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

tag_button

FMODB ID: 3922L

Calculation Name: 1Q0U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Q0U

Chain ID: A

ChEMBL ID:

UniProt ID: P83699

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2581735.527944
FMO2-HF: Nuclear repulsion 2498169.96059
FMO2-HF: Total energy -83565.567354
FMO2-MP2: Total energy -83807.689616


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:THR)


Summations of interaction energy for fragment #1(A:4:THR)
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.
-11.492-0.6866.914-6.171-11.551-0.024
Interaction energy analysis for fragmet #1(A:4:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.023
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].
3A6PHE00.0380.0102.371-2.1020.8361.422-1.596-2.7640.001
4A7THR00.0220.0183.5860.1930.4620.0010.026-0.2970.000
5A8ARG10.7800.8745.5210.8290.8290.0000.0000.0000.000
6A9PHE0-0.006-0.0036.9310.3040.3040.0000.0000.0000.000
7A10PRO00.0030.0118.169-0.197-0.1970.0000.0000.0000.000
8A11PHE0-0.011-0.0206.3420.1260.1260.0000.0000.0000.000
9A12GLN00.0530.0039.653-0.060-0.0600.0000.0000.0000.000
10A13PRO00.011-0.0108.539-0.020-0.0200.0000.0000.0000.000
11A14PHE00.0370.0147.9540.0110.0110.0000.0000.0000.000
12A15ILE00.0240.0277.5240.1360.1360.0000.0000.0000.000
13A16ILE00.0020.0033.074-0.3820.0680.050-0.083-0.4170.000
14A17GLU-1-0.778-0.8813.806-0.1050.2270.003-0.143-0.192-0.001
15A18ALA00.0110.0216.4500.3660.3660.0000.0000.0000.000
16A19ILE0-0.025-0.0152.527-0.158-0.0451.159-0.249-1.023-0.001
17A20LYS10.8140.8892.646-0.3621.3940.772-0.692-1.8360.004
18A21THR0-0.043-0.0214.222-0.589-0.4850.001-0.029-0.0760.000
19A22LEU0-0.089-0.0507.087-0.163-0.1630.0000.0000.0000.000
20A23ARG10.9010.9636.265-1.033-1.0330.0000.0000.0000.000
21A24PHE0-0.016-0.0014.381-0.1030.021-0.001-0.020-0.1040.000
22A25TYR00.0650.0402.482-5.334-2.0741.975-1.893-3.342-0.009
23A26LYS10.8370.8842.569-2.256-0.8571.533-1.490-1.442-0.018
24A27PRO0-0.0180.0115.304-0.0030.058-0.001-0.002-0.0580.000
25A28THR00.005-0.0087.8130.1100.1100.0000.0000.0000.000
26A29GLU-1-0.770-0.87611.1270.0180.0180.0000.0000.0000.000
27A30ILE00.0150.01014.124-0.042-0.0420.0000.0000.0000.000
28A31GLN0-0.019-0.0039.071-0.019-0.0190.0000.0000.0000.000
29A32GLU-1-0.746-0.8599.970-0.089-0.0890.0000.0000.0000.000
30A33ARG10.7960.88212.410-0.073-0.0730.0000.0000.0000.000
31A34ILE00.0150.01714.6590.0040.0040.0000.0000.0000.000
32A35ILE00.0060.0069.563-0.007-0.0070.0000.0000.0000.000
33A36PRO0-0.009-0.01212.544-0.018-0.0180.0000.0000.0000.000
34A37GLY00.0270.02414.7130.0020.0020.0000.0000.0000.000
35A38ALA00.0470.00315.6320.0050.0050.0000.0000.0000.000
36A39LEU0-0.018-0.00911.5690.0040.0040.0000.0000.0000.000
37A40ARG10.8320.91916.1910.1940.1940.0000.0000.0000.000
38A41GLY0-0.010-0.00219.4640.0070.0070.0000.0000.0000.000
39A42GLU-1-0.773-0.84920.962-0.113-0.1130.0000.0000.0000.000
40A43SER00.0780.04321.862-0.003-0.0030.0000.0000.0000.000
41A44MET0-0.086-0.03418.676-0.006-0.0060.0000.0000.0000.000
42A45VAL00.0100.00723.2750.0070.0070.0000.0000.0000.000
43A46GLY00.0210.00921.0410.0000.0000.0000.0000.0000.000
44A47GLN0-0.020-0.01822.0370.0130.0130.0000.0000.0000.000
45A48SER00.006-0.02518.9200.0070.0070.0000.0000.0000.000
46A49GLN0-0.0030.00920.716-0.011-0.0110.0000.0000.0000.000
47A50THR0-0.003-0.02119.8450.0060.0060.0000.0000.0000.000
48A51GLY00.0480.01717.4160.0170.0170.0000.0000.0000.000
49A52THR00.0060.00013.621-0.014-0.0140.0000.0000.0000.000
50A53GLY00.0250.01511.574-0.011-0.0110.0000.0000.0000.000
51A54LYS10.8460.91212.622-0.117-0.1170.0000.0000.0000.000
52A55THR00.0050.00615.228-0.019-0.0190.0000.0000.0000.000
53A56HIS10.8070.87510.199-0.174-0.1740.0000.0000.0000.000
54A57ALA0-0.0020.00911.970-0.058-0.0580.0000.0000.0000.000
55A58TYR00.015-0.01613.409-0.037-0.0370.0000.0000.0000.000
56A59LEU0-0.014-0.01313.821-0.022-0.0220.0000.0000.0000.000
57A60LEU0-0.058-0.0157.755-0.001-0.0010.0000.0000.0000.000
58A61PRO00.009-0.00211.594-0.039-0.0390.0000.0000.0000.000
59A62ILE00.0130.01213.6900.0010.0010.0000.0000.0000.000
60A63MET0-0.021-0.02113.0860.0060.0060.0000.0000.0000.000
61A64GLU-1-0.819-0.88611.791-0.438-0.4380.0000.0000.0000.000
62A65LYS10.8650.94414.3780.1770.1770.0000.0000.0000.000
63A66ILE0-0.049-0.01517.6790.0210.0210.0000.0000.0000.000
64A67LYS10.8660.93319.2650.1080.1080.0000.0000.0000.000
65A68PRO00.0050.00919.3330.0130.0130.0000.0000.0000.000
66A69GLU-1-0.857-0.93422.212-0.119-0.1190.0000.0000.0000.000
67A70ARG10.8440.91725.2760.0840.0840.0000.0000.0000.000
68A71ALA0-0.011-0.00726.2100.0010.0010.0000.0000.0000.000
69A72GLU-1-0.833-0.90827.106-0.056-0.0560.0000.0000.0000.000
70A73VAL00.0070.01026.325-0.005-0.0050.0000.0000.0000.000
71A74GLN0-0.018-0.00723.106-0.016-0.0160.0000.0000.0000.000
72A75ALA0-0.017-0.00921.542-0.006-0.0060.0000.0000.0000.000
73A76VAL00.0260.01523.5450.0080.0080.0000.0000.0000.000
74A77ILE0-0.015-0.01519.887-0.002-0.0020.0000.0000.0000.000
75A78THR0-0.007-0.01224.2010.0060.0060.0000.0000.0000.000
76A79ALA00.0280.00624.4730.0020.0020.0000.0000.0000.000
77A80PRO00.0230.01726.515-0.002-0.0020.0000.0000.0000.000
78A81THR00.0430.00928.1050.0000.0000.0000.0000.0000.000
79A82ARG10.9170.93427.686-0.046-0.0460.0000.0000.0000.000
80A83GLU-1-0.936-0.94125.4840.0940.0940.0000.0000.0000.000
81A84LEU00.0360.01723.1400.0080.0080.0000.0000.0000.000
82A85ALA00.0570.02822.6070.0040.0040.0000.0000.0000.000
83A86THR0-0.019-0.02923.170-0.003-0.0030.0000.0000.0000.000
84A87GLN00.0190.01919.6580.0170.0170.0000.0000.0000.000
85A88ILE00.0380.01818.4710.0140.0140.0000.0000.0000.000
86A89TYR00.0150.00518.391-0.004-0.0040.0000.0000.0000.000
87A90HIS0-0.018-0.02418.321-0.007-0.0070.0000.0000.0000.000
88A91GLU-1-0.826-0.89013.4690.2880.2880.0000.0000.0000.000
89A92THR00.004-0.00813.863-0.006-0.0060.0000.0000.0000.000
90A93LEU00.0090.00815.174-0.009-0.0090.0000.0000.0000.000
91A94LYS10.7700.86712.162-0.288-0.2880.0000.0000.0000.000
92A95ILE0-0.015-0.00510.2700.0480.0480.0000.0000.0000.000
93A96THR00.0550.01012.159-0.017-0.0170.0000.0000.0000.000
94A97LYS10.9020.96313.359-0.221-0.2210.0000.0000.0000.000
95A98PHE0-0.014-0.01710.7180.0300.0300.0000.0000.0000.000
96A99CYS0-0.0380.01013.187-0.036-0.0360.0000.0000.0000.000
97A100PRO00.009-0.00414.6530.0160.0160.0000.0000.0000.000
98A101LYS10.9510.97217.4580.0470.0470.0000.0000.0000.000
99A102ASP-1-0.875-0.93520.781-0.091-0.0910.0000.0000.0000.000
100A103ARG10.8460.91216.2190.2120.2120.0000.0000.0000.000
101A104MET0-0.0250.01017.873-0.004-0.0040.0000.0000.0000.000
102A105ILE00.0220.00316.082-0.001-0.0010.0000.0000.0000.000
103A106VAL0-0.029-0.01919.7170.0170.0170.0000.0000.0000.000
104A107ALA00.0290.01220.094-0.004-0.0040.0000.0000.0000.000
105A108ARG10.8450.92022.134-0.003-0.0030.0000.0000.0000.000
106A109CYS0-0.040-0.00724.281-0.003-0.0030.0000.0000.0000.000
107A110LEU0-0.037-0.00426.0690.0000.0000.0000.0000.0000.000
108A111ILE00.015-0.00627.9520.0000.0000.0000.0000.0000.000
109A112GLY00.0150.01531.1810.0020.0020.0000.0000.0000.000
110A113GLY0-0.041-0.02433.8280.0050.0050.0000.0000.0000.000
111A114THR00.028-0.00136.273-0.003-0.0030.0000.0000.0000.000
112A115ASP-1-0.791-0.89338.9670.0210.0210.0000.0000.0000.000
113A116LYS10.9750.98240.864-0.024-0.0240.0000.0000.0000.000
114A117GLN00.0400.03234.620-0.002-0.0020.0000.0000.0000.000
115A118LYS10.8520.91236.196-0.022-0.0220.0000.0000.0000.000
116A119ALA0-0.0100.00037.675-0.002-0.0020.0000.0000.0000.000
117A120LEU0-0.0150.00035.378-0.002-0.0020.0000.0000.0000.000
118A121GLU-1-0.752-0.85132.3000.0230.0230.0000.0000.0000.000
119A122LYS10.8750.93334.194-0.009-0.0090.0000.0000.0000.000
120A123LEU00.0210.00030.1040.0030.0030.0000.0000.0000.000
121A124ASN0-0.013-0.00231.9210.0000.0000.0000.0000.0000.000
122A125VAL00.0280.01828.709-0.002-0.0020.0000.0000.0000.000
123A126GLN00.0310.00929.9220.0040.0040.0000.0000.0000.000
124A127PRO0-0.033-0.01225.331-0.004-0.0040.0000.0000.0000.000
125A128HIS00.0750.05321.8080.0040.0040.0000.0000.0000.000
126A129ILE0-0.010-0.00418.139-0.005-0.0050.0000.0000.0000.000
127A130VAL00.0070.00522.5480.0100.0100.0000.0000.0000.000
128A131ILE00.0100.00720.457-0.001-0.0010.0000.0000.0000.000
129A132GLY00.0530.00524.7750.0020.0020.0000.0000.0000.000
130A133THR00.0030.01527.6920.0000.0000.0000.0000.0000.000
131A134PRO00.0530.02530.065-0.003-0.0030.0000.0000.0000.000
132A135GLY00.0660.03931.900-0.003-0.0030.0000.0000.0000.000
133A136ARG10.7220.84932.569-0.016-0.0160.0000.0000.0000.000
134A137ILE00.0410.01027.952-0.002-0.0020.0000.0000.0000.000
135A138ASN0-0.020-0.02532.522-0.006-0.0060.0000.0000.0000.000
136A139ASP-1-0.797-0.86935.9630.0080.0080.0000.0000.0000.000
137A140PHE0-0.024-0.01733.414-0.001-0.0010.0000.0000.0000.000
138A141ILE00.0020.01033.462-0.002-0.0020.0000.0000.0000.000
139A142ARG10.8420.90736.915-0.005-0.0050.0000.0000.0000.000
140A143GLU-1-0.882-0.94438.5830.0050.0050.0000.0000.0000.000
141A144GLN0-0.048-0.01939.3750.0000.0000.0000.0000.0000.000
142A145ALA0-0.0010.01136.320-0.002-0.0020.0000.0000.0000.000
143A146LEU0-0.063-0.02930.0810.0000.0000.0000.0000.0000.000
144A147ASP-1-0.791-0.89033.183-0.032-0.0320.0000.0000.0000.000
145A148VAL0-0.037-0.04230.3510.0000.0000.0000.0000.0000.000
146A149HIS0-0.049-0.03630.976-0.006-0.0060.0000.0000.0000.000
147A150THR0-0.041-0.02429.215-0.002-0.0020.0000.0000.0000.000
148A151ALA0-0.081-0.02726.711-0.008-0.0080.0000.0000.0000.000
149A152HIS00.0210.00825.5280.0020.0020.0000.0000.0000.000
150A153ILE0-0.024-0.00820.167-0.004-0.0040.0000.0000.0000.000
151A154LEU00.0120.01024.1630.0070.0070.0000.0000.0000.000
152A155VAL0-0.035-0.01220.336-0.001-0.0010.0000.0000.0000.000
153A156VAL00.0050.00323.5350.0060.0060.0000.0000.0000.000
154A157ASP-1-0.735-0.83720.5520.0520.0520.0000.0000.0000.000
155A158GLU-1-0.783-0.89522.2830.0820.0820.0000.0000.0000.000
156A159ALA00.030-0.00125.612-0.001-0.0010.0000.0000.0000.000
157A160ASP-1-0.776-0.86428.2210.0440.0440.0000.0000.0000.000
158A161LEU00.0360.01628.561-0.001-0.0010.0000.0000.0000.000
159A162MET0-0.096-0.03327.404-0.003-0.0030.0000.0000.0000.000
160A163LEU00.001-0.01231.438-0.004-0.0040.0000.0000.0000.000
161A164ASP-1-0.931-0.95534.1520.0320.0320.0000.0000.0000.000
162A165MET0-0.096-0.04233.0050.0010.0010.0000.0000.0000.000
163A166GLY0-0.0020.00535.877-0.001-0.0010.0000.0000.0000.000
164A167PHE0-0.014-0.01932.850-0.003-0.0030.0000.0000.0000.000
165A168ILE00.0400.02831.236-0.003-0.0030.0000.0000.0000.000
166A169THR00.0040.00234.583-0.004-0.0040.0000.0000.0000.000
167A170ASP-1-0.922-0.95734.7690.0080.0080.0000.0000.0000.000
168A171VAL00.024-0.00630.137-0.003-0.0030.0000.0000.0000.000
169A172ASP-1-0.823-0.87032.801-0.014-0.0140.0000.0000.0000.000
170A173GLN00.0100.00035.279-0.004-0.0040.0000.0000.0000.000
171A174ILE0-0.048-0.01230.298-0.002-0.0020.0000.0000.0000.000
172A175ALA00.0520.01431.692-0.004-0.0040.0000.0000.0000.000
173A176ALA0-0.056-0.02032.717-0.004-0.0040.0000.0000.0000.000
174A177ARG10.8370.91335.0920.0100.0100.0000.0000.0000.000
175A178MET0-0.0310.01527.4690.0010.0010.0000.0000.0000.000
176A179PRO00.0070.00730.3360.0020.0020.0000.0000.0000.000
177A180LYS10.9340.94532.2220.0350.0350.0000.0000.0000.000
178A181ASP-1-0.963-0.95730.077-0.072-0.0720.0000.0000.0000.000
179A182LEU0-0.0010.01027.537-0.005-0.0050.0000.0000.0000.000
180A183GLN0-0.020-0.01719.640-0.002-0.0020.0000.0000.0000.000
181A184MET0-0.012-0.00424.4680.0050.0050.0000.0000.0000.000
182A185LEU0-0.039-0.02719.096-0.006-0.0060.0000.0000.0000.000
183A186VAL00.0200.01222.9110.0090.0090.0000.0000.0000.000
184A187PHE0-0.022-0.01718.658-0.002-0.0020.0000.0000.0000.000
185A188SER0-0.018-0.01723.0890.0040.0040.0000.0000.0000.000
186A189ALA00.0140.01824.5450.0020.0020.0000.0000.0000.000
187A190THR0-0.058-0.03726.045-0.001-0.0010.0000.0000.0000.000
188A191ILE00.0130.00128.029-0.004-0.0040.0000.0000.0000.000
189A192PRO00.0490.03131.240-0.002-0.0020.0000.0000.0000.000
190A193GLU-1-0.790-0.89234.7420.0110.0110.0000.0000.0000.000
191A194LYS10.9560.96437.711-0.020-0.0200.0000.0000.0000.000
192A195LEU00.0230.02430.242-0.002-0.0020.0000.0000.0000.000
193A196LYS10.8550.91334.076-0.015-0.0150.0000.0000.0000.000
194A197PRO0-0.0070.00235.090-0.004-0.0040.0000.0000.0000.000
195A198PHE00.0210.00730.009-0.003-0.0030.0000.0000.0000.000
196A199LEU0-0.006-0.01129.079-0.003-0.0030.0000.0000.0000.000
197A200LYS10.8440.90332.1870.0190.0190.0000.0000.0000.000
198A201LYS10.7910.87934.6840.0080.0080.0000.0000.0000.000
199A202TYR0-0.024-0.03731.484-0.002-0.0020.0000.0000.0000.000
200A203MET0-0.044-0.00627.564-0.007-0.0070.0000.0000.0000.000
201A204GLU-1-0.794-0.86631.012-0.025-0.0250.0000.0000.0000.000
202A205ASN0-0.088-0.05128.639-0.001-0.0010.0000.0000.0000.000
203A206PRO00.0250.02926.516-0.007-0.0070.0000.0000.0000.000
204A207THR0-0.025-0.04321.4770.0080.0080.0000.0000.0000.000
205A208PHE0-0.012-0.00423.5310.0040.0040.0000.0000.0000.000
206A209VAL0-0.011-0.01019.029-0.002-0.0020.0000.0000.0000.000
207A210HIS00.0490.03122.3390.0100.0100.0000.0000.0000.000
208A211VAL0-0.028-0.01617.815-0.006-0.0060.0000.0000.0000.000
209A212LEU0-0.0290.00520.7960.0160.0160.0000.0000.0000.000