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: 858ZY

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2237437.22148
FMO2-HF: Nuclear repulsion 2153475.052819
FMO2-HF: Total energy -83962.168661
FMO2-MP2: Total energy -84206.599494


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.
-2.5821.8240.177-1.642-2.942-0.002
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 : -0.003 / q_NPA : -0.007
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].
3A3ILE00.0220.0012.924-2.8810.0950.145-1.216-1.9050.000
4A4GLY0-0.0040.0054.8390.1920.321-0.001-0.009-0.1190.000
5A5ASN0-0.038-0.0048.4300.2270.2270.0000.0000.0000.000
6A6LYS10.9931.0018.923-0.072-0.0720.0000.0000.0000.000
7A7THR00.013-0.0018.8420.1390.1390.0000.0000.0000.000
8A8ASN0-0.026-0.01510.164-0.123-0.1230.0000.0000.0000.000
9A9GLU-1-0.892-0.94513.0700.2100.2100.0000.0000.0000.000
10A10ASN0-0.057-0.01716.088-0.043-0.0430.0000.0000.0000.000
11A11VAL0-0.002-0.00314.2440.0630.0630.0000.0000.0000.000
12A12ILE00.0160.00817.357-0.047-0.0470.0000.0000.0000.000
13A13SER0-0.022-0.01218.9820.0470.0470.0000.0000.0000.000
14A14PHE0-0.037-0.02020.634-0.023-0.0230.0000.0000.0000.000
15A15PHE0-0.009-0.01323.5230.0050.0050.0000.0000.0000.000
16A16ASP-1-0.881-0.91725.4080.1510.1510.0000.0000.0000.000
17A17SER0-0.074-0.05423.0650.0110.0110.0000.0000.0000.000
18A18THR0-0.015-0.02224.020-0.013-0.0130.0000.0000.0000.000
19A19ASP-1-0.839-0.88722.8320.1250.1250.0000.0000.0000.000
20A20ALA0-0.036-0.04119.706-0.006-0.0060.0000.0000.0000.000
21A21GLU-1-0.940-0.98018.6030.1360.1360.0000.0000.0000.000
22A22THR00.0170.00921.334-0.012-0.0120.0000.0000.0000.000
23A23GLN00.0370.02024.7290.0000.0000.0000.0000.0000.000
24A24ASN00.0090.00419.265-0.007-0.0070.0000.0000.0000.000
25A25HIS0-0.022-0.01323.297-0.004-0.0040.0000.0000.0000.000
26A26ASP-1-0.884-0.95524.9480.0720.0720.0000.0000.0000.000
27A27VAL0-0.022-0.01025.501-0.007-0.0070.0000.0000.0000.000
28A28LEU0-0.015-0.01022.380-0.005-0.0050.0000.0000.0000.000
29A29MET0-0.020-0.00226.653-0.011-0.0110.0000.0000.0000.000
30A30LYS10.8730.93929.837-0.073-0.0730.0000.0000.0000.000
31A31GLY0-0.015-0.00129.697-0.003-0.0030.0000.0000.0000.000
32A32CYS0-0.118-0.03325.0280.0040.0040.0000.0000.0000.000
33A33GLY00.0120.00928.273-0.006-0.0060.0000.0000.0000.000
34A34GLU-1-0.968-0.98124.5770.0270.0270.0000.0000.0000.000
35A35PHE00.019-0.01418.7310.0100.0100.0000.0000.0000.000
36A36ILE00.0000.00817.856-0.013-0.0130.0000.0000.0000.000
37A37VAL00.0410.03115.3790.0150.0150.0000.0000.0000.000
38A38ASN00.0050.00013.497-0.020-0.0200.0000.0000.0000.000
39A39LEU00.0960.03911.523-0.004-0.0040.0000.0000.0000.000
40A40ARG10.9290.95913.2270.2320.2320.0000.0000.0000.000
41A41THR0-0.007-0.01416.6080.0040.0040.0000.0000.0000.000
42A42LEU00.0360.01617.3190.0050.0050.0000.0000.0000.000
43A43LEU0-0.060-0.02615.943-0.003-0.0030.0000.0000.0000.000
44A44ARG10.8220.92720.1020.1190.1190.0000.0000.0000.000
45A45THR0-0.0180.00223.2120.0080.0080.0000.0000.0000.000
46A46PHE00.0190.00924.467-0.006-0.0060.0000.0000.0000.000
47A47ARG10.9070.95423.9560.0120.0120.0000.0000.0000.000
48A48THR00.0090.00126.890-0.007-0.0070.0000.0000.0000.000
49A49ILE0-0.011-0.01025.3540.0030.0030.0000.0000.0000.000
50A50THR0-0.002-0.01427.8320.0030.0030.0000.0000.0000.000
51A51ASP-1-0.867-0.93331.319-0.004-0.0040.0000.0000.0000.000
52A52ASN0-0.062-0.04834.4320.0010.0010.0000.0000.0000.000
53A53TRP00.0190.02034.056-0.001-0.0010.0000.0000.0000.000
54A54ILE00.0240.00636.1600.0000.0000.0000.0000.0000.000
55A55LEU00.0160.01036.796-0.003-0.0030.0000.0000.0000.000
56A56GLN00.0040.00640.5990.0010.0010.0000.0000.0000.000
57A57ALA0-0.009-0.00443.490-0.001-0.0010.0000.0000.0000.000
58A58ASN0-0.020-0.02645.7140.0000.0000.0000.0000.0000.000
59A59THR00.0330.02140.340-0.001-0.0010.0000.0000.0000.000
60A60LYS10.8530.93639.7180.0510.0510.0000.0000.0000.000
61A61THR00.0620.02234.9730.0000.0000.0000.0000.0000.000
62A62PRO00.0160.02132.542-0.001-0.0010.0000.0000.0000.000
63A63ILE00.0180.00928.2360.0020.0020.0000.0000.0000.000
64A64THR00.0300.01727.052-0.001-0.0010.0000.0000.0000.000
65A65ASP-1-0.864-0.92928.477-0.063-0.0630.0000.0000.0000.000
66A66LEU0-0.067-0.02729.1550.0040.0040.0000.0000.0000.000
67A67THR0-0.068-0.05124.2280.0000.0000.0000.0000.0000.000
68A68ASN00.0140.00024.458-0.013-0.0130.0000.0000.0000.000
69A69THR00.0060.01424.202-0.004-0.0040.0000.0000.0000.000
70A70THR00.007-0.01124.5280.0020.0020.0000.0000.0000.000
71A71ASP-1-0.857-0.92620.368-0.117-0.1170.0000.0000.0000.000
72A72ALA0-0.0080.03019.644-0.011-0.0110.0000.0000.0000.000
73A73GLN0-0.026-0.01020.4860.0070.0070.0000.0000.0000.000
74A74GLY00.0540.03219.5270.0110.0110.0000.0000.0000.000
75A75ARG10.8880.95220.2350.0180.0180.0000.0000.0000.000
76A76ASP-1-0.775-0.87521.772-0.061-0.0610.0000.0000.0000.000
77A77TYR00.0730.01019.129-0.005-0.0050.0000.0000.0000.000
78A78MET0-0.040-0.01517.838-0.014-0.0140.0000.0000.0000.000
79A79SER0-0.013-0.00317.492-0.021-0.0210.0000.0000.0000.000
80A80TYR00.0030.01915.545-0.018-0.0180.0000.0000.0000.000
81A81LEU00.001-0.01713.391-0.009-0.0090.0000.0000.0000.000
82A82SER0-0.085-0.05012.458-0.066-0.0660.0000.0000.0000.000
83A83TYR0-0.012-0.02712.449-0.065-0.0650.0000.0000.0000.000
84A84LEU00.0070.0168.286-0.020-0.0200.0000.0000.0000.000
85A85TYR0-0.053-0.0167.285-0.275-0.2750.0000.0000.0000.000
86A86ARG11.0221.0258.9940.6010.6010.0000.0000.0000.000
87A87PHE0-0.022-0.00710.5380.0790.0790.0000.0000.0000.000
88A88TYR00.007-0.01212.937-0.015-0.0150.0000.0000.0000.000
89A89ARG10.9350.96315.6890.2220.2220.0000.0000.0000.000
90A90GLY00.0510.03518.3750.0030.0030.0000.0000.0000.000
91A91GLY00.0400.01921.643-0.001-0.0010.0000.0000.0000.000
92A92ARG10.8820.94220.0190.1470.1470.0000.0000.0000.000
93A93ARG10.8890.95625.3940.0820.0820.0000.0000.0000.000
94A94TYR00.0140.00126.370-0.003-0.0030.0000.0000.0000.000
95A95LYS10.8110.88130.2870.0440.0440.0000.0000.0000.000
96A96PHE0-0.011-0.00232.7770.0010.0010.0000.0000.0000.000
97A97PHE00.0250.00933.2950.0010.0010.0000.0000.0000.000
98A98ASN00.0420.00337.9840.0000.0000.0000.0000.0000.000
99A99THR0-0.073-0.05739.7740.0020.0020.0000.0000.0000.000
100A100THR00.0070.00442.6090.0010.0010.0000.0000.0000.000
101A101PRO0-0.005-0.00145.1600.0000.0000.0000.0000.0000.000
102A102LEU00.0040.01147.293-0.001-0.0010.0000.0000.0000.000
103A103LYS10.9730.98950.6360.0150.0150.0000.0000.0000.000
104A104GLN00.0690.03053.948-0.001-0.0010.0000.0000.0000.000
105A105SER0-0.067-0.02456.379-0.001-0.0010.0000.0000.0000.000
106A106GLN0-0.015-0.02151.6280.0000.0000.0000.0000.0000.000
107A107THR00.0410.02451.4390.0010.0010.0000.0000.0000.000
108A108CYS0-0.056-0.01546.474-0.001-0.0010.0000.0000.0000.000
109A109TYR00.0180.00045.2450.0000.0000.0000.0000.0000.000
110A110ILE0-0.0080.00039.5430.0000.0000.0000.0000.0000.000
111A111ARG10.9100.95841.4260.0410.0410.0000.0000.0000.000
112A112SER0-0.0010.00635.8790.0000.0000.0000.0000.0000.000
113A113PHE00.026-0.00636.7870.0010.0010.0000.0000.0000.000
114A114LEU00.0330.00931.595-0.003-0.0030.0000.0000.0000.000
115A115MET0-0.038-0.00932.1930.0030.0030.0000.0000.0000.000
116A116PRO00.0190.02530.365-0.005-0.0050.0000.0000.0000.000
117A117ARG10.8890.91823.6440.1440.1440.0000.0000.0000.000
118A118ASN0-0.039-0.03824.8010.0030.0030.0000.0000.0000.000
119A119TYR00.0140.02229.103-0.001-0.0010.0000.0000.0000.000
120A120SER00.0390.02532.6960.0000.0000.0000.0000.0000.000
121A121ALA00.009-0.01635.5550.0000.0000.0000.0000.0000.000
122A122ASP-1-0.975-0.99038.050-0.055-0.0550.0000.0000.0000.000
123A123GLU-1-0.856-0.92335.085-0.076-0.0760.0000.0000.0000.000
124A124ILE0-0.046-0.03136.293-0.005-0.0050.0000.0000.0000.000
125A125ASN0-0.030-0.00938.8810.0040.0040.0000.0000.0000.000
126A126VAL0-0.028-0.03439.951-0.002-0.0020.0000.0000.0000.000
127A127ASP-1-0.897-0.93041.292-0.049-0.0490.0000.0000.0000.000
128A128GLY0-0.025-0.01338.952-0.003-0.0030.0000.0000.0000.000
129A129PRO0-0.028-0.03036.2270.0030.0030.0000.0000.0000.000
130A130SER0-0.023-0.01138.4070.0010.0010.0000.0000.0000.000
131A131HIS00.0210.02637.5600.0010.0010.0000.0000.0000.000
132A132ILE0-0.023-0.03440.1310.0000.0000.0000.0000.0000.000
133A133THR0-0.049-0.00640.7510.0020.0020.0000.0000.0000.000
134A134TYR00.0790.02543.6800.0000.0000.0000.0000.0000.000
135A135PRO00.0310.01343.4520.0010.0010.0000.0000.0000.000
136A136VAL0-0.012-0.01945.4150.0010.0010.0000.0000.0000.000
137A137ILE0-0.020-0.00847.4380.0010.0010.0000.0000.0000.000
138A138ASN0-0.027-0.02141.2030.0020.0020.0000.0000.0000.000
139A139PRO0-0.0090.00242.203-0.002-0.0020.0000.0000.0000.000
140A140VAL00.0220.02436.718-0.001-0.0010.0000.0000.0000.000
141A141HIS00.0240.03636.3450.0020.0020.0000.0000.0000.000
142A142GLU-1-0.820-0.90134.544-0.038-0.0380.0000.0000.0000.000
143A143VAL00.0040.00132.6880.0000.0000.0000.0000.0000.000
144A144GLU-1-0.850-0.95028.767-0.089-0.0890.0000.0000.0000.000
145A145VAL0-0.030-0.00627.9530.0020.0020.0000.0000.0000.000
146A146PRO00.0390.01627.461-0.009-0.0090.0000.0000.0000.000
147A147PHE00.001-0.01121.051-0.006-0.0060.0000.0000.0000.000
148A148TYR00.0010.00725.852-0.002-0.0020.0000.0000.0000.000
149A149SER00.024-0.01522.8400.0020.0020.0000.0000.0000.000
150A150GLN00.0310.02825.819-0.001-0.0010.0000.0000.0000.000
151A151TYR0-0.0250.00320.842-0.013-0.0130.0000.0000.0000.000
152A152ARG10.9380.96718.1680.2670.2670.0000.0000.0000.000
153A153LYS10.8990.94513.1770.4320.4320.0000.0000.0000.000
154A154ILE00.0470.04317.447-0.002-0.0020.0000.0000.0000.000
155A155PRO0-0.019-0.01714.863-0.027-0.0270.0000.0000.0000.000
156A156ILE0-0.003-0.01812.5410.0440.0440.0000.0000.0000.000
157A157ALA0-0.0020.00815.839-0.006-0.0060.0000.0000.0000.000
158A158SER0-0.040-0.01618.5290.0030.0030.0000.0000.0000.000
159A159THR00.0250.01519.2480.0120.0120.0000.0000.0000.000
160A160SER0-0.011-0.01321.7430.0110.0110.0000.0000.0000.000
161A161ASP-1-0.872-0.96422.058-0.167-0.1670.0000.0000.0000.000
162A162LYS10.9080.97323.9360.1050.1050.0000.0000.0000.000
163A163GLY00.0110.00627.7190.0040.0040.0000.0000.0000.000
164A164TYR0-0.0380.01323.1160.0000.0000.0000.0000.0000.000
165A165ASP-1-0.762-0.87423.816-0.163-0.1630.0000.0000.0000.000
166A166SER00.0060.00926.1870.0070.0070.0000.0000.0000.000
167A167SER0-0.022-0.01327.046-0.008-0.0080.0000.0000.0000.000
168A168LEU0-0.018-0.00829.0200.0040.0040.0000.0000.0000.000
169A169MET0-0.023-0.00231.6540.0000.0000.0000.0000.0000.000
170A170TYR0-0.027-0.03434.8730.0010.0010.0000.0000.0000.000
171A171PHE00.0090.01536.9220.0010.0010.0000.0000.0000.000
172A172SER00.0620.03940.7080.0010.0010.0000.0000.0000.000
173A173ASN00.0180.00743.6470.0000.0000.0000.0000.0000.000
174A174THR00.0130.00846.4720.0010.0010.0000.0000.0000.000
175A175SER0-0.039-0.02744.672-0.001-0.0010.0000.0000.0000.000
176A176THR0-0.043-0.02440.7470.0020.0020.0000.0000.0000.000
177A177THR00.1080.05940.1450.0000.0000.0000.0000.0000.000
178A178GLN0-0.0210.01837.163-0.001-0.0010.0000.0000.0000.000
179A179ILE00.0550.05733.713-0.001-0.0010.0000.0000.0000.000
180A180VAL0-0.0020.00630.231-0.002-0.0020.0000.0000.0000.000
181A181ALA00.0170.01329.1660.0030.0030.0000.0000.0000.000
182A182ARG10.7410.85121.8720.0880.0880.0000.0000.0000.000
183A183ALA00.0190.00223.6520.0060.0060.0000.0000.0000.000
184A184GLY00.0360.01822.098-0.005-0.0050.0000.0000.0000.000
185A185ASN0-0.003-0.00823.1220.0010.0010.0000.0000.0000.000
186A186ASP-1-0.901-0.97323.502-0.097-0.0970.0000.0000.0000.000
187A187ASP-1-0.921-0.94622.035-0.141-0.1410.0000.0000.0000.000
188A188PHE0-0.129-0.04217.945-0.027-0.0270.0000.0000.0000.000
189A189THR0-0.018-0.01214.3280.0160.0160.0000.0000.0000.000
190A190PHE00.0220.01911.897-0.005-0.0050.0000.0000.0000.000
191A191GLY0-0.007-0.01510.2410.0050.0050.0000.0000.0000.000
192A192TRP0-0.034-0.0375.6710.1790.1790.0000.0000.0000.000
193A193MET00.0060.0064.128-0.514-0.0460.006-0.077-0.3980.000
194A194ILE0-0.050-0.0213.434-1.307-0.5890.028-0.332-0.414-0.002
195A195GLY0-0.0010.0054.858-0.149-0.034-0.001-0.008-0.1060.000
196A196PRO00.000-0.0046.0510.0010.0010.0000.0000.0000.000
197A197PRO00.0130.0199.2450.0590.0590.0000.0000.0000.000
198A198GLN0-0.011-0.01412.5490.0410.0410.0000.0000.0000.000
199A199LEU0-0.004-0.00215.057-0.035-0.0350.0000.0000.0000.000
200A200GLN00.0010.00617.4340.0060.0060.0000.0000.0000.000
201A201GLY00.0110.00821.1960.0000.0000.0000.0000.0000.000
202A202GLU-1-0.950-0.97923.5260.0700.0700.0000.0000.0000.000
203A203THR0-0.024-0.01627.2470.0010.0010.0000.0000.0000.000
204A204ARG10.9560.97429.507-0.079-0.0790.0000.0000.0000.000
205A205SER00.0230.02433.1040.0000.0000.0000.0000.0000.000
206A206VAL0-0.067-0.05834.5660.0030.0030.0000.0000.0000.000
207A207VAL0-0.094-0.04937.339-0.002-0.0020.0000.0000.0000.000
208A208PRO00.1560.10338.191-0.001-0.0010.0000.0000.0000.000