Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: N974Q

Calculation Name: 5HC1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5HC1

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 -2494555.412688
FMO2-HF: Nuclear repulsion 2409334.794473
FMO2-HF: Total energy -85220.618215
FMO2-MP2: Total energy -85465.898956


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:0:GLY)


Summations of interaction energy for fragment #1(A:0:GLY)
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.
0.7651.749-0.011-0.48-0.4930
Interaction energy analysis for fragmet #1(A:0:GLY)
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 : -0.005
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].
3A2ASN0-0.0060.0123.8631.5742.558-0.011-0.480-0.4930.000
4A3LYS10.8060.8716.309-0.479-0.4790.0000.0000.0000.000
5A4ILE0-0.0110.0149.6800.0010.0010.0000.0000.0000.000
6A5SER00.0470.00712.267-0.049-0.0490.0000.0000.0000.000
7A6CYS00.0000.00815.760-0.004-0.0040.0000.0000.0000.000
8A7LEU00.0160.01419.3400.0270.0270.0000.0000.0000.000
9A8PRO00.0240.01520.335-0.016-0.0160.0000.0000.0000.000
10A9ARG10.8580.90022.302-0.050-0.0500.0000.0000.0000.000
11A10VAL0-0.024-0.00323.200-0.006-0.0060.0000.0000.0000.000
12A11ALA00.0570.01721.194-0.009-0.0090.0000.0000.0000.000
13A12GLN0-0.0120.00123.317-0.004-0.0040.0000.0000.0000.000
14A13ASN0-0.098-0.06025.8130.0000.0000.0000.0000.0000.000
15A14LEU0-0.072-0.01925.164-0.003-0.0030.0000.0000.0000.000
16A15GLY00.0120.01127.133-0.005-0.0050.0000.0000.0000.000
17A16TYR0-0.071-0.06321.5420.0020.0020.0000.0000.0000.000
18A17HIS00.012-0.01323.1440.0140.0140.0000.0000.0000.000
19A18TYR00.0070.00820.1140.0120.0120.0000.0000.0000.000
20A19SER00.023-0.00714.808-0.009-0.0090.0000.0000.0000.000
21A20PRO00.0090.00512.0910.0310.0310.0000.0000.0000.000
22A21ASP-1-0.772-0.8579.3690.1640.1640.0000.0000.0000.000
23A22LEU0-0.027-0.00311.3820.1350.1350.0000.0000.0000.000
24A23PRO0-0.023-0.02012.870-0.028-0.0280.0000.0000.0000.000
25A24GLY0-0.0040.00415.701-0.017-0.0170.0000.0000.0000.000
26A25PHE0-0.027-0.01617.186-0.038-0.0380.0000.0000.0000.000
27A26CYS0-0.026-0.00819.5480.0240.0240.0000.0000.0000.000
28A27PRO00.0360.02217.612-0.007-0.0070.0000.0000.0000.000
29A28ILE00.000-0.00617.154-0.024-0.0240.0000.0000.0000.000
30A29PRO0-0.018-0.00816.2280.0230.0230.0000.0000.0000.000
31A30LYS10.9160.93311.868-0.256-0.2560.0000.0000.0000.000
32A31GLU-1-0.811-0.89414.4150.1270.1270.0000.0000.0000.000
33A32LEU0-0.012-0.01917.302-0.016-0.0160.0000.0000.0000.000
34A33ALA0-0.0090.01115.532-0.007-0.0070.0000.0000.0000.000
35A34GLU-1-0.932-0.96617.063-0.061-0.0610.0000.0000.0000.000
36A35HIS0-0.086-0.04218.977-0.008-0.0080.0000.0000.0000.000
37A36TRP0-0.035-0.01621.2020.0040.0040.0000.0000.0000.000
38A37PRO00.0010.00720.849-0.006-0.0060.0000.0000.0000.000
39A38VAL0-0.039-0.00616.6300.0180.0180.0000.0000.0000.000
40A39VAL00.0060.00617.492-0.026-0.0260.0000.0000.0000.000
41A40SER0-0.013-0.01712.1750.0140.0140.0000.0000.0000.000
42A41ASN0-0.028-0.0309.4330.0760.0760.0000.0000.0000.000
43A42ASP-1-0.848-0.8868.793-0.534-0.5340.0000.0000.0000.000
44A43ARG10.8300.91611.6180.2820.2820.0000.0000.0000.000
45A44TYR00.001-0.02811.2390.0180.0180.0000.0000.0000.000
46A45PRO0-0.010-0.01116.915-0.007-0.0070.0000.0000.0000.000
47A46ASN0-0.002-0.00620.662-0.004-0.0040.0000.0000.0000.000
48A47CYS0-0.067-0.01415.8180.0190.0190.0000.0000.0000.000
49A48LEU00.0200.02919.530-0.017-0.0170.0000.0000.0000.000
50A49GLN00.001-0.01012.5360.0560.0560.0000.0000.0000.000
51A50ILE0-0.015-0.01314.8550.0130.0130.0000.0000.0000.000
52A51THR00.003-0.00112.975-0.086-0.0860.0000.0000.0000.000
53A52LEU00.0290.00710.5920.0540.0540.0000.0000.0000.000
54A53GLN0-0.016-0.00714.2130.0330.0330.0000.0000.0000.000
55A54GLN00.0090.02016.3190.0000.0000.0000.0000.0000.000
56A55VAL0-0.010-0.00515.483-0.036-0.0360.0000.0000.0000.000
57A56CYS0-0.060-0.01718.2110.0100.0100.0000.0000.0000.000
58A57GLU-1-0.859-0.94521.963-0.131-0.1310.0000.0000.0000.000
59A58LEU0-0.036-0.02324.6960.0120.0120.0000.0000.0000.000
60A59SER0-0.056-0.03320.0000.0010.0010.0000.0000.0000.000
61A60LYS10.8910.95222.2580.0660.0660.0000.0000.0000.000
62A61PRO00.0230.01922.228-0.004-0.0040.0000.0000.0000.000
63A62CYS0-0.029-0.01922.0810.0180.0180.0000.0000.0000.000
64A63SER0-0.0090.00022.221-0.002-0.0020.0000.0000.0000.000
65A64ALA0-0.021-0.01422.7440.0060.0060.0000.0000.0000.000
66A65GLY00.0740.04322.395-0.002-0.0020.0000.0000.0000.000
67A66TYR0-0.036-0.02815.981-0.010-0.0100.0000.0000.0000.000
68A67MET0-0.0140.00416.1960.0020.0020.0000.0000.0000.000
69A68VAL00.0230.01710.896-0.023-0.0230.0000.0000.0000.000
70A69GLY00.0010.00712.2670.0670.0670.0000.0000.0000.000
71A70GLN00.024-0.01312.946-0.086-0.0860.0000.0000.0000.000
72A71SER0-0.042-0.00814.938-0.033-0.0330.0000.0000.0000.000
73A72VAL00.009-0.00316.924-0.007-0.0070.0000.0000.0000.000
74A73PHE0-0.042-0.01915.5850.0010.0010.0000.0000.0000.000
75A74VAL0-0.017-0.00520.457-0.009-0.0090.0000.0000.0000.000
76A75GLN0-0.025-0.01422.5440.0010.0010.0000.0000.0000.000
77A76THR00.0050.00322.6150.0030.0030.0000.0000.0000.000
78A77PRO00.0070.00324.387-0.007-0.0070.0000.0000.0000.000
79A78GLY00.001-0.00426.813-0.004-0.0040.0000.0000.0000.000
80A79VAL0-0.0170.00121.248-0.009-0.0090.0000.0000.0000.000
81A80THR0-0.052-0.01420.1680.0170.0170.0000.0000.0000.000
82A81SER0-0.014-0.02719.198-0.015-0.0150.0000.0000.0000.000
83A82TYR0-0.007-0.01916.743-0.003-0.0030.0000.0000.0000.000
84A83TRP0-0.006-0.00117.5300.0130.0130.0000.0000.0000.000
85A84LEU0-0.0030.00317.770-0.007-0.0070.0000.0000.0000.000
86A85THR0-0.026-0.02518.483-0.015-0.0150.0000.0000.0000.000
87A86GLU-1-0.737-0.82319.615-0.053-0.0530.0000.0000.0000.000
88A87TRP0-0.030-0.02217.3420.0020.0020.0000.0000.0000.000
89A88VAL00.0300.00321.9880.0130.0130.0000.0000.0000.000
90A89ASP-1-0.856-0.91724.900-0.051-0.0510.0000.0000.0000.000
91A90GLY0-0.0130.00221.876-0.003-0.0030.0000.0000.0000.000
92A91LYS10.8960.94222.4560.0620.0620.0000.0000.0000.000
93A92ALA00.0190.02822.3060.0070.0070.0000.0000.0000.000
94A93ARG10.8220.87423.9440.0610.0610.0000.0000.0000.000
95A94ALA00.0100.00925.767-0.005-0.0050.0000.0000.0000.000
96A95LEU00.0180.01722.9300.0070.0070.0000.0000.0000.000
97A96PRO0-0.017-0.00527.442-0.001-0.0010.0000.0000.0000.000
98A97ASP-1-0.796-0.91228.924-0.057-0.0570.0000.0000.0000.000
99A98SER0-0.079-0.06729.1600.0080.0080.0000.0000.0000.000
100A99LEU0-0.0120.02030.075-0.004-0.0040.0000.0000.0000.000
101A100PHE00.0210.00425.9630.0010.0010.0000.0000.0000.000
102A101SER0-0.021-0.03727.514-0.001-0.0010.0000.0000.0000.000
103A102SER0-0.014-0.02826.236-0.002-0.0020.0000.0000.0000.000
104A103GLY00.0280.02024.8280.0010.0010.0000.0000.0000.000
105A104ARG10.7580.88825.871-0.004-0.0040.0000.0000.0000.000
106A105PHE0-0.021-0.02128.6050.0040.0040.0000.0000.0000.000
107A106GLU-1-0.792-0.88924.1940.0580.0580.0000.0000.0000.000
108A107THR0-0.018-0.02523.8010.0090.0090.0000.0000.0000.000
109A108ASN0-0.070-0.03626.532-0.005-0.0050.0000.0000.0000.000
110A109SER00.0270.03229.167-0.006-0.0060.0000.0000.0000.000
111A110ARG10.8920.92530.932-0.042-0.0420.0000.0000.0000.000
112A111ALA00.0210.02432.179-0.003-0.0030.0000.0000.0000.000
113A112PHE00.0220.00132.9630.0000.0000.0000.0000.0000.000
114A113LEU0-0.047-0.02828.0330.0020.0020.0000.0000.0000.000
115A114ASP-1-0.795-0.89430.158-0.025-0.0250.0000.0000.0000.000
116A115GLU-1-0.829-0.89232.714-0.010-0.0100.0000.0000.0000.000
117A116ALA00.0150.00234.8920.0010.0010.0000.0000.0000.000
118A117GLU-1-0.782-0.88933.3440.0000.0000.0000.0000.0000.000
119A118GLU-1-0.887-0.92836.160-0.001-0.0010.0000.0000.0000.000
120A119LYS10.8290.89038.8080.0090.0090.0000.0000.0000.000
121A120PHE0-0.0050.01638.3690.0000.0000.0000.0000.0000.000
122A121ALA00.0250.00639.6050.0000.0000.0000.0000.0000.000
123A122ALA0-0.027-0.01341.3780.0010.0010.0000.0000.0000.000
124A123ALA0-0.021-0.00743.4180.0000.0000.0000.0000.0000.000
125A124HIS10.7520.86442.1400.0110.0110.0000.0000.0000.000
126A125PRO00.0710.02744.9650.0010.0010.0000.0000.0000.000
127A126HIS0-0.039-0.03046.7960.0030.0030.0000.0000.0000.000
128A127ALA00.0230.02542.7240.0010.0010.0000.0000.0000.000
129A128CYS0-0.0380.00342.1740.0010.0010.0000.0000.0000.000
130A129LEU0-0.0090.01143.4450.0020.0020.0000.0000.0000.000
131A130GLY00.0060.00146.292-0.001-0.0010.0000.0000.0000.000
132A131GLU-1-0.757-0.89444.4610.0140.0140.0000.0000.0000.000
133A132ILE0-0.069-0.02847.4630.0000.0000.0000.0000.0000.000
134A133ASN0-0.027-0.01649.504-0.001-0.0010.0000.0000.0000.000
135A134LYS10.8900.95748.802-0.003-0.0030.0000.0000.0000.000
136A135SER00.0400.03146.180-0.002-0.0020.0000.0000.0000.000
137A136THR0-0.023-0.00848.3780.0010.0010.0000.0000.0000.000
138A137VAL0-0.012-0.00543.314-0.001-0.0010.0000.0000.0000.000
139A138GLY00.0150.01845.9440.0000.0000.0000.0000.0000.000
140A139GLY00.002-0.02342.1460.0020.0020.0000.0000.0000.000
141A140SER0-0.104-0.02941.791-0.002-0.0020.0000.0000.0000.000
142A141ALA00.0420.02141.036-0.001-0.0010.0000.0000.0000.000
143A142PHE00.0140.01535.7030.0010.0010.0000.0000.0000.000
144A143ILE0-0.046-0.02432.1780.0010.0010.0000.0000.0000.000
145A144PHE00.0110.00735.1410.0020.0020.0000.0000.0000.000
146A145SER0-0.055-0.03637.391-0.001-0.0010.0000.0000.0000.000
147A146GLN00.002-0.01241.1020.0010.0010.0000.0000.0000.000
148A147TYR0-0.009-0.00843.5290.0010.0010.0000.0000.0000.000
149A148LEU0-0.0100.01838.4770.0010.0010.0000.0000.0000.000
150A149PRO0-0.007-0.00441.3380.0000.0000.0000.0000.0000.000
151A150PRO00.0270.00639.1620.0010.0010.0000.0000.0000.000
152A151LEU0-0.0260.00236.6300.0030.0030.0000.0000.0000.000
153A152LEU00.012-0.00535.462-0.003-0.0030.0000.0000.0000.000
154A153PRO00.0380.02935.2210.0020.0020.0000.0000.0000.000
155A154ALA00.0950.02733.015-0.003-0.0030.0000.0000.0000.000
156A155ASP-1-0.935-0.96635.1610.0490.0490.0000.0000.0000.000
157A156ALA00.003-0.00137.882-0.003-0.0030.0000.0000.0000.000
158A157VAL0-0.024-0.00336.967-0.004-0.0040.0000.0000.0000.000
159A158ALA00.012-0.00436.6900.0030.0030.0000.0000.0000.000
160A159LEU0-0.0300.00129.955-0.004-0.0040.0000.0000.0000.000
161A160VAL00.0150.00333.4620.0000.0000.0000.0000.0000.000
162A161GLY00.0180.02230.8530.0010.0010.0000.0000.0000.000
163A162ALA00.0130.00830.2680.0020.0020.0000.0000.0000.000
164A163SER0-0.039-0.02131.729-0.005-0.0050.0000.0000.0000.000
165A164LEU0-0.0150.01934.6370.0030.0030.0000.0000.0000.000
166A165ALA00.0020.00634.1680.0010.0010.0000.0000.0000.000
167A166GLY00.0490.02336.094-0.002-0.0020.0000.0000.0000.000
168A167LYS10.8800.90138.100-0.042-0.0420.0000.0000.0000.000
169A168ALA00.0630.05841.703-0.002-0.0020.0000.0000.0000.000
170A169ALA00.007-0.00443.157-0.001-0.0010.0000.0000.0000.000
171A170LYS10.9040.94345.156-0.020-0.0200.0000.0000.0000.000
172A171ALA00.0180.02741.1450.0020.0020.0000.0000.0000.000
173A172ALA0-0.022-0.01242.923-0.002-0.0020.0000.0000.0000.000
174A173CYS0-0.034-0.00441.460-0.001-0.0010.0000.0000.0000.000
175A174SER00.003-0.01339.2570.0020.0020.0000.0000.0000.000
176A175VAL00.0140.01234.904-0.002-0.0020.0000.0000.0000.000
177A176VAL00.0330.00435.3810.0010.0010.0000.0000.0000.000
178A177ASP-1-0.735-0.86029.3920.0250.0250.0000.0000.0000.000
179A178VAL00.0190.01330.5420.0010.0010.0000.0000.0000.000
180A179TYR00.005-0.01529.8330.0000.0000.0000.0000.0000.000
181A180ALA00.0230.02031.784-0.004-0.0040.0000.0000.0000.000
182A181PRO00.017-0.00533.935-0.001-0.0010.0000.0000.0000.000
183A182SER0-0.061-0.03332.000-0.002-0.0020.0000.0000.0000.000
184A183PHE00.025-0.00434.075-0.001-0.0010.0000.0000.0000.000
185A184GLU-1-0.752-0.86737.407-0.017-0.0170.0000.0000.0000.000
186A185PRO0-0.019-0.01536.0050.0000.0000.0000.0000.0000.000
187A186TYR0-0.0090.00135.3160.0000.0000.0000.0000.0000.000
188A187LEU0-0.044-0.03141.0370.0020.0020.0000.0000.0000.000
189A188HIS0-0.048-0.02143.2760.0020.0020.0000.0000.0000.000
190A189PRO0-0.056-0.00546.117-0.001-0.0010.0000.0000.0000.000
191A190GLU-1-0.801-0.90947.788-0.019-0.0190.0000.0000.0000.000
192A191THR0-0.093-0.03650.8330.0010.0010.0000.0000.0000.000
193A192LEU00.0100.01151.6330.0000.0000.0000.0000.0000.000
194A193SER00.0140.00250.7360.0000.0000.0000.0000.0000.000
195A194ARG10.9340.97045.2200.0150.0150.0000.0000.0000.000
196A195VAL00.0310.00545.2500.0010.0010.0000.0000.0000.000
197A196TYR0-0.020-0.01641.320-0.002-0.0020.0000.0000.0000.000
198A197LYS10.9070.94840.4600.0160.0160.0000.0000.0000.000
199A198ILE00.0340.01236.204-0.003-0.0030.0000.0000.0000.000
200A199MET0-0.022-0.00832.1600.0020.0020.0000.0000.0000.000
201A200ILE00.0410.02331.055-0.003-0.0030.0000.0000.0000.000
202A201ASP-1-0.764-0.85327.5960.0170.0170.0000.0000.0000.000
203A202PHE00.027-0.00424.3960.0030.0030.0000.0000.0000.000
204A203LYS10.8850.95029.806-0.022-0.0220.0000.0000.0000.000
205A204PRO00.000-0.00532.647-0.002-0.0020.0000.0000.0000.000
206A205CYS0-0.077-0.02735.9120.0030.0030.0000.0000.0000.000
207A206ARG10.9440.97438.7170.0000.0000.0000.0000.0000.000
208A207LEU00.0370.02439.0480.0020.0020.0000.0000.0000.000
209A208MET0-0.0560.00242.027-0.002-0.0020.0000.0000.0000.000
210A209VAL0-0.0060.00143.7390.0010.0010.0000.0000.0000.000
211A210TRP00.014-0.00546.490-0.001-0.0010.0000.0000.0000.000
212A211ARG10.9230.94448.8120.0140.0140.0000.0000.0000.000
213A212ASN0-0.028-0.02048.6830.0000.0000.0000.0000.0000.000
214A213ALA0-0.0120.01949.7760.0010.0010.0000.0000.0000.000
215A214THR0-0.026-0.03947.1810.0010.0010.0000.0000.0000.000
216A215PHE00.001-0.00539.529-0.001-0.0010.0000.0000.0000.000
217A216TYR00.0640.02642.4750.0010.0010.0000.0000.0000.000
218A217VAL00.0410.02837.562-0.001-0.0010.0000.0000.0000.000
219A218GLN0-0.023-0.01640.8590.0000.0000.0000.0000.0000.000