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: LZ3M9

Calculation Name: 1CAX-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1CAX

Chain ID: B

ChEMBL ID:

UniProt ID: P50477

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 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 184
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1840336.961024
FMO2-HF: Nuclear repulsion 1768162.909101
FMO2-HF: Total energy -72174.051923
FMO2-MP2: Total energy -72385.970647


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(B:241:THR)


Summations of interaction energy for fragment #1(B:241:THR)
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.
-1.7110.546-0.036-1.132-1.087-0.003
Interaction energy analysis for fragmet #1(B:241:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.019
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].
3B243SER00.0360.0283.7920.1982.371-0.034-1.127-1.012-0.003
4B244SER00.008-0.0047.0030.1360.1360.0000.0000.0000.000
5B245GLN0-0.040-0.0214.728-1.000-0.953-0.001-0.005-0.0400.000
6B246ASP-1-0.885-0.9466.536-0.448-0.4480.0000.0000.0000.000
7B247LYS10.8650.9168.4820.8560.8560.0000.0000.0000.000
8B248PRO00.0160.07110.5500.0610.0610.0000.0000.0000.000
9B249PHE00.0320.0056.236-0.236-0.2360.0000.0000.0000.000
10B250ASN0-0.023-0.0195.075-0.570-0.533-0.0010.000-0.0350.000
11B251LEU00.0480.0297.7040.0280.0280.0000.0000.0000.000
12B252ARG10.9100.9346.799-0.666-0.6660.0000.0000.0000.000
13B253SER00.0590.01612.132-0.023-0.0230.0000.0000.0000.000
14B254ARG10.7750.86413.213-0.210-0.2100.0000.0000.0000.000
15B255ASP-1-0.787-0.85316.3300.1900.1900.0000.0000.0000.000
16B256PRO0-0.047-0.00920.033-0.019-0.0190.0000.0000.0000.000
17B257ILE0-0.037-0.03222.625-0.002-0.0020.0000.0000.0000.000
18B258TYR00.0210.00525.477-0.007-0.0070.0000.0000.0000.000
19B259SER00.0010.02326.0130.0100.0100.0000.0000.0000.000
20B260ASN0-0.012-0.02128.0490.0010.0010.0000.0000.0000.000
21B261ASN0-0.043-0.02829.9340.0020.0020.0000.0000.0000.000
22B262TYR00.0580.02831.8060.0000.0000.0000.0000.0000.000
23B263GLY00.0530.01628.433-0.004-0.0040.0000.0000.0000.000
24B264LYS10.8810.91922.958-0.139-0.1390.0000.0000.0000.000
25B265LEU00.0330.02324.157-0.007-0.0070.0000.0000.0000.000
26B266TYR0-0.0110.01919.4050.0150.0150.0000.0000.0000.000
27B267GLU-1-0.757-0.84921.218-0.020-0.0200.0000.0000.0000.000
28B268ILE0-0.069-0.03716.0240.0080.0080.0000.0000.0000.000
29B269THR00.010-0.01919.365-0.014-0.0140.0000.0000.0000.000
30B270PRO00.0710.04120.636-0.009-0.0090.0000.0000.0000.000
31B271GLU-1-0.788-0.88621.815-0.071-0.0710.0000.0000.0000.000
32B272LYS10.8830.94819.1580.0110.0110.0000.0000.0000.000
33B273ASN0-0.030-0.01413.745-0.030-0.0300.0000.0000.0000.000
34B274SER00.0500.02114.8210.0040.0040.0000.0000.0000.000
35B275GLN00.003-0.00911.2270.0350.0350.0000.0000.0000.000
36B276LEU00.0150.00315.7950.0060.0060.0000.0000.0000.000
37B277ARG10.9130.94118.7460.1320.1320.0000.0000.0000.000
38B278ASP-1-0.998-0.98520.108-0.234-0.2340.0000.0000.0000.000
39B279LEU0-0.085-0.05418.852-0.012-0.0120.0000.0000.0000.000
40B280ASP-1-0.873-0.93722.558-0.082-0.0820.0000.0000.0000.000
41B281ILE0-0.012-0.03220.7350.0120.0120.0000.0000.0000.000
42B282LEU0-0.070-0.01421.211-0.010-0.0100.0000.0000.0000.000
43B283LEU0-0.026-0.01416.296-0.007-0.0070.0000.0000.0000.000
44B284ASN0-0.088-0.07420.1850.0070.0070.0000.0000.0000.000
45B285CYM-1-0.820-0.86918.8440.0950.0950.0000.0000.0000.000
46B286LEU0-0.009-0.01221.0070.0100.0100.0000.0000.0000.000
47B287GLN0-0.014-0.03219.3910.0170.0170.0000.0000.0000.000
48B288MET0-0.071-0.03624.717-0.004-0.0040.0000.0000.0000.000
49B289ASN00.0000.00228.5540.0060.0060.0000.0000.0000.000
50B290GLU-1-0.887-0.94530.7710.0530.0530.0000.0000.0000.000
51B291GLY0-0.035-0.00933.5740.0010.0010.0000.0000.0000.000
52B292ALA0-0.069-0.02832.572-0.003-0.0030.0000.0000.0000.000
53B293LEU00.009-0.00634.734-0.005-0.0050.0000.0000.0000.000
54B294PHE0-0.0120.00129.8250.0010.0010.0000.0000.0000.000
55B295VAL00.0320.00633.732-0.005-0.0050.0000.0000.0000.000
56B296PRO00.0070.00035.749-0.002-0.0020.0000.0000.0000.000
57B297HIS10.8110.91732.369-0.012-0.0120.0000.0000.0000.000
58B298TYR00.0190.02235.299-0.001-0.0010.0000.0000.0000.000
59B299ASN00.0210.00730.9610.0070.0070.0000.0000.0000.000
60B300SER0-0.0290.00933.502-0.004-0.0040.0000.0000.0000.000
61B301ARG10.9350.94431.8970.0420.0420.0000.0000.0000.000
62B302ALA0-0.0210.01627.958-0.005-0.0050.0000.0000.0000.000
63B303THR0-0.012-0.01029.6780.0080.0080.0000.0000.0000.000
64B304VAL0-0.028-0.01626.331-0.009-0.0090.0000.0000.0000.000
65B305ILE00.0070.02625.8940.0060.0060.0000.0000.0000.000
66B306LEU00.010-0.01325.683-0.001-0.0010.0000.0000.0000.000
67B307VAL00.0100.00423.400-0.004-0.0040.0000.0000.0000.000
68B308ALA00.0030.01525.3870.0090.0090.0000.0000.0000.000
69B309ASN0-0.082-0.07119.981-0.010-0.0100.0000.0000.0000.000
70B310GLU-1-0.878-0.94223.6370.0900.0900.0000.0000.0000.000
71B311GLY00.1040.08125.3530.0030.0030.0000.0000.0000.000
72B312ARG10.8770.93429.094-0.034-0.0340.0000.0000.0000.000
73B313ALA00.018-0.00631.0590.0040.0040.0000.0000.0000.000
74B314GLU-1-0.841-0.91833.1310.0220.0220.0000.0000.0000.000
75B315VAL0-0.041-0.01933.0780.0020.0020.0000.0000.0000.000
76B316GLU-1-0.833-0.89736.2280.0080.0080.0000.0000.0000.000
77B317LEU0-0.007-0.02135.7520.0010.0010.0000.0000.0000.000
78B318VAL0-0.013-0.02339.0380.0000.0000.0000.0000.0000.000
79B319GLY00.0590.03041.215-0.001-0.0010.0000.0000.0000.000
80B320LEU0-0.0120.01243.1420.0010.0010.0000.0000.0000.000
81B321GLU-1-0.862-0.92741.600-0.026-0.0260.0000.0000.0000.000
82B322GLN00.0790.03944.241-0.001-0.0010.0000.0000.0000.000
83B323GLN00.0730.03646.6880.0020.0020.0000.0000.0000.000
84B324GLN0-0.025-0.00445.4180.0020.0020.0000.0000.0000.000
85B325GLN0-0.103-0.05549.8900.0020.0020.0000.0000.0000.000
86B326GLN0-0.017-0.00951.1150.0000.0000.0000.0000.0000.000
87B327GLY0-0.015-0.04553.7080.0000.0000.0000.0000.0000.000
88B328LEU00.0170.02353.5640.0010.0010.0000.0000.0000.000
89B329GLU-1-0.925-0.91854.566-0.011-0.0110.0000.0000.0000.000
90B330SER0-0.024-0.03955.8820.0000.0000.0000.0000.0000.000
91B331MET0-0.083-0.01547.275-0.002-0.0020.0000.0000.0000.000
92B332GLN00.0130.00547.1640.0010.0010.0000.0000.0000.000
93B333LEU00.0480.00746.249-0.001-0.0010.0000.0000.0000.000
94B334ARG10.8970.97645.1030.0160.0160.0000.0000.0000.000
95B335ARG10.8760.92643.214-0.005-0.0050.0000.0000.0000.000
96B336TYR0-0.137-0.10740.2660.0000.0000.0000.0000.0000.000
97B337ALA00.027-0.00639.4550.0010.0010.0000.0000.0000.000
98B338ALA0-0.023-0.00436.310-0.002-0.0020.0000.0000.0000.000
99B339THR0-0.0170.01236.7020.0020.0020.0000.0000.0000.000
100B340LEU0-0.077-0.02530.3360.0000.0000.0000.0000.0000.000
101B341SER00.008-0.00731.2130.0090.0090.0000.0000.0000.000
102B342GLU-1-0.874-0.95225.2540.0320.0320.0000.0000.0000.000
103B343GLY0-0.0290.00426.414-0.005-0.0050.0000.0000.0000.000
104B344ASP-1-0.883-0.92027.376-0.016-0.0160.0000.0000.0000.000
105B345ILE0-0.029-0.04126.3250.0010.0010.0000.0000.0000.000
106B346ILE0-0.067-0.02029.9450.0010.0010.0000.0000.0000.000
107B347VAL00.020-0.00130.318-0.003-0.0030.0000.0000.0000.000
108B348ILE0-0.053-0.04230.2060.0040.0040.0000.0000.0000.000
109B349PRO00.0290.00732.506-0.002-0.0020.0000.0000.0000.000
110B350SER00.0010.00233.9670.0030.0030.0000.0000.0000.000
111B351SER00.0070.00135.1940.0020.0020.0000.0000.0000.000
112B352PHE0-0.034-0.00237.4470.0030.0030.0000.0000.0000.000
113B353PRO0-0.028-0.00436.9070.0000.0000.0000.0000.0000.000
114B354VAL0-0.017-0.02433.3830.0000.0000.0000.0000.0000.000
115B355ALA00.0200.01335.9490.0020.0020.0000.0000.0000.000
116B356LEU0-0.035-0.01730.635-0.003-0.0030.0000.0000.0000.000
117B357LYS10.8790.91434.417-0.026-0.0260.0000.0000.0000.000
118B358ALA00.004-0.00931.973-0.001-0.0010.0000.0000.0000.000
119B359ALA0-0.045-0.01433.6980.0050.0050.0000.0000.0000.000
120B360SER00.0180.01530.873-0.003-0.0030.0000.0000.0000.000
121B361ASP-1-0.885-0.94328.1220.0930.0930.0000.0000.0000.000
122B362LEU0-0.033-0.01227.827-0.003-0.0030.0000.0000.0000.000
123B363ASN0-0.074-0.05221.0400.0070.0070.0000.0000.0000.000
124B364MET00.0120.02424.560-0.010-0.0100.0000.0000.0000.000
125B365VAL00.0320.02119.2220.0080.0080.0000.0000.0000.000
126B366GLY00.0140.00022.036-0.006-0.0060.0000.0000.0000.000
127B367ILE0-0.021-0.01520.838-0.011-0.0110.0000.0000.0000.000
128B368GLY00.0150.01423.1860.0090.0090.0000.0000.0000.000
129B369VAL00.0480.02724.916-0.013-0.0130.0000.0000.0000.000
130B370ASN0-0.037-0.02927.1140.0090.0090.0000.0000.0000.000
131B371ALA0-0.041-0.00424.9650.0100.0100.0000.0000.0000.000
132B372GLU-1-0.818-0.88526.886-0.068-0.0680.0000.0000.0000.000
133B373ASN0-0.082-0.05327.8870.0050.0050.0000.0000.0000.000
134B374ASN00.0160.03528.2560.0070.0070.0000.0000.0000.000
135B375GLU-1-0.890-0.93429.919-0.001-0.0010.0000.0000.0000.000
136B376ARG10.8270.87126.731-0.005-0.0050.0000.0000.0000.000
137B377ASN0-0.036-0.01832.7430.0070.0070.0000.0000.0000.000
138B378PHE0-0.016-0.00832.004-0.001-0.0010.0000.0000.0000.000
139B379LEU0-0.009-0.00137.426-0.001-0.0010.0000.0000.0000.000
140B380ALA00.000-0.01539.5910.0000.0000.0000.0000.0000.000
141B381GLY00.0310.02838.7380.0020.0020.0000.0000.0000.000
142B382HIS00.0240.01639.366-0.004-0.0040.0000.0000.0000.000
143B383LYS10.8530.90233.691-0.049-0.0490.0000.0000.0000.000
144B384GLU-1-0.781-0.86033.9520.0380.0380.0000.0000.0000.000
145B385ASN0-0.0030.00637.668-0.006-0.0060.0000.0000.0000.000
146B386VAL00.0680.01540.4660.0000.0000.0000.0000.0000.000
147B387ILE00.003-0.01342.085-0.001-0.0010.0000.0000.0000.000
148B388ARG10.7900.87241.620-0.030-0.0300.0000.0000.0000.000
149B389GLN0-0.101-0.03942.6300.0020.0020.0000.0000.0000.000
150B390ILE0-0.0170.02345.992-0.002-0.0020.0000.0000.0000.000
151B391PRO0-0.010-0.01149.1530.0010.0010.0000.0000.0000.000
152B392ARG10.8330.86652.135-0.018-0.0180.0000.0000.0000.000
153B393GLN00.0210.01655.2160.0000.0000.0000.0000.0000.000
154B394VAL0-0.0060.00652.895-0.001-0.0010.0000.0000.0000.000
155B395SER00.0610.03551.921-0.001-0.0010.0000.0000.0000.000
156B396ASP-1-0.847-0.92453.5770.0090.0090.0000.0000.0000.000
157B397LEU0-0.064-0.02757.091-0.001-0.0010.0000.0000.0000.000
158B398THR0-0.108-0.05251.510-0.002-0.0020.0000.0000.0000.000
159B399PHE0-0.048-0.02948.907-0.001-0.0010.0000.0000.0000.000
160B400PRO0-0.047-0.03254.9400.0000.0000.0000.0000.0000.000
161B401GLY00.0080.02456.4720.0000.0000.0000.0000.0000.000
162B402SER0-0.030-0.03257.480-0.001-0.0010.0000.0000.0000.000
163B403GLY00.028-0.01755.3580.0010.0010.0000.0000.0000.000
164B404GLU-1-0.926-0.95054.2720.0170.0170.0000.0000.0000.000
165B405GLU-1-0.842-0.93254.3690.0150.0150.0000.0000.0000.000
166B406VAL00.0180.01251.6350.0000.0000.0000.0000.0000.000
167B407GLU-1-0.812-0.87750.7840.0210.0210.0000.0000.0000.000
168B408GLU-1-1.010-0.98350.1570.0250.0250.0000.0000.0000.000
169B409LEU0-0.011-0.00748.4400.0020.0020.0000.0000.0000.000
170B410LEU0-0.048-0.01445.8550.0020.0020.0000.0000.0000.000
171B411GLU-1-0.801-0.86945.6580.0300.0300.0000.0000.0000.000
172B412ASN0-0.058-0.03746.7310.0030.0030.0000.0000.0000.000
173B413GLN0-0.113-0.04741.0040.0050.0050.0000.0000.0000.000
174B414LYS10.9420.97140.993-0.046-0.0460.0000.0000.0000.000
175B415GLU-1-0.863-0.92236.3030.0670.0670.0000.0000.0000.000
176B416SER0-0.023-0.02335.183-0.004-0.0040.0000.0000.0000.000
177B417TYR0-0.051-0.04631.7330.0000.0000.0000.0000.0000.000
178B418PHE00.0010.01227.741-0.006-0.0060.0000.0000.0000.000
179B419VAL0-0.023-0.01633.5790.0040.0040.0000.0000.0000.000
180B420ASP-1-0.854-0.94836.9180.0480.0480.0000.0000.0000.000
181B421GLY00.0040.01538.563-0.003-0.0030.0000.0000.0000.000
182B422GLN0-0.088-0.03540.276-0.001-0.0010.0000.0000.0000.000
183B423PRO0-0.038-0.02342.646-0.002-0.0020.0000.0000.0000.000
184B424ARG11.0421.03245.699-0.020-0.0200.0000.0000.0000.000