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: G5NG1

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1856611.099459
FMO2-HF: Nuclear repulsion 1784713.628519
FMO2-HF: Total energy -71897.470941
FMO2-MP2: Total energy -72105.899046


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.
-15.352-7.38319.477-9.417-18.0290.016
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 : -0.042 / q_NPA : -0.044
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].
3F6LEU0-0.028-0.0062.949-0.3732.0350.158-0.976-1.591-0.003
4F7ASP-1-0.797-0.8635.2590.0890.141-0.001-0.003-0.0480.000
5F8TYR0-0.037-0.0408.6620.1880.1880.0000.0000.0000.000
6F9ARG10.9520.96611.264-0.140-0.1400.0000.0000.0000.000
7F10ILE0-0.0030.00614.8280.0070.0070.0000.0000.0000.000
8F11LEU0-0.028-0.01317.2130.0180.0180.0000.0000.0000.000
9F12GLY00.0280.00720.178-0.014-0.0140.0000.0000.0000.000
10F13GLU-1-0.939-0.97023.144-0.010-0.0100.0000.0000.0000.000
11F14SER0-0.025-0.02524.947-0.008-0.0080.0000.0000.0000.000
12F15MET0-0.062-0.03324.917-0.009-0.0090.0000.0000.0000.000
13F16GLN0-0.0010.02520.150-0.008-0.0080.0000.0000.0000.000
14F17THR0-0.024-0.01417.405-0.006-0.0060.0000.0000.0000.000
15F18VAL00.0070.02912.2070.0150.0150.0000.0000.0000.000
16F19GLU-1-0.877-0.92813.7670.2860.2860.0000.0000.0000.000
17F20ILE0-0.010-0.0237.138-0.081-0.0810.0000.0000.0000.000
18F21GLU-1-0.854-0.9479.5930.6750.6750.0000.0000.0000.000
19F22LEU0-0.045-0.0295.475-0.016-0.0160.0000.0000.0000.000
20F23ASP-1-0.816-0.8926.5571.0131.0130.0000.0000.0000.000
21F24PRO0-0.093-0.0606.8230.8790.8790.0000.0000.0000.000
22F25GLY0-0.006-0.0035.2930.2670.2670.0000.0000.0000.000
23F26GLU-1-0.916-0.9512.546-0.7132.4972.600-2.555-3.2550.006
24F27THR0-0.042-0.0412.609-10.729-8.7701.440-0.236-3.1630.018
25F28VAL0-0.0060.0063.584-1.435-0.5990.024-0.247-0.614-0.001
26F29ILE0-0.018-0.0156.062-0.076-0.0760.0000.0000.0000.000
27F30ALA00.0420.0178.894-0.066-0.0660.0000.0000.0000.000
28F31GLU-1-0.851-0.91312.273-0.320-0.3200.0000.0000.0000.000
29F32ALA0-0.021-0.01615.8700.0450.0450.0000.0000.0000.000
30F33GLY0-0.053-0.03717.987-0.009-0.0090.0000.0000.0000.000
31F34ALA00.0480.03215.8390.0130.0130.0000.0000.0000.000
32F35MET0-0.0670.00315.1540.0160.0160.0000.0000.0000.000
33F36ASN0-0.029-0.01516.837-0.017-0.0170.0000.0000.0000.000
34F37TYR0-0.084-0.08417.052-0.027-0.0270.0000.0000.0000.000
35F38MET00.0250.00914.5570.0250.0250.0000.0000.0000.000
36F39THR0-0.027-0.00615.638-0.053-0.0530.0000.0000.0000.000
37F40GLY0-0.023-0.01715.6900.0570.0570.0000.0000.0000.000
38F41ASP-1-0.947-0.98614.5640.4680.4680.0000.0000.0000.000
39F42ILE00.0420.03910.6670.0790.0790.0000.0000.0000.000
40F43ARG10.8950.94311.005-0.490-0.4900.0000.0000.0000.000
41F44PHE00.0160.00610.8670.0740.0740.0000.0000.0000.000
42F45THR0-0.038-0.02811.144-0.027-0.0270.0000.0000.0000.000
43F46ALA0-0.038-0.01013.726-0.059-0.0590.0000.0000.0000.000
44F47ARG10.9731.00311.3500.3820.3820.0000.0000.0000.000
45F75MET0-0.070-0.03311.936-0.014-0.0140.0000.0000.0000.000
46F76THR0-0.076-0.05413.342-0.025-0.0250.0000.0000.0000.000
47F77HIS00.0310.0206.7930.1490.1490.0000.0000.0000.000
48F78PHE00.014-0.0149.001-0.084-0.0840.0000.0000.0000.000
49F79THR00.0340.0225.7150.5170.5170.0000.0000.0000.000
50F80ASN00.0010.0046.829-0.879-0.8790.0000.0000.0000.000
51F81GLU-1-0.938-0.9718.0000.4250.4250.0000.0000.0000.000
52F82GLY00.0490.05310.282-0.153-0.1530.0000.0000.0000.000
53F83GLN0-0.075-0.04711.6480.1340.1340.0000.0000.0000.000
54F84GLY0-0.040-0.02913.422-0.087-0.0870.0000.0000.0000.000
55F85LYS10.9470.97011.555-0.383-0.3830.0000.0000.0000.000
56F86GLN00.0070.03111.297-0.252-0.2520.0000.0000.0000.000
57F87HIS00.0090.00911.0500.1700.1700.0000.0000.0000.000
58F88VAL0-0.014-0.01010.694-0.053-0.0530.0000.0000.0000.000
59F89ALA0-0.0190.00612.418-0.038-0.0380.0000.0000.0000.000
60F90PHE00.0160.00410.340-0.035-0.0350.0000.0000.0000.000
61F91ALA0-0.009-0.02015.537-0.015-0.0150.0000.0000.0000.000
62F92ALA00.0320.02618.588-0.009-0.0090.0000.0000.0000.000
63F93PRO00.0130.00220.4030.0180.0180.0000.0000.0000.000
64F94TYR0-0.068-0.04222.6360.0090.0090.0000.0000.0000.000
65F95PRO00.0250.00524.616-0.003-0.0030.0000.0000.0000.000
66F96GLY0-0.007-0.01325.043-0.007-0.0070.0000.0000.0000.000
67F97SER0-0.006-0.00322.3560.0130.0130.0000.0000.0000.000
68F98VAL00.0060.00915.792-0.016-0.0160.0000.0000.0000.000
69F99VAL0-0.055-0.03717.3760.0190.0190.0000.0000.0000.000
70F100ALA00.0270.02213.014-0.035-0.0350.0000.0000.0000.000
71F101VAL0-0.057-0.03612.7780.0670.0670.0000.0000.0000.000
72F102ASP-1-0.811-0.9199.947-0.667-0.6670.0000.0000.0000.000
73F103LEU0-0.056-0.0238.3490.1170.1170.0000.0000.0000.000
74F104ASP-1-0.783-0.86310.354-0.045-0.0450.0000.0000.0000.000
75F105ASP-1-1.003-0.98312.234-0.148-0.1480.0000.0000.0000.000
76F106VAL0-0.127-0.08314.2460.0210.0210.0000.0000.0000.000
77F107GLY0-0.072-0.03715.1290.0050.0050.0000.0000.0000.000
78F108GLY00.0080.00211.6440.0170.0170.0000.0000.0000.000
79F109ARG10.7570.84812.5800.2150.2150.0000.0000.0000.000
80F110LEU00.0110.00914.4830.0400.0400.0000.0000.0000.000
81F111PHE0-0.034-0.00815.816-0.037-0.0370.0000.0000.0000.000
82F112CYS00.025-0.00316.7540.0030.0030.0000.0000.0000.000
83F113GLN00.0290.02318.873-0.004-0.0040.0000.0000.0000.000
84F114LYS10.9880.98819.3220.2210.2210.0000.0000.0000.000
85F115ASP-1-0.945-0.97619.445-0.173-0.1730.0000.0000.0000.000
86F116SER0-0.024-0.01019.6910.0180.0180.0000.0000.0000.000
87F117PHE00.0020.02010.6570.0050.0050.0000.0000.0000.000
88F118LEU0-0.022-0.00114.2920.0280.0280.0000.0000.0000.000
89F119CYS0-0.052-0.03410.0390.0230.0230.0000.0000.0000.000
90F120ALA0-0.011-0.0047.6980.0000.0000.0000.0000.0000.000
91F121ALA00.0900.0602.7140.3120.9010.094-0.203-0.4810.001
92F122TYR0-0.051-0.0151.691-0.202-1.6589.421-2.780-5.1850.027
93F123GLY00.0500.0202.319-7.475-7.2285.743-2.393-3.597-0.032
94F124THR0-0.046-0.0274.7671.0751.148-0.001-0.015-0.0560.000
95F125ARG10.8920.9376.9370.6360.6360.0000.0000.0000.000
96F126VAL00.0360.02110.4330.1130.1130.0000.0000.0000.000
97F127GLY0-0.0070.00212.8070.0240.0240.0000.0000.0000.000
98F128ILE0-0.020-0.01116.4210.0190.0190.0000.0000.0000.000
99F129ALA0-0.0040.00519.8910.0000.0000.0000.0000.0000.000
100F144PHE0-0.033-0.02924.7070.0010.0010.0000.0000.0000.000
101F145ILE00.0060.00522.4990.0030.0030.0000.0000.0000.000
102F146LEU0-0.0080.01121.201-0.011-0.0110.0000.0000.0000.000
103F147GLN0-0.027-0.02216.633-0.010-0.0100.0000.0000.0000.000
104F148LYS10.8370.91016.2340.3600.3600.0000.0000.0000.000
105F149LEU00.001-0.00911.348-0.039-0.0390.0000.0000.0000.000
106F150GLU-1-0.831-0.90011.615-0.315-0.3150.0000.0000.0000.000
107F151GLY0-0.002-0.0127.760-0.201-0.2010.0000.0000.0000.000
108F152ASP-1-0.874-0.9325.5991.0901.0900.0000.0000.0000.000
109F153GLY00.0840.0684.508-0.133-0.082-0.001-0.009-0.0390.000
110F154LEU00.004-0.0045.4170.4920.4920.0000.0000.0000.000
111F155VAL0-0.031-0.0117.238-0.241-0.2410.0000.0000.0000.000
112F156PHE00.005-0.0078.6050.1580.1580.0000.0000.0000.000
113F157VAL0-0.007-0.00213.0620.0110.0110.0000.0000.0000.000
114F158HIS00.0100.00616.3560.0240.0240.0000.0000.0000.000
115F159ALA0-0.060-0.04019.616-0.005-0.0050.0000.0000.0000.000
116F160GLY00.0360.01023.0820.0140.0140.0000.0000.0000.000
117F161GLY0-0.052-0.04126.1220.0010.0010.0000.0000.0000.000
118F162THR0-0.028-0.02627.7900.0050.0050.0000.0000.0000.000
119F163LEU00.0720.04122.245-0.006-0.0060.0000.0000.0000.000
120F164ILE0-0.040-0.03825.7760.0110.0110.0000.0000.0000.000
121F165ARG10.9761.00220.5830.1330.1330.0000.0000.0000.000
122F166ARG10.8990.93825.5800.0910.0910.0000.0000.0000.000
123F167GLN00.0340.00324.941-0.018-0.0180.0000.0000.0000.000
124F168LEU0-0.0290.00727.2180.0080.0080.0000.0000.0000.000
125F169ASN00.0410.01928.759-0.008-0.0080.0000.0000.0000.000
126F170GLY0-0.0170.00131.2170.0060.0060.0000.0000.0000.000
127F171GLU-1-0.942-0.97533.171-0.069-0.0690.0000.0000.0000.000
128F172THR0-0.021-0.02633.105-0.006-0.0060.0000.0000.0000.000
129F173LEU0-0.010-0.00130.2390.0050.0050.0000.0000.0000.000
130F174ARG10.9180.97132.7670.0680.0680.0000.0000.0000.000
131F175VAL00.0010.00329.3690.0040.0040.0000.0000.0000.000
132F176ASP-1-0.893-0.95432.720-0.090-0.0900.0000.0000.0000.000
133F177THR00.0280.01129.643-0.002-0.0020.0000.0000.0000.000
134F178GLY00.0230.02628.352-0.009-0.0090.0000.0000.0000.000
135F179CYS0-0.055-0.04027.710-0.001-0.0010.0000.0000.0000.000
136F180LEU0-0.0020.00423.9980.0000.0000.0000.0000.0000.000
137F181VAL0-0.0130.00720.152-0.005-0.0050.0000.0000.0000.000
138F182ALA00.0500.00718.403-0.026-0.0260.0000.0000.0000.000
139F183PHE0-0.038-0.02319.9810.0260.0260.0000.0000.0000.000
140F184THR00.0610.04318.556-0.017-0.0170.0000.0000.0000.000
141F185ASP-1-0.810-0.91219.225-0.199-0.1990.0000.0000.0000.000
142F186GLY0-0.0290.00220.9910.0120.0120.0000.0000.0000.000
143F187ILE0-0.039-0.02123.8350.0130.0130.0000.0000.0000.000
144F188ASP-1-0.945-0.96425.921-0.127-0.1270.0000.0000.0000.000
145F189TYR0-0.021-0.04224.0170.0020.0020.0000.0000.0000.000
146F190ASP-1-0.921-0.95029.521-0.101-0.1010.0000.0000.0000.000
147F191VAL0-0.015-0.00930.0410.0030.0030.0000.0000.0000.000
148F192GLN00.001-0.01033.081-0.001-0.0010.0000.0000.0000.000
149F193LEU00.0020.00536.7230.0000.0000.0000.0000.0000.000
150F194ALA0-0.0090.00839.6480.0020.0020.0000.0000.0000.000
151F207LEU0-0.021-0.02837.4200.0000.0000.0000.0000.0000.000
152F208LEU0-0.0060.01532.9120.0020.0020.0000.0000.0000.000
153F209LEU00.011-0.00234.7670.0000.0000.0000.0000.0000.000
154F210THR00.0170.00028.894-0.006-0.0060.0000.0000.0000.000
155F211THR0-0.022-0.01632.3240.0060.0060.0000.0000.0000.000
156F212LEU00.0320.02126.995-0.006-0.0060.0000.0000.0000.000
157F213LYS10.9210.95330.4840.0950.0950.0000.0000.0000.000
158F214GLY00.0750.04828.918-0.006-0.0060.0000.0000.0000.000
159F215SER0-0.042-0.03727.7240.0110.0110.0000.0000.0000.000
160F216GLY00.0600.05724.140-0.008-0.0080.0000.0000.0000.000
161F217THR0-0.032-0.02021.3990.0130.0130.0000.0000.0000.000
162F218VAL00.0050.00422.680-0.014-0.0140.0000.0000.0000.000
163F219TRP00.017-0.00418.5770.0180.0180.0000.0000.0000.000
164F220LEU0-0.009-0.01123.226-0.003-0.0030.0000.0000.0000.000
165F221GLN00.0400.03925.0810.0020.0020.0000.0000.0000.000
166F222SER0-0.0200.00226.9880.0030.0030.0000.0000.0000.000
167F223LEU0-0.095-0.05929.1260.0070.0070.0000.0000.0000.000
168F224PRO00.0360.03427.523-0.002-0.0020.0000.0000.0000.000
169F225PHE00.0750.03826.4230.0100.0100.0000.0000.0000.000
170F226SER00.0410.01028.4100.0090.0090.0000.0000.0000.000
171F227ARG10.9190.96630.7590.0840.0840.0000.0000.0000.000
172F228LEU00.0060.00429.9810.0070.0070.0000.0000.0000.000
173F229ALA00.0290.01831.4200.0060.0060.0000.0000.0000.000
174F230GLY00.0190.01533.3890.0040.0040.0000.0000.0000.000
175F231ARG10.9790.97736.2850.0550.0550.0000.0000.0000.000
176F232ILE0-0.0130.00534.9270.0050.0050.0000.0000.0000.000
177F233TYR00.0180.00837.4580.0040.0040.0000.0000.0000.000
178F234ASP-1-0.880-0.94239.208-0.052-0.0520.0000.0000.0000.000
179F235ALA0-0.020-0.00941.2260.0030.0030.0000.0000.0000.000
180F236THR0-0.089-0.04440.6290.0030.0030.0000.0000.0000.000
181F237PHE0-0.013-0.02043.5680.0010.0010.0000.0000.0000.000
182F238ARG10.9980.98946.2890.0250.0250.0000.0000.0000.000
183F239ALA0-0.055-0.03245.9970.0010.0010.0000.0000.0000.000
184F240ARG10.8840.95242.9720.0450.0450.0000.0000.0000.000
185F241GLU-1-1.004-0.97646.821-0.032-0.0320.0000.0000.0000.000
186F242GLU-1-0.996-0.99149.768-0.029-0.0290.0000.0000.0000.000