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

tag_button

FMODB ID: PKGV3

Calculation Name: 2LIS-A-Xray17

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2LIS

Chain ID: A

ChEMBL ID:

UniProt ID: P04552

Base Structure: X-ray

Registration Date: 2018-06-01

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 239
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1518607.937614
FMO2-HF: Nuclear repulsion 1455444.329781
FMO2-HF: Total energy -63163.607832
FMO2-MP2: Total energy -63343.932721


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:3:ACE)


Summations of interaction energy for fragment #1(A:3:ACE)
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.
0.7591.789-0.013-0.444-0.5730
Interaction energy analysis for fragmet #1(A:3:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.057 / q_NPA : 0.021
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].
3A5TYR00.0650.0433.8340.4711.501-0.013-0.444-0.5730.000
4A6VAL0-0.026-0.0116.861-0.067-0.0670.0000.0000.0000.000
5A7GLU-1-0.769-0.8049.928-0.458-0.4580.0000.0000.0000.000
6A8PRO00.0240.02613.2290.0400.0400.0000.0000.0000.000
7A9LYS10.9460.95915.8250.1790.1790.0000.0000.0000.000
8A10PHE00.0730.03119.1340.0140.0140.0000.0000.0000.000
9A11LEU00.0270.02922.4190.0140.0140.0000.0000.0000.000
10A12ASN00.0430.03921.498-0.013-0.0130.0000.0000.0000.000
11A13LYS10.8810.94320.9670.1240.1240.0000.0000.0000.000
12A14ALA00.0670.02522.8850.0040.0040.0000.0000.0000.000
13A15PHE00.0240.01425.3220.0040.0040.0000.0000.0000.000
14A16GLU-1-0.714-0.83225.311-0.099-0.0990.0000.0000.0000.000
15A17VAL0-0.024-0.01326.0420.0030.0030.0000.0000.0000.000
16A18ALA0-0.006-0.00228.5940.0030.0030.0000.0000.0000.000
17A19LEU0-0.009-0.00130.2740.0030.0030.0000.0000.0000.000
18A20LYS10.8010.88827.4320.0860.0860.0000.0000.0000.000
19A21VAL00.0040.00931.8650.0020.0020.0000.0000.0000.000
20A22GLN00.0410.02934.3400.0040.0040.0000.0000.0000.000
21A23ILE00.0370.02035.0200.0020.0020.0000.0000.0000.000
22A24ILE00.0200.01334.7110.0020.0020.0000.0000.0000.000
23A25ALA0-0.0110.01238.3250.0020.0020.0000.0000.0000.000
24A26GLY00.0060.00440.2400.0020.0020.0000.0000.0000.000
25A27PHE00.0190.00340.2950.0010.0010.0000.0000.0000.000
26A28ASP-1-0.699-0.81841.282-0.037-0.0370.0000.0000.0000.000
27A29ARG10.8560.91941.3360.0270.0270.0000.0000.0000.000
28A30GLY00.0630.04346.3620.0020.0020.0000.0000.0000.000
29A31LEU00.0260.02045.9040.0010.0010.0000.0000.0000.000
30A32VAL0-0.028-0.00647.3620.0010.0010.0000.0000.0000.000
31A33LYS10.9360.96749.9200.0210.0210.0000.0000.0000.000
32A34TRP00.008-0.00951.8500.0000.0000.0000.0000.0000.000
33A35LEU00.000-0.00449.6060.0010.0010.0000.0000.0000.000
34A36ARG10.9250.97353.6400.0170.0170.0000.0000.0000.000
35A37VAL00.0470.03655.9760.0010.0010.0000.0000.0000.000
36A38HIS00.0510.04655.8780.0010.0010.0000.0000.0000.000
37A39GLY00.0110.01055.013-0.001-0.0010.0000.0000.0000.000
38A40ARG10.9080.92955.8030.0170.0170.0000.0000.0000.000
39A41THR0-0.041-0.00858.4440.0000.0000.0000.0000.0000.000
40A42LEU00.0220.02352.902-0.001-0.0010.0000.0000.0000.000
41A43SER00.0430.00953.5990.0000.0000.0000.0000.0000.000
42A44THR00.018-0.01149.687-0.001-0.0010.0000.0000.0000.000
43A45VAL00.0400.01548.754-0.001-0.0010.0000.0000.0000.000
44A46GLN00.0150.01148.523-0.001-0.0010.0000.0000.0000.000
45A47LYS10.9130.96149.3170.0240.0240.0000.0000.0000.000
46A48LYS10.8600.93244.6590.0350.0350.0000.0000.0000.000
47A49ALA00.0420.02744.478-0.002-0.0020.0000.0000.0000.000
48A50LEU00.0140.01145.016-0.002-0.0020.0000.0000.0000.000
49A51TYR0-0.013-0.00142.457-0.001-0.0010.0000.0000.0000.000
50A52PHE00.0080.01238.381-0.002-0.0020.0000.0000.0000.000
51A53VAL00.001-0.00240.668-0.002-0.0020.0000.0000.0000.000
52A54ASN00.0110.02941.406-0.001-0.0010.0000.0000.0000.000
53A55ARG10.7910.87236.6860.0430.0430.0000.0000.0000.000
54A56ARG10.9030.94335.4670.0610.0610.0000.0000.0000.000
55A57TYR00.0080.00138.329-0.002-0.0020.0000.0000.0000.000
56A58MET00.0040.00333.2780.0000.0000.0000.0000.0000.000
57A59GLN0-0.028-0.01332.3080.0030.0030.0000.0000.0000.000
58A60THR0-0.026-0.01734.643-0.002-0.0020.0000.0000.0000.000
59A61HIS10.8950.96637.1390.0440.0440.0000.0000.0000.000
60A62TRP00.0140.01729.0700.0040.0040.0000.0000.0000.000
61A63ALA00.0560.02733.0240.0010.0010.0000.0000.0000.000
62A64ASN00.0250.00633.9520.0020.0020.0000.0000.0000.000
63A65TYR00.0310.00635.5350.0030.0030.0000.0000.0000.000
64A66MET00.0280.01829.3440.0030.0030.0000.0000.0000.000
65A67LEU0-0.0130.01933.4690.0020.0020.0000.0000.0000.000
66A68TRP0-0.027-0.00335.4880.0020.0020.0000.0000.0000.000
67A69ILE00.006-0.01532.4200.0030.0030.0000.0000.0000.000
68A70ASN00.0420.01930.1750.0030.0030.0000.0000.0000.000
69A71LYS10.9390.98833.3970.0290.0290.0000.0000.0000.000
70A72LYS10.8810.94836.7320.0240.0240.0000.0000.0000.000
71A73ILE00.000-0.01330.5880.0030.0030.0000.0000.0000.000
72A74ASP-1-0.843-0.90932.426-0.026-0.0260.0000.0000.0000.000
73A75ALA0-0.058-0.01434.6000.0030.0030.0000.0000.0000.000
74A76LEU0-0.091-0.03733.3650.0020.0020.0000.0000.0000.000
75A77GLY00.0570.04536.1270.0020.0020.0000.0000.0000.000
76A78ARG10.8550.95033.0270.0130.0130.0000.0000.0000.000
77A79THR00.0260.01426.773-0.004-0.0040.0000.0000.0000.000
78A80PRO0-0.0140.02328.1530.0010.0010.0000.0000.0000.000
79A81VAL00.0310.01128.3240.0000.0000.0000.0000.0000.000
80A82VAL00.0460.01028.126-0.003-0.0030.0000.0000.0000.000
81A83GLY00.0250.01329.855-0.002-0.0020.0000.0000.0000.000
82A84ASP-1-0.706-0.82432.532-0.016-0.0160.0000.0000.0000.000
83A85TYR00.0400.01228.496-0.002-0.0020.0000.0000.0000.000
84A86THR0-0.0250.00032.901-0.002-0.0020.0000.0000.0000.000
85A87ARG10.9210.96434.9110.0160.0160.0000.0000.0000.000
86A88LEU00.0320.01034.7030.0000.0000.0000.0000.0000.000
87A89GLY00.0530.02635.928-0.001-0.0010.0000.0000.0000.000
88A90ALA0-0.044-0.01736.7530.0000.0000.0000.0000.0000.000
89A91GLU-1-0.801-0.88839.852-0.022-0.0220.0000.0000.0000.000
90A92ILE00.008-0.00737.0950.0000.0000.0000.0000.0000.000
91A93GLY00.0150.00740.3460.0000.0000.0000.0000.0000.000
92A94ARG10.9450.99241.6320.0220.0220.0000.0000.0000.000
93A95ARG10.8860.94144.4240.0250.0250.0000.0000.0000.000
94A96ILE0-0.0330.00242.5710.0000.0000.0000.0000.0000.000
95A97ASP-1-0.819-0.89145.774-0.024-0.0240.0000.0000.0000.000
96A98MET0-0.005-0.01144.1410.0000.0000.0000.0000.0000.000
97A99ALA00.0100.00048.0700.0000.0000.0000.0000.0000.000
98A100TYR00.0370.04251.5430.0000.0000.0000.0000.0000.000
99A101PHE00.0130.00045.5590.0000.0000.0000.0000.0000.000
100A102TYR0-0.022-0.05745.6910.0000.0000.0000.0000.0000.000
101A103ASP-1-0.704-0.80651.561-0.022-0.0220.0000.0000.0000.000
102A104PHE00.0320.02451.7770.0000.0000.0000.0000.0000.000
103A105LEU0-0.035-0.01948.4430.0000.0000.0000.0000.0000.000
104A106LYS10.9080.96353.0680.0220.0220.0000.0000.0000.000
105A107ASP-1-0.887-0.95455.732-0.021-0.0210.0000.0000.0000.000
106A108LYS10.9000.94956.2140.0230.0230.0000.0000.0000.000
107A109ASN0-0.033-0.01156.687-0.001-0.0010.0000.0000.0000.000
108A110MET00.0200.01751.725-0.001-0.0010.0000.0000.0000.000
109A111ILE0-0.0190.00349.711-0.002-0.0020.0000.0000.0000.000
110A112PRO00.0060.01446.1600.0000.0000.0000.0000.0000.000
111A113LYS11.0051.01048.5500.0320.0320.0000.0000.0000.000
112A114TYR0-0.023-0.03542.669-0.002-0.0020.0000.0000.0000.000
113A115LEU00.0410.01242.6820.0010.0010.0000.0000.0000.000
114A116PRO00.0850.02639.951-0.001-0.0010.0000.0000.0000.000
115A117TYR00.0520.01736.775-0.001-0.0010.0000.0000.0000.000
116A118MET0-0.0160.02037.336-0.001-0.0010.0000.0000.0000.000
117A119GLU-1-0.770-0.84939.342-0.043-0.0430.0000.0000.0000.000
118A120GLU-1-0.899-0.93732.195-0.080-0.0800.0000.0000.0000.000
119A121ILE0-0.010-0.01734.348-0.001-0.0010.0000.0000.0000.000
120A122ASN0-0.030-0.04435.7810.0000.0000.0000.0000.0000.000
121A123ARG10.9010.96136.3860.0460.0460.0000.0000.0000.000
122A124MET0-0.0100.04630.832-0.001-0.0010.0000.0000.0000.000
123A125ARG10.9230.94226.4350.0730.0730.0000.0000.0000.000
124A126PRO00.0520.01931.782-0.005-0.0050.0000.0000.0000.000
125A127ALA00.001-0.00628.187-0.003-0.0030.0000.0000.0000.000
126A128ASP-1-0.796-0.87626.757-0.089-0.0890.0000.0000.0000.000
127A129VAL00.0170.02828.473-0.006-0.0060.0000.0000.0000.000
128A130PRO00.0170.01927.755-0.001-0.0010.0000.0000.0000.000
129A131VAL00.0250.04027.6580.0080.0080.0000.0000.0000.000
130A132LYS10.9560.97327.1970.1010.1010.0000.0000.0000.000
131A133TYR0-0.010-0.01925.0300.0110.0110.0000.0000.0000.000
132A134MET00.0300.00527.877-0.009-0.0090.0000.0000.0000.000
133A135NME00.0240.02930.0260.0030.0030.0000.0000.0000.000
134A2002HOH00.0190.01031.978-0.002-0.0020.0000.0000.0000.000
135A2003HOH0-0.025-0.03146.4810.0000.0000.0000.0000.0000.000
136A2006HOH00.0310.01743.0020.0000.0000.0000.0000.0000.000
137A2008HOH0-0.062-0.03845.8610.0000.0000.0000.0000.0000.000
138A2009HOH00.0040.00032.9800.0000.0000.0000.0000.0000.000
139A2010HOH0-0.007-0.01439.7330.0010.0010.0000.0000.0000.000
140A2011HOH0-0.033-0.02242.8650.0000.0000.0000.0000.0000.000
141A2012HOH0-0.030-0.02152.6450.0000.0000.0000.0000.0000.000
142A2013HOH00.0480.02723.7910.0010.0010.0000.0000.0000.000
143A2015HOH0-0.025-0.01928.322-0.001-0.0010.0000.0000.0000.000
144A2016HOH0-0.030-0.02625.6750.0010.0010.0000.0000.0000.000
145A2017HOH0-0.046-0.03132.3310.0000.0000.0000.0000.0000.000
146A2018HOH0-0.004-0.00549.494-0.001-0.0010.0000.0000.0000.000
147A2019HOH0-0.0020.00050.0830.0000.0000.0000.0000.0000.000
148A2021HOH0-0.071-0.04824.188-0.004-0.0040.0000.0000.0000.000
149A2023HOH0-0.064-0.04155.0000.0000.0000.0000.0000.0000.000
150A2024HOH0-0.027-0.03444.1390.0010.0010.0000.0000.0000.000
151A2026HOH00.0500.02732.6390.0020.0020.0000.0000.0000.000
152A2029HOH00.0340.01631.864-0.001-0.0010.0000.0000.0000.000
153A2030HOH0-0.030-0.02149.0430.0000.0000.0000.0000.0000.000
154A2031HOH0-0.032-0.02133.1140.0010.0010.0000.0000.0000.000
155A2032HOH00.008-0.00354.806-0.001-0.0010.0000.0000.0000.000
156A2033HOH00.0380.03048.211-0.001-0.0010.0000.0000.0000.000
157A2034HOH0-0.015-0.01140.9720.0000.0000.0000.0000.0000.000
158A2035HOH00.0410.02953.7540.0000.0000.0000.0000.0000.000
159A2036HOH0-0.011-0.01433.2530.0000.0000.0000.0000.0000.000
160A2037HOH0-0.006-0.01129.5870.0030.0030.0000.0000.0000.000
161A2039HOH0-0.035-0.02636.977-0.001-0.0010.0000.0000.0000.000
162A2040HOH0-0.007-0.00334.5900.0010.0010.0000.0000.0000.000
163A2042HOH00.0450.02527.140-0.002-0.0020.0000.0000.0000.000
164A2044HOH0-0.031-0.02849.5910.0000.0000.0000.0000.0000.000
165A2045HOH0-0.004-0.00746.0490.0000.0000.0000.0000.0000.000
166A2046HOH0-0.012-0.00643.8920.0000.0000.0000.0000.0000.000
167A2047HOH0-0.007-0.01548.7180.0000.0000.0000.0000.0000.000
168A2048HOH0-0.043-0.02140.0240.0010.0010.0000.0000.0000.000
169A2049HOH0-0.035-0.02539.0510.0000.0000.0000.0000.0000.000
170A2051HOH0-0.017-0.01245.1460.0000.0000.0000.0000.0000.000
171A2052HOH0-0.065-0.05531.3830.0000.0000.0000.0000.0000.000
172A2054HOH0-0.004-0.00551.2460.0000.0000.0000.0000.0000.000
173A2059HOH0-0.009-0.01456.7590.0000.0000.0000.0000.0000.000
174A2060HOH0-0.003-0.00339.385-0.001-0.0010.0000.0000.0000.000
175A2061HOH00.0390.03356.6650.0000.0000.0000.0000.0000.000
176A2062HOH0-0.012-0.00441.8780.0010.0010.0000.0000.0000.000
177A2064HOH0-0.012-0.01432.8790.0000.0000.0000.0000.0000.000
178A2065HOH00.009-0.00525.9410.0030.0030.0000.0000.0000.000
179A2066HOH0-0.054-0.03457.8300.0000.0000.0000.0000.0000.000
180A2068HOH0-0.057-0.06357.3650.0000.0000.0000.0000.0000.000
181A2069HOH0-0.022-0.02049.3500.0000.0000.0000.0000.0000.000
182A2072HOH0-0.029-0.01925.4160.0010.0010.0000.0000.0000.000
183A2075HOH0-0.004-0.00924.176-0.001-0.0010.0000.0000.0000.000
184A2077HOH00.0410.0497.779-0.053-0.0530.0000.0000.0000.000
185A2078HOH00.0140.00948.2150.0010.0010.0000.0000.0000.000
186A2084HOH00.004-0.00241.1230.0000.0000.0000.0000.0000.000
187A2086HOH0-0.002-0.00361.1940.0000.0000.0000.0000.0000.000
188A2087HOH0-0.059-0.03636.0550.0010.0010.0000.0000.0000.000
189A2089HOH0-0.025-0.02247.8080.0000.0000.0000.0000.0000.000
190A2091HOH0-0.017-0.0228.8700.0390.0390.0000.0000.0000.000
191A2093HOH0-0.041-0.03536.3110.0010.0010.0000.0000.0000.000
192A2095HOH0-0.029-0.01539.5870.0010.0010.0000.0000.0000.000
193A2099HOH0-0.024-0.01556.6460.0000.0000.0000.0000.0000.000
194A2104HOH00.0420.02441.1350.0000.0000.0000.0000.0000.000
195A2105HOH0-0.067-0.04841.7350.0000.0000.0000.0000.0000.000
196A2106HOH0-0.009-0.00122.857-0.005-0.0050.0000.0000.0000.000
197A2107HOH0-0.0010.01148.1050.0010.0010.0000.0000.0000.000
198A2108HOH00.0290.02030.610-0.001-0.0010.0000.0000.0000.000
199A2109HOH0-0.028-0.02429.446-0.002-0.0020.0000.0000.0000.000
200A2110HOH00.013-0.01049.7170.0000.0000.0000.0000.0000.000
201A2111HOH0-0.069-0.04934.387-0.001-0.0010.0000.0000.0000.000
202A2115HOH0-0.016-0.00910.3750.0110.0110.0000.0000.0000.000
203A2116HOH0-0.103-0.1089.4170.0040.0040.0000.0000.0000.000
204A2117HOH00.0460.02411.0930.0370.0370.0000.0000.0000.000
205A2118HOH0-0.021-0.01320.8200.0010.0010.0000.0000.0000.000
206A2122HOH00.0150.00533.867-0.001-0.0010.0000.0000.0000.000
207A2128HOH0-0.001-0.00152.1860.0000.0000.0000.0000.0000.000
208A2130HOH00.001-0.00343.5110.0010.0010.0000.0000.0000.000
209A2131HOH00.0880.09246.604-0.001-0.0010.0000.0000.0000.000
210A2132HOH00.0270.02335.0200.0010.0010.0000.0000.0000.000
211A2133HOH0-0.031-0.02338.2460.0000.0000.0000.0000.0000.000
212A2134HOH0-0.034-0.02830.1270.0000.0000.0000.0000.0000.000
213A2135HOH0-0.037-0.02736.8550.0000.0000.0000.0000.0000.000
214A2138HOH00.002-0.00860.8450.0000.0000.0000.0000.0000.000
215A2140HOH0-0.033-0.02514.6240.0190.0190.0000.0000.0000.000
216A2141HOH00.0010.00018.5860.0040.0040.0000.0000.0000.000
217A2143HOH0-0.0030.00320.9960.0050.0050.0000.0000.0000.000
218A2146HOH0-0.031-0.03213.6180.0160.0160.0000.0000.0000.000
219A2154HOH0-0.033-0.01925.264-0.001-0.0010.0000.0000.0000.000
220A2155HOH00.0010.01639.4990.0000.0000.0000.0000.0000.000
221A2160HOH00.0270.01148.1290.0000.0000.0000.0000.0000.000
222A2161HOH00.0080.01759.7510.0000.0000.0000.0000.0000.000
223A2162HOH0-0.086-0.06858.6960.0000.0000.0000.0000.0000.000
224A2165HOH00.0080.02756.3710.0000.0000.0000.0000.0000.000
225A2167HOH0-0.044-0.06645.227-0.001-0.0010.0000.0000.0000.000
226A2169HOH00.0180.00831.2440.0020.0020.0000.0000.0000.000
227A2172HOH00.0150.00539.398-0.001-0.0010.0000.0000.0000.000
228A2175HOH0-0.047-0.03452.1220.0000.0000.0000.0000.0000.000
229A2184HOH0-0.031-0.02639.6610.0000.0000.0000.0000.0000.000
230A2190HOH0-0.026-0.02124.5870.0010.0010.0000.0000.0000.000
231A2206HOH0-0.014-0.01727.995-0.003-0.0030.0000.0000.0000.000
232A2240HOH0-0.038-0.02360.0920.0000.0000.0000.0000.0000.000
233A2241HOH0-0.003-0.01534.4720.0010.0010.0000.0000.0000.000
234A2245HOH0-0.020-0.01642.3670.0000.0000.0000.0000.0000.000
235A2248HOH0-0.002-0.00457.2100.0000.0000.0000.0000.0000.000
236A2259HOH0-0.028-0.02013.8160.0240.0240.0000.0000.0000.000
237A2268HOH00.0090.01357.2130.0000.0000.0000.0000.0000.000
238A2271HOH00.0200.01262.5920.0000.0000.0000.0000.0000.000
239A2278HOH0-0.056-0.08434.8230.0000.0000.0000.0000.0000.000