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: JL6Z9

Calculation Name: 5CDD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CDD

Chain ID: A

ChEMBL ID:

UniProt ID: D1FK67

Base Structure: X-ray

Registration Date: 2023-06-21

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2239426.073171
FMO2-HF: Nuclear repulsion 2155461.36483
FMO2-HF: Total energy -83964.708341
FMO2-MP2: Total energy -84208.897345


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(A:1:ILE)


Summations of interaction energy for fragment #1(A:1: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.
-3.9970.9510.923-2.099-3.771-0.007
Interaction energy analysis for fragmet #1(A:1:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.012
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].
3A3ILE00.001-0.0092.561-3.994-0.5470.878-1.718-2.607-0.006
4A4GLY00.0100.0084.9100.1770.307-0.001-0.009-0.1200.000
5A5ASN0-0.0300.0048.0900.1510.1510.0000.0000.0000.000
6A6LYS10.8850.9368.404-0.116-0.1160.0000.0000.0000.000
7A7THR00.0180.0059.0960.1380.1380.0000.0000.0000.000
8A8ASN0-0.035-0.02910.211-0.114-0.1140.0000.0000.0000.000
9A9GLU-1-0.805-0.89813.2830.1330.1330.0000.0000.0000.000
10A10ASN0-0.049-0.01316.207-0.039-0.0390.0000.0000.0000.000
11A11VAL0-0.017-0.00314.3570.0530.0530.0000.0000.0000.000
12A12ILE00.0050.00017.487-0.040-0.0400.0000.0000.0000.000
13A13SER00.0120.00819.0030.0470.0470.0000.0000.0000.000
14A14PHE0-0.043-0.02320.883-0.018-0.0180.0000.0000.0000.000
15A15PHE00.010-0.00823.6880.0030.0030.0000.0000.0000.000
16A16ASP-1-0.896-0.93925.6830.1240.1240.0000.0000.0000.000
17A17SER0-0.067-0.02523.2610.0060.0060.0000.0000.0000.000
18A18THR0-0.005-0.02024.360-0.008-0.0080.0000.0000.0000.000
19A19ASP-1-0.817-0.88322.9910.0950.0950.0000.0000.0000.000
20A20ALA00.001-0.01320.262-0.006-0.0060.0000.0000.0000.000
21A21GLU-1-0.962-0.97718.3360.0970.0970.0000.0000.0000.000
22A22THR0-0.006-0.02921.239-0.010-0.0100.0000.0000.0000.000
23A23GLN00.0140.02324.7420.0000.0000.0000.0000.0000.000
24A24ASN0-0.009-0.00519.474-0.001-0.0010.0000.0000.0000.000
25A25HIS0-0.0080.00023.322-0.005-0.0050.0000.0000.0000.000
26A26ASP-1-0.799-0.89925.0400.0570.0570.0000.0000.0000.000
27A27VAL00.0090.01026.003-0.005-0.0050.0000.0000.0000.000
28A28LEU00.009-0.00522.330-0.005-0.0050.0000.0000.0000.000
29A29MET0-0.056-0.03126.766-0.009-0.0090.0000.0000.0000.000
30A30LYS10.7460.85329.908-0.063-0.0630.0000.0000.0000.000
31A31GLY0-0.0140.00429.944-0.001-0.0010.0000.0000.0000.000
32A32CYS0-0.122-0.03525.1680.0030.0030.0000.0000.0000.000
33A33GLY00.0090.01028.404-0.005-0.0050.0000.0000.0000.000
34A34GLU-1-0.943-0.97524.9140.0110.0110.0000.0000.0000.000
35A35PHE00.035-0.00819.0210.0080.0080.0000.0000.0000.000
36A36ILE0-0.0060.00518.072-0.012-0.0120.0000.0000.0000.000
37A37VAL00.0270.03215.9680.0100.0100.0000.0000.0000.000
38A38ASN0-0.012-0.01912.906-0.020-0.0200.0000.0000.0000.000
39A39LEU00.0820.04011.457-0.004-0.0040.0000.0000.0000.000
40A40ARG10.9080.94612.6610.2230.2230.0000.0000.0000.000
41A41THR00.013-0.00916.8300.0060.0060.0000.0000.0000.000
42A42LEU00.0560.03116.8690.0020.0020.0000.0000.0000.000
43A43LEU0-0.066-0.02115.219-0.001-0.0010.0000.0000.0000.000
44A44ARG10.7810.88819.4630.1090.1090.0000.0000.0000.000
45A45THR0-0.025-0.00423.2370.0070.0070.0000.0000.0000.000
46A46PHE00.0420.01724.346-0.002-0.0020.0000.0000.0000.000
47A47ARG10.9000.95024.0470.0170.0170.0000.0000.0000.000
48A48THR00.0250.00626.758-0.006-0.0060.0000.0000.0000.000
49A49ILE0-0.019-0.00324.8080.0030.0030.0000.0000.0000.000
50A50THR00.018-0.00727.3970.0040.0040.0000.0000.0000.000
51A51ASP-1-0.812-0.87630.800-0.006-0.0060.0000.0000.0000.000
52A52ASN0-0.056-0.03933.8270.0000.0000.0000.0000.0000.000
53A53TRP00.0270.02533.720-0.002-0.0020.0000.0000.0000.000
54A54ILE00.0380.01936.104-0.001-0.0010.0000.0000.0000.000
55A55LEU00.0040.00936.689-0.002-0.0020.0000.0000.0000.000
56A56GLN00.0080.00540.5810.0010.0010.0000.0000.0000.000
57A57ALA00.0080.00443.448-0.001-0.0010.0000.0000.0000.000
58A58ASN0-0.022-0.02345.525-0.001-0.0010.0000.0000.0000.000
59A59THR0-0.0050.01140.197-0.001-0.0010.0000.0000.0000.000
60A60LYS10.8300.93039.2670.0450.0450.0000.0000.0000.000
61A61THR00.0220.00634.8810.0000.0000.0000.0000.0000.000
62A62PRO00.0320.02332.382-0.001-0.0010.0000.0000.0000.000
63A63ILE0-0.058-0.02027.4370.0020.0020.0000.0000.0000.000
64A64THR00.0150.00826.860-0.001-0.0010.0000.0000.0000.000
65A65ASP-1-0.846-0.90728.066-0.052-0.0520.0000.0000.0000.000
66A66LEU0-0.0110.00328.8710.0040.0040.0000.0000.0000.000
67A67THR0-0.013-0.02223.8710.0010.0010.0000.0000.0000.000
68A68ASN0-0.006-0.01323.889-0.009-0.0090.0000.0000.0000.000
69A69THR0-0.014-0.00123.769-0.002-0.0020.0000.0000.0000.000
70A70THR0-0.034-0.03524.4870.0030.0030.0000.0000.0000.000
71A71ASP-1-0.778-0.88620.019-0.106-0.1060.0000.0000.0000.000
72A72ALA00.0000.03419.227-0.008-0.0080.0000.0000.0000.000
73A73GLN0-0.0020.00520.2180.0080.0080.0000.0000.0000.000
74A74GLY00.0200.01818.6480.0120.0120.0000.0000.0000.000
75A75ARG10.8000.87419.4580.0170.0170.0000.0000.0000.000
76A76ASP-1-0.724-0.84721.809-0.056-0.0560.0000.0000.0000.000
77A77TYR00.0370.01018.851-0.007-0.0070.0000.0000.0000.000
78A78MET0-0.033-0.00317.440-0.015-0.0150.0000.0000.0000.000
79A79SER00.006-0.00517.107-0.018-0.0180.0000.0000.0000.000
80A80TYR0-0.0110.00614.436-0.021-0.0210.0000.0000.0000.000
81A81LEU00.005-0.01113.244-0.009-0.0090.0000.0000.0000.000
82A82SER0-0.069-0.03612.097-0.058-0.0580.0000.0000.0000.000
83A83TYR0-0.025-0.04012.022-0.057-0.0570.0000.0000.0000.000
84A84LEU00.0010.0138.456-0.005-0.0050.0000.0000.0000.000
85A85TYR0-0.047-0.0257.071-0.230-0.2300.0000.0000.0000.000
86A86ARG10.9831.0068.5720.4510.4510.0000.0000.0000.000
87A87PHE0-0.011-0.01910.2840.0650.0650.0000.0000.0000.000
88A88TYR0-0.041-0.05112.511-0.017-0.0170.0000.0000.0000.000
89A89ARG10.8120.89415.2810.1790.1790.0000.0000.0000.000
90A90GLY00.0380.02317.8050.0010.0010.0000.0000.0000.000
91A91GLY00.0290.01421.047-0.001-0.0010.0000.0000.0000.000
92A92ARG10.8510.92320.5110.1220.1220.0000.0000.0000.000
93A93ARG10.7850.87624.7120.0780.0780.0000.0000.0000.000
94A94TYR00.004-0.01126.209-0.003-0.0030.0000.0000.0000.000
95A95LYS10.8170.90729.8020.0380.0380.0000.0000.0000.000
96A96PHE0-0.004-0.00632.0570.0010.0010.0000.0000.0000.000
97A97PHE00.0250.01132.8970.0010.0010.0000.0000.0000.000
98A98ASN00.0290.01137.7020.0000.0000.0000.0000.0000.000
99A99THR0-0.036-0.02139.7140.0020.0020.0000.0000.0000.000
100A100THR0-0.001-0.00442.4370.0010.0010.0000.0000.0000.000
101A101PRO00.0230.00245.0800.0000.0000.0000.0000.0000.000
102A102LEU0-0.0240.00546.544-0.001-0.0010.0000.0000.0000.000
103A103LYS10.9120.94550.2240.0130.0130.0000.0000.0000.000
104A104GLN00.0500.02353.8170.0000.0000.0000.0000.0000.000
105A105SER0-0.018-0.00156.4400.0000.0000.0000.0000.0000.000
106A106GLN00.0200.00951.9400.0000.0000.0000.0000.0000.000
107A107THR00.014-0.00351.2550.0000.0000.0000.0000.0000.000
108A108CYS0-0.0430.00546.291-0.001-0.0010.0000.0000.0000.000
109A109TYR00.013-0.00344.8680.0000.0000.0000.0000.0000.000
110A110ILE00.0080.01439.0750.0000.0000.0000.0000.0000.000
111A111ARG10.8810.92641.0270.0370.0370.0000.0000.0000.000
112A112SER00.0220.01435.5260.0000.0000.0000.0000.0000.000
113A113PHE0-0.0020.00836.2340.0020.0020.0000.0000.0000.000
114A114LEU00.0170.00331.213-0.003-0.0030.0000.0000.0000.000
115A115MET0-0.0130.01031.5510.0030.0030.0000.0000.0000.000
116A116PRO00.0200.02129.776-0.005-0.0050.0000.0000.0000.000
117A117ARG10.7960.88023.2620.1250.1250.0000.0000.0000.000
118A118ASN0-0.025-0.03324.8820.0050.0050.0000.0000.0000.000
119A119TYR0-0.028-0.00128.9980.0000.0000.0000.0000.0000.000
120A120SER00.000-0.02832.6010.0000.0000.0000.0000.0000.000
121A121ALA00.011-0.01735.450-0.001-0.0010.0000.0000.0000.000
122A122ASP-1-0.886-0.93137.949-0.045-0.0450.0000.0000.0000.000
123A123GLU-1-0.799-0.85634.787-0.065-0.0650.0000.0000.0000.000
124A124ILE0-0.036-0.01535.794-0.003-0.0030.0000.0000.0000.000
125A125ASN0-0.032-0.03138.5400.0010.0010.0000.0000.0000.000
126A126VAL0-0.028-0.03440.1800.0000.0000.0000.0000.0000.000
127A127ASP-1-0.825-0.89840.800-0.043-0.0430.0000.0000.0000.000
128A128GLY00.0040.00638.786-0.003-0.0030.0000.0000.0000.000
129A129PRO0-0.027-0.02835.2990.0030.0030.0000.0000.0000.000
130A130SER0-0.020-0.01537.3460.0000.0000.0000.0000.0000.000
131A131HIS00.0240.02437.1240.0000.0000.0000.0000.0000.000
132A132ILE0-0.036-0.02639.7910.0000.0000.0000.0000.0000.000
133A133THR0-0.011-0.01440.3850.0010.0010.0000.0000.0000.000
134A134TYR00.0720.02343.0830.0000.0000.0000.0000.0000.000
135A135PRO00.0100.00143.0840.0010.0010.0000.0000.0000.000
136A136VAL0-0.008-0.00745.1940.0010.0010.0000.0000.0000.000
137A137ILE0-0.016-0.01047.5230.0010.0010.0000.0000.0000.000
138A138ASN00.007-0.00540.4780.0010.0010.0000.0000.0000.000
139A139PRO0-0.0280.00242.078-0.001-0.0010.0000.0000.0000.000
140A140VAL00.0120.01236.5180.0000.0000.0000.0000.0000.000
141A141HIS00.0340.05035.9600.0010.0010.0000.0000.0000.000
142A142GLU-1-0.813-0.91134.158-0.035-0.0350.0000.0000.0000.000
143A143VAL0-0.029-0.01732.2630.0000.0000.0000.0000.0000.000
144A144GLU-1-0.797-0.89127.984-0.082-0.0820.0000.0000.0000.000
145A145VAL0-0.0120.00727.2210.0030.0030.0000.0000.0000.000
146A146PRO00.0340.01326.693-0.009-0.0090.0000.0000.0000.000
147A147PHE00.001-0.00220.075-0.004-0.0040.0000.0000.0000.000
148A148TYR00.0090.00325.195-0.003-0.0030.0000.0000.0000.000
149A149SER00.017-0.00522.3360.0020.0020.0000.0000.0000.000
150A150GLN00.0240.01625.354-0.004-0.0040.0000.0000.0000.000
151A151TYR0-0.0080.00420.534-0.011-0.0110.0000.0000.0000.000
152A152ARG10.9300.95917.9220.2260.2260.0000.0000.0000.000
153A153LYS10.8830.94912.4800.3770.3770.0000.0000.0000.000
154A154ILE00.0440.03917.0950.0000.0000.0000.0000.0000.000
155A155PRO0-0.001-0.01314.770-0.023-0.0230.0000.0000.0000.000
156A156ILE0-0.026-0.01211.8750.0360.0360.0000.0000.0000.000
157A157ALA00.001-0.00415.486-0.005-0.0050.0000.0000.0000.000
158A158SER0-0.0170.00218.3500.0050.0050.0000.0000.0000.000
159A159THR00.0130.00419.3400.0090.0090.0000.0000.0000.000
160A160SER0-0.004-0.00220.9770.0070.0070.0000.0000.0000.000
161A161ASP-1-0.845-0.92622.195-0.138-0.1380.0000.0000.0000.000
162A162LYS10.8300.90324.0720.0840.0840.0000.0000.0000.000
163A163GLY00.0440.02026.8890.0050.0050.0000.0000.0000.000
164A164TYR0-0.086-0.04422.4500.0000.0000.0000.0000.0000.000
165A165ASP-1-0.746-0.83422.836-0.144-0.1440.0000.0000.0000.000
166A166SER00.0220.01425.4580.0060.0060.0000.0000.0000.000
167A167SER0-0.022-0.01626.431-0.007-0.0070.0000.0000.0000.000
168A168LEU00.0030.00328.5910.0040.0040.0000.0000.0000.000
169A169MET0-0.0160.00831.3960.0000.0000.0000.0000.0000.000
170A170TYR00.020-0.01134.6010.0000.0000.0000.0000.0000.000
171A171PHE00.0090.00836.7220.0000.0000.0000.0000.0000.000
172A172SER00.0540.01940.5220.0010.0010.0000.0000.0000.000
173A173ASN00.0310.01743.4490.0000.0000.0000.0000.0000.000
174A174THR0-0.031-0.01146.3050.0010.0010.0000.0000.0000.000
175A175SER00.007-0.00944.765-0.001-0.0010.0000.0000.0000.000
176A176THR0-0.077-0.05040.8430.0010.0010.0000.0000.0000.000
177A177THR00.0580.02640.0900.0000.0000.0000.0000.0000.000
178A178GLN00.0060.02736.5570.0010.0010.0000.0000.0000.000
179A179ILE00.0450.04533.7300.0000.0000.0000.0000.0000.000
180A180VAL0-0.027-0.01730.275-0.003-0.0030.0000.0000.0000.000
181A181ALA00.0070.00228.8210.0020.0020.0000.0000.0000.000
182A182ARG10.7150.81721.2940.0750.0750.0000.0000.0000.000
183A183ALA00.0280.01623.4200.0050.0050.0000.0000.0000.000
184A184GLY00.0500.01721.409-0.005-0.0050.0000.0000.0000.000
185A185ASN0-0.030-0.03522.3780.0000.0000.0000.0000.0000.000
186A186ASP-1-0.777-0.89522.583-0.088-0.0880.0000.0000.0000.000
187A187ASP-1-0.845-0.88521.709-0.140-0.1400.0000.0000.0000.000
188A188PHE0-0.092-0.02017.360-0.024-0.0240.0000.0000.0000.000
189A189THR0-0.019-0.02213.4360.0120.0120.0000.0000.0000.000
190A190PHE00.0510.03711.545-0.003-0.0030.0000.0000.0000.000
191A191GLY00.0190.0069.4770.0070.0070.0000.0000.0000.000
192A192TRP0-0.018-0.0215.8190.1240.1240.0000.0000.0000.000
193A193MET00.0200.0133.277-0.6110.0460.024-0.124-0.5570.000
194A194ILE0-0.059-0.0233.572-0.873-0.2960.023-0.238-0.362-0.001
195A195GLY00.0110.0104.686-0.181-0.044-0.001-0.010-0.1250.000
196A196PRO00.0040.0065.810-0.018-0.0180.0000.0000.0000.000
197A197PRO0-0.0050.0079.1480.0610.0610.0000.0000.0000.000
198A198GLN0-0.009-0.01212.6340.0280.0280.0000.0000.0000.000
199A199LEU00.000-0.00614.843-0.034-0.0340.0000.0000.0000.000
200A200GLN0-0.025-0.00517.6430.0080.0080.0000.0000.0000.000
201A201GLY00.0340.01021.4750.0030.0030.0000.0000.0000.000
202A202GLU-1-0.885-0.93723.7720.0640.0640.0000.0000.0000.000
203A203THR0-0.037-0.03127.0650.0010.0010.0000.0000.0000.000
204A204ARG10.8950.95129.548-0.077-0.0770.0000.0000.0000.000
205A205SER00.0340.02633.2500.0010.0010.0000.0000.0000.000
206A206VAL0-0.049-0.02934.6850.0020.0020.0000.0000.0000.000
207A207VAL00.0400.02737.484-0.003-0.0030.0000.0000.0000.000
208A208PRO00.0060.00538.2210.0020.0020.0000.0000.0000.000