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

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FMODB ID: 497RN

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 OptAll
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 -1753855.597529
FMO2-HF: Nuclear repulsion 1687414.170543
FMO2-HF: Total energy -66441.426986
FMO2-MP2: Total energy -66633.192059


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.
-29.996-15.70220.956-13.747-21.501-0.077
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 : -0.027 / q_NPA : -0.002
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].
3E18GLY00.0550.0193.377-2.2121.4280.023-2.033-1.6300.004
4E19GLY00.003-0.0266.0940.2310.2310.0000.0000.0000.000
5E29ASP-1-0.810-0.8512.361-2.214-0.6122.456-1.597-2.461-0.008
6E30ALA0-0.020-0.0173.988-0.519-0.2410.005-0.072-0.2100.000
7E31ILE0-0.0380.0012.861-1.4070.0940.358-0.675-1.184-0.007
8E32TYR00.004-0.0084.993-0.287-0.249-0.001-0.002-0.0340.000
9E33SER00.0960.0528.2900.0460.0460.0000.0000.0000.000
10E34SER00.007-0.01111.4360.0410.0410.0000.0000.0000.000
11E39THR00.0160.01214.5840.0080.0080.0000.0000.0000.000
12E40GLY00.0160.00413.425-0.010-0.0100.0000.0000.0000.000
13E41ARG10.8050.8907.961-0.153-0.1530.0000.0000.0000.000
14E42CYS0-0.093-0.0148.537-0.014-0.0140.0000.0000.0000.000
15E43SER00.0260.0096.2950.1180.1180.0000.0000.0000.000
16E44LEU0-0.0030.0202.391-0.892-0.2061.693-0.436-1.943-0.003
17E45GLY00.0620.0355.799-0.024-0.0240.0000.0000.0000.000
18E46PHE00.003-0.0237.831-0.106-0.1060.0000.0000.0000.000
19E47ASN0-0.0120.0043.0890.4011.2820.024-0.451-0.4540.001
20E48VAL0-0.022-0.0136.6820.2160.2160.0000.0000.0000.000
21E48ARG10.8620.9299.9230.7370.7370.0000.0000.0000.000
22E48SER00.0590.01312.5060.0660.0660.0000.0000.0000.000
23E48GLY00.0320.02616.1160.0240.0240.0000.0000.0000.000
24E48SER0-0.016-0.01015.421-0.068-0.0680.0000.0000.0000.000
25E49THR0-0.0130.00713.416-0.001-0.0010.0000.0000.0000.000
26E50TYR00.009-0.0048.415-0.033-0.0330.0000.0000.0000.000
27E51TYR00.003-0.0158.7500.1930.1930.0000.0000.0000.000
28E52PHE00.0220.0164.901-0.331-0.3310.0000.0000.0000.000
29E53LEU00.0160.0157.3610.2450.2450.0000.0000.0000.000
30E54THR0-0.007-0.0228.769-0.096-0.0960.0000.0000.0000.000
31E55ALA00.0700.03910.8340.0150.0150.0000.0000.0000.000
32E56GLY00.0100.01813.8430.0160.0160.0000.0000.0000.000
33E57HIS00.022-0.01615.9050.0380.0380.0000.0000.0000.000
34E59THR0-0.074-0.03511.9800.0220.0220.0000.0000.0000.000
35E60ASP-1-0.836-0.90914.065-0.028-0.0280.0000.0000.0000.000
36E62GLY0-0.0150.00017.2490.0210.0210.0000.0000.0000.000
37E63ALA0-0.050-0.01013.2010.0310.0310.0000.0000.0000.000
38E64THR00.0470.02514.298-0.015-0.0150.0000.0000.0000.000
39E65THR0-0.053-0.01411.498-0.035-0.0350.0000.0000.0000.000
40E66TRP00.0290.0096.8510.0190.0190.0000.0000.0000.000
41E67TRP0-0.001-0.0097.0120.0110.0110.0000.0000.0000.000
42E68ALA00.0620.0232.766-0.578-0.1030.194-0.145-0.5240.001
43E78ASN0-0.010-0.0224.084-0.209-0.110-0.0010.008-0.1060.000
44E79SER00.0580.0327.389-0.114-0.1140.0000.0000.0000.000
45E80ALA0-0.008-0.00310.810-0.096-0.0960.0000.0000.0000.000
46E81ARG10.8530.92410.209-0.475-0.4750.0000.0000.0000.000
47E82THR00.0260.02510.8200.0040.0040.0000.0000.0000.000
48E83THR0-0.029-0.0076.0290.0110.0110.0000.0000.0000.000
49E84VAL00.0150.0086.9260.1730.1730.0000.0000.0000.000
50E85LEU0-0.0070.0062.488-0.809-0.0841.442-0.334-1.8330.003
51E86GLY00.0620.0095.927-0.267-0.2670.0000.0000.0000.000
52E87THR0-0.080-0.0388.7250.0860.0860.0000.0000.0000.000
53E88THR00.015-0.01911.971-0.087-0.0870.0000.0000.0000.000
54E89SER0-0.094-0.05313.3640.0190.0190.0000.0000.0000.000
55E90GLY00.0260.01215.3670.0000.0000.0000.0000.0000.000
56E91SER0-0.032-0.03315.622-0.018-0.0180.0000.0000.0000.000
57E93SER0-0.011-0.00217.8080.0120.0120.0000.0000.0000.000
58E94PHE00.0180.03019.482-0.019-0.0190.0000.0000.0000.000
59E99PRO00.0360.05021.3220.0070.0070.0000.0000.0000.000
60E100ASN0-0.038-0.03923.912-0.004-0.0040.0000.0000.0000.000
61E101ASN0-0.034-0.02121.8690.0010.0010.0000.0000.0000.000
62E102ASP-1-0.697-0.83017.816-0.152-0.1520.0000.0000.0000.000
63E103TYR0-0.060-0.02315.800-0.038-0.0380.0000.0000.0000.000
64E104GLY00.0590.02814.3880.0490.0490.0000.0000.0000.000
65E105ILE0-0.059-0.01411.419-0.085-0.0850.0000.0000.0000.000
66E106VAL00.0120.0188.0190.1010.1010.0000.0000.0000.000
67E107ARG10.9620.9918.9450.0310.0310.0000.0000.0000.000
68E108TYR0-0.033-0.0412.765-0.7590.2030.848-0.476-1.334-0.005
69E109THR0-0.074-0.0488.4560.0350.0350.0000.0000.0000.000
70E110ASN0-0.0200.0076.399-0.140-0.1400.0000.0000.0000.000
71E111THR00.0550.0107.415-0.177-0.1770.0000.0000.0000.000
72E112THR0-0.018-0.0118.814-0.174-0.1740.0000.0000.0000.000
73E113ILE0-0.0250.0062.602-1.658-0.0540.829-0.509-1.9240.004
74E114PRO00.0580.0292.245-1.843-0.7931.294-0.938-1.4060.003
75E115LYS10.8300.9141.991-6.343-7.0558.257-3.731-3.814-0.039
76E116ASP-1-0.819-0.8872.111-10.764-9.3143.536-2.348-2.638-0.031
77E117GLY00.0240.0204.8130.1300.145-0.001-0.008-0.0060.000
78E118THR0-0.027-0.0326.7980.1620.1620.0000.0000.0000.000
79E119VAL0-0.004-0.0067.757-0.345-0.3450.0000.0000.0000.000
80E120GLY00.0190.0156.5250.3900.3900.0000.0000.0000.000
81E121GLY0-0.0040.0007.496-0.307-0.3070.0000.0000.0000.000
82E122GLN0-0.102-0.04410.2200.1170.1170.0000.0000.0000.000
83E123ASP-1-0.817-0.92211.142-1.128-1.1280.0000.0000.0000.000
84E124ILE0-0.042-0.01511.6480.1440.1440.0000.0000.0000.000
85E125THR00.0250.01913.608-0.049-0.0490.0000.0000.0000.000
86E126SER0-0.034-0.01016.3940.0670.0670.0000.0000.0000.000
87E127ALA00.0300.00916.517-0.061-0.0610.0000.0000.0000.000
88E128ALA0-0.025-0.01118.2050.0410.0410.0000.0000.0000.000
89E129ASN00.0450.03020.827-0.027-0.0270.0000.0000.0000.000
90E130ALA00.0500.02022.2670.0030.0030.0000.0000.0000.000
91E131THR00.0280.00823.8370.0090.0090.0000.0000.0000.000
92E132VAL00.006-0.00726.890-0.004-0.0040.0000.0000.0000.000
93E133GLY00.0130.01028.4950.0030.0030.0000.0000.0000.000
94E134MET0-0.100-0.02923.028-0.010-0.0100.0000.0000.0000.000
95E135ALA00.0520.02424.1620.0010.0010.0000.0000.0000.000
96E136VAL0-0.043-0.01319.402-0.028-0.0280.0000.0000.0000.000
97E137THR00.0210.01315.3590.0520.0520.0000.0000.0000.000
98E138ARG10.8210.92813.4020.1130.1130.0000.0000.0000.000
99E139ARG10.8180.8865.4770.4460.4460.0000.0000.0000.000
100E140GLY0-0.031-0.0299.554-0.065-0.0650.0000.0000.0000.000
101E141SER0-0.002-0.0036.7810.0950.0950.0000.0000.0000.000
102E142THR0-0.070-0.0408.8940.1070.1070.0000.0000.0000.000
103E143THR00.024-0.01212.5250.0090.0090.0000.0000.0000.000
104E156GLY00.0140.03511.8640.0090.0090.0000.0000.0000.000
105E157THR0-0.035-0.03712.810-0.064-0.0640.0000.0000.0000.000
106E158HIS00.0070.00214.5090.0260.0260.0000.0000.0000.000
107E159SER0-0.004-0.02117.684-0.033-0.0330.0000.0000.0000.000
108E160GLY00.0010.00220.2360.0260.0260.0000.0000.0000.000
109E161SER0-0.026-0.00723.258-0.011-0.0110.0000.0000.0000.000
110E162VAL00.0150.00222.9470.0070.0070.0000.0000.0000.000
111E163THR0-0.050-0.03325.1740.0060.0060.0000.0000.0000.000
112E164ALA0-0.014-0.01027.2330.0110.0110.0000.0000.0000.000
113E165LEU00.0050.00025.732-0.015-0.0150.0000.0000.0000.000
114E166ASN0-0.007-0.00327.3350.0070.0070.0000.0000.0000.000
115E167ALA00.0030.02126.9680.0110.0110.0000.0000.0000.000
116E168THR0-0.011-0.01027.669-0.006-0.0060.0000.0000.0000.000
117E169VAL0-0.045-0.01524.7290.0070.0070.0000.0000.0000.000
118E170ASN00.018-0.00327.443-0.001-0.0010.0000.0000.0000.000
119E171TYR0-0.015-0.01721.1730.0090.0090.0000.0000.0000.000
120E172GLY00.0340.03026.1460.0090.0090.0000.0000.0000.000
121E173GLY0-0.003-0.01728.194-0.003-0.0030.0000.0000.0000.000
122E174GLY0-0.009-0.00629.6090.0030.0030.0000.0000.0000.000
123E175ASP-1-0.891-0.93224.472-0.060-0.0600.0000.0000.0000.000
124E176VAL0-0.063-0.03526.295-0.003-0.0030.0000.0000.0000.000
125E177VAL0-0.014-0.00322.683-0.005-0.0050.0000.0000.0000.000
126E178TYR00.0230.00025.9690.0090.0090.0000.0000.0000.000
127E179GLY00.0600.02525.345-0.012-0.0120.0000.0000.0000.000
128E180MET0-0.069-0.01220.616-0.019-0.0190.0000.0000.0000.000
129E181ILE00.0010.00020.2320.0120.0120.0000.0000.0000.000
130E182ARG10.8930.94622.9480.0990.0990.0000.0000.0000.000
131E183THR00.009-0.00520.987-0.007-0.0070.0000.0000.0000.000
132E184ASN00.011-0.00224.1150.0010.0010.0000.0000.0000.000
133E190VAL00.0500.03718.4440.0110.0110.0000.0000.0000.000
134E191CYS0-0.0420.00319.292-0.010-0.0100.0000.0000.0000.000
135E192ALA00.0450.00616.334-0.027-0.0270.0000.0000.0000.000
136E192GLU-1-0.818-0.90416.1220.0270.0270.0000.0000.0000.000
137E192PRO00.0370.00615.157-0.010-0.0100.0000.0000.0000.000
138E193GLY00.0520.05512.0190.0380.0380.0000.0000.0000.000
139E194ASP-1-0.769-0.86310.419-0.078-0.0780.0000.0000.0000.000
140E195SER00.011-0.00711.796-0.065-0.0650.0000.0000.0000.000
141E196GLY0-0.023-0.02010.6860.0040.0040.0000.0000.0000.000
142E197GLY00.0010.0169.181-0.111-0.1110.0000.0000.0000.000
143E198PRO0-0.0470.0098.5770.0830.0830.0000.0000.0000.000
144E199LEU0-0.0200.00011.4920.0690.0690.0000.0000.0000.000
145E200TYR00.037-0.00813.011-0.050-0.0500.0000.0000.0000.000
146E201SER0-0.007-0.01415.9090.0640.0640.0000.0000.0000.000
147E202GLY00.0460.03918.6130.0130.0130.0000.0000.0000.000
148E207THR00.006-0.00116.019-0.024-0.0240.0000.0000.0000.000
149E208ARG10.8770.92617.0320.3030.3030.0000.0000.0000.000
150E209ALA00.0370.01213.9800.0140.0140.0000.0000.0000.000
151E210ILE0-0.025-0.02115.6140.0570.0570.0000.0000.0000.000
152E211GLY00.012-0.01315.9340.0410.0410.0000.0000.0000.000
153E212LEU0-0.0280.00011.759-0.083-0.0830.0000.0000.0000.000
154E213THR0-0.036-0.03913.3660.0650.0650.0000.0000.0000.000
155E214SER0-0.017-0.02115.1130.0130.0130.0000.0000.0000.000
156E215GLY00.0820.03117.8740.0230.0230.0000.0000.0000.000
157E216GLY0-0.009-0.01519.842-0.017-0.0170.0000.0000.0000.000
158E217SER0-0.042-0.00322.4450.0140.0140.0000.0000.0000.000
159E218GLY00.0380.01424.623-0.009-0.0090.0000.0000.0000.000
160E219ASN0-0.020-0.02022.0880.0060.0060.0000.0000.0000.000
161E221SER0-0.0070.01221.9700.0020.0020.0000.0000.0000.000
162E222SER0-0.072-0.03625.0130.0050.0050.0000.0000.0000.000
163E223GLY00.0310.04125.667-0.004-0.0040.0000.0000.0000.000
164E224GLY00.032-0.00624.7550.0090.0090.0000.0000.0000.000
165E225THR0-0.087-0.02424.628-0.007-0.0070.0000.0000.0000.000
166E226THR0-0.016-0.00618.1770.0130.0130.0000.0000.0000.000
167E227PHE00.022-0.00321.243-0.007-0.0070.0000.0000.0000.000
168E228PHE0-0.007-0.01815.617-0.005-0.0050.0000.0000.0000.000
169E229GLN00.0680.02917.6030.0400.0400.0000.0000.0000.000
170E230PRO00.0260.00317.991-0.047-0.0470.0000.0000.0000.000
171E231VAL0-0.0110.00713.975-0.004-0.0040.0000.0000.0000.000
172E232THR0-0.009-0.02017.077-0.021-0.0210.0000.0000.0000.000
173E233GLU-1-0.862-0.92719.551-0.231-0.2310.0000.0000.0000.000
174E234ALA00.0150.01315.8470.0090.0090.0000.0000.0000.000
175E235LEU0-0.062-0.03213.816-0.022-0.0220.0000.0000.0000.000
176E235VAL00.0040.00016.9950.0080.0080.0000.0000.0000.000
177E236ALA0-0.023-0.00319.4200.0140.0140.0000.0000.0000.000
178E237TYR00.002-0.01115.3630.0200.0200.0000.0000.0000.000
179E238GLY00.0160.03017.923-0.008-0.0080.0000.0000.0000.000
180E239VAL0-0.052-0.01213.765-0.024-0.0240.0000.0000.0000.000
181E240SER0-0.041-0.03014.5600.0520.0520.0000.0000.0000.000
182E241VAL00.0260.01011.826-0.095-0.0950.0000.0000.0000.000
183E242TYR0-0.059-0.0397.1660.2940.2940.0000.0000.0000.000