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: ZVRRN

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1881627.320891
FMO2-HF: Nuclear repulsion 1810669.746906
FMO2-HF: Total energy -70957.573985
FMO2-MP2: Total energy -71164.690783


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.
-5.582-2.8140.038-1.325-1.4810.003
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 : -0.006 / q_NPA : -0.010
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].
3A7SER00.006-0.0143.190-1.4300.8840.034-1.188-1.1600.003
4A8ARG10.8560.9294.337-2.200-1.977-0.001-0.051-0.1710.000
5A9GLU-1-0.793-0.8765.973-0.544-0.5440.0000.0000.0000.000
6A10LYS10.8720.9237.8410.3410.3410.0000.0000.0000.000
7A11ILE0-0.054-0.0208.046-0.103-0.1030.0000.0000.0000.000
8A12LEU00.0180.01710.413-0.117-0.1170.0000.0000.0000.000
9A13HIS00.0330.04511.840-0.045-0.0450.0000.0000.0000.000
10A14THR00.0300.01113.560-0.049-0.0490.0000.0000.0000.000
11A15ALA0-0.010-0.01014.850-0.034-0.0340.0000.0000.0000.000
12A16SER0-0.011-0.01115.418-0.036-0.0360.0000.0000.0000.000
13A17ARG10.8360.90617.480-0.155-0.1550.0000.0000.0000.000
14A18LEU0-0.036-0.01718.915-0.013-0.0130.0000.0000.0000.000
15A19SER0-0.022-0.01520.015-0.009-0.0090.0000.0000.0000.000
16A20GLN0-0.0030.00921.562-0.023-0.0230.0000.0000.0000.000
17A21LEU0-0.035-0.02123.947-0.010-0.0100.0000.0000.0000.000
18A22GLN0-0.043-0.04123.783-0.013-0.0130.0000.0000.0000.000
19A23GLY00.0800.05325.662-0.005-0.0050.0000.0000.0000.000
20A24TYR0-0.044-0.04122.7210.0250.0250.0000.0000.0000.000
21A25HIS0-0.012-0.01325.0550.0200.0200.0000.0000.0000.000
22A26ALA0-0.0010.00827.1920.0060.0060.0000.0000.0000.000
23A27THR00.0350.02920.8890.0040.0040.0000.0000.0000.000
24A28GLY00.0000.00822.6150.0100.0100.0000.0000.0000.000
25A29LEU00.046-0.00817.7590.0080.0080.0000.0000.0000.000
26A30ASN0-0.008-0.01317.6810.0570.0570.0000.0000.0000.000
27A31GLN0-0.022-0.00818.9240.0160.0160.0000.0000.0000.000
28A32ILE00.0560.03214.5690.0010.0010.0000.0000.0000.000
29A33VAL0-0.037-0.01813.5170.0340.0340.0000.0000.0000.000
30A34LYS10.9280.96014.693-0.147-0.1470.0000.0000.0000.000
31A35GLU-1-0.816-0.89717.1920.1210.1210.0000.0000.0000.000
32A36SER0-0.0350.00511.8280.0220.0220.0000.0000.0000.000
33A37GLY00.0000.01112.338-0.030-0.0300.0000.0000.0000.000
34A38ALA0-0.028-0.0108.2360.0270.0270.0000.0000.0000.000
35A39PRO00.0200.0077.614-0.066-0.0660.0000.0000.0000.000
36A40LYS10.9320.9409.240-0.196-0.1960.0000.0000.0000.000
37A41GLY00.0830.0457.994-0.004-0.0040.0000.0000.0000.000
38A42SER0-0.030-0.0128.9220.0860.0860.0000.0000.0000.000
39A43LEU00.0520.00111.5840.0210.0210.0000.0000.0000.000
40A44TYR0-0.045-0.0055.712-0.148-0.1480.0000.0000.0000.000
41A45HIS00.011-0.0203.684-1.135-0.9040.005-0.086-0.1500.000
42A46PHE0-0.043-0.0098.928-0.096-0.0960.0000.0000.0000.000
43A47PHE00.0740.03110.690-0.046-0.0460.0000.0000.0000.000
44A48PRO0-0.039-0.01913.990-0.056-0.0560.0000.0000.0000.000
45A49ASN00.0450.06116.892-0.020-0.0200.0000.0000.0000.000
46A50GLY0-0.038-0.03217.737-0.027-0.0270.0000.0000.0000.000
47A51LYS10.8090.87918.130-0.158-0.1580.0000.0000.0000.000
48A52GLU-1-0.806-0.86619.7710.1600.1600.0000.0000.0000.000
49A53GLU-1-0.853-0.93315.1360.3940.3940.0000.0000.0000.000
50A54LEU0-0.023-0.01113.4920.0050.0050.0000.0000.0000.000
51A55ALA00.004-0.00516.284-0.015-0.0150.0000.0000.0000.000
52A56ILE00.0220.01918.111-0.026-0.0260.0000.0000.0000.000
53A57GLU-1-0.815-0.89712.4540.2720.2720.0000.0000.0000.000
54A58ALA00.001-0.00515.673-0.028-0.0280.0000.0000.0000.000
55A59VAL00.0150.01316.785-0.035-0.0350.0000.0000.0000.000
56A60THR00.0120.00216.809-0.032-0.0320.0000.0000.0000.000
57A61TYR0-0.128-0.10211.682-0.010-0.0100.0000.0000.0000.000
58A62THR0-0.003-0.02016.205-0.032-0.0320.0000.0000.0000.000
59A63GLY00.014-0.00919.329-0.017-0.0170.0000.0000.0000.000
60A64LYS10.9450.98613.512-0.021-0.0210.0000.0000.0000.000
61A65ILE00.0010.01316.314-0.014-0.0140.0000.0000.0000.000
62A66VAL0-0.009-0.00619.961-0.009-0.0090.0000.0000.0000.000
63A67GLU-1-0.865-0.92622.581-0.020-0.0200.0000.0000.0000.000
64A68HIS00.017-0.00717.856-0.002-0.0020.0000.0000.0000.000
65A69LEU0-0.021-0.00122.880-0.005-0.0050.0000.0000.0000.000
66A70ILE0-0.0010.02725.420-0.001-0.0010.0000.0000.0000.000
67A71GLN00.0330.00925.7060.0030.0030.0000.0000.0000.000
68A72GLN0-0.019-0.02925.7180.0010.0010.0000.0000.0000.000
69A73SER0-0.038-0.05127.7120.0010.0010.0000.0000.0000.000
70A74MET0-0.058-0.01330.7340.0030.0030.0000.0000.0000.000
71A75ASP-1-0.857-0.92029.001-0.047-0.0470.0000.0000.0000.000
72A76GLU-1-0.888-0.91231.507-0.039-0.0390.0000.0000.0000.000
73A77SER0-0.022-0.04634.1280.0010.0010.0000.0000.0000.000
74A78SER0-0.0120.00037.1610.0000.0000.0000.0000.0000.000
75A79ASP-1-0.809-0.90939.452-0.013-0.0130.0000.0000.0000.000
76A80PRO00.0220.01538.3460.0000.0000.0000.0000.0000.000
77A81VAL0-0.0040.01038.6620.0010.0010.0000.0000.0000.000
78A82GLU-1-0.880-0.91639.522-0.020-0.0200.0000.0000.0000.000
79A83ALA00.0050.00335.1880.0000.0000.0000.0000.0000.000
80A84ILE0-0.016-0.01635.2080.0000.0000.0000.0000.0000.000
81A85GLN0-0.009-0.01235.9500.0000.0000.0000.0000.0000.000
82A86LEU00.0010.01734.7700.0020.0020.0000.0000.0000.000
83A87PHE00.0090.01028.1530.0000.0000.0000.0000.0000.000
84A88ILE00.0110.00432.5240.0020.0020.0000.0000.0000.000
85A89LYS10.9040.94934.8910.0140.0140.0000.0000.0000.000
86A90LYS10.8200.90429.3090.0350.0350.0000.0000.0000.000
87A91THR0-0.074-0.02829.5730.0030.0030.0000.0000.0000.000
88A92ALA00.0500.01431.4760.0040.0040.0000.0000.0000.000
89A93SER0-0.088-0.05532.1480.0010.0010.0000.0000.0000.000
90A94GLN00.0180.01329.4500.0030.0030.0000.0000.0000.000
91A95PHE00.011-0.02031.1890.0030.0030.0000.0000.0000.000
92A96ASP-1-0.868-0.90234.226-0.006-0.0060.0000.0000.0000.000
93A97ASN0-0.011-0.00733.0140.0010.0010.0000.0000.0000.000
94A98THR00.026-0.01632.5140.0020.0020.0000.0000.0000.000
95A99GLU-1-0.995-0.98928.7370.0100.0100.0000.0000.0000.000
96A100SER0-0.033-0.01327.9690.0010.0010.0000.0000.0000.000
97A101ILE0-0.065-0.00628.377-0.001-0.0010.0000.0000.0000.000
98A102LYS10.8920.96924.777-0.011-0.0110.0000.0000.0000.000
99A103GLY00.0300.00526.522-0.002-0.0020.0000.0000.0000.000
100A104ILE0-0.0050.01228.098-0.007-0.0070.0000.0000.0000.000
101A105PRO0-0.062-0.05123.8750.0070.0070.0000.0000.0000.000
102A106VAL00.0280.01723.2560.0120.0120.0000.0000.0000.000
103A107GLY00.0640.03925.5710.0070.0070.0000.0000.0000.000
104A108LEU0-0.0370.01227.8250.0000.0000.0000.0000.0000.000
105A109LEU00.0850.03722.7820.0040.0040.0000.0000.0000.000
106A110ALA0-0.007-0.00126.9920.0040.0040.0000.0000.0000.000
107A111SER0-0.041-0.03428.811-0.003-0.0030.0000.0000.0000.000
108A112GLU-1-0.821-0.89928.4590.1010.1010.0000.0000.0000.000
109A113THR0-0.080-0.07826.4370.0020.0020.0000.0000.0000.000
110A114ALA00.0350.03129.7670.0000.0000.0000.0000.0000.000
111A115LEU0-0.018-0.01631.929-0.001-0.0010.0000.0000.0000.000
112A116ILE0-0.073-0.01930.0130.0010.0010.0000.0000.0000.000
113A117SER0-0.002-0.04226.139-0.003-0.0030.0000.0000.0000.000
114A118GLU-1-0.716-0.82128.8420.0680.0680.0000.0000.0000.000
115A119PRO0-0.029-0.00324.308-0.005-0.0050.0000.0000.0000.000
116A120LEU00.0310.01522.4800.0010.0010.0000.0000.0000.000
117A121ARG10.8470.91025.282-0.070-0.0700.0000.0000.0000.000
118A122THR0-0.014-0.02726.231-0.010-0.0100.0000.0000.0000.000
119A123VAL0-0.046-0.02820.841-0.009-0.0090.0000.0000.0000.000
120A124CYS0-0.0030.00524.169-0.006-0.0060.0000.0000.0000.000
121A125MET0-0.031-0.00125.995-0.010-0.0100.0000.0000.0000.000
122A126LYS10.9300.95622.333-0.075-0.0750.0000.0000.0000.000
123A127VAL00.0040.03122.003-0.007-0.0070.0000.0000.0000.000
124A128PHE00.0390.04024.890-0.007-0.0070.0000.0000.0000.000
125A129LYS10.8340.90528.371-0.031-0.0310.0000.0000.0000.000
126A130SER0-0.049-0.04024.788-0.006-0.0060.0000.0000.0000.000
127A131TRP00.004-0.02123.709-0.003-0.0030.0000.0000.0000.000
128A132GLU-1-0.757-0.85228.1830.0180.0180.0000.0000.0000.000
129A133ALA00.0200.00329.088-0.003-0.0030.0000.0000.0000.000
130A134VAL0-0.040-0.00127.223-0.004-0.0040.0000.0000.0000.000
131A135PHE00.003-0.00930.222-0.003-0.0030.0000.0000.0000.000
132A136ALA00.0120.00633.599-0.002-0.0020.0000.0000.0000.000
133A137ARG10.8480.92026.5790.0210.0210.0000.0000.0000.000
134A138LYS10.8900.95734.0450.0260.0260.0000.0000.0000.000
135A139LEU0-0.029-0.01635.5380.0000.0000.0000.0000.0000.000
136A140MET0-0.039-0.02035.9880.0000.0000.0000.0000.0000.000
137A141GLU-1-0.976-0.98133.751-0.027-0.0270.0000.0000.0000.000
138A142ASN0-0.068-0.04938.612-0.002-0.0020.0000.0000.0000.000
139A143GLY0-0.026-0.00241.4540.0010.0010.0000.0000.0000.000
140A144PHE0-0.051-0.02041.3490.0020.0020.0000.0000.0000.000
141A145ALA00.0340.01842.088-0.001-0.0010.0000.0000.0000.000
142A146GLU-1-0.899-0.97037.6660.0010.0010.0000.0000.0000.000
143A147GLU-1-0.968-0.98739.7560.0070.0070.0000.0000.0000.000
144A148GLU-1-0.865-0.94341.2740.0000.0000.0000.0000.0000.000
145A149ALA00.0050.01938.1510.0010.0010.0000.0000.0000.000
146A150ASN00.017-0.00835.5500.0000.0000.0000.0000.0000.000
147A151GLN0-0.055-0.02037.3260.0020.0020.0000.0000.0000.000
148A152LEU00.0050.00039.5950.0020.0020.0000.0000.0000.000
149A153GLY00.0390.02935.4670.0000.0000.0000.0000.0000.000
150A154THR0-0.095-0.06135.1250.0020.0020.0000.0000.0000.000
151A155LEU00.0100.01536.2630.0020.0020.0000.0000.0000.000
152A156ILE00.0190.01134.9570.0010.0010.0000.0000.0000.000
153A157ASN0-0.040-0.02731.3480.0000.0000.0000.0000.0000.000
154A158SER0-0.074-0.04634.0630.0030.0030.0000.0000.0000.000
155A159MET0-0.009-0.01436.3470.0010.0010.0000.0000.0000.000
156A160ILE00.0160.01232.3340.0000.0000.0000.0000.0000.000
157A161GLU-1-0.797-0.92129.7820.0400.0400.0000.0000.0000.000
158A162GLY00.0140.00033.7880.0030.0030.0000.0000.0000.000
159A163GLY00.045-0.00237.0860.0000.0000.0000.0000.0000.000
160A164ILE0-0.0100.00930.3580.0000.0000.0000.0000.0000.000
161A165MET0-0.0320.00033.8540.0020.0020.0000.0000.0000.000
162A166LEU00.0120.00135.7080.0010.0010.0000.0000.0000.000
163A167SER0-0.010-0.01835.771-0.001-0.0010.0000.0000.0000.000
164A168LEU0-0.025-0.01031.7090.0000.0000.0000.0000.0000.000
165A169THR0-0.112-0.05935.3110.0020.0020.0000.0000.0000.000
166A170ASN0-0.032-0.02038.3000.0010.0010.0000.0000.0000.000
167A171LYS10.9010.96034.912-0.034-0.0340.0000.0000.0000.000
168A172ASP-1-0.785-0.87537.7390.0070.0070.0000.0000.0000.000
169A173LYS10.8530.91436.6990.0050.0050.0000.0000.0000.000
170A174THR0-0.035-0.04438.513-0.002-0.0020.0000.0000.0000.000
171A175PRO0-0.025-0.00739.654-0.001-0.0010.0000.0000.0000.000
172A176LEU00.0210.01434.4220.0000.0000.0000.0000.0000.000
173A177LEU0-0.039-0.01638.744-0.002-0.0020.0000.0000.0000.000
174A178LEU00.0300.03240.923-0.001-0.0010.0000.0000.0000.000
175A179ILE0-0.0040.00238.767-0.001-0.0010.0000.0000.0000.000
176A180ALA0-0.015-0.01039.367-0.001-0.0010.0000.0000.0000.000
177A181GLU-1-0.945-0.98440.931-0.002-0.0020.0000.0000.0000.000
178A182GLN0-0.047-0.02443.7860.0000.0000.0000.0000.0000.000
179A183ILE00.000-0.00139.9910.0000.0000.0000.0000.0000.000
180A184PRO00.0010.00443.0000.0000.0000.0000.0000.0000.000
181A185VAL0-0.0070.00945.7890.0000.0000.0000.0000.0000.000
182A186LEU0-0.039-0.01543.1120.0010.0010.0000.0000.0000.000
183A187VAL0-0.024-0.00240.6690.0010.0010.0000.0000.0000.000
184A188ARG10.9100.95944.116-0.002-0.0020.0000.0000.0000.000