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: JLLZ9

Calculation Name: 5LKQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LKQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DRP0

Base Structure: X-ray

Registration Date: 2023-06-21

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1792726.807065
FMO2-HF: Nuclear repulsion 1726477.002185
FMO2-HF: Total energy -66249.804881
FMO2-MP2: Total energy -66444.989615


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:277:SER)


Summations of interaction energy for fragment #1(A:277: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.
-24.341-27.25334.78-14.716-17.151-0.066
Interaction energy analysis for fragmet #1(A:277:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.012
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].
3A279VAL00.0780.0333.774-3.246-0.660-0.015-1.217-1.3540.003
4A280PHE0-0.021-0.0212.858-1.880-0.9140.139-0.333-0.7720.001
5A281LEU0-0.062-0.0482.456-1.688-1.2262.051-0.779-1.7350.010
6A282GLU-1-0.967-0.9726.0581.2331.2330.0000.0000.0000.000
7A283GLU-1-0.949-0.9608.2580.9540.9540.0000.0000.0000.000
8A284ARG10.7800.9208.325-1.367-1.3670.0000.0000.0000.000
9A285LEU00.0300.00210.522-0.060-0.0600.0000.0000.0000.000
10A286ASP-1-0.898-0.95813.1540.4520.4520.0000.0000.0000.000
11A287GLY0-0.0030.00213.732-0.059-0.0590.0000.0000.0000.000
12A288ALA0-0.021-0.00414.002-0.059-0.0590.0000.0000.0000.000
13A289THR0-0.091-0.04614.3330.0550.0550.0000.0000.0000.000
14A290GLY00.0250.00516.6040.0130.0130.0000.0000.0000.000
15A291SER00.0040.00511.715-0.010-0.0100.0000.0000.0000.000
16A292SER0-0.068-0.03910.478-0.020-0.0200.0000.0000.0000.000
17A293ILE00.0380.0465.201-0.010-0.0100.0000.0000.0000.000
18A294VAL0-0.003-0.0058.432-0.215-0.2150.0000.0000.0000.000
19A295VAL00.0080.0158.0910.0660.0660.0000.0000.0000.000
20A296THR0-0.041-0.03410.228-0.015-0.0150.0000.0000.0000.000
21A297MET0-0.062-0.01812.267-0.057-0.0570.0000.0000.0000.000
22A298GLU-1-0.916-0.93114.8180.2920.2920.0000.0000.0000.000
23A299GLY00.0170.00116.352-0.017-0.0170.0000.0000.0000.000
24A300THR0-0.068-0.05218.181-0.017-0.0170.0000.0000.0000.000
25A301ARG10.9710.99510.042-0.374-0.3740.0000.0000.0000.000
26A302PRO00.0300.00610.5060.0570.0570.0000.0000.0000.000
27A303ILE0-0.006-0.0209.004-0.002-0.0020.0000.0000.0000.000
28A304LEU00.0080.0124.279-0.173-0.078-0.001-0.009-0.0840.000
29A305ALA00.0250.0117.3620.2570.2570.0000.0000.0000.000
30A306GLU-1-0.803-0.9088.4821.1601.1600.0000.0000.0000.000
31A307VAL0-0.045-0.0239.934-0.081-0.0810.0000.0000.0000.000
32A308GLN0-0.024-0.03012.834-0.031-0.0310.0000.0000.0000.000
33A309ALA0-0.037-0.02915.536-0.052-0.0520.0000.0000.0000.000
34A310LEU00.0220.02318.9280.0200.0200.0000.0000.0000.000
35A311VAL0-0.025-0.02121.821-0.020-0.0200.0000.0000.0000.000
36A312THR00.0170.01424.8390.0070.0070.0000.0000.0000.000
37A313PRO00.0400.02728.144-0.005-0.0050.0000.0000.0000.000
38A314THR0-0.0310.00731.7440.0040.0040.0000.0000.0000.000
39A315MET0-0.047-0.02133.799-0.007-0.0070.0000.0000.0000.000
40A316PHE00.025-0.00336.975-0.007-0.0070.0000.0000.0000.000
41A317GLY0-0.022-0.00937.5320.0050.0050.0000.0000.0000.000
42A318ASN00.000-0.00535.478-0.004-0.0040.0000.0000.0000.000
43A319ALA00.0070.00731.9810.0050.0050.0000.0000.0000.000
44A320LYS10.8520.92929.976-0.119-0.1190.0000.0000.0000.000
45A321ARG10.8770.93127.526-0.108-0.1080.0000.0000.0000.000
46A322THR0-0.0170.00026.311-0.010-0.0100.0000.0000.0000.000
47A323THR0-0.029-0.01722.5980.0110.0110.0000.0000.0000.000
48A324THR00.008-0.00121.2310.0030.0030.0000.0000.0000.000
49A325GLY00.0200.01219.0760.0240.0240.0000.0000.0000.000
50A326LEU00.0240.01417.834-0.002-0.0020.0000.0000.0000.000
51A327ASP-1-0.850-0.93620.8900.1050.1050.0000.0000.0000.000
52A328PHE00.0140.01824.1950.0020.0020.0000.0000.0000.000
53A329ASN00.024-0.00326.499-0.004-0.0040.0000.0000.0000.000
54A330ARG10.9300.97421.305-0.083-0.0830.0000.0000.0000.000
55A331ALA00.0460.02623.085-0.007-0.0070.0000.0000.0000.000
56A332SER00.0040.00424.256-0.005-0.0050.0000.0000.0000.000
57A333LEU0-0.022-0.01527.047-0.008-0.0080.0000.0000.0000.000
58A334ILE0-0.0210.00420.791-0.009-0.0090.0000.0000.0000.000
59A335MET0-0.018-0.01124.779-0.003-0.0030.0000.0000.0000.000
60A336ALA00.0260.02426.401-0.006-0.0060.0000.0000.0000.000
61A337VAL0-0.035-0.01626.186-0.009-0.0090.0000.0000.0000.000
62A338LEU0-0.013-0.01322.069-0.011-0.0110.0000.0000.0000.000
63A339GLU-1-0.806-0.88726.4260.0560.0560.0000.0000.0000.000
64A340LYS10.9010.94729.853-0.022-0.0220.0000.0000.0000.000
65A341ARG10.8140.89828.354-0.004-0.0040.0000.0000.0000.000
66A342ALA0-0.047-0.03226.126-0.011-0.0110.0000.0000.0000.000
67A343GLY00.0020.01628.0740.0020.0020.0000.0000.0000.000
68A344LEU0-0.067-0.02623.6610.0040.0040.0000.0000.0000.000
69A345LEU00.0080.00928.447-0.001-0.0010.0000.0000.0000.000
70A346LEU00.0650.01225.4620.0100.0100.0000.0000.0000.000
71A347GLN0-0.060-0.02629.5660.0060.0060.0000.0000.0000.000
72A348ASN0-0.024-0.00432.8050.0030.0030.0000.0000.0000.000
73A349GLN00.0250.00828.3660.0090.0090.0000.0000.0000.000
74A350ASP-1-0.781-0.88029.0650.1240.1240.0000.0000.0000.000
75A351ALA0-0.019-0.02224.2850.0070.0070.0000.0000.0000.000
76A352TYR0-0.016-0.00923.223-0.011-0.0110.0000.0000.0000.000
77A353LEU00.012-0.00519.1720.0140.0140.0000.0000.0000.000
78A354LYS10.9490.97216.409-0.520-0.5200.0000.0000.0000.000
79A355SER0-0.013-0.03214.5480.0210.0210.0000.0000.0000.000
80A356ALA0-0.010-0.01311.388-0.027-0.0270.0000.0000.0000.000
81A357GLY00.0310.00213.1780.0230.0230.0000.0000.0000.000
82A358GLY0-0.035-0.00414.646-0.039-0.0390.0000.0000.0000.000
83A359VAL00.0160.01712.510-0.055-0.0550.0000.0000.0000.000
84A360LYS10.9411.00015.925-0.231-0.2310.0000.0000.0000.000
85A361LEU0-0.006-0.00113.840-0.011-0.0110.0000.0000.0000.000
86A362ASP-1-0.929-0.97617.7680.0900.0900.0000.0000.0000.000
87A363GLU-1-0.767-0.88316.257-0.053-0.0530.0000.0000.0000.000
88A364PRO00.020-0.00919.9540.0110.0110.0000.0000.0000.000
89A365ALA00.0070.00416.670-0.001-0.0010.0000.0000.0000.000
90A366ILE00.0470.01615.503-0.016-0.0160.0000.0000.0000.000
91A367ASP-1-0.800-0.89016.6030.0710.0710.0000.0000.0000.000
92A368LEU0-0.035-0.01215.8580.0220.0220.0000.0000.0000.000
93A369ALA00.0490.02912.7000.0150.0150.0000.0000.0000.000
94A370VAL00.0510.03514.4800.0550.0550.0000.0000.0000.000
95A371ALA0-0.009-0.00917.2140.0120.0120.0000.0000.0000.000
96A372VAL0-0.030-0.01714.3670.0030.0030.0000.0000.0000.000
97A373ALA00.0090.01714.7130.0140.0140.0000.0000.0000.000
98A374ILE00.0360.00416.2790.0050.0050.0000.0000.0000.000
99A375ALA0-0.023-0.01319.726-0.005-0.0050.0000.0000.0000.000
100A376SER0-0.038-0.00916.4950.0120.0120.0000.0000.0000.000
101A377SER00.0700.02918.540-0.004-0.0040.0000.0000.0000.000
102A378TYR0-0.009-0.01320.502-0.017-0.0170.0000.0000.0000.000
103A379LYS10.8140.90321.047-0.094-0.0940.0000.0000.0000.000
104A380ASP-1-0.856-0.91121.3100.2020.2020.0000.0000.0000.000
105A381LYS10.9020.95518.698-0.103-0.1030.0000.0000.0000.000
106A382PRO00.0420.03513.694-0.004-0.0040.0000.0000.0000.000
107A383THR0-0.017-0.02811.526-0.015-0.0150.0000.0000.0000.000
108A384ASN00.0520.0376.7910.4780.4780.0000.0000.0000.000
109A385PRO00.0360.0095.742-0.242-0.2420.0000.0000.0000.000
110A386GLN0-0.0090.0072.187-0.6880.9050.895-0.946-1.5420.008
111A387GLU-1-0.882-0.9643.971-2.436-2.3050.000-0.017-0.1140.000
112A388CYS0-0.036-0.0046.8170.3040.3040.0000.0000.0000.000
113A389PHE0-0.006-0.0158.727-0.166-0.1660.0000.0000.0000.000
114A390VAL00.009-0.00312.0740.0410.0410.0000.0000.0000.000
115A391GLY0-0.011-0.02614.525-0.031-0.0310.0000.0000.0000.000
116A392GLU-1-0.902-0.93318.257-0.005-0.0050.0000.0000.0000.000
117A393LEU0-0.058-0.02721.414-0.017-0.0170.0000.0000.0000.000
118A394GLY00.0210.01923.3630.0100.0100.0000.0000.0000.000
119A395LEU00.0560.01827.1300.0040.0040.0000.0000.0000.000
120A396THR0-0.113-0.09229.8380.0050.0050.0000.0000.0000.000
121A397GLY00.008-0.00126.629-0.004-0.0040.0000.0000.0000.000
122A398GLU-1-0.759-0.83425.750-0.044-0.0440.0000.0000.0000.000
123A399ILE0-0.003-0.00619.7290.0110.0110.0000.0000.0000.000
124A400ARG10.8640.92423.0690.0330.0330.0000.0000.0000.000
125A401ARG10.9330.95021.8110.1250.1250.0000.0000.0000.000
126A402VAL00.0480.04317.4240.0210.0210.0000.0000.0000.000
127A403ASN00.0310.01220.158-0.026-0.0260.0000.0000.0000.000
128A404ARG10.9280.93817.3510.1430.1430.0000.0000.0000.000
129A405ILE00.0460.02415.909-0.025-0.0250.0000.0000.0000.000
130A406GLU-1-0.822-0.92415.167-0.582-0.5820.0000.0000.0000.000
131A407GLN0-0.004-0.00113.776-0.052-0.0520.0000.0000.0000.000
132A408ARG10.7880.91611.2840.0860.0860.0000.0000.0000.000
133A409ILE00.0380.01710.071-0.169-0.1690.0000.0000.0000.000
134A410ASN00.0010.0089.788-0.365-0.3650.0000.0000.0000.000
135A411GLU-1-0.863-0.9446.927-0.960-0.9600.0000.0000.0000.000
136A412ALA00.000-0.0095.797-0.566-0.5660.0000.0000.0000.000
137A413ALA00.0170.0004.870-1.593-1.467-0.001-0.004-0.1210.000
138A414LYS10.8820.9516.255-0.003-0.0030.0000.0000.0000.000
139A415LEU0-0.094-0.0432.471-0.9200.3460.700-0.877-1.088-0.001
140A416GLY00.0510.0291.736-4.161-18.83227.319-7.447-5.201-0.058
141A417PHE0-0.040-0.0232.573-9.324-4.8533.678-3.137-5.012-0.029
142A418THR00.0130.0143.5621.3761.4390.0150.050-0.1280.000
143A419LYS10.8580.9416.2370.9610.9610.0000.0000.0000.000
144A420ILE00.0180.0088.2180.0910.0910.0000.0000.0000.000
145A421TYR0-0.047-0.02010.3720.0390.0390.0000.0000.0000.000
146A422VAL00.0300.01513.8400.0270.0270.0000.0000.0000.000
147A423PRO00.0140.00816.1040.0180.0180.0000.0000.0000.000
148A424LYS11.0181.00219.8940.1740.1740.0000.0000.0000.000
149A425ASN0-0.053-0.03221.592-0.015-0.0150.0000.0000.0000.000
150A426SER0-0.023-0.02519.6810.0220.0220.0000.0000.0000.000
151A427LEU00.0120.01517.276-0.015-0.0150.0000.0000.0000.000
152A428THR0-0.089-0.05920.973-0.002-0.0020.0000.0000.0000.000
153A429GLY00.0170.03224.4710.0080.0080.0000.0000.0000.000
154A430ILE0-0.0140.01318.9290.0020.0020.0000.0000.0000.000
155A431THR00.000-0.01019.1930.0150.0150.0000.0000.0000.000
156A432LEU0-0.024-0.00916.245-0.030-0.0300.0000.0000.0000.000
157A433PRO00.0160.01612.3910.0730.0730.0000.0000.0000.000
158A434LYS10.9330.94513.8550.5670.5670.0000.0000.0000.000
159A435GLU-1-0.895-0.9329.456-1.162-1.1620.0000.0000.0000.000
160A436ILE0-0.021-0.0046.883-0.253-0.2530.0000.0000.0000.000
161A437GLN0-0.0050.0009.8340.2680.2680.0000.0000.0000.000
162A438VAL00.0250.00211.490-0.020-0.0200.0000.0000.0000.000
163A439ILE0-0.047-0.01813.8740.0890.0890.0000.0000.0000.000
164A440GLY00.002-0.00215.9690.0210.0210.0000.0000.0000.000
165A441VAL0-0.037-0.01517.9960.0250.0250.0000.0000.0000.000
166A442THR0-0.034-0.02320.5600.0040.0040.0000.0000.0000.000
167A443THR00.0220.01823.5050.0180.0180.0000.0000.0000.000
168A444ILE00.0790.03020.791-0.010-0.0100.0000.0000.0000.000
169A445GLN00.026-0.00222.5150.0010.0010.0000.0000.0000.000
170A446GLU-1-0.893-0.95221.465-0.153-0.1530.0000.0000.0000.000
171A447VAL00.0350.01117.199-0.012-0.0120.0000.0000.0000.000
172A448LEU0-0.013-0.00618.7060.0080.0080.0000.0000.0000.000
173A449LYS10.9190.96220.3750.0530.0530.0000.0000.0000.000
174A450LYS10.8730.94817.3210.1730.1730.0000.0000.0000.000
175A451VAL00.0060.01414.136-0.013-0.0130.0000.0000.0000.000
176A452PHE0-0.048-0.00916.3010.0170.0170.0000.0000.0000.000