0.8465.116-2.809-2.8090.0000.0000.0000.000
210A210THR0-0.048-0.0377.757-0.086-0.0860.0000.0000.0000.000
211A211TYR00.0550.0228.5760.3220.3220.0000.0000.0000.000
212A212HIS0-0.031-0.03510.194-0.006-0.0060.0000.0000.0000.000
213A213SER0-0.050-0.0367.3640.1510.1510.0000.0000.0000.000
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