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: 98G92

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 OptH
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 -1901141.698935
FMO2-HF: Nuclear repulsion 1827977.05754
FMO2-HF: Total energy -73164.641396
FMO2-MP2: Total energy -73376.81792


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.
192.459196.5790.062-1.402-2.7770.002
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 : -1.005 / q_NPA : -1.017
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-1-0.795-0.8653.84626.51828.139-0.008-0.746-0.8670.000
4A8TYR0-0.045-0.0506.642-0.466-0.4660.0000.0000.0000.000
5A9ARG10.9320.9659.656-18.713-18.7130.0000.0000.0000.000
6A10ILE0-0.008-0.00212.9840.0760.0760.0000.0000.0000.000
7A11LEU0-0.042-0.00815.407-0.917-0.9170.0000.0000.0000.000
8A12GLY00.0530.02318.862-0.035-0.0350.0000.0000.0000.000
9A13GLU-1-0.923-0.97121.26211.48011.4800.0000.0000.0000.000
10A14SER0-0.060-0.04023.0730.1130.1130.0000.0000.0000.000
11A15MET0-0.086-0.04124.087-0.086-0.0860.0000.0000.0000.000
12A16GLN0-0.0150.00918.8060.3070.3070.0000.0000.0000.000
13A17THR00.0090.01618.1790.2150.2150.0000.0000.0000.000
14A18VAL0-0.021-0.01011.630-0.198-0.1980.0000.0000.0000.000
15A19GLU-1-0.887-0.93713.72617.68417.6840.0000.0000.0000.000
16A20ILE00.007-0.0097.5050.2330.2330.0000.0000.0000.000
17A21GLU-1-0.981-1.0048.60123.69323.6930.0000.0000.0000.000
18A22LEU0-0.034-0.0125.8292.2452.2450.0000.0000.0000.000
19A23ASP-1-0.792-0.8956.82323.38923.3890.0000.0000.0000.000
20A24PRO0-0.131-0.0677.8651.8081.8080.0000.0000.0000.000
21A25GLY0-0.028-0.0078.2810.6860.6860.0000.0000.0000.000
22A26GLU-1-0.835-0.8963.39745.60346.0170.018-0.111-0.3210.000
23A27THR0-0.034-0.0584.730-7.800-7.727-0.001-0.006-0.0660.000
24A28VAL00.0060.0045.1537.3717.454-0.001-0.002-0.0800.000
25A29ILE0-0.075-0.0417.680-4.597-4.5970.0000.0000.0000.000
26A30ALA00.0750.03110.204-0.081-0.0810.0000.0000.0000.000
27A31GLU-1-0.924-0.96513.72715.48515.4850.0000.0000.0000.000
28A32ALA0-0.020-0.02817.3220.0070.0070.0000.0000.0000.000
29A33GLY0-0.042-0.02819.586-0.507-0.5070.0000.0000.0000.000
30A34ALA00.0700.05517.347-0.443-0.4430.0000.0000.0000.000
31A35MET0-0.089-0.00516.394-0.166-0.1660.0000.0000.0000.000
32A36ASN0-0.053-0.02918.003-0.621-0.6210.0000.0000.0000.000
33A37TYR0-0.048-0.06717.147-0.959-0.9590.0000.0000.0000.000
34A38MET00.0280.00615.7790.8390.8390.0000.0000.0000.000
35A39THR0-0.035-0.01215.716-0.890-0.8900.0000.0000.0000.000
36A40GLY00.001-0.00816.3900.7710.7710.0000.0000.0000.000
37A41ASP-1-0.860-0.93415.52816.00416.0040.0000.0000.0000.000
38A42ILE0-0.0160.01911.5240.7640.7640.0000.0000.0000.000
39A43ARG10.8310.92614.172-18.490-18.4900.0000.0000.0000.000
40A44PHE00.0200.01113.9861.3511.3510.0000.0000.0000.000
41A45THR00.0050.00314.059-1.610-1.6100.0000.0000.0000.000
42A46ALA0-0.015-0.00115.5860.9600.9600.0000.0000.0000.000
43A47ARG10.9620.98414.753-19.405-19.4050.0000.0000.0000.000
44A75MET0-0.075-0.03513.557-0.192-0.1920.0000.0000.0000.000
45A76THR0-0.037-0.01614.827-1.024-1.0240.0000.0000.0000.000
46A77HIS0-0.018-0.00710.270-0.567-0.5670.0000.0000.0000.000
47A78PHE00.020-0.00310.653-2.663-2.6630.0000.0000.0000.000
48A79THR00.0890.0538.6214.2334.2330.0000.0000.0000.000
49A80ASN0-0.069-0.0369.491-4.965-4.9650.0000.0000.0000.000
50A81GLU-1-0.880-0.95611.23123.54223.5420.0000.0000.0000.000
51A82GLY0-0.055-0.00614.127-1.332-1.3320.0000.0000.0000.000
52A83GLN0-0.047-0.03814.0751.2461.2460.0000.0000.0000.000
53A84GLY0-0.038-0.02613.852-1.440-1.4400.0000.0000.0000.000
54A85LYS11.0431.03211.645-16.342-16.3420.0000.0000.0000.000
55A86GLN0-0.098-0.05411.264-2.639-2.6390.0000.0000.0000.000
56A87HIS00.0920.05211.1750.9040.9040.0000.0000.0000.000
57A88VAL0-0.016-0.01811.051-1.253-1.2530.0000.0000.0000.000
58A89ALA0-0.0160.01512.7531.0741.0740.0000.0000.0000.000
59A90PHE00.002-0.00211.744-0.556-0.5560.0000.0000.0000.000
60A91ALA00.0320.00216.259-0.037-0.0370.0000.0000.0000.000
61A92ALA00.0480.04118.919-0.031-0.0310.0000.0000.0000.000
62A93PRO0-0.0010.00220.942-0.509-0.5090.0000.0000.0000.000
63A94TYR0-0.048-0.05222.628-0.854-0.8540.0000.0000.0000.000
64A95PRO0-0.0010.00124.4940.3780.3780.0000.0000.0000.000
65A96GLY00.0320.01124.022-0.293-0.2930.0000.0000.0000.000
66A97SER00.0270.02920.7300.2320.2320.0000.0000.0000.000
67A98VAL00.0340.00314.5920.1380.1380.0000.0000.0000.000
68A99VAL0-0.068-0.04015.117-0.355-0.3550.0000.0000.0000.000
69A100ALA00.0130.00910.0010.6370.6370.0000.0000.0000.000
70A101VAL0-0.080-0.05111.111-1.278-1.2780.0000.0000.0000.000
71A102ASP-1-0.786-0.9097.04232.27332.2730.0000.0000.0000.000
72A103LEU0-0.051-0.0308.363-2.760-2.7600.0000.0000.0000.000
73A104ASP-1-0.924-0.9458.14023.99423.9940.0000.0000.0000.000
74A105ASP-1-0.868-0.92910.24219.61219.6120.0000.0000.0000.000
75A106VAL0-0.182-0.10712.374-2.191-2.1910.0000.0000.0000.000
76A107GLY0-0.048-0.01814.412-0.638-0.6380.0000.0000.0000.000
77A108GLY00.0060.01111.754-0.340-0.3400.0000.0000.0000.000
78A109ARG10.8280.88412.677-17.200-17.2000.0000.0000.0000.000
79A110LEU00.0040.01213.771-0.899-0.8990.0000.0000.0000.000
80A111PHE0-0.058-0.02116.1530.4080.4080.0000.0000.0000.000
81A112CYS00.021-0.00517.2760.0830.0830.0000.0000.0000.000
82A113GLN00.0120.02619.3520.2160.2160.0000.0000.0000.000
83A114LYS10.9360.95820.420-13.664-13.6640.0000.0000.0000.000
84A115ASP-1-0.899-0.95020.47012.97212.9720.0000.0000.0000.000
85A116SER0-0.039-0.01819.800-0.027-0.0270.0000.0000.0000.000
86A117PHE0-0.0340.00012.6420.6620.6620.0000.0000.0000.000
87A118LEU00.0220.01814.364-0.589-0.5890.0000.0000.0000.000
88A119CYS0-0.059-0.04011.1650.0450.0450.0000.0000.0000.000
89A120ALA0-0.017-0.0088.431-0.741-0.7410.0000.0000.0000.000
90A121ALA00.0890.0563.322-2.499-2.0270.034-0.248-0.2570.002
91A122TYR0-0.039-0.0254.074-9.160-8.8910.000-0.077-0.1920.000
92A123GLY00.0180.0313.73210.40010.9350.021-0.126-0.4290.000
93A124THR00.0560.0376.388-1.149-1.1490.0000.0000.0000.000
94A125ARG10.8490.9248.661-22.346-22.3460.0000.0000.0000.000
95A126VAL00.0450.01412.211-0.834-0.8340.0000.0000.0000.000
96A127GLY0-0.039-0.01114.988-0.729-0.7290.0000.0000.0000.000
97A128ILE00.028-0.00318.6930.1510.1510.0000.0000.0000.000
98A129ALA0-0.030-0.00221.6690.0510.0510.0000.0000.0000.000
99A142GLU-1-0.946-0.99027.03111.64211.6420.0000.0000.0000.000
100A143GLY0-0.024-0.00330.817-0.037-0.0370.0000.0000.0000.000
101A144PHE00.008-0.00825.9760.3360.3360.0000.0000.0000.000
102A145ILE00.0140.01723.2290.0140.0140.0000.0000.0000.000
103A146LEU0-0.042-0.01122.3120.1620.1620.0000.0000.0000.000
104A147GLN0-0.022-0.03617.762-0.479-0.4790.0000.0000.0000.000
105A148LYS10.8930.96616.602-17.481-17.4810.0000.0000.0000.000
106A149LEU0-0.009-0.00612.7600.4670.4670.0000.0000.0000.000
107A150GLU-1-0.878-0.96012.22819.10519.1050.0000.0000.0000.000
108A151GLY0-0.026-0.0248.3081.4101.4100.0000.0000.0000.000
109A152ASP-1-0.897-0.9484.46953.18953.388-0.001-0.009-0.1890.000
110A153GLY00.0790.0594.1421.8092.0270.000-0.037-0.1810.000
111A154LEU00.0260.0224.011-7.838-7.6020.000-0.040-0.1950.000
112A155VAL0-0.057-0.0206.0411.6331.6330.0000.0000.0000.000
113A156PHE00.0150.0037.188-2.330-2.3300.0000.0000.0000.000
114A157VAL00.0150.00512.009-0.675-0.6750.0000.0000.0000.000
115A158HIS0-0.005-0.01015.651-0.398-0.3980.0000.0000.0000.000
116A159ALA0-0.017-0.01118.867-0.332-0.3320.0000.0000.0000.000
117A160GLY00.0280.01122.041-0.242-0.2420.0000.0000.0000.000
118A161GLY0-0.067-0.05225.217-0.302-0.3020.0000.0000.0000.000
119A162THR0-0.026-0.01926.3230.0670.0670.0000.0000.0000.000
120A163LEU00.0750.04520.180-0.003-0.0030.0000.0000.0000.000
121A164ILE0-0.053-0.04524.144-0.396-0.3960.0000.0000.0000.000
122A165ARG10.9641.00517.346-14.407-14.4070.0000.0000.0000.000
123A166ARG10.9220.95623.475-10.365-10.3650.0000.0000.0000.000
124A167GLN00.0540.02921.5540.7190.7190.0000.0000.0000.000
125A168LEU0-0.0270.00025.395-0.432-0.4320.0000.0000.0000.000
126A169ASN00.0190.03227.1870.5950.5950.0000.0000.0000.000
127A170GLY0-0.0200.00129.802-0.362-0.3620.0000.0000.0000.000
128A171GLU-1-0.954-0.99530.8629.5029.5020.0000.0000.0000.000
129A172THR0-0.016-0.01932.1240.1910.1910.0000.0000.0000.000
130A173LEU0-0.042-0.01129.000-0.230-0.2300.0000.0000.0000.000
131A174ARG10.9370.95932.473-8.265-8.2650.0000.0000.0000.000
132A175VAL00.0150.02128.681-0.103-0.1030.0000.0000.0000.000
133A176ASP-1-0.827-0.91832.1319.3819.3810.0000.0000.0000.000
134A177THR00.0150.00530.3220.4550.4550.0000.0000.0000.000
135A178GLY00.0300.01928.5510.3790.3790.0000.0000.0000.000
136A179CYS0-0.059-0.03827.5210.2530.2530.0000.0000.0000.000
137A180LEU0-0.0260.00224.4040.1190.1190.0000.0000.0000.000
138A181VAL0-0.0020.01919.6610.0790.0790.0000.0000.0000.000
139A182ALA00.0570.01118.1510.4920.4920.0000.0000.0000.000
140A183PHE0-0.043-0.02719.994-0.756-0.7560.0000.0000.0000.000
141A184THR00.0730.05018.0500.4750.4750.0000.0000.0000.000
142A185ASP-1-0.792-0.87519.77715.21915.2190.0000.0000.0000.000
143A186GLY0-0.0050.00122.096-0.028-0.0280.0000.0000.0000.000
144A187ILE0-0.072-0.03223.365-0.579-0.5790.0000.0000.0000.000
145A188ASP-1-0.887-0.94226.54010.84010.8400.0000.0000.0000.000
146A189TYR0-0.017-0.03725.515-0.169-0.1690.0000.0000.0000.000
147A190ASP-1-0.953-0.98629.5049.0249.0240.0000.0000.0000.000
148A191VAL0-0.0030.01230.533-0.103-0.1030.0000.0000.0000.000
149A192GLN0-0.014-0.00433.257-0.433-0.4330.0000.0000.0000.000
150A193LEU0-0.009-0.02136.8350.1430.1430.0000.0000.0000.000
151A194ALA00.0030.01639.592-0.145-0.1450.0000.0000.0000.000
152A195GLY0-0.0100.00542.665-0.135-0.1350.0000.0000.0000.000
153A207LEU00.011-0.00537.4080.0040.0040.0000.0000.0000.000
154A208LEU00.0230.00834.453-0.121-0.1210.0000.0000.0000.000
155A209LEU0-0.045-0.02334.7760.1480.1480.0000.0000.0000.000
156A210THR00.0610.02029.052-0.093-0.0930.0000.0000.0000.000
157A211THR0-0.091-0.04732.397-0.141-0.1410.0000.0000.0000.000
158A212LEU00.0280.00626.9780.1760.1760.0000.0000.0000.000
159A213LYS10.9210.97030.153-9.788-9.7880.0000.0000.0000.000
160A214GLY00.0820.06128.9460.2100.2100.0000.0000.0000.000
161A215SER00.015-0.02026.275-0.357-0.3570.0000.0000.0000.000
162A216GLY00.0330.02622.8740.3400.3400.0000.0000.0000.000
163A217THR0-0.049-0.02119.507-0.328-0.3280.0000.0000.0000.000
164A218VAL0-0.014-0.01221.7580.3320.3320.0000.0000.0000.000
165A219TRP00.028-0.00716.344-0.349-0.3490.0000.0000.0000.000
166A220LEU0-0.019-0.02122.278-0.115-0.1150.0000.0000.0000.000
167A221GLN00.0760.05124.2850.4780.4780.0000.0000.0000.000
168A222SER0-0.016-0.00726.033-0.250-0.2500.0000.0000.0000.000
169A223LEU0-0.116-0.06128.264-0.498-0.4980.0000.0000.0000.000
170A224PRO00.0160.02627.1130.2590.2590.0000.0000.0000.000
171A225PHE00.0960.04026.480-0.490-0.4900.0000.0000.0000.000
172A226SER00.0310.01128.351-0.371-0.3710.0000.0000.0000.000
173A227ARG10.8930.95030.991-9.645-9.6450.0000.0000.0000.000
174A228LEU00.0120.01030.609-0.375-0.3750.0000.0000.0000.000
175A229ALA00.0440.02031.867-0.322-0.3220.0000.0000.0000.000
176A230GLY00.0250.01233.717-0.273-0.2730.0000.0000.0000.000
177A231ARG10.9480.96436.316-8.070-8.0700.0000.0000.0000.000
178A232ILE0-0.0110.00635.035-0.282-0.2820.0000.0000.0000.000
179A233TYR00.0150.01737.949-0.287-0.2870.0000.0000.0000.000
180A234ASP-1-0.864-0.89939.7927.5057.5050.0000.0000.0000.000
181A235ALA0-0.047-0.03541.580-0.225-0.2250.0000.0000.0000.000
182A236THR0-0.040-0.02640.992-0.178-0.1780.0000.0000.0000.000
183A237PHE0-0.035-0.03644.153-0.086-0.0860.0000.0000.0000.000
184A238ARG11.0060.99847.027-6.136-6.1360.0000.0000.0000.000
185A239ALA00.0400.02446.841-0.080-0.0800.0000.0000.0000.000
186A240ARG10.8040.89243.639-7.320-7.3200.0000.0000.0000.000
187A241GLU-1-0.966-0.98548.2776.0336.0330.0000.0000.0000.000
188A242GLU-1-0.969-0.97651.4805.9995.9990.0000.0000.0000.000
189A243VAL0-0.065-0.01351.101-0.092-0.0920.0000.0000.0000.000
190A244ARG10.9370.96852.421-6.201-6.2010.0000.0000.0000.000