Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 2JQ9R

Calculation Name: 5LSK-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LSK

Chain ID: D

ChEMBL ID:

UniProt ID: Q03188

Base Structure: X-ray

Registration Date: 2023-09-19

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 OptH
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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1104079.369095
FMO2-HF: Nuclear repulsion 1030762.117968
FMO2-HF: Total energy -73317.251127
FMO2-MP2: Total energy -73527.70468


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(D:116:GLY)


Summations of interaction energy for fragment #1(D:116:GLY)
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.
-0.7131.2620.098-0.76-1.3140.001
Interaction energy analysis for fragmet #1(D:116:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.009
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].
3D118THR00.0340.0053.014-1.2850.1790.092-0.667-0.8890.001
4D119GLU-1-0.936-0.9633.676-0.840-0.3290.006-0.093-0.4250.000
5D120LEU0-0.0030.0105.5860.5100.5100.0000.0000.0000.000
6D121SER0-0.055-0.0037.8990.2920.2920.0000.0000.0000.000
7D122ARG10.9220.9587.6410.6160.6160.0000.0000.0000.000
8D123SER0-0.032-0.0309.082-0.002-0.0020.0000.0000.0000.000
9D124ILE0-0.017-0.01011.5320.0530.0530.0000.0000.0000.000
10D125SER0-0.026-0.04215.2200.0220.0220.0000.0000.0000.000
11D126VAL00.0550.04018.0880.0080.0080.0000.0000.0000.000
12D127ASP-1-0.917-0.95419.422-0.093-0.0930.0000.0000.0000.000
13D128LEU0-0.040-0.00320.5630.0120.0120.0000.0000.0000.000
14D129ALA0-0.013-0.01323.6370.0020.0020.0000.0000.0000.000
15D130GLU-1-0.818-0.90219.614-0.098-0.0980.0000.0000.0000.000
16D131SER00.0350.01320.838-0.010-0.0100.0000.0000.0000.000
17D132LYS10.9510.97622.0580.0950.0950.0000.0000.0000.000
18D133ARG10.9080.94915.1720.1460.1460.0000.0000.0000.000
19D134LEU00.0120.01517.364-0.031-0.0310.0000.0000.0000.000
20D135GLY00.0650.02518.179-0.007-0.0070.0000.0000.0000.000
21D136CYS0-0.041-0.03517.331-0.012-0.0120.0000.0000.0000.000
22D137LEU0-0.0180.00111.994-0.056-0.0560.0000.0000.0000.000
23D138LEU0-0.0100.00314.345-0.025-0.0250.0000.0000.0000.000
24D139LEU00.0410.00916.366-0.009-0.0090.0000.0000.0000.000
25D140SER0-0.005-0.00512.165-0.033-0.0330.0000.0000.0000.000
26D141SER0-0.034-0.00911.672-0.098-0.0980.0000.0000.0000.000
27D142PHE00.0270.01612.7460.0170.0170.0000.0000.0000.000
28D143GLN00.0230.00813.9670.0510.0510.0000.0000.0000.000
29D144PHE0-0.0070.0055.097-0.080-0.0800.0000.0000.0000.000
30D145SER0-0.039-0.03510.3620.0420.0420.0000.0000.0000.000
31D146ILE00.002-0.00512.3330.0300.0300.0000.0000.0000.000
32D147GLN0-0.012-0.01410.9590.0670.0670.0000.0000.0000.000
33D148LYS10.8920.9607.3070.0670.0670.0000.0000.0000.000
34D149LEU0-0.026-0.01810.8170.0710.0710.0000.0000.0000.000
35D150GLU-1-0.876-0.94114.323-0.217-0.2170.0000.0000.0000.000
36D151PRO0-0.104-0.04111.5190.0210.0210.0000.0000.0000.000
37D152PHE0-0.047-0.02712.5260.0320.0320.0000.0000.0000.000
38D153LEU00.0350.02217.4060.0130.0130.0000.0000.0000.000
39D154ARG10.9300.98620.6680.0000.0000.0000.0000.0000.000
40D155ASP-1-0.923-0.96223.856-0.029-0.0290.0000.0000.0000.000
41D156THR00.049-0.00225.506-0.005-0.0050.0000.0000.0000.000
42D157LYS10.8550.88726.8460.0470.0470.0000.0000.0000.000
43D158GLY0-0.0050.01629.990-0.001-0.0010.0000.0000.0000.000
44D159PHE00.0690.04427.0980.0010.0010.0000.0000.0000.000
45D160SER00.0160.02125.928-0.001-0.0010.0000.0000.0000.000
46D161LEU00.0030.00820.1900.0020.0020.0000.0000.0000.000
47D162GLU-1-0.960-0.99723.560-0.107-0.1070.0000.0000.0000.000
48D163SER00.0220.01726.0280.0000.0000.0000.0000.0000.000
49D164PHE0-0.020-0.00119.1510.0030.0030.0000.0000.0000.000
50D165ARG11.0010.99020.7690.1740.1740.0000.0000.0000.000
51D166ALA00.0400.03023.266-0.004-0.0040.0000.0000.0000.000
52D167LYS10.9560.98624.6640.0670.0670.0000.0000.0000.000
53D168ALA00.0550.05319.9590.0000.0000.0000.0000.0000.000
54D169SER00.0620.01221.943-0.014-0.0140.0000.0000.0000.000
55D170SER0-0.089-0.04123.3940.0050.0050.0000.0000.0000.000
56D171LEU00.0570.00722.4670.0000.0000.0000.0000.0000.000
57D172SER0-0.089-0.03420.537-0.005-0.0050.0000.0000.0000.000
58D173GLU-1-0.902-0.96422.245-0.140-0.1400.0000.0000.0000.000
59D174GLU-1-0.972-0.98225.178-0.058-0.0580.0000.0000.0000.000
60D175LEU0-0.026-0.01019.8450.0070.0070.0000.0000.0000.000
61D176LYS10.9060.95022.7680.1440.1440.0000.0000.0000.000
62D177HIS00.0090.00624.0280.0010.0010.0000.0000.0000.000
63D178PHE0-0.037-0.01225.5330.0090.0090.0000.0000.0000.000
64D179ALA0-0.034-0.02422.8540.0080.0080.0000.0000.0000.000
65D180ASP-1-0.853-0.94124.899-0.115-0.1150.0000.0000.0000.000
66D181GLY0-0.0120.00627.2520.0060.0060.0000.0000.0000.000
67D182LEU0-0.006-0.01828.2480.0070.0070.0000.0000.0000.000
68D183GLU-1-0.946-0.97025.872-0.079-0.0790.0000.0000.0000.000
69D184THR0-0.107-0.05927.8500.0060.0060.0000.0000.0000.000
70D185ASP-1-0.937-0.94931.553-0.020-0.0200.0000.0000.0000.000
71D186GLY00.0680.01131.1370.0040.0040.0000.0000.0000.000
72D187THR0-0.068-0.04027.7670.0050.0050.0000.0000.0000.000
73D188LEU00.0150.02922.5940.0040.0040.0000.0000.0000.000
74D189GLN00.014-0.00325.4320.0050.0050.0000.0000.0000.000
75D190LYS10.9370.96727.4900.0130.0130.0000.0000.0000.000
76D191CYS0-0.049-0.01822.1870.0080.0080.0000.0000.0000.000
77D192PHE0-0.061-0.02721.7470.0040.0040.0000.0000.0000.000
78D193GLU-1-0.966-0.95626.0040.0150.0150.0000.0000.0000.000
79D203SER00.0440.00636.6560.0010.0010.0000.0000.0000.000
80D204LEU00.0280.01935.8960.0010.0010.0000.0000.0000.000
81D205GLU-1-0.884-0.95432.0450.0490.0490.0000.0000.0000.000
82D206ALA00.0110.01435.6550.0020.0020.0000.0000.0000.000
83D207SER00.0360.01937.9710.0010.0010.0000.0000.0000.000
84D208VAL0-0.022-0.01636.6020.0010.0010.0000.0000.0000.000
85D209ALA0-0.014-0.00736.3310.0020.0020.0000.0000.0000.000
86D210GLU-1-0.904-0.95938.1450.0310.0310.0000.0000.0000.000
87D211MET0-0.035-0.00741.6880.0000.0000.0000.0000.0000.000
88D212LYS10.9060.92934.534-0.069-0.0690.0000.0000.0000.000
89D213GLU-1-0.899-0.94239.7560.0470.0470.0000.0000.0000.000
90D214TYR0-0.037-0.01842.092-0.002-0.0020.0000.0000.0000.000
91D215ILE0-0.0240.00342.553-0.001-0.0010.0000.0000.0000.000
92D216THR00.0400.01541.206-0.001-0.0010.0000.0000.0000.000
93D217LYS10.9901.00544.504-0.033-0.0330.0000.0000.0000.000
94D218PHE00.026-0.00147.128-0.001-0.0010.0000.0000.0000.000
95D219SER0-0.084-0.03646.3840.0000.0000.0000.0000.0000.000
96D220LEU00.011-0.00145.619-0.001-0.0010.0000.0000.0000.000
97D221GLU-1-0.904-0.94149.2670.0280.0280.0000.0000.0000.000
98D222ARG10.9590.97849.007-0.041-0.0410.0000.0000.0000.000
99D223GLN00.0120.00448.806-0.001-0.0010.0000.0000.0000.000
100D224THR0-0.027-0.02252.825-0.001-0.0010.0000.0000.0000.000
101D225TRP0-0.056-0.02555.063-0.002-0.0020.0000.0000.0000.000
102D226ASP-1-0.915-0.95255.5640.0320.0320.0000.0000.0000.000
103D227GLN0-0.036-0.01855.2260.0000.0000.0000.0000.0000.000
104D228LEU0-0.012-0.01058.047-0.001-0.0010.0000.0000.0000.000
105D229LEU0-0.0120.00560.490-0.001-0.0010.0000.0000.0000.000
106D230LEU00.026-0.00859.303-0.001-0.0010.0000.0000.0000.000
107D231HIS0-0.036-0.00161.8910.0000.0000.0000.0000.0000.000
108D232TYR00.0520.01163.595-0.001-0.0010.0000.0000.0000.000
109D233GLN0-0.029-0.00264.8360.0000.0000.0000.0000.0000.000
110D234GLN0-0.030-0.02462.9580.0000.0000.0000.0000.0000.000
111D235GLU-1-0.924-0.95167.6200.0200.0200.0000.0000.0000.000
112D236ALA00.0180.01069.313-0.001-0.0010.0000.0000.0000.000
113D237LYS10.8830.92670.353-0.022-0.0220.0000.0000.0000.000
114D238GLU-1-0.868-0.93770.4700.0200.0200.0000.0000.0000.000
115D239ILE00.003-0.00672.429-0.001-0.0010.0000.0000.0000.000
116D240LEU0-0.074-0.03175.027-0.001-0.0010.0000.0000.0000.000
117D241SER0-0.065-0.04075.1530.0000.0000.0000.0000.0000.000
118D242ARG10.9100.98174.422-0.018-0.0180.0000.0000.0000.000
119D243GLY0-0.042-0.02177.5620.0000.0000.0000.0000.0000.000
120D244SER0-0.047-0.00980.759-0.001-0.0010.0000.0000.0000.000
121D245THR00.0220.01377.9600.0000.0000.0000.0000.0000.000
122D258THR00.006-0.01691.6510.0000.0000.0000.0000.0000.000
123D259TYR00.0110.01384.7700.0000.0000.0000.0000.0000.000
124D260LEU00.0110.00382.5880.0000.0000.0000.0000.0000.000
125D261GLY00.0280.00885.2050.0000.0000.0000.0000.0000.000
126D262SER0-0.029-0.00786.2220.0000.0000.0000.0000.0000.000
127D263SER00.0530.02189.3300.0000.0000.0000.0000.0000.000
128D264GLN00.0320.01291.2440.0000.0000.0000.0000.0000.000
129D265ASN0-0.043-0.02289.9340.0000.0000.0000.0000.0000.000
130D266GLU-1-0.868-0.93592.7090.0090.0090.0000.0000.0000.000
131D267VAL00.015-0.00295.2720.0000.0000.0000.0000.0000.000
132D268LEU0-0.083-0.04594.1490.0000.0000.0000.0000.0000.000
133D269ASN0-0.029-0.01192.2580.0000.0000.0000.0000.0000.000
134D270THR0-0.049-0.00496.5710.0000.0000.0000.0000.0000.000
135D271LYS10.9530.991100.084-0.009-0.0090.0000.0000.0000.000
136D272PRO0-0.0020.005101.8690.0000.0000.0000.0000.0000.000
137D273ASP-1-0.853-0.934105.0570.0080.0080.0000.0000.0000.000
138D274TYR00.0520.006104.8740.0000.0000.0000.0000.0000.000
139D275GLN00.0180.010106.7170.0000.0000.0000.0000.0000.000
140D276LYS10.9640.976107.338-0.008-0.0080.0000.0000.0000.000
141D277ILE0-0.0010.005110.4090.0000.0000.0000.0000.0000.000
142D278LEU00.0180.003112.3380.0000.0000.0000.0000.0000.000
143D279GLN00.0030.003110.6920.0000.0000.0000.0000.0000.000
144D280ASN0-0.040-0.029113.6180.0000.0000.0000.0000.0000.000
145D281GLN00.008-0.003116.3770.0000.0000.0000.0000.0000.000
146D282SER0-0.002-0.001117.7190.0000.0000.0000.0000.0000.000
147D283LYS10.9700.999115.495-0.007-0.0070.0000.0000.0000.000
148D284VAL0-0.043-0.014120.3220.0000.0000.0000.0000.0000.000
149D285PHE0-0.021-0.024122.3450.0000.0000.0000.0000.0000.000
150D286ASP-1-0.833-0.897122.5510.0060.0060.0000.0000.0000.000
151D287CYS0-0.096-0.058124.3040.0000.0000.0000.0000.0000.000
152D288MET0-0.004-0.010126.0820.0000.0000.0000.0000.0000.000
153D289GLU-1-0.923-0.956128.2060.0060.0060.0000.0000.0000.000
154D290LEU00.0020.016126.5810.0000.0000.0000.0000.0000.000
155D291VAL0-0.006-0.005129.5650.0000.0000.0000.0000.0000.000
156D292MET0-0.052-0.020132.0610.0000.0000.0000.0000.0000.000
157D293ASP-1-0.867-0.941133.2540.0050.0050.0000.0000.0000.000
158D294GLU-1-0.983-0.986133.6150.0050.0050.0000.0000.0000.000
159D295LEU0-0.024-0.014136.0710.0000.0000.0000.0000.0000.000
160D296GLN0-0.019-0.026138.1640.0000.0000.0000.0000.0000.000
161D297GLY00.0190.011139.1500.0000.0000.0000.0000.0000.000
162D298SER0-0.020-0.019139.5240.0000.0000.0000.0000.0000.000
163D299VAL0-0.029-0.008142.0820.0000.0000.0000.0000.0000.000
164D300LYS10.9490.974144.072-0.005-0.0050.0000.0000.0000.000
165D301GLN0-0.0180.004143.9620.0000.0000.0000.0000.0000.000
166D302LEU0-0.010-0.002145.9620.0000.0000.0000.0000.0000.000
167D303GLN0-0.026-0.015148.1000.0000.0000.0000.0000.0000.000
168D304ALA00.0160.006149.5630.0000.0000.0000.0000.0000.000
169D305PHE00.0380.025150.8600.0000.0000.0000.0000.0000.000
170D306MET0-0.012-0.003151.3760.0000.0000.0000.0000.0000.000
171D307ASP-1-0.882-0.947154.1520.0040.0040.0000.0000.0000.000
172D308GLU-1-0.971-0.986154.7660.0040.0040.0000.0000.0000.000
173D309SER0-0.050-0.039155.9730.0000.0000.0000.0000.0000.000
174D310THR0-0.039-0.014158.2070.0000.0000.0000.0000.0000.000
175D311GLN0-0.023-0.005159.9160.0000.0000.0000.0000.0000.000
176D312CYS0-0.035-0.025160.9850.0000.0000.0000.0000.0000.000
177D313PHE00.000-0.016160.8600.0000.0000.0000.0000.0000.000
178D314GLN00.0240.028164.3150.0000.0000.0000.0000.0000.000
179D315LYS10.8600.926164.714-0.003-0.0030.0000.0000.0000.000
180D316VAL0-0.0130.004167.5770.0000.0000.0000.0000.0000.000
181D317SER0-0.053-0.010169.9840.0000.0000.0000.0000.0000.000