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: 6692Z

Calculation Name: 4HUD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HUD

Chain ID: A

ChEMBL ID:

UniProt ID: P11112

Base Structure: X-ray

Registration Date: 2023-06-20

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 -2647946.996647
FMO2-HF: Nuclear repulsion 2559331.950919
FMO2-HF: Total energy -88615.045729
FMO2-MP2: Total energy -88873.088186


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:3:GLY)


Summations of interaction energy for fragment #1(A:3: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.
1.8433.308-0.023-0.814-0.6290
Interaction energy analysis for fragmet #1(A:3:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.009
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].
3A5PHE0-0.0150.0153.8021.0712.536-0.023-0.814-0.6290.000
4A6TYR0-0.055-0.0606.730-0.434-0.4340.0000.0000.0000.000
5A7ASN00.014-0.0047.894-0.235-0.2350.0000.0000.0000.000
6A8SER0-0.043-0.01610.462-0.054-0.0540.0000.0000.0000.000
7A9SER00.059-0.00112.221-0.024-0.0240.0000.0000.0000.000
8A10PHE00.0110.01014.289-0.015-0.0150.0000.0000.0000.000
9A11ARG10.9600.9927.3360.9400.9400.0000.0000.0000.000
10A12ARG10.8820.96112.698-0.041-0.0410.0000.0000.0000.000
11A13TYR0-0.002-0.01114.9910.0030.0030.0000.0000.0000.000
12A14ALA0-0.003-0.00214.4320.0040.0040.0000.0000.0000.000
13A15THR0-0.011-0.01613.171-0.031-0.0310.0000.0000.0000.000
14A16LEU00.0190.01115.5360.0160.0160.0000.0000.0000.000
15A17MET0-0.032-0.01718.8610.0130.0130.0000.0000.0000.000
16A18GLY00.014-0.00718.0230.0080.0080.0000.0000.0000.000
17A19ASP-1-0.754-0.86218.040-0.128-0.1280.0000.0000.0000.000
18A20LEU0-0.033-0.01119.8600.0150.0150.0000.0000.0000.000
19A21PHE0-0.035-0.02622.5590.0120.0120.0000.0000.0000.000
20A22SER0-0.0130.02219.760-0.002-0.0020.0000.0000.0000.000
21A23ASN0-0.072-0.03921.944-0.002-0.0020.0000.0000.0000.000
22A24ILE00.0600.04124.9550.0110.0110.0000.0000.0000.000
23A25GLN0-0.001-0.00927.561-0.011-0.0110.0000.0000.0000.000
24A26ILE00.0120.03930.0190.0050.0050.0000.0000.0000.000
25A27LYS10.8210.89733.0230.0500.0500.0000.0000.0000.000
26A28ARG10.8750.91533.9080.0830.0830.0000.0000.0000.000
27A29GLN0-0.013-0.00937.3510.0020.0020.0000.0000.0000.000
28A30LEU0-0.026-0.01137.112-0.001-0.0010.0000.0000.0000.000
29A31GLU-1-0.964-0.97941.563-0.039-0.0390.0000.0000.0000.000
30A32SER00.0160.00640.8130.0010.0010.0000.0000.0000.000
31A33GLY00.0110.00141.8500.0020.0020.0000.0000.0000.000
32A34ASP-1-0.853-0.91538.779-0.053-0.0530.0000.0000.0000.000
33A35LYS10.9280.97232.9100.0760.0760.0000.0000.0000.000
34A36PHE00.0120.00032.5020.0000.0000.0000.0000.0000.000
35A37ILE0-0.045-0.02429.371-0.002-0.0020.0000.0000.0000.000
36A38ARG10.9280.95824.8830.1090.1090.0000.0000.0000.000
37A39VAL00.0170.00725.487-0.003-0.0030.0000.0000.0000.000
38A40PRO0-0.0100.02821.345-0.006-0.0060.0000.0000.0000.000
39A41ILE00.0230.00418.6590.0050.0050.0000.0000.0000.000
40A42THR0-0.007-0.01717.159-0.024-0.0240.0000.0000.0000.000
41A43TYR00.0270.00913.9110.0430.0430.0000.0000.0000.000
42A44ALA0-0.029-0.02114.957-0.063-0.0630.0000.0000.0000.000
43A45SER00.0330.02717.0730.0410.0410.0000.0000.0000.000
44A46LYS10.8530.90019.4680.1200.1200.0000.0000.0000.000
45A47GLU-1-0.885-0.94722.850-0.134-0.1340.0000.0000.0000.000
46A48HIS0-0.017-0.00815.2250.0370.0370.0000.0000.0000.000
47A49PHE00.0210.00419.9660.0060.0060.0000.0000.0000.000
48A50MET00.0310.01421.1220.0080.0080.0000.0000.0000.000
49A51MET0-0.043-0.01521.5890.0110.0110.0000.0000.0000.000
50A52LYS10.8610.91716.6580.3110.3110.0000.0000.0000.000
51A53LEU0-0.0100.01422.0180.0080.0080.0000.0000.0000.000
52A54ASN00.016-0.00524.6430.0150.0150.0000.0000.0000.000
53A55LYS10.9420.97820.9640.1840.1840.0000.0000.0000.000
54A56TRP0-0.022-0.00618.7930.0110.0110.0000.0000.0000.000
55A57THR0-0.012-0.00125.4150.0080.0080.0000.0000.0000.000
56A58SER0-0.046-0.01628.0970.0110.0110.0000.0000.0000.000
57A59ILE00.0150.00130.151-0.003-0.0030.0000.0000.0000.000
58A60ASN0-0.057-0.01929.2890.0070.0070.0000.0000.0000.000
59A61SER0-0.057-0.04031.7360.0070.0070.0000.0000.0000.000
60A62GLN00.023-0.01334.138-0.002-0.0020.0000.0000.0000.000
61A63GLU-1-0.864-0.91329.477-0.097-0.0970.0000.0000.0000.000
62A64ASP-1-0.785-0.87629.539-0.109-0.1090.0000.0000.0000.000
63A65VAL00.0050.00131.918-0.003-0.0030.0000.0000.0000.000
64A66ALA0-0.019-0.00434.2250.0000.0000.0000.0000.0000.000
65A67LYS10.8070.86726.8200.1130.1130.0000.0000.0000.000
66A68VAL00.0420.03829.301-0.009-0.0090.0000.0000.0000.000
67A69GLU-1-0.856-0.90030.433-0.088-0.0880.0000.0000.0000.000
68A70THR0-0.088-0.04128.417-0.001-0.0010.0000.0000.0000.000
69A71ILE0-0.0210.01225.066-0.008-0.0080.0000.0000.0000.000
70A72LEU0-0.043-0.00326.615-0.008-0.0080.0000.0000.0000.000
71A73PRO0-0.005-0.00228.9580.0050.0050.0000.0000.0000.000
72A74ARG10.7980.84120.7160.1960.1960.0000.0000.0000.000
73A75ILE00.0260.01923.2630.0120.0120.0000.0000.0000.000
74A76ASN00.0240.02919.805-0.042-0.0420.0000.0000.0000.000
75A77LEU0-0.030-0.01019.0980.0190.0190.0000.0000.0000.000
76A78HIS0-0.029-0.02415.680-0.036-0.0360.0000.0000.0000.000
77A79LEU0-0.0320.00518.4060.0270.0270.0000.0000.0000.000
78A80VAL0-0.038-0.03120.533-0.010-0.0100.0000.0000.0000.000
79A81ASP-1-0.878-0.94123.424-0.074-0.0740.0000.0000.0000.000
80A82PHE0-0.031-0.01520.489-0.003-0.0030.0000.0000.0000.000
81A83SER00.0240.02724.6850.0060.0060.0000.0000.0000.000
82A84TYR0-0.025-0.02427.1720.0010.0010.0000.0000.0000.000
83A85ASN0-0.039-0.02428.640-0.002-0.0020.0000.0000.0000.000
84A86ALA0-0.007-0.00630.5290.0040.0040.0000.0000.0000.000
85A87PRO0-0.0030.01533.524-0.002-0.0020.0000.0000.0000.000
86A105VAL0-0.005-0.02032.1570.0020.0020.0000.0000.0000.000
87A106VAL00.0080.01526.995-0.003-0.0030.0000.0000.0000.000
88A107SER0-0.031-0.02424.787-0.006-0.0060.0000.0000.0000.000
89A108GLN00.0440.01020.6280.0120.0120.0000.0000.0000.000
90A109TYR0-0.066-0.01620.2000.0040.0040.0000.0000.0000.000
91A110ASN0-0.014-0.01425.4940.0000.0000.0000.0000.0000.000
92A111PRO00.0150.02423.9630.0070.0070.0000.0000.0000.000
93A112SER00.011-0.00224.829-0.005-0.0050.0000.0000.0000.000
94A113PRO0-0.0010.02125.421-0.004-0.0040.0000.0000.0000.000
95A114ILE0-0.012-0.00621.731-0.001-0.0010.0000.0000.0000.000
96A115LYS10.8230.91625.8300.0470.0470.0000.0000.0000.000
97A116MET0-0.059-0.02821.081-0.006-0.0060.0000.0000.0000.000
98A117ILE00.0230.01524.1200.0040.0040.0000.0000.0000.000
99A118TYR00.013-0.01218.207-0.005-0.0050.0000.0000.0000.000
100A119GLU-1-0.836-0.90523.676-0.115-0.1150.0000.0000.0000.000
101A120LEU0-0.025-0.00923.662-0.020-0.0200.0000.0000.0000.000
102A121SER00.017-0.01724.7540.0090.0090.0000.0000.0000.000
103A122ILE00.0050.00226.014-0.011-0.0110.0000.0000.0000.000
104A123PHE00.0400.01925.3610.0070.0070.0000.0000.0000.000
105A124THR0-0.013-0.03329.452-0.003-0.0030.0000.0000.0000.000
106A125ARG10.8370.91432.1190.0810.0810.0000.0000.0000.000
107A126TYR0-0.075-0.06534.7280.0070.0070.0000.0000.0000.000
108A127GLU-1-0.888-0.94936.687-0.062-0.0620.0000.0000.0000.000
109A128ASP-1-0.869-0.92238.286-0.062-0.0620.0000.0000.0000.000
110A129ASP-1-0.745-0.87833.423-0.086-0.0860.0000.0000.0000.000
111A130MET0-0.025-0.00732.433-0.005-0.0050.0000.0000.0000.000
112A131PHE0-0.005-0.00734.772-0.001-0.0010.0000.0000.0000.000
113A132GLN00.0250.01135.0940.0000.0000.0000.0000.0000.000
114A133ILE00.0150.00729.5490.0000.0000.0000.0000.0000.000
115A134VAL0-0.007-0.00532.2340.0000.0000.0000.0000.0000.000
116A135GLU-1-0.958-0.97133.633-0.053-0.0530.0000.0000.0000.000
117A136GLN0-0.096-0.06631.6100.0010.0010.0000.0000.0000.000
118A137ILE0-0.029-0.00828.157-0.001-0.0010.0000.0000.0000.000
119A138LEU0-0.015-0.02631.4940.0040.0040.0000.0000.0000.000
120A139PRO00.0140.02334.4830.0030.0030.0000.0000.0000.000
121A140TYR0-0.069-0.03232.0250.0050.0050.0000.0000.0000.000
122A141PHE0-0.003-0.01328.1100.0000.0000.0000.0000.0000.000
123A142GLN0-0.059-0.00734.2170.0030.0030.0000.0000.0000.000
124A143PRO0-0.030-0.01836.1780.0040.0040.0000.0000.0000.000
125A144HIS00.014-0.00733.156-0.005-0.0050.0000.0000.0000.000
126A145PHE00.0720.05326.9960.0020.0020.0000.0000.0000.000
127A146ASN0-0.042-0.02830.187-0.003-0.0030.0000.0000.0000.000
128A147THR00.019-0.00625.4740.0010.0010.0000.0000.0000.000
129A148THR0-0.029-0.00727.4370.0020.0020.0000.0000.0000.000
130A149MET0-0.0080.00420.087-0.008-0.0080.0000.0000.0000.000
131A150TYR0-0.019-0.02322.9100.0100.0100.0000.0000.0000.000
132A151GLU-1-0.716-0.82119.0550.0280.0280.0000.0000.0000.000
133A152GLN0-0.039-0.03419.8310.0000.0000.0000.0000.0000.000
134A153PHE00.0670.02617.5810.0110.0110.0000.0000.0000.000
135A154GLY00.0800.04617.899-0.004-0.0040.0000.0000.0000.000
136A155ASN0-0.064-0.04219.162-0.016-0.0160.0000.0000.0000.000
137A156ASP-1-0.889-0.92022.6810.1120.1120.0000.0000.0000.000
138A157ILE0-0.018-0.01624.611-0.006-0.0060.0000.0000.0000.000
139A158PRO0-0.007-0.00523.5930.0040.0040.0000.0000.0000.000
140A159PHE00.0190.00522.180-0.010-0.0100.0000.0000.0000.000
141A160LYS10.8380.90724.442-0.005-0.0050.0000.0000.0000.000
142A161ARG10.8030.90722.334-0.035-0.0350.0000.0000.0000.000
143A162ASP-1-0.821-0.89825.968-0.012-0.0120.0000.0000.0000.000
144A163ILE00.0100.01523.555-0.002-0.0020.0000.0000.0000.000
145A164LYS10.8780.94326.9090.0330.0330.0000.0000.0000.000
146A165ILE00.0250.01224.789-0.003-0.0030.0000.0000.0000.000
147A166VAL00.000-0.02028.6190.0040.0040.0000.0000.0000.000
148A167LEU0-0.0110.00830.731-0.006-0.0060.0000.0000.0000.000
149A168MET0-0.047-0.02231.2610.0070.0070.0000.0000.0000.000
150A169SER0-0.019-0.01633.0290.0030.0030.0000.0000.0000.000
151A170ALA00.0090.00433.020-0.005-0.0050.0000.0000.0000.000
152A171ALA0-0.015-0.00533.0120.0040.0040.0000.0000.0000.000
153A172ILE0-0.017-0.00733.987-0.005-0.0050.0000.0000.0000.000
154A173ASP-1-0.840-0.90934.370-0.075-0.0750.0000.0000.0000.000
155A174GLU-1-0.912-0.95835.693-0.070-0.0700.0000.0000.0000.000
156A175ALA00.004-0.00633.841-0.003-0.0030.0000.0000.0000.000
157A176ILE00.0030.00835.835-0.003-0.0030.0000.0000.0000.000
158A177ASP-1-0.875-0.93937.809-0.072-0.0720.0000.0000.0000.000
159A178GLY00.0720.04739.6420.0000.0000.0000.0000.0000.000
160A179ASP-1-0.892-0.94242.759-0.054-0.0540.0000.0000.0000.000
161A180ASN0-0.082-0.04145.0540.0020.0020.0000.0000.0000.000
162A181LEU0-0.068-0.03440.8710.0020.0020.0000.0000.0000.000
163A182SER00.009-0.01537.027-0.001-0.0010.0000.0000.0000.000
164A183ARG10.8160.93437.7410.0640.0640.0000.0000.0000.000
165A184ARG10.8500.92432.9350.0900.0900.0000.0000.0000.000
166A185ARG10.8800.91629.1320.1150.1150.0000.0000.0000.000
167A186ILE00.0180.02834.2240.0010.0010.0000.0000.0000.000
168A187GLU-1-0.805-0.88429.373-0.123-0.1230.0000.0000.0000.000
169A188TRP00.0400.01631.6130.0070.0070.0000.0000.0000.000
170A189SER00.006-0.01029.072-0.012-0.0120.0000.0000.0000.000
171A190LEU0-0.028-0.01029.1020.0090.0090.0000.0000.0000.000
172A191THR00.0090.01728.312-0.011-0.0110.0000.0000.0000.000
173A192PHE00.010-0.01326.3620.0080.0080.0000.0000.0000.000
174A193GLU-1-0.773-0.87426.955-0.058-0.0580.0000.0000.0000.000
175A194VAL00.0070.01122.9390.0070.0070.0000.0000.0000.000
176A195ASN0-0.088-0.06526.0800.0050.0050.0000.0000.0000.000
177A196GLY00.0470.02023.8460.0030.0030.0000.0000.0000.000
178A197TRP0-0.034-0.03122.8560.0100.0100.0000.0000.0000.000
179A198MET00.0160.02018.1280.0030.0030.0000.0000.0000.000
180A199TYR0-0.028-0.06317.8140.0060.0060.0000.0000.0000.000
181A200PRO0-0.028-0.01118.702-0.006-0.0060.0000.0000.0000.000
182A201PRO0-0.008-0.00313.299-0.002-0.0020.0000.0000.0000.000
183A202VAL00.0540.03614.8980.0070.0070.0000.0000.0000.000
184A203ASP-1-0.841-0.92011.2970.8430.8430.0000.0000.0000.000
185A204ASP-1-0.731-0.8667.2811.3011.3010.0000.0000.0000.000
186A205ALA0-0.085-0.05110.372-0.036-0.0360.0000.0000.0000.000
187A206GLU-1-1.012-1.00012.1670.2010.2010.0000.0000.0000.000
188A207GLY0-0.026-0.00913.496-0.077-0.0770.0000.0000.0000.000
189A208LEU0-0.041-0.0178.883-0.004-0.0040.0000.0000.0000.000
190A209ILE0-0.042-0.00712.857-0.066-0.0660.0000.0000.0000.000
191A210ARG10.8610.92914.445-0.143-0.1430.0000.0000.0000.000
192A211THR00.027-0.00416.073-0.005-0.0050.0000.0000.0000.000
193A212THR0-0.0210.01418.393-0.014-0.0140.0000.0000.0000.000
194A213TYR0-0.041-0.06020.4680.0050.0050.0000.0000.0000.000
195A214THR0-0.0190.01523.7300.0020.0020.0000.0000.0000.000
196A215ASP-1-0.757-0.88225.870-0.061-0.0610.0000.0000.0000.000
197A216PHE00.011-0.00826.9540.0060.0060.0000.0000.0000.000
198A217HIS0-0.043-0.00629.9790.0050.0050.0000.0000.0000.000
199A218ALA0-0.055-0.02330.6420.0040.0040.0000.0000.0000.000
200A219ASN0-0.012-0.00129.2510.0100.0100.0000.0000.0000.000
201A220THR0-0.052-0.04025.572-0.003-0.0030.0000.0000.0000.000
202A221ARG10.8470.94220.4140.1100.1100.0000.0000.0000.000
203A222ASP-1-0.904-0.97919.615-0.022-0.0220.0000.0000.0000.000
204A223LEU0-0.072-0.04215.291-0.011-0.0110.0000.0000.0000.000
205A224PRO00.0150.02415.4200.0130.0130.0000.0000.0000.000
206A225ASP-1-0.783-0.8838.696-0.229-0.2290.0000.0000.0000.000
207A226GLY00.0230.00310.162-0.026-0.0260.0000.0000.0000.000
208A227GLU-1-0.997-1.0098.352-0.969-0.9690.0000.0000.0000.000
209A228GLY0-0.048-0.01410.3650.0490.0490.0000.0000.0000.000
210A229VAL0-0.063-0.01613.7990.0400.0400.0000.0000.0000.000
211A230PHE0-0.053-0.02113.3660.0330.0330.0000.0000.0000.000
212A231GLU-1-0.790-0.85314.097-0.283-0.2830.0000.0000.0000.000
213A232SER00.010-0.00712.2490.0020.0020.0000.0000.0000.000
214A233VAL00.0470.02914.0280.0500.0500.0000.0000.0000.000
215A234ASP-1-0.948-0.97611.760-0.416-0.4160.0000.0000.0000.000