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: 76G7K

Calculation Name: 1YOX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YOX

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HXU4

Base Structure: X-ray

Registration Date: 2023-09-21

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1904506.691698
FMO2-HF: Nuclear repulsion 1831339.740363
FMO2-HF: Total energy -73166.951335
FMO2-MP2: Total energy -73378.961724


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:5:GLU)


Summations of interaction energy for fragment #1(A:5:GLU)
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.
145.014152.9561.267-4.046-5.1640.021
Interaction energy analysis for fragmet #1(A:5:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.959 / q_NPA : -1.004
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].
3A7ASP-1-0.843-0.9123.74922.41923.5940.004-0.453-0.7270.001
4A8TYR0-0.069-0.0476.582-0.463-0.4630.0000.0000.0000.000
5A9ARG10.7910.8739.807-22.248-22.2480.0000.0000.0000.000
6A10ILE0-0.002-0.00213.420-0.116-0.1160.0000.0000.0000.000
7A11LEU0-0.032-0.00615.839-1.034-1.0340.0000.0000.0000.000
8A12GLY00.0520.02619.326-0.032-0.0320.0000.0000.0000.000
9A13GLU-1-0.886-0.94621.64112.37312.3730.0000.0000.0000.000
10A14SER0-0.095-0.07024.189-0.311-0.3110.0000.0000.0000.000
11A15MET0-0.080-0.02824.652-0.312-0.3120.0000.0000.0000.000
12A16GLN0-0.037-0.01519.4990.1930.1930.0000.0000.0000.000
13A17THR00.000-0.00417.9130.2740.2740.0000.0000.0000.000
14A18VAL0-0.015-0.00811.955-0.348-0.3480.0000.0000.0000.000
15A19GLU-1-0.834-0.88413.29119.39519.3950.0000.0000.0000.000
16A20ILE00.0040.0027.5160.4940.4940.0000.0000.0000.000
17A21GLU-1-0.839-0.9118.71019.98819.9880.0000.0000.0000.000
18A22LEU00.0010.0065.9773.6293.6290.0000.0000.0000.000
19A23ASP-1-0.837-0.9396.47520.56020.5600.0000.0000.0000.000
20A24PRO0-0.110-0.0567.8652.2732.2730.0000.0000.0000.000
21A25GLY0-0.0080.0008.6980.8380.8380.0000.0000.0000.000
22A26GLU-1-0.841-0.8982.89251.04252.6090.316-0.907-0.975-0.010
23A27THR0-0.037-0.0494.599-8.653-8.560-0.001-0.017-0.0750.000
24A28VAL00.0210.0144.27812.18812.4090.000-0.018-0.2040.000
25A29ILE0-0.074-0.0386.601-6.203-6.2030.0000.0000.0000.000
26A30ALA00.0720.0309.4200.3230.3230.0000.0000.0000.000
27A31GLU-1-0.882-0.95412.64815.90915.9090.0000.0000.0000.000
28A32ALA0-0.053-0.03416.3830.1600.1600.0000.0000.0000.000
29A33GLY0-0.033-0.03218.350-1.030-1.0300.0000.0000.0000.000
30A34ALA00.0340.03216.287-0.372-0.3720.0000.0000.0000.000
31A35MET0-0.0510.01415.625-0.105-0.1050.0000.0000.0000.000
32A36ASN0-0.037-0.02017.129-0.752-0.7520.0000.0000.0000.000
33A37TYR0-0.051-0.06216.848-1.255-1.2550.0000.0000.0000.000
34A38MET00.0330.00315.4751.0911.0910.0000.0000.0000.000
35A39THR0-0.029-0.00715.415-0.929-0.9290.0000.0000.0000.000
36A40GLY0-0.010-0.01916.7720.5890.5890.0000.0000.0000.000
37A41ASP-1-0.821-0.91715.29316.87816.8780.0000.0000.0000.000
38A42ILE0-0.0480.00511.5111.0981.0980.0000.0000.0000.000
39A43ARG10.7760.89613.833-20.084-20.0840.0000.0000.0000.000
40A44PHE00.007-0.00613.5781.6471.6470.0000.0000.0000.000
41A45THR00.0020.00614.312-1.863-1.8630.0000.0000.0000.000
42A46ALA0-0.0040.00915.4771.0381.0380.0000.0000.0000.000
43A47ARG10.9090.95813.745-21.231-21.2310.0000.0000.0000.000
44A75MET0-0.049-0.00812.366-0.426-0.4260.0000.0000.0000.000
45A76THR0-0.036-0.02114.582-1.343-1.3430.0000.0000.0000.000
46A77HIS00.002-0.00210.420-0.077-0.0770.0000.0000.0000.000
47A78PHE00.0490.00210.062-3.165-3.1650.0000.0000.0000.000
48A79THR00.0450.0378.7615.7155.7150.0000.0000.0000.000
49A80ASN0-0.008-0.0079.432-5.260-5.2600.0000.0000.0000.000
50A81GLU-1-0.883-0.96511.10224.39524.3950.0000.0000.0000.000
51A82GLY0-0.0040.01513.610-1.399-1.3990.0000.0000.0000.000
52A83GLN0-0.061-0.04213.8610.8850.8850.0000.0000.0000.000
53A84GLY0-0.024-0.02513.451-1.216-1.2160.0000.0000.0000.000
54A85LYS10.9921.02110.791-17.945-17.9450.0000.0000.0000.000
55A86GLN0-0.064-0.00810.944-3.012-3.0120.0000.0000.0000.000
56A87HIS00.020-0.00510.9931.3951.3950.0000.0000.0000.000
57A88VAL0-0.006-0.01510.712-1.366-1.3660.0000.0000.0000.000
58A89ALA0-0.0180.02812.7361.2461.2460.0000.0000.0000.000
59A90PHE00.002-0.00310.820-0.515-0.5150.0000.0000.0000.000
60A91ALA00.0380.00915.6050.0510.0510.0000.0000.0000.000
61A92ALA00.0570.04018.5450.0280.0280.0000.0000.0000.000
62A93PRO0-0.014-0.00320.378-0.619-0.6190.0000.0000.0000.000
63A94TYR0-0.088-0.07522.085-0.956-0.9560.0000.0000.0000.000
64A95PRO00.0080.01224.4230.4000.4000.0000.0000.0000.000
65A96GLY00.0330.00424.308-0.354-0.3540.0000.0000.0000.000
66A97SER00.0060.01621.4680.1200.1200.0000.0000.0000.000
67A98VAL00.017-0.00315.1470.1110.1110.0000.0000.0000.000
68A99VAL0-0.051-0.02915.433-0.384-0.3840.0000.0000.0000.000
69A100ALA00.0400.02810.6590.8300.8300.0000.0000.0000.000
70A101VAL0-0.069-0.04611.097-2.125-2.1250.0000.0000.0000.000
71A102ASP-1-0.793-0.8936.32236.72836.7280.0000.0000.0000.000
72A103LEU0-0.030-0.0178.351-3.513-3.5130.0000.0000.0000.000
73A104ASP-1-0.917-0.9508.36320.78820.7880.0000.0000.0000.000
74A105ASP-1-0.945-0.96810.25419.10119.1010.0000.0000.0000.000
75A106VAL0-0.156-0.07712.771-1.978-1.9780.0000.0000.0000.000
76A107GLY0-0.030-0.00714.058-0.577-0.5770.0000.0000.0000.000
77A108GLY00.0210.01611.782-0.594-0.5940.0000.0000.0000.000
78A109ARG10.7470.84712.866-17.154-17.1540.0000.0000.0000.000
79A110LEU00.0120.01514.076-0.928-0.9280.0000.0000.0000.000
80A111PHE0-0.034-0.01315.9970.4520.4520.0000.0000.0000.000
81A112CYS0-0.010-0.02017.5890.1920.1920.0000.0000.0000.000
82A113GLN00.0100.03019.6360.0570.0570.0000.0000.0000.000
83A114LYS10.8460.90220.138-12.982-12.9820.0000.0000.0000.000
84A115ASP-1-0.882-0.94719.79213.77813.7780.0000.0000.0000.000
85A116SER0-0.0160.00219.773-0.188-0.1880.0000.0000.0000.000
86A117PHE0-0.012-0.00111.3180.4760.4760.0000.0000.0000.000
87A118LEU0-0.0070.01114.124-1.060-1.0600.0000.0000.0000.000
88A119CYS0-0.055-0.0299.969-0.004-0.0040.0000.0000.0000.000
89A120ALA0-0.014-0.0077.805-1.447-1.4470.0000.0000.0000.000
90A121ALA00.1040.0642.556-5.583-3.2750.882-1.549-1.6400.021
91A122TYR0-0.0030.0023.163-22.311-20.6160.054-0.861-0.8890.008
92A123GLY00.0170.0144.2586.9387.1850.000-0.031-0.2160.000
93A124THR0-0.047-0.0226.308-6.654-6.6540.0000.0000.0000.000
94A125ARG10.8560.9268.344-22.414-22.4140.0000.0000.0000.000
95A126VAL00.0550.01711.869-0.643-0.6430.0000.0000.0000.000
96A127GLY0-0.014-0.00214.411-1.021-1.0210.0000.0000.0000.000
97A128ILE0-0.002-0.01118.1980.1840.1840.0000.0000.0000.000
98A129ALA00.0170.01021.2460.1050.1050.0000.0000.0000.000
99A142GLU-1-0.856-0.92826.11612.55012.5500.0000.0000.0000.000
100A143GLY00.0080.01029.794-0.198-0.1980.0000.0000.0000.000
101A144PHE0-0.006-0.01025.5040.3850.3850.0000.0000.0000.000
102A145ILE0-0.0070.00022.800-0.117-0.1170.0000.0000.0000.000
103A146LEU0-0.0150.01022.2770.3050.3050.0000.0000.0000.000
104A147GLN0-0.022-0.02517.392-0.224-0.2240.0000.0000.0000.000
105A148LYS10.8200.90816.740-19.056-19.0560.0000.0000.0000.000
106A149LEU0-0.0170.00112.5120.2930.2930.0000.0000.0000.000
107A150GLU-1-0.785-0.89412.66718.37618.3760.0000.0000.0000.000
108A151GLY0-0.017-0.0169.5861.4331.4330.0000.0000.0000.000
109A152ASP-1-0.904-0.9566.05439.36639.3660.0000.0000.0000.000
110A153GLY00.0680.0514.1962.5912.7500.000-0.038-0.1210.000
111A154LEU00.0180.0013.900-8.214-7.7370.012-0.172-0.3170.001
112A155VAL0-0.044-0.0216.0502.6622.6620.0000.0000.0000.000
113A156PHE00.0160.0017.210-2.751-2.7510.0000.0000.0000.000
114A157VAL0-0.006-0.00612.056-0.577-0.5770.0000.0000.0000.000
115A158HIS00.007-0.01115.759-0.313-0.3130.0000.0000.0000.000
116A159ALA0-0.017-0.01119.160-0.379-0.3790.0000.0000.0000.000
117A160GLY00.0260.01822.522-0.190-0.1900.0000.0000.0000.000
118A161GLY0-0.044-0.04225.655-0.416-0.4160.0000.0000.0000.000
119A162THR0-0.034-0.01926.2400.1750.1750.0000.0000.0000.000
120A163LEU00.0790.04720.572-0.116-0.1160.0000.0000.0000.000
121A164ILE0-0.047-0.03124.513-0.464-0.4640.0000.0000.0000.000
122A165ARG10.8790.95317.821-14.864-14.8640.0000.0000.0000.000
123A166ARG10.7990.87823.993-10.862-10.8620.0000.0000.0000.000
124A167GLN00.0610.05221.9440.7920.7920.0000.0000.0000.000
125A168LEU0-0.028-0.01125.766-0.435-0.4350.0000.0000.0000.000
126A169ASN00.009-0.00527.4780.4400.4400.0000.0000.0000.000
127A170GLY0-0.0030.01330.149-0.351-0.3510.0000.0000.0000.000
128A171GLU-1-0.824-0.89131.3439.7089.7080.0000.0000.0000.000
129A172THR0-0.027-0.03032.9380.1880.1880.0000.0000.0000.000
130A173LEU0-0.0120.00629.399-0.243-0.2430.0000.0000.0000.000
131A174ARG10.9090.94133.044-8.512-8.5120.0000.0000.0000.000
132A175VAL00.0110.01628.927-0.072-0.0720.0000.0000.0000.000
133A176ASP-1-0.794-0.88832.4199.7389.7380.0000.0000.0000.000
134A177THR00.017-0.00330.5080.4230.4230.0000.0000.0000.000
135A178GLY00.0080.00928.7950.4140.4140.0000.0000.0000.000
136A179CYS0-0.068-0.04527.8510.2840.2840.0000.0000.0000.000
137A180LEU0-0.025-0.00324.3930.1100.1100.0000.0000.0000.000
138A181VAL00.0020.01619.7280.0160.0160.0000.0000.0000.000
139A182ALA00.027-0.00618.3910.6050.6050.0000.0000.0000.000
140A183PHE0-0.049-0.03020.054-0.787-0.7870.0000.0000.0000.000
141A184THR00.0760.04617.9940.6500.6500.0000.0000.0000.000
142A185ASP-1-0.790-0.89319.56815.14915.1490.0000.0000.0000.000
143A186GLY00.0100.01021.763-0.032-0.0320.0000.0000.0000.000
144A187ILE0-0.077-0.02823.685-0.612-0.6120.0000.0000.0000.000
145A188ASP-1-0.841-0.90826.33010.95610.9560.0000.0000.0000.000
146A189TYR00.0040.00125.563-0.192-0.1920.0000.0000.0000.000
147A190ASP-1-0.859-0.93529.3438.9618.9610.0000.0000.0000.000
148A191VAL0-0.023-0.00130.5290.1480.1480.0000.0000.0000.000
149A192GLN0-0.031-0.01633.638-0.403-0.4030.0000.0000.0000.000
150A193LEU00.000-0.00836.9020.1780.1780.0000.0000.0000.000
151A194ALA00.0250.02839.579-0.177-0.1770.0000.0000.0000.000
152A195GLY0-0.042-0.02142.608-0.232-0.2320.0000.0000.0000.000
153A207LEU00.014-0.00737.1360.0000.0000.0000.0000.0000.000
154A208LEU00.0240.01833.871-0.147-0.1470.0000.0000.0000.000
155A209LEU0-0.033-0.02134.6960.1360.1360.0000.0000.0000.000
156A210THR00.0370.01629.068-0.070-0.0700.0000.0000.0000.000
157A211THR0-0.061-0.03932.564-0.192-0.1920.0000.0000.0000.000
158A212LEU00.0180.00826.9780.1490.1490.0000.0000.0000.000
159A213LYS10.8360.90830.162-10.376-10.3760.0000.0000.0000.000
160A214GLY00.0610.04529.1470.2410.2410.0000.0000.0000.000
161A215SER0-0.010-0.02926.566-0.387-0.3870.0000.0000.0000.000
162A216GLY00.0180.02223.1160.3590.3590.0000.0000.0000.000
163A217THR0-0.051-0.03419.589-0.386-0.3860.0000.0000.0000.000
164A218VAL0-0.013-0.01122.1680.2600.2600.0000.0000.0000.000
165A219TRP00.0990.03616.699-0.418-0.4180.0000.0000.0000.000
166A220LEU0-0.009-0.00322.541-0.076-0.0760.0000.0000.0000.000
167A221GLN00.0690.03524.1990.2960.2960.0000.0000.0000.000
168A222SER0-0.029-0.01026.473-0.304-0.3040.0000.0000.0000.000
169A223LEU0-0.054-0.03828.719-0.552-0.5520.0000.0000.0000.000
170A224PRO00.0450.03826.9840.2430.2430.0000.0000.0000.000
171A225PHE00.0590.02825.876-0.536-0.5360.0000.0000.0000.000
172A226SER00.0350.01727.897-0.422-0.4220.0000.0000.0000.000
173A227ARG10.8370.92030.518-10.126-10.1260.0000.0000.0000.000
174A228LEU00.0050.00630.599-0.408-0.4080.0000.0000.0000.000
175A229ALA00.0360.00831.163-0.343-0.3430.0000.0000.0000.000
176A230GLY00.0260.01433.114-0.299-0.2990.0000.0000.0000.000
177A231ARG10.8840.91935.911-8.274-8.2740.0000.0000.0000.000
178A232ILE00.0190.02434.894-0.293-0.2930.0000.0000.0000.000
179A233TYR00.0250.01637.363-0.321-0.3210.0000.0000.0000.000
180A234ASP-1-0.860-0.91439.1197.7317.7310.0000.0000.0000.000
181A235ALA0-0.044-0.02540.889-0.233-0.2330.0000.0000.0000.000
182A236THR0-0.031-0.02140.516-0.195-0.1950.0000.0000.0000.000
183A237PHE0-0.029-0.01043.246-0.085-0.0850.0000.0000.0000.000
184A238ARG10.9870.98146.036-6.227-6.2270.0000.0000.0000.000
185A239ALA00.0360.01845.605-0.109-0.1090.0000.0000.0000.000
186A240ARG10.8110.90742.448-7.522-7.5220.0000.0000.0000.000
187A241GLU-1-0.934-0.96747.6476.1726.1720.0000.0000.0000.000
188A242GLU-1-0.969-0.97850.8236.2186.2180.0000.0000.0000.000
189A243VAL0-0.0170.00349.981-0.100-0.1000.0000.0000.0000.000
190A244ARG10.8930.95152.045-6.317-6.3170.0000.0000.0000.000