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: J2KG9

Calculation Name: 1F3U-B-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1F3U

Chain ID: B

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 OptAll
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 263
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1093401.089865
FMO2-HF: Nuclear repulsion 1036559.284187
FMO2-HF: Total energy -56841.805678
FMO2-MP2: Total energy -57008.780624


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(B:5:GLY)


Summations of interaction energy for fragment #1(B: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.
-0.9490.25-0.004-0.68-0.5140.003
Interaction energy analysis for fragmet #1(B:5:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.019
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].
3B7SER00.0690.0103.873-1.300-0.101-0.004-0.680-0.5140.003
4B7SER0-0.0130.0776.7370.2410.2410.0000.0000.0000.000
5B8SER00.055-0.0676.2710.5720.5720.0000.0000.0000.000
6B8SER0-0.0530.0629.2570.1290.1290.0000.0000.0000.000
7B9GLN0-0.015-0.1037.011-0.254-0.2540.0000.0000.0000.000
8B9GLN0-0.0350.1125.012-0.203-0.2030.0000.0000.0000.000
9B10ASN00.149-0.0448.1970.0810.0810.0000.0000.0000.000
10B10ASN0-0.1310.05012.6200.0510.0510.0000.0000.0000.000
11B11VAL00.043-0.11910.513-0.016-0.0160.0000.0000.0000.000
12B11VAL0-0.0450.1208.769-0.009-0.0090.0000.0000.0000.000
13B12THR00.012-0.08211.605-0.017-0.0170.0000.0000.0000.000
14B12THR0-0.0200.06315.3190.0010.0010.0000.0000.0000.000
15B13GLU0-0.002-0.13414.6310.0390.0390.0000.0000.0000.000
16B13GLU-1-0.970-0.82911.9410.1500.1500.0000.0000.0000.000
17B14TYR00.031-0.13715.950-0.033-0.0330.0000.0000.0000.000
18B14TYR0-0.0920.10418.357-0.004-0.0040.0000.0000.0000.000
19B15VAL00.161-0.06919.3620.0370.0370.0000.0000.0000.000
20B15VAL0-0.0590.11321.901-0.002-0.0020.0000.0000.0000.000
21B16VAL00.052-0.10821.845-0.020-0.0200.0000.0000.0000.000
22B16VAL0-0.0750.10720.6280.0020.0020.0000.0000.0000.000
23B17ARG00.022-0.11323.3620.0120.0120.0000.0000.0000.000
24B17ARG10.6890.91826.746-0.068-0.0680.0000.0000.0000.000
25B18VAL00.107-0.10826.992-0.003-0.0030.0000.0000.0000.000
26B18VAL0-0.0970.11926.6690.0010.0010.0000.0000.0000.000
27B19PRO00.005-0.10929.2420.0010.0010.0000.0000.0000.000
28B20LYS00.0530.01732.8370.0060.0060.0000.0000.0000.000
29B20LYS10.8521.04031.393-0.120-0.1200.0000.0000.0000.000
30B21ASN00.108-0.05436.007-0.002-0.0020.0000.0000.0000.000
31B21ASN0-0.0430.10035.4470.0050.0050.0000.0000.0000.000
32B22THR00.040-0.08837.251-0.004-0.0040.0000.0000.0000.000
33B22THR0-0.0490.07836.2980.0000.0000.0000.0000.0000.000
34B23THR00.011-0.08038.3700.0020.0020.0000.0000.0000.000
35B23THR0-0.0190.06841.7790.0000.0000.0000.0000.0000.000
36B24LYS00.053-0.12839.256-0.004-0.0040.0000.0000.0000.000
37B24LYS10.9331.10837.759-0.042-0.0420.0000.0000.0000.000
38B25LYS00.076-0.08738.7240.0050.0050.0000.0000.0000.000
39B25LYS10.8331.05539.587-0.070-0.0700.0000.0000.0000.000
40B26TYR00.108-0.08235.115-0.007-0.0070.0000.0000.0000.000
41B26TYR0-0.0630.12034.383-0.002-0.0020.0000.0000.0000.000
42B27ASN00.046-0.07836.5670.0060.0060.0000.0000.0000.000
43B27ASN0-0.0550.04938.7560.0010.0010.0000.0000.0000.000
44B28ILE00.087-0.08334.999-0.003-0.0030.0000.0000.0000.000
45B28ILE0-0.0660.12631.8400.0000.0000.0000.0000.0000.000
46B29MET00.148-0.08935.9880.0010.0010.0000.0000.0000.000
47B29MET0-0.1160.09038.370-0.002-0.0020.0000.0000.0000.000
48B30ALA00.125-0.09136.062-0.004-0.0040.0000.0000.0000.000
49B30ALA0-0.0670.11635.4730.0010.0010.0000.0000.0000.000
50B31PHE00.003-0.13536.6670.0000.0000.0000.0000.0000.000
51B31PHE0-0.0430.11237.982-0.001-0.0010.0000.0000.0000.000
52B32ASN00.205-0.03436.8870.0020.0020.0000.0000.0000.000
53B32ASN0-0.1210.07638.909-0.002-0.0020.0000.0000.0000.000
54B33ALA00.133-0.10236.178-0.003-0.0030.0000.0000.0000.000
55B33ALA0-0.0300.14135.3010.0000.0000.0000.0000.0000.000
56B34ALA00.085-0.10237.453-0.005-0.0050.0000.0000.0000.000
57B34ALA0-0.0630.11740.3160.0000.0000.0000.0000.0000.000
58B35ASP0-0.022-0.09740.637-0.004-0.0040.0000.0000.0000.000
59B35ASP-1-0.891-0.82442.1380.0260.0260.0000.0000.0000.000
60B36LYS00.084-0.06839.9860.0000.0000.0000.0000.0000.000
61B36LYS10.8431.04140.322-0.010-0.0100.0000.0000.0000.000
62B37VAL00.109-0.12440.223-0.003-0.0030.0000.0000.0000.000
63B37VAL0-0.0830.12139.8820.0000.0000.0000.0000.0000.000
64B38ASN00.125-0.06739.2820.0010.0010.0000.0000.0000.000
65B38ASN0-0.0750.08940.4620.0000.0000.0000.0000.0000.000
66B39PHE00.128-0.08339.620-0.001-0.0010.0000.0000.0000.000
67B39PHE0-0.0510.10336.5240.0010.0010.0000.0000.0000.000
68B40ALA00.133-0.07940.7100.0010.0010.0000.0000.0000.000
69B40ALA0-0.0560.12240.383-0.001-0.0010.0000.0000.0000.000
70B41THR0-0.022-0.08742.061-0.002-0.0020.0000.0000.0000.000
71B41THR0-0.0860.03444.2020.0010.0010.0000.0000.0000.000
72B42TRP00.031-0.06844.3970.0000.0000.0000.0000.0000.000
73B42TRP0-0.0890.06242.4570.0020.0020.0000.0000.0000.000
74B43ASN00.196-0.03245.9290.0000.0000.0000.0000.0000.000
75B43ASN0-0.1140.05749.324-0.001-0.0010.0000.0000.0000.000
76B44GLN00.099-0.07648.7410.0000.0000.0000.0000.0000.000
77B44GLN0-0.0870.08650.9280.0010.0010.0000.0000.0000.000
78B45ALA00.072-0.10047.200-0.001-0.0010.0000.0000.0000.000
79B45ALA0-0.0460.10746.5860.0000.0000.0000.0000.0000.000
80B46ARG0-0.007-0.10848.6660.0000.0000.0000.0000.0000.000
81B46ARG10.8211.01551.366-0.019-0.0190.0000.0000.0000.000
82B47LEU00.135-0.07946.717-0.001-0.0010.0000.0000.0000.000
83B47LEU0-0.0780.11143.9950.0000.0000.0000.0000.0000.000
84B48GLU00.061-0.09948.1770.0010.0010.0000.0000.0000.000
85B48GLU-1-0.838-0.74851.4720.0210.0210.0000.0000.0000.000
86B49ARG00.080-0.11050.1640.0000.0000.0000.0000.0000.000
87B49ARG10.7581.01845.726-0.048-0.0480.0000.0000.0000.000
88B50ASP00.161-0.09051.135-0.002-0.0020.0000.0000.0000.000
89B50ASP-1-0.949-0.78052.1400.0300.0300.0000.0000.0000.000
90B51LEU00.033-0.10953.3280.0020.0020.0000.0000.0000.000
91B51LEU0-0.0830.08553.8380.0000.0000.0000.0000.0000.000
92B52SER00.039-0.08956.0260.0000.0000.0000.0000.0000.000
93B52SER0-0.0390.05256.740-0.001-0.0010.0000.0000.0000.000
94B53ASN00.134-0.05356.896-0.001-0.0010.0000.0000.0000.000
95B53ASN0-0.1120.05954.841-0.001-0.0010.0000.0000.0000.000
96B54LYS00.094-0.06158.2000.0000.0000.0000.0000.0000.000
97B54LYS10.7811.02958.762-0.033-0.0330.0000.0000.0000.000
98B55LYS00.028-0.09060.0370.0000.0000.0000.0000.0000.000
99B55LYS10.8821.04863.359-0.024-0.0240.0000.0000.0000.000
100B56ILE00.145-0.09161.314-0.002-0.0020.0000.0000.0000.000
101B56ILE0-0.1120.10359.0580.0000.0000.0000.0000.0000.000
102B57TYR00.074-0.09262.0000.0020.0020.0000.0000.0000.000
103B57TYR0-0.0530.10265.8980.0000.0000.0000.0000.0000.000
104B58GLN00.024-0.11961.702-0.001-0.0010.0000.0000.0000.000
105B58GLN0-0.0990.08359.5780.0000.0000.0000.0000.0000.000
106B59GLU00.151-0.08563.0630.0000.0000.0000.0000.0000.000
107B59GLU-1-1.021-0.84965.6100.0270.0270.0000.0000.0000.000
108B60GLU00.041-0.12963.6280.0010.0010.0000.0000.0000.000
109B60GLU-1-0.920-0.79461.3190.0380.0380.0000.0000.0000.000
110B61GLU00.070-0.11564.510-0.001-0.0010.0000.0000.0000.000
111B61GLU-1-0.865-0.76465.4940.0340.0340.0000.0000.0000.000
112B62MET0-0.100-0.13466.1110.0020.0020.0000.0000.0000.000
113B62MET00.0300.01669.4210.0000.0000.0000.0000.0000.000
114B73ARG00.1710.02879.0940.0000.0000.0000.0000.0000.000
115B73ARG10.8811.08073.303-0.030-0.0300.0000.0000.0000.000
116B74LYS00.021-0.11978.319-0.001-0.0010.0000.0000.0000.000
117B74LYS10.7811.01578.181-0.024-0.0240.0000.0000.0000.000
118B75LEU00.087-0.11477.3740.0010.0010.0000.0000.0000.000
119B75LEU0-0.0220.14478.0090.0000.0000.0000.0000.0000.000
120B76ARG00.078-0.08673.0190.0000.0000.0000.0000.0000.000
121B76ARG10.9251.06467.748-0.034-0.0340.0000.0000.0000.000
122B77GLU00.047-0.10673.6920.0000.0000.0000.0000.0000.000
123B77GLU-1-0.887-0.79172.6420.0300.0300.0000.0000.0000.000
124B78GLU00.138-0.10875.3970.0000.0000.0000.0000.0000.000
125B78GLU-1-0.935-0.79278.6550.0240.0240.0000.0000.0000.000
126B79ALA00.034-0.12275.172-0.001-0.0010.0000.0000.0000.000
127B79ALA0-0.0950.10174.4140.0000.0000.0000.0000.0000.000
128B80ARG00.005-0.13372.8530.0010.0010.0000.0000.0000.000
129B80ARG10.8111.02972.102-0.028-0.0280.0000.0000.0000.000
130B81ARG00.146-0.05172.3490.0010.0010.0000.0000.0000.000
131B81ARG10.8651.07675.070-0.023-0.0230.0000.0000.0000.000
132B82LYS00.109-0.07870.282-0.001-0.0010.0000.0000.0000.000
133B82LYS10.7581.00566.193-0.034-0.0340.0000.0000.0000.000
134B83LYS00.026-0.12770.734-0.001-0.0010.0000.0000.0000.000
135B83LYS10.7771.01272.473-0.027-0.0270.0000.0000.0000.000
136B84TYR00.057-0.09369.1660.0010.0010.0000.0000.0000.000
137B84TYR0-0.0240.10565.7610.0000.0000.0000.0000.0000.000
138B85GLY00.038-0.08168.652-0.001-0.0010.0000.0000.0000.000
139B86ILE00.1030.02066.9300.0010.0010.0000.0000.0000.000
140B86ILE0-0.0870.09767.4820.0000.0000.0000.0000.0000.000
141B87VAL00.068-0.13664.238-0.001-0.0010.0000.0000.0000.000
142B87VAL0-0.0630.13363.0250.0000.0000.0000.0000.0000.000
143B88LEU00.134-0.10763.0370.0000.0000.0000.0000.0000.000
144B88LEU0-0.1440.10862.6690.0000.0000.0000.0000.0000.000
145B89LYS00.049-0.11058.8990.0000.0000.0000.0000.0000.000
146B89LYS10.7320.99158.104-0.040-0.0400.0000.0000.0000.000
147B90GLU00.091-0.13557.556-0.002-0.0020.0000.0000.0000.000
148B90GLU-1-0.922-0.78556.2420.0430.0430.0000.0000.0000.000
149B91PHE00.098-0.09055.8250.0020.0020.0000.0000.0000.000
150B91PHE0-0.0980.08355.985-0.001-0.0010.0000.0000.0000.000
151B92ARG00.136-0.08452.442-0.001-0.0010.0000.0000.0000.000
152B92ARG10.7911.04146.734-0.058-0.0580.0000.0000.0000.000
153B93PRO00.005-0.12251.6600.0010.0010.0000.0000.0000.000
154B94GLU00.091-0.00947.718-0.002-0.0020.0000.0000.0000.000
155B94GLU-1-0.900-0.79745.2850.0560.0560.0000.0000.0000.000
156B95ASP00.055-0.06446.6060.0020.0020.0000.0000.0000.000
157B95ASP-1-0.847-0.79246.1940.0610.0610.0000.0000.0000.000
158B96GLN00.039-0.12248.4390.0000.0000.0000.0000.0000.000
159B96GLN0-0.0350.12351.464-0.002-0.0020.0000.0000.0000.000
160B97PRO0-0.020-0.09247.8640.0010.0010.0000.0000.0000.000
161B98TRP00.0790.00146.588-0.002-0.0020.0000.0000.0000.000
162B98TRP0-0.0610.09944.491-0.001-0.0010.0000.0000.0000.000
163B99LEU00.145-0.09047.9720.0000.0000.0000.0000.0000.000
164B99LEU0-0.1350.09750.6100.0000.0000.0000.0000.0000.000
165B100LEU00.135-0.09346.4670.0000.0000.0000.0000.0000.000
166B100LEU0-0.1360.09843.8280.0000.0000.0000.0000.0000.000
167B101ARG00.018-0.10747.9210.0000.0000.0000.0000.0000.000
168B101ARG10.7440.97651.555-0.021-0.0210.0000.0000.0000.000
169B102VAL00.192-0.08247.8940.0000.0000.0000.0000.0000.000
170B102VAL0-0.0930.11045.8710.0000.0000.0000.0000.0000.000
171B103ASN00.003-0.08149.0390.0000.0000.0000.0000.0000.000
172B103ASN0-0.1400.04948.8140.0000.0000.0000.0000.0000.000
173B104GLY00.147-0.06651.581-0.001-0.0010.0000.0000.0000.000
174B105LYS00.011-0.03854.6230.0010.0010.0000.0000.0000.000
175B105LYS10.9411.09658.186-0.012-0.0120.0000.0000.0000.000
176B106SER00.035-0.08656.4790.0010.0010.0000.0000.0000.000
177B106SER00.0280.12355.7850.0000.0000.0000.0000.0000.000
178B107GLY00.013-0.06352.103-0.001-0.0010.0000.0000.0000.000
179B108ARG00.0870.02648.6290.0010.0010.0000.0000.0000.000
180B108ARG10.8051.00544.192-0.013-0.0130.0000.0000.0000.000
181B109LYS00.068-0.09649.7010.0000.0000.0000.0000.0000.000
182B109LYS10.7480.99551.653-0.013-0.0130.0000.0000.0000.000
183B110PHE00.009-0.10246.327-0.001-0.0010.0000.0000.0000.000
184B110PHE0-0.0400.08544.6020.0000.0000.0000.0000.0000.000
185B111LYS00.177-0.07847.7790.0000.0000.0000.0000.0000.000
186B111LYS10.8011.06048.279-0.031-0.0310.0000.0000.0000.000
187B112GLY0-0.031-0.11544.3310.0000.0000.0000.0000.0000.000
188B113ILE00.089-0.01643.7420.0000.0000.0000.0000.0000.000
189B113ILE0-0.0660.11344.3860.0000.0000.0000.0000.0000.000
190B114LYS00.141-0.08841.7660.0010.0010.0000.0000.0000.000
191B114LYS10.7161.00641.568-0.064-0.0640.0000.0000.0000.000
192B115LYS00.066-0.10038.000-0.002-0.0020.0000.0000.0000.000
193B115LYS10.7821.03834.021-0.097-0.0970.0000.0000.0000.000
194B116GLY0-0.016-0.12138.4940.0060.0060.0000.0000.0000.000
195B117GLY00.0100.01336.9920.0000.0000.0000.0000.0000.000
196B118VAL00.027-0.01136.0940.0040.0040.0000.0000.0000.000
197B118VAL0-0.0830.08138.328-0.001-0.0010.0000.0000.0000.000
198B119THR00.065-0.07333.8600.0010.0010.0000.0000.0000.000
199B119THR0-0.0740.06333.168-0.005-0.0050.0000.0000.0000.000
200B120GLU00.061-0.06532.379-0.010-0.0100.0000.0000.0000.000
201B120GLU-1-0.873-0.80029.8200.1740.1740.0000.0000.0000.000
202B121ASN00.033-0.10530.090-0.008-0.0080.0000.0000.0000.000
203B121ASN0-0.0880.06729.4100.0030.0030.0000.0000.0000.000
204B122THR00.010-0.07328.0450.0120.0120.0000.0000.0000.000
205B122THR0-0.0560.04226.2280.0000.0000.0000.0000.0000.000
206B123SER00.091-0.07928.761-0.013-0.0130.0000.0000.0000.000
207B123SER0-0.0210.07930.9070.0010.0010.0000.0000.0000.000
208B124TYR00.096-0.07028.5450.0140.0140.0000.0000.0000.000
209B124TYR0-0.0840.08528.155-0.004-0.0040.0000.0000.0000.000
210B125TYR00.056-0.12828.088-0.011-0.0110.0000.0000.0000.000
211B125TYR0-0.0390.12527.1730.0000.0000.0000.0000.0000.000
212B126ILE00.031-0.10227.7610.0070.0070.0000.0000.0000.000
213B126ILE0-0.0740.09030.142-0.002-0.0020.0000.0000.0000.000
214B127PHE00.109-0.09125.2170.0010.0010.0000.0000.0000.000
215B127PHE0-0.0650.10522.8170.0030.0030.0000.0000.0000.000
216B128THR0-0.022-0.09826.712-0.007-0.0070.0000.0000.0000.000
217B128THR0-0.0450.05629.3580.0000.0000.0000.0000.0000.000
218B129GLN00.191-0.04226.0850.0110.0110.0000.0000.0000.000
219B129GLN0-0.0670.10923.697-0.002-0.0020.0000.0000.0000.000
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