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

tag_button

FMODB ID: 3JQRL

Calculation Name: 1YOX-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YOX

Chain ID: B

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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2098972.355075
FMO2-HF: Nuclear repulsion 2022308.680233
FMO2-HF: Total energy -76663.674843
FMO2-MP2: Total energy -76885.530642


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(B:2:ALA)


Summations of interaction energy for fragment #1(B:2:ALA)
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.
-14.025-8.5974.548-5.487-4.489-0.038
Interaction energy analysis for fragmet #1(B:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.009
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].
3B4HIS0-0.019-0.0093.583-1.5140.695-0.004-1.181-1.0240.006
4B5GLU-1-0.931-0.9625.168-1.389-1.3890.0000.0000.0000.000
5B6LEU0-0.039-0.0097.4580.2940.2940.0000.0000.0000.000
6B7ASP-1-0.814-0.88811.029-0.544-0.5440.0000.0000.0000.000
7B8TYR0-0.072-0.06614.1490.0240.0240.0000.0000.0000.000
8B9ARG10.8380.89717.2180.3370.3370.0000.0000.0000.000
9B10ILE0-0.007-0.00720.153-0.010-0.0100.0000.0000.0000.000
10B11LEU0-0.042-0.01122.8410.0280.0280.0000.0000.0000.000
11B12GLY00.0570.02726.252-0.003-0.0030.0000.0000.0000.000
12B13GLU-1-0.916-0.97528.861-0.175-0.1750.0000.0000.0000.000
13B14SER0-0.035-0.02829.974-0.003-0.0030.0000.0000.0000.000
14B15MET0-0.096-0.04630.266-0.001-0.0010.0000.0000.0000.000
15B16GLN0-0.019-0.00425.670-0.010-0.0100.0000.0000.0000.000
16B17THR0-0.019-0.00924.4100.0050.0050.0000.0000.0000.000
17B18VAL00.0070.02518.2260.0120.0120.0000.0000.0000.000
18B19GLU-1-0.784-0.83820.981-0.326-0.3260.0000.0000.0000.000
19B20ILE00.004-0.00914.758-0.009-0.0090.0000.0000.0000.000
20B21GLU-1-0.805-0.88816.041-0.355-0.3550.0000.0000.0000.000
21B22LEU0-0.044-0.01913.203-0.084-0.0840.0000.0000.0000.000
22B23ASP-1-0.816-0.91213.078-0.383-0.3830.0000.0000.0000.000
23B24PRO0-0.086-0.05214.259-0.049-0.0490.0000.0000.0000.000
24B25GLY0-0.0010.00113.155-0.036-0.0360.0000.0000.0000.000
25B26GLU-1-0.832-0.9039.284-1.427-1.4270.0000.0000.0000.000
26B27THR0-0.046-0.04110.8630.2400.2400.0000.0000.0000.000
27B28VAL00.0140.01611.067-0.242-0.2420.0000.0000.0000.000
28B29ILE0-0.058-0.02811.6530.1470.1470.0000.0000.0000.000
29B30ALA00.0860.04114.5540.0030.0030.0000.0000.0000.000
30B31GLU-1-0.919-0.96618.031-0.372-0.3720.0000.0000.0000.000
31B32ALA00.025-0.01020.917-0.002-0.0020.0000.0000.0000.000
32B33GLY0-0.062-0.03723.6040.0130.0130.0000.0000.0000.000
33B34ALA00.0470.03922.1550.0150.0150.0000.0000.0000.000
34B35MET0-0.053-0.01222.7750.0030.0030.0000.0000.0000.000
35B36ASN0-0.057-0.03624.1090.0150.0150.0000.0000.0000.000
36B37TYR0-0.041-0.06124.8850.0280.0280.0000.0000.0000.000
37B38MET00.0110.00123.003-0.037-0.0370.0000.0000.0000.000
38B39THR0-0.017-0.01522.8140.0220.0220.0000.0000.0000.000
39B40GLY0-0.001-0.01324.451-0.009-0.0090.0000.0000.0000.000
40B41ASP-1-0.791-0.88521.783-0.252-0.2520.0000.0000.0000.000
41B42ILE0-0.0140.02318.936-0.026-0.0260.0000.0000.0000.000
42B43ARG10.8010.89220.1620.3410.3410.0000.0000.0000.000
43B44PHE00.0240.00519.568-0.042-0.0420.0000.0000.0000.000
44B45THR00.0070.01918.2420.0460.0460.0000.0000.0000.000
45B46ALA0-0.016-0.01019.167-0.038-0.0380.0000.0000.0000.000
46B47ARG10.8930.94813.1980.5040.5040.0000.0000.0000.000
47B75MET0-0.070-0.04214.2750.0210.0210.0000.0000.0000.000
48B76THR0-0.017-0.00617.528-0.007-0.0070.0000.0000.0000.000
49B77HIS00.0290.03012.889-0.045-0.0450.0000.0000.0000.000
50B78PHE00.013-0.01616.0910.0960.0960.0000.0000.0000.000
51B79THR00.0540.01414.358-0.080-0.0800.0000.0000.0000.000
52B80ASN0-0.033-0.01915.7590.1360.1360.0000.0000.0000.000
53B81GLU-1-0.927-0.98216.787-0.467-0.4670.0000.0000.0000.000
54B82GLY0-0.045-0.01419.2670.0470.0470.0000.0000.0000.000
55B83GLN0-0.110-0.05019.349-0.002-0.0020.0000.0000.0000.000
56B84GLY0-0.007-0.00919.9520.0040.0040.0000.0000.0000.000
57B85LYS10.8840.92417.9370.3470.3470.0000.0000.0000.000
58B86GLN0-0.0160.02618.3030.0530.0530.0000.0000.0000.000
59B87HIS00.022-0.01218.541-0.037-0.0370.0000.0000.0000.000
60B88VAL0-0.011-0.00418.4020.0390.0390.0000.0000.0000.000
61B89ALA0-0.0330.00020.310-0.028-0.0280.0000.0000.0000.000
62B90PHE00.0150.00518.1010.0110.0110.0000.0000.0000.000
63B91ALA00.0070.00322.5540.0040.0040.0000.0000.0000.000
64B92ALA00.0540.03524.671-0.002-0.0020.0000.0000.0000.000
65B93PRO0-0.021-0.01025.9020.0140.0140.0000.0000.0000.000
66B94TYR0-0.056-0.04925.7630.0240.0240.0000.0000.0000.000
67B95PRO00.0240.01229.502-0.012-0.0120.0000.0000.0000.000
68B96GLY00.009-0.01328.7630.0100.0100.0000.0000.0000.000
69B97SER00.0250.03426.182-0.005-0.0050.0000.0000.0000.000
70B98VAL00.0290.01620.302-0.004-0.0040.0000.0000.0000.000
71B99VAL0-0.060-0.03219.2100.0220.0220.0000.0000.0000.000
72B100ALA00.0210.01516.087-0.026-0.0260.0000.0000.0000.000
73B101VAL0-0.072-0.05114.1970.0690.0690.0000.0000.0000.000
74B102ASP-1-0.819-0.90610.148-0.948-0.9480.0000.0000.0000.000
75B103LEU0-0.014-0.0238.3750.1670.1670.0000.0000.0000.000
76B104ASP-1-0.847-0.9197.810-0.046-0.0460.0000.0000.0000.000
77B105ASP-1-0.989-0.97410.235-0.157-0.1570.0000.0000.0000.000
78B106VAL0-0.157-0.09112.7790.0620.0620.0000.0000.0000.000
79B107GLY0-0.023-0.00412.7310.0160.0160.0000.0000.0000.000
80B108GLY00.0350.0289.2950.1060.1060.0000.0000.0000.000
81B109ARG10.6900.80610.022-0.108-0.1080.0000.0000.0000.000
82B110LEU0-0.0060.01012.8520.0300.0300.0000.0000.0000.000
83B111PHE0-0.056-0.03115.355-0.014-0.0140.0000.0000.0000.000
84B112CYS00.0320.01617.848-0.009-0.0090.0000.0000.0000.000
85B113GLN0-0.072-0.04219.8340.0170.0170.0000.0000.0000.000
86B114LYS10.9640.96921.6250.1960.1960.0000.0000.0000.000
87B115ASP-1-0.902-0.96122.353-0.212-0.2120.0000.0000.0000.000
88B116SER0-0.036-0.00922.2790.0050.0050.0000.0000.0000.000
89B117PHE0-0.032-0.00114.437-0.026-0.0260.0000.0000.0000.000
90B118LEU00.0000.01618.4910.0230.0230.0000.0000.0000.000
91B119CYS0-0.030-0.01216.122-0.005-0.0050.0000.0000.0000.000
92B120ALA00.002-0.00111.2630.0240.0240.0000.0000.0000.000
93B121ALA00.0770.0567.9850.1020.1020.0000.0000.0000.000
94B122TYR00.0150.0157.0250.1610.1610.0000.0000.0000.000
95B123GLY00.0300.0214.908-0.899-0.8990.0000.0000.0000.000
96B124THR0-0.063-0.0365.6420.4250.4250.0000.0000.0000.000
97B125ARG10.8030.8896.4840.4040.4040.0000.0000.0000.000
98B126VAL00.0230.0099.6550.0860.0860.0000.0000.0000.000
99B127GLY0-0.0060.00113.3910.0560.0560.0000.0000.0000.000
100B128ILE0-0.046-0.03415.867-0.019-0.0190.0000.0000.0000.000
101B129ALA0-0.030-0.01319.2720.0260.0260.0000.0000.0000.000
102B130PHE00.0180.00720.5860.0250.0250.0000.0000.0000.000
103B131THR0-0.020-0.02424.227-0.021-0.0210.0000.0000.0000.000
104B132LYS10.8680.94726.9640.0590.0590.0000.0000.0000.000
105B133ARG10.9610.98130.3380.0790.0790.0000.0000.0000.000
106B134LEU00.020-0.00533.5860.0060.0060.0000.0000.0000.000
107B135GLY00.0190.03236.5790.0030.0030.0000.0000.0000.000
108B144PHE0-0.011-0.01227.314-0.001-0.0010.0000.0000.0000.000
109B145ILE00.007-0.01222.6800.0100.0100.0000.0000.0000.000
110B146LEU00.0150.02221.923-0.012-0.0120.0000.0000.0000.000
111B147GLN00.0270.00717.3740.0210.0210.0000.0000.0000.000
112B148LYS10.9050.96114.5990.0600.0600.0000.0000.0000.000
113B149LEU00.0130.00112.321-0.017-0.0170.0000.0000.0000.000
114B150GLU-1-0.750-0.8709.6590.1320.1320.0000.0000.0000.000
115B151GLY0-0.032-0.0135.658-0.199-0.1990.0000.0000.0000.000
116B152ASP-1-0.751-0.8502.301-9.230-6.0484.553-4.303-3.432-0.044
117B153GLY00.0680.0595.216-0.132-0.095-0.001-0.003-0.0330.000
118B154LEU0-0.0070.0016.8160.4710.4710.0000.0000.0000.000
119B155VAL0-0.035-0.02510.564-0.084-0.0840.0000.0000.0000.000
120B156PHE00.0150.00912.9720.1080.1080.0000.0000.0000.000
121B157VAL00.002-0.00216.6770.0170.0170.0000.0000.0000.000
122B158HIS00.0060.00319.510-0.008-0.0080.0000.0000.0000.000
123B159ALA0-0.031-0.02423.1900.0160.0160.0000.0000.0000.000
124B160GLY00.0310.00826.1300.0040.0040.0000.0000.0000.000
125B161GLY0-0.061-0.03129.5770.0110.0110.0000.0000.0000.000
126B162THR0-0.016-0.02230.839-0.005-0.0050.0000.0000.0000.000
127B163LEU00.0450.03324.2460.0050.0050.0000.0000.0000.000
128B164ILE0-0.032-0.02628.0550.0130.0130.0000.0000.0000.000
129B165ARG10.9801.00021.0810.1990.1990.0000.0000.0000.000
130B166ARG10.9250.95826.4510.0890.0890.0000.0000.0000.000
131B167GLN00.0610.04923.431-0.023-0.0230.0000.0000.0000.000
132B168LEU0-0.057-0.01426.7470.0040.0040.0000.0000.0000.000
133B169ASN0-0.035-0.04727.5410.0060.0060.0000.0000.0000.000
134B170GLY00.0210.01729.6450.0030.0030.0000.0000.0000.000
135B171GLU-1-0.877-0.91831.156-0.040-0.0400.0000.0000.0000.000
136B172THR0-0.039-0.03431.652-0.001-0.0010.0000.0000.0000.000
137B173LEU0-0.0040.00030.272-0.001-0.0010.0000.0000.0000.000
138B174ARG10.9250.96032.8060.0410.0410.0000.0000.0000.000
139B175VAL00.0210.01029.931-0.002-0.0020.0000.0000.0000.000
140B176ASP-1-0.781-0.87633.437-0.093-0.0930.0000.0000.0000.000
141B177THR00.0290.00030.490-0.005-0.0050.0000.0000.0000.000
142B178GLY00.0270.03129.750-0.008-0.0080.0000.0000.0000.000
143B179CYS0-0.088-0.05129.509-0.009-0.0090.0000.0000.0000.000
144B180LEU0-0.0190.01325.328-0.004-0.0040.0000.0000.0000.000
145B181VAL0-0.0020.01321.997-0.003-0.0030.0000.0000.0000.000
146B182ALA00.0500.01119.409-0.020-0.0200.0000.0000.0000.000
147B183PHE0-0.023-0.01520.2980.0180.0180.0000.0000.0000.000
148B184THR00.0650.04917.786-0.025-0.0250.0000.0000.0000.000
149B185ASP-1-0.778-0.88916.6410.0150.0150.0000.0000.0000.000
150B186GLY0-0.0050.00519.590-0.006-0.0060.0000.0000.0000.000
151B187ILE0-0.070-0.02522.8530.0020.0020.0000.0000.0000.000
152B188ASP-1-0.886-0.94024.491-0.003-0.0030.0000.0000.0000.000
153B189TYR0-0.020-0.03823.249-0.013-0.0130.0000.0000.0000.000
154B190ASP-1-0.887-0.93328.517-0.032-0.0320.0000.0000.0000.000
155B191VAL00.0090.02029.881-0.003-0.0030.0000.0000.0000.000
156B192GLN0-0.014-0.02132.6460.0040.0040.0000.0000.0000.000
157B193LEU00.0150.01036.473-0.005-0.0050.0000.0000.0000.000
158B194ALA0-0.034-0.00139.3810.0040.0040.0000.0000.0000.000
159B195GLY00.0020.00540.8950.0040.0040.0000.0000.0000.000
160B196GLY00.0100.00744.4070.0000.0000.0000.0000.0000.000
161B197LEU0-0.058-0.04640.696-0.002-0.0020.0000.0000.0000.000
162B198LYS10.9250.96043.0400.0450.0450.0000.0000.0000.000
163B199SER00.023-0.00543.106-0.004-0.0040.0000.0000.0000.000
164B200MET0-0.020-0.00941.7020.0020.0020.0000.0000.0000.000
165B201LEU0-0.049-0.03345.6920.0010.0010.0000.0000.0000.000
166B202PHE0-0.039-0.02545.9220.0010.0010.0000.0000.0000.000
167B203GLY00.0920.05844.8880.0010.0010.0000.0000.0000.000
168B204GLY0-0.0280.00345.9230.0020.0020.0000.0000.0000.000
169B205GLU-1-0.938-0.99143.288-0.056-0.0560.0000.0000.0000.000
170B206GLY00.0430.05441.260-0.003-0.0030.0000.0000.0000.000
171B207LEU0-0.0210.00438.157-0.004-0.0040.0000.0000.0000.000
172B208LEU00.0240.01633.9350.0040.0040.0000.0000.0000.000
173B209LEU0-0.054-0.03535.457-0.004-0.0040.0000.0000.0000.000
174B210THR00.026-0.00729.0450.0010.0010.0000.0000.0000.000
175B211THR0-0.028-0.00832.516-0.001-0.0010.0000.0000.0000.000
176B212LEU00.0070.00427.0580.0010.0010.0000.0000.0000.000
177B213LYS10.9420.95229.1410.0150.0150.0000.0000.0000.000
178B214GLY00.0440.06227.5720.0020.0020.0000.0000.0000.000
179B215SER0-0.035-0.03825.948-0.005-0.0050.0000.0000.0000.000
180B216GLY00.0530.03622.8890.0070.0070.0000.0000.0000.000
181B217THR0-0.039-0.02421.010-0.001-0.0010.0000.0000.0000.000
182B218VAL0-0.024-0.01922.443-0.007-0.0070.0000.0000.0000.000
183B219TRP00.010-0.01518.759-0.001-0.0010.0000.0000.0000.000
184B220LEU00.006-0.00424.4450.0020.0020.0000.0000.0000.000
185B221GLN00.0610.04727.160-0.018-0.0180.0000.0000.0000.000
186B222SER00.0080.00329.1850.0080.0080.0000.0000.0000.000
187B223LEU0-0.079-0.05331.9510.0120.0120.0000.0000.0000.000
188B224PRO00.0370.03730.419-0.009-0.0090.0000.0000.0000.000
189B225PHE00.0660.03630.0250.0110.0110.0000.0000.0000.000
190B226SER00.0440.02431.6490.0080.0080.0000.0000.0000.000
191B227ARG10.8500.91333.4010.1080.1080.0000.0000.0000.000
192B228LEU00.0060.00134.4530.0070.0070.0000.0000.0000.000
193B229ALA00.0170.00335.0250.0060.0060.0000.0000.0000.000
194B230GLY00.0210.00436.9290.0060.0060.0000.0000.0000.000
195B231ARG10.8270.90438.9820.0790.0790.0000.0000.0000.000
196B232ILE00.0300.01139.0790.0050.0050.0000.0000.0000.000
197B233TYR0-0.034-0.00740.7740.0040.0040.0000.0000.0000.000
198B234ASP-1-0.798-0.90742.618-0.064-0.0640.0000.0000.0000.000
199B235ALA0-0.049-0.01644.9630.0040.0040.0000.0000.0000.000
200B236THR0-0.095-0.05144.8910.0010.0010.0000.0000.0000.000
201B237PHE0-0.0140.00842.7920.0030.0030.0000.0000.0000.000