FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 6GR5Z

Calculation Name: 2GSC-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2GSC

Chain ID: A

ChEMBL ID:

UniProt ID: Q8PD29

Base Structure: X-ray

Registration Date: 2025-07-08

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 226
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -976420.127302
FMO2-HF: Nuclear repulsion 929367.950756
FMO2-HF: Total energy -47052.176547
FMO2-MP2: Total energy -47189.54603


3D Structure Molmil
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:9:ARG)


Summations of interaction energy for fragment #1(A:9:ARG)
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.
-9.102-9.4560.0761.811-1.5320.003
Interaction energy analysis for fragmet #1(A:9:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.117 / q_NPA : -0.015
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].
4A11HIS00.1750.0063.831-1.675-0.310-0.006-0.748-0.6110.004
5A11HIS0-0.0470.1233.741-1.142-1.2490.0090.421-0.323-0.001
6A12GLU00.017-0.1183.9321.9282.032-0.001-0.026-0.0760.000
7A12GLU-1-0.923-0.8142.957-7.468-9.2640.0762.167-0.4470.000
8A13ARG00.090-0.0825.2670.4750.555-0.002-0.003-0.0750.000
9A13ARG10.8471.0455.110-0.498-0.4980.0000.0000.0000.000
10A14LEU00.024-0.1137.8010.4280.4280.0000.0000.0000.000
11A14LEU0-0.1140.0888.4220.0630.0630.0000.0000.0000.000
12A15ASP00.187-0.10810.129-0.285-0.2850.0000.0000.0000.000
13A15ASP-1-0.949-0.81014.508-0.562-0.5620.0000.0000.0000.000
14A16ALA00.128-0.06813.274-0.055-0.0550.0000.0000.0000.000
15A16ALA0-0.0900.09513.1890.0200.0200.0000.0000.0000.000
16A17TRP00.089-0.0969.3630.1690.1690.0000.0000.0000.000
17A17TRP0-0.1040.0987.536-0.327-0.3270.0000.0000.0000.000
18A18ARG00.083-0.06510.837-0.081-0.0810.0000.0000.0000.000
19A18ARG10.8921.0569.7201.1501.1500.0000.0000.0000.000
20A19ASP00.153-0.08211.698-0.020-0.0200.0000.0000.0000.000
21A19ASP-1-0.902-0.80415.924-0.628-0.6280.0000.0000.0000.000
22A20SER00.005-0.06913.9830.0950.0950.0000.0000.0000.000
23A20SER0-0.0440.03612.6520.0040.0040.0000.0000.0000.000
24A21MET00.081-0.12512.0990.1510.1510.0000.0000.0000.000
25A21MET0-0.1260.10910.011-0.016-0.0160.0000.0000.0000.000
26A22GLU00.143-0.09413.4140.0330.0330.0000.0000.0000.000
27A22GLU-1-1.013-0.83416.149-0.642-0.6420.0000.0000.0000.000
28A23LEU00.117-0.10116.2620.0680.0680.0000.0000.0000.000
29A23LEU0-0.1230.07517.7340.0060.0060.0000.0000.0000.000
30A24VAL00.053-0.10516.4010.0940.0940.0000.0000.0000.000
31A24VAL0-0.0860.08815.111-0.001-0.0010.0000.0000.0000.000
32A25GLU00.091-0.11017.0900.0680.0680.0000.0000.0000.000
33A25GLU-1-0.936-0.80616.878-0.728-0.7280.0000.0000.0000.000
34A26MET00.028-0.13018.5330.0400.0400.0000.0000.0000.000
35A26MET0-0.0690.10820.5050.0040.0040.0000.0000.0000.000
36A27ILE00.058-0.05821.0060.0500.0500.0000.0000.0000.000
37A27ILE0-0.0760.08420.9610.0020.0020.0000.0000.0000.000
38A28TYR00.112-0.11021.1650.0510.0510.0000.0000.0000.000
39A28TYR0-0.1230.07318.4710.0100.0100.0000.0000.0000.000
40A29ARG00.157-0.05622.5320.0300.0300.0000.0000.0000.000
41A29ARG10.8031.03020.6030.5060.5060.0000.0000.0000.000
42A30LEU00.158-0.09924.5530.0280.0280.0000.0000.0000.000
43A30LEU0-0.1790.08725.8700.0030.0030.0000.0000.0000.000
44A31THR0-0.080-0.07225.8910.0260.0260.0000.0000.0000.000
45A31THR0-0.0670.03525.164-0.004-0.0040.0000.0000.0000.000
46A32GLU00.068-0.11627.3720.0180.0180.0000.0000.0000.000
47A32GLU-1-1.022-0.85724.814-0.378-0.3780.0000.0000.0000.000
48A33VAL00.008-0.09928.5600.0110.0110.0000.0000.0000.000
49A33VAL0-0.0730.07730.7140.0010.0010.0000.0000.0000.000
50A34PHE00.033-0.11231.1130.0160.0160.0000.0000.0000.000
51A34PHE0-0.0270.10230.084-0.002-0.0020.0000.0000.0000.000
52A35PRO0-0.001-0.08032.6770.0020.0020.0000.0000.0000.000
53A36ASP00.154-0.00233.974-0.010-0.0100.0000.0000.0000.000
54A36ASP-1-1.001-0.84033.844-0.198-0.1980.0000.0000.0000.000
55A37GLN00.023-0.13335.051-0.002-0.0020.0000.0000.0000.000
56A37GLN0-0.0750.09637.623-0.004-0.0040.0000.0000.0000.000
57A38GLU00.123-0.09333.8340.0060.0060.0000.0000.0000.000
58A38GLU-1-0.912-0.78832.388-0.173-0.1730.0000.0000.0000.000
59A39ARG00.041-0.11630.457-0.011-0.0110.0000.0000.0000.000
60A39ARG10.8911.09526.1320.2720.2720.0000.0000.0000.000
61A40TYR00.052-0.12029.194-0.023-0.0230.0000.0000.0000.000
62A40TYR0-0.0830.09529.406-0.003-0.0030.0000.0000.0000.000
63A41GLY0-0.005-0.10230.7140.0080.0080.0000.0000.0000.000
64A42LEU00.175-0.02729.697-0.013-0.0130.0000.0000.0000.000
65A42LEU0-0.1220.13329.571-0.001-0.0010.0000.0000.0000.000
66A43THR0-0.069-0.08727.758-0.016-0.0160.0000.0000.0000.000
67A43THR0-0.0030.07728.027-0.009-0.0090.0000.0000.0000.000
68A44ALA00.154-0.09925.609-0.036-0.0360.0000.0000.0000.000
69A44ALA0-0.0850.11226.5870.0030.0030.0000.0000.0000.000
70A45GLN0-0.017-0.13124.855-0.025-0.0250.0000.0000.0000.000
71A45GLN0-0.0760.09727.6730.0030.0030.0000.0000.0000.000
72A46LEU00.092-0.11124.708-0.009-0.0090.0000.0000.0000.000
73A46LEU0-0.0660.12724.932-0.003-0.0030.0000.0000.0000.000
74A47ARG00.078-0.12721.620-0.030-0.0300.0000.0000.0000.000
75A47ARG10.8111.06721.5880.3750.3750.0000.0000.0000.000
76A48ARG00.077-0.07720.143-0.062-0.0620.0000.0000.0000.000
77A48ARG10.8801.06121.3530.2350.2350.0000.0000.0000.000
78A49ALA00.108-0.12620.025-0.029-0.0290.0000.0000.0000.000
79A49ALA0-0.0520.15222.8090.0050.0050.0000.0000.0000.000
80A50ALA00.097-0.11719.266-0.009-0.0090.0000.0000.0000.000
81A50ALA0-0.0530.11819.041-0.002-0.0020.0000.0000.0000.000
82A51VAL00.035-0.11515.806-0.071-0.0710.0000.0000.0000.000
83A51VAL0-0.0540.12415.0230.0000.0000.0000.0000.0000.000
84A52SER00.034-0.07614.868-0.111-0.1110.0000.0000.0000.000
85A52SER0-0.0260.07218.2370.0140.0140.0000.0000.0000.000
86A53ILE00.058-0.07915.5330.0200.0200.0000.0000.0000.000
87A53ILE0-0.0620.09715.381-0.005-0.0050.0000.0000.0000.000
88A54PRO00.009-0.09710.9370.0040.0040.0000.0000.0000.000
89A55SER00.009-0.01610.649-0.180-0.1800.0000.0000.0000.000
90A55SER0-0.0500.06413.031-0.010-0.0100.0000.0000.0000.000
91A56ASN00.114-0.05611.2530.0210.0210.0000.0000.0000.000
92A56ASN0-0.1380.07214.8680.0710.0710.0000.0000.0000.000
93A57ILE00.127-0.08911.5660.1980.1980.0000.0000.0000.000
94A57ILE0-0.0930.0779.645-0.005-0.0050.0000.0000.0000.000
95A58ALA00.073-0.1497.4670.2120.2120.0000.0000.0000.000
96A58ALA0-0.0910.1186.976-0.103-0.1030.0000.0000.0000.000
97A59GLU00.050-0.1697.4260.2980.2980.0000.0000.0000.000
98A59GLU-1-0.995-0.80210.665-0.038-0.0380.0000.0000.0000.000
99A60GLY00.001-0.1009.9810.2470.2470.0000.0000.0000.000
100A61ALA0-0.005-0.0207.6340.2700.2700.0000.0000.0000.000
101A61ALA0-0.0550.1096.849-0.077-0.0770.0000.0000.0000.000
102A62ALA00.106-0.1376.8670.7570.7570.0000.0000.0000.000
103A62ALA0-0.0140.1647.126-0.025-0.0250.0000.0000.0000.000
104A63ARG00.001-0.1437.8300.1910.1910.0000.0000.0000.000
105A63ARG10.8471.08311.444-0.378-0.3780.0000.0000.0000.000
106A64ARG0-0.089-0.1419.968-0.171-0.1710.0000.0000.0000.000
107A64ARG10.8221.0437.289-1.581-1.5810.0000.0000.0000.000
108A65SER00.136-0.03611.1290.0170.0170.0000.0000.0000.000
109A65SER0-0.0860.02514.594-0.055-0.0550.0000.0000.0000.000
110A66THR0-0.028-0.07914.845-0.033-0.0330.0000.0000.0000.000
111A66THR0-0.0170.07617.466-0.015-0.0150.0000.0000.0000.000
112A67PRO00.125-0.06917.065-0.047-0.0470.0000.0000.0000.000
113A68ASP00.0560.00317.156-0.037-0.0370.0000.0000.0000.000
114A68ASP-1-0.890-0.81315.5570.3070.3070.0000.0000.0000.000
115A69TYR00.217-0.09013.771-0.035-0.0350.0000.0000.0000.000
116A69TYR0-0.1060.11810.7970.0500.0500.0000.0000.0000.000
117A70SER00.002-0.12414.564-0.082-0.0820.0000.0000.0000.000
118A70SER0-0.0480.08118.167-0.007-0.0070.0000.0000.0000.000
119A71ARG00.081-0.06817.603-0.052-0.0520.0000.0000.0000.000
120A71ARG10.8871.07218.126-0.065-0.0650.0000.0000.0000.000
121A72PHE00.037-0.13114.502-0.030-0.0300.0000.0000.0000.000
122A72PHE0-0.0660.13513.8930.0150.0150.0000.0000.0000.000
123A73LEU00.133-0.08915.811-0.080-0.0800.0000.0000.0000.000
124A73LEU0-0.0900.10112.901-0.002-0.0020.0000.0000.0000.000
125A74SER00.088-0.05516.396-0.047-0.0470.0000.0000.0000.000
126A74SER0-0.0840.04020.6520.0020.0020.0000.0000.0000.000
127A75ILE00.068-0.07818.955-0.009-0.0090.0000.0000.0000.000
128A75ILE0-0.0730.09417.9560.0080.0080.0000.0000.0000.000
129A76ALA00.145-0.08716.5140.0000.0000.0000.0000.0000.000
130A76ALA0-0.0740.11215.742-0.013-0.0130.0000.0000.0000.000
131A77ARG00.026-0.13817.825-0.036-0.0360.0000.0000.0000.000
132A77ARG10.8701.08920.3510.1630.1630.0000.0000.0000.000
133A78GLY0-0.011-0.10820.7330.0060.0060.0000.0000.0000.000
134A79SER00.0750.02720.2920.0210.0210.0000.0000.0000.000
135A79SER0-0.0210.11319.481-0.013-0.0130.0000.0000.0000.000
136A80LEU00.122-0.09120.968-0.011-0.0110.0000.0000.0000.000
137A80LEU0-0.1140.10120.018-0.001-0.0010.0000.0000.0000.000
138A81SER00.042-0.08621.860-0.007-0.0070.0000.0000.0000.000
139A81SER0-0.0640.07024.8800.0110.0110.0000.0000.0000.000
140A82GLU00.090-0.08224.8270.0150.0150.0000.0000.0000.000
141A82GLU-1-1.019-0.84924.132-0.237-0.2370.0000.0000.0000.000
142A83LEU00.134-0.12623.3060.0170.0170.0000.0000.0000.000
143A83LEU0-0.1240.10821.573-0.006-0.0060.0000.0000.0000.000
144A84ASP00.049-0.11624.6750.0010.0010.0000.0000.0000.000
145A84ASP-1-0.954-0.83325.949-0.221-0.2210.0000.0000.0000.000
146A85THR00.016-0.07726.8970.0070.0070.0000.0000.0000.000
147A85THR0-0.0450.05929.3050.0080.0080.0000.0000.0000.000
148A86GLN00.040-0.12428.2010.0170.0170.0000.0000.0000.000
149A86GLN0-0.0530.09826.494-0.017-0.0170.0000.0000.0000.000
150A87VAL00.102-0.09227.9900.0070.0070.0000.0000.0000.000
151A87VAL0-0.0440.11225.892-0.004-0.0040.0000.0000.0000.000
152A88GLN00.080-0.10728.9770.0030.0030.0000.0000.0000.000
153A88GLN0-0.1650.06630.9040.0140.0140.0000.0000.0000.000
154A89ILE00.052-0.08232.1840.0110.0110.0000.0000.0000.000
155A89ILE0-0.0900.07932.1390.0010.0010.0000.0000.0000.000
156A90ALA00.130-0.07731.4810.0150.0150.0000.0000.0000.000
157A90ALA0-0.0700.09330.838-0.004-0.0040.0000.0000.0000.000
158A91ALA00.058-0.10232.8740.0050.0050.0000.0000.0000.000
159A91ALA0-0.0730.10333.2120.0000.0000.0000.0000.0000.000
160A92ARG00.001-0.12334.5650.0060.0060.0000.0000.0000.000
161A92ARG10.8451.03636.6580.1310.1310.0000.0000.0000.000
162A93LEU0-0.027-0.11736.4610.0100.0100.0000.0000.0000.000
163A93LEU0-0.0650.10935.3370.0000.0000.0000.0000.0000.000
164A94GLY00.019-0.09537.4630.0040.0040.0000.0000.0000.000
165A95TYR00.015-0.01034.2490.0030.0030.0000.0000.0000.000
166A95TYR0-0.0530.08533.6130.0010.0010.0000.0000.0000.000
167A96SER00.017-0.07232.385-0.011-0.0110.0000.0000.0000.000
168A96SER0-0.0180.07031.7860.0020.0020.0000.0000.0000.000
169A97ARG00.117-0.07233.5710.0110.0110.0000.0000.0000.000
170A97ARG10.8661.09132.5680.2240.2240.0000.0000.0000.000
171A98SER00.133-0.04133.425-0.015-0.0150.0000.0000.0000.000
172A98SER0-0.0500.04536.324-0.001-0.0010.0000.0000.0000.000
173A99GLU00.035-0.12233.096-0.007-0.0070.0000.0000.0000.000
174A99GLU-1-0.940-0.82132.891-0.206-0.2060.0000.0000.0000.000
175A100ASP00.106-0.10929.548-0.013-0.0130.0000.0000.0000.000
176A100ASP-1-0.979-0.83429.383-0.261-0.2610.0000.0000.0000.000
177A101ASP00.084-0.11928.759-0.026-0.0260.0000.0000.0000.000
178A101ASP-1-0.994-0.85031.351-0.207-0.2070.0000.0000.0000.000
179A102GLN00.046-0.11829.532-0.010-0.0100.0000.0000.0000.000
180A102GLN0-0.1320.06631.6230.0060.0060.0000.0000.0000.000
181A103SER0-0.030-0.13027.3230.0000.0000.0000.0000.0000.000
182A103SER0-0.0240.07826.390-0.003-0.0030.0000.0000.0000.000
183A104VAL00.072-0.06824.642-0.026-0.0260.0000.0000.0000.000
184A104VAL0-0.0510.11324.238-0.002-0.0020.0000.0000.0000.000
185A105ARG00.134-0.08824.816-0.026-0.0260.0000.0000.0000.000
186A105ARG10.8941.08328.9170.2010.2010.0000.0000.0000.000
187A106ARG00.085-0.06526.2600.0000.0000.0000.0000.0000.000
188A106ARG10.8781.05326.4630.2490.2490.0000.0000.0000.000
189A107GLN00.111-0.09922.2830.0090.0090.0000.0000.0000.000
190A107GLN0-0.0830.12318.3230.0350.0350.0000.0000.0000.000
191A108VAL00.012-0.14121.330-0.048-0.0480.0000.0000.0000.000
192A108VAL0-0.0530.12222.997-0.001-0.0010.0000.0000.0000.000
193A109ASP00.141-0.10622.641-0.009-0.0090.0000.0000.0000.000
194A109ASP-1-0.997-0.84025.847-0.231-0.2310.0000.0000.0000.000
195A110LEU00.059-0.14521.5320.0260.0260.0000.0000.0000.000
196A110LEU0-0.1040.12819.6440.0030.0030.0000.0000.0000.000
197A111VAL00.038-0.10018.3110.0010.0010.0000.0000.0000.000
198A111VAL0-0.0440.09917.021-0.009-0.0090.0000.0000.0000.000
199A112PHE00.112-0.09318.994-0.009-0.0090.0000.0000.0000.000
200A112PHE0-0.0790.09723.1390.0150.0150.0000.0000.0000.000
201A113ALA00.064-0.13421.5000.0270.0270.0000.0000.0000.000
202A113ALA0-0.0570.13622.1340.0020.0020.0000.0000.0000.000
203A114LYS00.012-0.15317.5330.0590.0590.0000.0000.0000.000
204A114LYS10.7411.03816.6390.4670.4670.0000.0000.0000.000
205A115LEU00.115-0.09716.8850.0080.0080.0000.0000.0000.000
206A115LEU0-0.0950.12115.793-0.002-0.0020.0000.0000.0000.000
207A116THR00.007-0.10017.8950.0380.0380.0000.0000.0000.000
208A116THR0-0.0710.06622.0900.0180.0180.0000.0000.0000.000
209A117ALA00.068-0.12320.3470.0510.0510.0000.0000.0000.000
210A117ALA0-0.0340.14619.499-0.002-0.0020.0000.0000.0000.000
211A118LEU00.072-0.10915.8200.0590.0590.0000.0000.0000.000
212A118LEU0-0.0850.11512.776-0.013-0.0130.0000.0000.0000.000
213A119MET00.077-0.12617.0740.0650.0650.0000.0000.0000.000
214A119MET0-0.1200.10417.994-0.007-0.0070.0000.0000.0000.000
215A120ASN00.077-0.10318.8170.0470.0470.0000.0000.0000.000
216A120ASN0-0.1160.06122.0370.0060.0060.0000.0000.0000.000
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