Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: QYQ7Y

Calculation Name: 1CT4-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1CT4

Chain ID: E

ChEMBL ID:

UniProt ID: P68390

Base Structure: X-ray

Registration Date: 2023-09-20

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1751845.168629
FMO2-HF: Nuclear repulsion 1685403.98382
FMO2-HF: Total energy -66441.184809
FMO2-MP2: Total energy -66632.933333


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(E:16:ILE)


Summations of interaction energy for fragment #1(E:16:ILE)
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.
-28.267-14.42920.24-14.04-20.035-0.064
Interaction energy analysis for fragmet #1(E:16:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : 0.005
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].
3E18GLY00.0650.0293.318-3.5111.3540.015-2.762-2.1180.009
4E19GLY0-0.026-0.0365.8880.1690.1690.0000.0000.0000.000
5E29ASP-1-0.840-0.8982.483-4.791-1.9833.145-2.500-3.453-0.024
6E30ALA0-0.024-0.0254.316-0.199-0.0330.000-0.038-0.1280.000
7E31ILE0-0.0270.0072.947-1.329-0.0110.253-0.537-1.034-0.005
8E32TYR0-0.019-0.0174.908-0.298-0.266-0.001-0.003-0.0270.000
9E33SER00.1140.0718.2290.1010.1010.0000.0000.0000.000
10E34SER0-0.029-0.02011.1940.0310.0310.0000.0000.0000.000
11E39THR00.0390.01914.4010.0040.0040.0000.0000.0000.000
12E40GLY00.0260.01213.309-0.011-0.0110.0000.0000.0000.000
13E41ARG10.8230.9028.225-0.049-0.0490.0000.0000.0000.000
14E42CYS0-0.099-0.0258.417-0.012-0.0120.0000.0000.0000.000
15E43SER00.019-0.0066.3610.0640.0640.0000.0000.0000.000
16E44LEU0-0.0040.0182.323-0.843-0.0411.269-0.357-1.713-0.001
17E45GLY00.0740.0365.777-0.099-0.0990.0000.0000.0000.000
18E46PHE0-0.019-0.0327.874-0.190-0.1900.0000.0000.0000.000
19E47ASN00.0160.0242.7600.7811.3860.065-0.214-0.4560.001
20E48VAL0-0.025-0.0246.6620.1270.1270.0000.0000.0000.000
21E48ARG10.9250.9619.7200.6640.6640.0000.0000.0000.000
22E48SER00.0680.03912.3300.0400.0400.0000.0000.0000.000
23E48GLY00.0250.02015.8620.0330.0330.0000.0000.0000.000
24E48SER0-0.052-0.04114.915-0.055-0.0550.0000.0000.0000.000
25E49THR00.0060.02213.1770.0270.0270.0000.0000.0000.000
26E50TYR00.001-0.0058.111-0.061-0.0610.0000.0000.0000.000
27E51TYR00.003-0.0158.9190.1810.1810.0000.0000.0000.000
28E52PHE00.0060.0105.213-0.235-0.2350.0000.0000.0000.000
29E53LEU00.0050.0077.4260.2110.2110.0000.0000.0000.000
30E54THR0-0.002-0.0178.530-0.104-0.1040.0000.0000.0000.000
31E55ALA00.0600.03010.5690.0130.0130.0000.0000.0000.000
32E56GLY00.0210.02413.6270.0270.0270.0000.0000.0000.000
33E57HIS00.0020.01715.7760.0360.0360.0000.0000.0000.000
34E59THR0-0.041-0.03911.7720.0300.0300.0000.0000.0000.000
35E60ASP-1-0.955-0.95613.9620.0020.0020.0000.0000.0000.000
36E62GLY00.0370.02917.5260.0150.0150.0000.0000.0000.000
37E63ALA0-0.045-0.00913.1280.0330.0330.0000.0000.0000.000
38E64THR00.0060.00314.846-0.005-0.0050.0000.0000.0000.000
39E65THR0-0.020-0.00911.109-0.011-0.0110.0000.0000.0000.000
40E66TRP00.0330.0146.8040.0040.0040.0000.0000.0000.000
41E67TRP0-0.009-0.0237.0410.0830.0830.0000.0000.0000.000
42E68ALA00.0540.0142.808-0.530-0.0690.151-0.133-0.4790.001
43E78ASN00.016-0.0044.160-0.269-0.158-0.0010.002-0.1120.000
44E79SER00.0520.0227.431-0.089-0.0890.0000.0000.0000.000
45E80ALA0-0.0080.00210.836-0.087-0.0870.0000.0000.0000.000
46E81ARG10.8260.90210.120-0.515-0.5150.0000.0000.0000.000
47E82THR00.0180.01910.2680.0040.0040.0000.0000.0000.000
48E83THR0-0.0090.0065.9260.0190.0190.0000.0000.0000.000
49E84VAL00.0090.0057.0440.1450.1450.0000.0000.0000.000
50E85LEU00.0050.0132.616-0.871-0.0441.155-0.291-1.6920.003
51E86GLY00.0500.0026.234-0.242-0.2420.0000.0000.0000.000
52E87THR0-0.027-0.0099.0480.0520.0520.0000.0000.0000.000
53E88THR0-0.024-0.02411.859-0.059-0.0590.0000.0000.0000.000
54E89SER0-0.074-0.04313.0710.0070.0070.0000.0000.0000.000
55E90GLY00.0120.00514.922-0.003-0.0030.0000.0000.0000.000
56E91SER00.006-0.00115.315-0.019-0.0190.0000.0000.0000.000
57E93SER0-0.0260.00817.4860.0100.0100.0000.0000.0000.000
58E94PHE00.0630.04919.292-0.022-0.0220.0000.0000.0000.000
59E99PRO00.0360.03021.2370.0100.0100.0000.0000.0000.000
60E100ASN0-0.029-0.02023.625-0.003-0.0030.0000.0000.0000.000
61E101ASN0-0.034-0.02521.205-0.011-0.0110.0000.0000.0000.000
62E102ASP-1-0.713-0.86417.475-0.150-0.1500.0000.0000.0000.000
63E103TYR0-0.044-0.01315.484-0.041-0.0410.0000.0000.0000.000
64E104GLY00.0620.03613.9970.0480.0480.0000.0000.0000.000
65E105ILE0-0.064-0.01411.478-0.076-0.0760.0000.0000.0000.000
66E106VAL00.0140.0127.9280.0890.0890.0000.0000.0000.000
67E107ARG10.9530.9869.316-0.099-0.0990.0000.0000.0000.000
68E108TYR0-0.032-0.0472.801-0.7630.2580.834-0.461-1.393-0.004
69E109THR0-0.063-0.0468.220-0.021-0.0210.0000.0000.0000.000
70E110ASN0-0.0350.0046.376-0.127-0.1270.0000.0000.0000.000
71E111THR00.042-0.0087.806-0.088-0.0880.0000.0000.0000.000
72E112THR0-0.017-0.0059.091-0.065-0.0650.0000.0000.0000.000
73E113ILE0-0.0340.0022.594-1.753-0.1650.620-0.453-1.7540.003
74E114PRO00.0940.0513.004-2.079-0.8510.102-0.532-0.7980.002
75E115LYS10.8330.9131.844-5.906-10.03312.554-4.645-3.782-0.040
76E116ASP-1-0.838-0.8943.084-6.005-3.8760.080-1.111-1.099-0.009
77E117GLY0-0.0070.0125.144-0.131-0.127-0.001-0.0050.0030.000
78E118THR0-0.001-0.0266.8830.1810.1810.0000.0000.0000.000
79E119VAL00.000-0.0027.559-0.447-0.4470.0000.0000.0000.000
80E120GLY00.0040.0086.8410.4600.4600.0000.0000.0000.000
81E121GLY0-0.0020.0007.571-0.326-0.3260.0000.0000.0000.000
82E122GLN0-0.078-0.0279.8820.1150.1150.0000.0000.0000.000
83E123ASP-1-0.831-0.91811.088-1.242-1.2420.0000.0000.0000.000
84E124ILE0-0.039-0.02011.3760.1610.1610.0000.0000.0000.000
85E125THR0-0.033-0.02313.604-0.004-0.0040.0000.0000.0000.000
86E126SER0-0.023-0.00916.2400.0620.0620.0000.0000.0000.000
87E127ALA00.0380.02916.755-0.051-0.0510.0000.0000.0000.000
88E128ALA0-0.022-0.01318.2070.0400.0400.0000.0000.0000.000
89E129ASN00.0340.01420.915-0.018-0.0180.0000.0000.0000.000
90E130ALA00.0330.01422.2760.0010.0010.0000.0000.0000.000
91E131THR00.0180.00123.8870.0120.0120.0000.0000.0000.000
92E132VAL00.030-0.00326.833-0.007-0.0070.0000.0000.0000.000
93E133GLY0-0.0040.00128.4380.0040.0040.0000.0000.0000.000
94E134MET0-0.077-0.00922.979-0.012-0.0120.0000.0000.0000.000
95E135ALA00.0320.01823.9350.0020.0020.0000.0000.0000.000
96E136VAL0-0.033-0.02119.166-0.025-0.0250.0000.0000.0000.000
97E137THR00.002-0.00215.4160.0320.0320.0000.0000.0000.000
98E138ARG10.8480.92313.5600.2330.2330.0000.0000.0000.000
99E139ARG10.8450.9166.0111.0171.0170.0000.0000.0000.000
100E140GLY0-0.024-0.02310.075-0.074-0.0740.0000.0000.0000.000
101E141SER0-0.017-0.0017.2250.0890.0890.0000.0000.0000.000
102E142THR0-0.054-0.0479.1580.1100.1100.0000.0000.0000.000
103E143THR00.005-0.01312.7650.0040.0040.0000.0000.0000.000
104E156GLY00.0230.03212.0020.0110.0110.0000.0000.0000.000
105E157THR0-0.041-0.04113.070-0.075-0.0750.0000.0000.0000.000
106E158HIS00.0100.01214.8040.0480.0480.0000.0000.0000.000
107E159SER00.006-0.00617.706-0.051-0.0510.0000.0000.0000.000
108E160GLY00.0140.01220.2910.0280.0280.0000.0000.0000.000
109E161SER0-0.057-0.02023.177-0.011-0.0110.0000.0000.0000.000
110E162VAL00.0180.01123.0570.0070.0070.0000.0000.0000.000
111E163THR0-0.029-0.03325.2730.0090.0090.0000.0000.0000.000
112E164ALA0-0.014-0.01127.3530.0130.0130.0000.0000.0000.000
113E165LEU0-0.004-0.00125.985-0.015-0.0150.0000.0000.0000.000
114E166ASN00.0080.01027.2220.0070.0070.0000.0000.0000.000
115E167ALA00.0070.01226.9110.0120.0120.0000.0000.0000.000
116E168THR00.0030.00327.334-0.005-0.0050.0000.0000.0000.000
117E169VAL0-0.037-0.01424.3670.0050.0050.0000.0000.0000.000
118E170ASN00.009-0.00226.7120.0020.0020.0000.0000.0000.000
119E171TYR0-0.020-0.02620.8630.0040.0040.0000.0000.0000.000
120E172GLY00.0110.01026.0740.0080.0080.0000.0000.0000.000
121E173GLY00.010-0.00427.7920.0000.0000.0000.0000.0000.000
122E174GLY0-0.020-0.00629.5130.0020.0020.0000.0000.0000.000
123E175ASP-1-0.886-0.93124.501-0.049-0.0490.0000.0000.0000.000
124E176VAL0-0.066-0.03626.287-0.005-0.0050.0000.0000.0000.000
125E177VAL00.0050.01122.086-0.003-0.0030.0000.0000.0000.000
126E178TYR0-0.005-0.02225.3850.0060.0060.0000.0000.0000.000
127E179GLY00.0600.02625.407-0.010-0.0100.0000.0000.0000.000
128E180MET0-0.054-0.00720.187-0.022-0.0220.0000.0000.0000.000
129E181ILE0-0.029-0.00720.3450.0120.0120.0000.0000.0000.000
130E182ARG10.9740.98722.8270.1140.1140.0000.0000.0000.000
131E183THR00.0040.00521.185-0.008-0.0080.0000.0000.0000.000
132E184ASN0-0.0060.00124.168-0.002-0.0020.0000.0000.0000.000
133E190VAL00.0480.03718.4810.0070.0070.0000.0000.0000.000
134E191CYS0-0.055-0.00519.693-0.011-0.0110.0000.0000.0000.000
135E192ALA00.0520.00516.600-0.035-0.0350.0000.0000.0000.000
136E192GLU-1-0.810-0.90816.378-0.035-0.0350.0000.0000.0000.000
137E192PRO00.0500.01915.330-0.020-0.0200.0000.0000.0000.000
138E193GLY00.0400.05611.9710.0260.0260.0000.0000.0000.000
139E194ASP-1-0.769-0.86910.463-0.230-0.2300.0000.0000.0000.000
140E195SER00.006-0.04111.946-0.075-0.0750.0000.0000.0000.000
141E196GLY0-0.034-0.02110.583-0.002-0.0020.0000.0000.0000.000
142E197GLY00.0030.0189.141-0.120-0.1200.0000.0000.0000.000
143E198PRO0-0.0380.0098.4620.1100.1100.0000.0000.0000.000
144E199LEU00.0100.00811.4030.0480.0480.0000.0000.0000.000
145E200TYR00.001-0.02812.930-0.034-0.0340.0000.0000.0000.000
146E201SER00.0160.00315.8880.0610.0610.0000.0000.0000.000
147E202GLY00.0220.02118.5600.0120.0120.0000.0000.0000.000
148E207THR00.0250.01116.242-0.044-0.0440.0000.0000.0000.000
149E208ARG10.9000.95116.7540.3180.3180.0000.0000.0000.000
150E209ALA00.0320.01213.899-0.004-0.0040.0000.0000.0000.000
151E210ILE0-0.013-0.02315.6610.0630.0630.0000.0000.0000.000
152E211GLY00.020-0.00815.8950.0480.0480.0000.0000.0000.000
153E212LEU0-0.035-0.00411.730-0.091-0.0910.0000.0000.0000.000
154E213THR0-0.050-0.03513.3640.0680.0680.0000.0000.0000.000
155E214SER0-0.022-0.01414.9150.0130.0130.0000.0000.0000.000
156E215GLY00.1100.04517.6140.0220.0220.0000.0000.0000.000
157E216GLY0-0.003-0.00419.660-0.017-0.0170.0000.0000.0000.000
158E217SER0-0.060-0.01122.7840.0160.0160.0000.0000.0000.000
159E218GLY00.0340.01224.296-0.010-0.0100.0000.0000.0000.000
160E219ASN0-0.014-0.00822.2320.0010.0010.0000.0000.0000.000
161E221SER0-0.0480.00622.342-0.003-0.0030.0000.0000.0000.000
162E222SER0-0.012-0.02525.3890.0010.0010.0000.0000.0000.000
163E223GLY00.0240.03525.576-0.002-0.0020.0000.0000.0000.000
164E224GLY00.010-0.01924.4950.0110.0110.0000.0000.0000.000
165E225THR0-0.100-0.03124.874-0.007-0.0070.0000.0000.0000.000
166E226THR0-0.022-0.02318.3310.0130.0130.0000.0000.0000.000
167E227PHE00.000-0.02021.254-0.005-0.0050.0000.0000.0000.000
168E228PHE0-0.007-0.01415.752-0.010-0.0100.0000.0000.0000.000
169E229GLN00.0640.02917.4980.0430.0430.0000.0000.0000.000
170E230PRO00.0150.00217.853-0.052-0.0520.0000.0000.0000.000
171E231VAL00.0220.00714.0340.0050.0050.0000.0000.0000.000
172E232THR0-0.018-0.01017.195-0.007-0.0070.0000.0000.0000.000
173E233GLU-1-0.871-0.94319.719-0.208-0.2080.0000.0000.0000.000
174E234ALA00.0110.01615.8650.0140.0140.0000.0000.0000.000
175E235LEU0-0.079-0.04514.001-0.004-0.0040.0000.0000.0000.000
176E235VAL00.0100.00317.2140.0130.0130.0000.0000.0000.000
177E236ALA0-0.0300.00119.6140.0170.0170.0000.0000.0000.000
178E237TYR0-0.008-0.02115.3300.0190.0190.0000.0000.0000.000
179E238GLY00.0230.03418.0660.0030.0030.0000.0000.0000.000
180E239VAL0-0.075-0.02813.711-0.017-0.0170.0000.0000.0000.000
181E240SER0-0.028-0.02314.6580.0330.0330.0000.0000.0000.000
182E241VAL00.0190.00911.946-0.073-0.0730.0000.0000.0000.000
183E242TYR0-0.041-0.0356.8980.2820.2820.0000.0000.0000.000