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: YZ3R2

Calculation Name: 4UOS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4UOS

Chain ID: A

ChEMBL ID:

UniProt ID:

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2056850.019445
FMO2-HF: Nuclear repulsion 1977282.53446
FMO2-HF: Total energy -79567.484985
FMO2-MP2: Total energy -79788.986896


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.
7.53410.5720.246-1.34-1.9440.004
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 : 0.107 / q_NPA : 0.051
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].
3A2ASN00.026-0.0083.8660.6972.103-0.002-0.708-0.6960.002
4A3GLU-1-0.787-0.8632.599-0.7570.2380.245-0.492-0.7480.002
5A4GLU-1-0.844-0.9203.463-2.406-1.7690.003-0.140-0.5000.000
6A5VAL00.0190.0035.7401.1951.1950.0000.0000.0000.000
7A6LYS10.7940.8827.6931.7481.7480.0000.0000.0000.000
8A7LYS10.8600.9146.7851.6081.6080.0000.0000.0000.000
9A8MET0-0.0070.0008.8440.3800.3800.0000.0000.0000.000
10A9LEU00.0080.00211.8490.2410.2410.0000.0000.0000.000
11A10GLU-1-0.829-0.90910.374-0.828-0.8280.0000.0000.0000.000
12A11LYS10.8710.92412.2790.8480.8480.0000.0000.0000.000
13A12MET0-0.054-0.00715.5730.0690.0690.0000.0000.0000.000
14A13ILE0-0.002-0.00316.9320.0690.0690.0000.0000.0000.000
15A14GLU-1-0.802-0.88218.218-0.245-0.2450.0000.0000.0000.000
16A15GLU-1-0.823-0.89419.586-0.247-0.2470.0000.0000.0000.000
17A16ILE0-0.007-0.00921.2890.0400.0400.0000.0000.0000.000
18A17LYS10.8050.88322.6270.2640.2640.0000.0000.0000.000
19A18LYS10.9100.94422.6040.2940.2940.0000.0000.0000.000
20A19MET0-0.136-0.05625.3600.0200.0200.0000.0000.0000.000
21A20LEU00.0440.02226.7130.0210.0210.0000.0000.0000.000
22A21GLU-1-0.818-0.90126.573-0.184-0.1840.0000.0000.0000.000
23A22LYS10.8580.90727.0290.2130.2130.0000.0000.0000.000
24A23ALA0-0.016-0.00431.5410.0110.0110.0000.0000.0000.000
25A24ILE00.0310.00931.6930.0110.0110.0000.0000.0000.000
26A25LYS10.8630.91334.3400.1120.1120.0000.0000.0000.000
27A26LYS10.9110.94134.8750.1420.1420.0000.0000.0000.000
28A27VAL00.0050.00637.6200.0070.0070.0000.0000.0000.000
29A28LYS10.8660.92239.0290.0900.0900.0000.0000.0000.000
30A29GLU-1-0.820-0.89239.082-0.089-0.0890.0000.0000.0000.000
31A30MET0-0.085-0.03141.8160.0040.0040.0000.0000.0000.000
32A31LEU00.0320.01942.6010.0050.0050.0000.0000.0000.000
33A32GLU-1-0.801-0.89343.416-0.074-0.0740.0000.0000.0000.000
34A33LYS10.8750.94043.2510.0840.0840.0000.0000.0000.000
35A34MET0-0.024-0.00248.0550.0020.0020.0000.0000.0000.000
36A35ILE00.0150.00748.3150.0030.0030.0000.0000.0000.000
37A36LYS10.9530.97650.6180.0580.0580.0000.0000.0000.000
38A37GLU-1-0.864-0.94352.429-0.051-0.0510.0000.0000.0000.000
39A38ILE0-0.011-0.01153.1520.0020.0020.0000.0000.0000.000
40A39LYS10.8250.89854.9860.0460.0460.0000.0000.0000.000
41A40LYS10.9500.97656.6500.0470.0470.0000.0000.0000.000
42A41MET0-0.062-0.01256.7010.0010.0010.0000.0000.0000.000
43A42LEU00.0100.00358.7620.0010.0010.0000.0000.0000.000
44A43GLU-1-0.868-0.91959.494-0.041-0.0410.0000.0000.0000.000
45A44ASN0-0.106-0.05362.8290.0020.0020.0000.0000.0000.000
46A45GLY00.0100.01264.7240.0010.0010.0000.0000.0000.000
47A46GLU-1-0.825-0.88562.105-0.044-0.0440.0000.0000.0000.000
48A47ASP-1-0.800-0.89265.435-0.042-0.0420.0000.0000.0000.000
49A48SER00.022-0.03863.160-0.001-0.0010.0000.0000.0000.000
50A49GLU-1-0.878-0.90962.116-0.045-0.0450.0000.0000.0000.000
51A50LYS10.8220.88960.4840.0430.0430.0000.0000.0000.000
52A51ILE00.0280.00758.545-0.003-0.0030.0000.0000.0000.000
53A52LEU00.008-0.00457.643-0.003-0.0030.0000.0000.0000.000
54A53LYS10.9230.96956.8930.0510.0510.0000.0000.0000.000
55A54LYS10.8350.91752.7320.0580.0580.0000.0000.0000.000
56A55ALA00.0350.01353.385-0.003-0.0030.0000.0000.0000.000
57A56LYS10.9740.97152.0210.0560.0560.0000.0000.0000.000
58A57GLU-1-0.853-0.90551.327-0.067-0.0670.0000.0000.0000.000
59A58MET0-0.029-0.01148.527-0.003-0.0030.0000.0000.0000.000
60A59ALA00.0400.01147.542-0.004-0.0040.0000.0000.0000.000
61A60GLU-1-0.816-0.90246.569-0.092-0.0920.0000.0000.0000.000
62A61LYS10.8760.93845.4170.0690.0690.0000.0000.0000.000
63A62ILE00.0060.00142.311-0.005-0.0050.0000.0000.0000.000
64A63LEU0-0.0010.00541.670-0.007-0.0070.0000.0000.0000.000
65A64LYS10.8720.91041.1940.0850.0850.0000.0000.0000.000
66A65MET0-0.0040.03238.385-0.009-0.0090.0000.0000.0000.000
67A66VAL00.012-0.00136.994-0.009-0.0090.0000.0000.0000.000
68A67ILE0-0.007-0.00336.284-0.009-0.0090.0000.0000.0000.000
69A68GLU-1-0.848-0.93534.711-0.155-0.1550.0000.0000.0000.000
70A69LEU0-0.012-0.00332.778-0.010-0.0100.0000.0000.0000.000
71A70ALA00.0170.01031.647-0.015-0.0150.0000.0000.0000.000
72A71GLU-1-0.852-0.92531.228-0.164-0.1640.0000.0000.0000.000
73A72LYS10.7880.89129.4540.1430.1430.0000.0000.0000.000
74A73ILE00.0270.01126.615-0.021-0.0210.0000.0000.0000.000
75A74LEU00.0350.02326.153-0.027-0.0270.0000.0000.0000.000
76A75LYS10.9030.94826.3180.2260.2260.0000.0000.0000.000
77A76LYS10.8680.91521.7040.2990.2990.0000.0000.0000.000
78A77ALA00.0530.02321.953-0.040-0.0400.0000.0000.0000.000
79A78LYS10.9700.97221.4410.2340.2340.0000.0000.0000.000
80A79GLU-1-0.781-0.87221.764-0.346-0.3460.0000.0000.0000.000
81A80MET0-0.060-0.02917.386-0.037-0.0370.0000.0000.0000.000
82A81ALA00.0520.02517.094-0.077-0.0770.0000.0000.0000.000
83A82GLU-1-0.797-0.88717.809-0.514-0.5140.0000.0000.0000.000
84A83LYS10.8620.93715.1750.4390.4390.0000.0000.0000.000
85A84ILE00.0200.00612.886-0.095-0.0950.0000.0000.0000.000
86A85LEU00.0250.01313.181-0.104-0.1040.0000.0000.0000.000
87A86LYS10.8290.89312.2890.7430.7430.0000.0000.0000.000
88A87LYS10.7770.8845.8382.5302.5300.0000.0000.0000.000
89A88VAL00.012-0.00810.602-0.037-0.0370.0000.0000.0000.000
90A89LYS10.8010.89212.2420.5650.5650.0000.0000.0000.000
91A90GLU-1-0.832-0.8968.834-1.088-1.0880.0000.0000.0000.000
92A91LEU0-0.029-0.0147.311-0.006-0.0060.0000.0000.0000.000
93A92GLY00.0090.00211.4150.0730.0730.0000.0000.0000.000
94A93VAL0-0.019-0.01215.245-0.027-0.0270.0000.0000.0000.000
95A94ASP-1-0.911-0.95718.741-0.275-0.2750.0000.0000.0000.000
96A95ASN00.0600.05814.6980.0670.0670.0000.0000.0000.000
97A96GLU-1-0.744-0.87518.430-0.314-0.3140.0000.0000.0000.000
98A97GLU-1-0.873-0.93519.225-0.317-0.3170.0000.0000.0000.000
99A98VAL00.0280.01014.821-0.003-0.0030.0000.0000.0000.000
100A99LYS10.8780.94518.0540.2750.2750.0000.0000.0000.000
101A100LYS10.8990.94720.5190.2510.2510.0000.0000.0000.000
102A101MET0-0.010-0.00218.9920.0250.0250.0000.0000.0000.000
103A102LEU00.0210.01116.3530.0080.0080.0000.0000.0000.000
104A103GLU-1-0.884-0.96320.602-0.260-0.2600.0000.0000.0000.000
105A104LYS10.8340.90924.1520.2920.2920.0000.0000.0000.000
106A105MET0-0.050-0.01418.0720.0040.0040.0000.0000.0000.000
107A106ILE0-0.023-0.00722.5760.0140.0140.0000.0000.0000.000
108A107GLU-1-0.821-0.89525.230-0.181-0.1810.0000.0000.0000.000
109A108GLU-1-0.834-0.90426.161-0.202-0.2020.0000.0000.0000.000
110A109ILE0-0.020-0.00623.2020.0140.0140.0000.0000.0000.000
111A110LYS10.7750.86427.8190.2010.2010.0000.0000.0000.000
112A111LYS10.9450.97030.6830.2050.2050.0000.0000.0000.000
113A112MET0-0.045-0.02130.5930.0190.0190.0000.0000.0000.000
114A113LEU00.0120.00529.4210.0110.0110.0000.0000.0000.000
115A114GLU-1-0.833-0.91233.326-0.156-0.1560.0000.0000.0000.000
116A115LYS10.9020.96235.8970.1420.1420.0000.0000.0000.000
117A116ALA00.0240.00735.2180.0090.0090.0000.0000.0000.000
118A117ILE00.0160.01036.2570.0090.0090.0000.0000.0000.000
119A118LYS10.9510.98139.2930.1130.1130.0000.0000.0000.000
120A119LYS10.8280.87640.4980.1030.1030.0000.0000.0000.000
121A120VAL00.0280.02139.6650.0060.0060.0000.0000.0000.000
122A121LYS10.9040.94942.5400.0910.0910.0000.0000.0000.000
123A122GLU-1-0.850-0.89645.222-0.086-0.0860.0000.0000.0000.000
124A123MET00.002-0.01643.7740.0030.0030.0000.0000.0000.000
125A124LEU00.0270.02144.7240.0040.0040.0000.0000.0000.000
126A125GLU-1-0.833-0.90548.173-0.075-0.0750.0000.0000.0000.000
127A126LYS10.8330.90950.0150.0790.0790.0000.0000.0000.000
128A127MET00.0010.01549.4090.0020.0020.0000.0000.0000.000
129A128ILE0-0.023-0.01151.8650.0030.0030.0000.0000.0000.000
130A129LYS10.9240.95754.2120.0610.0610.0000.0000.0000.000
131A130GLU-1-0.786-0.86954.838-0.050-0.0500.0000.0000.0000.000
132A131ILE00.005-0.00853.2740.0020.0020.0000.0000.0000.000
133A132LYS10.7850.87057.4140.0490.0490.0000.0000.0000.000
134A133LYS10.8210.89659.6920.0500.0500.0000.0000.0000.000
135A134MET0-0.124-0.00258.2610.0000.0000.0000.0000.0000.000
136A135LEU00.0110.01460.3610.0010.0010.0000.0000.0000.000
137A136GLU-1-0.803-0.88163.619-0.044-0.0440.0000.0000.0000.000
138A137ASN0-0.061-0.04663.4920.0010.0010.0000.0000.0000.000
139A138GLY00.0400.03766.1810.0010.0010.0000.0000.0000.000
140A139GLU-1-0.760-0.86861.050-0.045-0.0450.0000.0000.0000.000
141A140ASP-1-0.764-0.88362.849-0.040-0.0400.0000.0000.0000.000
142A141SER00.0570.01161.030-0.002-0.0020.0000.0000.0000.000
143A142GLU-1-0.872-0.91758.836-0.042-0.0420.0000.0000.0000.000
144A143LYS10.8410.90957.9730.0370.0370.0000.0000.0000.000
145A144ILE00.018-0.01157.340-0.003-0.0030.0000.0000.0000.000
146A145LEU0-0.001-0.00354.910-0.003-0.0030.0000.0000.0000.000
147A146LYS10.8880.94353.4590.0470.0470.0000.0000.0000.000
148A147LYS10.8000.86352.7220.0470.0470.0000.0000.0000.000
149A148ALA00.0120.00052.170-0.003-0.0030.0000.0000.0000.000
150A149LYS10.9840.98247.7100.0570.0570.0000.0000.0000.000
151A150GLU-1-0.824-0.89947.951-0.061-0.0610.0000.0000.0000.000
152A151MET0-0.046-0.02047.726-0.004-0.0040.0000.0000.0000.000
153A152ALA00.0280.01245.865-0.004-0.0040.0000.0000.0000.000
154A153GLU-1-0.857-0.92242.910-0.087-0.0870.0000.0000.0000.000
155A154LYS10.8540.91542.6880.0620.0620.0000.0000.0000.000
156A155ILE0-0.011-0.01142.075-0.005-0.0050.0000.0000.0000.000
157A156LEU0-0.001-0.00338.271-0.007-0.0070.0000.0000.0000.000
158A157LYS10.9180.94338.1780.0760.0760.0000.0000.0000.000
159A158MET0-0.0350.01037.768-0.003-0.0030.0000.0000.0000.000
160A159VAL0-0.011-0.01434.875-0.008-0.0080.0000.0000.0000.000
161A160ILE00.0060.00333.323-0.011-0.0110.0000.0000.0000.000
162A161GLU-1-0.792-0.89732.814-0.138-0.1380.0000.0000.0000.000
163A162LEU0-0.029-0.02532.814-0.008-0.0080.0000.0000.0000.000
164A163ALA00.0140.01029.833-0.015-0.0150.0000.0000.0000.000
165A164GLU-1-0.900-0.95428.237-0.160-0.1600.0000.0000.0000.000
166A165LYS10.8120.90627.7490.1230.1230.0000.0000.0000.000
167A166ILE0-0.026-0.00925.819-0.016-0.0160.0000.0000.0000.000
168A167LEU00.0000.00623.147-0.027-0.0270.0000.0000.0000.000
169A168LYS10.8430.91422.8570.1750.1750.0000.0000.0000.000
170A169LYS10.9050.94623.3390.2280.2280.0000.0000.0000.000
171A170ALA00.011-0.00121.122-0.022-0.0220.0000.0000.0000.000
172A171LYS10.8720.91918.1740.2810.2810.0000.0000.0000.000
173A172GLU-1-0.768-0.87418.718-0.264-0.2640.0000.0000.0000.000
174A173MET0-0.087-0.02720.4250.0090.0090.0000.0000.0000.000
175A174ALA00.0810.03615.265-0.025-0.0250.0000.0000.0000.000
176A175GLU-1-0.819-0.89415.214-0.448-0.4480.0000.0000.0000.000
177A176LYS10.7920.89016.3550.3680.3680.0000.0000.0000.000
178A177ILE00.0200.00514.426-0.007-0.0070.0000.0000.0000.000
179A178LEU00.010-0.0018.667-0.016-0.0160.0000.0000.0000.000
180A179LYS10.8670.94811.8280.3230.3230.0000.0000.0000.000
181A180LYS10.8660.91213.8040.3620.3620.0000.0000.0000.000
182A181VAL00.0020.0039.4340.0120.0120.0000.0000.0000.000
183A182LYS10.9210.9598.4690.8450.8450.0000.0000.0000.000
184A183GLU-1-0.872-0.93310.599-0.288-0.2880.0000.0000.0000.000
185A184LEU0-0.0390.00011.6030.0540.0540.0000.0000.0000.000
186A185GLY0-0.0160.00410.0490.0140.0140.0000.0000.0000.000
187A186VAL00.0010.00210.6910.0490.0490.0000.0000.0000.000
188A187GLY0-0.032-0.01212.1380.0560.0560.0000.0000.0000.000