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: NN1QQ

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 OptAll
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 -1859723.037643
FMO2-HF: Nuclear repulsion 1787823.34833
FMO2-HF: Total energy -71899.689313
FMO2-MP2: Total energy -72107.96235


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.
-36.962-23.18921.663-12.881-22.556-0.006
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 : -0.005 / q_NPA : 0.001
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].
3F6LEU0-0.046-0.0253.4331.0113.1750.007-0.913-1.2590.002
4F7ASP-1-0.791-0.8775.333-0.345-0.296-0.001-0.002-0.0450.000
5F8TYR0-0.071-0.0528.7680.4100.4100.0000.0000.0000.000
6F9ARG10.8640.92111.164-0.294-0.2940.0000.0000.0000.000
7F10ILE00.0110.00614.9000.0690.0690.0000.0000.0000.000
8F11LEU0-0.032-0.00917.224-0.010-0.0100.0000.0000.0000.000
9F12GLY00.0480.02220.2240.0110.0110.0000.0000.0000.000
10F13GLU-1-0.883-0.94323.2350.0090.0090.0000.0000.0000.000
11F14SER0-0.070-0.04525.950-0.015-0.0150.0000.0000.0000.000
12F15MET0-0.0370.00225.180-0.004-0.0040.0000.0000.0000.000
13F16GLN0-0.023-0.01020.564-0.011-0.0110.0000.0000.0000.000
14F17THR0-0.026-0.01717.6830.0340.0340.0000.0000.0000.000
15F18VAL00.0070.01112.303-0.050-0.0500.0000.0000.0000.000
16F19GLU-1-0.800-0.86513.7130.4860.4860.0000.0000.0000.000
17F20ILE00.003-0.0037.193-0.155-0.1550.0000.0000.0000.000
18F21GLU-1-0.809-0.9019.1060.5070.5070.0000.0000.0000.000
19F22LEU0-0.010-0.0015.3430.0320.0320.0000.0000.0000.000
20F23ASP-1-0.806-0.9047.3540.3530.3530.0000.0000.0000.000
21F24PRO0-0.073-0.0427.1430.9400.9400.0000.0000.0000.000
22F25GLY0-0.0140.0034.765-0.424-0.339-0.001-0.023-0.0610.000
23F26GLU-1-0.849-0.9292.512-10.674-2.8945.443-5.956-7.267-0.051
24F27THR0-0.055-0.0432.092-13.081-16.45413.139-3.438-6.3280.029
25F28VAL0-0.0010.0063.264-1.075-0.3870.1150.420-1.2230.001
26F29ILE0-0.046-0.0245.952-0.336-0.3360.0000.0000.0000.000
27F30ALA00.0650.0318.857-0.315-0.3150.0000.0000.0000.000
28F31GLU-1-0.804-0.88812.3000.4340.4340.0000.0000.0000.000
29F32ALA0-0.015-0.02315.8440.0190.0190.0000.0000.0000.000
30F33GLY0-0.021-0.01317.988-0.068-0.0680.0000.0000.0000.000
31F34ALA0-0.0130.00916.096-0.033-0.0330.0000.0000.0000.000
32F35MET0-0.046-0.00514.827-0.003-0.0030.0000.0000.0000.000
33F36ASN0-0.021-0.01416.944-0.051-0.0510.0000.0000.0000.000
34F37TYR0-0.071-0.07416.980-0.063-0.0630.0000.0000.0000.000
35F38MET00.0200.00114.6620.1320.1320.0000.0000.0000.000
36F39THR0-0.014-0.00615.092-0.091-0.0910.0000.0000.0000.000
37F40GLY0-0.001-0.00815.2610.0920.0920.0000.0000.0000.000
38F41ASP-1-0.840-0.91314.3060.6810.6810.0000.0000.0000.000
39F42ILE00.0150.02610.0170.0890.0890.0000.0000.0000.000
40F43ARG10.7510.86710.639-1.080-1.0800.0000.0000.0000.000
41F44PHE00.012-0.00610.6170.2710.2710.0000.0000.0000.000
42F45THR0-0.005-0.00710.137-0.124-0.1240.0000.0000.0000.000
43F46ALA0-0.032-0.00412.866-0.093-0.0930.0000.0000.0000.000
44F47ARG10.9570.99312.123-0.573-0.5730.0000.0000.0000.000
45F75MET0-0.061-0.02812.6110.0590.0590.0000.0000.0000.000
46F76THR0-0.087-0.05313.179-0.072-0.0720.0000.0000.0000.000
47F77HIS00.0370.0227.729-0.044-0.0440.0000.0000.0000.000
48F78PHE00.027-0.0108.431-0.586-0.5860.0000.0000.0000.000
49F79THR00.013-0.0175.0231.2681.2680.0000.0000.0000.000
50F80ASN0-0.003-0.0136.397-1.072-1.0720.0000.0000.0000.000
51F81GLU-1-0.867-0.9077.2341.1091.1090.0000.0000.0000.000
52F82GLY00.0280.0359.548-0.228-0.2280.0000.0000.0000.000
53F83GLN0-0.100-0.05411.816-0.028-0.0280.0000.0000.0000.000
54F84GLY00.000-0.00513.872-0.014-0.0140.0000.0000.0000.000
55F85LYS10.8450.91611.382-0.074-0.0740.0000.0000.0000.000
56F86GLN0-0.0410.00511.368-0.196-0.1960.0000.0000.0000.000
57F87HIS00.003-0.02311.0250.2200.2200.0000.0000.0000.000
58F88VAL0-0.010-0.01210.9320.0070.0070.0000.0000.0000.000
59F89ALA0-0.0110.01912.370-0.048-0.0480.0000.0000.0000.000
60F90PHE00.010-0.00510.3610.0090.0090.0000.0000.0000.000
61F91ALA00.002-0.00315.627-0.085-0.0850.0000.0000.0000.000
62F92ALA00.0580.03918.6510.0340.0340.0000.0000.0000.000
63F93PRO0-0.017-0.01920.508-0.016-0.0160.0000.0000.0000.000
64F94TYR0-0.067-0.05322.464-0.028-0.0280.0000.0000.0000.000
65F95PRO00.0150.00924.8740.0010.0010.0000.0000.0000.000
66F96GLY00.018-0.00925.033-0.014-0.0140.0000.0000.0000.000
67F97SER0-0.042-0.01422.9260.0110.0110.0000.0000.0000.000
68F98VAL00.003-0.00316.4500.0040.0040.0000.0000.0000.000
69F99VAL0-0.054-0.02917.423-0.022-0.0220.0000.0000.0000.000
70F100ALA00.0410.02513.2330.0320.0320.0000.0000.0000.000
71F101VAL0-0.058-0.04013.0900.0240.0240.0000.0000.0000.000
72F102ASP-1-0.819-0.91210.012-1.688-1.6880.0000.0000.0000.000
73F103LEU0-0.038-0.0219.7270.2220.2220.0000.0000.0000.000
74F104ASP-1-0.891-0.92510.270-0.945-0.9450.0000.0000.0000.000
75F105ASP-1-0.944-0.97212.094-0.507-0.5070.0000.0000.0000.000
76F106VAL0-0.138-0.07214.5830.1340.1340.0000.0000.0000.000
77F107GLY0-0.033-0.01115.4960.0620.0620.0000.0000.0000.000
78F108GLY00.0190.01011.8750.0410.0410.0000.0000.0000.000
79F109ARG10.7290.82412.6690.3890.3890.0000.0000.0000.000
80F110LEU00.0050.01214.8660.0100.0100.0000.0000.0000.000
81F111PHE0-0.017-0.00516.5610.0400.0400.0000.0000.0000.000
82F112CYS00.0280.00117.284-0.013-0.0130.0000.0000.0000.000
83F113GLN0-0.031-0.01919.8280.0250.0250.0000.0000.0000.000
84F114LYS10.8970.93319.578-0.233-0.2330.0000.0000.0000.000
85F115ASP-1-0.911-0.96019.4340.1630.1630.0000.0000.0000.000
86F116SER0-0.0350.00420.0080.0080.0080.0000.0000.0000.000
87F117PHE0-0.0020.01010.885-0.022-0.0220.0000.0000.0000.000
88F118LEU0-0.042-0.00714.5470.0320.0320.0000.0000.0000.000
89F119CYS0-0.046-0.03010.1520.0660.0660.0000.0000.0000.000
90F120ALA0-0.004-0.0017.782-0.291-0.2910.0000.0000.0000.000
91F121ALA00.1040.0632.7850.8421.2970.114-0.142-0.4280.000
92F122TYR0-0.038-0.0112.828-7.043-3.2022.419-1.905-4.3550.022
93F123GLY00.0270.0152.882-3.398-1.3140.428-0.922-1.590-0.009
94F124THR0-0.040-0.0245.445-0.527-0.5270.0000.0000.0000.000
95F125ARG10.9100.9477.8390.5720.5720.0000.0000.0000.000
96F126VAL00.0200.01710.865-0.089-0.0890.0000.0000.0000.000
97F127GLY0-0.013-0.00313.2780.0370.0370.0000.0000.0000.000
98F128ILE0-0.014-0.01416.952-0.018-0.0180.0000.0000.0000.000
99F129ALA0-0.0040.00420.588-0.021-0.0210.0000.0000.0000.000
100F144PHE0-0.014-0.01226.3740.0050.0050.0000.0000.0000.000
101F145ILE00.006-0.00123.219-0.004-0.0040.0000.0000.0000.000
102F146LEU0-0.0240.00922.2810.0100.0100.0000.0000.0000.000
103F147GLN0-0.009-0.01917.1700.0160.0160.0000.0000.0000.000
104F148LYS10.8460.91417.2130.1280.1280.0000.0000.0000.000
105F149LEU00.0230.01712.1120.0700.0700.0000.0000.0000.000
106F150GLU-1-0.809-0.88412.149-0.324-0.3240.0000.0000.0000.000
107F151GLY0-0.039-0.0268.1660.1330.1330.0000.0000.0000.000
108F152ASP-1-0.884-0.9385.372-2.135-2.1350.0000.0000.0000.000
109F153GLY00.0920.0525.272-0.651-0.6510.0000.0000.0000.000
110F154LEU0-0.036-0.0106.3020.8510.8510.0000.0000.0000.000
111F155VAL0-0.028-0.0157.4550.2300.2300.0000.0000.0000.000
112F156PHE00.0080.0008.390-0.029-0.0290.0000.0000.0000.000
113F157VAL0-0.003-0.00513.0410.0920.0920.0000.0000.0000.000
114F158HIS0-0.006-0.00916.496-0.005-0.0050.0000.0000.0000.000
115F159ALA0-0.009-0.00819.938-0.011-0.0110.0000.0000.0000.000
116F160GLY00.0300.01823.5450.0050.0050.0000.0000.0000.000
117F161GLY0-0.032-0.02526.487-0.015-0.0150.0000.0000.0000.000
118F162THR0-0.044-0.03028.614-0.002-0.0020.0000.0000.0000.000
119F163LEU00.0630.04822.647-0.002-0.0020.0000.0000.0000.000
120F164ILE0-0.022-0.01025.957-0.006-0.0060.0000.0000.0000.000
121F165ARG10.9230.96221.9180.2040.2040.0000.0000.0000.000
122F166ARG10.9000.94926.5970.0830.0830.0000.0000.0000.000
123F167GLN00.0950.04925.549-0.016-0.0160.0000.0000.0000.000
124F168LEU0-0.060-0.01127.8330.0160.0160.0000.0000.0000.000
125F169ASN0-0.048-0.05029.342-0.023-0.0230.0000.0000.0000.000
126F170GLY00.0310.01932.0360.0040.0040.0000.0000.0000.000
127F171GLU-1-0.894-0.92733.352-0.092-0.0920.0000.0000.0000.000
128F172THR0-0.023-0.03033.948-0.002-0.0020.0000.0000.0000.000
129F173LEU0-0.0110.00431.0170.0040.0040.0000.0000.0000.000
130F174ARG10.9190.94934.3460.0410.0410.0000.0000.0000.000
131F175VAL0-0.0150.00630.1880.0010.0010.0000.0000.0000.000
132F176ASP-1-0.765-0.88232.4670.0170.0170.0000.0000.0000.000
133F177THR00.0180.00229.8760.0000.0000.0000.0000.0000.000
134F178GLY00.0480.03828.635-0.001-0.0010.0000.0000.0000.000
135F179CYS0-0.093-0.04627.7930.0080.0080.0000.0000.0000.000
136F180LEU00.0050.01224.309-0.008-0.0080.0000.0000.0000.000
137F181VAL0-0.0170.01020.5720.0120.0120.0000.0000.0000.000
138F182ALA00.033-0.00819.3280.0090.0090.0000.0000.0000.000
139F183PHE0-0.050-0.02920.9790.0050.0050.0000.0000.0000.000
140F184THR00.0480.03619.425-0.005-0.0050.0000.0000.0000.000
141F185ASP-1-0.790-0.88719.214-0.246-0.2460.0000.0000.0000.000
142F186GLY00.0140.01221.629-0.005-0.0050.0000.0000.0000.000
143F187ILE0-0.060-0.02425.2530.0150.0150.0000.0000.0000.000
144F188ASP-1-0.809-0.88926.682-0.102-0.1020.0000.0000.0000.000
145F189TYR0-0.031-0.03125.7540.0020.0020.0000.0000.0000.000
146F190ASP-1-0.875-0.91130.542-0.044-0.0440.0000.0000.0000.000
147F191VAL00.004-0.01530.7160.0010.0010.0000.0000.0000.000
148F192GLN00.0130.01134.0310.0050.0050.0000.0000.0000.000
149F193LEU00.0050.00837.5010.0020.0020.0000.0000.0000.000
150F194ALA0-0.028-0.00240.159-0.003-0.0030.0000.0000.0000.000
151F207LEU0-0.006-0.01737.9620.0010.0010.0000.0000.0000.000
152F208LEU00.0080.01334.253-0.004-0.0040.0000.0000.0000.000
153F209LEU0-0.022-0.01735.4110.0010.0010.0000.0000.0000.000
154F210THR00.028-0.00729.8990.0020.0020.0000.0000.0000.000
155F211THR0-0.065-0.04633.3780.0000.0000.0000.0000.0000.000
156F212LEU00.0040.00428.189-0.001-0.0010.0000.0000.0000.000
157F213LYS10.8520.90231.1310.0860.0860.0000.0000.0000.000
158F214GLY00.0560.04729.615-0.002-0.0020.0000.0000.0000.000
159F215SER0-0.078-0.05428.3550.0070.0070.0000.0000.0000.000
160F216GLY00.0750.05324.560-0.013-0.0130.0000.0000.0000.000
161F217THR0-0.047-0.03021.9580.0130.0130.0000.0000.0000.000
162F218VAL00.001-0.00323.416-0.001-0.0010.0000.0000.0000.000
163F219TRP00.0440.01119.6260.0120.0120.0000.0000.0000.000
164F220LEU0-0.016-0.01223.9840.0110.0110.0000.0000.0000.000
165F221GLN00.0600.02824.9870.0060.0060.0000.0000.0000.000
166F222SER0-0.038-0.02127.5300.0040.0040.0000.0000.0000.000
167F223LEU0-0.045-0.03429.6340.0010.0010.0000.0000.0000.000
168F224PRO00.0250.02227.6530.0100.0100.0000.0000.0000.000
169F225PHE00.0550.03826.1250.0000.0000.0000.0000.0000.000
170F226SER00.0410.01628.1750.0000.0000.0000.0000.0000.000
171F227ARG10.8310.90930.695-0.025-0.0250.0000.0000.0000.000
172F228LEU00.0000.00030.137-0.002-0.0020.0000.0000.0000.000
173F229ALA00.0320.01031.225-0.001-0.0010.0000.0000.0000.000
174F230GLY00.0260.01833.229-0.001-0.0010.0000.0000.0000.000
175F231ARG10.9500.97236.000-0.043-0.0430.0000.0000.0000.000
176F232ILE00.0000.00834.952-0.003-0.0030.0000.0000.0000.000
177F233TYR00.0150.00837.290-0.002-0.0020.0000.0000.0000.000
178F234ASP-1-0.895-0.94938.9810.0500.0500.0000.0000.0000.000
179F235ALA0-0.033-0.01841.026-0.002-0.0020.0000.0000.0000.000
180F236THR0-0.059-0.03540.677-0.001-0.0010.0000.0000.0000.000
181F237PHE0-0.026-0.00843.4110.0010.0010.0000.0000.0000.000
182F238ARG10.9790.97946.024-0.052-0.0520.0000.0000.0000.000
183F239ALA0-0.077-0.04145.678-0.001-0.0010.0000.0000.0000.000
184F240ARG10.8520.94242.563-0.061-0.0610.0000.0000.0000.000
185F241GLU-1-0.896-0.93646.8630.0430.0430.0000.0000.0000.000
186F242GLU-1-1.017-1.01049.9880.0560.0560.0000.0000.0000.000