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: 5G33Z

Calculation Name: 5A8F-B-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5A8F

Chain ID: B

ChEMBL ID:

UniProt ID: C0MHL9

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 188
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1992403.377793
FMO2-HF: Nuclear repulsion 1918809.13819
FMO2-HF: Total energy -73594.239604
FMO2-MP2: Total energy -73807.324822


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:44:LEU)


Summations of interaction energy for fragment #1(B:44:LEU)
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.
63.86269.882.354-2.439-5.933-0.011
Interaction energy analysis for fragmet #1(B:44:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.889 / q_NPA : 0.934
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].
3B46SER00.0210.0043.1030.0852.6610.003-1.194-1.384-0.004
4B47LEU00.0300.0172.8025.1926.7080.423-0.515-1.425-0.002
5B48CYS0-0.0110.0064.7923.5643.8310.000-0.054-0.2130.000
54B98VAL0-0.028-0.0192.562-3.056-1.9290.439-0.358-1.209-0.004
58B102PHE0-0.019-0.0152.312-3.541-3.1111.490-0.314-1.606-0.001
176B220LEU00.0170.0034.6511.6731.775-0.001-0.004-0.0960.000
6B49LYS10.8790.9606.92836.89036.8900.0000.0000.0000.000
7B50ILE00.0160.0238.0682.3412.3410.0000.0000.0000.000
8B51PRO0-0.034-0.01510.5170.0310.0310.0000.0000.0000.000
9B52THR0-0.029-0.00611.829-0.027-0.0270.0000.0000.0000.000
10B53PHE00.013-0.00614.2960.1900.1900.0000.0000.0000.000
11B54LEU0-0.0220.00416.911-0.723-0.7230.0000.0000.0000.000
12B55GLY0-0.004-0.00119.2080.5310.5310.0000.0000.0000.000
13B56ASN00.0220.03021.2320.2060.2060.0000.0000.0000.000
14B57LEU0-0.036-0.02724.764-0.051-0.0510.0000.0000.0000.000
15B58ASP-1-0.749-0.85927.761-9.302-9.3020.0000.0000.0000.000
16B59SER0-0.019-0.01430.5230.1260.1260.0000.0000.0000.000
17B60ASN0-0.066-0.04333.3890.3460.3460.0000.0000.0000.000
18B61LYS10.8920.93930.2729.0149.0140.0000.0000.0000.000
19B62LYS10.9861.00128.1729.8819.8810.0000.0000.0000.000
20B63ARG10.8630.92522.13012.75512.7550.0000.0000.0000.000
21B64ILE00.0110.01424.778-0.050-0.0500.0000.0000.0000.000
22B65PRO00.0010.00721.394-0.150-0.1500.0000.0000.0000.000
23B66TYR00.0260.00322.850-0.405-0.4050.0000.0000.0000.000
24B67PHE0-0.0010.00725.9010.0770.0770.0000.0000.0000.000
25B68SER00.013-0.01628.749-0.041-0.0410.0000.0000.0000.000
26B69ALA0-0.0010.00432.4150.0100.0100.0000.0000.0000.000
27B70THR00.0590.00234.5710.1410.1410.0000.0000.0000.000
28B71ASN00.0040.01438.334-0.119-0.1190.0000.0000.0000.000
29B72SER0-0.050-0.03040.2830.1940.1940.0000.0000.0000.000
30B73THR00.032-0.00439.031-0.153-0.1530.0000.0000.0000.000
31B74PRO0-0.0190.00136.9540.1610.1610.0000.0000.0000.000
32B75ALA00.0120.00837.956-0.137-0.1370.0000.0000.0000.000
33B76THR0-0.030-0.02335.201-0.010-0.0100.0000.0000.0000.000
34B77PRO0-0.0160.00630.2740.0360.0360.0000.0000.0000.000
35B78LEU0-0.017-0.01330.5990.0600.0600.0000.0000.0000.000
36B79VAL0-0.030-0.01425.785-0.117-0.1170.0000.0000.0000.000
37B80THR00.0050.00026.0560.0070.0070.0000.0000.0000.000
38B81TYR0-0.042-0.06220.942-0.351-0.3510.0000.0000.0000.000
39B82GLN00.0200.00921.9880.3820.3820.0000.0000.0000.000
40B83VAL0-0.0230.00218.971-0.702-0.7020.0000.0000.0000.000
41B84THR0-0.011-0.02317.1510.3850.3850.0000.0000.0000.000
42B85LEU00.0120.00010.265-0.058-0.0580.0000.0000.0000.000
43B86SER00.009-0.00113.915-0.473-0.4730.0000.0000.0000.000
44B87CYS0-0.0580.01616.2910.9270.9270.0000.0000.0000.000
45B88SER00.025-0.00617.783-0.534-0.5340.0000.0000.0000.000
46B90MET00.0760.04514.514-0.543-0.5430.0000.0000.0000.000
47B91ALA00.0060.03614.475-1.438-1.4380.0000.0000.0000.000
48B92ASN00.0200.00013.546-1.625-1.6250.0000.0000.0000.000
49B93SER00.0530.01712.653-0.825-0.8250.0000.0000.0000.000
50B94MET00.0440.0146.936-2.101-2.1010.0000.0000.0000.000
51B95LEU0-0.0050.0027.584-3.636-3.6360.0000.0000.0000.000
52B96ALA00.0330.0098.057-1.876-1.8760.0000.0000.0000.000
53B97ALA0-0.035-0.0088.2320.0820.0820.0000.0000.0000.000
55B99ALA00.0330.0085.4550.1260.1260.0000.0000.0000.000
56B100ARG10.8920.9447.59322.93922.9390.0000.0000.0000.000
57B101ASN0-0.073-0.0254.9583.8693.8690.0000.0000.0000.000
59B103ASN00.0230.0257.7242.0192.0190.0000.0000.0000.000
60B104GLN00.0180.00610.6160.9760.9760.0000.0000.0000.000
61B105TYR00.0510.01910.255-2.668-2.6680.0000.0000.0000.000
62B106ARG10.8660.91611.50919.73819.7380.0000.0000.0000.000
63B107GLY00.0180.02912.240-1.958-1.9580.0000.0000.0000.000
64B108SER0-0.029-0.03514.7010.7190.7190.0000.0000.0000.000
65B109LEU0-0.042-0.02212.806-1.991-1.9910.0000.0000.0000.000
66B110ASN00.0230.02814.7382.1662.1660.0000.0000.0000.000
67B111TYR00.022-0.00316.140-1.040-1.0400.0000.0000.0000.000
68B112LEU0-0.0150.00418.0950.6110.6110.0000.0000.0000.000
69B113PHE0-0.001-0.00119.9800.0030.0030.0000.0000.0000.000
70B114VAL00.0240.00022.0720.0380.0380.0000.0000.0000.000
71B115PHE00.0110.00724.9270.1510.1510.0000.0000.0000.000
72B116THR0-0.042-0.02427.661-0.198-0.1980.0000.0000.0000.000
73B117GLY00.0360.01929.9070.2400.2400.0000.0000.0000.000
74B118SER0-0.0010.00233.622-0.041-0.0410.0000.0000.0000.000
75B119ALA00.0550.01535.781-0.024-0.0240.0000.0000.0000.000
76B120MET0-0.044-0.01836.7260.1780.1780.0000.0000.0000.000
77B121THR0-0.049-0.02436.4450.2500.2500.0000.0000.0000.000
78B122LYS10.9340.97137.1167.6357.6350.0000.0000.0000.000
79B123GLY00.0850.03737.2390.1240.1240.0000.0000.0000.000
80B124LYS10.7970.89934.6898.3518.3510.0000.0000.0000.000
81B125PHE00.0090.00030.9090.1470.1470.0000.0000.0000.000
82B126LEU00.0040.00931.330-0.039-0.0390.0000.0000.0000.000
83B127ILE0-0.010-0.00125.012-0.035-0.0350.0000.0000.0000.000
84B128SER0-0.007-0.03727.951-0.079-0.0790.0000.0000.0000.000
85B129TYR0-0.021-0.02722.949-0.222-0.2220.0000.0000.0000.000
86B130THR00.0460.01025.6700.4140.4140.0000.0000.0000.000
87B131PRO00.0310.01825.500-0.240-0.2400.0000.0000.0000.000
88B132PRO0-0.006-0.00824.9410.4070.4070.0000.0000.0000.000
89B133GLY0-0.033-0.01527.6990.1200.1200.0000.0000.0000.000
90B134ALA00.0250.00931.0640.2800.2800.0000.0000.0000.000
91B135GLY0-0.031-0.00831.2340.2260.2260.0000.0000.0000.000
92B136GLU-1-0.854-0.92929.377-10.156-10.1560.0000.0000.0000.000
93B137PRO0-0.022-0.00330.0720.3120.3120.0000.0000.0000.000
94B138LYS10.8780.91732.9929.1359.1350.0000.0000.0000.000
95B139THR00.0340.01536.1990.1100.1100.0000.0000.0000.000
96B140LEU00.0630.02635.039-0.218-0.2180.0000.0000.0000.000
97B141ASP-1-0.870-0.94136.235-7.897-7.8970.0000.0000.0000.000
98B142GLN0-0.0030.01035.113-0.204-0.2040.0000.0000.0000.000
99B143ALA00.0130.01431.947-0.211-0.2110.0000.0000.0000.000
100B144MET0-0.050-0.00432.069-0.353-0.3530.0000.0000.0000.000
101B145GLN0-0.031-0.02734.5410.1240.1240.0000.0000.0000.000
102B146ALA0-0.0360.00829.549-0.092-0.0920.0000.0000.0000.000
103B147THR0-0.020-0.01225.385-0.014-0.0140.0000.0000.0000.000
104B148TYR0-0.017-0.01027.519-0.353-0.3530.0000.0000.0000.000
105B149ALA00.0040.00827.700-0.011-0.0110.0000.0000.0000.000
106B150ILE0-0.005-0.00329.6160.0450.0450.0000.0000.0000.000
107B151TRP0-0.026-0.00227.693-0.274-0.2740.0000.0000.0000.000
108B152ASP-1-0.807-0.91230.828-8.588-8.5880.0000.0000.0000.000
109B153LEU0-0.0200.00931.296-0.316-0.3160.0000.0000.0000.000
110B154GLY00.027-0.00632.9960.3310.3310.0000.0000.0000.000
111B155LEU0-0.041-0.00331.293-0.152-0.1520.0000.0000.0000.000
112B156ASN0-0.008-0.01028.0010.0300.0300.0000.0000.0000.000
113B157SER00.0630.03626.626-0.074-0.0740.0000.0000.0000.000
114B158SER0-0.012-0.01423.393-0.232-0.2320.0000.0000.0000.000
115B159TYR00.0280.01424.6080.3120.3120.0000.0000.0000.000
116B160ASN0-0.010-0.00917.998-0.629-0.6290.0000.0000.0000.000
117B161PHE00.006-0.00121.5380.2450.2450.0000.0000.0000.000
118B162THR0-0.003-0.00618.261-0.549-0.5490.0000.0000.0000.000
119B163VAL00.0000.00418.6010.7980.7980.0000.0000.0000.000
120B164PRO00.0260.00418.660-1.010-1.0100.0000.0000.0000.000
121B165PHE0-0.003-0.00616.069-0.091-0.0910.0000.0000.0000.000
122B166ILE0-0.0190.00019.3180.3480.3480.0000.0000.0000.000
123B167SER00.0380.02019.9530.3480.3480.0000.0000.0000.000
124B168PRO0-0.020-0.00522.0730.1220.1220.0000.0000.0000.000
125B169THR0-0.015-0.01819.9310.3780.3780.0000.0000.0000.000
126B170HIS00.0550.03618.380-1.090-1.0900.0000.0000.0000.000
127B171TYR00.0130.00512.691-0.609-0.6090.0000.0000.0000.000
128B172ARG10.8530.93115.29015.61115.6110.0000.0000.0000.000
129B173GLN0-0.015-0.01714.542-1.371-1.3710.0000.0000.0000.000
130B174THR0-0.033-0.02310.3820.3410.3410.0000.0000.0000.000
131B175SER0-0.020-0.02613.3580.6040.6040.0000.0000.0000.000
132B176TYR00.004-0.00316.0450.1590.1590.0000.0000.0000.000
133B177ASN00.0110.01519.483-0.274-0.2740.0000.0000.0000.000
134B178THR00.017-0.00222.4940.2000.2000.0000.0000.0000.000
135B179PRO00.0170.02223.231-0.335-0.3350.0000.0000.0000.000
136B180THR00.0420.03322.3310.3090.3090.0000.0000.0000.000
137B181ILE00.0740.03523.331-0.457-0.4570.0000.0000.0000.000
138B182THR0-0.0010.00420.536-0.083-0.0830.0000.0000.0000.000
139B183SER0-0.012-0.02818.633-0.833-0.8330.0000.0000.0000.000
140B184VAL00.0050.01719.044-0.559-0.5590.0000.0000.0000.000
141B185ASP-1-0.876-0.94419.888-13.916-13.9160.0000.0000.0000.000
142B186GLY00.0340.04121.9250.1670.1670.0000.0000.0000.000
143B187TRP0-0.007-0.02423.408-0.396-0.3960.0000.0000.0000.000
144B188LEU0-0.0100.01721.4320.1510.1510.0000.0000.0000.000
145B189THR0-0.033-0.00724.2930.1820.1820.0000.0000.0000.000
146B190VAL00.0100.00826.409-0.100-0.1000.0000.0000.0000.000
147B191TRP00.0320.01129.0480.3650.3650.0000.0000.0000.000
148B192GLN00.007-0.00232.855-0.255-0.2550.0000.0000.0000.000
149B193LEU0-0.0070.00435.3140.2230.2230.0000.0000.0000.000
150B194THR0-0.010-0.01637.0540.2750.2750.0000.0000.0000.000
151B195PRO00.0130.02438.045-0.237-0.2370.0000.0000.0000.000
152B196LEU0-0.055-0.02034.366-0.043-0.0430.0000.0000.0000.000
153B197THR0-0.003-0.01138.7600.2270.2270.0000.0000.0000.000
154B198TYR00.001-0.02040.433-0.233-0.2330.0000.0000.0000.000
155B199PRO0-0.0090.01442.7420.1710.1710.0000.0000.0000.000
156B200LEU00.0400.00444.960-0.093-0.0930.0000.0000.0000.000
157B201GLY0-0.001-0.01045.692-0.041-0.0410.0000.0000.0000.000
158B202VAL0-0.041-0.00439.687-0.153-0.1530.0000.0000.0000.000
159B203PRO0-0.011-0.01238.6110.1210.1210.0000.0000.0000.000
160B204ASN00.0540.03139.765-0.057-0.0570.0000.0000.0000.000
161B205ASP-1-0.923-0.92435.955-8.462-8.4620.0000.0000.0000.000
162B206SER0-0.013-0.01433.604-0.046-0.0460.0000.0000.0000.000
163B207HIS00.0330.02629.442-0.206-0.2060.0000.0000.0000.000
164B208ILE0-0.016-0.00526.071-0.087-0.0870.0000.0000.0000.000
165B209LEU00.0100.00822.765-0.229-0.2290.0000.0000.0000.000
166B210THR00.0060.01021.8910.1470.1470.0000.0000.0000.000
167B211LEU0-0.025-0.01116.607-0.337-0.3370.0000.0000.0000.000
168B212VAL00.0020.00013.8160.4250.4250.0000.0000.0000.000
169B213SER0-0.0190.00111.586-1.073-1.0730.0000.0000.0000.000
170B214GLY00.015-0.00510.2801.4331.4330.0000.0000.0000.000
171B215GLY00.019-0.00411.2320.3210.3210.0000.0000.0000.000
172B216ASP-1-0.928-0.96911.947-24.005-24.0050.0000.0000.0000.000
173B217ASP-1-0.789-0.88511.870-21.955-21.9550.0000.0000.0000.000
174B218PHE0-0.071-0.0137.123-0.790-0.7900.0000.0000.0000.000
175B219THR0-0.044-0.0407.939-3.206-3.2060.0000.0000.0000.000
177B221ARG10.8610.9257.08018.43818.4380.0000.0000.0000.000
178B222MET00.001-0.0018.5651.4971.4970.0000.0000.0000.000
179B223PRO00.0330.0225.2900.2090.2090.0000.0000.0000.000
180B224VAL0-0.0110.0027.4112.4042.4040.0000.0000.0000.000
181B225THR0-0.031-0.0188.731-1.217-1.2170.0000.0000.0000.000
182B226PHE00.0190.00910.9161.0461.0460.0000.0000.0000.000
183B227THR00.011-0.00212.5590.4290.4290.0000.0000.0000.000
184B228LYS10.9470.97415.59815.61115.6110.0000.0000.0000.000
185B229TYR00.0010.00514.5270.1930.1930.0000.0000.0000.000
186B230VAL00.0280.01419.036-0.375-0.3750.0000.0000.0000.000
187B231PRO0-0.049-0.03117.5230.0910.0910.0000.0000.0000.000
188B232GLN-1-0.940-0.95219.933-12.014-12.0140.0000.0000.0000.000