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: MN3YZ

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 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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1902769.580168
FMO2-HF: Nuclear repulsion 1829603.495977
FMO2-HF: Total energy -73166.08419
FMO2-MP2: Total energy -73378.166475


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.
166.406173.3790.658-3.424-4.2070.024
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 : -0.976 / q_NPA : -1.007
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-1-0.845-0.9023.73324.00825.589-0.002-0.745-0.8350.002
4A8TYR0-0.054-0.0506.710-0.699-0.6990.0000.0000.0000.000
5A9ARG10.8070.90510.070-21.042-21.0420.0000.0000.0000.000
6A10ILE0-0.008-0.00413.5350.2000.2000.0000.0000.0000.000
7A11LEU0-0.031-0.00315.981-1.063-1.0630.0000.0000.0000.000
8A12GLY00.0550.02419.337-0.011-0.0110.0000.0000.0000.000
9A13GLU-1-0.916-0.95921.92712.04412.0440.0000.0000.0000.000
10A14SER0-0.056-0.03923.6920.1050.1050.0000.0000.0000.000
11A15MET0-0.088-0.04724.271-0.072-0.0720.0000.0000.0000.000
12A16GLN0-0.021-0.00719.0870.3660.3660.0000.0000.0000.000
13A17THR0-0.0050.00318.1470.2480.2480.0000.0000.0000.000
14A18VAL0-0.020-0.00711.921-0.182-0.1820.0000.0000.0000.000
15A19GLU-1-0.855-0.91713.21318.41618.4160.0000.0000.0000.000
16A20ILE00.000-0.0107.1860.3720.3720.0000.0000.0000.000
17A21GLU-1-0.820-0.9228.49920.19320.1930.0000.0000.0000.000
18A22LEU0-0.034-0.0065.8322.8582.8580.0000.0000.0000.000
19A23ASP-1-0.815-0.9256.54221.33321.3330.0000.0000.0000.000
20A24PRO0-0.108-0.0447.7922.0722.0720.0000.0000.0000.000
21A25GLY0-0.033-0.0108.0610.5350.5350.0000.0000.0000.000
22A26GLU-1-0.849-0.9093.51148.53149.4230.071-0.395-0.568-0.002
23A27THR0-0.034-0.0484.806-7.767-7.704-0.001-0.005-0.0560.000
24A28VAL00.0140.0044.5659.8049.971-0.001-0.006-0.1600.000
25A29ILE0-0.074-0.0416.870-5.890-5.8900.0000.0000.0000.000
26A30ALA00.0760.0339.4200.1170.1170.0000.0000.0000.000
27A31GLU-1-0.929-0.96512.79215.98515.9850.0000.0000.0000.000
28A32ALA0-0.027-0.03316.4280.0380.0380.0000.0000.0000.000
29A33GLY0-0.035-0.02318.790-0.539-0.5390.0000.0000.0000.000
30A34ALA00.0710.05316.412-0.495-0.4950.0000.0000.0000.000
31A35MET0-0.0710.00215.934-0.177-0.1770.0000.0000.0000.000
32A36ASN0-0.057-0.03317.467-0.686-0.6860.0000.0000.0000.000
33A37TYR0-0.018-0.04216.764-1.070-1.0700.0000.0000.0000.000
34A38MET00.026-0.00215.6590.9690.9690.0000.0000.0000.000
35A39THR0-0.032-0.01215.309-0.957-0.9570.0000.0000.0000.000
36A40GLY00.011-0.00216.1520.8130.8130.0000.0000.0000.000
37A41ASP-1-0.812-0.90615.62216.08716.0870.0000.0000.0000.000
38A42ILE0-0.0350.01611.5080.7890.7890.0000.0000.0000.000
39A43ARG10.7750.89614.118-18.988-18.9880.0000.0000.0000.000
40A44PHE00.0110.00413.7921.4641.4640.0000.0000.0000.000
41A45THR00.0170.00813.985-1.755-1.7550.0000.0000.0000.000
42A46ALA0-0.027-0.00515.3201.0821.0820.0000.0000.0000.000
43A47ARG10.9500.98014.092-20.526-20.5260.0000.0000.0000.000
44A75MET0-0.043-0.00712.390-0.226-0.2260.0000.0000.0000.000
45A76THR0-0.049-0.03414.188-1.271-1.2710.0000.0000.0000.000
46A77HIS0-0.036-0.0129.898-0.595-0.5950.0000.0000.0000.000
47A78PHE00.026-0.00510.132-2.968-2.9680.0000.0000.0000.000
48A79THR00.0810.0468.9945.0875.0870.0000.0000.0000.000
49A80ASN0-0.050-0.0299.465-5.008-5.0080.0000.0000.0000.000
50A81GLU-1-0.873-0.95811.17623.63023.6300.0000.0000.0000.000
51A82GLY0-0.041-0.00114.097-1.402-1.4020.0000.0000.0000.000
52A83GLN0-0.036-0.03514.0431.1261.1260.0000.0000.0000.000
53A84GLY0-0.033-0.02313.715-1.502-1.5020.0000.0000.0000.000
54A85LYS11.0371.03211.384-16.378-16.3780.0000.0000.0000.000
55A86GLN0-0.091-0.04810.995-2.595-2.5950.0000.0000.0000.000
56A87HIS00.0200.00910.8161.0051.0050.0000.0000.0000.000
57A88VAL0-0.017-0.01410.527-1.374-1.3740.0000.0000.0000.000
58A89ALA0-0.0240.01512.3871.3131.3130.0000.0000.0000.000
59A90PHE0-0.004-0.00511.225-0.607-0.6070.0000.0000.0000.000
60A91ALA00.0300.00815.952-0.046-0.0460.0000.0000.0000.000
61A92ALA00.0480.03818.867-0.038-0.0380.0000.0000.0000.000
62A93PRO0-0.007-0.00220.765-0.545-0.5450.0000.0000.0000.000
63A94TYR0-0.056-0.04722.180-0.879-0.8790.0000.0000.0000.000
64A95PRO0-0.0020.00024.6820.4110.4110.0000.0000.0000.000
65A96GLY00.0330.01024.184-0.317-0.3170.0000.0000.0000.000
66A97SER00.0480.03520.8280.2320.2320.0000.0000.0000.000
67A98VAL00.002-0.00414.7270.1260.1260.0000.0000.0000.000
68A99VAL0-0.049-0.03315.372-0.382-0.3820.0000.0000.0000.000
69A100ALA00.0240.01510.6590.7960.7960.0000.0000.0000.000
70A101VAL0-0.079-0.05611.176-1.538-1.5380.0000.0000.0000.000
71A102ASP-1-0.811-0.9036.99236.18336.1830.0000.0000.0000.000
72A103LEU0-0.019-0.0138.288-3.367-3.3670.0000.0000.0000.000
73A104ASP-1-0.919-0.9538.57522.34222.3420.0000.0000.0000.000
74A105ASP-1-0.930-0.95510.51019.44319.4430.0000.0000.0000.000
75A106VAL0-0.171-0.09612.936-2.197-2.1970.0000.0000.0000.000
76A107GLY0-0.027-0.00514.690-0.654-0.6540.0000.0000.0000.000
77A108GLY00.0120.01411.793-0.399-0.3990.0000.0000.0000.000
78A109ARG10.8110.88812.818-17.447-17.4470.0000.0000.0000.000
79A110LEU00.0110.01413.926-0.864-0.8640.0000.0000.0000.000
80A111PHE0-0.060-0.02116.1030.5480.5480.0000.0000.0000.000
81A112CYS00.008-0.01417.2880.1550.1550.0000.0000.0000.000
82A113GLN0-0.0030.01919.3850.1610.1610.0000.0000.0000.000
83A114LYS10.8850.92419.762-13.315-13.3150.0000.0000.0000.000
84A115ASP-1-0.896-0.95419.79213.51613.5160.0000.0000.0000.000
85A116SER0-0.012-0.00519.7590.0000.0000.0000.0000.0000.000
86A117PHE0-0.0370.00211.4120.6610.6610.0000.0000.0000.000
87A118LEU00.0020.01114.369-0.690-0.6900.0000.0000.0000.000
88A119CYS0-0.049-0.03410.268-0.112-0.1120.0000.0000.0000.000
89A120ALA0-0.010-0.0098.024-1.004-1.0040.0000.0000.0000.000
90A121ALA00.0720.0522.659-7.077-4.3080.551-1.807-1.5130.023
91A122TYR0-0.026-0.0163.651-13.890-13.2960.014-0.242-0.3660.001
92A123GLY00.0150.0293.7169.52910.0140.026-0.136-0.3760.000
93A124THR00.0390.0206.392-1.749-1.7490.0000.0000.0000.000
94A125ARG10.8030.8998.405-22.486-22.4860.0000.0000.0000.000
95A126VAL00.0590.02112.091-0.817-0.8170.0000.0000.0000.000
96A127GLY0-0.031-0.01514.464-0.847-0.8470.0000.0000.0000.000
97A128ILE00.011-0.00918.2220.2130.2130.0000.0000.0000.000
98A129ALA00.0060.01121.3680.0330.0330.0000.0000.0000.000
99A142GLU-1-0.897-0.96026.15512.15412.1540.0000.0000.0000.000
100A143GLY0-0.0140.00129.918-0.023-0.0230.0000.0000.0000.000
101A144PHE00.007-0.00525.9640.3650.3650.0000.0000.0000.000
102A145ILE00.0100.01122.479-0.013-0.0130.0000.0000.0000.000
103A146LEU0-0.032-0.00422.2260.1990.1990.0000.0000.0000.000
104A147GLN0-0.022-0.02917.408-0.514-0.5140.0000.0000.0000.000
105A148LYS10.8590.95316.865-18.813-18.8130.0000.0000.0000.000
106A149LEU0-0.006-0.00512.4360.4700.4700.0000.0000.0000.000
107A150GLU-1-0.849-0.94212.50818.94418.9440.0000.0000.0000.000
108A151GLY0-0.010-0.0179.1431.4221.4220.0000.0000.0000.000
109A152ASP-1-0.894-0.9485.64644.55444.5540.0000.0000.0000.000
110A153GLY00.0650.0543.9962.2242.3760.000-0.034-0.1180.000
111A154LEU00.0360.0144.096-8.161-7.8910.000-0.054-0.2150.000
112A155VAL0-0.049-0.0246.0801.8661.8660.0000.0000.0000.000
113A156PHE00.0100.0067.474-2.569-2.5690.0000.0000.0000.000
114A157VAL00.0130.00212.139-0.820-0.8200.0000.0000.0000.000
115A158HIS0-0.007-0.00815.768-0.462-0.4620.0000.0000.0000.000
116A159ALA0-0.022-0.01219.008-0.397-0.3970.0000.0000.0000.000
117A160GLY00.0410.01622.162-0.243-0.2430.0000.0000.0000.000
118A161GLY0-0.056-0.04125.358-0.317-0.3170.0000.0000.0000.000
119A162THR0-0.039-0.02326.4600.0800.0800.0000.0000.0000.000
120A163LEU00.0780.05420.486-0.037-0.0370.0000.0000.0000.000
121A164ILE0-0.044-0.04324.396-0.426-0.4260.0000.0000.0000.000
122A165ARG10.8880.96518.147-14.833-14.8330.0000.0000.0000.000
123A166ARG10.8280.89724.052-10.746-10.7460.0000.0000.0000.000
124A167GLN00.0370.03722.3540.6840.6840.0000.0000.0000.000
125A168LEU0-0.0050.00126.175-0.479-0.4790.0000.0000.0000.000
126A169ASN00.0130.03327.7930.5160.5160.0000.0000.0000.000
127A170GLY0-0.0110.00530.492-0.373-0.3730.0000.0000.0000.000
128A171GLU-1-0.855-0.92731.4179.7509.7500.0000.0000.0000.000
129A172THR0-0.010-0.02132.3780.1850.1850.0000.0000.0000.000
130A173LEU0-0.029-0.00629.220-0.213-0.2130.0000.0000.0000.000
131A174ARG10.9230.95832.457-8.424-8.4240.0000.0000.0000.000
132A175VAL00.0120.01628.651-0.090-0.0900.0000.0000.0000.000
133A176ASP-1-0.796-0.89632.1589.6839.6830.0000.0000.0000.000
134A177THR00.0300.01130.3800.4550.4550.0000.0000.0000.000
135A178GLY00.0110.00828.6080.4110.4110.0000.0000.0000.000
136A179CYS0-0.063-0.03927.6090.2720.2720.0000.0000.0000.000
137A180LEU0-0.024-0.00224.4560.1430.1430.0000.0000.0000.000
138A181VAL00.0060.02519.7040.0740.0740.0000.0000.0000.000
139A182ALA00.0450.00418.1470.5350.5350.0000.0000.0000.000
140A183PHE0-0.044-0.02819.993-0.786-0.7860.0000.0000.0000.000
141A184THR00.0730.04917.9370.5020.5020.0000.0000.0000.000
142A185ASP-1-0.790-0.88419.71215.32015.3200.0000.0000.0000.000
143A186GLY00.0020.00321.990-0.033-0.0330.0000.0000.0000.000
144A187ILE0-0.063-0.03023.339-0.568-0.5680.0000.0000.0000.000
145A188ASP-1-0.864-0.93126.46610.94010.9400.0000.0000.0000.000
146A189TYR0-0.027-0.03325.655-0.199-0.1990.0000.0000.0000.000
147A190ASP-1-0.919-0.95629.4629.1159.1150.0000.0000.0000.000
148A191VAL0-0.0030.01330.454-0.094-0.0940.0000.0000.0000.000
149A192GLN0-0.044-0.02933.258-0.437-0.4370.0000.0000.0000.000
150A193LEU0-0.006-0.01936.8370.1520.1520.0000.0000.0000.000
151A194ALA00.0250.02739.578-0.163-0.1630.0000.0000.0000.000
152A195GLY0-0.045-0.01542.701-0.266-0.2660.0000.0000.0000.000
153A207LEU00.005-0.00837.416-0.005-0.0050.0000.0000.0000.000
154A208LEU00.0310.01734.080-0.142-0.1420.0000.0000.0000.000
155A209LEU0-0.036-0.02134.7950.1540.1540.0000.0000.0000.000
156A210THR00.0480.01629.027-0.090-0.0900.0000.0000.0000.000
157A211THR0-0.039-0.03132.406-0.116-0.1160.0000.0000.0000.000
158A212LEU00.0090.00127.0400.1920.1920.0000.0000.0000.000
159A213LYS10.8830.94230.060-10.325-10.3250.0000.0000.0000.000
160A214GLY00.0750.06129.0390.2060.2060.0000.0000.0000.000
161A215SER00.006-0.02226.716-0.348-0.3480.0000.0000.0000.000
162A216GLY00.0330.02223.3780.3390.3390.0000.0000.0000.000
163A217THR0-0.050-0.03519.891-0.418-0.4180.0000.0000.0000.000
164A218VAL0-0.014-0.00921.8420.3630.3630.0000.0000.0000.000
165A219TRP00.0750.02216.726-0.487-0.4870.0000.0000.0000.000
166A220LEU0-0.012-0.01922.306-0.113-0.1130.0000.0000.0000.000
167A221GLN00.0720.04824.3470.3670.3670.0000.0000.0000.000
168A222SER0-0.049-0.02526.125-0.310-0.3100.0000.0000.0000.000
169A223LEU0-0.069-0.04528.393-0.525-0.5250.0000.0000.0000.000
170A224PRO00.0180.03027.2440.2750.2750.0000.0000.0000.000
171A225PHE00.0910.03626.251-0.521-0.5210.0000.0000.0000.000
172A226SER00.0270.01028.241-0.404-0.4040.0000.0000.0000.000
173A227ARG10.8720.93530.730-10.056-10.0560.0000.0000.0000.000
174A228LEU00.0060.01030.978-0.390-0.3900.0000.0000.0000.000
175A229ALA00.0440.01931.378-0.339-0.3390.0000.0000.0000.000
176A230GLY00.0180.00933.361-0.288-0.2880.0000.0000.0000.000
177A231ARG10.8900.92336.120-8.221-8.2210.0000.0000.0000.000
178A232ILE0-0.0010.00635.056-0.288-0.2880.0000.0000.0000.000
179A233TYR00.0190.01637.544-0.313-0.3130.0000.0000.0000.000
180A234ASP-1-0.839-0.88739.2987.6537.6530.0000.0000.0000.000
181A235ALA0-0.045-0.02741.350-0.238-0.2380.0000.0000.0000.000
182A236THR0-0.045-0.03740.806-0.168-0.1680.0000.0000.0000.000
183A237PHE0-0.051-0.03743.712-0.093-0.0930.0000.0000.0000.000
184A238ARG10.9970.99546.533-6.207-6.2070.0000.0000.0000.000
185A239ALA00.0480.02546.253-0.086-0.0860.0000.0000.0000.000
186A240ARG10.8450.92843.019-7.477-7.4770.0000.0000.0000.000
187A241GLU-1-0.968-0.98147.5006.1426.1420.0000.0000.0000.000
188A242GLU-1-0.974-0.98750.7516.1346.1340.0000.0000.0000.000
189A243VAL0-0.058-0.00950.194-0.095-0.0950.0000.0000.0000.000
190A244ARG10.9500.97751.902-6.306-6.3060.0000.0000.0000.000