Manual

About

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: K3L83

Calculation Name: 4C47-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4C47

Chain ID: A

ChEMBL ID:

UniProt ID: Q8ZL65

Base Structure: X-ray

Registration Date: 2023-06-19

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1674291.449447
FMO2-HF: Nuclear repulsion 1598348.771508
FMO2-HF: Total energy -75942.677939
FMO2-MP2: Total energy -76166.550283


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:23:ASP)


Summations of interaction energy for fragment #1(A:23:ASP)
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.
-23.198-13.9841.641-5.305-5.5490.049
Interaction energy analysis for fragmet #1(A:23:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.839 / q_NPA : -0.917
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].
3A25PHE0-0.057-0.0292.451-31.409-22.8991.609-4.895-5.2240.052
4A26ALA0-0.016-0.0043.476-1.769-1.0650.032-0.410-0.325-0.003
5A27ASP-1-0.788-0.9075.98030.51830.5180.0000.0000.0000.000
6A28LYS10.8620.9186.882-23.784-23.7840.0000.0000.0000.000
7A29HIS0-0.039-0.03310.013-1.526-1.5260.0000.0000.0000.000
8A30LEU00.0250.0169.314-1.700-1.7000.0000.0000.0000.000
9A31VAL00.002-0.00610.181-1.584-1.5840.0000.0000.0000.000
10A32GLU-1-0.888-0.93612.63716.28116.2810.0000.0000.0000.000
11A33GLU-1-0.861-0.91214.50315.03615.0360.0000.0000.0000.000
12A34MET0-0.050-0.02513.256-0.598-0.5980.0000.0000.0000.000
13A35LYS10.9420.97716.412-16.017-16.0170.0000.0000.0000.000
14A36GLU-1-0.760-0.86518.61512.42112.4210.0000.0000.0000.000
15A37GLN00.0110.00419.493-0.381-0.3810.0000.0000.0000.000
16A38GLN0-0.013-0.00320.263-0.415-0.4150.0000.0000.0000.000
17A39LYS10.8000.87922.072-13.612-13.6120.0000.0000.0000.000
18A40GLU-1-0.875-0.92124.34010.60010.6000.0000.0000.0000.000
19A41GLN0-0.035-0.03522.074-0.371-0.3710.0000.0000.0000.000
20A42GLU-1-0.857-0.91426.27710.00510.0050.0000.0000.0000.000
21A43THR0-0.044-0.01228.142-0.518-0.5180.0000.0000.0000.000
22A44LYS10.8370.89727.294-10.736-10.7360.0000.0000.0000.000
23A45ILE00.0350.02327.840-0.356-0.3560.0000.0000.0000.000
24A46ASN0-0.029-0.02431.549-0.557-0.5570.0000.0000.0000.000
25A47LEU0-0.060-0.02134.178-0.338-0.3380.0000.0000.0000.000
26A48LEU00.016-0.00332.692-0.290-0.2900.0000.0000.0000.000
27A49GLU-1-0.815-0.89035.1398.1738.1730.0000.0000.0000.000
28A50LYS10.8640.94337.681-7.515-7.5150.0000.0000.0000.000
29A51GLN0-0.030-0.03538.638-0.106-0.1060.0000.0000.0000.000
30A52GLN00.0320.02239.815-0.105-0.1050.0000.0000.0000.000
31A53LYS10.9030.94338.895-7.974-7.9740.0000.0000.0000.000
32A54GLU-1-0.872-0.93143.9196.6136.6130.0000.0000.0000.000
33A55GLN0-0.041-0.03142.533-0.188-0.1880.0000.0000.0000.000
34A56GLU-1-0.880-0.92545.5896.4836.4830.0000.0000.0000.000
35A57ALA0-0.025-0.01647.424-0.173-0.1730.0000.0000.0000.000
36A58LYS10.8310.89647.473-6.543-6.5430.0000.0000.0000.000
37A59ILE00.0580.03747.625-0.149-0.1490.0000.0000.0000.000
38A60ASN00.0650.03351.360-0.234-0.2340.0000.0000.0000.000
39A61LEU0-0.060-0.02753.589-0.148-0.1480.0000.0000.0000.000
40A62LEU00.004-0.00152.841-0.132-0.1320.0000.0000.0000.000
41A63GLU-1-0.890-0.93453.6035.6635.6630.0000.0000.0000.000
42A64LYS10.8910.93755.647-5.679-5.6790.0000.0000.0000.000
43A65GLN0-0.001-0.01058.719-0.117-0.1170.0000.0000.0000.000
44A66GLN00.0310.02358.085-0.105-0.1050.0000.0000.0000.000
45A67ALA00.0230.01861.407-0.094-0.0940.0000.0000.0000.000
46A68THR0-0.039-0.02763.377-0.119-0.1190.0000.0000.0000.000
47A69ILE00.0260.02162.564-0.108-0.1080.0000.0000.0000.000
48A70ILE00.0230.03362.786-0.102-0.1020.0000.0000.0000.000
49A71ASN0-0.011-0.00566.864-0.146-0.1460.0000.0000.0000.000
50A72THR0-0.011-0.02269.067-0.096-0.0960.0000.0000.0000.000
51A73THR00.014-0.00668.469-0.076-0.0760.0000.0000.0000.000
52A74LYS10.9710.99670.902-4.461-4.4610.0000.0000.0000.000
53A75LYS10.8950.94372.884-4.321-4.3210.0000.0000.0000.000
54A76VAL00.0310.01873.868-0.071-0.0710.0000.0000.0000.000
55A77THR0-0.026-0.01773.755-0.044-0.0440.0000.0000.0000.000
56A78GLU-1-0.894-0.93776.4403.8173.8170.0000.0000.0000.000
57A79VAL0-0.030-0.01478.960-0.068-0.0680.0000.0000.0000.000
58A80VAL00.0260.00778.104-0.060-0.0600.0000.0000.0000.000
59A81GLY00.0560.03780.534-0.042-0.0420.0000.0000.0000.000
60A82ARG10.8170.89182.129-3.862-3.8620.0000.0000.0000.000
61A83VAL0-0.004-0.00584.246-0.054-0.0540.0000.0000.0000.000
62A84GLU-1-0.763-0.85483.3073.7483.7480.0000.0000.0000.000
63A85ARG10.9200.94684.100-3.726-3.7260.0000.0000.0000.000
64A86LYS10.9330.96387.932-3.515-3.5150.0000.0000.0000.000
65A87GLN00.001-0.00687.099-0.010-0.0100.0000.0000.0000.000
66A88ARG10.8080.89584.263-3.697-3.6970.0000.0000.0000.000
67A89LEU0-0.088-0.03791.438-0.025-0.0250.0000.0000.0000.000
68A90PHE0-0.0150.00094.376-0.034-0.0340.0000.0000.0000.000
69A91ASP-1-0.886-0.92490.8003.4583.4580.0000.0000.0000.000
70A92TYR0-0.052-0.04990.3930.0070.0070.0000.0000.0000.000
71A93THR00.012-0.00496.3300.0160.0160.0000.0000.0000.000
72A94GLU-1-0.904-0.94192.4893.4413.4410.0000.0000.0000.000
73A95LEU0-0.0070.00497.116-0.010-0.0100.0000.0000.0000.000
74A96ASP-1-0.738-0.84299.1063.1893.1890.0000.0000.0000.000
75A97PRO00.0140.017100.531-0.023-0.0230.0000.0000.0000.000
76A98SER0-0.032-0.037102.545-0.029-0.0290.0000.0000.0000.000
77A99GLN0-0.081-0.043102.082-0.033-0.0330.0000.0000.0000.000
78A100THR0-0.009-0.014103.3310.0140.0140.0000.0000.0000.000
79A101HIS0-0.0140.008105.921-0.028-0.0280.0000.0000.0000.000
80A102TYR00.0280.003108.564-0.005-0.0050.0000.0000.0000.000
81A103PHE0-0.026-0.008103.6090.0320.0320.0000.0000.0000.000
82A104ILE00.0140.002103.508-0.027-0.0270.0000.0000.0000.000
83A105ILE00.0150.030100.6160.0370.0370.0000.0000.0000.000
84A106ASN00.008-0.009100.777-0.023-0.0230.0000.0000.0000.000
85A107ASN00.0980.03298.0000.0090.0090.0000.0000.0000.000
86A108GLY0-0.0250.00098.1000.0290.0290.0000.0000.0000.000
87A109ASN0-0.113-0.05499.717-0.002-0.0020.0000.0000.0000.000
88A110ILE00.0600.030102.435-0.034-0.0340.0000.0000.0000.000
89A111GLY0-0.0060.001103.6350.0300.0300.0000.0000.0000.000
90A112LEU00.0120.008105.591-0.034-0.0340.0000.0000.0000.000
91A113ALA0-0.007-0.006106.3870.0290.0290.0000.0000.0000.000
92A114GLY00.0300.011108.244-0.016-0.0160.0000.0000.0000.000
93A115ARG10.7930.881109.059-2.736-2.7360.0000.0000.0000.000
94A116ILE0-0.017-0.012105.828-0.011-0.0110.0000.0000.0000.000
95A117LEU0-0.052-0.016110.520-0.011-0.0110.0000.0000.0000.000
96A118SER0-0.023-0.035112.423-0.012-0.0120.0000.0000.0000.000
97A119ILE0-0.039-0.020106.6060.0210.0210.0000.0000.0000.000
98A120GLU-1-0.829-0.906109.8842.7922.7920.0000.0000.0000.000
99A121PRO0-0.036-0.012108.7920.0340.0340.0000.0000.0000.000
100A122ILE00.0030.000107.167-0.030-0.0300.0000.0000.0000.000
101A123ASP-1-0.829-0.918107.3432.9932.9930.0000.0000.0000.000
102A124ASN0-0.015-0.002100.8190.0270.0270.0000.0000.0000.000
103A125GLY00.0090.015103.1420.0390.0390.0000.0000.0000.000
104A126SER0-0.020-0.017104.340-0.030-0.0300.0000.0000.0000.000
105A127VAL0-0.027-0.019106.4020.0140.0140.0000.0000.0000.000
106A128ILE0-0.0090.010104.352-0.011-0.0110.0000.0000.0000.000
107A129HIS00.0510.038108.9120.0040.0040.0000.0000.0000.000
108A130LEU0-0.022-0.022107.8490.0080.0080.0000.0000.0000.000
109A131ASP-1-0.757-0.847111.8282.7302.7300.0000.0000.0000.000
110A132LEU0-0.003-0.007107.4620.0290.0290.0000.0000.0000.000
111A133VAL00.0100.009110.936-0.029-0.0290.0000.0000.0000.000
112A134ASN0-0.007-0.012110.5900.0540.0540.0000.0000.0000.000
113A135LEU0-0.033-0.029107.359-0.023-0.0230.0000.0000.0000.000
114A136LEU0-0.0230.002107.216-0.004-0.0040.0000.0000.0000.000
115A137SER00.000-0.012111.319-0.014-0.0140.0000.0000.0000.000
116A138ILE00.0190.006110.471-0.027-0.0270.0000.0000.0000.000
117A139PRO0-0.0050.001112.9700.0210.0210.0000.0000.0000.000
118A140VAL0-0.0110.015108.7210.0200.0200.0000.0000.0000.000
119A141SER00.0550.018110.525-0.017-0.0170.0000.0000.0000.000
120A142ASN0-0.026-0.014108.2030.0070.0070.0000.0000.0000.000
121A143LEU00.0350.036105.0090.0300.0300.0000.0000.0000.000
122A144ALA00.0500.038102.266-0.014-0.0140.0000.0000.0000.000
123A145PHE0-0.016-0.007101.7250.0230.0230.0000.0000.0000.000
124A146ASN0-0.037-0.00496.3500.0040.0040.0000.0000.0000.000
125A147MET00.0190.00898.481-0.011-0.0110.0000.0000.0000.000
126A148THR0-0.021-0.02692.7400.0330.0330.0000.0000.0000.000
127A149TRP0-0.011-0.00296.192-0.011-0.0110.0000.0000.0000.000
128A150GLY00.0330.00695.4990.0250.0250.0000.0000.0000.000
129A151THR00.0500.02693.045-0.019-0.0190.0000.0000.0000.000
130A152LYS10.8700.92094.276-3.256-3.2560.0000.0000.0000.000
131A153LYS10.9470.98687.562-3.540-3.5400.0000.0000.0000.000
132A154PRO0-0.0160.00987.124-0.009-0.0090.0000.0000.0000.000
133A155SER00.0260.00287.6540.0040.0040.0000.0000.0000.000
134A156GLU-1-0.849-0.90480.8913.9073.9070.0000.0000.0000.000
135A157ALA00.033-0.00280.099-0.014-0.0140.0000.0000.0000.000
136A158LYS10.8600.91879.052-3.874-3.8740.0000.0000.0000.000
137A159ASP-1-0.838-0.92280.3043.7923.7920.0000.0000.0000.000
138A160LEU0-0.033-0.00882.415-0.041-0.0410.0000.0000.0000.000
139A161PRO0-0.017-0.01479.785-0.037-0.0370.0000.0000.0000.000
140A162ARG10.9450.95879.895-3.872-3.8720.0000.0000.0000.000
141A163TRP00.0340.01684.865-0.004-0.0040.0000.0000.0000.000
142A164LYS10.9490.96682.100-3.812-3.8120.0000.0000.0000.000
143A165GLN0-0.036-0.01982.004-0.024-0.0240.0000.0000.0000.000
144A166LEU0-0.029-0.00787.264-0.021-0.0210.0000.0000.0000.000
145A167LEU0-0.085-0.01590.301-0.045-0.0450.0000.0000.0000.000
146A168LEU0-0.0040.01792.4030.0120.0120.0000.0000.0000.000
147A169ASN0-0.015-0.03093.709-0.015-0.0150.0000.0000.0000.000
148A170THR0-0.021-0.00795.890-0.002-0.0020.0000.0000.0000.000
149A171LYS10.8900.93596.659-3.230-3.2300.0000.0000.0000.000
150A172MET0-0.048-0.014100.115-0.014-0.0140.0000.0000.0000.000
151A173ASP-1-0.861-0.932103.4233.0813.0810.0000.0000.0000.000
152A174SER0-0.090-0.052105.581-0.034-0.0340.0000.0000.0000.000
153A175THR00.0420.009108.8860.0130.0130.0000.0000.0000.000
154A176ILE0-0.048-0.026111.381-0.026-0.0260.0000.0000.0000.000
155A177GLU-1-0.886-0.937112.1042.7462.7460.0000.0000.0000.000
156A178LEU0-0.051-0.024110.046-0.018-0.0180.0000.0000.0000.000
157A179LEU00.0710.024114.0520.0100.0100.0000.0000.0000.000
158A180PRO0-0.028-0.015114.9990.0080.0080.0000.0000.0000.000
159A181GLY0-0.0070.007115.228-0.026-0.0260.0000.0000.0000.000
160A182ALA0-0.033-0.013116.930-0.015-0.0150.0000.0000.0000.000
161A183TRP0-0.028-0.032112.0580.0290.0290.0000.0000.0000.000
162A184THR00.002-0.001114.452-0.031-0.0310.0000.0000.0000.000
163A185ASN0-0.063-0.033114.1950.0250.0250.0000.0000.0000.000
164A186VAL00.0200.010109.1280.0040.0040.0000.0000.0000.000
165A187THR00.0000.003110.611-0.003-0.0030.0000.0000.0000.000
166A188LEU00.000-0.004104.4300.0190.0190.0000.0000.0000.000
167A189THR0-0.008-0.009105.906-0.008-0.0080.0000.0000.0000.000
168A190LEU0-0.0110.000101.6040.0270.0270.0000.0000.0000.000
169A191LYS10.8530.900102.153-3.021-3.0210.0000.0000.0000.000
170A192GLY00.018-0.00699.3240.0320.0320.0000.0000.0000.000
171A193VAL0-0.013-0.00698.1590.0270.0270.0000.0000.0000.000
172A194SER00.0270.028100.894-0.017-0.0170.0000.0000.0000.000
173A195PRO00.1290.046102.9660.0300.0300.0000.0000.0000.000
174A196ASN0-0.0210.007103.0120.0000.0000.0000.0000.0000.000
175A197ASN0-0.071-0.04699.1220.0420.0420.0000.0000.0000.000
176A198LEU0-0.0270.00199.1180.0430.0430.0000.0000.0000.000
177A199LYS10.8910.94298.039-3.142-3.1420.0000.0000.0000.000
178A200TYR0-0.129-0.08892.7220.0250.0250.0000.0000.0000.000
179A201LEU00.0400.01997.454-0.007-0.0070.0000.0000.0000.000
180A202LYS10.8790.96690.788-3.454-3.4540.0000.0000.0000.000
181A203ILE00.008-0.00297.089-0.002-0.0020.0000.0000.0000.000
182A204GLY00.0500.01497.6360.0100.0100.0000.0000.0000.000
183A205ILE0-0.024-0.00798.680-0.020-0.0200.0000.0000.0000.000
184A206ASP-1-0.832-0.91097.8083.2793.2790.0000.0000.0000.000
185A207MET00.0050.00299.261-0.043-0.0430.0000.0000.0000.000
186A208GLU-1-0.938-0.94198.3023.2133.2130.0000.0000.0000.000
187A209ASN0-0.043-0.029100.823-0.018-0.0180.0000.0000.0000.000
188A210VAL00.0050.011104.199-0.033-0.0330.0000.0000.0000.000
189A211ILE0-0.037-0.012106.0960.0040.0040.0000.0000.0000.000
190A212PHE0-0.017-0.025105.323-0.007-0.0070.0000.0000.0000.000
191A213ASP-1-0.943-0.962110.7662.7322.7320.0000.0000.0000.000