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: N28QQ

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 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 219
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -778466.976389
FMO2-HF: Nuclear repulsion 734570.328861
FMO2-HF: Total energy -43896.647528
FMO2-MP2: Total energy -44026.369894


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.
-1.7512.0962.268-3.264-2.851-0.019
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 : 0.160 / q_NPA : 0.044
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-1-1.012-0.8453.585-0.652-0.1600.003-0.153-0.3430.000
5A4ARG00.153-0.0923.800-1.0150.204-0.014-0.676-0.5290.003
6A4ARG10.8241.0518.1230.6710.6710.0000.0000.0000.000
7A5GLY0-0.054-0.1166.7940.2710.2710.0000.0000.0000.000
8A6GLU00.085-0.0174.3330.2460.310-0.001-0.015-0.0480.000
9A6GLU-1-0.962-0.8142.529-1.9670.0562.281-2.409-1.895-0.022
10A7LEU00.114-0.1115.449-0.311-0.3110.0000.0000.0000.000
11A7LEU0-0.1630.0888.5210.0330.0330.0000.0000.0000.000
12A8ASP00.093-0.1055.7080.3000.3000.0000.0000.0000.000
13A8ASP-1-0.920-0.8145.387-0.945-0.9450.0000.0000.0000.000
14A9LEU00.019-0.1236.325-0.013-0.0130.0000.0000.0000.000
15A9LEU0-0.0750.1058.4990.0270.0270.0000.0000.0000.000
16A10THR00.022-0.1299.0960.0740.0740.0000.0000.0000.000
17A10THR0-0.0340.1028.3990.0190.0190.0000.0000.0000.000
18A11GLY00.086-0.04811.0260.0580.0580.0000.0000.0000.000
19A12ALA00.124-0.00213.3460.0410.0410.0000.0000.0000.000
20A12ALA0-0.0690.10913.965-0.002-0.0020.0000.0000.0000.000
21A13LYS00.052-0.09314.0640.0150.0150.0000.0000.0000.000
22A13LYS10.8671.05712.659-0.036-0.0360.0000.0000.0000.000
23A14GLN00.020-0.11615.2270.0350.0350.0000.0000.0000.000
24A14GLN0-0.0860.09114.1940.0170.0170.0000.0000.0000.000
25A15ASN00.069-0.07316.6270.0060.0060.0000.0000.0000.000
26A15ASN0-0.1240.06020.202-0.003-0.0030.0000.0000.0000.000
27A16THR00.003-0.12117.8910.0190.0190.0000.0000.0000.000
28A16THR0-0.0270.10816.8560.0020.0020.0000.0000.0000.000
29A17GLY0-0.004-0.08119.272-0.013-0.0130.0000.0000.0000.000
30A18VAL00.026-0.03222.0120.0040.0040.0000.0000.0000.000
31A18VAL0-0.0210.13120.065-0.002-0.0020.0000.0000.0000.000
32A19TRP00.094-0.10223.0870.0090.0090.0000.0000.0000.000
33A19TRP0-0.0630.08826.6260.0040.0040.0000.0000.0000.000
34A20LEU00.124-0.09525.382-0.013-0.0130.0000.0000.0000.000
35A20LEU0-0.1010.11124.8300.0010.0010.0000.0000.0000.000
36A21VAL00.008-0.12526.7390.0100.0100.0000.0000.0000.000
37A21VAL0-0.0600.09728.8840.0010.0010.0000.0000.0000.000
38A22LYS00.147-0.05729.792-0.009-0.0090.0000.0000.0000.000
39A22LYS10.8601.05432.5050.0920.0920.0000.0000.0000.000
40A23VAL00.012-0.15432.1550.0090.0090.0000.0000.0000.000
41A23VAL0-0.0510.14330.9980.0000.0000.0000.0000.0000.000
42A24PRO00.002-0.09133.609-0.003-0.0030.0000.0000.0000.000
43A25LYS00.117-0.00735.162-0.003-0.0030.0000.0000.0000.000
44A25LYS10.9381.11431.8950.1260.1260.0000.0000.0000.000
45A26TYR00.105-0.07536.202-0.005-0.0050.0000.0000.0000.000
46A26TYR0-0.0220.11140.1660.0010.0010.0000.0000.0000.000
47A27LEU00.129-0.08436.7830.0010.0010.0000.0000.0000.000
48A27LEU0-0.0870.10835.3080.0000.0000.0000.0000.0000.000
49A28SER00.030-0.07732.6070.0010.0010.0000.0000.0000.000
50A28SER0-0.0400.06531.779-0.002-0.0020.0000.0000.0000.000
51A29GLN00.091-0.09433.054-0.007-0.0070.0000.0000.0000.000
52A29GLN0-0.1150.07035.529-0.002-0.0020.0000.0000.0000.000
53A30GLN00.084-0.11835.373-0.002-0.0020.0000.0000.0000.000
54A30GLN0-0.1360.08637.094-0.002-0.0020.0000.0000.0000.000
55A31TRP00.040-0.08932.3480.0040.0040.0000.0000.0000.000
56A31TRP0-0.0630.06629.961-0.003-0.0030.0000.0000.0000.000
57A32ALA00.106-0.07231.576-0.003-0.0030.0000.0000.0000.000
58A32ALA0-0.0840.09932.3440.0000.0000.0000.0000.0000.000
59A33LYS0-0.020-0.11632.624-0.004-0.0040.0000.0000.0000.000
60A33LYS10.8161.04536.8360.0870.0870.0000.0000.0000.000
61A34ALA00.118-0.09232.6640.0080.0080.0000.0000.0000.000
62A34ALA0-0.0500.11331.748-0.001-0.0010.0000.0000.0000.000
63A35SER0-0.039-0.09532.889-0.006-0.0060.0000.0000.0000.000
64A35SER00.0010.09334.8880.0020.0020.0000.0000.0000.000
65A36GLY00.021-0.09032.7940.0010.0010.0000.0000.0000.000
66A37ARG00.053-0.02329.543-0.007-0.0070.0000.0000.0000.000
67A37ARG10.9001.07929.9680.0770.0770.0000.0000.0000.000
68A38GLY00.004-0.07128.531-0.008-0.0080.0000.0000.0000.000
69A39GLU00.063-0.03729.923-0.008-0.0080.0000.0000.0000.000
70A39GLU-1-1.015-0.84331.181-0.079-0.0790.0000.0000.0000.000
71A40VAL00.054-0.13731.8330.0040.0040.0000.0000.0000.000
72A40VAL0-0.0300.13431.4450.0000.0000.0000.0000.0000.000
73A41GLY00.009-0.10233.6790.0050.0050.0000.0000.0000.000
74A42LYS00.024-0.02333.972-0.004-0.0040.0000.0000.0000.000
75A42LYS10.8861.07635.2980.0640.0640.0000.0000.0000.000
76A43LEU00.140-0.09833.0880.0020.0020.0000.0000.0000.000
77A43LEU0-0.1040.12631.026-0.001-0.0010.0000.0000.0000.000
78A44ARG00.062-0.11634.4950.0010.0010.0000.0000.0000.000
79A44ARG10.8531.08138.6130.0460.0460.0000.0000.0000.000
80A45ILE00.114-0.11436.095-0.002-0.0020.0000.0000.0000.000
81A45ILE0-0.0840.11132.7140.0000.0000.0000.0000.0000.000
82A46ALA00.090-0.11037.3090.0020.0020.0000.0000.0000.000
83A46ALA0-0.1070.12041.7400.0000.0000.0000.0000.0000.000
84A47LYS00.051-0.13340.833-0.001-0.0010.0000.0000.0000.000
85A47LYS10.8861.08835.5300.0430.0430.0000.0000.0000.000
86A48THR00.032-0.04741.7840.0020.0020.0000.0000.0000.000
87A48THR0-0.0070.07045.308-0.001-0.0010.0000.0000.0000.000
88A49GLN00.136-0.09944.292-0.001-0.0010.0000.0000.0000.000
89A49GLN0-0.0870.12447.7160.0010.0010.0000.0000.0000.000
90A50GLY0-0.016-0.10043.6870.0000.0000.0000.0000.0000.000
91A51ARG00.128-0.02943.498-0.001-0.0010.0000.0000.0000.000
92A51ARG10.7861.07644.0680.0410.0410.0000.0000.0000.000
93A52THR0-0.038-0.08739.5040.0020.0020.0000.0000.0000.000
94A52THR0-0.0030.06437.4950.0000.0000.0000.0000.0000.000
95A53GLU00.088-0.10240.927-0.002-0.0020.0000.0000.0000.000
96A53GLU-1-0.942-0.81442.326-0.043-0.0430.0000.0000.0000.000
97A54VAL00.048-0.10536.7960.0020.0020.0000.0000.0000.000
98A54VAL0-0.0460.09134.702-0.001-0.0010.0000.0000.0000.000
99A55SER00.012-0.09037.742-0.001-0.0010.0000.0000.0000.000
100A55SER00.0170.08639.9140.0000.0000.0000.0000.0000.000
101A56PHE00.092-0.07536.0360.0000.0000.0000.0000.0000.000
102A56PHE0-0.0500.10533.657-0.001-0.0010.0000.0000.0000.000
103A57THR0-0.023-0.08837.0580.0010.0010.0000.0000.0000.000
104A57THR00.0030.08039.6910.0020.0020.0000.0000.0000.000
105A58LEU00.070-0.10537.572-0.003-0.0030.0000.0000.0000.000
106A58LEU0-0.0730.09736.7560.0000.0000.0000.0000.0000.000
107A59ASN00.089-0.02137.7030.0050.0050.0000.0000.0000.000
108A59ASN0-0.0220.06435.8760.0010.0010.0000.0000.0000.000
109A60GLU00.112-0.13339.006-0.001-0.0010.0000.0000.0000.000
110A60GLU-1-0.994-0.82742.253-0.047-0.0470.0000.0000.0000.000
111A61ASP00.128-0.09739.5040.0020.0020.0000.0000.0000.000
112A61ASP-1-1.023-0.84238.675-0.065-0.0650.0000.0000.0000.000
113A62LEU00.052-0.10438.3320.0020.0020.0000.0000.0000.000
114A62LEU0-0.0930.09234.972-0.001-0.0010.0000.0000.0000.000
115A63ALA00.077-0.10039.621-0.002-0.0020.0000.0000.0000.000
116A63ALA0-0.0910.09542.3180.0010.0010.0000.0000.0000.000
117A64ASN0-0.018-0.10842.6760.0020.0020.0000.0000.0000.000
118A64ASN0-0.1380.05844.4020.0020.0020.0000.0000.0000.000
119A65ILE00.147-0.08541.9080.0030.0030.0000.0000.0000.000
120A65ILE0-0.0920.11639.427-0.001-0.0010.0000.0000.0000.000
121A66HIS00.034-0.11343.129-0.003-0.0030.0000.0000.0000.000
122A66HIS0-0.0600.08245.7860.0000.0000.0000.0000.0000.000
123A67ASP00.118-0.05945.2300.0000.0000.0000.0000.0000.000
124A67ASP-1-1.006-0.87742.995-0.071-0.0710.0000.0000.0000.000
125A68ILE00.057-0.14845.7550.0020.0020.0000.0000.0000.000
126A68ILE0-0.0680.12447.6530.0000.0000.0000.0000.0000.000
127A69GLY0-0.010-0.10549.1890.0000.0000.0000.0000.0000.000
128A70GLY0-0.006-0.00549.7250.0020.0020.0000.0000.0000.000
129A71LYS00.028-0.00150.2750.0010.0010.0000.0000.0000.000
130A71LYS10.8541.07346.9690.0500.0500.0000.0000.0000.000
131A72PRO00.026-0.09651.1770.0010.0010.0000.0000.0000.000
132A73ALA00.1860.01354.4980.0000.0000.0000.0000.0000.000
133A73ALA0-0.1040.12955.4710.0000.0000.0000.0000.0000.000
134A74SER0-0.010-0.06154.093-0.001-0.0010.0000.0000.0000.000
135A74SER0-0.0090.05554.6280.0000.0000.0000.0000.0000.000
136A75VAL0-0.036-0.15851.3850.0000.0000.0000.0000.0000.000
137A75VAL00.0110.13550.2010.0000.0000.0000.0000.0000.000
138A76SER00.009-0.02550.513-0.001-0.0010.0000.0000.0000.000
139A76SER0-0.119-0.04149.8470.0000.0000.0000.0000.0000.000
140A77ALA00.162-0.03448.1800.0000.0000.0000.0000.0000.000
141A77ALA0-0.0400.10847.4840.0000.0000.0000.0000.0000.000
142A78PRO0-0.008-0.11242.6720.0000.0000.0000.0000.0000.000
143A79ARG00.0450.00344.3620.0020.0020.0000.0000.0000.000
144A79ARG10.9011.07044.2950.0460.0460.0000.0000.0000.000
145A80GLU00.127-0.11742.040-0.004-0.0040.0000.0000.0000.000
146A80GLU-1-1.004-0.82541.858-0.050-0.0500.0000.0000.0000.000
147A81HIS0-0.031-0.14339.5910.0030.0030.0000.0000.0000.000
148A81HIS0-0.0910.10138.760-0.002-0.0020.0000.0000.0000.000
149A82PRO00.093-0.05339.229-0.003-0.0030.0000.0000.0000.000
150A83PHE00.092-0.03836.782-0.003-0.0030.0000.0000.0000.000
151A83PHE0-0.0480.10732.455-0.001-0.0010.0000.0000.0000.000
152A84VAL00.037-0.08237.5810.0040.0040.0000.0000.0000.000
153A84VAL0-0.0730.10438.4890.0000.0000.0000.0000.0000.000
154A85LEU00.054-0.12935.354-0.006-0.0060.0000.0000.0000.000
155A85LEU0-0.0560.12634.5150.0000.0000.0000.0000.0000.000
156A86GLN00.074-0.09934.2530.0050.0050.0000.0000.0000.000
157A86GLN0-0.1010.08633.518-0.005-0.0050.0000.0000.0000.000
158A87SER00.061-0.06933.333-0.002-0.0020.0000.0000.0000.000
159A87SER0-0.0080.06733.8290.0000.0000.0000.0000.0000.000
160A88VAL0-0.007-0.13528.895-0.002-0.0020.0000.0000.0000.000
161A88VAL0-0.0110.13426.800-0.001-0.0010.0000.0000.0000.000
162A89GLY0-0.013-0.09728.874-0.002-0.0020.0000.0000.0000.000
163A90GLY0-0.0010.00630.1710.0020.0020.0000.0000.0000.000
164A91GLN00.107-0.02727.5850.0010.0010.0000.0000.0000.000
165A91GLN0-0.1060.10026.5290.0010.0010.0000.0000.0000.000
166A92THR00.017-0.07323.3430.0030.0030.0000.0000.0000.000
167A92THR00.0090.08821.3010.0030.0030.0000.0000.0000.000
168A93LEU00.010-0.09522.314-0.007-0.0070.0000.0000.0000.000
169A93LEU0-0.0850.07523.1870.0010.0010.0000.0000.0000.000
170A94THR00.066-0.05417.9650.0150.0150.0000.0000.0000.000
171A94THR00.0050.06917.089-0.003-0.0030.0000.0000.0000.000
172A95VAL00.086-0.09617.5590.0040.0040.0000.0000.0000.000
173A95VAL0-0.0830.10016.8300.0040.0040.0000.0000.0000.000
174A96PHE00.035-0.08613.7830.0010.0010.0000.0000.0000.000
175A96PHE0-0.0690.09012.7690.0140.0140.0000.0000.0000.000
176A97THR00.018-0.09612.7720.0610.0610.0000.0000.0000.000
177A97THR0-0.0740.03612.445-0.035-0.0350.0000.0000.0000.000
178A98GLU00.152-0.09911.764-0.112-0.1120.0000.0000.0000.000
179A98GLU-1-0.995-0.81412.628-0.562-0.5620.0000.0000.0000.000
180A99SER0-0.058-0.08211.1990.1270.1270.0000.0000.0000.000
181A99SER0-0.0620.03810.030-0.063-0.0630.0000.0000.0000.000
182A100SER00.087-0.05212.436-0.029-0.0290.0000.0000.0000.000
183A100SER0-0.0580.03814.5660.0120.0120.0000.0000.0000.000
184A101SER0-0.022-0.05710.4170.1150.1150.0000.0000.0000.000
185A101SER0-0.0440.0379.588-0.101-0.1010.0000.0000.0000.000
186A102ASP00.062-0.1049.900-0.165-0.1650.0000.0000.0000.000
187A102ASP-1-0.969-0.84510.472-0.707-0.7070.0000.0000.0000.000
188A103LYS00.162-0.0767.202-0.060-0.0600.0000.0000.0000.000
189A103LYS10.8071.0494.6192.8452.894-0.001-0.011-0.0360.000
190A104LEU00.088-0.1167.1250.2210.2210.0000.0000.0000.000
191A104LEU0-0.0570.1388.1990.0400.0400.0000.0000.0000.000
192A105SER00.060-0.1037.118-0.171-0.1710.0000.0000.0000.000
193A105SER0-0.0630.0748.158-0.038-0.0380.0000.0000.0000.000
194A106LEU00.049-0.1009.2240.0600.0600.0000.0000.0000.000
195A106LEU0-0.1180.09111.3750.0210.0210.0000.0000.0000.000
196A107GLU00.120-0.11112.0420.0180.0180.0000.0000.0000.000
197A107GLU-1-0.937-0.79112.113-0.568-0.5680.0000.0000.0000.000
198A108GLY0-0.023-0.11914.2700.0400.0400.0000.0000.0000.000
199A109ILE00.076-0.03317.213-0.023-0.0230.0000.0000.0000.000
200A109ILE0-0.0640.12918.4460.0010.0010.0000.0000.0000.000
201A110VAL00.036-0.11920.1420.0060.0060.0000.0000.0000.000
202A110VAL0-0.0940.09622.1160.0000.0000.0000.0000.0000.000
203A111VAL00.016-0.11623.4500.0060.0060.0000.0000.0000.000
204A111VAL0-0.0800.11723.8580.0020.0020.0000.0000.0000.000
205A112GLN00.118-0.12526.1610.0100.0100.0000.0000.0000.000
206A112GLN0-0.1290.09529.0300.0040.0040.0000.0000.0000.000
207A113ARG00.095-0.09828.125-0.011-0.0110.0000.0000.0000.000
208A113ARG10.8671.08528.3190.1070.1070.0000.0000.0000.000
209A114ALA00.079-0.08230.2910.0080.0080.0000.0000.0000.000
210A114ALA0-0.0460.10732.7140.0010.0010.0000.0000.0000.000
211A115GLU00.078-0.10232.569-0.009-0.0090.0000.0000.0000.000
212A115GLU-1-0.995-0.84335.616-0.078-0.0780.0000.0000.0000.000
213A116CYS00.107-0.09235.0260.0060.0060.0000.0000.0000.000
214A116CYS0-0.1670.09534.8230.0010.0010.0000.0000.0000.000
215A117ARG00.041-0.16336.551-0.004-0.0040.0000.0000.0000.000
216A117ARG10.8091.08239.3690.0690.0690.0000.0000.0000.000
217A118PRO00.024-0.10640.1890.0000.0000.0000.0000.0000.000
218A119ALA0-0.070-0.01342.0370.0030.0030.0000.0000.0000.000
219A119ALA00.0620.03442.9660.0000.0000.0000.0000.0000.000