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: GYRG1

Calculation Name: 1F3U-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1F3U

Chain ID: A

ChEMBL ID:

UniProt ID: P35269

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 OptHSide
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 219
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -778679.20221
FMO2-HF: Nuclear repulsion 734780.807969
FMO2-HF: Total energy -43898.394241
FMO2-MP2: Total energy -44028.070346


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:2:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-1.8930.9384.459-4.021-3.27-0.025
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.171 / q_NPA : 0.056
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].
4A3GLU-1-1.026-0.8683.944-0.4040.0040.000-0.119-0.2890.000
5A4ARG00.159-0.0903.800-1.0220.179-0.014-0.652-0.5350.002
6A4ARG10.8301.0468.0590.6090.6090.0000.0000.0000.000
7A5GLY0-0.046-0.1166.8000.2620.2620.0000.0000.0000.000
8A6GLU00.098-0.0214.2270.2750.3570.000-0.027-0.0550.000
9A6GLU-1-0.945-0.8092.369-2.049-0.9884.474-3.195-2.341-0.027
10A7LEU00.098-0.0925.467-0.313-0.3130.0000.0000.0000.000
11A7LEU0-0.1620.0888.5320.0380.0380.0000.0000.0000.000
12A8ASP00.122-0.1015.7180.2910.2910.0000.0000.0000.000
13A8ASP-1-0.887-0.7765.390-1.534-1.5340.0000.0000.0000.000
14A9LEU00.029-0.1196.3420.0160.0160.0000.0000.0000.000
15A9LEU0-0.0580.1008.4130.0330.0330.0000.0000.0000.000
16A10THR0-0.014-0.1149.0940.0960.0960.0000.0000.0000.000
17A10THR0-0.0370.0988.4670.0160.0160.0000.0000.0000.000
18A11GLY00.096-0.06211.0290.0720.0720.0000.0000.0000.000
19A12ALA00.1210.01413.3610.0490.0490.0000.0000.0000.000
20A12ALA0-0.0780.10313.951-0.002-0.0020.0000.0000.0000.000
21A13LYS00.063-0.09314.0710.0220.0220.0000.0000.0000.000
22A13LYS10.8791.05312.7230.0100.0100.0000.0000.0000.000
23A14GLN00.019-0.11115.2480.0410.0410.0000.0000.0000.000
24A14GLN0-0.0630.09413.8770.0070.0070.0000.0000.0000.000
25A15ASN00.104-0.04516.6310.0090.0090.0000.0000.0000.000
26A15ASN0-0.1580.05120.0980.0040.0040.0000.0000.0000.000
27A16THR0-0.032-0.13217.8820.0250.0250.0000.0000.0000.000
28A16THR0-0.0020.08916.3230.0120.0120.0000.0000.0000.000
29A17GLY00.014-0.06219.290-0.013-0.0130.0000.0000.0000.000
30A18VAL00.024-0.03422.0020.0040.0040.0000.0000.0000.000
31A18VAL0-0.0360.13520.099-0.002-0.0020.0000.0000.0000.000
32A19TRP00.097-0.10523.1010.0090.0090.0000.0000.0000.000
33A19TRP0-0.0710.08326.6260.0050.0050.0000.0000.0000.000
34A20LEU00.149-0.08425.393-0.013-0.0130.0000.0000.0000.000
35A20LEU0-0.1000.11324.7790.0010.0010.0000.0000.0000.000
36A21VAL00.008-0.13626.7670.0100.0100.0000.0000.0000.000
37A21VAL0-0.0860.10028.8840.0010.0010.0000.0000.0000.000
38A22LYS00.200-0.04229.818-0.009-0.0090.0000.0000.0000.000
39A22LYS10.7380.99932.3650.0960.0960.0000.0000.0000.000
40A23VAL0-0.003-0.15932.1610.0090.0090.0000.0000.0000.000
41A23VAL0-0.0580.13831.1290.0000.0000.0000.0000.0000.000
42A24PRO00.013-0.09833.567-0.002-0.0020.0000.0000.0000.000
43A25LYS00.1040.00735.138-0.003-0.0030.0000.0000.0000.000
44A25LYS10.9341.10831.7410.1330.1330.0000.0000.0000.000
45A26TYR00.123-0.07236.182-0.005-0.0050.0000.0000.0000.000
46A26TYR0-0.0330.08440.1470.0010.0010.0000.0000.0000.000
47A27LEU00.117-0.07336.8000.0010.0010.0000.0000.0000.000
48A27LEU0-0.0860.10235.4310.0000.0000.0000.0000.0000.000
49A28SER00.037-0.07932.5810.0010.0010.0000.0000.0000.000
50A28SER0-0.0420.05831.699-0.003-0.0030.0000.0000.0000.000
51A29GLN00.075-0.09333.035-0.007-0.0070.0000.0000.0000.000
52A29GLN0-0.0990.07235.4000.0000.0000.0000.0000.0000.000
53A30GLN00.121-0.09135.358-0.002-0.0020.0000.0000.0000.000
54A30GLN0-0.1500.07637.115-0.001-0.0010.0000.0000.0000.000
55A31TRP00.051-0.08732.3770.0040.0040.0000.0000.0000.000
56A31TRP0-0.0880.06330.077-0.004-0.0040.0000.0000.0000.000
57A32ALA00.120-0.07331.571-0.004-0.0040.0000.0000.0000.000
58A32ALA0-0.0870.09832.2630.0000.0000.0000.0000.0000.000
59A33LYS0-0.021-0.10632.614-0.004-0.0040.0000.0000.0000.000
60A33LYS10.7520.98636.7510.0840.0840.0000.0000.0000.000
61A34ALA00.120-0.08632.6800.0090.0090.0000.0000.0000.000
62A34ALA0-0.0580.11031.752-0.001-0.0010.0000.0000.0000.000
63A35SER0-0.035-0.09732.855-0.006-0.0060.0000.0000.0000.000
64A35SER0-0.0130.09334.7860.0020.0020.0000.0000.0000.000
65A36GLY00.027-0.09832.7840.0000.0000.0000.0000.0000.000
66A37ARG00.050-0.02029.527-0.008-0.0080.0000.0000.0000.000
67A37ARG10.8961.07829.9770.0840.0840.0000.0000.0000.000
68A38GLY0-0.001-0.07428.508-0.009-0.0090.0000.0000.0000.000
69A39GLU00.064-0.02729.895-0.008-0.0080.0000.0000.0000.000
70A39GLU-1-0.993-0.85031.104-0.088-0.0880.0000.0000.0000.000
71A40VAL00.067-0.13031.8000.0050.0050.0000.0000.0000.000
72A40VAL0-0.0560.13931.2290.0000.0000.0000.0000.0000.000
73A41GLY00.010-0.10733.6380.0060.0060.0000.0000.0000.000
74A42LYS00.016-0.00733.922-0.005-0.0050.0000.0000.0000.000
75A42LYS10.8971.06534.9810.0730.0730.0000.0000.0000.000
76A43LEU00.142-0.08232.9950.0030.0030.0000.0000.0000.000
77A43LEU0-0.1050.11130.850-0.001-0.0010.0000.0000.0000.000
78A44ARG00.070-0.10934.4310.0010.0010.0000.0000.0000.000
79A44ARG10.8291.07238.5170.0540.0540.0000.0000.0000.000
80A45ILE00.124-0.09435.950-0.001-0.0010.0000.0000.0000.000
81A45ILE0-0.0970.09532.6330.0000.0000.0000.0000.0000.000
82A46ALA00.098-0.10037.2300.0020.0020.0000.0000.0000.000
83A46ALA0-0.0970.10841.6120.0000.0000.0000.0000.0000.000
84A47LYS00.062-0.11940.724-0.001-0.0010.0000.0000.0000.000
85A47LYS10.8831.08035.4330.0550.0550.0000.0000.0000.000
86A48THR00.072-0.02241.6950.0020.0020.0000.0000.0000.000
87A48THR0-0.0380.06245.3580.0000.0000.0000.0000.0000.000
88A49GLN00.123-0.12544.312-0.001-0.0010.0000.0000.0000.000
89A49GLN0-0.0780.12247.8310.0010.0010.0000.0000.0000.000
90A50GLY0-0.027-0.10343.7050.0000.0000.0000.0000.0000.000
91A51ARG00.107-0.00743.503-0.001-0.0010.0000.0000.0000.000
92A51ARG10.7621.00444.4000.0470.0470.0000.0000.0000.000
93A52THR0-0.034-0.08839.5240.0020.0020.0000.0000.0000.000
94A52THR0-0.0080.05637.519-0.001-0.0010.0000.0000.0000.000
95A53GLU00.117-0.08640.950-0.002-0.0020.0000.0000.0000.000
96A53GLU-1-0.937-0.76442.335-0.049-0.0490.0000.0000.0000.000
97A54VAL00.055-0.10136.7060.0020.0020.0000.0000.0000.000
98A54VAL0-0.0660.08834.576-0.001-0.0010.0000.0000.0000.000
99A55SER00.006-0.09637.665-0.001-0.0010.0000.0000.0000.000
100A55SER0-0.0640.01039.8600.0000.0000.0000.0000.0000.000
101A56PHE00.096-0.06735.9290.0000.0000.0000.0000.0000.000
102A56PHE0-0.0520.09733.534-0.001-0.0010.0000.0000.0000.000
103A57THR00.002-0.09337.0000.0010.0010.0000.0000.0000.000
104A57THR0-0.0140.08639.6490.0020.0020.0000.0000.0000.000
105A58LEU00.087-0.09537.529-0.003-0.0030.0000.0000.0000.000
106A58LEU0-0.0740.08736.6030.0000.0000.0000.0000.0000.000
107A59ASN00.075-0.03737.6550.0050.0050.0000.0000.0000.000
108A59ASN0-0.0400.06335.7090.0010.0010.0000.0000.0000.000
109A60GLU00.106-0.12638.966-0.001-0.0010.0000.0000.0000.000
110A60GLU-1-0.989-0.82442.329-0.052-0.0520.0000.0000.0000.000
111A61ASP00.059-0.11539.4420.0030.0030.0000.0000.0000.000
112A61ASP-1-0.962-0.84438.577-0.071-0.0710.0000.0000.0000.000
113A62LEU00.073-0.09238.3000.0020.0020.0000.0000.0000.000
114A62LEU0-0.0770.09735.130-0.001-0.0010.0000.0000.0000.000
115A63ALA00.071-0.09539.595-0.001-0.0010.0000.0000.0000.000
116A63ALA0-0.0770.10042.2370.0010.0010.0000.0000.0000.000
117A64ASN0-0.003-0.08442.6450.0020.0020.0000.0000.0000.000
118A64ASN0-0.1390.05044.4310.0020.0020.0000.0000.0000.000
119A65ILE00.163-0.08741.8790.0040.0040.0000.0000.0000.000
120A65ILE0-0.0820.11739.588-0.001-0.0010.0000.0000.0000.000
121A66HIS00.027-0.10143.111-0.003-0.0030.0000.0000.0000.000
122A66HIS0-0.0400.07945.7150.0000.0000.0000.0000.0000.000
123A67ASP00.199-0.02345.0770.0000.0000.0000.0000.0000.000
124A67ASP-1-0.972-0.85342.758-0.076-0.0760.0000.0000.0000.000
125A68ILE0-0.008-0.16445.7450.0020.0020.0000.0000.0000.000
126A68ILE0-0.0680.11647.7220.0000.0000.0000.0000.0000.000
127A69GLY00.004-0.10949.1820.0000.0000.0000.0000.0000.000
128A70GLY0-0.014-0.00849.7100.0020.0020.0000.0000.0000.000
129A71LYS00.0180.03050.1190.0010.0010.0000.0000.0000.000
130A71LYS10.7831.02046.3200.0560.0560.0000.0000.0000.000
131A72PRO00.048-0.11051.1520.0010.0010.0000.0000.0000.000
132A73ALA00.1690.03754.4690.0000.0000.0000.0000.0000.000
133A73ALA0-0.0960.11155.3970.0000.0000.0000.0000.0000.000
134A74SER0-0.020-0.05054.055-0.001-0.0010.0000.0000.0000.000
135A74SER0-0.0100.05454.8480.0000.0000.0000.0000.0000.000
136A75VAL00.039-0.13851.3410.0000.0000.0000.0000.0000.000
137A75VAL0-0.0120.12950.0860.0000.0000.0000.0000.0000.000
138A76SER0-0.0180.00250.476-0.001-0.0010.0000.0000.0000.000
139A76SER0-0.091-0.01550.4910.0000.0000.0000.0000.0000.000
140A77ALA00.181-0.06548.1320.0000.0000.0000.0000.0000.000
141A77ALA0-0.0580.10147.5310.0000.0000.0000.0000.0000.000
142A78PRO00.000-0.11842.6420.0000.0000.0000.0000.0000.000
143A79ARG00.0700.02344.3400.0020.0020.0000.0000.0000.000
144A79ARG10.8441.03944.4290.0500.0500.0000.0000.0000.000
145A80GLU00.138-0.12341.986-0.004-0.0040.0000.0000.0000.000
146A80GLU-1-0.920-0.74441.719-0.057-0.0570.0000.0000.0000.000
147A81HIS0-0.024-0.13739.5760.0030.0030.0000.0000.0000.000
148A81HIS0-0.0960.10638.738-0.002-0.0020.0000.0000.0000.000
149A82PRO00.096-0.06539.171-0.003-0.0030.0000.0000.0000.000
150A83PHE00.071-0.01736.689-0.002-0.0020.0000.0000.0000.000
151A83PHE0-0.0520.09832.309-0.002-0.0020.0000.0000.0000.000
152A84VAL00.105-0.07037.6080.0040.0040.0000.0000.0000.000
153A84VAL0-0.1110.09138.6960.0000.0000.0000.0000.0000.000
154A85LEU00.025-0.13235.382-0.006-0.0060.0000.0000.0000.000
155A85LEU0-0.0430.12034.4460.0000.0000.0000.0000.0000.000
156A86GLN00.081-0.11434.2780.0060.0060.0000.0000.0000.000
157A86GLN0-0.0440.09833.391-0.006-0.0060.0000.0000.0000.000
158A87SER00.064-0.03933.354-0.003-0.0030.0000.0000.0000.000
159A87SER0-0.0090.06633.9520.0000.0000.0000.0000.0000.000
160A88VAL00.010-0.12028.932-0.002-0.0020.0000.0000.0000.000
161A88VAL0-0.0390.12626.913-0.001-0.0010.0000.0000.0000.000
162A89GLY0-0.003-0.10628.889-0.003-0.0030.0000.0000.0000.000
163A90GLY00.0020.00630.1810.0020.0020.0000.0000.0000.000
164A91GLN00.123-0.01727.6020.0010.0010.0000.0000.0000.000
165A91GLN0-0.0760.08126.044-0.002-0.0020.0000.0000.0000.000
166A92THR0-0.020-0.06623.3830.0030.0030.0000.0000.0000.000
167A92THR0-0.0090.09021.4950.0030.0030.0000.0000.0000.000
168A93LEU00.050-0.07622.316-0.008-0.0080.0000.0000.0000.000
169A93LEU0-0.1020.07723.2780.0010.0010.0000.0000.0000.000
170A94THR00.033-0.06217.9890.0150.0150.0000.0000.0000.000
171A94THR00.0020.06217.067-0.002-0.0020.0000.0000.0000.000
172A95VAL00.115-0.08317.5850.0070.0070.0000.0000.0000.000
173A95VAL0-0.1050.09516.9730.0050.0050.0000.0000.0000.000
174A96PHE00.062-0.09113.822-0.005-0.0050.0000.0000.0000.000
175A96PHE0-0.0820.09612.7730.0150.0150.0000.0000.0000.000
176A97THR00.019-0.11312.8060.0690.0690.0000.0000.0000.000
177A97THR0-0.0760.02012.424-0.035-0.0350.0000.0000.0000.000
178A98GLU00.160-0.08611.798-0.122-0.1220.0000.0000.0000.000
179A98GLU-1-1.000-0.81712.493-0.546-0.5460.0000.0000.0000.000
180A99SER0-0.061-0.09111.2050.1330.1330.0000.0000.0000.000
181A99SER0-0.0470.04210.086-0.048-0.0480.0000.0000.0000.000
182A100SER00.111-0.05612.452-0.023-0.0230.0000.0000.0000.000
183A100SER0-0.0360.05814.6310.0150.0150.0000.0000.0000.000
184A101SER0-0.053-0.06310.4730.1180.1180.0000.0000.0000.000
185A101SER0-0.0530.0339.537-0.110-0.1100.0000.0000.0000.000
186A102ASP0-0.015-0.0999.969-0.151-0.1510.0000.0000.0000.000
187A102ASP-1-0.953-0.85210.554-0.670-0.6700.0000.0000.0000.000
188A103LYS00.172-0.0627.089-0.018-0.0180.0000.0000.0000.000
189A103LYS10.7380.9864.0453.0283.107-0.001-0.028-0.0500.000
190A104LEU00.105-0.1187.1600.2180.2180.0000.0000.0000.000
191A104LEU0-0.0810.1308.1480.0370.0370.0000.0000.0000.000
192A105SER00.078-0.1247.148-0.209-0.2090.0000.0000.0000.000
193A105SER0-0.0650.0608.373-0.077-0.0770.0000.0000.0000.000
194A106LEU00.059-0.0709.2530.0780.0780.0000.0000.0000.000
195A106LEU0-0.1470.07311.3220.0260.0260.0000.0000.0000.000
196A107GLU00.079-0.12812.0640.0090.0090.0000.0000.0000.000
197A107GLU-1-0.900-0.75111.913-0.664-0.6640.0000.0000.0000.000
198A108GLY0-0.017-0.11514.2970.0410.0410.0000.0000.0000.000
199A109ILE00.066-0.02017.235-0.023-0.0230.0000.0000.0000.000
200A109ILE0-0.0750.11618.6270.0010.0010.0000.0000.0000.000
201A110VAL00.059-0.10920.1600.0060.0060.0000.0000.0000.000
202A110VAL0-0.1040.09522.0920.0010.0010.0000.0000.0000.000
203A111VAL00.036-0.11823.4720.0080.0080.0000.0000.0000.000
204A111VAL0-0.0890.11323.8870.0020.0020.0000.0000.0000.000
205A112GLN00.118-0.11026.1800.0110.0110.0000.0000.0000.000
206A112GLN0-0.1430.07629.0880.0040.0040.0000.0000.0000.000
207A113ARG00.133-0.10328.150-0.012-0.0120.0000.0000.0000.000
208A113ARG10.8001.06628.5010.1150.1150.0000.0000.0000.000
209A114ALA00.067-0.08630.3160.0090.0090.0000.0000.0000.000
210A114ALA0-0.0440.11232.6900.0010.0010.0000.0000.0000.000
211A115GLU00.089-0.08432.598-0.009-0.0090.0000.0000.0000.000
212A115GLU-1-0.921-0.79935.462-0.086-0.0860.0000.0000.0000.000
213A116CYS00.101-0.11035.0170.0070.0070.0000.0000.0000.000
214A116CYS0-0.1320.11634.7400.0000.0000.0000.0000.0000.000
215A117ARG00.010-0.16636.497-0.003-0.0030.0000.0000.0000.000
216A117ARG10.8171.07639.4100.0760.0760.0000.0000.0000.000
217A118PRO00.022-0.10540.1380.0000.0000.0000.0000.0000.000
218A119ALA0-0.070-0.01541.9920.0040.0040.0000.0000.0000.000
219A119ALA00.0650.03542.8350.0000.0000.0000.0000.0000.000