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: 6YLLZ

Calculation Name: 1SGM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SGM

Chain ID: A

ChEMBL ID:

UniProt ID: P42105

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1881143.190409
FMO2-HF: Nuclear repulsion 1810186.738684
FMO2-HF: Total energy -70956.451725
FMO2-MP2: Total energy -71163.677463


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:5:GLY)


Summations of interaction energy for fragment #1(A:5:GLY)
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.
-5.24-2.2220.051-1.485-1.5860.004
Interaction energy analysis for fragmet #1(A:5:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.008
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].
3A7SER0-0.003-0.0163.344-3.282-0.8170.033-1.329-1.1700.004
4A8ARG10.9650.9973.770-0.2050.011-0.001-0.034-0.1820.000
5A9GLU-1-0.807-0.8715.673-0.549-0.5490.0000.0000.0000.000
6A10LYS10.9510.9857.6050.0810.0810.0000.0000.0000.000
7A11ILE0-0.0260.0127.580-0.018-0.0180.0000.0000.0000.000
8A12LEU00.0300.0159.821-0.022-0.0220.0000.0000.0000.000
9A13HIS00.0130.03311.5510.0420.0420.0000.0000.0000.000
10A14THR00.006-0.00813.1440.0180.0180.0000.0000.0000.000
11A15ALA0-0.015-0.01414.2830.0000.0000.0000.0000.0000.000
12A16SER0-0.020-0.02315.279-0.006-0.0060.0000.0000.0000.000
13A17ARG10.9050.96017.441-0.048-0.0480.0000.0000.0000.000
14A18LEU0-0.036-0.01718.2290.0030.0030.0000.0000.0000.000
15A19SER0-0.0030.00419.7360.0000.0000.0000.0000.0000.000
16A20GLN00.0200.01721.6620.0000.0000.0000.0000.0000.000
17A21LEU0-0.038-0.02323.4640.0010.0010.0000.0000.0000.000
18A22GLN0-0.045-0.04423.2660.0090.0090.0000.0000.0000.000
19A23GLY00.0830.05025.0380.0010.0010.0000.0000.0000.000
20A24TYR0-0.024-0.02321.7780.0070.0070.0000.0000.0000.000
21A25HIS0-0.022-0.02624.2800.0090.0090.0000.0000.0000.000
22A26ALA00.0080.01326.4410.0070.0070.0000.0000.0000.000
23A27THR00.0170.01120.1840.0120.0120.0000.0000.0000.000
24A28GLY0-0.013-0.00621.916-0.004-0.0040.0000.0000.0000.000
25A29LEU00.048-0.00916.9170.0080.0080.0000.0000.0000.000
26A30ASN0-0.004-0.00917.0270.0370.0370.0000.0000.0000.000
27A31GLN0-0.0270.00218.4660.0210.0210.0000.0000.0000.000
28A32ILE00.0490.03113.9190.0150.0150.0000.0000.0000.000
29A33VAL0-0.044-0.01813.2410.0320.0320.0000.0000.0000.000
30A34LYS10.9250.95514.534-0.109-0.1090.0000.0000.0000.000
31A35GLU-1-0.850-0.94117.0240.1080.1080.0000.0000.0000.000
32A36SER0-0.0140.01211.5340.0360.0360.0000.0000.0000.000
33A37GLY0-0.028-0.00312.4310.0110.0110.0000.0000.0000.000
34A38ALA0-0.022-0.0138.0930.1610.1610.0000.0000.0000.000
35A39PRO00.0090.0068.134-0.205-0.2050.0000.0000.0000.000
36A40LYS10.9360.9489.195-0.177-0.1770.0000.0000.0000.000
37A41GLY00.0800.0397.363-0.050-0.0500.0000.0000.0000.000
38A42SER0-0.025-0.0158.261-0.179-0.1790.0000.0000.0000.000
39A43LEU00.049-0.00210.784-0.054-0.0540.0000.0000.0000.000
40A44TYR0-0.061-0.0085.1330.0340.0340.0000.0000.0000.000
41A45HIS00.011-0.0233.225-0.721-0.3840.019-0.122-0.2340.000
42A46PHE0-0.065-0.0148.130-0.104-0.1040.0000.0000.0000.000
43A47PHE00.0970.04211.0200.0410.0410.0000.0000.0000.000
44A48PRO0-0.0160.00513.3880.0000.0000.0000.0000.0000.000
45A49ASN0-0.0130.02616.095-0.015-0.0150.0000.0000.0000.000
46A50GLY0-0.026-0.03316.8740.0100.0100.0000.0000.0000.000
47A51LYS10.8340.90917.175-0.034-0.0340.0000.0000.0000.000
48A52GLU-1-0.803-0.87318.859-0.046-0.0460.0000.0000.0000.000
49A53GLU-1-0.815-0.91215.051-0.095-0.0950.0000.0000.0000.000
50A54LEU0-0.025-0.01312.717-0.020-0.0200.0000.0000.0000.000
51A55ALA0-0.007-0.00815.471-0.022-0.0220.0000.0000.0000.000
52A56ILE00.0110.01418.456-0.009-0.0090.0000.0000.0000.000
53A57GLU-1-0.914-0.96513.302-0.274-0.2740.0000.0000.0000.000
54A58ALA0-0.019-0.01115.723-0.026-0.0260.0000.0000.0000.000
55A59VAL00.0170.00616.600-0.007-0.0070.0000.0000.0000.000
56A60THR00.0290.01916.5820.0020.0020.0000.0000.0000.000
57A61TYR0-0.135-0.11611.7190.0200.0200.0000.0000.0000.000
58A62THR0-0.001-0.01216.2500.0020.0020.0000.0000.0000.000
59A63GLY00.012-0.00719.3760.0070.0070.0000.0000.0000.000
60A64LYS10.9590.98913.5050.3560.3560.0000.0000.0000.000
61A65ILE0-0.0100.01116.6950.0060.0060.0000.0000.0000.000
62A66VAL0-0.017-0.00919.9970.0100.0100.0000.0000.0000.000
63A67GLU-1-0.923-0.95222.360-0.143-0.1430.0000.0000.0000.000
64A68HIS00.011-0.01217.6360.0190.0190.0000.0000.0000.000
65A69LEU0-0.039-0.01222.9450.0090.0090.0000.0000.0000.000
66A70ILE0-0.0110.00725.4500.0070.0070.0000.0000.0000.000
67A71GLN00.0500.01825.7340.0040.0040.0000.0000.0000.000
68A72GLN0-0.026-0.04325.7750.0050.0050.0000.0000.0000.000
69A73SER0-0.023-0.02827.7330.0090.0090.0000.0000.0000.000
70A74MET0-0.051-0.01430.7580.0080.0080.0000.0000.0000.000
71A75ASP-1-0.885-0.93629.222-0.089-0.0890.0000.0000.0000.000
72A76GLU-1-0.938-0.94531.290-0.062-0.0620.0000.0000.0000.000
73A77SER0-0.023-0.03734.1460.0040.0040.0000.0000.0000.000
74A78SER0-0.005-0.00137.180-0.003-0.0030.0000.0000.0000.000
75A79ASP-1-0.831-0.92339.468-0.040-0.0400.0000.0000.0000.000
76A80PRO00.0160.01238.368-0.001-0.0010.0000.0000.0000.000
77A81VAL00.0050.01338.689-0.001-0.0010.0000.0000.0000.000
78A82GLU-1-0.844-0.90039.719-0.040-0.0400.0000.0000.0000.000
79A83ALA00.0030.00235.179-0.001-0.0010.0000.0000.0000.000
80A84ILE0-0.024-0.02035.237-0.002-0.0020.0000.0000.0000.000
81A85GLN0-0.050-0.03235.9830.0000.0000.0000.0000.0000.000
82A86LEU00.0080.02134.7850.0020.0020.0000.0000.0000.000
83A87PHE00.0000.00928.163-0.001-0.0010.0000.0000.0000.000
84A88ILE00.0290.01432.5600.0010.0010.0000.0000.0000.000
85A89LYS10.9440.97834.9300.0350.0350.0000.0000.0000.000
86A90LYS10.8730.94829.0970.0720.0720.0000.0000.0000.000
87A91THR0-0.109-0.05830.0530.0030.0030.0000.0000.0000.000
88A92ALA00.0620.01831.5170.0030.0030.0000.0000.0000.000
89A93SER0-0.118-0.06532.1240.0040.0040.0000.0000.0000.000
90A94GLN00.0430.02129.5320.0030.0030.0000.0000.0000.000
91A95PHE0-0.013-0.02931.1890.0040.0040.0000.0000.0000.000
92A96ASP-1-0.977-0.96934.059-0.014-0.0140.0000.0000.0000.000
93A97ASN00.0530.03432.9660.0050.0050.0000.0000.0000.000
94A98THR00.002-0.04132.5140.0000.0000.0000.0000.0000.000
95A99GLU-1-1.007-0.99728.6420.0190.0190.0000.0000.0000.000
96A100SER0-0.031-0.01127.9690.0020.0020.0000.0000.0000.000
97A101ILE0-0.0570.00328.377-0.006-0.0060.0000.0000.0000.000
98A102LYS10.8700.96225.2460.0620.0620.0000.0000.0000.000
99A103GLY00.0250.00026.2790.0010.0010.0000.0000.0000.000
100A104ILE00.0000.01227.850-0.004-0.0040.0000.0000.0000.000
101A105PRO0-0.057-0.04024.136-0.001-0.0010.0000.0000.0000.000
102A106VAL00.0220.01323.447-0.003-0.0030.0000.0000.0000.000
103A107GLY00.0590.02825.5990.0040.0040.0000.0000.0000.000
104A108LEU0-0.0110.02527.3900.0030.0030.0000.0000.0000.000
105A109LEU00.0490.01822.1810.0030.0030.0000.0000.0000.000
106A110ALA00.0220.00126.5620.0020.0020.0000.0000.0000.000
107A111SER0-0.036-0.02128.5640.0020.0020.0000.0000.0000.000
108A112GLU-1-0.850-0.91727.809-0.005-0.0050.0000.0000.0000.000
109A113THR0-0.080-0.07225.7870.0010.0010.0000.0000.0000.000
110A114ALA00.0370.03029.180-0.001-0.0010.0000.0000.0000.000
111A115LEU0-0.019-0.01531.546-0.001-0.0010.0000.0000.0000.000
112A116ILE0-0.074-0.01628.9850.0030.0030.0000.0000.0000.000
113A117SER0-0.013-0.03425.470-0.005-0.0050.0000.0000.0000.000
114A118GLU-1-0.693-0.82328.403-0.044-0.0440.0000.0000.0000.000
115A119PRO0-0.0330.01724.026-0.006-0.0060.0000.0000.0000.000
116A120LEU00.0500.01521.938-0.010-0.0100.0000.0000.0000.000
117A121ARG10.8280.90724.9620.0390.0390.0000.0000.0000.000
118A122THR0-0.030-0.05626.298-0.003-0.0030.0000.0000.0000.000
119A123VAL0-0.035-0.02020.835-0.006-0.0060.0000.0000.0000.000
120A124CYS0-0.0010.01424.213-0.006-0.0060.0000.0000.0000.000
121A125MET0-0.0300.00126.0420.0010.0010.0000.0000.0000.000
122A126LYS10.9290.95122.5080.1240.1240.0000.0000.0000.000
123A127VAL00.0120.03422.196-0.005-0.0050.0000.0000.0000.000
124A128PHE00.0390.05524.930-0.002-0.0020.0000.0000.0000.000
125A129LYS10.9390.97428.4120.0630.0630.0000.0000.0000.000
126A130SER0-0.057-0.05824.914-0.002-0.0020.0000.0000.0000.000
127A131TRP00.007-0.01823.8290.0030.0030.0000.0000.0000.000
128A132GLU-1-0.864-0.94628.218-0.058-0.0580.0000.0000.0000.000
129A133ALA00.0080.00029.1090.0030.0030.0000.0000.0000.000
130A134VAL0-0.043-0.00327.0570.0010.0010.0000.0000.0000.000
131A135PHE00.011-0.00530.2490.0030.0030.0000.0000.0000.000
132A136ALA00.0230.01233.6280.0030.0030.0000.0000.0000.000
133A137ARG10.9130.95027.1240.1050.1050.0000.0000.0000.000
134A138LYS10.8840.95734.0780.0650.0650.0000.0000.0000.000
135A139LEU0-0.018-0.00935.5590.0030.0030.0000.0000.0000.000
136A140MET0-0.043-0.02336.0860.0020.0020.0000.0000.0000.000
137A141GLU-1-0.994-0.98634.143-0.073-0.0730.0000.0000.0000.000
138A142ASN0-0.053-0.03938.628-0.001-0.0010.0000.0000.0000.000
139A143GLY0-0.026-0.00541.4710.0030.0030.0000.0000.0000.000
140A144PHE0-0.036-0.01541.3610.0020.0020.0000.0000.0000.000
141A145ALA00.0360.02142.110-0.002-0.0020.0000.0000.0000.000
142A146GLU-1-0.915-0.97537.823-0.059-0.0590.0000.0000.0000.000
143A147GLU-1-0.964-0.98539.782-0.041-0.0410.0000.0000.0000.000
144A148GLU-1-0.876-0.95141.305-0.038-0.0380.0000.0000.0000.000
145A149ALA00.0010.01938.1350.0000.0000.0000.0000.0000.000
146A150ASN00.0400.00035.867-0.004-0.0040.0000.0000.0000.000
147A151GLN0-0.051-0.02937.3590.0000.0000.0000.0000.0000.000
148A152LEU00.004-0.00139.6320.0010.0010.0000.0000.0000.000
149A153GLY00.0340.02635.5010.0000.0000.0000.0000.0000.000
150A154THR0-0.051-0.00635.1620.0000.0000.0000.0000.0000.000
151A155LEU00.0020.00336.3020.0010.0010.0000.0000.0000.000
152A156ILE00.0210.00635.1080.0020.0020.0000.0000.0000.000
153A157ASN0-0.043-0.02631.0790.0000.0000.0000.0000.0000.000
154A158SER0-0.079-0.04434.1040.0030.0030.0000.0000.0000.000
155A159MET0-0.016-0.01736.3910.0020.0020.0000.0000.0000.000
156A160ILE00.0190.01332.3220.0030.0030.0000.0000.0000.000
157A161GLU-1-0.809-0.92030.083-0.048-0.0480.0000.0000.0000.000
158A162GLY00.003-0.00733.8360.0030.0030.0000.0000.0000.000
159A163GLY00.042-0.00337.1340.0030.0030.0000.0000.0000.000
160A164ILE0-0.014-0.00330.4560.0030.0030.0000.0000.0000.000
161A165MET0-0.039-0.00433.9630.0050.0050.0000.0000.0000.000
162A166LEU00.013-0.00435.6170.0030.0030.0000.0000.0000.000
163A167SER0-0.014-0.01235.8820.0030.0030.0000.0000.0000.000
164A168LEU0-0.017-0.01031.5860.0020.0020.0000.0000.0000.000
165A169THR0-0.098-0.04435.1120.0040.0040.0000.0000.0000.000
166A170ASN0-0.035-0.02337.9620.0040.0040.0000.0000.0000.000
167A171LYS10.9060.96234.713-0.004-0.0040.0000.0000.0000.000
168A172ASP-1-0.782-0.87737.604-0.011-0.0110.0000.0000.0000.000
169A173LYS10.9680.97436.9090.0210.0210.0000.0000.0000.000
170A174THR0-0.036-0.02838.529-0.003-0.0030.0000.0000.0000.000
171A175PRO0-0.036-0.01539.658-0.001-0.0010.0000.0000.0000.000
172A176LEU00.0210.01434.572-0.002-0.0020.0000.0000.0000.000
173A177LEU0-0.041-0.01738.790-0.002-0.0020.0000.0000.0000.000
174A178LEU00.0400.03140.9640.0000.0000.0000.0000.0000.000
175A179ILE00.0050.01138.6360.0000.0000.0000.0000.0000.000
176A180ALA0-0.022-0.01839.456-0.001-0.0010.0000.0000.0000.000
177A181GLU-1-0.974-0.99440.970-0.022-0.0220.0000.0000.0000.000
178A182GLN0-0.030-0.01843.8260.0010.0010.0000.0000.0000.000
179A183ILE0-0.0050.00840.1800.0000.0000.0000.0000.0000.000
180A184PRO00.001-0.00143.035-0.001-0.0010.0000.0000.0000.000
181A185VAL00.0040.01945.8210.0000.0000.0000.0000.0000.000
182A186LEU0-0.045-0.00843.0470.0010.0010.0000.0000.0000.000
183A187VAL0-0.020-0.00140.736-0.001-0.0010.0000.0000.0000.000
184A188ARG10.8880.93644.1480.0290.0290.0000.0000.0000.000