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: K9N73

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 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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1751773.22429
FMO2-HF: Nuclear repulsion 1685331.901508
FMO2-HF: Total energy -66441.322782
FMO2-MP2: Total energy -66633.052889


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.
-27.429-14.20118.631-12.995-18.864-0.052
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 : -0.014 / q_NPA : -0.001
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].
3E18GLY00.0750.0263.339-3.3511.5350.011-2.772-2.1250.008
4E19GLY0-0.016-0.0275.9270.1770.1770.0000.0000.0000.000
5E29ASP-1-0.822-0.8702.433-2.598-0.9262.011-1.495-2.187-0.008
6E30ALA0-0.009-0.0144.189-0.401-0.1980.001-0.046-0.1580.000
7E31ILE0-0.0310.0042.883-1.538-0.0960.336-0.607-1.171-0.006
8E32TYR0-0.013-0.0154.913-0.287-0.255-0.001-0.003-0.0270.000
9E33SER00.1110.0728.2310.0810.0810.0000.0000.0000.000
10E34SER0-0.006-0.02111.2510.0370.0370.0000.0000.0000.000
11E39THR00.0190.00914.4560.0060.0060.0000.0000.0000.000
12E40GLY00.0200.01013.310-0.009-0.0090.0000.0000.0000.000
13E41ARG10.8020.8918.044-0.136-0.1360.0000.0000.0000.000
14E42CYS0-0.096-0.0248.403-0.014-0.0140.0000.0000.0000.000
15E43SER00.0270.0046.3200.0930.0930.0000.0000.0000.000
16E44LEU0-0.0140.0192.459-0.982-0.0110.830-0.304-1.497-0.001
17E45GLY00.0750.0355.807-0.060-0.0600.0000.0000.0000.000
18E46PHE0-0.007-0.0297.983-0.161-0.1610.0000.0000.0000.000
19E47ASN00.0050.0192.8550.7701.3720.044-0.222-0.4240.001
20E48VAL0-0.016-0.0186.7920.1420.1420.0000.0000.0000.000
21E48ARG10.8940.9479.8060.6680.6680.0000.0000.0000.000
22E48SER00.0630.02912.4190.0520.0520.0000.0000.0000.000
23E48GLY00.0210.02515.9350.0310.0310.0000.0000.0000.000
24E48SER0-0.019-0.02715.016-0.060-0.0600.0000.0000.0000.000
25E49THR0-0.0170.00713.2950.0200.0200.0000.0000.0000.000
26E50TYR00.008-0.0028.223-0.038-0.0380.0000.0000.0000.000
27E51TYR00.005-0.0138.9030.1940.1940.0000.0000.0000.000
28E52PHE00.0110.0125.368-0.256-0.2560.0000.0000.0000.000
29E53LEU00.0110.0117.4500.2140.2140.0000.0000.0000.000
30E54THR0-0.006-0.0238.566-0.088-0.0880.0000.0000.0000.000
31E55ALA00.0670.03410.6270.0100.0100.0000.0000.0000.000
32E56GLY00.0280.02213.6560.0240.0240.0000.0000.0000.000
33E57HIS00.027-0.00515.7980.0390.0390.0000.0000.0000.000
34E59THR0-0.086-0.03511.8630.0230.0230.0000.0000.0000.000
35E60ASP-1-0.885-0.92813.9970.0000.0000.0000.0000.0000.000
36E62GLY00.0330.02617.5450.0180.0180.0000.0000.0000.000
37E63ALA0-0.055-0.01213.1240.0330.0330.0000.0000.0000.000
38E64THR00.0220.01414.880-0.010-0.0100.0000.0000.0000.000
39E65THR0-0.0070.00211.181-0.021-0.0210.0000.0000.0000.000
40E66TRP00.0270.0156.8210.0080.0080.0000.0000.0000.000
41E67TRP0-0.012-0.0257.0770.0530.0530.0000.0000.0000.000
42E68ALA00.0550.0162.810-0.540-0.0690.139-0.131-0.4800.001
43E78ASN00.010-0.0044.106-0.240-0.130-0.0010.006-0.1150.000
44E79SER00.0560.0287.309-0.103-0.1030.0000.0000.0000.000
45E80ALA0-0.004-0.00210.728-0.096-0.0960.0000.0000.0000.000
46E81ARG10.8430.92510.048-0.528-0.5280.0000.0000.0000.000
47E82THR00.0210.01310.2250.0000.0000.0000.0000.0000.000
48E83THR0-0.0230.0006.0130.0270.0270.0000.0000.0000.000
49E84VAL00.0150.0097.0650.1400.1400.0000.0000.0000.000
50E85LEU00.0050.0132.611-0.894-0.0351.096-0.289-1.6660.003
51E86GLY00.0470.0006.108-0.244-0.2440.0000.0000.0000.000
52E87THR0-0.089-0.0358.9900.0520.0520.0000.0000.0000.000
53E88THR00.012-0.02311.972-0.064-0.0640.0000.0000.0000.000
54E89SER0-0.084-0.04913.1820.0060.0060.0000.0000.0000.000
55E90GLY00.0130.00615.054-0.001-0.0010.0000.0000.0000.000
56E91SER0-0.043-0.03215.427-0.011-0.0110.0000.0000.0000.000
57E93SER00.0230.01617.5800.0130.0130.0000.0000.0000.000
58E94PHE00.0050.02619.329-0.021-0.0210.0000.0000.0000.000
59E99PRO00.0220.02721.2830.0090.0090.0000.0000.0000.000
60E100ASN0-0.020-0.01923.668-0.004-0.0040.0000.0000.0000.000
61E101ASN0-0.037-0.02821.590-0.004-0.0040.0000.0000.0000.000
62E102ASP-1-0.704-0.84317.544-0.137-0.1370.0000.0000.0000.000
63E103TYR0-0.041-0.01115.553-0.037-0.0370.0000.0000.0000.000
64E104GLY00.0580.02914.0950.0470.0470.0000.0000.0000.000
65E105ILE0-0.065-0.01611.549-0.079-0.0790.0000.0000.0000.000
66E106VAL00.0070.0128.0320.0910.0910.0000.0000.0000.000
67E107ARG10.9720.9929.392-0.047-0.0470.0000.0000.0000.000
68E108TYR0-0.030-0.0402.729-0.7040.2130.953-0.457-1.413-0.004
69E109THR0-0.067-0.0508.281-0.007-0.0070.0000.0000.0000.000
70E110ASN0-0.0310.0106.358-0.122-0.1220.0000.0000.0000.000
71E111THR00.047-0.0057.704-0.121-0.1210.0000.0000.0000.000
72E112THR0-0.017-0.0039.019-0.083-0.0830.0000.0000.0000.000
73E113ILE0-0.040-0.0032.541-1.655-0.1710.848-0.455-1.8770.003
74E114PRO00.0880.0432.987-1.692-0.6380.080-0.431-0.7030.001
75E115LYS10.8220.9151.843-5.950-9.77212.073-4.608-3.643-0.039
76E116ASP-1-0.836-0.8942.830-7.281-4.9330.212-1.175-1.385-0.011
77E117GLY00.0050.0145.122-0.082-0.083-0.001-0.0060.0070.000
78E118THR0-0.007-0.0256.8490.2000.2000.0000.0000.0000.000
79E119VAL0-0.001-0.0027.609-0.419-0.4190.0000.0000.0000.000
80E120GLY00.0200.0176.8350.4240.4240.0000.0000.0000.000
81E121GLY0-0.007-0.0087.577-0.355-0.3550.0000.0000.0000.000
82E122GLN0-0.104-0.0479.8890.1080.1080.0000.0000.0000.000
83E123ASP-1-0.839-0.92111.084-1.203-1.2030.0000.0000.0000.000
84E124ILE0-0.036-0.01211.6780.1670.1670.0000.0000.0000.000
85E125THR0-0.001-0.00913.606-0.014-0.0140.0000.0000.0000.000
86E126SER0-0.029-0.01016.3640.0620.0620.0000.0000.0000.000
87E127ALA00.0240.02216.847-0.046-0.0460.0000.0000.0000.000
88E128ALA0-0.018-0.01018.3630.0380.0380.0000.0000.0000.000
89E129ASN00.0370.01921.048-0.021-0.0210.0000.0000.0000.000
90E130ALA00.0390.01922.3010.0020.0020.0000.0000.0000.000
91E131THR00.0350.00823.9390.0100.0100.0000.0000.0000.000
92E132VAL00.006-0.01026.874-0.005-0.0050.0000.0000.0000.000
93E133GLY00.0020.00328.4700.0030.0030.0000.0000.0000.000
94E134MET0-0.082-0.01423.054-0.012-0.0120.0000.0000.0000.000
95E135ALA00.0410.02324.0270.0030.0030.0000.0000.0000.000
96E136VAL0-0.026-0.01519.225-0.028-0.0280.0000.0000.0000.000
97E137THR00.0000.00015.4090.0440.0440.0000.0000.0000.000
98E138ARG10.8390.93313.5740.1530.1530.0000.0000.0000.000
99E139ARG10.8290.9005.6440.6890.6890.0000.0000.0000.000
100E140GLY0-0.028-0.02310.007-0.073-0.0730.0000.0000.0000.000
101E141SER0-0.009-0.0096.9630.0890.0890.0000.0000.0000.000
102E142THR0-0.062-0.0389.0070.1120.1120.0000.0000.0000.000
103E143THR00.004-0.02212.6070.0040.0040.0000.0000.0000.000
104E156GLY00.0280.03511.9250.0040.0040.0000.0000.0000.000
105E157THR0-0.040-0.03912.993-0.059-0.0590.0000.0000.0000.000
106E158HIS00.0100.01114.7810.0360.0360.0000.0000.0000.000
107E159SER0-0.002-0.01917.703-0.034-0.0340.0000.0000.0000.000
108E160GLY00.0100.00720.2900.0270.0270.0000.0000.0000.000
109E161SER0-0.019-0.01023.183-0.013-0.0130.0000.0000.0000.000
110E162VAL0-0.007-0.00123.0270.0080.0080.0000.0000.0000.000
111E163THR0-0.042-0.03725.3010.0070.0070.0000.0000.0000.000
112E164ALA0-0.008-0.00627.3830.0110.0110.0000.0000.0000.000
113E165LEU0-0.006-0.00325.970-0.014-0.0140.0000.0000.0000.000
114E166ASN0-0.010-0.00227.2700.0080.0080.0000.0000.0000.000
115E167ALA00.0160.01926.9190.0120.0120.0000.0000.0000.000
116E168THR0-0.0010.00027.371-0.006-0.0060.0000.0000.0000.000
117E169VAL0-0.036-0.01424.4390.0060.0060.0000.0000.0000.000
118E170ASN00.009-0.00326.7660.0010.0010.0000.0000.0000.000
119E171TYR0-0.018-0.02520.8930.0060.0060.0000.0000.0000.000
120E172GLY00.0170.01526.1050.0090.0090.0000.0000.0000.000
121E173GLY00.008-0.00527.8400.0000.0000.0000.0000.0000.000
122E174GLY0-0.016-0.00429.5810.0020.0020.0000.0000.0000.000
123E175ASP-1-0.864-0.92724.452-0.045-0.0450.0000.0000.0000.000
124E176VAL0-0.076-0.03926.347-0.003-0.0030.0000.0000.0000.000
125E177VAL0-0.0030.00922.159-0.004-0.0040.0000.0000.0000.000
126E178TYR00.000-0.02025.4700.0070.0070.0000.0000.0000.000
127E179GLY00.0530.02625.454-0.010-0.0100.0000.0000.0000.000
128E180MET0-0.046-0.00520.296-0.022-0.0220.0000.0000.0000.000
129E181ILE0-0.032-0.01220.4280.0110.0110.0000.0000.0000.000
130E182ARG10.9410.97822.8570.1000.1000.0000.0000.0000.000
131E183THR00.0050.00021.144-0.008-0.0080.0000.0000.0000.000
132E184ASN0-0.009-0.00124.1850.0000.0000.0000.0000.0000.000
133E190VAL00.0460.04018.4570.0070.0070.0000.0000.0000.000
134E191CYS0-0.044-0.00319.563-0.012-0.0120.0000.0000.0000.000
135E192ALA00.0580.01216.586-0.029-0.0290.0000.0000.0000.000
136E192GLU-1-0.816-0.90616.2820.0070.0070.0000.0000.0000.000
137E192PRO00.0570.02315.240-0.014-0.0140.0000.0000.0000.000
138E193GLY00.0370.04811.8900.0300.0300.0000.0000.0000.000
139E194ASP-1-0.766-0.86410.387-0.126-0.1260.0000.0000.0000.000
140E195SER00.008-0.01011.917-0.067-0.0670.0000.0000.0000.000
141E196GLY0-0.030-0.02310.5940.0050.0050.0000.0000.0000.000
142E197GLY00.0070.0209.159-0.115-0.1150.0000.0000.0000.000
143E198PRO0-0.0340.0128.5240.0900.0900.0000.0000.0000.000
144E199LEU0-0.0080.00811.4390.0540.0540.0000.0000.0000.000
145E200TYR00.025-0.01912.850-0.043-0.0430.0000.0000.0000.000
146E201SER00.005-0.01215.9280.0610.0610.0000.0000.0000.000
147E202GLY00.0200.02118.6040.0070.0070.0000.0000.0000.000
148E207THR00.0270.01416.236-0.039-0.0390.0000.0000.0000.000
149E208ARG10.9030.95216.9380.2990.2990.0000.0000.0000.000
150E209ALA00.0280.00514.0970.0020.0020.0000.0000.0000.000
151E210ILE0-0.023-0.02815.7500.0590.0590.0000.0000.0000.000
152E211GLY00.027-0.00315.9490.0440.0440.0000.0000.0000.000
153E212LEU0-0.046-0.00811.643-0.083-0.0830.0000.0000.0000.000
154E213THR0-0.048-0.04113.3040.0630.0630.0000.0000.0000.000
155E214SER0-0.016-0.01614.9540.0130.0130.0000.0000.0000.000
156E215GLY00.0950.03817.6490.0230.0230.0000.0000.0000.000
157E216GLY00.000-0.00319.658-0.017-0.0170.0000.0000.0000.000
158E217SER0-0.061-0.01222.7600.0150.0150.0000.0000.0000.000
159E218GLY00.0350.01324.231-0.009-0.0090.0000.0000.0000.000
160E219ASN0-0.015-0.00422.1220.0040.0040.0000.0000.0000.000
161E221SER0-0.0200.01622.2140.0010.0010.0000.0000.0000.000
162E222SER0-0.048-0.04025.2450.0000.0000.0000.0000.0000.000
163E223GLY00.0290.03525.478-0.004-0.0040.0000.0000.0000.000
164E224GLY00.015-0.01624.4170.0100.0100.0000.0000.0000.000
165E225THR0-0.088-0.02824.831-0.009-0.0090.0000.0000.0000.000
166E226THR0-0.017-0.01918.3270.0140.0140.0000.0000.0000.000
167E227PHE00.009-0.01721.263-0.007-0.0070.0000.0000.0000.000
168E228PHE00.004-0.01215.629-0.007-0.0070.0000.0000.0000.000
169E229GLN00.0470.01817.5400.0390.0390.0000.0000.0000.000
170E230PRO00.0220.00317.905-0.049-0.0490.0000.0000.0000.000
171E231VAL00.0070.00314.1720.0010.0010.0000.0000.0000.000
172E232THR0-0.012-0.01417.293-0.011-0.0110.0000.0000.0000.000
173E233GLU-1-0.861-0.92619.828-0.208-0.2080.0000.0000.0000.000
174E234ALA00.0070.01215.9110.0130.0130.0000.0000.0000.000
175E235LEU0-0.071-0.04114.126-0.008-0.0080.0000.0000.0000.000
176E235VAL00.004-0.00217.3030.0100.0100.0000.0000.0000.000
177E236ALA0-0.0270.00519.6310.0160.0160.0000.0000.0000.000
178E237TYR00.005-0.01515.6560.0170.0170.0000.0000.0000.000
179E238GLY00.0270.03718.112-0.001-0.0010.0000.0000.0000.000
180E239VAL0-0.072-0.02813.810-0.021-0.0210.0000.0000.0000.000
181E240SER0-0.022-0.01814.7440.0390.0390.0000.0000.0000.000
182E241VAL00.0130.00312.098-0.081-0.0810.0000.0000.0000.000
183E242TYR0-0.038-0.0317.0970.2980.2980.0000.0000.0000.000