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: N1ZGQ

Calculation Name: 1DUS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DUS

Chain ID: A

ChEMBL ID:

UniProt ID: Q58292

Base Structure: X-ray

Registration Date: 2023-03-13

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2219727.362194
FMO2-HF: Nuclear repulsion 2144416.459244
FMO2-HF: Total energy -75310.90295
FMO2-MP2: Total energy -75534.633688


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:4:PHE)


Summations of interaction energy for fragment #1(A:4:PHE)
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.
-9.736-2.451.491-3.937-4.839-0.014
Interaction energy analysis for fragmet #1(A:4:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.038
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].
3A6GLU-1-0.889-0.9552.489-14.264-7.0821.491-3.907-4.766-0.014
4A7LYS10.8900.9384.2411.3941.4980.000-0.030-0.0730.000
5A8PRO00.0350.0167.5650.0550.0550.0000.0000.0000.000
6A9THR00.0360.0188.7360.1740.1740.0000.0000.0000.000
7A10THR0-0.016-0.00111.2230.1610.1610.0000.0000.0000.000
8A11LYS10.9600.98813.4790.4210.4210.0000.0000.0000.000
9A12SER00.010-0.00215.372-0.046-0.0460.0000.0000.0000.000
10A13ASP-1-0.850-0.87517.705-0.390-0.3900.0000.0000.0000.000
11A14VAL0-0.029-0.02921.131-0.001-0.0010.0000.0000.0000.000
12A15LYS10.9160.97323.3490.2590.2590.0000.0000.0000.000
13A16ILE00.0140.01626.796-0.006-0.0060.0000.0000.0000.000
14A17VAL0-0.040-0.00728.8140.0060.0060.0000.0000.0000.000
15A18GLU-1-0.811-0.89431.202-0.124-0.1240.0000.0000.0000.000
16A19ASP-1-0.816-0.89934.058-0.111-0.1110.0000.0000.0000.000
17A20ILE0-0.040-0.02235.9110.0030.0030.0000.0000.0000.000
18A21LEU0-0.034-0.01732.442-0.002-0.0020.0000.0000.0000.000
19A22ARG10.7930.85935.5520.0460.0460.0000.0000.0000.000
20A23GLY00.0010.00538.9440.0030.0030.0000.0000.0000.000
21A24LYS10.7610.84135.8500.0560.0560.0000.0000.0000.000
22A25LYS10.8650.92637.8380.0620.0620.0000.0000.0000.000
23A26LEU00.0470.03432.5490.0000.0000.0000.0000.0000.000
24A27LYS10.8540.91331.4590.1240.1240.0000.0000.0000.000
25A28PHE00.005-0.00127.441-0.003-0.0030.0000.0000.0000.000
26A29LYS10.8600.91922.5730.2800.2800.0000.0000.0000.000
27A30THR0-0.041-0.02923.738-0.009-0.0090.0000.0000.0000.000
28A31ASP-1-0.735-0.89618.000-0.510-0.5100.0000.0000.0000.000
29A32SER0-0.047-0.05819.5170.0030.0030.0000.0000.0000.000
30A33GLY0-0.0060.01616.303-0.006-0.0060.0000.0000.0000.000
31A34VAL0-0.073-0.04516.669-0.023-0.0230.0000.0000.0000.000
32A35PHE00.0130.00219.3390.0150.0150.0000.0000.0000.000
33A36SER0-0.039-0.03721.7680.0110.0110.0000.0000.0000.000
34A37TYR00.0840.03622.8540.0190.0190.0000.0000.0000.000
35A38GLY0-0.024-0.02524.8270.0120.0120.0000.0000.0000.000
36A39LYS10.9530.97728.0810.1860.1860.0000.0000.0000.000
37A40VAL00.0630.05828.995-0.010-0.0100.0000.0000.0000.000
38A41ASP-1-0.781-0.89128.066-0.121-0.1210.0000.0000.0000.000
39A42LYS10.9620.97830.0380.1140.1140.0000.0000.0000.000
40A43GLY00.0270.01331.0720.0090.0090.0000.0000.0000.000
41A44THR00.004-0.03128.0440.0070.0070.0000.0000.0000.000
42A45LYS10.8100.89430.2680.1120.1120.0000.0000.0000.000
43A46ILE0-0.063-0.01833.6430.0070.0070.0000.0000.0000.000
44A47LEU0-0.002-0.00129.3200.0070.0070.0000.0000.0000.000
45A48VAL00.0180.00431.1260.0060.0060.0000.0000.0000.000
46A49GLU-1-0.852-0.91433.686-0.061-0.0610.0000.0000.0000.000
47A50ASN0-0.097-0.07136.6350.0080.0080.0000.0000.0000.000
48A51VAL00.0020.02133.1070.0050.0050.0000.0000.0000.000
49A52VAL0-0.0030.00736.082-0.002-0.0020.0000.0000.0000.000
50A53VAL0-0.031-0.02334.0390.0030.0030.0000.0000.0000.000
51A54ASP-1-0.805-0.91637.219-0.001-0.0010.0000.0000.0000.000
52A55LYS10.8920.94037.392-0.002-0.0020.0000.0000.0000.000
53A56ASP-1-0.866-0.92637.7440.0090.0090.0000.0000.0000.000
54A57ASP-1-0.840-0.90033.7370.0070.0070.0000.0000.0000.000
55A58ASP-1-0.757-0.81630.0320.0210.0210.0000.0000.0000.000
56A59ILE0-0.021-0.02928.5740.0050.0050.0000.0000.0000.000
57A60LEU0-0.001-0.00221.691-0.001-0.0010.0000.0000.0000.000
58A61ASP-1-0.826-0.91724.549-0.097-0.0970.0000.0000.0000.000
59A62LEU00.002-0.01719.547-0.008-0.0080.0000.0000.0000.000
60A63GLY0-0.0250.00818.833-0.005-0.0050.0000.0000.0000.000
61A64CYS0-0.018-0.00519.892-0.012-0.0120.0000.0000.0000.000
62A65GLY00.0230.01819.650-0.006-0.0060.0000.0000.0000.000
63A66TYR0-0.081-0.06420.5570.0000.0000.0000.0000.0000.000
64A67GLY00.0460.00622.5330.0060.0060.0000.0000.0000.000
65A68VAL0-0.049-0.00624.5430.0130.0130.0000.0000.0000.000
66A69ILE00.0380.01126.1460.0080.0080.0000.0000.0000.000
67A70GLY00.0430.00826.6580.0090.0090.0000.0000.0000.000
68A71ILE0-0.044-0.02826.4490.0060.0060.0000.0000.0000.000
69A72ALA0-0.015-0.01129.5700.0050.0050.0000.0000.0000.000
70A73LEU0-0.001-0.00330.7260.0060.0060.0000.0000.0000.000
71A74ALA00.0160.01730.3360.0070.0070.0000.0000.0000.000
72A75ASP-1-0.866-0.90932.195-0.047-0.0470.0000.0000.0000.000
73A76GLU-1-0.799-0.85635.387-0.039-0.0390.0000.0000.0000.000
74A77VAL0-0.085-0.03132.0280.0050.0050.0000.0000.0000.000
75A78LYS10.8290.92733.999-0.019-0.0190.0000.0000.0000.000
76A79SER0-0.026-0.04029.5150.0010.0010.0000.0000.0000.000
77A80THR00.0140.00926.504-0.002-0.0020.0000.0000.0000.000
78A81THR0-0.0200.01021.9690.0040.0040.0000.0000.0000.000
79A82MET0-0.0330.00821.755-0.008-0.0080.0000.0000.0000.000
80A83ALA00.0320.01217.8550.0050.0050.0000.0000.0000.000
81A84ASP-1-0.795-0.89815.832-0.272-0.2720.0000.0000.0000.000
82A85ILE00.0830.05710.041-0.009-0.0090.0000.0000.0000.000
83A86ASN0-0.033-0.01711.068-0.174-0.1740.0000.0000.0000.000
84A87ARG11.0230.9896.2140.9700.9700.0000.0000.0000.000
85A88ARG10.8440.92812.6760.5420.5420.0000.0000.0000.000
86A89ALA00.0190.00415.4200.0520.0520.0000.0000.0000.000
87A90ILE00.0160.01814.5640.0380.0380.0000.0000.0000.000
88A91LYS10.8860.95116.5510.4370.4370.0000.0000.0000.000
89A92LEU0-0.012-0.01118.4460.0290.0290.0000.0000.0000.000
90A93ALA00.0580.03720.6150.0260.0260.0000.0000.0000.000
91A94LYS10.9320.96117.2560.1830.1830.0000.0000.0000.000
92A95GLU-1-0.866-0.92521.319-0.290-0.2900.0000.0000.0000.000
93A96ASN00.0170.00124.5400.0130.0130.0000.0000.0000.000
94A97ILE00.0350.03824.7680.0110.0110.0000.0000.0000.000
95A98LYS10.8550.91426.4480.1180.1180.0000.0000.0000.000
96A99LEU0-0.092-0.04128.0460.0050.0050.0000.0000.0000.000
97A100ASN0-0.039-0.03529.9500.0080.0080.0000.0000.0000.000
98A101ASN0-0.0280.00032.8790.0070.0070.0000.0000.0000.000
99A102LEU00.0420.02130.5350.0070.0070.0000.0000.0000.000
100A103ASP-1-0.832-0.92029.686-0.087-0.0870.0000.0000.0000.000
101A104ASN0-0.041-0.00831.7910.0010.0010.0000.0000.0000.000
102A105TYR00.0220.02432.1670.0050.0050.0000.0000.0000.000
103A106ASP-1-0.888-0.93628.8400.0000.0000.0000.0000.0000.000
104A107ILE00.0170.00025.689-0.001-0.0010.0000.0000.0000.000
105A108ARG10.7530.83622.610-0.052-0.0520.0000.0000.0000.000
106A109VAL0-0.020-0.01818.845-0.007-0.0070.0000.0000.0000.000
107A110VAL0-0.041-0.02816.443-0.005-0.0050.0000.0000.0000.000
108A111HIS0-0.070-0.0408.3970.0440.0440.0000.0000.0000.000
109A112SER00.020-0.02713.5260.0910.0910.0000.0000.0000.000
110A113ASP-1-0.866-0.91611.0550.0490.0490.0000.0000.0000.000
111A114LEU00.030-0.00813.0910.0430.0430.0000.0000.0000.000
112A115TYR0-0.041-0.03816.814-0.023-0.0230.0000.0000.0000.000
113A116GLU-1-0.861-0.91113.1650.3560.3560.0000.0000.0000.000
114A117ASN0-0.056-0.02814.2380.0630.0630.0000.0000.0000.000
115A118VAL0-0.023-0.00416.405-0.024-0.0240.0000.0000.0000.000
116A119LYS10.8550.91819.910-0.194-0.1940.0000.0000.0000.000
117A120ASP-1-0.783-0.84321.8310.1030.1030.0000.0000.0000.000
118A121ARG10.8990.95723.484-0.050-0.0500.0000.0000.0000.000
119A122LYS10.9630.99125.955-0.094-0.0940.0000.0000.0000.000
120A123TYR0-0.009-0.02223.295-0.013-0.0130.0000.0000.0000.000
121A124ASN0-0.0120.00529.5840.0090.0090.0000.0000.0000.000
122A125LYS10.8540.91030.984-0.001-0.0010.0000.0000.0000.000
123A126ILE00.0030.02525.3630.0000.0000.0000.0000.0000.000
124A127ILE00.000-0.00627.151-0.001-0.0010.0000.0000.0000.000
125A128THR0-0.007-0.02823.369-0.006-0.0060.0000.0000.0000.000
126A129ASN0-0.009-0.00425.1450.0120.0120.0000.0000.0000.000
127A130PRO0-0.0150.00323.077-0.014-0.0140.0000.0000.0000.000
128A131PRO00.0410.02319.139-0.010-0.0100.0000.0000.0000.000
129A132ILE00.020-0.01522.1010.0170.0170.0000.0000.0000.000
130A133ARG10.9380.95220.5280.2560.2560.0000.0000.0000.000
131A134ALA00.0080.01918.796-0.002-0.0020.0000.0000.0000.000
132A135GLY00.0690.05020.1870.0200.0200.0000.0000.0000.000
133A136LYS10.9170.92223.1300.0220.0220.0000.0000.0000.000
134A137GLU-1-0.855-0.92321.7460.0190.0190.0000.0000.0000.000
135A138VAL00.0460.02518.4520.0140.0140.0000.0000.0000.000
136A139LEU0-0.029-0.01321.0820.0040.0040.0000.0000.0000.000
137A140HIS10.8690.92624.321-0.025-0.0250.0000.0000.0000.000
138A141ARG10.8500.91115.514-0.196-0.1960.0000.0000.0000.000
139A142ILE00.0110.01020.9560.0060.0060.0000.0000.0000.000
140A143ILE0-0.028-0.01423.4800.0010.0010.0000.0000.0000.000
141A144GLU-1-0.875-0.93325.8610.0920.0920.0000.0000.0000.000
142A145GLU-1-0.730-0.84120.0910.1720.1720.0000.0000.0000.000
143A146GLY00.0220.01324.6020.0010.0010.0000.0000.0000.000
144A147LYS10.8760.93226.205-0.062-0.0620.0000.0000.0000.000
145A148GLU-1-0.892-0.94624.3960.1450.1450.0000.0000.0000.000
146A149LEU0-0.024-0.00822.5440.0050.0050.0000.0000.0000.000
147A150LEU0-0.0480.00027.207-0.007-0.0070.0000.0000.0000.000
148A151LYS10.8130.90030.498-0.029-0.0290.0000.0000.0000.000
149A152ASP-1-0.833-0.92533.4450.0520.0520.0000.0000.0000.000
150A153ASN0-0.035-0.02136.748-0.007-0.0070.0000.0000.0000.000
151A154GLY00.0550.04133.756-0.006-0.0060.0000.0000.0000.000
152A155GLU-1-0.839-0.93433.494-0.001-0.0010.0000.0000.0000.000
153A156ILE0-0.0190.00026.970-0.001-0.0010.0000.0000.0000.000
154A157TRP0-0.012-0.01930.347-0.005-0.0050.0000.0000.0000.000
155A158VAL00.0170.00227.983-0.005-0.0050.0000.0000.0000.000
156A159VAL0-0.033-0.00229.2810.0020.0020.0000.0000.0000.000
157A160ILE00.0230.00229.030-0.005-0.0050.0000.0000.0000.000
158A161GLN0-0.025-0.00830.6540.0000.0000.0000.0000.0000.000
159A162THR0-0.045-0.05333.0670.0070.0070.0000.0000.0000.000
160A163LYS10.9570.98135.6720.0550.0550.0000.0000.0000.000
161A164GLN00.1110.03936.2580.0040.0040.0000.0000.0000.000
162A165GLY00.0360.03532.7670.0050.0050.0000.0000.0000.000
163A166ALA00.0660.03332.7330.0050.0050.0000.0000.0000.000
164A167LYS10.9180.95734.3500.0310.0310.0000.0000.0000.000
165A168SER0-0.067-0.02332.8730.0050.0050.0000.0000.0000.000
166A169LEU00.0470.02528.2620.0060.0060.0000.0000.0000.000
167A170ALA00.0490.02532.1580.0060.0060.0000.0000.0000.000
168A171LYS10.9240.95535.2570.0050.0050.0000.0000.0000.000
169A172TYR0-0.005-0.00628.229-0.001-0.0010.0000.0000.0000.000
170A173MET00.0080.00231.3080.0030.0030.0000.0000.0000.000
171A174LYS10.8600.92433.250-0.017-0.0170.0000.0000.0000.000
172A175ASP-1-0.885-0.93534.2620.0300.0300.0000.0000.0000.000
173A176VAL00.0080.02030.1220.0040.0040.0000.0000.0000.000
174A177PHE0-0.022-0.02430.3600.0060.0060.0000.0000.0000.000
175A178GLY00.0110.03035.3170.0000.0000.0000.0000.0000.000
176A179ASN0-0.053-0.03537.755-0.007-0.0070.0000.0000.0000.000
177A180VAL0-0.0240.00935.7730.0010.0010.0000.0000.0000.000
178A181GLU-1-0.802-0.87337.884-0.009-0.0090.0000.0000.0000.000
179A182THR0-0.066-0.04938.060-0.004-0.0040.0000.0000.0000.000
180A183VAL00.0210.01637.6980.0000.0000.0000.0000.0000.000
181A184THR00.0260.01638.179-0.002-0.0020.0000.0000.0000.000
182A185ILE0-0.021-0.02038.736-0.001-0.0010.0000.0000.0000.000
183A186LYS10.9960.99938.9140.0600.0600.0000.0000.0000.000
184A187GLY00.0410.02138.338-0.004-0.0040.0000.0000.0000.000
185A188GLY00.0130.00837.722-0.005-0.0050.0000.0000.0000.000
186A189TYR0-0.0180.00831.1540.0000.0000.0000.0000.0000.000
187A190ARG10.9470.97034.7530.0380.0380.0000.0000.0000.000
188A191VAL00.0380.03134.075-0.004-0.0040.0000.0000.0000.000
189A192LEU0-0.076-0.03332.8870.0040.0040.0000.0000.0000.000
190A193LYS10.8880.94333.6310.0040.0040.0000.0000.0000.000
191A194SER0-0.001-0.02533.5230.0000.0000.0000.0000.0000.000
192A195LYS10.8390.92034.538-0.016-0.0160.0000.0000.0000.000
193A196LYS10.8210.91231.448-0.066-0.0660.0000.0000.0000.000
194A197LEU00.0030.00835.6960.0000.0000.0000.0000.0000.000