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: 4JNNN

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2122974.671075
FMO2-HF: Nuclear repulsion 2044455.612134
FMO2-HF: Total energy -78519.05894
FMO2-MP2: Total energy -78744.790466


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.
-9.4541.3154.065-5.321-9.515-0.007
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 : 0.032 / q_NPA : 0.021
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].
3A11ASN0-0.105-0.0552.456-7.210-0.7891.702-3.665-4.459-0.006
4A12ILE00.0290.0072.412-0.1801.3021.177-0.579-2.0800.002
5A13ARG10.8120.8893.1482.6483.5440.029-0.274-0.6510.000
6A14ASP-1-0.841-0.9375.047-1.689-1.538-0.001-0.007-0.1430.000
7A15THR0-0.0040.0097.4040.3740.3740.0000.0000.0000.000
8A16ILE00.0140.0016.9690.4100.4100.0000.0000.0000.000
9A17ILE0-0.025-0.0049.2670.2610.2610.0000.0000.0000.000
10A18GLU-1-0.899-0.93911.637-1.000-1.0000.0000.0000.0000.000
11A19ARG10.8070.85312.6611.0011.0010.0000.0000.0000.000
12A20ALA0-0.029-0.01314.2010.1140.1140.0000.0000.0000.000
13A21ALA00.015-0.00115.5450.0860.0860.0000.0000.0000.000
14A22ALA00.0240.01617.4550.0700.0700.0000.0000.0000.000
15A23MET0-0.042-0.01417.8180.0720.0720.0000.0000.0000.000
16A24PHE0-0.027-0.02816.6340.0470.0470.0000.0000.0000.000
17A25ALA00.0180.02221.3500.0330.0330.0000.0000.0000.000
18A26ARG10.6980.82422.5780.4050.4050.0000.0000.0000.000
19A27GLN00.0410.02122.6770.0030.0030.0000.0000.0000.000
20A28GLY00.0600.04324.4390.0220.0220.0000.0000.0000.000
21A29TYR00.0320.00418.415-0.003-0.0030.0000.0000.0000.000
22A30SER0-0.047-0.04822.3880.0020.0020.0000.0000.0000.000
23A31GLU-1-0.873-0.90524.531-0.128-0.1280.0000.0000.0000.000
24A32THR00.0110.01019.180-0.011-0.0110.0000.0000.0000.000
25A33SER0-0.049-0.05320.6660.0120.0120.0000.0000.0000.000
26A34ILE00.0630.00714.675-0.031-0.0310.0000.0000.0000.000
27A35GLY0-0.031-0.02116.1350.0010.0010.0000.0000.0000.000
28A36ASP-1-0.763-0.82918.245-0.153-0.1530.0000.0000.0000.000
29A37ILE00.0420.02113.201-0.019-0.0190.0000.0000.0000.000
30A38ALA0-0.026-0.01013.316-0.057-0.0570.0000.0000.0000.000
31A39ARG10.8560.90614.3970.1070.1070.0000.0000.0000.000
32A40ALA00.0100.01416.410-0.005-0.0050.0000.0000.0000.000
33A41CYS0-0.0590.00411.059-0.140-0.1400.0000.0000.0000.000
34A42GLU-1-0.845-0.90012.246-0.535-0.5350.0000.0000.0000.000
35A43CYS0-0.0310.00810.9230.1960.1960.0000.0000.0000.000
36A44SER00.0290.00012.881-0.006-0.0060.0000.0000.0000.000
37A45LYS10.9730.96112.574-0.052-0.0520.0000.0000.0000.000
38A46SER00.013-0.00213.151-0.045-0.0450.0000.0000.0000.000
39A47ARG10.9290.9515.383-1.213-1.2130.0000.0000.0000.000
40A48LEU00.0210.0217.8740.0320.0320.0000.0000.0000.000
41A49TYR00.0210.0028.791-0.090-0.0900.0000.0000.0000.000
42A50HIS0-0.067-0.0214.520-0.0170.128-0.001-0.016-0.1280.000
43A51TYR0-0.016-0.0112.656-1.976-0.3021.159-0.780-2.054-0.003
44A52PHE00.0270.0065.710-0.411-0.4110.0000.0000.0000.000
45A53ASP-1-0.795-0.8849.2550.0770.0770.0000.0000.0000.000
46A54SER0-0.028-0.05312.4860.0200.0200.0000.0000.0000.000
47A55LYS10.8120.89213.7420.1090.1090.0000.0000.0000.000
48A56GLU-1-0.825-0.88615.923-0.135-0.1350.0000.0000.0000.000
49A57ALA0-0.037-0.00811.912-0.041-0.0410.0000.0000.0000.000
50A58VAL00.0050.00211.227-0.090-0.0900.0000.0000.0000.000
51A59LEU00.0070.01012.666-0.091-0.0910.0000.0000.0000.000
52A60ARG10.8660.90812.9230.1560.1560.0000.0000.0000.000
53A61ASP-1-0.846-0.8809.763-1.275-1.2750.0000.0000.0000.000
54A62MET00.0110.02012.729-0.031-0.0310.0000.0000.0000.000
55A63LEU0-0.0150.00214.2580.0190.0190.0000.0000.0000.000
56A64THR0-0.027-0.03414.4840.0500.0500.0000.0000.0000.000
57A65THR0-0.019-0.02511.1260.0290.0290.0000.0000.0000.000
58A66HIS0-0.030-0.00814.546-0.028-0.0280.0000.0000.0000.000
59A67VAL00.009-0.00817.7040.0390.0390.0000.0000.0000.000
60A68ASP-1-0.781-0.89317.415-0.319-0.3190.0000.0000.0000.000
61A69SER0-0.0450.00216.9530.0420.0420.0000.0000.0000.000
62A70LEU00.008-0.00118.8830.0390.0390.0000.0000.0000.000
63A71LEU0-0.036-0.00922.0990.0340.0340.0000.0000.0000.000
64A72GLU-1-0.856-0.91520.950-0.267-0.2670.0000.0000.0000.000
65A73ARG10.8190.86821.3240.4700.4700.0000.0000.0000.000
66A74CYS0-0.048-0.02724.3780.0280.0280.0000.0000.0000.000
67A75ARG10.7820.86921.7670.3010.3010.0000.0000.0000.000
68A76GLN00.003-0.01022.8150.0070.0070.0000.0000.0000.000
69A77VAL0-0.0140.00027.6840.0150.0150.0000.0000.0000.000
70A78LEU0-0.057-0.03030.4110.0180.0180.0000.0000.0000.000
71A79TYR0-0.056-0.03227.9300.0190.0190.0000.0000.0000.000
72A80GLY00.0300.03332.5350.0040.0040.0000.0000.0000.000
73A81SER0-0.0010.00533.5030.0130.0130.0000.0000.0000.000
74A82ASN00.0190.00636.9500.0050.0050.0000.0000.0000.000
75A83GLU-1-0.830-0.88740.036-0.132-0.1320.0000.0000.0000.000
76A84PRO00.0140.00239.738-0.009-0.0090.0000.0000.0000.000
77A85LYS10.8480.90239.5220.1210.1210.0000.0000.0000.000
78A86THR0-0.042-0.03737.721-0.007-0.0070.0000.0000.0000.000
79A87ARG10.8450.91235.4190.1360.1360.0000.0000.0000.000
80A88PHE00.0200.00634.821-0.013-0.0130.0000.0000.0000.000
81A89LEU00.0100.00735.422-0.010-0.0100.0000.0000.0000.000
82A90GLN00.011-0.01032.574-0.005-0.0050.0000.0000.0000.000
83A91ILE00.0180.01830.657-0.019-0.0190.0000.0000.0000.000
84A92VAL0-0.030-0.01130.931-0.016-0.0160.0000.0000.0000.000
85A93LYS10.7790.85432.0550.2050.2050.0000.0000.0000.000
86A94LEU0-0.0020.01425.054-0.019-0.0190.0000.0000.0000.000
87A95PHE0-0.006-0.01427.073-0.026-0.0260.0000.0000.0000.000
88A96LEU00.0000.00327.706-0.017-0.0170.0000.0000.0000.000
89A97GLU-1-0.790-0.84924.567-0.451-0.4510.0000.0000.0000.000
90A98ILE00.0200.00722.170-0.036-0.0360.0000.0000.0000.000
91A99TYR0-0.063-0.02723.620-0.038-0.0380.0000.0000.0000.000
92A100ALA0-0.012-0.02425.251-0.014-0.0140.0000.0000.0000.000
93A101THR0-0.042-0.01421.162-0.029-0.0290.0000.0000.0000.000
94A102SER0-0.015-0.00819.601-0.089-0.0890.0000.0000.0000.000
95A103ARG10.8790.95320.9020.3470.3470.0000.0000.0000.000
96A104ASP-1-0.758-0.86319.987-0.443-0.4430.0000.0000.0000.000
97A105ARG10.9680.98412.2221.2171.2170.0000.0000.0000.000
98A106HIS00.0530.02819.1610.0120.0120.0000.0000.0000.000
99A107VAL0-0.010-0.00822.6470.0340.0340.0000.0000.0000.000
100A108VAL00.0240.00619.0470.0310.0310.0000.0000.0000.000
101A109MET0-0.052-0.01821.2670.0240.0240.0000.0000.0000.000
102A110LEU0-0.039-0.01422.6800.0320.0320.0000.0000.0000.000
103A111THR0-0.081-0.03625.0370.0250.0250.0000.0000.0000.000
104A112CYS0-0.0040.01022.1010.0050.0050.0000.0000.0000.000
105A113LEU00.0070.01822.6130.0010.0010.0000.0000.0000.000
106A114ASP-1-0.885-0.95323.919-0.173-0.1730.0000.0000.0000.000
107A115ALA0-0.0190.00122.7600.0210.0210.0000.0000.0000.000
108A116LEU0-0.038-0.00618.3030.0030.0030.0000.0000.0000.000
109A117PRO00.0270.00720.7770.0120.0120.0000.0000.0000.000
110A118GLU-1-0.774-0.88123.690-0.106-0.1060.0000.0000.0000.000
111A119ASP-1-0.824-0.88921.745-0.093-0.0930.0000.0000.0000.000
112A120GLN00.022-0.02018.306-0.043-0.0430.0000.0000.0000.000
113A121ARG10.8540.93221.3530.0990.0990.0000.0000.0000.000
114A122LYS10.8710.90923.8290.0730.0730.0000.0000.0000.000
115A123ALA0-0.0090.00521.762-0.001-0.0010.0000.0000.0000.000
116A124LEU00.0260.01218.699-0.011-0.0110.0000.0000.0000.000
117A125ILE0-0.006-0.00522.763-0.003-0.0030.0000.0000.0000.000
118A126ALA0-0.060-0.03325.6540.0040.0040.0000.0000.0000.000
119A127LYS10.8400.91120.0470.2880.2880.0000.0000.0000.000
120A128GLN00.0460.01424.7550.0110.0110.0000.0000.0000.000
121A129ARG10.9140.95526.9680.1410.1410.0000.0000.0000.000
122A130GLU-1-0.778-0.84724.466-0.228-0.2280.0000.0000.0000.000
123A131LEU00.0310.01925.9670.0060.0060.0000.0000.0000.000
124A132ILE0-0.025-0.02228.5060.0080.0080.0000.0000.0000.000
125A133ALA0-0.017-0.00731.7680.0090.0090.0000.0000.0000.000
126A134TYR0-0.026-0.03226.4250.0080.0080.0000.0000.0000.000
127A135VAL00.0210.02231.7550.0030.0030.0000.0000.0000.000
128A136ARG10.8170.89134.2370.1270.1270.0000.0000.0000.000
129A137ASP-1-0.834-0.90636.077-0.117-0.1170.0000.0000.0000.000
130A138ALA00.0080.01335.4770.0060.0060.0000.0000.0000.000
131A139LEU00.009-0.00137.5000.0050.0050.0000.0000.0000.000
132A140LEU0-0.026-0.01440.1320.0080.0080.0000.0000.0000.000
133A141GLN0-0.0150.00037.2390.0030.0030.0000.0000.0000.000
134A142LEU0-0.043-0.00741.0260.0020.0020.0000.0000.0000.000
135A143ARG10.8200.88044.2890.0980.0980.0000.0000.0000.000
136A144PRO00.0520.03445.9380.0010.0010.0000.0000.0000.000
137A145ASP-1-0.827-0.88846.868-0.085-0.0850.0000.0000.0000.000
138A146MET00.004-0.00245.9820.0040.0040.0000.0000.0000.000
139A147ALA0-0.020-0.00644.6900.0000.0000.0000.0000.0000.000
140A148ALA0-0.016-0.00845.6160.0010.0010.0000.0000.0000.000
141A149ASN00.0110.01248.0120.0010.0010.0000.0000.0000.000
142A150ARG10.9830.97140.8510.0830.0830.0000.0000.0000.000
143A151THR00.0160.01342.983-0.005-0.0050.0000.0000.0000.000
144A152LEU00.0280.01143.940-0.004-0.0040.0000.0000.0000.000
145A153ALA00.0610.03942.385-0.005-0.0050.0000.0000.0000.000
146A154HIS0-0.043-0.00136.616-0.003-0.0030.0000.0000.0000.000
147A155VAL00.0280.00639.814-0.007-0.0070.0000.0000.0000.000
148A156ASP-1-0.869-0.93941.399-0.112-0.1120.0000.0000.0000.000
149A157THR0-0.024-0.03336.129-0.008-0.0080.0000.0000.0000.000
150A158MET0-0.039-0.02534.284-0.013-0.0130.0000.0000.0000.000
151A159LEU0-0.0120.00237.687-0.006-0.0060.0000.0000.0000.000
152A160PHE00.0160.00934.223-0.006-0.0060.0000.0000.0000.000
153A161PHE00.017-0.01330.429-0.008-0.0080.0000.0000.0000.000
154A162GLY0-0.0130.00334.244-0.011-0.0110.0000.0000.0000.000
155A163MET0-0.043-0.02035.958-0.005-0.0050.0000.0000.0000.000
156A164ILE00.0130.01331.503-0.008-0.0080.0000.0000.0000.000
157A165ASN0-0.0090.00530.349-0.029-0.0290.0000.0000.0000.000
158A166TRP00.0300.01631.278-0.012-0.0120.0000.0000.0000.000
159A167THR0-0.005-0.01531.405-0.006-0.0060.0000.0000.0000.000
160A168TYR0-0.016-0.01228.2810.0020.0020.0000.0000.0000.000
161A169THR0-0.046-0.02030.258-0.003-0.0030.0000.0000.0000.000
162A170TRP0-0.013-0.00733.0630.0050.0050.0000.0000.0000.000
163A171TYR0-0.028-0.02731.554-0.002-0.0020.0000.0000.0000.000
164A172LYS10.8940.94830.9650.2130.2130.0000.0000.0000.000
165A173ALA00.0030.00328.2530.0110.0110.0000.0000.0000.000
166A174ASP-1-0.888-0.94329.066-0.297-0.2970.0000.0000.0000.000
167A175GLY00.0110.00930.9460.0130.0130.0000.0000.0000.000
168A176SER0-0.038-0.03834.639-0.002-0.0020.0000.0000.0000.000
169A177VAL0-0.0190.00336.5330.0100.0100.0000.0000.0000.000
170A178SER00.0730.05833.488-0.008-0.0080.0000.0000.0000.000
171A179PRO00.0550.01329.6430.0120.0120.0000.0000.0000.000
172A180ASP-1-0.827-0.89932.662-0.231-0.2310.0000.0000.0000.000
173A181ALA00.0490.02434.4630.0120.0120.0000.0000.0000.000
174A182LEU0-0.0060.00234.4240.0130.0130.0000.0000.0000.000
175A183ALA00.0140.02534.1380.0100.0100.0000.0000.0000.000
176A184GLU-1-0.834-0.91336.231-0.173-0.1730.0000.0000.0000.000
177A185ARG10.8260.92239.5290.1480.1480.0000.0000.0000.000
178A186THR0-0.012-0.02337.2620.0090.0090.0000.0000.0000.000
179A187VAL00.001-0.00938.1460.0080.0080.0000.0000.0000.000
180A188GLN00.0220.01640.8090.0110.0110.0000.0000.0000.000
181A189LEU0-0.024-0.01942.4560.0080.0080.0000.0000.0000.000
182A190PHE0-0.040-0.02241.1120.0050.0050.0000.0000.0000.000
183A191LEU0-0.045-0.01641.5290.0040.0040.0000.0000.0000.000
184A192ASP-1-0.825-0.88645.094-0.118-0.1180.0000.0000.0000.000
185A193GLY00.0460.03847.3010.0060.0060.0000.0000.0000.000
186A194TYR00.003-0.02347.775-0.001-0.0010.0000.0000.0000.000
187A195LEU0-0.035-0.02749.6530.0010.0010.0000.0000.0000.000
188A196ASN0-0.047-0.01551.6240.0070.0070.0000.0000.0000.000
189A197LEU0-0.053-0.00746.338-0.002-0.0020.0000.0000.0000.000
190A198LEU00.0260.01350.3210.0020.0020.0000.0000.0000.000
191A199SER0-0.014-0.01649.896-0.007-0.0070.0000.0000.0000.000
192A200ALA00.0160.01749.7820.0040.0040.0000.0000.0000.000