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: LJ5M9

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 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 220
LigandCharge DGL=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2879353.510922
FMO2-HF: Nuclear repulsion 2790657.678598
FMO2-HF: Total energy -88695.832324
FMO2-MP2: Total energy -88956.811914


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.
-20.183-12.3763.64-4.906-6.54-0.013
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 : 0.044 / q_NPA : -0.005
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].
3A3ILE00.0230.0243.849-1.747-0.644-0.005-0.481-0.6180.002
4A4ILE0-0.083-0.0435.6910.9090.9090.0000.0000.0000.000
5A5GLY00.0440.0428.4770.3860.3860.0000.0000.0000.000
6A6PRO0-0.0050.01711.1080.0130.0130.0000.0000.0000.000
7A7LYS10.7770.85711.7870.7930.7930.0000.0000.0000.000
8A8TYR0-0.002-0.00415.2280.0380.0380.0000.0000.0000.000
9A9ARG10.8710.92318.3460.2500.2500.0000.0000.0000.000
10A10LYS10.8810.96421.3480.2580.2580.0000.0000.0000.000
11A11LYS10.8550.91521.6850.2240.2240.0000.0000.0000.000
12A12ARG10.9150.96027.1350.1480.1480.0000.0000.0000.000
13A13LEU00.0130.01930.7360.0030.0030.0000.0000.0000.000
14A14THR0-0.018-0.01627.851-0.001-0.0010.0000.0000.0000.000
15A15ASP-1-0.797-0.88529.233-0.074-0.0740.0000.0000.0000.000
16A16ALA00.0650.02329.794-0.009-0.0090.0000.0000.0000.000
17A17LEU0-0.006-0.01830.380-0.005-0.0050.0000.0000.0000.000
18A18LYS10.8060.89125.4870.0820.0820.0000.0000.0000.000
19A19GLU-1-0.791-0.83225.840-0.163-0.1630.0000.0000.0000.000
20A20ARG10.7350.81922.3630.2360.2360.0000.0000.0000.000
21A21SER0-0.028-0.03324.265-0.019-0.0190.0000.0000.0000.000
22A22LEU0-0.011-0.02217.7750.0040.0040.0000.0000.0000.000
23A23ALA00.0230.01722.238-0.007-0.0070.0000.0000.0000.000
24A24PHE0-0.005-0.02517.679-0.010-0.0100.0000.0000.0000.000
25A25PRO00.0410.03516.2490.0200.0200.0000.0000.0000.000
26A26PHE00.0150.00117.829-0.057-0.0570.0000.0000.0000.000
27A27ILE0-0.030-0.00911.8590.0060.0060.0000.0000.0000.000
28A28SER00.004-0.02811.748-0.078-0.0780.0000.0000.0000.000
29A29THR0-0.045-0.01814.5810.0550.0550.0000.0000.0000.000
30A30SER00.030-0.00518.2160.0320.0320.0000.0000.0000.000
31A31THR0-0.070-0.04317.8410.0200.0200.0000.0000.0000.000
32A32PHE0-0.039-0.02411.2470.0680.0680.0000.0000.0000.000
33A33GLY00.0260.02315.599-0.025-0.0250.0000.0000.0000.000
34A34PHE0-0.004-0.00411.573-0.036-0.0360.0000.0000.0000.000
35A35ASN00.0710.04116.3000.0340.0340.0000.0000.0000.000
36A36ILE00.0870.02118.685-0.046-0.0460.0000.0000.0000.000
37A37ASP-1-0.889-0.91620.986-0.319-0.3190.0000.0000.0000.000
38A38ASP-1-0.829-0.90717.092-0.566-0.5660.0000.0000.0000.000
39A39ALA0-0.027-0.02516.664-0.059-0.0590.0000.0000.0000.000
40A40THR0-0.042-0.04817.643-0.006-0.0060.0000.0000.0000.000
41A41GLU-1-0.831-0.88818.946-0.567-0.5670.0000.0000.0000.000
42A42ILE0-0.033-0.01513.780-0.023-0.0230.0000.0000.0000.000
43A43SER00.0130.01317.342-0.022-0.0220.0000.0000.0000.000
44A44ALA00.007-0.00418.1780.0160.0160.0000.0000.0000.000
45A45ASN00.016-0.00319.5160.0580.0580.0000.0000.0000.000
46A46ALA0-0.0130.00016.0890.0110.0110.0000.0000.0000.000
47A47ILE0-0.023-0.00917.9820.0280.0280.0000.0000.0000.000
48A48SER00.0270.00620.5400.0460.0460.0000.0000.0000.000
49A49GLU-1-0.879-0.90517.072-0.696-0.6960.0000.0000.0000.000
50A50TYR0-0.027-0.03818.4150.0420.0420.0000.0000.0000.000
51A51LEU0-0.022-0.02820.5470.0400.0400.0000.0000.0000.000
52A52HIS00.0240.01724.1920.0390.0390.0000.0000.0000.000
53A53PHE00.0090.00922.1170.0300.0300.0000.0000.0000.000
54A54HIS10.6990.84620.4390.3550.3550.0000.0000.0000.000
55A55GLU-1-0.738-0.83325.486-0.170-0.1700.0000.0000.0000.000
56A56LYS10.7770.85428.8940.1770.1770.0000.0000.0000.000
57A57GLU-1-0.718-0.82325.783-0.228-0.2280.0000.0000.0000.000
58A58ASP-1-0.848-0.92928.644-0.173-0.1730.0000.0000.0000.000
59A59ASP-1-0.762-0.85126.667-0.193-0.1930.0000.0000.0000.000
60A60ILE0-0.059-0.00523.799-0.004-0.0040.0000.0000.0000.000
61A61LYS10.8390.90925.5430.1690.1690.0000.0000.0000.000
62A62LEU0-0.011-0.00121.071-0.012-0.0120.0000.0000.0000.000
63A63LYS10.8170.89123.7690.1880.1880.0000.0000.0000.000
64A64MET0-0.0090.01620.447-0.029-0.0290.0000.0000.0000.000
65A65MET0-0.007-0.00221.1370.0340.0340.0000.0000.0000.000
66A66VAL0-0.008-0.01122.099-0.030-0.0300.0000.0000.0000.000
67A67GLU-1-0.803-0.87922.032-0.172-0.1720.0000.0000.0000.000
68A68LYS10.8380.88625.4790.1020.1020.0000.0000.0000.000
69A69SER0-0.045-0.02626.058-0.003-0.0030.0000.0000.0000.000
70A70ILE00.0160.01222.6930.0000.0000.0000.0000.0000.000
71A71TYR0-0.015-0.00825.998-0.010-0.0100.0000.0000.0000.000
72A72SER00.0350.01328.2130.0130.0130.0000.0000.0000.000
73A73ASP-1-0.842-0.93430.539-0.163-0.1630.0000.0000.0000.000
74A74ASN0-0.012-0.01730.5070.0000.0000.0000.0000.0000.000
75A75LEU0-0.0040.02023.855-0.012-0.0120.0000.0000.0000.000
76A76ILE00.0270.00927.543-0.018-0.0180.0000.0000.0000.000
77A77GLN0-0.014-0.02229.542-0.007-0.0070.0000.0000.0000.000
78A78SER00.0210.02625.735-0.007-0.0070.0000.0000.0000.000
79A79PHE00.0180.00621.679-0.017-0.0170.0000.0000.0000.000
80A80LYS10.9550.97926.7760.1740.1740.0000.0000.0000.000
81A81LYS10.9570.98928.4340.2680.2680.0000.0000.0000.000
82A82HIS0-0.048-0.03724.116-0.015-0.0150.0000.0000.0000.000
83A83PHE0-0.0120.00824.193-0.010-0.0100.0000.0000.0000.000
84A84ASN0-0.101-0.05228.4570.0250.0250.0000.0000.0000.000
85A85ASP-1-0.895-0.95531.535-0.178-0.1780.0000.0000.0000.000
86A86LYS10.8580.94232.0030.2220.2220.0000.0000.0000.000
87A87TRP0-0.042-0.02828.214-0.017-0.0170.0000.0000.0000.000
88A88ASP-1-0.753-0.86527.916-0.224-0.2240.0000.0000.0000.000
89A89LYS10.8850.92229.8250.1590.1590.0000.0000.0000.000
90A90ARG10.7200.83527.1270.2470.2470.0000.0000.0000.000
91A91PHE00.0030.01223.079-0.016-0.0160.0000.0000.0000.000
92A92GLU-1-0.792-0.87026.878-0.162-0.1620.0000.0000.0000.000
93A93ILE0-0.0070.00125.099-0.018-0.0180.0000.0000.0000.000
94A94ILE0-0.008-0.00426.4850.0200.0200.0000.0000.0000.000
95A95LYS10.9330.97726.8040.1260.1260.0000.0000.0000.000
96A96ILE00.0130.00923.9300.0110.0110.0000.0000.0000.000
97A97GLU-1-0.840-0.90828.075-0.113-0.1130.0000.0000.0000.000
98A98ASN0-0.005-0.02226.1140.0020.0020.0000.0000.0000.000
99A99SER00.018-0.01321.4590.0050.0050.0000.0000.0000.000
100A100ASN0-0.061-0.02723.5460.0080.0080.0000.0000.0000.000
101A101SER0-0.056-0.04025.9120.0160.0160.0000.0000.0000.000
102A102LEU00.0810.02028.046-0.007-0.0070.0000.0000.0000.000
103A103GLU-1-0.847-0.88129.618-0.121-0.1210.0000.0000.0000.000
104A104GLN0-0.062-0.05623.489-0.023-0.0230.0000.0000.0000.000
105A105PHE00.005-0.00124.114-0.010-0.0100.0000.0000.0000.000
106A106ASN0-0.0060.00627.9590.0000.0000.0000.0000.0000.000
107A107LEU0-0.003-0.00426.3650.0000.0000.0000.0000.0000.000
108A108GLY00.0500.03529.745-0.008-0.0080.0000.0000.0000.000
109A109CYS0-0.089-0.04924.635-0.005-0.0050.0000.0000.0000.000
110A110LYS10.9530.99025.4190.1150.1150.0000.0000.0000.000
111A111LEU0-0.055-0.01919.4180.0080.0080.0000.0000.0000.000
112A112PHE00.0360.01520.939-0.015-0.0150.0000.0000.0000.000
113A113ALA00.0050.00316.1500.0090.0090.0000.0000.0000.000
114A114THR00.002-0.00316.3790.0250.0250.0000.0000.0000.000
115A115GLU-1-0.809-0.89413.190-0.475-0.4750.0000.0000.0000.000
116A116SER0-0.004-0.01612.2050.1260.1260.0000.0000.0000.000
117A117THR00.0430.01010.202-0.025-0.0250.0000.0000.0000.000
118A118TRP00.0900.0297.9530.0050.0050.0000.0000.0000.000
119A119ARG10.9190.9629.141-0.389-0.3890.0000.0000.0000.000
120A120LEU0-0.043-0.00810.273-0.037-0.0370.0000.0000.0000.000
121A121LYS10.8440.93213.561-0.387-0.3870.0000.0000.0000.000
122A122LYS10.8600.94216.753-0.076-0.0760.0000.0000.0000.000
123A123THR0-0.029-0.02315.7010.0190.0190.0000.0000.0000.000
124A124PRO00.001-0.02219.007-0.012-0.0120.0000.0000.0000.000
125A125GLN00.0650.03818.9030.0140.0140.0000.0000.0000.000
126A126ASN00.0810.06216.8880.0150.0150.0000.0000.0000.000
127A127LYS10.8760.92021.0860.0100.0100.0000.0000.0000.000
128A128GLN00.0060.00623.8870.0120.0120.0000.0000.0000.000
129A129LEU00.0480.01820.3690.0040.0040.0000.0000.0000.000
130A130TYR00.008-0.01317.5710.0040.0040.0000.0000.0000.000
131A131GLU-1-0.813-0.88523.8110.0230.0230.0000.0000.0000.000
132A132MET00.0030.02927.1900.0040.0040.0000.0000.0000.000
133A133LEU0-0.037-0.00122.141-0.002-0.0020.0000.0000.0000.000
134A134ASP-1-0.782-0.86026.3150.0690.0690.0000.0000.0000.000
135A135THR00.006-0.01322.9320.0060.0060.0000.0000.0000.000
136A136GLY00.0430.03423.5840.0150.0150.0000.0000.0000.000
137A137THR0-0.048-0.05224.2200.0220.0220.0000.0000.0000.000
138A138PHE00.0400.01218.2700.0150.0150.0000.0000.0000.000
139A139GLU-1-0.827-0.91819.4380.1780.1780.0000.0000.0000.000
140A140LYS10.8740.94019.198-0.081-0.0810.0000.0000.0000.000
141A141VAL00.0060.00219.9980.0210.0210.0000.0000.0000.000
142A142THR0-0.018-0.02114.9220.0030.0030.0000.0000.0000.000
143A143LYS10.8470.92715.092-0.452-0.4520.0000.0000.0000.000
144A144ASN0-0.032-0.02916.2900.0590.0590.0000.0000.0000.000
145A145LEU0-0.0090.01315.5100.0130.0130.0000.0000.0000.000
146A146TYR0-0.027-0.03111.0030.0210.0210.0000.0000.0000.000
147A147PRO0-0.0020.01912.6100.0770.0770.0000.0000.0000.000
148A148ASN00.0480.0039.223-0.067-0.0670.0000.0000.0000.000
149A149CYS0-0.071-0.0258.9070.2330.2330.0000.0000.0000.000
150A150GLY00.0290.0157.336-0.036-0.0360.0000.0000.0000.000
151A151LYS10.8080.8962.490-5.165-3.1011.758-1.426-2.3960.017
152A152ILE00.0690.0233.093-2.986-1.9730.150-0.402-0.7600.001
153A153GLY00.0360.0262.242-13.133-10.2841.700-2.415-2.134-0.033
154A154LYS10.7590.8653.2745.2745.8730.037-0.153-0.4820.000
155A155VAL00.0090.0036.0600.3190.3190.0000.0000.0000.000
156A156TYR0-0.022-0.0106.0140.2140.2140.0000.0000.0000.000
157A157PRO00.0300.03011.8760.0260.0260.0000.0000.0000.000
158A158ILE00.0020.01115.3960.0600.0600.0000.0000.0000.000
159A159SER00.0000.01218.250-0.014-0.0140.0000.0000.0000.000
160A160LEU00.011-0.02021.5060.0250.0250.0000.0000.0000.000
161A161GLN0-0.0040.01724.7090.0110.0110.0000.0000.0000.000
162A162ASN0-0.064-0.00522.7850.0110.0110.0000.0000.0000.000
163A163ASN00.054-0.02321.1290.0070.0070.0000.0000.0000.000
164A164LYS10.8790.92125.365-0.036-0.0360.0000.0000.0000.000
165A165GLN00.0260.03026.6610.0100.0100.0000.0000.0000.000
166A166LEU00.0300.02523.0960.0010.0010.0000.0000.0000.000
167A167VAL00.0140.01327.650-0.010-0.0100.0000.0000.0000.000
168A168ASN0-0.016-0.03029.764-0.011-0.0110.0000.0000.0000.000
169A169SER0-0.0180.00328.560-0.004-0.0040.0000.0000.0000.000
170A170ILE00.0760.03830.514-0.005-0.0050.0000.0000.0000.000
171A171LEU0-0.027-0.01325.125-0.008-0.0080.0000.0000.0000.000
172A172HIS0-0.079-0.04627.994-0.002-0.0020.0000.0000.0000.000
173A173LYS10.8790.95429.3960.0160.0160.0000.0000.0000.000
174A174GLU-1-0.873-0.94532.964-0.036-0.0360.0000.0000.0000.000
175A175TYR0-0.063-0.04329.808-0.004-0.0040.0000.0000.0000.000
176A176GLY00.0070.02629.920-0.012-0.0120.0000.0000.0000.000
177A177ILE0-0.030-0.00823.871-0.010-0.0100.0000.0000.0000.000
178A178ASP-1-0.785-0.90424.915-0.070-0.0700.0000.0000.0000.000
179A179ILE0-0.057-0.03018.7310.0190.0190.0000.0000.0000.000
180A180VAL00.0470.03418.464-0.020-0.0200.0000.0000.0000.000
181A181ILE0-0.020-0.01813.7080.0150.0150.0000.0000.0000.000
182A182LEU0-0.025-0.00313.004-0.018-0.0180.0000.0000.0000.000
183A183VAL00.024-0.00510.939-0.056-0.0560.0000.0000.0000.000
184A184LEU0-0.039-0.0096.6970.2010.2010.0000.0000.0000.000
185A185GLY00.0770.0396.962-0.610-0.6100.0000.0000.0000.000
186A186VAL0-0.041-0.0087.2680.1140.1140.0000.0000.0000.000
187A187ASN00.0230.0179.1590.0980.0980.0000.0000.0000.000
188A188MET00.0350.02611.788-0.060-0.0600.0000.0000.0000.000
189A189ASN00.0020.01014.4140.0920.0920.0000.0000.0000.000
190A190PRO00.0480.00516.2910.0380.0380.0000.0000.0000.000
191A191ASN0-0.079-0.03117.9530.0550.0550.0000.0000.0000.000
192A192LYS10.8490.92615.2120.0630.0630.0000.0000.0000.000
193A193PRO0-0.019-0.02812.1410.0030.0030.0000.0000.0000.000
194A194ASP-1-0.879-0.9348.5600.8290.8290.0000.0000.0000.000
195A195ALA0-0.0160.0089.939-0.149-0.1490.0000.0000.0000.000
196A196PHE0-0.046-0.0275.747-0.013-0.0130.0000.0000.0000.000
197A197LYS10.9610.96711.9040.0910.0910.0000.0000.0000.000
198A198DGL-1-0.898-0.96614.580-0.410-0.4100.0000.0000.0000.000
199A199ASN00.0300.02516.582-0.033-0.0330.0000.0000.0000.000
200A200SER0-0.044-0.01510.659-0.047-0.0470.0000.0000.0000.000
201A201GLU-1-0.883-0.95112.734-0.564-0.5640.0000.0000.0000.000
202A202LEU0-0.047-0.0336.008-0.149-0.1490.0000.0000.0000.000
203A203ALA00.0110.0198.712-0.437-0.4370.0000.0000.0000.000
204A204LYS10.8700.89510.2930.4070.4070.0000.0000.0000.000
205A205PRO0-0.002-0.0048.926-0.091-0.0910.0000.0000.0000.000
206A206LEU00.0030.0053.864-0.648-0.4690.000-0.029-0.1500.000
207A207LEU00.0290.0387.326-0.137-0.1370.0000.0000.0000.000
208A208LEU00.0220.00910.1120.1000.1000.0000.0000.0000.000
209A209GLU-1-0.713-0.8355.458-3.006-3.0060.0000.0000.0000.000
210A210THR0-0.036-0.0348.0200.1050.1050.0000.0000.0000.000
211A211TYR00.0150.0069.1710.2770.2770.0000.0000.0000.000
212A212HIS0-0.012-0.02010.477-0.011-0.0110.0000.0000.0000.000
213A213SER0-0.008-0.0027.6100.1750.1750.0000.0000.0000.000
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