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: 7G31K

Calculation Name: 3CYG-A-Xray320

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 217
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2633580.559561
FMO2-HF: Nuclear repulsion 2545844.859062
FMO2-HF: Total energy -87735.700499
FMO2-MP2: Total energy -87996.10929


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:35:ACE )


Summations of interaction energy for fragment #1(A:35:ACE )
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.
2.0592.74-0.006-0.366-0.3090
Interaction energy analysis for fragmet #1(A:35:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / 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].
3A37ARG 10.9000.9803.8472.1052.786-0.006-0.366-0.3090.000
4A38MET 00.0040.0087.248-0.013-0.0130.0000.0000.0000.000
5A39LYS 10.8530.9159.3480.4840.4840.0000.0000.0000.000
6A40VAL 00.0500.00711.5740.0500.0500.0000.0000.0000.000
7A41PHE 00.0270.03114.6960.0340.0340.0000.0000.0000.000
8A42GLU -1-0.845-0.91714.888-0.117-0.1170.0000.0000.0000.000
9A43ILE 00.0310.01616.6420.0120.0120.0000.0000.0000.000
10A44VAL 0-0.017-0.00518.8450.0060.0060.0000.0000.0000.000
11A45LYS 10.9440.97919.9240.0920.0920.0000.0000.0000.000
12A46SER 0-0.055-0.02523.0840.0100.0100.0000.0000.0000.000
13A47SER 00.0250.01426.335-0.002-0.0020.0000.0000.0000.000
14A48THR 0-0.070-0.04529.5890.0050.0050.0000.0000.0000.000
15A49GLU -1-0.854-0.96033.058-0.021-0.0210.0000.0000.0000.000
16A50ASN 0-0.0180.00636.1920.0020.0020.0000.0000.0000.000
17A51GLU -1-0.908-0.95439.862-0.009-0.0090.0000.0000.0000.000
18A52ILE 00.0210.03542.358-0.001-0.0010.0000.0000.0000.000
19A53VAL 0-0.013-0.01437.846-0.002-0.0020.0000.0000.0000.000
20A54ARG 10.9000.96432.5240.0270.0270.0000.0000.0000.000
21A55ILE 0-0.056-0.01232.125-0.003-0.0030.0000.0000.0000.000
22A56HIS 00.0190.00028.8430.0000.0000.0000.0000.0000.000
23A57VAL 00.0040.00327.045-0.003-0.0030.0000.0000.0000.000
24A58GLU -1-0.893-0.94223.176-0.095-0.0950.0000.0000.0000.000
25A59LEU 00.011-0.00224.002-0.004-0.0040.0000.0000.0000.000
26A60PRO 0-0.0070.01221.742-0.007-0.0070.0000.0000.0000.000
27A61ARG 10.8980.94119.8280.0690.0690.0000.0000.0000.000
28A62LEU 0-0.024-0.01219.213-0.020-0.0200.0000.0000.0000.000
29A63LYS 10.8480.93813.0730.1610.1610.0000.0000.0000.000
30A64TYR 0-0.023-0.02915.205-0.017-0.0170.0000.0000.0000.000
31A65LEU 00.0150.01317.496-0.023-0.0230.0000.0000.0000.000
32A66LYS 10.8340.92920.0800.1370.1370.0000.0000.0000.000
33A67ASP -1-0.875-0.94721.865-0.048-0.0480.0000.0000.0000.000
34A68SER 00.0830.02524.269-0.005-0.0050.0000.0000.0000.000
35A69ASN 00.0460.02625.1600.0030.0030.0000.0000.0000.000
36A70PHE 0-0.057-0.01624.769-0.001-0.0010.0000.0000.0000.000
37A71GLU -1-0.846-0.94621.280-0.074-0.0740.0000.0000.0000.000
38A72GLU -1-0.954-0.97124.838-0.029-0.0290.0000.0000.0000.000
39A73LYS 10.9210.97927.3990.0640.0640.0000.0000.0000.000
40A74PHE 0-0.030-0.01224.682-0.001-0.0010.0000.0000.0000.000
41A75ASN 00.0630.01122.278-0.008-0.0080.0000.0000.0000.000
42A76SER 00.003-0.00126.3920.0020.0020.0000.0000.0000.000
43A77GLU -1-0.900-0.94929.734-0.049-0.0490.0000.0000.0000.000
44A78VAL 0-0.044-0.01926.3760.0020.0020.0000.0000.0000.000
45A79GLU -1-0.933-0.97427.571-0.035-0.0350.0000.0000.0000.000
46A80GLU -1-0.978-1.00329.717-0.026-0.0260.0000.0000.0000.000
47A81LYS 10.8780.93832.4940.0580.0580.0000.0000.0000.000
48A82ILE 00.0040.01828.8300.0020.0020.0000.0000.0000.000
49A83LYS 10.9360.96832.2410.0300.0300.0000.0000.0000.000
50A84LYS 10.8980.97134.2100.0290.0290.0000.0000.0000.000
51A85PHE 00.0690.03134.0660.0020.0020.0000.0000.0000.000
52A86VAL 00.0240.00132.7740.0020.0020.0000.0000.0000.000
53A87ASN 0-0.065-0.06036.1240.0030.0030.0000.0000.0000.000
54A88GLU -1-0.940-0.95939.107-0.029-0.0290.0000.0000.0000.000
55A89VAL 00.0110.00137.8720.0010.0010.0000.0000.0000.000
56A90LYS 10.9140.97237.3380.0200.0200.0000.0000.0000.000
57A91GLY 0-0.010-0.00241.1800.0020.0020.0000.0000.0000.000
58A92ILE 00.0280.01143.4580.0010.0010.0000.0000.0000.000
59A93ALA 00.0390.01142.7040.0000.0000.0000.0000.0000.000
60A94GLN 0-0.058-0.03244.7660.0010.0010.0000.0000.0000.000
61A95GLU -1-0.910-0.94646.666-0.015-0.0150.0000.0000.0000.000
62A96ASP -1-0.835-0.86647.959-0.018-0.0180.0000.0000.0000.000
63A97HIS 0-0.0020.00347.7060.0010.0010.0000.0000.0000.000
64A98ASP -1-0.906-0.94849.708-0.010-0.0100.0000.0000.0000.000
65A99LYS 10.7420.86852.0510.0160.0160.0000.0000.0000.000
66A100ASP -1-0.967-0.98853.018-0.011-0.0110.0000.0000.0000.000
67A101VAL 0-0.023-0.02352.2690.0000.0000.0000.0000.0000.000
68A102GLN 0-0.061-0.01544.115-0.001-0.0010.0000.0000.0000.000
69A103HIS 0-0.088-0.04948.8550.0010.0010.0000.0000.0000.000
70A104THR 0-0.041-0.02843.8840.0010.0010.0000.0000.0000.000
71A105PRO 00.0090.00740.9400.0000.0000.0000.0000.0000.000
72A106TYR 0-0.047-0.04641.319-0.002-0.0020.0000.0000.0000.000
73A107GLU -1-0.961-0.98135.240-0.035-0.0350.0000.0000.0000.000
74A108ALA 00.0090.00235.099-0.001-0.0010.0000.0000.0000.000
75A109TYR 0-0.034-0.02526.4060.0020.0020.0000.0000.0000.000
76A110VAL 00.0190.00828.132-0.003-0.0030.0000.0000.0000.000
77A111SER 0-0.017-0.00825.9790.0000.0000.0000.0000.0000.000
78A112VAL 0-0.003-0.01421.858-0.001-0.0010.0000.0000.0000.000
79A113ASP -1-0.831-0.89422.755-0.146-0.1460.0000.0000.0000.000
80A114VAL 0-0.028-0.01918.0190.0030.0030.0000.0000.0000.000
81A115ARG 10.7940.88121.0590.1190.1190.0000.0000.0000.000
82A116TYR 0-0.041-0.03019.294-0.029-0.0290.0000.0000.0000.000
83A117GLU -1-0.844-0.93014.223-0.377-0.3770.0000.0000.0000.000
84A118GLY 0-0.047-0.02115.528-0.061-0.0610.0000.0000.0000.000
85A119LYS 10.7560.86414.7300.2260.2260.0000.0000.0000.000
86A120ASP -1-0.841-0.94816.178-0.182-0.1820.0000.0000.0000.000
87A121PHE 00.0390.02719.3240.0220.0220.0000.0000.0000.000
88A122LEU 0-0.0190.00718.275-0.034-0.0340.0000.0000.0000.000
89A123SER 00.000-0.00821.1610.0230.0230.0000.0000.0000.000
90A124PHE 00.000-0.00122.079-0.015-0.0150.0000.0000.0000.000
91A125VAL 00.0600.03324.1340.0110.0110.0000.0000.0000.000
92A126VAL 0-0.043-0.01325.982-0.005-0.0050.0000.0000.0000.000
93A127TYR 00.007-0.01327.5540.0080.0080.0000.0000.0000.000
94A128TYR 00.003-0.00830.5930.0020.0020.0000.0000.0000.000
95A129TYR 00.0160.01033.1310.0020.0020.0000.0000.0000.000
96A130GLN 00.0440.00134.9120.0040.0040.0000.0000.0000.000
97A131PHE 0-0.056-0.00738.001-0.001-0.0010.0000.0000.0000.000
98A132THR 00.0340.00740.5420.0020.0020.0000.0000.0000.000
99A133GLY 00.0450.04243.6080.0020.0020.0000.0000.0000.000
100A134GLY 0-0.022-0.00444.950-0.002-0.0020.0000.0000.0000.000
101A135ALA 0-0.024-0.02445.6590.0000.0000.0000.0000.0000.000
102A136HIS 10.8950.95341.1010.0350.0350.0000.0000.0000.000
103A137GLY 00.0720.03539.8000.0020.0020.0000.0000.0000.000
104A138ILE 0-0.080-0.03939.782-0.002-0.0020.0000.0000.0000.000
105A139THR 00.0440.00633.9530.0010.0010.0000.0000.0000.000
106A140PHE 0-0.0260.00435.4610.0000.0000.0000.0000.0000.000
107A141PHE 0-0.018-0.03031.495-0.001-0.0010.0000.0000.0000.000
108A142GLU -1-0.808-0.88931.317-0.058-0.0580.0000.0000.0000.000
109A143THR 0-0.022-0.01328.869-0.007-0.0070.0000.0000.0000.000
110A144TYR 0-0.059-0.02526.0590.0070.0070.0000.0000.0000.000
111A145ASN 0-0.0050.01625.882-0.023-0.0230.0000.0000.0000.000
112A146ILE 00.0180.00523.2870.0110.0110.0000.0000.0000.000
113A147ASP -1-0.764-0.88123.553-0.135-0.1350.0000.0000.0000.000
114A148LEU 00.015-0.00618.4230.0100.0100.0000.0000.0000.000
115A149LYS 10.8260.92721.6030.1500.1500.0000.0000.0000.000
116A150ASN 0-0.016-0.03423.2960.0110.0110.0000.0000.0000.000
117A151SER 0-0.0280.00425.1390.0040.0040.0000.0000.0000.000
118A152LYS 10.9900.99326.1650.0790.0790.0000.0000.0000.000
119A153VAL 0-0.032-0.01327.893-0.008-0.0080.0000.0000.0000.000
120A154LEU 0-0.043-0.02828.5730.0070.0070.0000.0000.0000.000
121A155LYS 11.0001.00531.2710.0650.0650.0000.0000.0000.000
122A156LEU 00.0840.04333.954-0.002-0.0020.0000.0000.0000.000
123A157TYR 00.0200.01535.138-0.001-0.0010.0000.0000.0000.000
124A158ASP -1-0.903-0.97233.851-0.065-0.0650.0000.0000.0000.000
125A159ILE 0-0.074-0.04530.283-0.001-0.0010.0000.0000.0000.000
126A160ILE 0-0.021-0.01134.040-0.001-0.0010.0000.0000.0000.000
127A161LYS 10.9050.96937.0650.0600.0600.0000.0000.0000.000
128A162GLU -1-0.797-0.89940.753-0.053-0.0530.0000.0000.0000.000
129A163GLU -1-0.924-0.96743.317-0.048-0.0480.0000.0000.0000.000
130A164ALA 0-0.082-0.04439.7220.0000.0000.0000.0000.0000.000
131A165GLU -1-0.886-0.96541.615-0.049-0.0490.0000.0000.0000.000
132A166ASP -1-0.873-0.93243.062-0.044-0.0440.0000.0000.0000.000
133A167THR 0-0.080-0.04640.3640.0010.0010.0000.0000.0000.000
134A168ILE 00.0210.00637.545-0.002-0.0020.0000.0000.0000.000
135A169LYS 10.8760.95640.6640.0450.0450.0000.0000.0000.000
136A170SER 0-0.048-0.00943.4290.0010.0010.0000.0000.0000.000
137A171ASN 0-0.035-0.02637.7840.0000.0000.0000.0000.0000.000
138A172ILE 00.0960.04038.6030.0000.0000.0000.0000.0000.000
139A173LEU 0-0.021-0.00841.1740.0010.0010.0000.0000.0000.000
140A174LYS 10.8980.95642.8430.0520.0520.0000.0000.0000.000
141A175GLN 0-0.018-0.02936.597-0.002-0.0020.0000.0000.0000.000
142A176ILE 0-0.0190.01041.4010.0000.0000.0000.0000.0000.000
143A177GLU -1-1.000-1.01643.593-0.042-0.0420.0000.0000.0000.000
144A178GLN 0-0.0270.00241.9170.0030.0030.0000.0000.0000.000
145A179ASN 0-0.067-0.05440.738-0.001-0.0010.0000.0000.0000.000
146A180ASN 00.0620.03244.2110.0000.0000.0000.0000.0000.000
147A181THR 0-0.092-0.03645.5460.0010.0010.0000.0000.0000.000
148A182ASP -1-0.874-0.90642.243-0.049-0.0490.0000.0000.0000.000
149A183PHE 0-0.027-0.03040.145-0.001-0.0010.0000.0000.0000.000
150A184PHE 0-0.0090.00945.4090.0020.0020.0000.0000.0000.000
151A185PRO 00.0150.00048.458-0.001-0.0010.0000.0000.0000.000
152A186ASP -1-0.904-0.96450.669-0.035-0.0350.0000.0000.0000.000
153A187ALA 00.0170.01345.652-0.001-0.0010.0000.0000.0000.000
154A188PRO 00.015-0.00647.226-0.001-0.0010.0000.0000.0000.000
155A189MET 0-0.006-0.00348.2610.0000.0000.0000.0000.0000.000
156A190ASN 00.012-0.00946.8890.0010.0010.0000.0000.0000.000
157A191ILE 00.0260.03142.467-0.001-0.0010.0000.0000.0000.000
158A192LEU 0-0.052-0.02845.565-0.001-0.0010.0000.0000.0000.000
159A193LYS 10.9090.94848.4580.0340.0340.0000.0000.0000.000
160A194ASP -1-0.813-0.85942.167-0.052-0.0520.0000.0000.0000.000
161A195ASP -1-0.847-0.90743.486-0.048-0.0480.0000.0000.0000.000
162A196ILE 00.017-0.01539.048-0.002-0.0020.0000.0000.0000.000
163A197PHE 0-0.061-0.02338.837-0.005-0.0050.0000.0000.0000.000
164A198SER 0-0.075-0.02839.103-0.001-0.0010.0000.0000.0000.000
165A199ARG 10.8320.91737.4660.0550.0550.0000.0000.0000.000
166A200GLU -1-0.851-0.90933.249-0.075-0.0750.0000.0000.0000.000
167A201PHE 0-0.019-0.02530.501-0.001-0.0010.0000.0000.0000.000
168A202THR 00.0290.02126.619-0.006-0.0060.0000.0000.0000.000
169A203ILE 0-0.009-0.01124.9100.0040.0040.0000.0000.0000.000
170A204SER 00.0280.00723.391-0.022-0.0220.0000.0000.0000.000
171A205LYS 10.9270.96221.4410.2140.2140.0000.0000.0000.000
172A206ASP -1-0.934-0.98323.597-0.160-0.1600.0000.0000.0000.000
173A207GLY 0-0.009-0.02626.2600.0120.0120.0000.0000.0000.000
174A208LEU 0-0.0010.01328.000-0.009-0.0090.0000.0000.0000.000
175A209ILE 0-0.022-0.00827.2320.0030.0030.0000.0000.0000.000
176A210ILE 00.0260.01431.1620.0000.0000.0000.0000.0000.000
177A211MET 0-0.0370.00829.633-0.002-0.0020.0000.0000.0000.000
178A212TYR 0-0.052-0.06434.4970.0030.0030.0000.0000.0000.000
179A213PRO 0-0.0130.00736.507-0.003-0.0030.0000.0000.0000.000
180A214HIS 00.0450.00436.6160.0020.0020.0000.0000.0000.000
181A215TYR 0-0.030-0.03040.5630.0010.0010.0000.0000.0000.000
182A216ASP -1-0.848-0.91242.190-0.045-0.0450.0000.0000.0000.000
183A217LEU 0-0.034-0.02340.7750.0010.0010.0000.0000.0000.000
184A218ALA 00.0390.01641.9970.0010.0010.0000.0000.0000.000
185A219PRO 0-0.0040.00543.7730.0010.0010.0000.0000.0000.000
186A220TYR 00.020-0.00538.948-0.002-0.0020.0000.0000.0000.000
187A221ALA 0-0.054-0.02740.420-0.002-0.0020.0000.0000.0000.000
188A222SER 0-0.003-0.00740.176-0.001-0.0010.0000.0000.0000.000
189A223GLY 0-0.0160.01836.894-0.003-0.0030.0000.0000.0000.000
190A224MET 0-0.054-0.02633.9630.0030.0030.0000.0000.0000.000
191A225PRO 00.0080.00634.807-0.004-0.0040.0000.0000.0000.000
192A226GLU -1-0.832-0.91730.057-0.103-0.1030.0000.0000.0000.000
193A227PHE 0-0.023-0.01534.2800.0010.0010.0000.0000.0000.000
194A228VAL 00.0250.01730.314-0.004-0.0040.0000.0000.0000.000
195A229ILE 0-0.032-0.01732.4340.0070.0070.0000.0000.0000.000
196A230PRO 0-0.013-0.00231.582-0.006-0.0060.0000.0000.0000.000
197A231TRP 00.0970.05026.9880.0110.0110.0000.0000.0000.000
198A232ASN 00.0190.00431.9560.0010.0010.0000.0000.0000.000
199A233VAL 0-0.062-0.03234.3750.0060.0060.0000.0000.0000.000
200A234ILE 00.0040.00033.5690.0050.0050.0000.0000.0000.000
201A235GLU -1-0.938-0.95833.473-0.084-0.0840.0000.0000.0000.000
202A236LYS 10.9500.97535.4230.0540.0540.0000.0000.0000.000
203A237PHE 0-0.087-0.06738.0640.0040.0040.0000.0000.0000.000
204A238LEU 00.0620.04732.6180.0010.0010.0000.0000.0000.000
205A239LYS 10.8590.94035.3290.0640.0640.0000.0000.0000.000
206A240TYR 0-0.060-0.02728.2500.0040.0040.0000.0000.0000.000
207A241ASP -1-0.852-0.94227.527-0.107-0.1070.0000.0000.0000.000
208A242ILE 00.0450.03327.395-0.004-0.0040.0000.0000.0000.000
209A243LEU 0-0.045-0.03224.528-0.014-0.0140.0000.0000.0000.000
210A244SER 0-0.040-0.01023.000-0.010-0.0100.0000.0000.0000.000
211A245LEU 00.003-0.00821.392-0.023-0.0230.0000.0000.0000.000
212A246LEU 0-0.0430.01120.407-0.028-0.0280.0000.0000.0000.000
213A247LYS 10.9130.93914.2260.4310.4310.0000.0000.0000.000
214A248GLU -1-0.917-0.93016.810-0.267-0.2670.0000.0000.0000.000
215A249GLY 00.0130.02318.5240.0170.0170.0000.0000.0000.000
216A250HIS 0-0.047-0.06619.6980.0300.0300.0000.0000.0000.000
217A251NME 0-0.0180.00616.926-0.002-0.0020.0000.0000.0000.000