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

tag_button

FMODB ID: V56L1

Calculation Name: 5F17-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5F17

Chain ID: A

ChEMBL ID:

UniProt ID: P19811

Base Structure: X-ray

Registration Date: 2023-06-26

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2498212.991479
FMO2-HF: Nuclear repulsion 2412675.439978
FMO2-HF: Total energy -85537.551501
FMO2-MP2: Total energy -85783.813139


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:1:SER)


Summations of interaction energy for fragment #1(A:1:SER)
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.
1.2072.6273.186-1.01-3.5940.003
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.010
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].
3A3LYS10.8120.9002.647-0.5522.3290.266-1.397-1.7500.001
4A4ILE00.0060.0124.223-0.894-0.811-0.001-0.014-0.0680.000
5A5SER00.0160.0017.1650.3990.3990.0000.0000.0000.000
6A6CYS0-0.0010.0028.993-0.036-0.0360.0000.0000.0000.000
7A7LEU00.0160.02011.097-0.090-0.0900.0000.0000.0000.000
8A8PRO00.0330.02211.0820.0720.0720.0000.0000.0000.000
9A9ARG10.8120.87813.5270.4340.4340.0000.0000.0000.000
10A10VAL0-0.018-0.00115.9740.0460.0460.0000.0000.0000.000
11A11ALA00.0520.01414.7730.0370.0370.0000.0000.0000.000
12A12GLN0-0.028-0.01615.9270.0050.0050.0000.0000.0000.000
13A13ASN0-0.065-0.04118.3910.0430.0430.0000.0000.0000.000
14A14LEU0-0.051-0.01319.4810.0200.0200.0000.0000.0000.000
15A15GLY00.0020.00821.0940.0170.0170.0000.0000.0000.000
16A16TYR0-0.087-0.07216.4200.0280.0280.0000.0000.0000.000
17A17HIS00.0370.00516.275-0.043-0.0430.0000.0000.0000.000
18A18TYR00.0030.01014.439-0.010-0.0100.0000.0000.0000.000
19A19SER00.018-0.0019.5960.0010.0010.0000.0000.0000.000
20A20PRO0-0.0320.00110.8690.0690.0690.0000.0000.0000.000
21A21ASP-1-0.789-0.8547.0140.3960.3960.0000.0000.0000.000
22A22LEU00.0100.0045.0700.2540.328-0.001-0.001-0.0710.000
23A23PRO0-0.013-0.0133.405-0.3890.0500.017-0.119-0.3360.000
24A24GLY0-0.0190.0016.380-0.217-0.2170.0000.0000.0000.000
25A25PHE0-0.014-0.0079.1820.0130.0130.0000.0000.0000.000
26A26CYS0-0.0160.00111.2610.0480.0480.0000.0000.0000.000
27A27PRO00.0190.01410.6500.0360.0360.0000.0000.0000.000
28A28ILE00.007-0.00612.154-0.070-0.0700.0000.0000.0000.000
29A29PRO0-0.0020.00713.2580.0880.0880.0000.0000.0000.000
30A30LYS10.9280.93811.686-0.578-0.5780.0000.0000.0000.000
31A31GLU-1-0.814-0.90615.1980.3480.3480.0000.0000.0000.000
32A32LEU0-0.031-0.01918.158-0.031-0.0310.0000.0000.0000.000
33A33ALA00.0020.00315.322-0.029-0.0290.0000.0000.0000.000
34A34GLU-1-0.913-0.96517.3410.1160.1160.0000.0000.0000.000
35A35HIS0-0.071-0.03319.944-0.032-0.0320.0000.0000.0000.000
36A36TRP0-0.045-0.02518.182-0.013-0.0130.0000.0000.0000.000
37A37PRO00.0150.00918.6620.0080.0080.0000.0000.0000.000
38A38VAL0-0.052-0.01113.8530.0030.0030.0000.0000.0000.000
39A39VAL00.0160.01011.700-0.028-0.0280.0000.0000.0000.000
40A40SER0-0.006-0.0299.9510.0850.0850.0000.0000.0000.000
41A41ASN0-0.034-0.0316.867-0.238-0.2380.0000.0000.0000.000
42A42ASP-1-0.911-0.9389.5900.2110.2110.0000.0000.0000.000
43A43ARG10.8430.91712.383-0.045-0.0450.0000.0000.0000.000
44A44TYR00.0480.00912.1810.0420.0420.0000.0000.0000.000
45A45PRO0-0.008-0.00218.119-0.029-0.0290.0000.0000.0000.000
46A46ASN0-0.001-0.01420.646-0.026-0.0260.0000.0000.0000.000
47A47CYS0-0.0640.00315.9850.0090.0090.0000.0000.0000.000
48A48LEU00.0440.02815.673-0.014-0.0140.0000.0000.0000.000
49A49GLN0-0.004-0.00313.683-0.008-0.0080.0000.0000.0000.000
50A50ILE0-0.018-0.01211.010-0.018-0.0180.0000.0000.0000.000
51A51THR00.000-0.01411.428-0.050-0.0500.0000.0000.0000.000
52A52LEU00.0170.00411.754-0.011-0.0110.0000.0000.0000.000
53A53GLN0-0.007-0.01113.8630.0380.0380.0000.0000.0000.000
54A54GLN0-0.031-0.00517.225-0.014-0.0140.0000.0000.0000.000
55A55VAL0-0.021-0.00417.0380.0100.0100.0000.0000.0000.000
56A56CYS0-0.046-0.02020.2700.0270.0270.0000.0000.0000.000
57A57GLU-1-0.855-0.93023.635-0.097-0.0970.0000.0000.0000.000
58A58LEU0-0.053-0.03824.964-0.005-0.0050.0000.0000.0000.000
59A59SER0-0.038-0.02120.086-0.002-0.0020.0000.0000.0000.000
60A60LYS10.9000.92921.2630.1730.1730.0000.0000.0000.000
61A61PRO0-0.0080.00920.114-0.030-0.0300.0000.0000.0000.000
62A62CYS0-0.012-0.01018.0220.0240.0240.0000.0000.0000.000
63A63SER0-0.0230.00618.394-0.040-0.0400.0000.0000.0000.000
64A64ALA0-0.002-0.00817.0750.0310.0310.0000.0000.0000.000
65A65GLY00.0730.04615.676-0.039-0.0390.0000.0000.0000.000
66A66TYR0-0.041-0.02510.274-0.002-0.0020.0000.0000.0000.000
67A67MET00.0000.0116.8810.1880.1880.0000.0000.0000.000
68A68VAL00.0110.0005.0270.1570.1570.0000.0000.0000.000
69A69GLY00.0170.0072.241-2.248-1.9682.746-2.092-0.9340.006
70A70GLN0-0.009-0.0162.7373.9151.5780.1592.613-0.435-0.004
71A71SER0-0.0320.0045.6580.7180.7180.0000.0000.0000.000
72A72VAL00.0250.0117.680-0.114-0.1140.0000.0000.0000.000
73A73PHE0-0.043-0.0228.1490.0880.0880.0000.0000.0000.000
74A74VAL00.0040.00112.9990.0250.0250.0000.0000.0000.000
75A75GLN0-0.018-0.00716.619-0.006-0.0060.0000.0000.0000.000
76A76THR00.0220.00818.2590.0260.0260.0000.0000.0000.000
77A77PRO00.0170.00020.5680.0030.0030.0000.0000.0000.000
78A78GLY0-0.0100.00124.0920.0070.0070.0000.0000.0000.000
79A79VAL0-0.032-0.00819.6920.0140.0140.0000.0000.0000.000
80A80THR0-0.047-0.01818.158-0.016-0.0160.0000.0000.0000.000
81A81SER0-0.025-0.03114.6690.0120.0120.0000.0000.0000.000
82A82TYR0-0.012-0.02412.951-0.067-0.0670.0000.0000.0000.000
83A83TRP0-0.001-0.00415.3510.0500.0500.0000.0000.0000.000
84A84LEU0-0.022-0.00215.265-0.034-0.0340.0000.0000.0000.000
85A85THR00.0250.01717.1980.0300.0300.0000.0000.0000.000
86A86GLU-1-0.759-0.81818.267-0.088-0.0880.0000.0000.0000.000
87A87TRP0-0.024-0.03318.1100.0180.0180.0000.0000.0000.000
88A88VAL00.0270.00621.6040.0030.0030.0000.0000.0000.000
89A89ASP-1-0.853-0.91624.3730.0040.0040.0000.0000.0000.000
90A90GLY0-0.031-0.00923.5310.0040.0040.0000.0000.0000.000
91A91LYS10.8930.93624.5640.0200.0200.0000.0000.0000.000
92A92ALA00.0220.02123.355-0.003-0.0030.0000.0000.0000.000
93A93ARG10.8260.88023.7590.0790.0790.0000.0000.0000.000
94A94ALA00.0200.01424.189-0.011-0.0110.0000.0000.0000.000
95A95LEU00.0030.00720.5030.0010.0010.0000.0000.0000.000
96A96PRO00.0100.00424.9510.0000.0000.0000.0000.0000.000
97A97ASP-1-0.853-0.91825.741-0.157-0.1570.0000.0000.0000.000
98A98SER0-0.037-0.03523.8820.0100.0100.0000.0000.0000.000
99A99LEU0-0.0340.00225.081-0.008-0.0080.0000.0000.0000.000
100A100PHE00.0150.00319.911-0.005-0.0050.0000.0000.0000.000
101A101SER0-0.031-0.04519.5770.0190.0190.0000.0000.0000.000
102A102SER0-0.041-0.02319.037-0.035-0.0350.0000.0000.0000.000
103A103GLY00.0600.01516.299-0.050-0.0500.0000.0000.0000.000
104A104ARG10.6950.80717.0330.2410.2410.0000.0000.0000.000
105A105PHE0-0.009-0.00919.7940.0100.0100.0000.0000.0000.000
106A106GLU-1-0.759-0.87614.349-0.459-0.4590.0000.0000.0000.000
107A107THR0-0.048-0.01715.642-0.065-0.0650.0000.0000.0000.000
108A108ASN0-0.040-0.02417.0580.0450.0450.0000.0000.0000.000
109A109SER00.0080.02420.1680.0430.0430.0000.0000.0000.000
110A110ARG10.8630.90821.8170.2150.2150.0000.0000.0000.000
111A111ALA00.0140.02224.8010.0190.0190.0000.0000.0000.000
112A112PHE00.011-0.00125.570-0.015-0.0150.0000.0000.0000.000
113A113LEU0-0.044-0.02421.935-0.007-0.0070.0000.0000.0000.000
114A114ASP-1-0.769-0.86624.985-0.191-0.1910.0000.0000.0000.000
115A115GLU-1-0.737-0.85628.046-0.114-0.1140.0000.0000.0000.000
116A116ALA0-0.0060.00630.8130.0110.0110.0000.0000.0000.000
117A117GLU-1-0.739-0.84726.994-0.219-0.2190.0000.0000.0000.000
118A118GLU-1-0.929-0.94230.700-0.135-0.1350.0000.0000.0000.000
119A119LYS10.8020.86132.9780.1190.1190.0000.0000.0000.000
120A120PHE0-0.0110.00332.9340.0070.0070.0000.0000.0000.000
121A121ALA00.0300.00832.9230.0060.0060.0000.0000.0000.000
122A122ALA0-0.004-0.01134.9250.0060.0060.0000.0000.0000.000
123A123ALA0-0.027-0.00938.1060.0060.0060.0000.0000.0000.000
124A124HIS10.7360.85236.8310.1180.1180.0000.0000.0000.000
125A125PRO00.0780.04938.060-0.004-0.0040.0000.0000.0000.000
126A126HIS10.8260.86638.6950.0810.0810.0000.0000.0000.000
127A127ALA0-0.036-0.00136.3370.0020.0020.0000.0000.0000.000
128A128CYS0-0.067-0.00433.264-0.007-0.0070.0000.0000.0000.000
129A129LEU00.0440.04233.849-0.007-0.0070.0000.0000.0000.000
130A130GLY00.0450.03535.878-0.005-0.0050.0000.0000.0000.000
131A131GLU-1-0.883-0.92137.605-0.085-0.0850.0000.0000.0000.000
132A132ILE00.0120.00141.236-0.001-0.0010.0000.0000.0000.000
133A133ASN00.0220.02143.3700.0020.0020.0000.0000.0000.000
134A134LYS10.8530.90346.2610.0670.0670.0000.0000.0000.000
135A135SER00.0640.03946.8130.0000.0000.0000.0000.0000.000
136A136THR00.0190.02243.1490.0000.0000.0000.0000.0000.000
137A137VAL0-0.026-0.01437.8480.0010.0010.0000.0000.0000.000
138A138GLY00.0440.01239.4690.0000.0000.0000.0000.0000.000
139A139GLY00.0690.02037.776-0.002-0.0020.0000.0000.0000.000
140A140SER0-0.061-0.03734.317-0.003-0.0030.0000.0000.0000.000
141A141HIS0-0.043-0.02332.2510.0020.0020.0000.0000.0000.000
142A142PHE00.0550.03128.123-0.005-0.0050.0000.0000.0000.000
143A143ILE0-0.0030.00722.8430.0090.0090.0000.0000.0000.000
144A144PHE0-0.0020.00226.9850.0020.0020.0000.0000.0000.000
145A145SER0-0.079-0.03929.1030.0110.0110.0000.0000.0000.000
146A146GLN0-0.029-0.01532.162-0.001-0.0010.0000.0000.0000.000
147A147TYR0-0.057-0.02934.8510.0030.0030.0000.0000.0000.000
148A148LEU00.0380.02229.2020.0050.0050.0000.0000.0000.000
149A149PRO00.0100.01529.6230.0010.0010.0000.0000.0000.000
150A150PRO00.031-0.00128.840-0.012-0.0120.0000.0000.0000.000
151A151LEU0-0.038-0.00624.559-0.015-0.0150.0000.0000.0000.000
152A152LEU00.015-0.00224.1180.0200.0200.0000.0000.0000.000
153A153PRO00.0020.01022.382-0.022-0.0220.0000.0000.0000.000
154A154ALA00.016-0.00217.9920.0070.0070.0000.0000.0000.000
155A155ASP-1-0.836-0.89919.603-0.228-0.2280.0000.0000.0000.000
156A156ALA0-0.030-0.01421.821-0.005-0.0050.0000.0000.0000.000
157A157VAL0-0.045-0.04323.3900.0050.0050.0000.0000.0000.000
158A158ALA00.0120.03125.1060.0080.0080.0000.0000.0000.000
159A159LEU0-0.017-0.01626.7840.0110.0110.0000.0000.0000.000
160A160VAL0-0.006-0.00528.244-0.003-0.0030.0000.0000.0000.000
161A161GLY0-0.015-0.00531.2960.0090.0090.0000.0000.0000.000
162A162ALA00.0320.02933.886-0.005-0.0050.0000.0000.0000.000
163A163SER0-0.086-0.07235.5660.0090.0090.0000.0000.0000.000
164A164LEU00.0360.02937.954-0.004-0.0040.0000.0000.0000.000
165A165ALA00.0580.01740.3050.0050.0050.0000.0000.0000.000
166A166GLY00.0230.01741.9630.0030.0030.0000.0000.0000.000
167A167LYS10.8360.91444.5260.0730.0730.0000.0000.0000.000
168A168ALA00.0230.01242.9540.0030.0030.0000.0000.0000.000
169A169ALA00.0030.01040.232-0.004-0.0040.0000.0000.0000.000
170A170ALA00.0000.00238.3570.0050.0050.0000.0000.0000.000
171A171ALA00.0260.01236.779-0.007-0.0070.0000.0000.0000.000
172A172ALA0-0.013-0.00634.1940.0030.0030.0000.0000.0000.000
173A173CYS0-0.0340.00334.0280.0010.0010.0000.0000.0000.000
174A174SER00.002-0.02031.179-0.005-0.0050.0000.0000.0000.000
175A175VAL0-0.020-0.00127.6910.0050.0050.0000.0000.0000.000
176A176VAL00.0040.01025.617-0.011-0.0110.0000.0000.0000.000
177A177ASP-1-0.667-0.84020.857-0.351-0.3510.0000.0000.0000.000
178A178VAL00.0220.01423.349-0.014-0.0140.0000.0000.0000.000
179A179TYR0-0.014-0.02624.0220.0160.0160.0000.0000.0000.000
180A180ALA00.0280.02225.6680.0130.0130.0000.0000.0000.000
181A181PRO00.015-0.00228.8480.0100.0100.0000.0000.0000.000
182A182SER0-0.036-0.02827.1370.0070.0070.0000.0000.0000.000
183A183PHE0-0.001-0.01228.6840.0070.0070.0000.0000.0000.000
184A184GLU-1-0.757-0.86932.426-0.102-0.1020.0000.0000.0000.000
185A185PRO0-0.010-0.01032.9380.0080.0080.0000.0000.0000.000
186A186TYR00.0010.00631.6150.0040.0040.0000.0000.0000.000
187A187LEU0-0.049-0.02335.8180.0060.0060.0000.0000.0000.000
188A188HIS0-0.054-0.03439.0800.0090.0090.0000.0000.0000.000
189A189PRO0-0.0130.01541.7080.0020.0020.0000.0000.0000.000
190A190GLU-1-0.851-0.92443.549-0.058-0.0580.0000.0000.0000.000
191A191THR0-0.066-0.05445.7990.0020.0020.0000.0000.0000.000
192A192LEU0-0.0070.00046.336-0.003-0.0030.0000.0000.0000.000
193A193SER00.0220.00044.711-0.004-0.0040.0000.0000.0000.000
194A194ARG10.9160.96840.6210.0800.0800.0000.0000.0000.000
195A195VAL00.0410.03538.874-0.004-0.0040.0000.0000.0000.000
196A196TYR0-0.005-0.02335.9930.0050.0050.0000.0000.0000.000
197A197LYS10.8500.91932.7430.1030.1030.0000.0000.0000.000
198A198ILE00.0330.01629.7110.0030.0030.0000.0000.0000.000
199A199MET0-0.0290.00425.9350.0030.0030.0000.0000.0000.000
200A200ILE00.0400.02223.829-0.001-0.0010.0000.0000.0000.000
201A201ASP-1-0.743-0.84519.830-0.316-0.3160.0000.0000.0000.000
202A202PHE00.028-0.01119.4180.0020.0020.0000.0000.0000.000
203A203LYS10.8490.91223.4820.2060.2060.0000.0000.0000.000
204A204PRO0-0.029-0.01325.2980.0020.0020.0000.0000.0000.000
205A205CYS0-0.0070.00427.7850.0000.0000.0000.0000.0000.000
206A206ARG10.8420.91430.7100.1000.1000.0000.0000.0000.000
207A207LEU00.0080.02032.979-0.004-0.0040.0000.0000.0000.000
208A208MET0-0.019-0.00534.9950.0080.0080.0000.0000.0000.000
209A209VAL00.0200.00437.747-0.004-0.0040.0000.0000.0000.000
210A210TRP00.0020.00240.1360.0050.0050.0000.0000.0000.000
211A211ARG10.8960.94242.9840.0660.0660.0000.0000.0000.000
212A212ASN0-0.036-0.02843.2040.0040.0040.0000.0000.0000.000
213A213ALA00.0100.04043.6120.0010.0010.0000.0000.0000.000
214A214THR0-0.049-0.05539.613-0.002-0.0020.0000.0000.0000.000
215A215PHE00.0050.00432.7660.0040.0040.0000.0000.0000.000
216A216TYR00.0340.02234.829-0.002-0.0020.0000.0000.0000.000
217A217VAL00.0440.02029.9810.0040.0040.0000.0000.0000.000
218A218GLN00.0400.03932.6890.0050.0050.0000.0000.0000.000
219A219GLU-1-0.771-0.87126.938-0.166-0.1660.0000.0000.0000.000