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

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FMODB ID: JQ1G9

Calculation Name: 3CYG-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3CYG

Chain ID: A

ChEMBL ID:
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UniProt ID: A7HM60

Base Structure: X-ray

Registration Date: 2023-09-24

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2628794.592465
FMO2-HF: Nuclear repulsion 2541226.930648
FMO2-HF: Total energy -87567.661817
FMO2-MP2: Total energy -87827.507632


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:36:LEU)


Summations of interaction energy for fragment #1(A:36:LEU)
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.
-2.6510.340.022-1.484-1.5290.005
Interaction energy analysis for fragmet #1(A:36:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.074 / q_NPA : 0.031
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].
3A38MET00.0070.0143.463-2.8880.1030.022-1.484-1.5290.005
4A39LYS10.7690.8795.2580.7310.7310.0000.0000.0000.000
5A40VAL00.0420.0086.891-0.003-0.0030.0000.0000.0000.000
6A41PHE00.0080.0159.6540.0700.0700.0000.0000.0000.000
7A42GLU-1-0.829-0.8869.944-0.514-0.5140.0000.0000.0000.000
8A43ILE00.0230.00612.0870.0400.0400.0000.0000.0000.000
9A44VAL0-0.019-0.00314.671-0.013-0.0130.0000.0000.0000.000
10A45LYS10.8650.93415.4980.1370.1370.0000.0000.0000.000
11A46SER0-0.020-0.01019.287-0.008-0.0080.0000.0000.0000.000
12A47SER00.0050.00622.9110.0020.0020.0000.0000.0000.000
13A48THR0-0.060-0.03926.064-0.002-0.0020.0000.0000.0000.000
14A49GLU-1-0.835-0.92029.774-0.038-0.0380.0000.0000.0000.000
15A50ASN0-0.0010.00632.8660.0010.0010.0000.0000.0000.000
16A51GLU-1-0.919-0.96136.615-0.028-0.0280.0000.0000.0000.000
17A52ILE00.0380.04138.7070.0020.0020.0000.0000.0000.000
18A53VAL0-0.028-0.02233.7930.0000.0000.0000.0000.0000.000
19A54ARG10.7940.87928.9250.0340.0340.0000.0000.0000.000
20A55ILE0-0.066-0.02027.994-0.001-0.0010.0000.0000.0000.000
21A56HIS00.0180.00824.487-0.008-0.0080.0000.0000.0000.000
22A57VAL00.0050.00022.6920.0030.0030.0000.0000.0000.000
23A58GLU-1-0.823-0.90818.278-0.107-0.1070.0000.0000.0000.000
24A59LEU00.0320.00819.6450.0050.0050.0000.0000.0000.000
25A60PRO0-0.0180.00516.607-0.026-0.0260.0000.0000.0000.000
26A61ARG10.9040.93715.7260.2810.2810.0000.0000.0000.000
27A62LEU0-0.025-0.01914.221-0.037-0.0370.0000.0000.0000.000
28A63LYS10.8480.92310.2530.6500.6500.0000.0000.0000.000
29A64TYR0-0.014-0.02111.515-0.076-0.0760.0000.0000.0000.000
30A65LEU00.0090.00913.488-0.011-0.0110.0000.0000.0000.000
31A66LYS10.8040.90015.6210.1530.1530.0000.0000.0000.000
32A67ASP-1-0.857-0.93717.680-0.138-0.1380.0000.0000.0000.000
33A68SER00.0630.02120.170-0.002-0.0020.0000.0000.0000.000
34A69ASN00.0130.00821.2470.0050.0050.0000.0000.0000.000
35A70PHE0-0.041-0.01519.0110.0090.0090.0000.0000.0000.000
36A71GLU-1-0.858-0.95216.948-0.307-0.3070.0000.0000.0000.000
37A72GLU-1-0.938-0.96220.210-0.170-0.1700.0000.0000.0000.000
38A73LYS10.8130.90323.2840.1060.1060.0000.0000.0000.000
39A74PHE0-0.0030.00119.6290.0090.0090.0000.0000.0000.000
40A75ASN00.0370.00818.3150.0100.0100.0000.0000.0000.000
41A76SER00.001-0.00321.9010.0080.0080.0000.0000.0000.000
42A77GLU-1-0.794-0.87825.556-0.086-0.0860.0000.0000.0000.000
43A78VAL0-0.029-0.01821.1930.0090.0090.0000.0000.0000.000
44A79GLU-1-0.901-0.96423.873-0.132-0.1320.0000.0000.0000.000
45A80GLU-1-0.914-0.96025.183-0.075-0.0750.0000.0000.0000.000
46A81LYS10.8290.89826.8930.0790.0790.0000.0000.0000.000
47A82ILE0-0.0140.00923.8190.0060.0060.0000.0000.0000.000
48A83LYS10.8400.92127.2780.1010.1010.0000.0000.0000.000
49A84LYS10.8430.91929.7390.0580.0580.0000.0000.0000.000
50A85PHE00.0580.02528.9590.0040.0040.0000.0000.0000.000
51A86VAL00.0330.00428.2070.0040.0040.0000.0000.0000.000
52A87ASN0-0.033-0.03531.3970.0040.0040.0000.0000.0000.000
53A88GLU-1-0.864-0.89834.470-0.045-0.0450.0000.0000.0000.000
54A89VAL00.006-0.00733.0110.0030.0030.0000.0000.0000.000
55A90LYS10.8700.94833.1220.0630.0630.0000.0000.0000.000
56A91GLY00.0030.00436.7510.0020.0020.0000.0000.0000.000
57A92ILE00.0100.00238.4000.0020.0020.0000.0000.0000.000
58A93ALA00.0310.01438.1740.0020.0020.0000.0000.0000.000
59A94GLN0-0.084-0.04840.2490.0000.0000.0000.0000.0000.000
60A95GLU-1-0.826-0.88142.442-0.027-0.0270.0000.0000.0000.000
61A96ASP-1-0.814-0.89043.294-0.024-0.0240.0000.0000.0000.000
62A97HIS0-0.0180.00143.5940.0020.0020.0000.0000.0000.000
63A98ASP-1-0.855-0.93145.454-0.030-0.0300.0000.0000.0000.000
64A99LYS10.6160.79846.5400.0260.0260.0000.0000.0000.000
65A100ASP-1-0.969-0.99148.728-0.018-0.0180.0000.0000.0000.000
66A101VAL0-0.015-0.01947.7230.0020.0020.0000.0000.0000.000
67A102GLN0-0.062-0.01839.6790.0000.0000.0000.0000.0000.000
68A103HIS0-0.079-0.04544.1980.0020.0020.0000.0000.0000.000
69A104THR0-0.045-0.02839.2040.0010.0010.0000.0000.0000.000
70A105PRO00.0330.02136.676-0.001-0.0010.0000.0000.0000.000
71A106TYR0-0.057-0.03136.6550.0010.0010.0000.0000.0000.000
72A107GLU-1-0.843-0.91831.011-0.034-0.0340.0000.0000.0000.000
73A108ALA00.0050.00030.3060.0020.0020.0000.0000.0000.000
74A109TYR0-0.051-0.03421.215-0.001-0.0010.0000.0000.0000.000
75A110VAL00.0100.00722.8050.0030.0030.0000.0000.0000.000
76A111SER00.013-0.00120.278-0.008-0.0080.0000.0000.0000.000
77A112VAL0-0.017-0.00715.7650.0010.0010.0000.0000.0000.000
78A113ASP-1-0.812-0.87516.425-0.035-0.0350.0000.0000.0000.000
79A114VAL0-0.035-0.02711.559-0.001-0.0010.0000.0000.0000.000
80A115ARG10.7500.82914.2830.0290.0290.0000.0000.0000.000
81A116TYR0-0.049-0.04511.4970.0420.0420.0000.0000.0000.000
82A117GLU-1-0.766-0.8776.340-0.195-0.1950.0000.0000.0000.000
83A118GLY0-0.016-0.0068.2050.0660.0660.0000.0000.0000.000
84A119LYS10.7550.8558.679-0.021-0.0210.0000.0000.0000.000
85A120ASP-1-0.778-0.9009.620-0.095-0.0950.0000.0000.0000.000
86A121PHE00.0280.02012.409-0.004-0.0040.0000.0000.0000.000
87A122LEU0-0.030-0.00311.5340.0040.0040.0000.0000.0000.000
88A123SER00.0090.00214.1750.0030.0030.0000.0000.0000.000
89A124PHE0-0.007-0.00815.619-0.003-0.0030.0000.0000.0000.000
90A125VAL00.0720.03817.5730.0000.0000.0000.0000.0000.000
91A126VAL0-0.031-0.01019.692-0.011-0.0110.0000.0000.0000.000
92A127TYR0-0.040-0.04220.8380.0090.0090.0000.0000.0000.000
93A128TYR0-0.030-0.04524.507-0.008-0.0080.0000.0000.0000.000
94A129TYR0-0.015-0.00127.4920.0060.0060.0000.0000.0000.000
95A130GLN00.017-0.00329.217-0.002-0.0020.0000.0000.0000.000
96A131PHE0-0.034-0.00632.5410.0040.0040.0000.0000.0000.000
97A132THR00.0410.01135.240-0.002-0.0020.0000.0000.0000.000
98A133GLY00.0520.04038.4180.0010.0010.0000.0000.0000.000
99A134GLY0-0.016-0.00239.5050.0000.0000.0000.0000.0000.000
100A135ALA0-0.026-0.02540.3300.0000.0000.0000.0000.0000.000
101A136HIS10.8460.91735.3620.0140.0140.0000.0000.0000.000
102A137GLY00.0860.05034.187-0.001-0.0010.0000.0000.0000.000
103A138ILE0-0.055-0.02134.1450.0030.0030.0000.0000.0000.000
104A139THR00.0390.00227.713-0.002-0.0020.0000.0000.0000.000
105A140PHE0-0.0220.00829.6820.0040.0040.0000.0000.0000.000
106A141PHE0-0.010-0.02425.131-0.004-0.0040.0000.0000.0000.000
107A142GLU-1-0.747-0.80525.039-0.066-0.0660.0000.0000.0000.000
108A143THR0-0.034-0.03222.369-0.003-0.0030.0000.0000.0000.000
109A144TYR0-0.047-0.03619.796-0.004-0.0040.0000.0000.0000.000
110A145ASN0-0.0040.00819.0880.0010.0010.0000.0000.0000.000
111A146ILE00.0170.00416.8580.0000.0000.0000.0000.0000.000
112A147ASP-1-0.729-0.84316.650-0.056-0.0560.0000.0000.0000.000
113A148LEU00.003-0.00912.070-0.013-0.0130.0000.0000.0000.000
114A149LYS10.7910.91115.9870.0010.0010.0000.0000.0000.000
115A150ASN0-0.008-0.02817.351-0.014-0.0140.0000.0000.0000.000
116A151SER0-0.0250.00719.046-0.003-0.0030.0000.0000.0000.000
117A152LYS10.8900.92420.1510.0590.0590.0000.0000.0000.000
118A153VAL0-0.016-0.00321.2120.0020.0020.0000.0000.0000.000
119A154LEU0-0.034-0.01821.6680.0040.0040.0000.0000.0000.000
120A155LYS10.9550.97724.3090.0430.0430.0000.0000.0000.000
121A156LEU00.0590.03326.5620.0020.0020.0000.0000.0000.000
122A157TYR00.0410.02327.9580.0030.0030.0000.0000.0000.000
123A158ASP-1-0.838-0.92326.742-0.040-0.0400.0000.0000.0000.000
124A159ILE0-0.075-0.04122.8950.0010.0010.0000.0000.0000.000
125A160ILE00.0080.00426.8790.0050.0050.0000.0000.0000.000
126A161LYS10.8520.94529.757-0.004-0.0040.0000.0000.0000.000
127A162GLU-1-0.722-0.86933.477-0.011-0.0110.0000.0000.0000.000
128A163GLU-1-0.891-0.95635.976-0.002-0.0020.0000.0000.0000.000
129A164ALA0-0.069-0.03132.1880.0020.0020.0000.0000.0000.000
130A165GLU-1-0.817-0.92834.087-0.004-0.0040.0000.0000.0000.000
131A166ASP-1-0.886-0.94135.5610.0040.0040.0000.0000.0000.000
132A167THR0-0.077-0.04333.2080.0020.0020.0000.0000.0000.000
133A168ILE00.0170.00030.0140.0030.0030.0000.0000.0000.000
134A169LYS10.8380.92833.1360.0050.0050.0000.0000.0000.000
135A170SER0-0.048-0.01535.9490.0020.0020.0000.0000.0000.000
136A171ASN0-0.038-0.02030.4280.0010.0010.0000.0000.0000.000
137A172ILE00.0840.03431.3260.0020.0020.0000.0000.0000.000
138A173LEU0-0.0190.00233.8230.0010.0010.0000.0000.0000.000
139A174LYS10.8970.96035.646-0.018-0.0180.0000.0000.0000.000
140A175GLN0-0.012-0.03129.1580.0010.0010.0000.0000.0000.000
141A176ILE0-0.0330.00534.2660.0000.0000.0000.0000.0000.000
142A177GLU-1-0.933-0.97636.4180.0200.0200.0000.0000.0000.000
143A178GLN0-0.096-0.04835.1480.0030.0030.0000.0000.0000.000
144A179ASN0-0.057-0.04233.2280.0020.0020.0000.0000.0000.000
145A180ASN00.0440.02137.1670.0000.0000.0000.0000.0000.000
146A181THR0-0.104-0.03938.458-0.001-0.0010.0000.0000.0000.000
147A182ASP-1-0.851-0.90234.8450.0170.0170.0000.0000.0000.000
148A183PHE0-0.029-0.02932.897-0.002-0.0020.0000.0000.0000.000
149A184PHE0-0.0100.00338.3180.0000.0000.0000.0000.0000.000
150A185PRO00.0250.00441.4170.0000.0000.0000.0000.0000.000
151A186ASP-1-0.898-0.95043.643-0.001-0.0010.0000.0000.0000.000
152A187ALA00.0170.01138.348-0.001-0.0010.0000.0000.0000.000
153A188PRO00.023-0.00640.072-0.001-0.0010.0000.0000.0000.000
154A189MET00.0010.00041.066-0.001-0.0010.0000.0000.0000.000
155A190ASN00.024-0.00839.993-0.001-0.0010.0000.0000.0000.000
156A191ILE00.0500.04335.013-0.001-0.0010.0000.0000.0000.000
157A192LEU0-0.046-0.02638.2930.0000.0000.0000.0000.0000.000
158A193LYS10.8410.91541.0890.0040.0040.0000.0000.0000.000
159A194ASP-1-0.830-0.88334.927-0.011-0.0110.0000.0000.0000.000
160A195ASP-1-0.816-0.86636.294-0.015-0.0150.0000.0000.0000.000
161A196ILE00.026-0.00431.615-0.001-0.0010.0000.0000.0000.000
162A197PHE0-0.076-0.02531.334-0.001-0.0010.0000.0000.0000.000
163A198SER0-0.087-0.06332.100-0.003-0.0030.0000.0000.0000.000
164A199ARG10.7770.88430.3340.0120.0120.0000.0000.0000.000
165A200GLU-1-0.817-0.88226.628-0.044-0.0440.0000.0000.0000.000
166A201PHE0-0.003-0.01723.4090.0050.0050.0000.0000.0000.000
167A202THR00.0230.02319.379-0.005-0.0050.0000.0000.0000.000
168A203ILE0-0.015-0.01817.5260.0070.0070.0000.0000.0000.000
169A204SER00.0320.01415.8770.0010.0010.0000.0000.0000.000
170A205LYS10.8180.89414.071-0.121-0.1210.0000.0000.0000.000
171A206ASP-1-0.852-0.93216.1160.1020.1020.0000.0000.0000.000
172A207GLY00.006-0.00718.884-0.001-0.0010.0000.0000.0000.000
173A208LEU0-0.0110.01020.470-0.004-0.0040.0000.0000.0000.000
174A209ILE0-0.009-0.00519.7890.0050.0050.0000.0000.0000.000
175A210ILE00.0310.02023.798-0.007-0.0070.0000.0000.0000.000
176A211MET0-0.0300.00923.1030.0010.0010.0000.0000.0000.000
177A212TYR0-0.042-0.04927.548-0.002-0.0020.0000.0000.0000.000
178A213PRO0-0.0140.00929.753-0.001-0.0010.0000.0000.0000.000
179A214HIS00.0600.00930.5760.0040.0040.0000.0000.0000.000
180A215TYR0-0.025-0.03234.024-0.002-0.0020.0000.0000.0000.000
181A216ASP-1-0.806-0.87735.338-0.013-0.0130.0000.0000.0000.000
182A217LEU0-0.038-0.02333.7600.0010.0010.0000.0000.0000.000
183A218ALA00.0330.01635.0260.0020.0020.0000.0000.0000.000
184A219PRO00.0050.00937.029-0.003-0.0030.0000.0000.0000.000
185A220TYR00.012-0.00533.0310.0010.0010.0000.0000.0000.000
186A221ALA0-0.054-0.02934.0370.0000.0000.0000.0000.0000.000
187A222SER0-0.003-0.00633.6920.0010.0010.0000.0000.0000.000
188A223GLY0-0.0160.01630.2520.0020.0020.0000.0000.0000.000
189A224MET0-0.046-0.02726.772-0.002-0.0020.0000.0000.0000.000
190A225PRO00.0140.01127.9080.0020.0020.0000.0000.0000.000
191A226GLU-1-0.766-0.85223.119-0.007-0.0070.0000.0000.0000.000
192A227PHE0-0.018-0.01427.1290.0040.0040.0000.0000.0000.000
193A228VAL00.0110.00923.200-0.002-0.0020.0000.0000.0000.000
194A229ILE0-0.004-0.00324.9700.0010.0010.0000.0000.0000.000
195A230PRO0-0.0030.00224.1670.0010.0010.0000.0000.0000.000
196A231TRP00.0960.04419.465-0.006-0.0060.0000.0000.0000.000
197A232ASN00.015-0.00124.515-0.003-0.0030.0000.0000.0000.000
198A233VAL0-0.064-0.03127.090-0.002-0.0020.0000.0000.0000.000
199A234ILE00.0140.00726.062-0.003-0.0030.0000.0000.0000.000
200A235GLU-1-0.935-0.95025.8690.0270.0270.0000.0000.0000.000
201A236LYS10.9420.96228.106-0.018-0.0180.0000.0000.0000.000
202A237PHE0-0.042-0.03730.723-0.002-0.0020.0000.0000.0000.000
203A238LEU00.0400.03625.059-0.004-0.0040.0000.0000.0000.000
204A239LYS10.7360.88428.2000.0150.0150.0000.0000.0000.000
205A240TYR0-0.051-0.05021.258-0.006-0.0060.0000.0000.0000.000
206A241ASP-1-0.785-0.89820.8570.0110.0110.0000.0000.0000.000
207A242ILE00.0490.02920.313-0.001-0.0010.0000.0000.0000.000
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