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: JQ3G9

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2098788.708501
FMO2-HF: Nuclear repulsion 2022126.261763
FMO2-HF: Total energy -76662.446738
FMO2-MP2: Total energy -76884.415459


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.
-16.362-10.9634.502-5.586-4.315-0.049
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 : -0.056 / q_NPA : -0.031
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].
3B4HIS00.0090.0073.488-1.667-0.0640.006-0.794-0.8150.002
4B5GLU-1-0.920-0.9635.259-1.681-1.6810.0000.0000.0000.000
5B6LEU0-0.058-0.0167.3770.2700.2700.0000.0000.0000.000
6B7ASP-1-0.789-0.86610.944-0.600-0.6000.0000.0000.0000.000
7B8TYR0-0.058-0.06814.0720.0660.0660.0000.0000.0000.000
8B9ARG10.8440.90617.1410.2230.2230.0000.0000.0000.000
9B10ILE0-0.007-0.00420.1980.0050.0050.0000.0000.0000.000
10B11LEU0-0.043-0.01422.7720.0110.0110.0000.0000.0000.000
11B12GLY00.0490.02426.1780.0060.0060.0000.0000.0000.000
12B13GLU-1-0.914-0.96728.797-0.110-0.1100.0000.0000.0000.000
13B14SER0-0.042-0.03829.947-0.001-0.0010.0000.0000.0000.000
14B15MET0-0.091-0.04130.2420.0050.0050.0000.0000.0000.000
15B16GLN0-0.0120.00325.660-0.005-0.0050.0000.0000.0000.000
16B17THR0-0.013-0.01224.0310.0110.0110.0000.0000.0000.000
17B18VAL0-0.0050.02518.182-0.003-0.0030.0000.0000.0000.000
18B19GLU-1-0.788-0.84920.943-0.208-0.2080.0000.0000.0000.000
19B20ILE0-0.003-0.01214.642-0.013-0.0130.0000.0000.0000.000
20B21GLU-1-0.914-0.98015.949-0.335-0.3350.0000.0000.0000.000
21B22LEU0-0.052-0.02313.020-0.059-0.0590.0000.0000.0000.000
22B23ASP-1-0.827-0.91712.678-0.453-0.4530.0000.0000.0000.000
23B24PRO0-0.105-0.07114.222-0.010-0.0100.0000.0000.0000.000
24B25GLY00.0070.00613.120-0.056-0.0560.0000.0000.0000.000
25B26GLU-1-0.836-0.8979.886-1.021-1.0210.0000.0000.0000.000
26B27THR0-0.026-0.00510.8270.2140.2140.0000.0000.0000.000
27B28VAL00.0120.01511.067-0.135-0.1350.0000.0000.0000.000
28B29ILE0-0.068-0.02911.5640.0940.0940.0000.0000.0000.000
29B30ALA00.0930.03914.604-0.010-0.0100.0000.0000.0000.000
30B31GLU-1-0.917-0.96218.038-0.036-0.0360.0000.0000.0000.000
31B32ALA00.019-0.01021.149-0.017-0.0170.0000.0000.0000.000
32B33GLY0-0.062-0.03823.8580.0090.0090.0000.0000.0000.000
33B34ALA00.0580.04022.159-0.001-0.0010.0000.0000.0000.000
34B35MET0-0.062-0.01122.802-0.011-0.0110.0000.0000.0000.000
35B36ASN0-0.063-0.03624.1440.0040.0040.0000.0000.0000.000
36B37TYR0-0.041-0.06624.8100.0160.0160.0000.0000.0000.000
37B38MET00.0150.00322.960-0.014-0.0140.0000.0000.0000.000
38B39THR0-0.0050.00322.6490.0120.0120.0000.0000.0000.000
39B40GLY0-0.024-0.02224.3510.0000.0000.0000.0000.0000.000
40B41ASP-1-0.809-0.90121.673-0.168-0.1680.0000.0000.0000.000
41B42ILE0-0.0290.01518.850-0.012-0.0120.0000.0000.0000.000
42B43ARG10.8170.90120.1260.1770.1770.0000.0000.0000.000
43B44PHE00.0270.00919.514-0.019-0.0190.0000.0000.0000.000
44B45THR00.0130.01918.2630.0160.0160.0000.0000.0000.000
45B46ALA0-0.029-0.01419.180-0.005-0.0050.0000.0000.0000.000
46B47ARG10.9180.97213.995-0.134-0.1340.0000.0000.0000.000
47B75MET0-0.089-0.04614.9810.0000.0000.0000.0000.0000.000
48B76THR0-0.017-0.01217.9390.0250.0250.0000.0000.0000.000
49B77HIS00.0090.01012.7120.0180.0180.0000.0000.0000.000
50B78PHE00.021-0.01216.0920.0340.0340.0000.0000.0000.000
51B79THR00.042-0.02214.163-0.041-0.0410.0000.0000.0000.000
52B80ASN0-0.028-0.00515.7180.1020.1020.0000.0000.0000.000
53B81GLU-1-0.919-0.98116.751-0.244-0.2440.0000.0000.0000.000
54B82GLY0-0.055-0.02019.2310.0290.0290.0000.0000.0000.000
55B83GLN0-0.049-0.01519.313-0.024-0.0240.0000.0000.0000.000
56B84GLY0-0.042-0.03419.8710.0090.0090.0000.0000.0000.000
57B85LYS11.0031.00217.7450.2750.2750.0000.0000.0000.000
58B86GLN0-0.0210.01618.2060.0580.0580.0000.0000.0000.000
59B87HIS00.0230.00418.445-0.016-0.0160.0000.0000.0000.000
60B88VAL00.0090.00918.1530.0330.0330.0000.0000.0000.000
61B89ALA0-0.045-0.00720.218-0.020-0.0200.0000.0000.0000.000
62B90PHE00.0140.00417.9280.0220.0220.0000.0000.0000.000
63B91ALA00.0180.00622.531-0.006-0.0060.0000.0000.0000.000
64B92ALA00.0500.03424.6780.0080.0080.0000.0000.0000.000
65B93PRO0-0.015-0.00825.8850.0000.0000.0000.0000.0000.000
66B94TYR0-0.053-0.05026.0020.0080.0080.0000.0000.0000.000
67B95PRO00.0240.01229.484-0.006-0.0060.0000.0000.0000.000
68B96GLY00.004-0.01728.7420.0080.0080.0000.0000.0000.000
69B97SER00.0100.02726.395-0.004-0.0040.0000.0000.0000.000
70B98VAL00.0520.02520.4670.0070.0070.0000.0000.0000.000
71B99VAL0-0.055-0.03419.3420.0010.0010.0000.0000.0000.000
72B100ALA00.0270.01915.9790.0050.0050.0000.0000.0000.000
73B101VAL0-0.086-0.05714.1130.0330.0330.0000.0000.0000.000
74B102ASP-1-0.802-0.88910.144-0.678-0.6780.0000.0000.0000.000
75B103LEU0-0.037-0.0398.4790.1240.1240.0000.0000.0000.000
76B104ASP-1-0.843-0.9147.827-0.477-0.4770.0000.0000.0000.000
77B105ASP-1-0.981-0.97610.224-0.199-0.1990.0000.0000.0000.000
78B106VAL0-0.157-0.08812.7750.0520.0520.0000.0000.0000.000
79B107GLY0-0.021-0.00612.7370.0540.0540.0000.0000.0000.000
80B108GLY00.0320.0259.2980.1050.1050.0000.0000.0000.000
81B109ARG10.7520.84710.027-0.229-0.2290.0000.0000.0000.000
82B110LEU0-0.0010.01512.859-0.057-0.0570.0000.0000.0000.000
83B111PHE0-0.055-0.03915.3560.0570.0570.0000.0000.0000.000
84B112CYS00.0440.03117.804-0.038-0.0380.0000.0000.0000.000
85B113GLN0-0.071-0.05019.8320.0220.0220.0000.0000.0000.000
86B114LYS10.9480.96321.623-0.070-0.0700.0000.0000.0000.000
87B115ASP-1-0.903-0.95822.3480.0020.0020.0000.0000.0000.000
88B116SER0-0.053-0.01822.315-0.006-0.0060.0000.0000.0000.000
89B117PHE0-0.0250.00114.369-0.014-0.0140.0000.0000.0000.000
90B118LEU00.0020.02218.4790.0060.0060.0000.0000.0000.000
91B119CYS0-0.028-0.01616.041-0.006-0.0060.0000.0000.0000.000
92B120ALA0-0.002-0.00211.1370.0110.0110.0000.0000.0000.000
93B121ALA00.0800.0587.8980.0740.0740.0000.0000.0000.000
94B122TYR00.0060.0227.2570.3880.3880.0000.0000.0000.000
95B123GLY00.0250.0205.256-0.717-0.748-0.001-0.0120.0450.000
96B124THR0-0.067-0.0576.2280.9160.9160.0000.0000.0000.000
97B125ARG10.8580.9327.216-1.735-1.7350.0000.0000.0000.000
98B126VAL00.0190.00610.450-0.105-0.1050.0000.0000.0000.000
99B127GLY00.0020.00614.0010.0280.0280.0000.0000.0000.000
100B128ILE0-0.049-0.03316.648-0.048-0.0480.0000.0000.0000.000
101B129ALA0-0.035-0.01919.4810.0210.0210.0000.0000.0000.000
102B130PHE00.0040.00220.983-0.010-0.0100.0000.0000.0000.000
103B131THR0-0.023-0.02524.602-0.004-0.0040.0000.0000.0000.000
104B132LYS10.9020.97127.434-0.061-0.0610.0000.0000.0000.000
105B133ARG10.9680.98531.035-0.071-0.0710.0000.0000.0000.000
106B134LEU00.008-0.01234.0280.0020.0020.0000.0000.0000.000
107B135GLY00.0150.03336.932-0.004-0.0040.0000.0000.0000.000
108B144PHE0-0.004-0.00526.8820.0020.0020.0000.0000.0000.000
109B145ILE00.009-0.01623.0240.0090.0090.0000.0000.0000.000
110B146LEU00.0080.02321.813-0.014-0.0140.0000.0000.0000.000
111B147GLN00.0310.00117.6580.0050.0050.0000.0000.0000.000
112B148LYS10.9080.96814.609-0.323-0.3230.0000.0000.0000.000
113B149LEU00.0120.00012.2740.0450.0450.0000.0000.0000.000
114B150GLU-1-0.856-0.9469.6890.6420.6420.0000.0000.0000.000
115B151GLY0-0.050-0.0285.6690.3340.3340.0000.0000.0000.000
116B152ASP-1-0.758-0.8822.270-9.583-5.7884.498-4.777-3.517-0.051
117B153GLY00.0790.0675.205-0.393-0.361-0.001-0.003-0.0280.000
118B154LEU0-0.012-0.0016.7900.4050.4050.0000.0000.0000.000
119B155VAL0-0.025-0.02110.5380.0370.0370.0000.0000.0000.000
120B156PHE00.0170.01112.9530.0210.0210.0000.0000.0000.000
121B157VAL00.0030.00016.6560.0350.0350.0000.0000.0000.000
122B158HIS00.0050.00219.494-0.024-0.0240.0000.0000.0000.000
123B159ALA0-0.048-0.03423.1730.0170.0170.0000.0000.0000.000
124B160GLY00.0310.00826.114-0.004-0.0040.0000.0000.0000.000
125B161GLY0-0.061-0.03729.5610.0050.0050.0000.0000.0000.000
126B162THR00.004-0.01630.784-0.006-0.0060.0000.0000.0000.000
127B163LEU00.0300.02224.1280.0070.0070.0000.0000.0000.000
128B164ILE0-0.040-0.02728.0380.0010.0010.0000.0000.0000.000
129B165ARG10.9690.99720.2470.1170.1170.0000.0000.0000.000
130B166ARG10.9140.95426.4380.0190.0190.0000.0000.0000.000
131B167GLN00.0590.03523.428-0.010-0.0100.0000.0000.0000.000
132B168LEU0-0.060-0.01426.7440.0010.0010.0000.0000.0000.000
133B169ASN0-0.004-0.01727.5390.0030.0030.0000.0000.0000.000
134B170GLY00.0220.02129.6500.0000.0000.0000.0000.0000.000
135B171GLU-1-0.870-0.92931.1600.0020.0020.0000.0000.0000.000
136B172THR0-0.047-0.04131.6540.0050.0050.0000.0000.0000.000
137B173LEU0-0.012-0.00230.075-0.005-0.0050.0000.0000.0000.000
138B174ARG10.9110.95232.807-0.012-0.0120.0000.0000.0000.000
139B175VAL00.0160.01030.010-0.005-0.0050.0000.0000.0000.000
140B176ASP-1-0.856-0.94133.4340.0100.0100.0000.0000.0000.000
141B177THR00.0500.02030.3260.0000.0000.0000.0000.0000.000
142B178GLY00.0220.02829.7480.0020.0020.0000.0000.0000.000
143B179CYS0-0.039-0.01529.503-0.007-0.0070.0000.0000.0000.000
144B180LEU0-0.0220.01125.265-0.007-0.0070.0000.0000.0000.000
145B181VAL0-0.0020.01721.9860.0070.0070.0000.0000.0000.000
146B182ALA00.0450.01219.3740.0070.0070.0000.0000.0000.000
147B183PHE0-0.018-0.01620.287-0.009-0.0090.0000.0000.0000.000
148B184THR00.0620.05017.7900.0050.0050.0000.0000.0000.000
149B185ASP-1-0.774-0.88016.5380.2170.2170.0000.0000.0000.000
150B186GLY0-0.0020.00319.598-0.021-0.0210.0000.0000.0000.000
151B187ILE0-0.079-0.02422.935-0.012-0.0120.0000.0000.0000.000
152B188ASP-1-0.893-0.94024.5000.0970.0970.0000.0000.0000.000
153B189TYR0-0.018-0.03823.353-0.014-0.0140.0000.0000.0000.000
154B190ASP-1-0.892-0.94628.5250.0620.0620.0000.0000.0000.000
155B191VAL00.0040.01929.861-0.007-0.0070.0000.0000.0000.000
156B192GLN0-0.025-0.02232.6530.0030.0030.0000.0000.0000.000
157B193LEU00.0300.01536.480-0.003-0.0030.0000.0000.0000.000
158B194ALA0-0.0350.00239.3860.0000.0000.0000.0000.0000.000
159B195GLY0-0.0040.00240.8980.0000.0000.0000.0000.0000.000
160B196GLY00.0110.00844.411-0.002-0.0020.0000.0000.0000.000
161B197LEU0-0.064-0.05140.968-0.002-0.0020.0000.0000.0000.000
162B198LYS10.9510.97543.035-0.006-0.0060.0000.0000.0000.000
163B199SER00.013-0.01743.329-0.002-0.0020.0000.0000.0000.000
164B200MET0-0.017-0.00841.757-0.002-0.0020.0000.0000.0000.000
165B201LEU0-0.049-0.03445.8110.0020.0020.0000.0000.0000.000
166B202PHE0-0.062-0.03745.920-0.001-0.0010.0000.0000.0000.000
167B203GLY00.0890.06444.8860.0010.0010.0000.0000.0000.000
168B204GLY0-0.0270.00245.9200.0010.0010.0000.0000.0000.000
169B205GLU-1-0.945-0.99743.2200.0200.0200.0000.0000.0000.000
170B206GLY00.0340.04741.266-0.001-0.0010.0000.0000.0000.000
171B207LEU0-0.0060.01438.282-0.002-0.0020.0000.0000.0000.000
172B208LEU00.0140.01133.6370.0030.0030.0000.0000.0000.000
173B209LEU0-0.031-0.03235.533-0.004-0.0040.0000.0000.0000.000
174B210THR00.001-0.01529.0780.0070.0070.0000.0000.0000.000
175B211THR0-0.048-0.01832.519-0.009-0.0090.0000.0000.0000.000
176B212LEU00.0240.01026.6650.0070.0070.0000.0000.0000.000
177B213LYS10.9470.95329.150-0.055-0.0550.0000.0000.0000.000
178B214GLY00.0420.05927.5780.0090.0090.0000.0000.0000.000
179B215SER0-0.039-0.03425.692-0.011-0.0110.0000.0000.0000.000
180B216GLY00.0450.02222.8800.0120.0120.0000.0000.0000.000
181B217THR0-0.029-0.01220.985-0.008-0.0080.0000.0000.0000.000
182B218VAL0-0.020-0.01922.4400.0110.0110.0000.0000.0000.000
183B219TRP00.023-0.01218.768-0.021-0.0210.0000.0000.0000.000
184B220LEU0-0.011-0.00824.4350.0110.0110.0000.0000.0000.000
185B221GLN00.0520.03927.480-0.017-0.0170.0000.0000.0000.000
186B222SER0-0.0050.00529.1720.0050.0050.0000.0000.0000.000
187B223LEU0-0.101-0.06131.9250.0050.0050.0000.0000.0000.000
188B224PRO00.0280.02930.422-0.003-0.0030.0000.0000.0000.000
189B225PHE00.0800.03729.9610.0010.0010.0000.0000.0000.000
190B226SER00.0340.01631.6260.0000.0000.0000.0000.0000.000
191B227ARG10.9390.98233.3950.0090.0090.0000.0000.0000.000
192B228LEU00.002-0.00234.0070.0010.0010.0000.0000.0000.000
193B229ALA00.0180.00435.0520.0010.0010.0000.0000.0000.000
194B230GLY00.0200.00436.9200.0010.0010.0000.0000.0000.000
195B231ARG10.9340.96538.9760.0080.0080.0000.0000.0000.000
196B232ILE00.0150.00638.8670.0000.0000.0000.0000.0000.000
197B233TYR0-0.035-0.01240.8120.0010.0010.0000.0000.0000.000
198B234ASP-1-0.861-0.94942.6110.0020.0020.0000.0000.0000.000
199B235ALA0-0.042-0.01644.9580.0000.0000.0000.0000.0000.000
200B236THR0-0.101-0.04244.830-0.001-0.0010.0000.0000.0000.000
201B237PHE0-0.021-0.00342.7240.0020.0020.0000.0000.0000.000