FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: QV88Y

Calculation Name: 3CCY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CCY

Chain ID: A

ChEMBL ID:

UniProt ID: Q7W6R8

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2112181.313658
FMO2-HF: Nuclear repulsion 2033663.889662
FMO2-HF: Total energy -78517.423996
FMO2-MP2: Total energy -78743.199633


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:9:TYR)


Summations of interaction energy for fragment #1(A:9:TYR)
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.
-14.401-7.3839.883-5.648-11.255-0.018
Interaction energy analysis for fragmet #1(A:9:TYR)
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 : -0.036
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].
3A11ASN00.0050.0202.305-7.816-2.9954.712-3.546-5.988-0.026
4A12ILE00.0210.0062.239-0.1920.8212.142-0.748-2.4070.003
5A13ARG10.9250.9663.8740.6321.0880.001-0.096-0.3610.000
6A14ASP-1-0.829-0.9305.571-1.688-1.6880.0000.0000.0000.000
7A15THR00.0170.0247.7400.1640.1640.0000.0000.0000.000
8A16ILE0-0.0010.0036.7910.1910.1910.0000.0000.0000.000
9A17ILE0-0.045-0.01310.0230.0370.0370.0000.0000.0000.000
10A18GLU-1-0.977-0.98611.834-0.657-0.6570.0000.0000.0000.000
11A19ARG10.9380.93613.0920.4020.4020.0000.0000.0000.000
12A20ALA0-0.034-0.01914.2360.0420.0420.0000.0000.0000.000
13A21ALA0-0.0060.00215.8940.0200.0200.0000.0000.0000.000
14A22ALA00.0270.02217.8320.0200.0200.0000.0000.0000.000
15A23MET0-0.056-0.02617.5100.0220.0220.0000.0000.0000.000
16A24PHE0-0.018-0.03317.6880.0190.0190.0000.0000.0000.000
17A25ALA00.0140.01221.8890.0050.0050.0000.0000.0000.000
18A26ARG10.7240.87622.1650.1490.1490.0000.0000.0000.000
19A27GLN00.0600.03223.567-0.013-0.0130.0000.0000.0000.000
20A28GLY00.0800.05424.9000.0090.0090.0000.0000.0000.000
21A29TYR00.0530.00419.6560.0150.0150.0000.0000.0000.000
22A30SER0-0.024-0.00923.2820.0170.0170.0000.0000.0000.000
23A31GLU-1-0.926-0.95125.8920.0430.0430.0000.0000.0000.000
24A32THR0-0.0190.00819.6290.0000.0000.0000.0000.0000.000
25A33SER0-0.036-0.03421.0950.0320.0320.0000.0000.0000.000
26A34ILE00.0580.00015.383-0.013-0.0130.0000.0000.0000.000
27A35GLY0-0.046-0.02616.5110.0350.0350.0000.0000.0000.000
28A36ASP-1-0.804-0.91418.2210.1010.1010.0000.0000.0000.000
29A37ILE00.0290.01613.156-0.019-0.0190.0000.0000.0000.000
30A38ALA0-0.055-0.03113.528-0.019-0.0190.0000.0000.0000.000
31A39ARG10.9270.97114.157-0.136-0.1360.0000.0000.0000.000
32A40ALA00.0650.05515.888-0.039-0.0390.0000.0000.0000.000
33A41CYS0-0.125-0.03710.901-0.098-0.0980.0000.0000.0000.000
34A42GLU-1-0.925-0.95412.416-0.156-0.1560.0000.0000.0000.000
35A43CYS0-0.0230.01710.8940.1690.1690.0000.0000.0000.000
36A44SER00.019-0.01113.005-0.009-0.0090.0000.0000.0000.000
37A45LYS10.9700.94812.978-0.275-0.2750.0000.0000.0000.000
38A46SER00.0240.00013.2060.0040.0040.0000.0000.0000.000
39A47ARG10.9650.9715.599-1.978-1.9780.0000.0000.0000.000
40A48LEU00.0380.0268.1320.3450.3450.0000.0000.0000.000
41A49TYR0-0.007-0.0119.5590.0990.0990.0000.0000.0000.000
42A50HIS0-0.0580.0024.267-1.061-0.876-0.001-0.020-0.1650.000
43A51TYR0-0.041-0.0252.184-2.549-2.0063.029-1.238-2.3340.005
44A52PHE00.003-0.0067.016-0.428-0.4280.0000.0000.0000.000
45A53ASP-1-0.829-0.90710.5180.7540.7540.0000.0000.0000.000
46A54SER0-0.029-0.02613.698-0.079-0.0790.0000.0000.0000.000
47A55LYS10.8470.91915.011-0.103-0.1030.0000.0000.0000.000
48A56GLU-1-0.908-0.96117.2130.1360.1360.0000.0000.0000.000
49A57ALA0-0.030-0.00313.035-0.041-0.0410.0000.0000.0000.000
50A58VAL00.0070.00912.304-0.041-0.0410.0000.0000.0000.000
51A59LEU00.0040.00613.868-0.078-0.0780.0000.0000.0000.000
52A60ARG10.9240.94613.900-0.228-0.2280.0000.0000.0000.000
53A61ASP-1-0.888-0.93910.293-0.255-0.2550.0000.0000.0000.000
54A62MET00.0090.00513.519-0.084-0.0840.0000.0000.0000.000
55A63LEU0-0.027-0.01314.998-0.040-0.0400.0000.0000.0000.000
56A64THR0-0.015-0.02215.258-0.004-0.0040.0000.0000.0000.000
57A65THR0-0.0060.00211.983-0.030-0.0300.0000.0000.0000.000
58A66HIS00.0230.01715.342-0.040-0.0400.0000.0000.0000.000
59A67VAL0-0.008-0.01418.3520.0010.0010.0000.0000.0000.000
60A68ASP-1-0.824-0.88617.298-0.179-0.1790.0000.0000.0000.000
61A69SER0-0.006-0.00917.9420.0030.0030.0000.0000.0000.000
62A70LEU0-0.026-0.00419.6120.0080.0080.0000.0000.0000.000
63A71LEU0-0.036-0.02522.7800.0110.0110.0000.0000.0000.000
64A72GLU-1-0.877-0.93421.133-0.196-0.1960.0000.0000.0000.000
65A73ARG10.9080.92921.4700.3120.3120.0000.0000.0000.000
66A74CYS0-0.029-0.01624.8180.0150.0150.0000.0000.0000.000
67A75ARG10.8770.94622.9870.1720.1720.0000.0000.0000.000
68A76GLN00.0030.00323.839-0.003-0.0030.0000.0000.0000.000
69A77VAL0-0.0060.00628.3220.0070.0070.0000.0000.0000.000
70A78LEU0-0.075-0.03530.9820.0110.0110.0000.0000.0000.000
71A79TYR0-0.061-0.05429.0960.0080.0080.0000.0000.0000.000
72A80GLY00.0430.04232.9220.0000.0000.0000.0000.0000.000
73A81SER0-0.029-0.01634.0570.0090.0090.0000.0000.0000.000
74A82ASN00.0490.01237.4240.0050.0050.0000.0000.0000.000
75A83GLU-1-0.935-0.96940.600-0.085-0.0850.0000.0000.0000.000
76A84PRO00.0290.00540.397-0.005-0.0050.0000.0000.0000.000
77A85LYS10.9360.97140.4060.0760.0760.0000.0000.0000.000
78A86THR0-0.008-0.00337.964-0.003-0.0030.0000.0000.0000.000
79A87ARG10.9000.96735.6720.0940.0940.0000.0000.0000.000
80A88PHE00.0200.01935.488-0.007-0.0070.0000.0000.0000.000
81A89LEU00.0140.00536.216-0.004-0.0040.0000.0000.0000.000
82A90GLN00.014-0.01633.277-0.005-0.0050.0000.0000.0000.000
83A91ILE00.0220.02531.494-0.011-0.0110.0000.0000.0000.000
84A92VAL0-0.036-0.01631.539-0.007-0.0070.0000.0000.0000.000
85A93LYS10.8560.92232.4800.1390.1390.0000.0000.0000.000
86A94LEU00.0210.02925.619-0.011-0.0110.0000.0000.0000.000
87A95PHE0-0.024-0.02727.696-0.012-0.0120.0000.0000.0000.000
88A96LEU00.006-0.00328.145-0.006-0.0060.0000.0000.0000.000
89A97GLU-1-0.843-0.88825.390-0.280-0.2800.0000.0000.0000.000
90A98ILE00.003-0.00622.600-0.022-0.0220.0000.0000.0000.000
91A99TYR0-0.055-0.02524.159-0.013-0.0130.0000.0000.0000.000
92A100ALA0-0.005-0.01825.681-0.004-0.0040.0000.0000.0000.000
93A101THR0-0.077-0.02521.549-0.019-0.0190.0000.0000.0000.000
94A102SER0-0.013-0.01320.075-0.039-0.0390.0000.0000.0000.000
95A103ARG10.9130.96321.5470.1690.1690.0000.0000.0000.000
96A104ASP-1-0.789-0.89520.059-0.193-0.1930.0000.0000.0000.000
97A105ARG11.0060.98813.2870.5080.5080.0000.0000.0000.000
98A106HIS00.0260.02220.2710.0120.0120.0000.0000.0000.000
99A107VAL0-0.019-0.02123.6640.0200.0200.0000.0000.0000.000
100A108VAL00.017-0.00120.0270.0200.0200.0000.0000.0000.000
101A109MET0-0.027-0.00522.1060.0180.0180.0000.0000.0000.000
102A110LEU0-0.086-0.04423.6010.0120.0120.0000.0000.0000.000
103A111THR0-0.047-0.02226.0500.0100.0100.0000.0000.0000.000
104A112CYS0-0.026-0.00523.0230.0120.0120.0000.0000.0000.000
105A113LEU0-0.0040.01323.5970.0160.0160.0000.0000.0000.000
106A114ASP-1-0.940-0.98124.9830.0190.0190.0000.0000.0000.000
107A115ALA00.0320.01023.6010.0110.0110.0000.0000.0000.000
108A116LEU0-0.057-0.01519.4790.0200.0200.0000.0000.0000.000
109A117PRO00.0190.00521.979-0.007-0.0070.0000.0000.0000.000
110A118GLU-1-0.851-0.91924.9240.0250.0250.0000.0000.0000.000
111A119ASP-1-0.910-0.96022.6930.0800.0800.0000.0000.0000.000
112A120GLN00.0680.02819.351-0.005-0.0050.0000.0000.0000.000
113A121ARG10.8740.95222.224-0.052-0.0520.0000.0000.0000.000
114A122LYS10.9780.97524.675-0.038-0.0380.0000.0000.0000.000
115A123ALA00.0030.02122.178-0.010-0.0100.0000.0000.0000.000
116A124LEU0-0.001-0.00219.386-0.016-0.0160.0000.0000.0000.000
117A125ILE0-0.009-0.00923.388-0.011-0.0110.0000.0000.0000.000
118A126ALA0-0.082-0.04426.150-0.006-0.0060.0000.0000.0000.000
119A127LYS10.9110.93320.1190.1210.1210.0000.0000.0000.000
120A128GLN00.0400.01325.3700.0000.0000.0000.0000.0000.000
121A129ARG10.9270.96027.3930.0290.0290.0000.0000.0000.000
122A130GLU-1-0.919-0.95226.059-0.096-0.0960.0000.0000.0000.000
123A131LEU00.0100.01326.518-0.002-0.0020.0000.0000.0000.000
124A132ILE0-0.017-0.02529.1310.0000.0000.0000.0000.0000.000
125A133ALA0-0.019-0.00632.3190.0020.0020.0000.0000.0000.000
126A134TYR00.0580.03127.563-0.002-0.0020.0000.0000.0000.000
127A135VAL00.0050.01632.5030.0000.0000.0000.0000.0000.000
128A136ARG10.8510.93135.0430.0610.0610.0000.0000.0000.000
129A137ASP-1-0.880-0.95036.541-0.066-0.0660.0000.0000.0000.000
130A138ALA00.0020.00236.4240.0020.0020.0000.0000.0000.000
131A139LEU00.003-0.00238.4100.0020.0020.0000.0000.0000.000
132A140LEU0-0.029-0.01841.0770.0040.0040.0000.0000.0000.000
133A141GLN0-0.031-0.01639.249-0.002-0.0020.0000.0000.0000.000
134A142LEU0-0.044-0.00241.8140.0000.0000.0000.0000.0000.000
135A143ARG10.8230.88344.9140.0530.0530.0000.0000.0000.000
136A144PRO00.0540.03246.6750.0020.0020.0000.0000.0000.000
137A145ASP-1-0.837-0.88747.625-0.046-0.0460.0000.0000.0000.000
138A146MET00.004-0.00446.7240.0030.0030.0000.0000.0000.000
139A147ALA0-0.025-0.00845.3590.0010.0010.0000.0000.0000.000
140A148ALA0-0.028-0.01746.5030.0010.0010.0000.0000.0000.000
141A149ASN00.0110.01048.6310.0030.0030.0000.0000.0000.000
142A150ARG10.9980.97640.9540.0390.0390.0000.0000.0000.000
143A151THR00.0090.01043.820-0.002-0.0020.0000.0000.0000.000
144A152LEU00.0300.00744.624-0.001-0.0010.0000.0000.0000.000
145A153ALA00.0710.05742.767-0.002-0.0020.0000.0000.0000.000
146A154HIS0-0.035-0.00837.294-0.003-0.0030.0000.0000.0000.000
147A155VAL00.0220.00940.484-0.002-0.0020.0000.0000.0000.000
148A156ASP-1-0.875-0.94142.160-0.052-0.0520.0000.0000.0000.000
149A157THR0-0.032-0.04136.660-0.005-0.0050.0000.0000.0000.000
150A158MET0-0.037-0.01734.671-0.006-0.0060.0000.0000.0000.000
151A159LEU0-0.025-0.00838.273-0.002-0.0020.0000.0000.0000.000
152A160PHE00.0220.01334.798-0.003-0.0030.0000.0000.0000.000
153A161PHE00.009-0.01031.277-0.004-0.0040.0000.0000.0000.000
154A162GLY0-0.0010.02134.826-0.005-0.0050.0000.0000.0000.000
155A163MET0-0.036-0.01736.767-0.001-0.0010.0000.0000.0000.000
156A164ILE00.0240.01931.973-0.005-0.0050.0000.0000.0000.000
157A165ASN00.0060.01531.231-0.015-0.0150.0000.0000.0000.000
158A166TRP00.0300.01432.158-0.001-0.0010.0000.0000.0000.000
159A167THR0-0.007-0.02932.478-0.001-0.0010.0000.0000.0000.000
160A168TYR00.0320.02129.312-0.004-0.0040.0000.0000.0000.000
161A169THR0-0.058-0.02531.2350.0000.0000.0000.0000.0000.000
162A170TRP0-0.019-0.01733.9700.0010.0010.0000.0000.0000.000
163A171TYR0-0.055-0.03231.702-0.004-0.0040.0000.0000.0000.000
164A172LYS10.9180.97631.5080.1030.1030.0000.0000.0000.000
165A173ALA00.0280.00228.7420.0030.0030.0000.0000.0000.000
166A174ASP-1-0.941-0.95329.357-0.179-0.1790.0000.0000.0000.000
167A175GLY00.0240.01631.3310.0050.0050.0000.0000.0000.000
168A176SER0-0.029-0.02935.040-0.004-0.0040.0000.0000.0000.000
169A177VAL0-0.029-0.00137.5510.0000.0000.0000.0000.0000.000
170A178SER00.0880.06433.969-0.003-0.0030.0000.0000.0000.000
171A179PRO00.0690.02129.9300.0090.0090.0000.0000.0000.000
172A180ASP-1-0.841-0.92932.947-0.162-0.1620.0000.0000.0000.000
173A181ALA00.0020.00435.0680.0090.0090.0000.0000.0000.000
174A182LEU0-0.010-0.00534.4380.0090.0090.0000.0000.0000.000
175A183ALA00.0200.02734.7280.0090.0090.0000.0000.0000.000
176A184GLU-1-0.861-0.94736.812-0.116-0.1160.0000.0000.0000.000
177A185ARG10.9360.98240.1280.0890.0890.0000.0000.0000.000
178A186THR0-0.033-0.03937.5690.0070.0070.0000.0000.0000.000
179A187VAL00.001-0.00438.6160.0060.0060.0000.0000.0000.000
180A188GLN0-0.006-0.00141.2800.0070.0070.0000.0000.0000.000
181A189LEU0-0.026-0.01043.0760.0050.0050.0000.0000.0000.000
182A190PHE0-0.036-0.02042.0530.0040.0040.0000.0000.0000.000
183A191LEU0-0.053-0.02342.6250.0030.0030.0000.0000.0000.000
184A192ASP-1-0.862-0.92845.717-0.067-0.0670.0000.0000.0000.000
185A193GLY00.0120.02847.8840.0040.0040.0000.0000.0000.000
186A194TYR0-0.012-0.03748.643-0.002-0.0020.0000.0000.0000.000
187A195LEU0-0.043-0.03550.1750.0000.0000.0000.0000.0000.000
188A196ASN0-0.034-0.01152.3420.0030.0030.0000.0000.0000.000
189A197LEU0-0.0410.00146.694-0.002-0.0020.0000.0000.0000.000
190A198LEU00.0150.00350.9200.0020.0020.0000.0000.0000.000
191A199SER0-0.052-0.02250.786-0.004-0.0040.0000.0000.0000.000
192A200ALA00.0070.01149.8890.0020.0020.0000.0000.0000.000