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

tag_button

FMODB ID: 8QL1Y

Calculation Name: 5HGW-A-Xray547

Preferred Name:

Target Type:

Ligand Name: fe (iii) ion

Ligand 3-letter code: FE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5HGW

Chain ID: A

ChEMBL ID:

UniProt ID: B1YSH1

Base Structure: X-ray

Registration Date: 2025-10-05

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 174
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1847403.64996
FMO2-HF: Nuclear repulsion 1778029.496637
FMO2-HF: Total energy -69374.153323
FMO2-MP2: Total energy -69574.082796


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:HIS)


Summations of interaction energy for fragment #1(A:-2:HIS)
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.
-46.732-44.3940.066-0.958-1.446-0.002
Interaction energy analysis for fragmet #1(A:-2:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.856 / q_NPA : 0.913
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].
3A0HIS10.8320.9063.75031.08933.4270.066-0.958-1.446-0.002
4A1MET0-0.0070.0034.9711.8291.8290.0000.0000.0000.000
5A2ILE00.0510.0367.032-0.531-0.5310.0000.0000.0000.000
6A3ARG10.7570.8745.19728.89228.8920.0000.0000.0000.000
7A4GLU-1-0.896-0.94411.172-16.224-16.2240.0000.0000.0000.000
8A5ILE0-0.0060.00213.9510.2040.2040.0000.0000.0000.000
9A6LEU0-0.060-0.01716.1940.3340.3340.0000.0000.0000.000
10A7LYS10.9750.98719.12513.98013.9800.0000.0000.0000.000
11A8MET00.007-0.01022.6780.0500.0500.0000.0000.0000.000
12A9GLY00.0110.01026.0320.1600.1600.0000.0000.0000.000
13A10ASP-1-0.793-0.86619.764-13.320-13.3200.0000.0000.0000.000
14A11PRO00.0190.00222.5850.2010.2010.0000.0000.0000.000
15A12ARG10.8750.90415.42014.87814.8780.0000.0000.0000.000
16A13LEU0-0.065-0.02621.5810.0550.0550.0000.0000.0000.000
17A14LEU0-0.057-0.02524.0480.3770.3770.0000.0000.0000.000
18A15GLU-1-0.943-0.96622.596-11.735-11.7350.0000.0000.0000.000
19A16VAL0-0.040-0.01625.8920.0160.0160.0000.0000.0000.000
20A17ALA0-0.0100.00022.979-0.145-0.1450.0000.0000.0000.000
21A18LYS10.9350.96122.16111.30611.3060.0000.0000.0000.000
22A19PRO0-0.0040.00222.930-0.321-0.3210.0000.0000.0000.000
23A20VAL00.0200.00619.880-0.286-0.2860.0000.0000.0000.000
24A21ALA00.0080.00821.8800.4210.4210.0000.0000.0000.000
25A22GLN0-0.057-0.03620.4140.3360.3360.0000.0000.0000.000
26A23PHE00.021-0.00120.348-0.374-0.3740.0000.0000.0000.000
27A24ASP-1-0.831-0.90319.441-13.516-13.5160.0000.0000.0000.000
28A25THR0-0.037-0.00514.859-0.193-0.1930.0000.0000.0000.000
29A26PRO00.001-0.01411.828-0.116-0.1160.0000.0000.0000.000
30A27GLU-1-0.813-0.90010.696-19.693-19.6930.0000.0000.0000.000
31A28LEU0-0.040-0.00811.892-0.243-0.2430.0000.0000.0000.000
32A29HIS10.8080.88213.80815.76915.7690.0000.0000.0000.000
33A30GLU-1-0.894-0.9316.229-32.187-32.1870.0000.0000.0000.000
34A31ILE0-0.003-0.00510.8460.3010.3010.0000.0000.0000.000
35A32VAL00.004-0.00612.8870.5060.5060.0000.0000.0000.000
36A33ALA0-0.0030.01012.0460.5680.5680.0000.0000.0000.000
37A34ASP-1-0.795-0.8999.469-25.206-25.2060.0000.0000.0000.000
38A35MET0-0.072-0.02612.2760.5970.5970.0000.0000.0000.000
39A36PHE00.0560.00715.8220.6320.6320.0000.0000.0000.000
40A37GLU-1-0.837-0.88411.035-23.263-23.2630.0000.0000.0000.000
41A38THR0-0.015-0.03413.8400.2520.2520.0000.0000.0000.000
42A39MET0-0.0370.00615.8230.7670.7670.0000.0000.0000.000
43A40HIS00.0010.00218.9580.6930.6930.0000.0000.0000.000
44A41HIS0-0.0050.00817.0940.4640.4640.0000.0000.0000.000
45A42ALA0-0.018-0.00619.0790.4350.4350.0000.0000.0000.000
46A43ASN00.0050.01320.9350.8670.8670.0000.0000.0000.000
47A44GLY00.0000.00122.6590.5890.5890.0000.0000.0000.000
48A45ALA0-0.027-0.00924.0060.1120.1120.0000.0000.0000.000
49A46GLY00.042-0.02224.3640.1840.1840.0000.0000.0000.000
50A47LEU0-0.0300.00317.221-0.184-0.1840.0000.0000.0000.000
51A48ALA00.0240.01221.501-0.021-0.0210.0000.0000.0000.000
52A49ALA00.0390.01717.487-0.334-0.3340.0000.0000.0000.000
53A50PRO00.003-0.00217.308-0.613-0.6130.0000.0000.0000.000
54A51GLN00.032-0.00218.960-0.084-0.0840.0000.0000.0000.000
55A52ILE00.0060.01412.854-0.164-0.1640.0000.0000.0000.000
56A53GLY0-0.027-0.01413.759-0.958-0.9580.0000.0000.0000.000
57A54ILE0-0.0050.00511.959-0.091-0.0910.0000.0000.0000.000
58A55GLY00.0550.03416.0940.5640.5640.0000.0000.0000.000
59A56LEU0-0.029-0.02316.6970.4990.4990.0000.0000.0000.000
60A57GLN0-0.057-0.04120.4020.1650.1650.0000.0000.0000.000
61A58ILE00.0330.00617.8420.2350.2350.0000.0000.0000.000
62A59ILE0-0.030-0.01421.526-0.144-0.1440.0000.0000.0000.000
63A60ILE00.0020.01319.1210.0860.0860.0000.0000.0000.000
64A61PHE00.020-0.01722.8390.1910.1910.0000.0000.0000.000
65A62GLY00.0050.01325.6500.0160.0160.0000.0000.0000.000
66A63PHE0-0.019-0.00726.180-0.442-0.4420.0000.0000.0000.000
67A64GLY00.0130.01028.4030.3260.3260.0000.0000.0000.000
68A65SER0-0.009-0.01630.2910.3110.3110.0000.0000.0000.000
69A66ASN00.019-0.01226.777-0.171-0.1710.0000.0000.0000.000
70A67ASN00.019-0.00427.0570.2350.2350.0000.0000.0000.000
71A68ARG10.9410.98225.96211.14111.1410.0000.0000.0000.000
72A69TYR0-0.042-0.02328.8000.2470.2470.0000.0000.0000.000
73A70PRO00.0410.03232.8670.0030.0030.0000.0000.0000.000
74A71ASP-1-0.903-0.94735.004-7.665-7.6650.0000.0000.0000.000
75A72ALA0-0.087-0.02933.6010.1560.1560.0000.0000.0000.000
76A73PRO0-0.006-0.00435.394-0.075-0.0750.0000.0000.0000.000
77A74PRO0-0.005-0.01333.325-0.191-0.1910.0000.0000.0000.000
78A75VAL0-0.0200.00430.3630.2100.2100.0000.0000.0000.000
79A76PRO0-0.010-0.00230.340-0.268-0.2680.0000.0000.0000.000
80A77GLU-1-0.910-0.94323.540-12.462-12.4620.0000.0000.0000.000
81A78THR0-0.045-0.02625.7600.2860.2860.0000.0000.0000.000
82A79VAL00.0160.02020.657-0.297-0.2970.0000.0000.0000.000
83A80LEU0-0.058-0.02623.4690.4240.4240.0000.0000.0000.000
84A81ILE0-0.013-0.00220.641-0.265-0.2650.0000.0000.0000.000
85A82ASN0-0.030-0.01624.4930.1760.1760.0000.0000.0000.000
86A83PRO0-0.013-0.00126.2760.3600.3600.0000.0000.0000.000
87A84LYS10.9180.95829.2268.9338.9330.0000.0000.0000.000
88A85LEU00.0240.00831.530-0.053-0.0530.0000.0000.0000.000
89A86GLU-1-0.914-0.95435.136-7.726-7.7260.0000.0000.0000.000
90A87TYR00.000-0.01235.1520.0070.0070.0000.0000.0000.000
91A88MET0-0.047-0.01840.4330.1220.1220.0000.0000.0000.000
92A89PRO00.0170.03243.6680.0210.0210.0000.0000.0000.000
93A90PRO0-0.030-0.02446.2090.0440.0440.0000.0000.0000.000
94A91ASP-1-0.868-0.93446.188-6.242-6.2420.0000.0000.0000.000
95A92MET0-0.063-0.02041.508-0.195-0.1950.0000.0000.0000.000
96A93GLU-1-0.862-0.94341.548-7.027-7.0270.0000.0000.0000.000
97A94GLU-1-0.845-0.89841.213-6.897-6.8970.0000.0000.0000.000
98A95GLY00.005-0.01138.9230.0210.0210.0000.0000.0000.000
99A96TRP00.0150.01536.728-0.102-0.1020.0000.0000.0000.000
100A97GLU-1-0.721-0.81532.420-8.842-8.8420.0000.0000.0000.000
101A98GLY00.0750.02630.4740.1500.1500.0000.0000.0000.000
102A99CYS-1-0.947-0.88425.901-10.996-10.9960.0000.0000.0000.000
103A100LEU00.006-0.00920.9650.0430.0430.0000.0000.0000.000
104A101SER00.035-0.00921.817-0.285-0.2850.0000.0000.0000.000
105A102VAL0-0.061-0.03723.6970.1690.1690.0000.0000.0000.000
106A103PRO00.0370.02624.0440.2370.2370.0000.0000.0000.000
107A104GLY00.0600.02826.4970.2130.2130.0000.0000.0000.000
108A105MET0-0.0690.00329.5870.2650.2650.0000.0000.0000.000
109A106ARG10.8520.92030.7439.0569.0560.0000.0000.0000.000
110A107GLY00.0290.00934.2990.1560.1560.0000.0000.0000.000
111A108VAL0-0.0450.00036.621-0.144-0.1440.0000.0000.0000.000
112A109VAL0-0.003-0.00535.1070.0400.0400.0000.0000.0000.000
113A110SER00.0120.01638.3810.0100.0100.0000.0000.0000.000
114A111ARG10.7400.82632.5968.3248.3240.0000.0000.0000.000
115A112TYR00.0300.00639.0980.2220.2220.0000.0000.0000.000
116A113ALA00.0370.02839.710-0.190-0.1900.0000.0000.0000.000
117A114LYS10.8710.92840.5896.8596.8590.0000.0000.0000.000
118A115VAL0-0.013-0.01135.6200.0120.0120.0000.0000.0000.000
119A116ARG10.9190.97537.4087.3027.3020.0000.0000.0000.000
120A117TYR00.016-0.01731.000-0.170-0.1700.0000.0000.0000.000
121A118SER0-0.016-0.00432.9180.0230.0230.0000.0000.0000.000
122A119GLY00.0210.00129.084-0.100-0.1000.0000.0000.0000.000
123A120TYR0-0.042-0.00826.0160.3600.3600.0000.0000.0000.000
124A121ASP-1-0.706-0.85424.373-11.441-11.4410.0000.0000.0000.000
125A122GLN00.045-0.00518.9030.3270.3270.0000.0000.0000.000
126A123PHE0-0.035-0.03120.276-0.643-0.6430.0000.0000.0000.000
127A124GLY00.0140.01622.7640.1420.1420.0000.0000.0000.000
128A125ALA0-0.032-0.00525.4260.4690.4690.0000.0000.0000.000
129A126LYS10.8240.90428.1718.2728.2720.0000.0000.0000.000
130A127ILE00.0050.00227.1460.1500.1500.0000.0000.0000.000
131A128ASP-1-0.883-0.96331.305-7.881-7.8810.0000.0000.0000.000
132A129ARG10.8610.92229.7069.4719.4710.0000.0000.0000.000
133A130VAL00.000-0.00336.1340.0670.0670.0000.0000.0000.000
134A131ALA0-0.036-0.00435.606-0.101-0.1010.0000.0000.0000.000
135A132GLU-1-0.827-0.93137.707-6.829-6.8290.0000.0000.0000.000
136A133GLY00.1000.06238.152-0.196-0.1960.0000.0000.0000.000
137A134PHE00.009-0.00731.423-0.134-0.1340.0000.0000.0000.000
138A135HIS00.0540.04832.575-0.462-0.4620.0000.0000.0000.000
139A136ALA00.0250.00833.629-0.216-0.2160.0000.0000.0000.000
140A137ARG10.8120.90133.7757.7657.7650.0000.0000.0000.000
141A138VAL0-0.0040.00128.395-0.138-0.1380.0000.0000.0000.000
142A139VAL00.0090.00629.602-0.243-0.2430.0000.0000.0000.000
143A140GLN0-0.011-0.02730.5220.0110.0110.0000.0000.0000.000
144A141HIS10.7630.83327.2849.8369.8360.0000.0000.0000.000
145A142GLU-1-0.853-0.94524.565-11.304-11.3040.0000.0000.0000.000
146A143TYR00.0090.00226.387-0.161-0.1610.0000.0000.0000.000
147A144ASP-1-0.726-0.83028.770-8.739-8.7390.0000.0000.0000.000
148A145HIS10.8450.91624.06710.93310.9330.0000.0000.0000.000
149A146LEU0-0.0120.01023.454-0.337-0.3370.0000.0000.0000.000
150A147ILE0-0.063-0.02726.1660.0620.0620.0000.0000.0000.000
151A148GLY00.0250.03627.2270.3090.3090.0000.0000.0000.000
152A149LYS10.9130.94628.2558.7228.7220.0000.0000.0000.000
153A150LEU00.038-0.00425.803-0.331-0.3310.0000.0000.0000.000
154A151TYR00.0650.02929.6600.2820.2820.0000.0000.0000.000
155A152PRO00.0460.00731.3270.2370.2370.0000.0000.0000.000
156A153MET0-0.064-0.00730.3850.2320.2320.0000.0000.0000.000
157A154ARG10.7800.86134.2778.3548.3540.0000.0000.0000.000
158A155ILE0-0.0320.01735.7260.1260.1260.0000.0000.0000.000
159A156THR0-0.010-0.00838.9050.0120.0120.0000.0000.0000.000
160A157ASP-1-0.771-0.84842.224-6.525-6.5250.0000.0000.0000.000
161A158PHE0-0.012-0.02337.383-0.119-0.1190.0000.0000.0000.000
162A159THR0-0.071-0.04642.008-0.017-0.0170.0000.0000.0000.000
163A160ARG10.7750.86841.9396.7076.7070.0000.0000.0000.000
164A161PHE00.017-0.02033.826-0.196-0.1960.0000.0000.0000.000
165A162GLY00.0310.02136.8030.1590.1590.0000.0000.0000.000
166A163PHE00.0350.00532.268-0.205-0.2050.0000.0000.0000.000
167A164THR00.002-0.03332.2220.1520.1520.0000.0000.0000.000
168A165GLU-1-0.918-0.95434.388-8.604-8.6040.0000.0000.0000.000
169A166VAL0-0.035-0.01436.0920.1960.1960.0000.0000.0000.000
170A167LEU0-0.051-0.02336.9810.1950.1950.0000.0000.0000.000
171A168PHE0-0.040-0.02736.3820.1300.1300.0000.0000.0000.000
172A169PRO0-0.010-0.01237.031-0.180-0.1800.0000.0000.0000.000
173A170GLY0-0.064-0.02537.799-0.060-0.0600.0000.0000.0000.000
174A171LEU-1-0.971-0.95932.605-9.321-9.3210.0000.0000.0000.000