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: 892MY

Calculation Name: 1YOX-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YOX

Chain ID: F

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1857679.248696
FMO2-HF: Nuclear repulsion 1785780.454561
FMO2-HF: Total energy -71898.794135
FMO2-MP2: Total energy -72107.142235


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(F:4:HIS)


Summations of interaction energy for fragment #1(F:4:HIS)
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.
-34.849-26.58125.286-12.605-20.9420.003
Interaction energy analysis for fragmet #1(F:4:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.006
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].
3F6LEU0-0.043-0.0173.2660.1182.8350.047-1.162-1.6010.001
4F7ASP-1-0.811-0.8805.369-0.534-0.492-0.001-0.002-0.0380.000
5F8TYR0-0.058-0.0488.7700.4630.4630.0000.0000.0000.000
6F9ARG10.8860.93311.301-0.338-0.3380.0000.0000.0000.000
7F10ILE0-0.0020.00014.9020.0650.0650.0000.0000.0000.000
8F11LEU0-0.028-0.00817.254-0.018-0.0180.0000.0000.0000.000
9F12GLY00.0280.00420.2140.0010.0010.0000.0000.0000.000
10F13GLU-1-0.929-0.96623.1850.0070.0070.0000.0000.0000.000
11F14SER0-0.022-0.02224.991-0.011-0.0110.0000.0000.0000.000
12F15MET0-0.065-0.03724.945-0.007-0.0070.0000.0000.0000.000
13F16GLN0-0.0170.00620.274-0.012-0.0120.0000.0000.0000.000
14F17THR0-0.0060.00317.7890.0200.0200.0000.0000.0000.000
15F18VAL00.0100.02812.204-0.031-0.0310.0000.0000.0000.000
16F19GLU-1-0.817-0.88513.9670.5410.5410.0000.0000.0000.000
17F20ILE0-0.006-0.0207.220-0.150-0.1500.0000.0000.0000.000
18F21GLU-1-0.783-0.8749.7130.6990.6990.0000.0000.0000.000
19F22LEU0-0.040-0.0235.4830.0290.0290.0000.0000.0000.000
20F23ASP-1-0.809-0.9056.6630.6140.6140.0000.0000.0000.000
21F24PRO0-0.069-0.0406.8281.0761.0760.0000.0000.0000.000
22F25GLY0-0.010-0.0065.157-0.130-0.059-0.001-0.013-0.0570.000
23F26GLU-1-0.897-0.9452.407-7.257-1.8765.685-5.047-6.019-0.032
24F27THR0-0.058-0.0511.987-16.118-20.46113.013-2.789-5.8800.038
25F28VAL0-0.0050.0033.574-0.849-0.1280.0270.000-0.7490.002
26F29ILE0-0.029-0.0186.066-0.367-0.3670.0000.0000.0000.000
27F30ALA00.0610.0268.899-0.290-0.2900.0000.0000.0000.000
28F31GLU-1-0.809-0.88812.2850.3110.3110.0000.0000.0000.000
29F32ALA0-0.007-0.01015.8800.0450.0450.0000.0000.0000.000
30F33GLY0-0.045-0.03217.991-0.058-0.0580.0000.0000.0000.000
31F34ALA00.0430.03015.878-0.025-0.0250.0000.0000.0000.000
32F35MET0-0.0600.00915.133-0.031-0.0310.0000.0000.0000.000
33F36ASN0-0.041-0.02216.818-0.067-0.0670.0000.0000.0000.000
34F37TYR0-0.053-0.07017.174-0.060-0.0600.0000.0000.0000.000
35F38MET00.018-0.00114.1910.1300.1300.0000.0000.0000.000
36F39THR0-0.0220.00315.342-0.099-0.0990.0000.0000.0000.000
37F40GLY0-0.014-0.01315.1910.1050.1050.0000.0000.0000.000
38F41ASP-1-0.873-0.93914.3490.7570.7570.0000.0000.0000.000
39F42ILE00.0340.0349.7880.1170.1170.0000.0000.0000.000
40F43ARG10.8120.89810.295-1.143-1.1430.0000.0000.0000.000
41F44PHE00.0210.00710.1170.2560.2560.0000.0000.0000.000
42F45THR0-0.017-0.01510.950-0.094-0.0940.0000.0000.0000.000
43F46ALA0-0.055-0.01713.066-0.088-0.0880.0000.0000.0000.000
44F47ARG10.9731.00511.682-0.336-0.3360.0000.0000.0000.000
45F75MET0-0.066-0.03512.5520.0530.0530.0000.0000.0000.000
46F76THR0-0.081-0.05312.974-0.060-0.0600.0000.0000.0000.000
47F77HIS00.0270.0187.434-0.004-0.0040.0000.0000.0000.000
48F78PHE00.020-0.0128.399-0.488-0.4880.0000.0000.0000.000
49F79THR00.0210.0015.2631.2011.2010.0000.0000.0000.000
50F80ASN0-0.016-0.0176.201-1.228-1.2280.0000.0000.0000.000
51F81GLU-1-0.915-0.9457.5931.0311.0310.0000.0000.0000.000
52F82GLY00.0280.0419.857-0.245-0.2450.0000.0000.0000.000
53F83GLN0-0.060-0.03611.3940.0610.0610.0000.0000.0000.000
54F84GLY0-0.019-0.01813.359-0.059-0.0590.0000.0000.0000.000
55F85LYS10.8710.90611.608-0.289-0.2890.0000.0000.0000.000
56F86GLN0-0.0140.01511.343-0.247-0.2470.0000.0000.0000.000
57F87HIS00.001-0.00811.1060.2690.2690.0000.0000.0000.000
58F88VAL0-0.010-0.00410.881-0.066-0.0660.0000.0000.0000.000
59F89ALA0-0.0160.00612.434-0.026-0.0260.0000.0000.0000.000
60F90PHE00.008-0.00310.548-0.020-0.0200.0000.0000.0000.000
61F91ALA0-0.008-0.01315.560-0.073-0.0730.0000.0000.0000.000
62F92ALA00.0370.02718.6150.0210.0210.0000.0000.0000.000
63F93PRO00.001-0.00420.431-0.004-0.0040.0000.0000.0000.000
64F94TYR0-0.066-0.04722.495-0.023-0.0230.0000.0000.0000.000
65F95PRO00.0200.00424.6490.0020.0020.0000.0000.0000.000
66F96GLY00.001-0.01025.084-0.011-0.0110.0000.0000.0000.000
67F97SER0-0.037-0.01522.5140.0100.0100.0000.0000.0000.000
68F98VAL00.0240.02215.896-0.002-0.0020.0000.0000.0000.000
69F99VAL0-0.036-0.03217.336-0.013-0.0130.0000.0000.0000.000
70F100ALA00.0170.01713.1330.0100.0100.0000.0000.0000.000
71F101VAL0-0.063-0.03813.1300.0390.0390.0000.0000.0000.000
72F102ASP-1-0.817-0.9189.970-1.701-1.7010.0000.0000.0000.000
73F103LEU0-0.044-0.0218.6960.2500.2500.0000.0000.0000.000
74F104ASP-1-0.805-0.87710.398-1.130-1.1300.0000.0000.0000.000
75F105ASP-1-0.995-0.97711.772-0.537-0.5370.0000.0000.0000.000
76F106VAL0-0.136-0.09014.1120.1360.1360.0000.0000.0000.000
77F107GLY0-0.061-0.02714.7580.0740.0740.0000.0000.0000.000
78F108GLY00.0070.00411.4080.0370.0370.0000.0000.0000.000
79F109ARG10.7270.81612.3190.4950.4950.0000.0000.0000.000
80F110LEU00.0030.00914.5650.0310.0310.0000.0000.0000.000
81F111PHE0-0.032-0.00816.0700.0230.0230.0000.0000.0000.000
82F112CYS00.0320.00316.729-0.009-0.0090.0000.0000.0000.000
83F113GLN0-0.010-0.00119.0680.0240.0240.0000.0000.0000.000
84F114LYS10.9160.94419.359-0.135-0.1350.0000.0000.0000.000
85F115ASP-1-0.931-0.97019.4550.0820.0820.0000.0000.0000.000
86F116SER0-0.016-0.00119.8370.0150.0150.0000.0000.0000.000
87F117PHE0-0.0080.01310.791-0.009-0.0090.0000.0000.0000.000
88F118LEU0-0.021-0.00114.4670.0500.0500.0000.0000.0000.000
89F119CYS0-0.053-0.03310.0820.0690.0690.0000.0000.0000.000
90F120ALA0-0.005-0.0037.796-0.248-0.2480.0000.0000.0000.000
91F121ALA00.0830.0562.9550.8121.4100.048-0.225-0.4200.001
92F122TYR0-0.025-0.0062.693-6.078-2.5631.133-1.314-3.3330.014
93F123GLY00.0500.0242.092-2.371-2.9755.338-2.033-2.700-0.021
94F124THR0-0.050-0.0284.691-0.380-0.334-0.001-0.007-0.0370.000
95F125ARG10.8870.9387.0040.7790.7790.0000.0000.0000.000
96F126VAL00.0250.01510.332-0.055-0.0550.0000.0000.0000.000
97F127GLY0-0.0040.00512.7910.0640.0640.0000.0000.0000.000
98F128ILE0-0.014-0.00916.406-0.021-0.0210.0000.0000.0000.000
99F129ALA0-0.0040.00519.923-0.017-0.0170.0000.0000.0000.000
100F144PHE0-0.022-0.01925.4940.0040.0040.0000.0000.0000.000
101F145ILE00.0100.00122.792-0.003-0.0030.0000.0000.0000.000
102F146LEU0-0.0180.00921.5120.0050.0050.0000.0000.0000.000
103F147GLN0-0.009-0.01516.9930.0180.0180.0000.0000.0000.000
104F148LYS10.8380.90716.4250.2610.2610.0000.0000.0000.000
105F149LEU00.008-0.00211.5920.0480.0480.0000.0000.0000.000
106F150GLU-1-0.818-0.88111.742-0.469-0.4690.0000.0000.0000.000
107F151GLY0-0.012-0.0157.7510.0670.0670.0000.0000.0000.000
108F152ASP-1-0.848-0.9214.791-2.774-2.703-0.001-0.002-0.0680.000
109F153GLY00.0640.0544.702-0.646-0.593-0.001-0.011-0.0400.000
110F154LEU00.003-0.0015.4361.0821.0820.0000.0000.0000.000
111F155VAL0-0.033-0.0177.4950.1770.1770.0000.0000.0000.000
112F156PHE00.005-0.0058.5300.0180.0180.0000.0000.0000.000
113F157VAL0-0.008-0.00413.1680.0780.0780.0000.0000.0000.000
114F158HIS00.0150.00916.5410.0020.0020.0000.0000.0000.000
115F159ALA0-0.062-0.03719.656-0.014-0.0140.0000.0000.0000.000
116F160GLY00.0390.01223.2140.0140.0140.0000.0000.0000.000
117F161GLY0-0.036-0.03026.161-0.014-0.0140.0000.0000.0000.000
118F162THR0-0.035-0.02327.8320.0010.0010.0000.0000.0000.000
119F163LEU00.0760.04922.508-0.001-0.0010.0000.0000.0000.000
120F164ILE0-0.037-0.04126.021-0.002-0.0020.0000.0000.0000.000
121F165ARG10.9791.00821.0650.2450.2450.0000.0000.0000.000
122F166ARG10.9060.94825.9510.1080.1080.0000.0000.0000.000
123F167GLN00.0540.01225.059-0.015-0.0150.0000.0000.0000.000
124F168LEU0-0.0290.00327.3360.0150.0150.0000.0000.0000.000
125F169ASN0-0.030-0.02228.747-0.027-0.0270.0000.0000.0000.000
126F170GLY00.0040.01031.1720.0100.0100.0000.0000.0000.000
127F171GLU-1-0.917-0.95232.964-0.112-0.1120.0000.0000.0000.000
128F172THR0-0.027-0.03233.234-0.003-0.0030.0000.0000.0000.000
129F173LEU0-0.0140.00230.5420.0050.0050.0000.0000.0000.000
130F174ARG10.9430.98133.0910.0630.0630.0000.0000.0000.000
131F175VAL0-0.001-0.00229.5260.0020.0020.0000.0000.0000.000
132F176ASP-1-0.803-0.89132.629-0.020-0.0200.0000.0000.0000.000
133F177THR00.0400.01629.6630.0000.0000.0000.0000.0000.000
134F178GLY00.0160.02528.531-0.005-0.0050.0000.0000.0000.000
135F179CYS0-0.073-0.05127.8620.0080.0080.0000.0000.0000.000
136F180LEU00.0020.00524.019-0.007-0.0070.0000.0000.0000.000
137F181VAL0-0.033-0.00220.3090.0090.0090.0000.0000.0000.000
138F182ALA00.0460.00218.676-0.001-0.0010.0000.0000.0000.000
139F183PHE0-0.041-0.02020.2910.0180.0180.0000.0000.0000.000
140F184THR00.0660.04418.627-0.009-0.0090.0000.0000.0000.000
141F185ASP-1-0.798-0.89918.864-0.315-0.3150.0000.0000.0000.000
142F186GLY0-0.029-0.00220.9700.0010.0010.0000.0000.0000.000
143F187ILE0-0.033-0.01824.5960.0150.0150.0000.0000.0000.000
144F188ASP-1-0.909-0.95326.078-0.148-0.1480.0000.0000.0000.000
145F189TYR0-0.009-0.03724.4170.0120.0120.0000.0000.0000.000
146F190ASP-1-0.907-0.94129.800-0.079-0.0790.0000.0000.0000.000
147F191VAL00.0150.00230.2360.0030.0030.0000.0000.0000.000
148F192GLN00.0140.00033.2720.0050.0050.0000.0000.0000.000
149F193LEU0-0.008-0.00236.8960.0010.0010.0000.0000.0000.000
150F194ALA0-0.0080.00739.808-0.002-0.0020.0000.0000.0000.000
151F207LEU0-0.018-0.02437.5560.0010.0010.0000.0000.0000.000
152F208LEU0-0.0030.01033.639-0.003-0.0030.0000.0000.0000.000
153F209LEU00.002-0.00634.9840.0000.0000.0000.0000.0000.000
154F210THR00.031-0.00129.129-0.001-0.0010.0000.0000.0000.000
155F211THR0-0.064-0.03232.5620.0010.0010.0000.0000.0000.000
156F212LEU00.0060.01327.769-0.004-0.0040.0000.0000.0000.000
157F213LYS10.9100.94230.6830.1200.1200.0000.0000.0000.000
158F214GLY00.0550.04228.942-0.004-0.0040.0000.0000.0000.000
159F215SER0-0.042-0.03427.6920.0140.0140.0000.0000.0000.000
160F216GLY00.0650.05724.115-0.015-0.0150.0000.0000.0000.000
161F217THR0-0.032-0.02221.5180.0230.0230.0000.0000.0000.000
162F218VAL0-0.005-0.00422.914-0.008-0.0080.0000.0000.0000.000
163F219TRP00.0160.00118.9100.0220.0220.0000.0000.0000.000
164F220LEU0-0.008-0.01523.5530.0110.0110.0000.0000.0000.000
165F221GLN00.0400.03924.9880.0050.0050.0000.0000.0000.000
166F222SER0-0.047-0.01927.2120.0040.0040.0000.0000.0000.000
167F223LEU0-0.048-0.04029.3110.0030.0030.0000.0000.0000.000
168F224PRO00.0310.03027.6420.0090.0090.0000.0000.0000.000
169F225PHE00.0640.03426.4150.0040.0040.0000.0000.0000.000
170F226SER00.0330.01028.4410.0030.0030.0000.0000.0000.000
171F227ARG10.8460.92530.7900.0080.0080.0000.0000.0000.000
172F228LEU00.0110.00230.1880.0010.0010.0000.0000.0000.000
173F229ALA00.0340.02131.4190.0010.0010.0000.0000.0000.000
174F230GLY00.0190.01733.4160.0010.0010.0000.0000.0000.000
175F231ARG10.9710.97536.303-0.021-0.0210.0000.0000.0000.000
176F232ILE0-0.0120.00134.8870.0000.0000.0000.0000.0000.000
177F233TYR00.0240.00937.477-0.001-0.0010.0000.0000.0000.000
178F234ASP-1-0.895-0.94239.2310.0280.0280.0000.0000.0000.000
179F235ALA0-0.023-0.01341.227-0.002-0.0020.0000.0000.0000.000
180F236THR0-0.092-0.04840.7410.0000.0000.0000.0000.0000.000
181F237PHE0-0.029-0.01643.5910.0020.0020.0000.0000.0000.000
182F238ARG11.0050.99246.312-0.041-0.0410.0000.0000.0000.000
183F239ALA0-0.051-0.03246.0040.0000.0000.0000.0000.0000.000
184F240ARG10.9170.96942.953-0.042-0.0420.0000.0000.0000.000
185F241GLU-1-0.996-0.96746.8390.0290.0290.0000.0000.0000.000
186F242GLU-1-1.020-1.01649.7630.0440.0440.0000.0000.0000.000