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: 39V3L

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 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 184
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1841862.558365
FMO2-HF: Nuclear repulsion 1769692.84401
FMO2-HF: Total energy -72169.714355
FMO2-MP2: Total energy -72382.317264


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.
-0.4331.635-0.032-1.077-0.96-0.003
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 : -0.027 / q_NPA : -0.025
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].
3B243SER00.0200.0193.7920.7812.849-0.032-1.077-0.960-0.003
4B244SER00.009-0.0037.0040.2050.2050.0000.0000.0000.000
5B245GLN0-0.031-0.0134.823-1.044-1.0440.0000.0000.0000.000
6B246ASP-1-0.858-0.9296.5400.7240.7240.0000.0000.0000.000
7B247LYS10.8860.9168.4880.2590.2590.0000.0000.0000.000
8B248PRO0-0.0210.05610.5520.0860.0860.0000.0000.0000.000
9B249PHE00.007-0.0096.013-0.265-0.2650.0000.0000.0000.000
10B250ASN0-0.005-0.0104.955-0.046-0.0460.0000.0000.0000.000
11B251LEU00.0380.0308.5000.3030.3030.0000.0000.0000.000
12B252ARG10.9150.9426.633-1.050-1.0500.0000.0000.0000.000
13B253SER00.0520.01212.612-0.080-0.0800.0000.0000.0000.000
14B254ARG10.8760.93613.380-0.531-0.5310.0000.0000.0000.000
15B255ASP-1-0.908-0.94516.4270.3370.3370.0000.0000.0000.000
16B256PRO0-0.0240.01120.033-0.021-0.0210.0000.0000.0000.000
17B257ILE0-0.031-0.03122.8570.0010.0010.0000.0000.0000.000
18B258TYR00.0390.00425.790-0.014-0.0140.0000.0000.0000.000
19B259SER0-0.102-0.01226.3380.0080.0080.0000.0000.0000.000
20B260ASN00.0580.01528.2750.0000.0000.0000.0000.0000.000
21B261ASN0-0.019-0.01830.1340.0010.0010.0000.0000.0000.000
22B262TYR00.0580.03731.917-0.005-0.0050.0000.0000.0000.000
23B263GLY00.0420.00628.472-0.010-0.0100.0000.0000.0000.000
24B264LYS10.8920.92923.341-0.195-0.1950.0000.0000.0000.000
25B265LEU00.0380.02324.371-0.014-0.0140.0000.0000.0000.000
26B266TYR0-0.0080.02919.0720.0210.0210.0000.0000.0000.000
27B267GLU-1-0.764-0.87321.8020.0610.0610.0000.0000.0000.000
28B268ILE0-0.084-0.04216.8840.0410.0410.0000.0000.0000.000
29B269THR00.0470.02120.182-0.017-0.0170.0000.0000.0000.000
30B270PRO00.0880.03621.1120.0170.0170.0000.0000.0000.000
31B271GLU-1-0.834-0.92921.9910.0740.0740.0000.0000.0000.000
32B272LYS10.8820.94619.470-0.176-0.1760.0000.0000.0000.000
33B273ASN0-0.051-0.02414.3620.0090.0090.0000.0000.0000.000
34B274SER00.0140.00315.449-0.025-0.0250.0000.0000.0000.000
35B275GLN00.0710.03112.3560.0370.0370.0000.0000.0000.000
36B276LEU0-0.029-0.01217.245-0.016-0.0160.0000.0000.0000.000
37B277ARG10.9160.93019.430-0.037-0.0370.0000.0000.0000.000
38B278ASP-1-0.979-0.98019.761-0.091-0.0910.0000.0000.0000.000
39B279LEU0-0.080-0.04419.447-0.028-0.0280.0000.0000.0000.000
40B280ASP-1-0.903-0.94123.298-0.003-0.0030.0000.0000.0000.000
41B281ILE0-0.003-0.03320.875-0.001-0.0010.0000.0000.0000.000
42B282LEU0-0.051-0.00121.9700.0090.0090.0000.0000.0000.000
43B283LEU0-0.048-0.03916.846-0.021-0.0210.0000.0000.0000.000
44B284ASN0-0.005-0.00820.6610.0330.0330.0000.0000.0000.000
45B285CYM-1-0.861-0.92919.0580.0880.0880.0000.0000.0000.000
46B286LEU0-0.053-0.01821.1510.0190.0190.0000.0000.0000.000
47B287GLN00.0900.03620.530-0.002-0.0020.0000.0000.0000.000
48B288MET0-0.057-0.03824.6540.0070.0070.0000.0000.0000.000
49B289ASN0-0.009-0.00128.441-0.005-0.0050.0000.0000.0000.000
50B290GLU-1-1.002-0.93530.5440.0380.0380.0000.0000.0000.000
51B291GLY0-0.032-0.01533.2240.0020.0020.0000.0000.0000.000
52B292ALA0-0.068-0.02532.5250.0000.0000.0000.0000.0000.000
53B293LEU00.0610.00434.645-0.008-0.0080.0000.0000.0000.000
54B294PHE0-0.056-0.02029.9750.0070.0070.0000.0000.0000.000
55B295VAL00.0490.01233.870-0.009-0.0090.0000.0000.0000.000
56B296PRO00.0010.00336.032-0.001-0.0010.0000.0000.0000.000
57B297HIS10.8560.93532.787-0.040-0.0400.0000.0000.0000.000
58B298TYR0-0.047-0.00935.699-0.005-0.0050.0000.0000.0000.000
59B299ASN00.0810.05931.2480.0150.0150.0000.0000.0000.000
60B300SER0-0.044-0.00434.096-0.008-0.0080.0000.0000.0000.000
61B301ARG10.9320.94333.183-0.021-0.0210.0000.0000.0000.000
62B302ALA0-0.0090.03928.594-0.007-0.0070.0000.0000.0000.000
63B303THR0-0.021-0.01330.2020.0020.0020.0000.0000.0000.000
64B304VAL0-0.026-0.01326.835-0.006-0.0060.0000.0000.0000.000
65B305ILE00.0030.02525.9180.0000.0000.0000.0000.0000.000
66B306LEU00.021-0.00725.7550.0030.0030.0000.0000.0000.000
67B307VAL00.0190.00722.926-0.010-0.0100.0000.0000.0000.000
68B308ALA0-0.0110.00325.1410.0160.0160.0000.0000.0000.000
69B309ASN0-0.076-0.06319.4910.0010.0010.0000.0000.0000.000
70B310GLU-1-0.860-0.92722.9320.0000.0000.0000.0000.0000.000
71B311GLY00.0970.07524.7290.0140.0140.0000.0000.0000.000
72B312ARG10.8530.91728.475-0.003-0.0030.0000.0000.0000.000
73B313ALA00.005-0.00530.8190.0080.0080.0000.0000.0000.000
74B314GLU-1-0.912-0.98032.7730.0050.0050.0000.0000.0000.000
75B315VAL0-0.046-0.01933.2220.0060.0060.0000.0000.0000.000
76B316GLU-1-0.920-0.95136.0940.0080.0080.0000.0000.0000.000
77B317LEU0-0.020-0.02236.1020.0030.0030.0000.0000.0000.000
78B318VAL00.009-0.01339.111-0.003-0.0030.0000.0000.0000.000
79B319GLY00.0410.01941.4470.0010.0010.0000.0000.0000.000
80B320LEU0-0.017-0.00143.364-0.001-0.0010.0000.0000.0000.000
81B321GLU-1-0.854-0.95141.633-0.019-0.0190.0000.0000.0000.000
82B322GLN00.0730.04044.5030.0010.0010.0000.0000.0000.000
83B323GLN00.0930.02446.9220.0020.0020.0000.0000.0000.000
84B324GLN0-0.069-0.01745.7850.0030.0030.0000.0000.0000.000
85B325GLN0-0.042-0.03849.823-0.001-0.0010.0000.0000.0000.000
86B326GLN0-0.012-0.01451.3650.0000.0000.0000.0000.0000.000
87B327GLY0-0.029-0.05754.0450.0000.0000.0000.0000.0000.000
88B328LEU00.0430.02754.0790.0010.0010.0000.0000.0000.000
89B329GLU-1-0.907-0.93654.868-0.003-0.0030.0000.0000.0000.000
90B330SER0-0.067-0.04056.121-0.001-0.0010.0000.0000.0000.000
91B331MET0-0.1170.02447.842-0.002-0.0020.0000.0000.0000.000
92B332GLN00.0340.01747.3170.0010.0010.0000.0000.0000.000
93B333LEU00.012-0.01545.9500.0000.0000.0000.0000.0000.000
94B334ARG10.8890.98144.8190.0180.0180.0000.0000.0000.000
95B335ARG10.9760.99442.912-0.004-0.0040.0000.0000.0000.000
96B336TYR0-0.130-0.08140.180-0.003-0.0030.0000.0000.0000.000
97B337ALA00.021-0.00739.2910.0030.0030.0000.0000.0000.000
98B338ALA0-0.028-0.00436.215-0.004-0.0040.0000.0000.0000.000
99B339THR00.0020.03436.2930.0040.0040.0000.0000.0000.000
100B340LEU0-0.051-0.00830.255-0.003-0.0030.0000.0000.0000.000
101B341SER00.042-0.00730.5730.0100.0100.0000.0000.0000.000
102B342GLU-1-0.868-0.95324.423-0.056-0.0560.0000.0000.0000.000
103B343GLY0-0.0380.00325.794-0.007-0.0070.0000.0000.0000.000
104B344ASP-1-0.926-0.94426.731-0.061-0.0610.0000.0000.0000.000
105B345ILE0-0.032-0.04325.8020.0040.0040.0000.0000.0000.000
106B346ILE0-0.058-0.01429.6430.0030.0030.0000.0000.0000.000
107B347VAL00.007-0.00330.271-0.001-0.0010.0000.0000.0000.000
108B348ILE0-0.075-0.05330.5500.0030.0030.0000.0000.0000.000
109B349PRO00.0470.01232.8300.0030.0030.0000.0000.0000.000
110B350SER00.0450.01834.7560.0050.0050.0000.0000.0000.000
111B351SER0-0.027-0.00935.6900.0040.0040.0000.0000.0000.000
112B352PHE0-0.0180.00337.7570.0030.0030.0000.0000.0000.000
113B353PRO0-0.032-0.01637.2800.0030.0030.0000.0000.0000.000
114B354VAL0-0.047-0.03133.630-0.004-0.0040.0000.0000.0000.000
115B355ALA00.0270.01736.0830.0060.0060.0000.0000.0000.000
116B356LEU0-0.019-0.01130.573-0.006-0.0060.0000.0000.0000.000
117B357LYS10.9900.98834.410-0.024-0.0240.0000.0000.0000.000
118B358ALA0-0.052-0.02531.694-0.004-0.0040.0000.0000.0000.000
119B359ALA0-0.041-0.01833.4550.0040.0040.0000.0000.0000.000
120B360SER00.054-0.07830.366-0.003-0.0030.0000.0000.0000.000
121B361ASP-1-0.859-0.86827.8610.0680.0680.0000.0000.0000.000
122B362LEU00.0130.00327.297-0.007-0.0070.0000.0000.0000.000
123B363ASN0-0.085-0.03320.6780.0120.0120.0000.0000.0000.000
124B364MET0-0.0260.02024.281-0.015-0.0150.0000.0000.0000.000
125B365VAL00.0700.02418.9650.0170.0170.0000.0000.0000.000
126B366GLY0-0.031-0.02122.067-0.014-0.0140.0000.0000.0000.000
127B367ILE0-0.023-0.01520.260-0.001-0.0010.0000.0000.0000.000
128B368GLY00.0220.00623.4690.0000.0000.0000.0000.0000.000
129B369VAL00.0530.03025.483-0.003-0.0030.0000.0000.0000.000
130B370ASN0-0.009-0.01627.6350.0010.0010.0000.0000.0000.000
131B371ALA0-0.066-0.02925.6820.0090.0090.0000.0000.0000.000
132B372GLU-1-0.823-0.87627.1660.0360.0360.0000.0000.0000.000
133B373ASN0-0.062-0.02928.487-0.002-0.0020.0000.0000.0000.000
134B374ASN0-0.0170.00429.093-0.007-0.0070.0000.0000.0000.000
135B375GLU-1-0.905-0.94730.6290.0620.0620.0000.0000.0000.000
136B376ARG10.8010.84927.396-0.077-0.0770.0000.0000.0000.000
137B377ASN0-0.0120.00933.4370.0080.0080.0000.0000.0000.000
138B378PHE0-0.013-0.01132.434-0.005-0.0050.0000.0000.0000.000
139B379LEU0-0.009-0.00437.995-0.001-0.0010.0000.0000.0000.000
140B380ALA00.006-0.01940.085-0.002-0.0020.0000.0000.0000.000
141B381GLY00.0290.03539.2020.0040.0040.0000.0000.0000.000
142B382HIS00.0250.01939.446-0.004-0.0040.0000.0000.0000.000
143B383LYS10.9560.96534.533-0.110-0.1100.0000.0000.0000.000
144B384GLU-1-0.883-0.93533.6370.0980.0980.0000.0000.0000.000
145B385ASN0-0.027-0.00838.100-0.007-0.0070.0000.0000.0000.000
146B386VAL00.0850.01541.0920.0000.0000.0000.0000.0000.000
147B387ILE00.009-0.02842.704-0.002-0.0020.0000.0000.0000.000
148B388ARG10.8740.95841.677-0.068-0.0680.0000.0000.0000.000
149B389GLN0-0.113-0.04942.8570.0050.0050.0000.0000.0000.000
150B390ILE0-0.0110.04846.423-0.001-0.0010.0000.0000.0000.000
151B391PRO00.0190.00449.6790.0010.0010.0000.0000.0000.000
152B392ARG10.8950.96652.548-0.043-0.0430.0000.0000.0000.000
153B393GLN00.0280.01755.647-0.001-0.0010.0000.0000.0000.000
154B394VAL00.0110.01453.545-0.001-0.0010.0000.0000.0000.000
155B395SER00.0220.03052.450-0.001-0.0010.0000.0000.0000.000
156B396ASP-1-0.896-0.96054.2130.0250.0250.0000.0000.0000.000
157B397LEU0-0.075-0.02357.730-0.001-0.0010.0000.0000.0000.000
158B398THR0-0.120-0.07652.179-0.002-0.0020.0000.0000.0000.000
159B399PHE0-0.023-0.02049.568-0.001-0.0010.0000.0000.0000.000
160B400PRO0-0.051-0.03655.3830.0000.0000.0000.0000.0000.000
161B401GLY00.0140.03356.9400.0000.0000.0000.0000.0000.000
162B402SER00.0570.03658.0180.0000.0000.0000.0000.0000.000
163B403GLY00.040-0.01955.8860.0010.0010.0000.0000.0000.000
164B404GLU-1-1.021-1.06254.7330.0370.0370.0000.0000.0000.000
165B405GLU-1-0.901-0.95454.7970.0300.0300.0000.0000.0000.000
166B406VAL00.0560.02352.0890.0000.0000.0000.0000.0000.000
167B407GLU-1-0.836-0.90851.3080.0470.0470.0000.0000.0000.000
168B408GLU-1-1.025-0.98950.5510.0410.0410.0000.0000.0000.000
169B409LEU00.027-0.02248.9830.0020.0020.0000.0000.0000.000
170B410LEU0-0.064-0.00646.7200.0030.0030.0000.0000.0000.000
171B411GLU-1-0.869-0.94445.9480.0620.0620.0000.0000.0000.000
172B412ASN0-0.045-0.00147.0580.0040.0040.0000.0000.0000.000
173B413GLN0-0.085-0.02541.3760.0040.0040.0000.0000.0000.000
174B414LYS10.9640.97540.882-0.060-0.0600.0000.0000.0000.000
175B415GLU-1-0.958-0.98137.0950.1010.1010.0000.0000.0000.000
176B416SER0-0.031-0.04035.580-0.002-0.0020.0000.0000.0000.000
177B417TYR0-0.035-0.02232.3540.0010.0010.0000.0000.0000.000
178B418PHE00.0300.00728.157-0.009-0.0090.0000.0000.0000.000
179B419VAL0-0.042-0.03333.7980.0050.0050.0000.0000.0000.000
180B420ASP-1-0.823-0.91637.0630.0540.0540.0000.0000.0000.000
181B421GLY0-0.0130.00038.532-0.002-0.0020.0000.0000.0000.000
182B422GLN0-0.093-0.04740.213-0.003-0.0030.0000.0000.0000.000
183B423PRO0-0.039-0.02642.476-0.001-0.0010.0000.0000.0000.000
184B424ARG11.0261.03145.507-0.024-0.0240.0000.0000.0000.000