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: PJ2J9

Calculation Name: 4LX3-A-Xray40

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LX3

Chain ID: A

ChEMBL ID:

UniProt ID: B2J066

Base Structure: X-ray

Registration Date: 2019-02-15

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 216
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1015885.228984
FMO2-HF: Nuclear repulsion 964806.885704
FMO2-HF: Total energy -51078.343281
FMO2-MP2: Total energy -51221.025774


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:-2:ACE)


Summations of interaction energy for fragment #1(A:-2: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.
24.891-6.87230.7324.792-3.76-0.026
Interaction energy analysis for fragmet #1(A:-2:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : -0.087
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].
3A0HIS00.1320.0603.6830.2500.800-0.0150.048-0.582-0.002
4A1CYS0-0.155-0.0387.360-0.002-0.0020.0000.0000.0000.000
5A2LEU00.0460.0379.6860.0170.0170.0000.0000.0000.000
6A3SER00.0320.02513.2280.0350.0350.0000.0000.0000.000
7A4TYR00.0420.01115.5210.0030.0030.0000.0000.0000.000
8A5GLU-1-0.760-0.88117.182-0.061-0.0610.0000.0000.0000.000
9A6THR00.0060.03517.327-0.002-0.0020.0000.0000.0000.000
10A7GLU-1-0.909-0.92919.519-0.056-0.0560.0000.0000.0000.000
11A8ILE00.0070.00617.117-0.010-0.0100.0000.0000.0000.000
12A9LEU00.0180.01721.6870.0120.0120.0000.0000.0000.000
13A10THR00.014-0.00923.202-0.001-0.0010.0000.0000.0000.000
14A11VAL0-0.0010.00025.7700.0020.0020.0000.0000.0000.000
15A12GLU-1-0.758-0.84727.036-0.028-0.0280.0000.0000.0000.000
16A13TYR0-0.054-0.04925.9610.0050.0050.0000.0000.0000.000
17A14GLY00.0810.06028.9740.0010.0010.0000.0000.0000.000
18A15LEU00.0110.00325.411-0.002-0.0020.0000.0000.0000.000
19A16LEU00.0010.00723.0360.0090.0090.0000.0000.0000.000
20A17PRO00.0220.02121.117-0.009-0.0090.0000.0000.0000.000
21A18ILE00.0600.02213.9340.0130.0130.0000.0000.0000.000
22A19GLY00.0300.00516.3870.0140.0140.0000.0000.0000.000
23A20LYS10.8630.93617.4200.0310.0310.0000.0000.0000.000
24A21ILE00.0380.01517.7270.0130.0130.0000.0000.0000.000
25A22VAL00.001-0.00212.7910.0140.0140.0000.0000.0000.000
26A23GLU-1-0.904-0.94716.1280.0910.0910.0000.0000.0000.000
27A24LYS10.8220.89417.689-0.010-0.0100.0000.0000.0000.000
28A25ARG10.8430.91414.250-0.105-0.1050.0000.0000.0000.000
29A26ILE00.0030.02519.1890.0010.0010.0000.0000.0000.000
30A27GLU-1-0.809-0.88821.1570.0080.0080.0000.0000.0000.000
31A28CYS0-0.054-0.01921.779-0.005-0.0050.0000.0000.0000.000
32A29THR0-0.011-0.01023.109-0.002-0.0020.0000.0000.0000.000
33A30VAL0-0.019-0.00120.2700.0000.0000.0000.0000.0000.000
34A31TYR0-0.027-0.05023.5590.0080.0080.0000.0000.0000.000
35A32SER0-0.031-0.01321.587-0.013-0.0130.0000.0000.0000.000
36A33VAL00.0400.02423.0930.0110.0110.0000.0000.0000.000
37A34ASP-1-0.787-0.88223.616-0.092-0.0920.0000.0000.0000.000
38A35ASN00.016-0.01023.289-0.011-0.0110.0000.0000.0000.000
39A36ASN0-0.0230.02226.3380.0000.0000.0000.0000.0000.000
40A37GLY00.0570.03928.2870.0050.0050.0000.0000.0000.000
41A38ASN0-0.074-0.01729.4270.0070.0070.0000.0000.0000.000
42A39ILE00.0380.01827.360-0.007-0.0070.0000.0000.0000.000
43A40TYR0-0.092-0.03422.6430.0070.0070.0000.0000.0000.000
44A41THR00.0550.03826.426-0.005-0.0050.0000.0000.0000.000
45A42GLN00.0260.00921.204-0.011-0.0110.0000.0000.0000.000
46A43PRO00.0520.04022.393-0.005-0.0050.0000.0000.0000.000
47A44VAL00.0240.03617.166-0.013-0.0130.0000.0000.0000.000
48A45ALA00.0200.03016.9650.0150.0150.0000.0000.0000.000
49A46GLN00.0130.00711.5700.0600.0600.0000.0000.0000.000
50A47TRP0-0.0150.01013.694-0.028-0.0280.0000.0000.0000.000
51A48HIS0-0.070-0.0618.2420.1220.1220.0000.0000.0000.000
52A49ASP-1-0.717-0.81110.1760.1000.1000.0000.0000.0000.000
53A50ARG10.8300.8914.8630.1990.1990.0000.0000.0000.000
54A51GLY00.0430.0326.4370.0470.0470.0000.0000.0000.000
55A52GLU-1-0.882-0.9038.919-0.033-0.0330.0000.0000.0000.000
56A53GLN0-0.013-0.0075.051-0.069-0.0690.0000.0000.0000.000
57A54GLU-1-0.793-0.85110.229-0.161-0.1610.0000.0000.0000.000
58A55VAL0-0.029-0.01312.622-0.063-0.0630.0000.0000.0000.000
59A56PHE00.0150.01615.0940.0280.0280.0000.0000.0000.000
60A57GLU-1-0.769-0.83618.026-0.101-0.1010.0000.0000.0000.000
61A58TYR0-0.030-0.02817.360-0.003-0.0030.0000.0000.0000.000
62A59CYS00.007-0.00422.5650.0040.0040.0000.0000.0000.000
63A60LEU00.0040.01624.3490.0000.0000.0000.0000.0000.000
64A61GLU-1-0.801-0.88627.988-0.068-0.0680.0000.0000.0000.000
65A62ASP-1-0.765-0.85730.006-0.079-0.0790.0000.0000.0000.000
66A63GLY0-0.012-0.00730.7200.0050.0050.0000.0000.0000.000
67A64SER0-0.036-0.01026.831-0.003-0.0030.0000.0000.0000.000
68A65LEU00.0170.01223.835-0.003-0.0030.0000.0000.0000.000
69A66ILE00.0250.02318.389-0.002-0.0020.0000.0000.0000.000
70A67ARG10.8490.93717.8390.0890.0890.0000.0000.0000.000
71A68ALA0-0.002-0.01214.079-0.003-0.0030.0000.0000.0000.000
72A69THR00.0300.0149.170-0.035-0.0350.0000.0000.0000.000
73A70LYS10.9340.97112.2920.2400.2400.0000.0000.0000.000
74A71ASP-1-0.735-0.7979.890-0.531-0.5310.0000.0000.0000.000
75A72HIS0-0.100-0.06710.368-0.033-0.0330.0000.0000.0000.000
76A73LYS10.8890.94512.0280.5650.5650.0000.0000.0000.000
77A74PHE00.0380.01414.4830.0080.0080.0000.0000.0000.000
78A75MET0-0.0060.00417.9560.0020.0020.0000.0000.0000.000
79A76THR00.030-0.00720.9710.0070.0070.0000.0000.0000.000
80A77VAL00.0440.02323.9010.0030.0030.0000.0000.0000.000
81A78ASP-1-0.889-0.92825.855-0.127-0.1270.0000.0000.0000.000
82A79GLY00.0070.00424.5680.0030.0030.0000.0000.0000.000
83A80GLN00.0320.04521.375-0.022-0.0220.0000.0000.0000.000
84A81MET0-0.002-0.00316.568-0.012-0.0120.0000.0000.0000.000
85A82LEU0-0.026-0.01517.099-0.030-0.0300.0000.0000.0000.000
86A83PRO0-0.0070.00013.808-0.014-0.0140.0000.0000.0000.000
87A84ILE00.0360.02215.3200.0420.0420.0000.0000.0000.000
88A85ASP-1-0.735-0.83316.387-0.188-0.1880.0000.0000.0000.000
89A86GLU-1-0.851-0.91517.773-0.209-0.2090.0000.0000.0000.000
90A87ILE0-0.042-0.02519.6040.0250.0250.0000.0000.0000.000
91A88PHE00.0210.02021.0940.0210.0210.0000.0000.0000.000
92A89GLU-1-0.848-0.90521.107-0.155-0.1550.0000.0000.0000.000
93A90ARG10.7980.89922.5470.1710.1710.0000.0000.0000.000
94A91GLU-1-0.999-0.98325.326-0.085-0.0850.0000.0000.0000.000
95A92LEU0-0.072-0.02122.7500.0060.0060.0000.0000.0000.000
96A93ASP-1-0.755-0.85526.187-0.098-0.0980.0000.0000.0000.000
97A94LEU0-0.029-0.01421.183-0.008-0.0080.0000.0000.0000.000
98A95MET0-0.069-0.02424.2900.0130.0130.0000.0000.0000.000
99A96ARG10.8320.91225.2690.0910.0910.0000.0000.0000.000
100A97VAL00.0370.02826.4890.0060.0060.0000.0000.0000.000
101A98ASP-1-0.895-0.95028.926-0.066-0.0660.0000.0000.0000.000
102A99ASN0-0.068-0.03327.2610.0040.0040.0000.0000.0000.000
103A100NME0-0.0100.00231.5320.0030.0030.0000.0000.0000.000
104A201HOH0-0.059-0.03922.573-0.005-0.0050.0000.0000.0000.000
105A202HOH00.014-0.00322.1920.0000.0000.0000.0000.0000.000
106A203HOH0-0.043-0.02726.182-0.001-0.0010.0000.0000.0000.000
107A204HOH00.0220.01710.485-0.003-0.0030.0000.0000.0000.000
108A205HOH0-0.027-0.01932.4900.0020.0020.0000.0000.0000.000
109A206HOH0-0.003-0.01127.3000.0010.0010.0000.0000.0000.000
110A207HOH00.0560.03022.743-0.005-0.0050.0000.0000.0000.000
111A208HOH00.013-0.00226.034-0.001-0.0010.0000.0000.0000.000
112A209HOH0-0.014-0.00812.229-0.013-0.0130.0000.0000.0000.000
113A210HOH0-0.029-0.0167.560-0.151-0.1510.0000.0000.0000.000
114A211HOH0-0.020-0.02512.404-0.024-0.0240.0000.0000.0000.000
115A212HOH00.0370.0259.5180.0140.0140.0000.0000.0000.000
116A213HOH0-0.008-0.01219.0280.0020.0020.0000.0000.0000.000
117A214HOH0-0.023-0.02721.428-0.003-0.0030.0000.0000.0000.000
118A215HOH00.009-0.00621.171-0.007-0.0070.0000.0000.0000.000
119A216HOH00.006-0.01410.336-0.044-0.0440.0000.0000.0000.000
120A217HOH0-0.0290.00234.9230.0000.0000.0000.0000.0000.000
121A218HOH0-0.059-0.04132.7490.0020.0020.0000.0000.0000.000
122A219HOH0-0.040-0.03420.3770.0030.0030.0000.0000.0000.000
123A221HOH0-0.084-0.06823.2340.0030.0030.0000.0000.0000.000
124A222HOH0-0.031-0.02628.3110.0020.0020.0000.0000.0000.000
125A224HOH0-0.014-0.00918.187-0.002-0.0020.0000.0000.0000.000
126A225HOH0-0.050-0.03313.457-0.002-0.0020.0000.0000.0000.000
127A226HOH0-0.046-0.02728.9570.0010.0010.0000.0000.0000.000
128A227HOH00.0220.0189.6720.0030.0030.0000.0000.0000.000
129A228HOH0-0.050-0.03532.0010.0010.0010.0000.0000.0000.000
130A229HOH00.005-0.00927.403-0.003-0.0030.0000.0000.0000.000
131A230HOH0-0.020-0.02429.6230.0030.0030.0000.0000.0000.000
132A233HOH00.001-0.00625.5340.0010.0010.0000.0000.0000.000
133A234HOH0-0.030-0.02629.351-0.001-0.0010.0000.0000.0000.000
134A235HOH0-0.016-0.01920.0950.0040.0040.0000.0000.0000.000
135A237HOH0-0.078-0.06113.9260.0110.0110.0000.0000.0000.000
136A238HOH00.0480.03519.2100.0040.0040.0000.0000.0000.000
137A239HOH0-0.0030.02626.1650.0000.0000.0000.0000.0000.000
138A240HOH0-0.028-0.02516.4620.0090.0090.0000.0000.0000.000
139A241HOH0-0.039-0.02929.7060.0030.0030.0000.0000.0000.000
140A242HOH0-0.043-0.02415.750-0.008-0.0080.0000.0000.0000.000
141A244HOH0-0.010-0.01229.4760.0010.0010.0000.0000.0000.000
142A245HOH00.0330.03321.350-0.004-0.0040.0000.0000.0000.000
143A246HOH0-0.052-0.03715.385-0.002-0.0020.0000.0000.0000.000
144A247HOH0-0.032-0.02329.0770.0010.0010.0000.0000.0000.000
145A248HOH00.0230.02030.255-0.001-0.0010.0000.0000.0000.000
146A249HOH0-0.008-0.0157.0250.0560.0560.0000.0000.0000.000
147A250HOH0-0.081-0.07434.9860.0020.0020.0000.0000.0000.000
148A251HOH0-0.022-0.02024.079-0.003-0.0030.0000.0000.0000.000
149A252HOH0-0.0130.0034.470-0.765-0.7190.000-0.045-0.0010.000
150A253HOH00.0380.02129.533-0.004-0.0040.0000.0000.0000.000
151A254HOH0-0.045-0.02728.4780.0010.0010.0000.0000.0000.000
152A255HOH00.0000.0045.939-0.303-0.3030.0000.0000.0000.000
153A257HOH0-0.067-0.04721.4000.0010.0010.0000.0000.0000.000
154A258HOH0-0.035-0.02622.718-0.006-0.0060.0000.0000.0000.000
155A260HOH0-0.034-0.01521.4680.0050.0050.0000.0000.0000.000
156A261HOH00.000-0.00611.972-0.013-0.0130.0000.0000.0000.000
157A262HOH0-0.024-0.01629.985-0.003-0.0030.0000.0000.0000.000
158A263HOH00.0340.01932.591-0.002-0.0020.0000.0000.0000.000
159A264HOH0-0.044-0.03129.4040.0020.0020.0000.0000.0000.000
160A265HOH0-0.031-0.01926.1670.0010.0010.0000.0000.0000.000
161A266HOH0-0.032-0.01534.3890.0020.0020.0000.0000.0000.000
162A267HOH00.0460.03726.970-0.001-0.0010.0000.0000.0000.000
163A268HOH00.0260.02323.081-0.004-0.0040.0000.0000.0000.000
164A270HOH0-0.031-0.01721.6810.0060.0060.0000.0000.0000.000
165A271HOH0-0.054-0.0258.6980.0470.0470.0000.0000.0000.000
166A272HOH0-0.017-0.03125.322-0.002-0.0020.0000.0000.0000.000
167A273HOH0-0.020-0.01226.6700.0020.0020.0000.0000.0000.000
168A274HOH00.0140.0371.9725.205-2.31012.222-3.232-1.475-0.012
169A275HOH00.0140.01319.890-0.008-0.0080.0000.0000.0000.000
170A276HOH0-0.023-0.02131.8570.0010.0010.0000.0000.0000.000
171A277HOH0-0.0170.0492.16620.728-4.13818.5258.026-1.685-0.012
172A279HOH0-0.032-0.02031.0580.0000.0000.0000.0000.0000.000
173A283HOH00.0130.02014.2350.0020.0020.0000.0000.0000.000
174A285HOH0-0.028-0.02720.0330.0050.0050.0000.0000.0000.000
175A287HOH0-0.065-0.04331.6950.0010.0010.0000.0000.0000.000
176A288HOH0-0.025-0.02031.217-0.001-0.0010.0000.0000.0000.000
177A289HOH0-0.023-0.02228.2680.0020.0020.0000.0000.0000.000
178A290HOH0-0.038-0.02527.8740.0030.0030.0000.0000.0000.000
179A292HOH0-0.025-0.03716.892-0.015-0.0150.0000.0000.0000.000
180A293HOH0-0.017-0.01429.3480.0010.0010.0000.0000.0000.000
181A294HOH00.0220.0217.641-0.016-0.0160.0000.0000.0000.000
182A299HOH00.0320.03532.677-0.001-0.0010.0000.0000.0000.000
183A301HOH0-0.005-0.01520.7540.0030.0030.0000.0000.0000.000
184A302HOH0-0.043-0.02521.135-0.008-0.0080.0000.0000.0000.000
185A303HOH0-0.076-0.05213.3010.0110.0110.0000.0000.0000.000
186A305HOH0-0.022-0.01829.2400.0010.0010.0000.0000.0000.000
187A306HOH0-0.037-0.02229.5280.0030.0030.0000.0000.0000.000
188A308HOH0-0.047-0.04913.9210.0050.0050.0000.0000.0000.000
189A313HOH0-0.026-0.02820.815-0.005-0.0050.0000.0000.0000.000
190A314HOH0-0.022-0.03426.0810.0000.0000.0000.0000.0000.000
191A315HOH0-0.062-0.05314.0820.0090.0090.0000.0000.0000.000
192A316HOH0-0.032-0.02323.194-0.003-0.0030.0000.0000.0000.000
193A317HOH0-0.038-0.01818.6380.0010.0010.0000.0000.0000.000
194A318HOH0-0.028-0.02513.8120.0130.0130.0000.0000.0000.000
195A320HOH0-0.054-0.04718.892-0.002-0.0020.0000.0000.0000.000
196A322HOH0-0.042-0.02231.8330.0020.0020.0000.0000.0000.000
197A323HOH0-0.052-0.03719.285-0.004-0.0040.0000.0000.0000.000
198A327HOH0-0.020-0.01429.4640.0010.0010.0000.0000.0000.000
199A331HOH0-0.070-0.07324.9150.0010.0010.0000.0000.0000.000
200A333HOH0-0.025-0.01928.816-0.001-0.0010.0000.0000.0000.000
201A337HOH0-0.054-0.03527.8850.0010.0010.0000.0000.0000.000
202A340HOH00.0140.0064.6480.3700.3920.000-0.005-0.0170.000
203A342HOH0-0.059-0.04531.299-0.001-0.0010.0000.0000.0000.000
204A343HOH0-0.050-0.06710.9670.0250.0250.0000.0000.0000.000
205A344HOH0-0.067-0.04221.4860.0040.0040.0000.0000.0000.000
206A347HOH0-0.034-0.0297.2190.0430.0430.0000.0000.0000.000
207A350HOH0-0.057-0.04026.7500.0000.0000.0000.0000.0000.000
208A353HOH0-0.030-0.01531.5440.0000.0000.0000.0000.0000.000
209B101HOH00.0270.02215.324-0.010-0.0100.0000.0000.0000.000
210B103HOH00.0410.02326.003-0.002-0.0020.0000.0000.0000.000
211B105HOH0-0.050-0.03324.2750.0020.0020.0000.0000.0000.000
212B106HOH00.0440.0218.702-0.064-0.0640.0000.0000.0000.000
213B109HOH0-0.016-0.01124.4410.0020.0020.0000.0000.0000.000
214B115HOH00.0390.02324.0910.0010.0010.0000.0000.0000.000
215B120HOH0-0.022-0.02611.0570.0160.0160.0000.0000.0000.000
216B143HOH00.0370.02315.3060.0030.0030.0000.0000.0000.000