FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: 7YJ2K

Calculation Name: 1C28-B-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 1C28

Chain ID: B

ChEMBL ID:

UniProt ID: Q60994

Base Structure: X-ray

Registration Date: 2025-07-11

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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 224
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1029399.291591
FMO2-HF: Nuclear repulsion 981542.6166
FMO2-HF: Total energy -47856.674991
FMO2-MP2: Total energy -47997.515668


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(B:113:MET)


Summations of interaction energy for fragment #1(B:113:MET)
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.
-1.075-0.5360.4881.638-2.6660.007
Interaction energy analysis for fragmet #1(B:113:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.122 / q_NPA : -0.006
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].
4B114TYR0-0.0480.1053.9670.2780.7690.004-0.224-0.2700.000
5B115ARG00.154-0.0813.881-3.686-0.442-0.017-2.012-1.2160.000
6B115ARG10.8211.0396.786-0.934-0.9340.0000.0000.0000.000
7B116SER00.092-0.0995.8570.7220.7220.0000.0000.0000.000
8B116SER0-0.0500.0856.3210.0610.0610.0000.0000.0000.000
9B117ALA00.124-0.0767.928-0.321-0.3210.0000.0000.0000.000
10B117ALA0-0.0800.09311.1320.0040.0040.0000.0000.0000.000
11B118PHE0-0.018-0.11811.6360.1460.1460.0000.0000.0000.000
12B118PHE0-0.0160.11713.876-0.001-0.0010.0000.0000.0000.000
13B119SER00.094-0.07315.233-0.069-0.0690.0000.0000.0000.000
14B119SER0-0.0790.05418.2480.0090.0090.0000.0000.0000.000
15B120VAL0-0.032-0.10918.8090.0430.0430.0000.0000.0000.000
16B120VAL0-0.0450.11719.3470.0000.0000.0000.0000.0000.000
17B121GLY00.105-0.08521.858-0.027-0.0270.0000.0000.0000.000
18B122LEU00.104-0.01525.6230.0150.0150.0000.0000.0000.000
19B122LEU0-0.0730.12128.161-0.001-0.0010.0000.0000.0000.000
20B123GLU00.018-0.12229.120-0.011-0.0110.0000.0000.0000.000
21B123GLU-1-0.819-0.77131.6290.0450.0450.0000.0000.0000.000
22B124THR0-0.016-0.09632.701-0.004-0.0040.0000.0000.0000.000
23B124THR00.0250.07833.320-0.002-0.0020.0000.0000.0000.000
24B125ARG00.001-0.09434.2310.0000.0000.0000.0000.0000.000
25B125ARG10.8050.98833.6500.0040.0040.0000.0000.0000.000
26B126VAL00.140-0.04435.260-0.008-0.0080.0000.0000.0000.000
27B126VAL0-0.1210.09335.2040.0010.0010.0000.0000.0000.000
28B127THR00.006-0.11431.7280.0070.0070.0000.0000.0000.000
29B127THR0-0.0510.04430.2520.0010.0010.0000.0000.0000.000
30B128VAL00.037-0.12231.236-0.001-0.0010.0000.0000.0000.000
31B128VAL0-0.0830.12430.1130.0010.0010.0000.0000.0000.000
32B129PRO00.042-0.09831.448-0.009-0.0090.0000.0000.0000.000
33B130ASN00.0310.03332.0290.0050.0050.0000.0000.0000.000
34B130ASN0-0.0740.08333.6740.0000.0000.0000.0000.0000.000
35B131VAL00.089-0.09029.262-0.005-0.0050.0000.0000.0000.000
36B131VAL0-0.0560.10428.8920.0020.0020.0000.0000.0000.000
37B132PRO0-0.015-0.12524.066-0.004-0.0040.0000.0000.0000.000
38B133ILE00.0870.01426.0660.0170.0170.0000.0000.0000.000
39B133ILE0-0.0950.09326.112-0.001-0.0010.0000.0000.0000.000
40B134ARG00.080-0.08624.992-0.004-0.0040.0000.0000.0000.000
41B134ARG10.7711.02725.677-0.023-0.0230.0000.0000.0000.000
42B135PHE00.097-0.11524.3720.0090.0090.0000.0000.0000.000
43B135PHE0-0.1100.09323.312-0.005-0.0050.0000.0000.0000.000
44B136THR00.042-0.05524.2510.0110.0110.0000.0000.0000.000
45B136THR0-0.0160.06327.134-0.002-0.0020.0000.0000.0000.000
46B137LYS00.138-0.06425.3750.0230.0230.0000.0000.0000.000
47B137LYS10.6620.98126.124-0.052-0.0520.0000.0000.0000.000
48B138ILE00.055-0.13121.707-0.026-0.0260.0000.0000.0000.000
49B138ILE0-0.0880.10819.6990.0050.0050.0000.0000.0000.000
50B139PHE00.086-0.09021.4550.0190.0190.0000.0000.0000.000
51B139PHE0-0.0990.09521.140-0.002-0.0020.0000.0000.0000.000
52B140TYR00.143-0.10017.2480.0260.0260.0000.0000.0000.000
53B140TYR0-0.1650.06611.5050.0260.0260.0000.0000.0000.000
54B141ASN00.068-0.07615.125-0.053-0.0530.0000.0000.0000.000
55B141ASN0-0.0770.07015.246-0.001-0.0010.0000.0000.0000.000
56B142GLN00.157-0.06513.446-0.009-0.0090.0000.0000.0000.000
57B142GLN0-0.1200.06912.825-0.035-0.0350.0000.0000.0000.000
58B143GLN00.023-0.08310.0230.1170.1170.0000.0000.0000.000
59B143GLN0-0.0270.1158.254-0.202-0.2020.0000.0000.0000.000
60B144ASN00.056-0.07211.1340.0420.0420.0000.0000.0000.000
61B144ASN0-0.1030.06914.133-0.074-0.0740.0000.0000.0000.000
62B145HIS00.157-0.07111.506-0.016-0.0160.0000.0000.0000.000
63B145HIS0-0.1200.0526.9690.2020.2020.0000.0000.0000.000
64B146TYR00.106-0.07812.774-0.098-0.0980.0000.0000.0000.000
65B146TYR0-0.1040.08116.356-0.008-0.0080.0000.0000.0000.000
66B147ASP00.064-0.09016.2730.0640.0640.0000.0000.0000.000
67B147ASP-1-0.813-0.70218.6170.0920.0920.0000.0000.0000.000
68B148GLY00.042-0.09519.248-0.033-0.0330.0000.0000.0000.000
69B149SER00.019-0.01722.689-0.018-0.0180.0000.0000.0000.000
70B149SER0-0.0580.06322.724-0.001-0.0010.0000.0000.0000.000
71B150THR0-0.037-0.12722.775-0.009-0.0090.0000.0000.0000.000
72B150THR0-0.0540.06221.391-0.012-0.0120.0000.0000.0000.000
73B151GLY00.029-0.08322.673-0.019-0.0190.0000.0000.0000.000
74B152LYS00.035-0.02419.716-0.023-0.0230.0000.0000.0000.000
75B152LYS10.7911.04419.1900.1110.1110.0000.0000.0000.000
76B153PHE00.155-0.05015.5530.0670.0670.0000.0000.0000.000
77B153PHE0-0.1170.08110.2720.0020.0020.0000.0000.0000.000
78B154TYR00.033-0.11814.058-0.072-0.0720.0000.0000.0000.000
79B154TYR0-0.1130.06114.093-0.001-0.0010.0000.0000.0000.000
80B155CYS00.118-0.11910.4580.1370.1370.0000.0000.0000.000
81B155CYS0-0.1670.1419.745-0.093-0.0930.0000.0000.0000.000
82B156ASN00.099-0.0838.602-0.176-0.1760.0000.0000.0000.000
83B156ASN0-0.1020.0708.087-0.063-0.0630.0000.0000.0000.000
84B157ILE00.049-0.0994.6850.1290.192-0.002-0.007-0.0560.000
85B157ILE0-0.0860.1002.5671.146-0.1530.4251.514-0.6400.003
86B158PRO00.018-0.0734.918-0.017-0.001-0.001-0.007-0.0070.000
87B159GLY00.0690.0205.455-1.594-1.616-0.002-0.0010.0250.000
88B160LEU00.1390.0177.7590.5040.5040.0000.0000.0000.000
89B160LEU0-0.1320.09910.7700.0080.0080.0000.0000.0000.000
90B161TYR00.064-0.13010.161-0.177-0.1770.0000.0000.0000.000
91B161TYR0-0.0750.0957.5860.1970.1970.0000.0000.0000.000
92B162TYR00.115-0.07912.0870.0270.0270.0000.0000.0000.000
93B162TYR0-0.0590.10515.2550.0180.0180.0000.0000.0000.000
94B163PHE00.008-0.11915.3330.0200.0200.0000.0000.0000.000
95B163PHE0-0.0530.10114.3780.0050.0050.0000.0000.0000.000
96B164SER00.086-0.07218.028-0.016-0.0160.0000.0000.0000.000
97B164SER0-0.0230.07820.593-0.001-0.0010.0000.0000.0000.000
98B165TYR00.010-0.10421.3790.0180.0180.0000.0000.0000.000
99B165TYR0-0.0520.08623.226-0.004-0.0040.0000.0000.0000.000
100B166HIS00.118-0.10124.328-0.015-0.0150.0000.0000.0000.000
101B166HIS0-0.0980.08828.0240.0080.0080.0000.0000.0000.000
102B167ILE0-0.033-0.08527.9830.0130.0130.0000.0000.0000.000
103B167ILE0-0.0400.09427.461-0.001-0.0010.0000.0000.0000.000
104B168THR00.121-0.06030.095-0.010-0.0100.0000.0000.0000.000
105B168THR0-0.0010.07734.0340.0050.0050.0000.0000.0000.000
106B169VAL0-0.002-0.08733.1540.0040.0040.0000.0000.0000.000
107B169VAL0-0.0900.08532.654-0.002-0.0020.0000.0000.0000.000
108B170TYR00.029-0.07535.1210.0020.0020.0000.0000.0000.000
109B170TYR0-0.0880.07738.9680.0030.0030.0000.0000.0000.000
110B171MET00.146-0.09638.3670.0060.0060.0000.0000.0000.000
111B171MET0-0.0730.09734.957-0.004-0.0040.0000.0000.0000.000
112B172LYS00.099-0.07439.519-0.005-0.0050.0000.0000.0000.000
113B172LYS10.7280.97243.3560.0550.0550.0000.0000.0000.000
114B173ASP00.003-0.10840.383-0.001-0.0010.0000.0000.0000.000
115B173ASP-1-0.845-0.74541.772-0.061-0.0610.0000.0000.0000.000
116B174VAL00.053-0.09236.849-0.002-0.0020.0000.0000.0000.000
117B174VAL0-0.0340.10834.9430.0000.0000.0000.0000.0000.000
118B175LYS00.092-0.09333.8660.0030.0030.0000.0000.0000.000
119B175LYS10.8221.00332.9400.1190.1190.0000.0000.0000.000
120B176VAL00.056-0.12030.3670.0060.0060.0000.0000.0000.000
121B176VAL0-0.0110.12428.3530.0010.0010.0000.0000.0000.000
122B177SER00.046-0.08126.909-0.005-0.0050.0000.0000.0000.000
123B177SER0-0.0840.01625.475-0.005-0.0050.0000.0000.0000.000
124B178LEU00.133-0.04322.2030.0260.0260.0000.0000.0000.000
125B178LEU0-0.0840.09620.315-0.007-0.0070.0000.0000.0000.000
126B179PHE00.007-0.11722.312-0.012-0.0120.0000.0000.0000.000
127B179PHE0-0.0350.11923.5890.0060.0060.0000.0000.0000.000
128B180LYS00.189-0.05219.1130.0180.0180.0000.0000.0000.000
129B180LYS10.6820.96415.3580.6430.6430.0000.0000.0000.000
130B181LYS00.016-0.08919.816-0.004-0.0040.0000.0000.0000.000
131B181LYS10.7921.00416.7880.4410.4410.0000.0000.0000.000
132B182ASP00.073-0.08021.224-0.006-0.0060.0000.0000.0000.000
133B182ASP-1-0.914-0.83024.474-0.158-0.1580.0000.0000.0000.000
134B183LYS00.076-0.13123.5350.0220.0220.0000.0000.0000.000
135B183LYS10.7371.02125.8790.1630.1630.0000.0000.0000.000
136B185VAL00.015-0.08222.674-0.026-0.0260.0000.0000.0000.000
137B185VAL0-0.0620.08920.814-0.005-0.0050.0000.0000.0000.000
138B186LEU00.140-0.09523.543-0.017-0.0170.0000.0000.0000.000
139B186LEU0-0.0670.12626.088-0.001-0.0010.0000.0000.0000.000
140B187PHE00.115-0.09026.9470.0150.0150.0000.0000.0000.000
141B187PHE0-0.1110.08529.5950.0000.0000.0000.0000.0000.000
142B188THR0-0.009-0.08530.408-0.006-0.0060.0000.0000.0000.000
143B188THR0-0.0380.06232.304-0.004-0.0040.0000.0000.0000.000
144B189TYR00.141-0.07633.1420.0100.0100.0000.0000.0000.000
145B189TYR0-0.0930.09532.3620.0040.0040.0000.0000.0000.000
146B190ASP00.066-0.10236.159-0.004-0.0040.0000.0000.0000.000
147B190ASP-1-0.868-0.79437.185-0.113-0.1130.0000.0000.0000.000
148B191GLN00.085-0.09738.9580.0010.0010.0000.0000.0000.000
149B191GLN0-0.1270.08243.2890.0000.0000.0000.0000.0000.000
150B192TYR00.109-0.09341.519-0.004-0.0040.0000.0000.0000.000
151B192TYR0-0.1520.04343.0860.0010.0010.0000.0000.0000.000
152B193GLN00.037-0.11842.3290.0040.0040.0000.0000.0000.000
153B193GLN0-0.0830.08441.2650.0030.0030.0000.0000.0000.000
154B194GLU00.004-0.11441.920-0.004-0.0040.0000.0000.0000.000
155B194GLU-1-0.925-0.81343.993-0.053-0.0530.0000.0000.0000.000
156B195LYS00.097-0.07840.9890.0000.0000.0000.0000.0000.000
157B195LYS10.7770.99841.4470.0510.0510.0000.0000.0000.000
158B197VAL00.052-0.12136.823-0.003-0.0030.0000.0000.0000.000
159B197VAL0-0.0750.10334.688-0.001-0.0010.0000.0000.0000.000
160B198ASP00.084-0.08138.0360.0030.0030.0000.0000.0000.000
161B198ASP-1-0.874-0.79439.048-0.049-0.0490.0000.0000.0000.000
162B199GLN00.093-0.08234.4250.0060.0060.0000.0000.0000.000
163B199GLN0-0.0510.09933.9080.0060.0060.0000.0000.0000.000
164B200ALA00.057-0.10131.799-0.002-0.0020.0000.0000.0000.000
165B200ALA0-0.0470.10731.242-0.002-0.0020.0000.0000.0000.000
166B201SER0-0.025-0.09128.3570.0080.0080.0000.0000.0000.000
167B201SER00.0250.08128.5410.0040.0040.0000.0000.0000.000
168B202GLY00.015-0.08826.175-0.003-0.0030.0000.0000.0000.000
169B203SER0-0.0150.00522.2090.0160.0160.0000.0000.0000.000
170B203SER00.0050.08121.354-0.006-0.0060.0000.0000.0000.000
171B204VAL00.012-0.09320.3060.0170.0170.0000.0000.0000.000
172B204VAL0-0.0650.09818.8850.0020.0020.0000.0000.0000.000
173B205LEU00.093-0.10816.5750.0100.0100.0000.0000.0000.000
174B205LEU0-0.0650.11415.600-0.005-0.0050.0000.0000.0000.000
175B206LEU00.040-0.12715.1730.0390.0390.0000.0000.0000.000
176B206LEU0-0.0500.11415.4220.0110.0110.0000.0000.0000.000
177B207HIS00.170-0.05012.191-0.099-0.0990.0000.0000.0000.000
178B207HIS10.6970.9329.6511.6031.6030.0000.0000.0000.000
179B208LEU0-0.041-0.12411.1530.2110.2110.0000.0000.0000.000
180B208LEU0-0.0600.08110.8720.0400.0400.0000.0000.0000.000
181B209GLU00.106-0.08010.211-0.378-0.3780.0000.0000.0000.000
182B209GLU-1-0.895-0.80112.656-1.044-1.0440.0000.0000.0000.000
183B210VAL00.108-0.10410.4180.0700.0700.0000.0000.0000.000
184B210VAL0-0.0500.1178.620-0.017-0.0170.0000.0000.0000.000
185B211GLY00.008-0.09811.0570.0840.0840.0000.0000.0000.000
186B212ASP00.036-0.03813.3620.0990.0990.0000.0000.0000.000
187B212ASP-1-0.859-0.76713.306-0.626-0.6260.0000.0000.0000.000
188B213GLN00.167-0.08114.601-0.010-0.0100.0000.0000.0000.000
189B213GLN0-0.0920.11017.5580.0170.0170.0000.0000.0000.000
190B214VAL00.030-0.12017.013-0.023-0.0230.0000.0000.0000.000
191B214VAL0-0.0910.09615.700-0.008-0.0080.0000.0000.0000.000
192B215TRP00.031-0.10318.1100.0330.0330.0000.0000.0000.000
193B215TRP0-0.0510.12120.325-0.003-0.0030.0000.0000.0000.000
194B216LEU00.140-0.09820.997-0.033-0.0330.0000.0000.0000.000
195B216LEU0-0.1050.11223.1000.0030.0030.0000.0000.0000.000
196B217GLN00.094-0.10224.0320.0210.0210.0000.0000.0000.000
197B217GLN0-0.0670.12826.681-0.004-0.0040.0000.0000.0000.000
198B218VAL00.084-0.12027.461-0.017-0.0170.0000.0000.0000.000
199B218VAL0-0.0510.13030.7670.0010.0010.0000.0000.0000.000
200B219TYR0-0.066-0.16431.0670.0040.0040.0000.0000.0000.000
201B219TYR00.0140.01730.1290.0000.0000.0000.0000.0000.000
202B234ASP00.1370.06030.353-0.002-0.0020.0000.0000.0000.000
203B234ASP-1-0.924-0.82729.3520.0360.0360.0000.0000.0000.000
204B235SER00.019-0.11429.241-0.007-0.0070.0000.0000.0000.000
205B235SER0-0.0460.08429.037-0.005-0.0050.0000.0000.0000.000
206B236THR0-0.021-0.08425.1880.0170.0170.0000.0000.0000.000
207B236THR0-0.0230.06524.149-0.006-0.0060.0000.0000.0000.000
208B237PHE00.155-0.06122.302-0.021-0.0210.0000.0000.0000.000
209B237PHE0-0.0820.09219.300-0.002-0.0020.0000.0000.0000.000
210B238THR0-0.011-0.09218.4620.0390.0390.0000.0000.0000.000
211B238THR0-0.0100.07517.6280.0120.0120.0000.0000.0000.000
212B239GLY0-0.003-0.08515.567-0.042-0.0420.0000.0000.0000.000
213B240PHE00.0570.00411.7140.1180.1180.0000.0000.0000.000
214B240PHE0-0.0720.08811.7480.0380.0380.0000.0000.0000.000
215B241LEU00.122-0.0987.9050.0170.0170.0000.0000.0000.000
216B241LEU0-0.1440.1014.615-0.069-0.035-0.001-0.008-0.0250.000
217B242LEU00.085-0.0999.3310.1400.1400.0000.0000.0000.000
218B242LEU0-0.1400.08711.8930.0440.0440.0000.0000.0000.000
219B243TYR00.020-0.1238.1880.0630.0630.0000.0000.0000.000
220B243TYR0-0.0420.0939.2170.0950.0950.0000.0000.0000.000
221B244HIS00.108-0.0773.6171.7211.479-0.0060.326-0.0780.000
222B244HIS0-0.0730.0852.8911.287-0.6550.0862.119-0.2630.004
223B245ASP0-0.116-0.1404.0490.3310.5270.002-0.062-0.1360.000
224B245ASP-1-0.771-0.8586.140-2.315-2.3150.0000.0000.0000.000