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

tag_button

FMODB ID: 3995L

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 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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1793031.194419
FMO2-HF: Nuclear repulsion 1726780.378573
FMO2-HF: Total energy -66250.815845
FMO2-MP2: Total energy -66445.947936


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.
-25.136-26.00833.239-14.128-18.239-0.066
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 : -0.038 / q_NPA : -0.016
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].
3A279VAL00.0830.0343.774-2.726-0.282-0.017-1.126-1.3020.003
4A280PHE0-0.029-0.0262.642-2.139-1.0240.307-0.484-0.9370.001
5A281LEU0-0.041-0.0352.586-1.649-0.7281.321-0.733-1.5090.009
6A282GLU-1-0.968-0.9776.1711.0481.0480.0000.0000.0000.000
7A283GLU-1-0.949-0.9638.2370.9090.9090.0000.0000.0000.000
8A284ARG10.7210.8728.713-1.376-1.3760.0000.0000.0000.000
9A285LEU00.0250.00210.525-0.070-0.0700.0000.0000.0000.000
10A286ASP-1-0.894-0.95413.2440.4740.4740.0000.0000.0000.000
11A287GLY0-0.009-0.00213.812-0.060-0.0600.0000.0000.0000.000
12A288ALA0-0.022-0.00313.885-0.058-0.0580.0000.0000.0000.000
13A289THR0-0.081-0.04514.4000.0640.0640.0000.0000.0000.000
14A290GLY00.0100.00516.6180.0130.0130.0000.0000.0000.000
15A291SER00.0060.00611.6110.0400.0400.0000.0000.0000.000
16A292SER0-0.074-0.03510.521-0.017-0.0170.0000.0000.0000.000
17A293ILE00.0490.0405.169-0.023-0.0230.0000.0000.0000.000
18A294VAL00.0000.0018.437-0.244-0.2440.0000.0000.0000.000
19A295VAL00.0100.0158.1260.1070.1070.0000.0000.0000.000
20A296THR0-0.045-0.05210.306-0.048-0.0480.0000.0000.0000.000
21A297MET0-0.047-0.00412.368-0.041-0.0410.0000.0000.0000.000
22A298GLU-1-0.845-0.89514.8260.3570.3570.0000.0000.0000.000
23A299GLY00.0260.00016.481-0.020-0.0200.0000.0000.0000.000
24A300THR0-0.052-0.03818.249-0.013-0.0130.0000.0000.0000.000
25A301ARG10.9210.96810.513-0.484-0.4840.0000.0000.0000.000
26A302PRO00.0120.00110.5470.0540.0540.0000.0000.0000.000
27A303ILE0-0.014-0.0239.1560.0100.0100.0000.0000.0000.000
28A304LEU0-0.0170.0054.242-0.233-0.131-0.001-0.010-0.0910.000
29A305ALA00.0270.0097.5130.2390.2390.0000.0000.0000.000
30A306GLU-1-0.752-0.8588.4211.2111.2110.0000.0000.0000.000
31A307VAL0-0.040-0.0209.919-0.098-0.0980.0000.0000.0000.000
32A308GLN00.001-0.02012.561-0.043-0.0430.0000.0000.0000.000
33A309ALA0-0.033-0.02615.531-0.054-0.0540.0000.0000.0000.000
34A310LEU00.0300.02618.9280.0190.0190.0000.0000.0000.000
35A311VAL0-0.015-0.01921.823-0.021-0.0210.0000.0000.0000.000
36A312THR00.0210.01924.8440.0060.0060.0000.0000.0000.000
37A313PRO00.0430.02628.150-0.004-0.0040.0000.0000.0000.000
38A314THR0-0.0220.00131.7500.0050.0050.0000.0000.0000.000
39A315MET0-0.039-0.01433.801-0.008-0.0080.0000.0000.0000.000
40A316PHE00.0300.00136.976-0.007-0.0070.0000.0000.0000.000
41A317GLY0-0.016-0.00437.5280.0050.0050.0000.0000.0000.000
42A318ASN00.0050.00235.565-0.004-0.0040.0000.0000.0000.000
43A319ALA00.0160.01732.0470.0060.0060.0000.0000.0000.000
44A320LYS10.7880.87029.908-0.132-0.1320.0000.0000.0000.000
45A321ARG10.8800.93427.517-0.126-0.1260.0000.0000.0000.000
46A322THR0-0.0060.00626.355-0.011-0.0110.0000.0000.0000.000
47A323THR0-0.034-0.02222.5460.0110.0110.0000.0000.0000.000
48A324THR00.006-0.00121.2940.0010.0010.0000.0000.0000.000
49A325GLY00.0150.00919.0590.0270.0270.0000.0000.0000.000
50A326LEU00.0240.01517.8280.0030.0030.0000.0000.0000.000
51A327ASP-1-0.768-0.88020.8710.1270.1270.0000.0000.0000.000
52A328PHE00.0250.02424.1840.0020.0020.0000.0000.0000.000
53A329ASN0-0.021-0.03526.486-0.009-0.0090.0000.0000.0000.000
54A330ARG10.8720.93821.136-0.126-0.1260.0000.0000.0000.000
55A331ALA00.0310.01923.061-0.006-0.0060.0000.0000.0000.000
56A332SER0-0.005-0.00124.253-0.006-0.0060.0000.0000.0000.000
57A333LEU0-0.014-0.01027.149-0.009-0.0090.0000.0000.0000.000
58A334ILE0-0.0210.00320.808-0.010-0.0100.0000.0000.0000.000
59A335MET0-0.016-0.01024.826-0.003-0.0030.0000.0000.0000.000
60A336ALA00.0210.01926.408-0.007-0.0070.0000.0000.0000.000
61A337VAL0-0.037-0.01726.343-0.011-0.0110.0000.0000.0000.000
62A338LEU0-0.005-0.00922.068-0.012-0.0120.0000.0000.0000.000
63A339GLU-1-0.782-0.86526.4420.0710.0710.0000.0000.0000.000
64A340LYS10.9080.95429.869-0.037-0.0370.0000.0000.0000.000
65A341ARG10.8290.90428.329-0.023-0.0230.0000.0000.0000.000
66A342ALA0-0.037-0.03126.122-0.011-0.0110.0000.0000.0000.000
67A343GLY00.0030.01828.0980.0020.0020.0000.0000.0000.000
68A344LEU0-0.059-0.01423.7710.0030.0030.0000.0000.0000.000
69A345LEU0-0.006-0.00228.4670.0000.0000.0000.0000.0000.000
70A346LEU00.048-0.00325.5130.0100.0100.0000.0000.0000.000
71A347GLN0-0.059-0.03929.5770.0070.0070.0000.0000.0000.000
72A348ASN0-0.040-0.01132.8130.0010.0010.0000.0000.0000.000
73A349GLN00.0140.00728.3320.0050.0050.0000.0000.0000.000
74A350ASP-1-0.780-0.86229.0280.1400.1400.0000.0000.0000.000
75A351ALA0-0.010-0.01824.3520.0080.0080.0000.0000.0000.000
76A352TYR0-0.016-0.00823.293-0.010-0.0100.0000.0000.0000.000
77A353LEU00.010-0.00419.5600.0160.0160.0000.0000.0000.000
78A354LYS10.9030.94116.150-0.589-0.5890.0000.0000.0000.000
79A355SER0-0.006-0.01314.6290.0200.0200.0000.0000.0000.000
80A356ALA0-0.018-0.01611.364-0.034-0.0340.0000.0000.0000.000
81A357GLY00.0410.00813.1460.0370.0370.0000.0000.0000.000
82A358GLY0-0.032-0.00314.610-0.044-0.0440.0000.0000.0000.000
83A359VAL00.0080.01212.566-0.060-0.0600.0000.0000.0000.000
84A360LYS10.9350.98415.891-0.279-0.2790.0000.0000.0000.000
85A361LEU0-0.0040.00013.732-0.006-0.0060.0000.0000.0000.000
86A362ASP-1-0.892-0.96217.7460.1200.1200.0000.0000.0000.000
87A363GLU-1-0.724-0.82016.2740.0090.0090.0000.0000.0000.000
88A364PRO00.011-0.01019.9450.0150.0150.0000.0000.0000.000
89A365ALA00.0040.00816.786-0.001-0.0010.0000.0000.0000.000
90A366ILE00.0390.01515.509-0.010-0.0100.0000.0000.0000.000
91A367ASP-1-0.800-0.89616.6000.1120.1120.0000.0000.0000.000
92A368LEU0-0.026-0.00516.2060.0200.0200.0000.0000.0000.000
93A369ALA00.0590.03212.7230.0140.0140.0000.0000.0000.000
94A370VAL00.0360.03214.4890.0530.0530.0000.0000.0000.000
95A371ALA0-0.009-0.01017.2180.0080.0080.0000.0000.0000.000
96A372VAL0-0.028-0.01614.436-0.001-0.0010.0000.0000.0000.000
97A373ALA00.0130.01914.7120.0110.0110.0000.0000.0000.000
98A374ILE00.0350.00616.2900.0000.0000.0000.0000.0000.000
99A375ALA0-0.028-0.02019.731-0.009-0.0090.0000.0000.0000.000
100A376SER0-0.036-0.02816.5330.0120.0120.0000.0000.0000.000
101A377SER00.0610.02618.561-0.007-0.0070.0000.0000.0000.000
102A378TYR0-0.019-0.01720.516-0.021-0.0210.0000.0000.0000.000
103A379LYS10.8470.92021.139-0.115-0.1150.0000.0000.0000.000
104A380ASP-1-0.869-0.91721.2470.2290.2290.0000.0000.0000.000
105A381LYS10.8990.95518.678-0.141-0.1410.0000.0000.0000.000
106A382PRO00.0460.05213.714-0.002-0.0020.0000.0000.0000.000
107A383THR0-0.029-0.03011.486-0.013-0.0130.0000.0000.0000.000
108A384ASN00.022-0.0017.2150.4430.4430.0000.0000.0000.000
109A385PRO00.0360.0165.849-0.193-0.1930.0000.0000.0000.000
110A386GLN00.0030.0192.832-0.7750.8740.151-0.753-1.0470.006
111A387GLU-1-0.816-0.8994.003-2.567-2.4240.000-0.017-0.1250.000
112A388CYS0-0.043-0.0056.8250.3070.3070.0000.0000.0000.000
113A389PHE00.004-0.0098.751-0.196-0.1960.0000.0000.0000.000
114A390VAL00.005-0.00611.9860.0510.0510.0000.0000.0000.000
115A391GLY0-0.013-0.02614.536-0.039-0.0390.0000.0000.0000.000
116A392GLU-1-0.839-0.89018.2670.0200.0200.0000.0000.0000.000
117A393LEU0-0.048-0.01921.420-0.019-0.0190.0000.0000.0000.000
118A394GLY00.0230.01523.3730.0100.0100.0000.0000.0000.000
119A395LEU00.0550.01727.1400.0040.0040.0000.0000.0000.000
120A396THR0-0.094-0.06629.8490.0050.0050.0000.0000.0000.000
121A397GLY0-0.0080.00026.645-0.005-0.0050.0000.0000.0000.000
122A398GLU-1-0.774-0.85825.771-0.025-0.0250.0000.0000.0000.000
123A399ILE0-0.004-0.00619.6440.0130.0130.0000.0000.0000.000
124A400ARG10.7960.87523.0060.0040.0040.0000.0000.0000.000
125A401ARG10.9290.95021.7430.1150.1150.0000.0000.0000.000
126A402VAL00.0490.03817.4070.0210.0210.0000.0000.0000.000
127A403ASN00.0190.00819.743-0.032-0.0320.0000.0000.0000.000
128A404ARG10.9220.92717.4840.1230.1230.0000.0000.0000.000
129A405ILE00.0580.02515.371-0.019-0.0190.0000.0000.0000.000
130A406GLU-1-0.819-0.92115.106-0.576-0.5760.0000.0000.0000.000
131A407GLN00.0120.02413.629-0.065-0.0650.0000.0000.0000.000
132A408ARG10.7390.85511.2740.0050.0050.0000.0000.0000.000
133A409ILE00.0500.02110.033-0.166-0.1660.0000.0000.0000.000
134A410ASN0-0.028-0.0159.725-0.343-0.3430.0000.0000.0000.000
135A411GLU-1-0.809-0.8916.835-0.821-0.8210.0000.0000.0000.000
136A412ALA0-0.006-0.0095.746-0.532-0.5320.0000.0000.0000.000
137A413ALA00.007-0.0024.810-1.728-1.588-0.001-0.005-0.1340.000
138A414LYS10.8130.8896.2470.0020.0020.0000.0000.0000.000
139A415LEU0-0.062-0.0282.293-0.7300.2410.928-0.824-1.0740.000
140A416GLY00.0480.0211.878-3.832-16.21223.562-5.916-5.267-0.053
141A417PHE0-0.036-0.0202.300-10.377-6.4066.972-4.322-6.621-0.032
142A418THR00.0250.0193.5451.5141.5660.0170.062-0.1320.000
143A419LYS10.8110.8966.1170.8940.8940.0000.0000.0000.000
144A420ILE00.0130.0078.1260.1130.1130.0000.0000.0000.000
145A421TYR0-0.064-0.02910.3110.0150.0150.0000.0000.0000.000
146A422VAL00.0300.01813.6640.0360.0360.0000.0000.0000.000
147A423PRO00.0310.01716.0260.0160.0160.0000.0000.0000.000
148A424LYS10.9970.99019.8160.1520.1520.0000.0000.0000.000
149A425ASN0-0.043-0.02621.525-0.019-0.0190.0000.0000.0000.000
150A426SER0-0.023-0.02119.6170.0210.0210.0000.0000.0000.000
151A427LEU00.0170.01617.094-0.016-0.0160.0000.0000.0000.000
152A428THR0-0.076-0.03620.907-0.005-0.0050.0000.0000.0000.000
153A429GLY00.0130.01424.4030.0080.0080.0000.0000.0000.000
154A430ILE0-0.0210.00618.7510.0010.0010.0000.0000.0000.000
155A431THR00.004-0.00219.2800.0120.0120.0000.0000.0000.000
156A432LEU00.0020.00616.271-0.032-0.0320.0000.0000.0000.000
157A433PRO00.0300.02312.3440.0760.0760.0000.0000.0000.000
158A434LYS10.8930.92213.8390.5980.5980.0000.0000.0000.000
159A435GLU-1-0.914-0.9459.624-1.190-1.1900.0000.0000.0000.000
160A436ILE0-0.0110.0046.821-0.270-0.2700.0000.0000.0000.000
161A437GLN0-0.004-0.0059.7940.3080.3080.0000.0000.0000.000
162A438VAL00.0260.00511.361-0.012-0.0120.0000.0000.0000.000
163A439ILE0-0.040-0.01013.6980.0920.0920.0000.0000.0000.000
164A440GLY00.005-0.00215.8610.0260.0260.0000.0000.0000.000
165A441VAL0-0.047-0.02417.9570.0230.0230.0000.0000.0000.000
166A442THR0-0.055-0.04720.4980.0020.0020.0000.0000.0000.000
167A443THR00.0200.01223.4450.0180.0180.0000.0000.0000.000
168A444ILE00.0750.03320.835-0.008-0.0080.0000.0000.0000.000
169A445GLN00.025-0.00322.4920.0030.0030.0000.0000.0000.000
170A446GLU-1-0.806-0.87721.639-0.138-0.1380.0000.0000.0000.000
171A447VAL00.0320.01217.124-0.013-0.0130.0000.0000.0000.000
172A448LEU0-0.007-0.00618.6860.0090.0090.0000.0000.0000.000
173A449LYS10.9150.96520.3790.0390.0390.0000.0000.0000.000
174A450LYS10.8260.90317.1310.1620.1620.0000.0000.0000.000
175A451VAL0-0.0190.00714.207-0.012-0.0120.0000.0000.0000.000
176A452PHE0-0.023-0.00316.3260.0180.0180.0000.0000.0000.000