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: QYQ4Y

Calculation Name: 1YO6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YO6

Chain ID: A

ChEMBL ID:

UniProt ID: P90780

Base Structure: X-ray

Registration Date: 2023-09-20

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 237
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2837186.819015
FMO2-HF: Nuclear repulsion 2748214.773496
FMO2-HF: Total energy -88972.045519
FMO2-MP2: Total energy -89232.961963


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(A:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-2.5312.4810.755-1.916-3.850.005
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.034
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].
3A3PRO0-0.0010.0063.688-0.0493.3760.483-1.490-2.4180.006
4A4GLY00.016-0.0036.0140.2150.2150.0000.0000.0000.000
5A5SER00.0300.0207.380-0.248-0.2480.0000.0000.0000.000
6A6VAL00.0210.00910.478-0.100-0.1000.0000.0000.0000.000
7A7VAL00.0100.02412.9060.0320.0320.0000.0000.0000.000
8A8VAL0-0.014-0.01416.336-0.046-0.0460.0000.0000.0000.000
9A9THR00.0460.02618.6480.0150.0150.0000.0000.0000.000
10A10GLY00.0130.01622.222-0.015-0.0150.0000.0000.0000.000
11A11ALA00.0300.00521.450-0.013-0.0130.0000.0000.0000.000
12A12ASN0-0.003-0.00623.388-0.004-0.0040.0000.0000.0000.000
13A13ARG11.0010.98926.1530.1060.1060.0000.0000.0000.000
14A14GLY0-0.014-0.00125.869-0.005-0.0050.0000.0000.0000.000
15A15ILE00.0380.00120.822-0.004-0.0040.0000.0000.0000.000
16A16GLY00.0910.04020.870-0.023-0.0230.0000.0000.0000.000
17A17LEU0-0.0360.00720.602-0.009-0.0090.0000.0000.0000.000
18A18GLY00.0250.00720.676-0.007-0.0070.0000.0000.0000.000
19A19LEU0-0.003-0.01515.914-0.028-0.0280.0000.0000.0000.000
20A20VAL00.0530.03915.910-0.035-0.0350.0000.0000.0000.000
21A21GLN00.005-0.00216.221-0.013-0.0130.0000.0000.0000.000
22A22GLN0-0.081-0.04214.134-0.025-0.0250.0000.0000.0000.000
23A23LEU00.008-0.00211.880-0.065-0.0650.0000.0000.0000.000
24A24VAL0-0.014-0.00111.5850.0020.0020.0000.0000.0000.000
25A25LYS10.7880.89312.5210.3200.3200.0000.0000.0000.000
26A26ASP-1-0.776-0.8476.265-1.161-1.1610.0000.0000.0000.000
27A27LYS10.9490.9518.6230.2770.2770.0000.0000.0000.000
28A28ASN0-0.041-0.0052.867-0.3710.1140.078-0.087-0.4770.000
29A29ILE0-0.0590.0074.7790.4250.555-0.001-0.004-0.1240.000
30A30ARG10.8770.9306.895-1.323-1.3230.0000.0000.0000.000
31A31HIS00.012-0.0049.160-0.087-0.0870.0000.0000.0000.000
32A32ILE00.002-0.00311.693-0.023-0.0230.0000.0000.0000.000
33A33ILE00.0090.00514.350-0.006-0.0060.0000.0000.0000.000
34A34ALA00.0130.01717.702-0.031-0.0310.0000.0000.0000.000
35A35THR00.0250.00320.4200.0110.0110.0000.0000.0000.000
36A36ALA0-0.006-0.01023.947-0.014-0.0140.0000.0000.0000.000
37A37ARG10.9651.00027.4120.0550.0550.0000.0000.0000.000
38A38ASP-1-0.820-0.90430.632-0.030-0.0300.0000.0000.0000.000
39A39VAL00.0630.01827.311-0.004-0.0040.0000.0000.0000.000
40A40GLU-1-0.920-0.96129.702-0.026-0.0260.0000.0000.0000.000
41A41LYS10.8930.92232.1920.0330.0330.0000.0000.0000.000
42A42ALA0-0.0170.01127.264-0.005-0.0050.0000.0000.0000.000
43A43THR0-0.011-0.02227.8490.0000.0000.0000.0000.0000.000
44A44GLU-1-0.876-0.93826.110-0.097-0.0970.0000.0000.0000.000
45A45LEU0-0.0150.00022.070-0.005-0.0050.0000.0000.0000.000
46A46LYS10.8750.94123.1550.0310.0310.0000.0000.0000.000
47A47SER0-0.101-0.03724.3960.0040.0040.0000.0000.0000.000
48A48ILE0-0.007-0.00118.7700.0010.0010.0000.0000.0000.000
49A49LYS10.8460.91020.5300.0460.0460.0000.0000.0000.000
50A50ASP-1-0.813-0.90614.053-0.019-0.0190.0000.0000.0000.000
51A51SER00.0680.03815.877-0.003-0.0030.0000.0000.0000.000
52A52ARG10.7320.8599.2290.0220.0220.0000.0000.0000.000
53A53VAL0-0.036-0.01114.9100.0070.0070.0000.0000.0000.000
54A54HIS00.0150.00816.248-0.012-0.0120.0000.0000.0000.000
55A55VAL0-0.004-0.01619.669-0.012-0.0120.0000.0000.0000.000
56A56LEU0-0.0080.00421.7750.0060.0060.0000.0000.0000.000
57A57PRO0-0.036-0.02224.535-0.011-0.0110.0000.0000.0000.000
58A58LEU0-0.011-0.02124.3120.0020.0020.0000.0000.0000.000
59A59THR0-0.028-0.01028.026-0.008-0.0080.0000.0000.0000.000
60A60VAL0-0.006-0.02526.5880.0040.0040.0000.0000.0000.000
61A61THR00.0890.04429.203-0.001-0.0010.0000.0000.0000.000
62A62CYM-1-0.866-0.83132.070-0.023-0.0230.0000.0000.0000.000
63A63ASP-1-0.762-0.91531.397-0.033-0.0330.0000.0000.0000.000
64A64LYS10.8760.92231.4250.0140.0140.0000.0000.0000.000
65A65SER0-0.020-0.04629.4700.0040.0040.0000.0000.0000.000
66A66LEU0-0.015-0.00726.2910.0010.0010.0000.0000.0000.000
67A67ASP-1-0.809-0.88526.566-0.010-0.0100.0000.0000.0000.000
68A68THR0-0.044-0.03127.4160.0090.0090.0000.0000.0000.000
69A69PHE0-0.004-0.00720.5200.0080.0080.0000.0000.0000.000
70A70VAL00.0200.00222.5040.0070.0070.0000.0000.0000.000
71A71SER0-0.008-0.00922.5140.0130.0130.0000.0000.0000.000
72A72LYS10.9300.97623.2020.0000.0000.0000.0000.0000.000
73A73VAL00.0180.00118.4510.0140.0140.0000.0000.0000.000
74A74GLY00.0110.00618.3820.0250.0250.0000.0000.0000.000
75A75GLU-1-1.015-1.01219.4500.1150.1150.0000.0000.0000.000
76A76ILE0-0.027-0.00616.1430.0140.0140.0000.0000.0000.000
77A77VAL0-0.076-0.03513.9160.0330.0330.0000.0000.0000.000
78A78GLY00.0730.05014.7160.0540.0540.0000.0000.0000.000
79A79SER0-0.045-0.04415.566-0.007-0.0070.0000.0000.0000.000
80A80ASP-1-0.825-0.88810.9780.5700.5700.0000.0000.0000.000
81A81GLY0-0.0100.00612.1100.0060.0060.0000.0000.0000.000
82A82LEU0-0.067-0.05012.8000.0600.0600.0000.0000.0000.000
83A83SER00.0160.0158.0520.0750.0750.0000.0000.0000.000
84A84LEU00.0090.0039.550-0.150-0.1500.0000.0000.0000.000
85A85LEU00.0120.02611.6180.0640.0640.0000.0000.0000.000
86A86ILE00.0010.00115.147-0.039-0.0390.0000.0000.0000.000
87A87ASN0-0.021-0.02816.8210.0420.0420.0000.0000.0000.000
88A88ASN0-0.035-0.04120.549-0.021-0.0210.0000.0000.0000.000
89A89ALA0-0.068-0.02322.2960.0080.0080.0000.0000.0000.000
90A90GLY00.0550.02625.488-0.002-0.0020.0000.0000.0000.000
91A91VAL0-0.058-0.03028.4720.0020.0020.0000.0000.0000.000
92A92LEU0-0.008-0.00431.838-0.003-0.0030.0000.0000.0000.000
93A93LEU0-0.0030.00334.1240.0030.0030.0000.0000.0000.000
94A94SER00.000-0.00137.675-0.002-0.0020.0000.0000.0000.000
95A95TYR00.017-0.01940.4220.0040.0040.0000.0000.0000.000
96A96GLY00.0340.00140.774-0.004-0.0040.0000.0000.0000.000
97A97THR0-0.021-0.01943.0700.0010.0010.0000.0000.0000.000
98A98ASN0-0.031-0.00345.6680.0020.0020.0000.0000.0000.000
99A99THR0-0.036-0.00145.2780.0000.0000.0000.0000.0000.000
100A100GLU-1-0.850-0.92547.717-0.036-0.0360.0000.0000.0000.000
101A101PRO0-0.009-0.01248.168-0.002-0.0020.0000.0000.0000.000
102A102ASN00.0350.01345.9420.0020.0020.0000.0000.0000.000
103A103ARG10.9750.97644.5390.0360.0360.0000.0000.0000.000
104A104ALA00.0280.01643.110-0.002-0.0020.0000.0000.0000.000
105A105VAL00.0630.03841.055-0.002-0.0020.0000.0000.0000.000
106A106ILE0-0.026-0.01239.741-0.004-0.0040.0000.0000.0000.000
107A107ALA0-0.026-0.03038.468-0.004-0.0040.0000.0000.0000.000
108A108GLU-1-0.885-0.93136.828-0.056-0.0560.0000.0000.0000.000
109A109GLN0-0.027-0.02033.217-0.004-0.0040.0000.0000.0000.000
110A110LEU0-0.004-0.01233.575-0.007-0.0070.0000.0000.0000.000
111A111ASP-1-0.871-0.91832.715-0.059-0.0590.0000.0000.0000.000
112A112VAL0-0.0160.01330.701-0.003-0.0030.0000.0000.0000.000
113A113ASN0-0.040-0.02829.012-0.008-0.0080.0000.0000.0000.000
114A114THR0-0.046-0.03528.372-0.008-0.0080.0000.0000.0000.000
115A115THR00.0360.01528.505-0.006-0.0060.0000.0000.0000.000
116A116SER00.0670.01928.8730.0030.0030.0000.0000.0000.000
117A117VAL0-0.035-0.00823.442-0.001-0.0010.0000.0000.0000.000
118A118VAL0-0.032-0.00624.268-0.005-0.0050.0000.0000.0000.000
119A119LEU00.0360.01425.5270.0030.0030.0000.0000.0000.000
120A120LEU0-0.042-0.01821.9310.0080.0080.0000.0000.0000.000
121A121THR0-0.005-0.02419.824-0.002-0.0020.0000.0000.0000.000
122A122GLN0-0.010-0.01121.3490.0070.0070.0000.0000.0000.000
123A123LYS10.8210.90123.5550.0360.0360.0000.0000.0000.000
124A124LEU0-0.014-0.00618.6480.0150.0150.0000.0000.0000.000
125A125LEU00.0260.02918.3890.0000.0000.0000.0000.0000.000
126A126PRO0-0.024-0.00218.4600.0040.0040.0000.0000.0000.000
127A127LEU00.014-0.00616.6990.0120.0120.0000.0000.0000.000
128A128LEU00.0270.03013.3530.0300.0300.0000.0000.0000.000
129A129LYS10.8270.89213.9400.0400.0400.0000.0000.0000.000
130A130ASN0-0.059-0.02815.2570.0140.0140.0000.0000.0000.000
131A131ALA00.0310.03110.2080.0350.0350.0000.0000.0000.000
132A132ALA0-0.001-0.00310.3490.0100.0100.0000.0000.0000.000
133A133SER0-0.050-0.02811.7100.0000.0000.0000.0000.0000.000
134A134LYS10.8360.94510.290-0.260-0.2600.0000.0000.0000.000
135A135GLU-1-0.923-0.9886.129-0.464-0.4640.0000.0000.0000.000
136A136SER0-0.033-0.0059.842-0.063-0.0630.0000.0000.0000.000
137A137GLY00.0200.00811.302-0.020-0.0200.0000.0000.0000.000
138A138ASP-1-0.918-0.95213.452-0.163-0.1630.0000.0000.0000.000
139A139GLN0-0.066-0.0409.590-0.007-0.0070.0000.0000.0000.000
140A140LEU00.0020.00210.215-0.049-0.0490.0000.0000.0000.000
141A141SER00.0750.0255.575-0.013-0.0130.0000.0000.0000.000
142A142VAL00.009-0.0186.9610.1950.1950.0000.0000.0000.000
143A143SER0-0.035-0.0122.727-0.928-0.1220.196-0.331-0.671-0.001
144A144ARG10.8050.9294.7970.8180.984-0.001-0.004-0.1600.000
145A145ALA00.053-0.0066.8660.2730.2730.0000.0000.0000.000
146A146ALA0-0.034-0.00410.229-0.081-0.0810.0000.0000.0000.000
147A147VAL0-0.0070.00112.1890.0550.0550.0000.0000.0000.000
148A148ILE0-0.031-0.02312.419-0.011-0.0110.0000.0000.0000.000
149A149THR00.0020.01316.5780.0410.0410.0000.0000.0000.000
150A150ILE0-0.0170.00018.543-0.018-0.0180.0000.0000.0000.000
151A151SER0-0.014-0.03421.6530.0330.0330.0000.0000.0000.000
152A152SER00.037-0.01724.5230.0040.0040.0000.0000.0000.000
153A153GLY00.0680.02926.8440.0020.0020.0000.0000.0000.000
154A154LEU0-0.089-0.03828.0910.0080.0080.0000.0000.0000.000
155A155GLY0-0.003-0.01529.2640.0090.0090.0000.0000.0000.000
156A156SER0-0.093-0.07928.7420.0030.0030.0000.0000.0000.000
157A157ILE00.004-0.03030.3500.0060.0060.0000.0000.0000.000
158A158THR00.0240.00431.5050.0070.0070.0000.0000.0000.000
159A159ASP-1-0.834-0.87129.948-0.125-0.1250.0000.0000.0000.000
160A160ASN0-0.066-0.03733.3760.0020.0020.0000.0000.0000.000
161A161THR00.0310.01635.8950.0050.0050.0000.0000.0000.000
162A162SER0-0.008-0.00436.8760.0030.0030.0000.0000.0000.000
163A163GLY00.0160.02538.9720.0040.0040.0000.0000.0000.000
164A164SER00.001-0.01639.290-0.003-0.0030.0000.0000.0000.000
165A165ALA0-0.022-0.00141.3790.0020.0020.0000.0000.0000.000
166A166GLN00.0230.01042.3740.0020.0020.0000.0000.0000.000
167A167PHE00.0420.02038.838-0.001-0.0010.0000.0000.0000.000
168A168PRO00.0380.04040.369-0.002-0.0020.0000.0000.0000.000
169A169VAL00.0310.00135.862-0.001-0.0010.0000.0000.0000.000
170A170LEU00.0090.01136.733-0.005-0.0050.0000.0000.0000.000
171A171ALA00.0280.01237.382-0.003-0.0030.0000.0000.0000.000
172A172TYR00.0300.01929.329-0.005-0.0050.0000.0000.0000.000
173A173ARG10.8690.93632.8910.0840.0840.0000.0000.0000.000
174A174MET0-0.0020.00032.915-0.004-0.0040.0000.0000.0000.000
175A175SER0-0.034-0.01832.159-0.004-0.0040.0000.0000.0000.000
176A176LYS10.9000.93625.8540.1400.1400.0000.0000.0000.000
177A177ALA00.0360.03528.452-0.009-0.0090.0000.0000.0000.000
178A178ALA0-0.002-0.00129.708-0.004-0.0040.0000.0000.0000.000
179A179ILE0-0.0060.00624.927-0.004-0.0040.0000.0000.0000.000
180A180ASN00.0140.01825.182-0.025-0.0250.0000.0000.0000.000
181A181MET00.0030.01125.732-0.009-0.0090.0000.0000.0000.000
182A182PHE00.0120.00722.7500.0000.0000.0000.0000.0000.000
183A183GLY00.0520.02922.090-0.001-0.0010.0000.0000.0000.000
184A184ARG10.8700.92822.0070.1450.1450.0000.0000.0000.000
185A185THR0-0.017-0.02624.1730.0030.0030.0000.0000.0000.000
186A186LEU0-0.0040.00719.7010.0050.0050.0000.0000.0000.000
187A187ALA00.028-0.00119.3310.0010.0010.0000.0000.0000.000
188A188VAL0-0.093-0.04820.2980.0000.0000.0000.0000.0000.000
189A189ASP-1-0.860-0.93422.844-0.082-0.0820.0000.0000.0000.000
190A190LEU0-0.065-0.02918.1490.0120.0120.0000.0000.0000.000
191A191LYS10.8910.94918.2930.1590.1590.0000.0000.0000.000
192A192ASP-1-0.896-0.95218.333-0.082-0.0820.0000.0000.0000.000
193A193ASP-1-0.845-0.90017.471-0.043-0.0430.0000.0000.0000.000
194A194ASN0-0.014-0.01913.177-0.024-0.0240.0000.0000.0000.000
195A195VAL00.0000.02312.920-0.055-0.0550.0000.0000.0000.000
196A196LEU0-0.037-0.01110.9570.0190.0190.0000.0000.0000.000
197A197VAL00.0130.02013.8510.0110.0110.0000.0000.0000.000
198A198VAL0-0.037-0.00314.6100.0060.0060.0000.0000.0000.000
199A199ASN00.0130.01117.385-0.003-0.0030.0000.0000.0000.000
200A200PHE00.0450.01214.595-0.004-0.0040.0000.0000.0000.000
201A201CYS0-0.0460.01020.1330.0350.0350.0000.0000.0000.000
202A202PRO0-0.0120.00721.882-0.019-0.0190.0000.0000.0000.000
203A203GLY00.010-0.00222.8080.0130.0130.0000.0000.0000.000
204A204TRP00.0260.02225.3700.0020.0020.0000.0000.0000.000
205A218VAL00.0320.00024.644-0.004-0.0040.0000.0000.0000.000
206A219GLU-1-0.805-0.89919.668-0.241-0.2410.0000.0000.0000.000
207A220GLN00.0160.00319.617-0.025-0.0250.0000.0000.0000.000
208A221SER00.0530.01619.591-0.021-0.0210.0000.0000.0000.000
209A222THR0-0.011-0.00717.781-0.028-0.0280.0000.0000.0000.000
210A223ALA00.0480.02815.537-0.059-0.0590.0000.0000.0000.000
211A224GLU-1-0.813-0.89514.584-0.340-0.3400.0000.0000.0000.000
212A225LEU0-0.037-0.01914.976-0.043-0.0430.0000.0000.0000.000
213A226ILE00.0240.01310.540-0.061-0.0610.0000.0000.0000.000
214A227SER00.0020.01310.272-0.196-0.1960.0000.0000.0000.000
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