FMODB

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

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: 1YQLZ

Calculation Name: 1DYT-A-Xray547

Preferred Name:

Target Type:

Ligand Name: citric acid | fe (iii) ion

Ligand 3-letter code: CIT | FE

Ligand of Interest (LOI):

PDB ID: 1DYT

Chain ID: A

ChEMBL ID:

UniProt ID: P12724

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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 129
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1248859.149014
FMO2-HF: Nuclear repulsion 1193051.585889
FMO2-HF: Total energy -55807.563125
FMO2-MP2: Total energy -55966.234428


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(A:1:ARG)


Summations of interaction energy for fragment #1(A:1:ARG)
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.
270.527284.32317.199-12.042-18.951-0.132
Interaction energy analysis for fragmet #1(A:1:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.717 / q_NPA : 1.850
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].
3A3PRO00.0580.0342.573-13.057-10.3341.216-1.513-2.425-0.015
4A4GLN00.0230.0194.228-0.300-0.045-0.001-0.016-0.2380.000
5A5PHE00.0060.0142.9534.6936.0650.092-0.556-0.907-0.002
6A6THR0-0.020-0.0261.818-48.337-47.93710.879-6.061-5.218-0.075
7A7ARG10.8280.8802.55454.91458.2042.328-1.545-4.073-0.015
8A8ALA00.0600.0463.6183.4753.5720.0060.135-0.2380.000
10A10TRP00.0240.0002.516-9.647-5.4032.535-1.886-4.893-0.022
11A11PHE00.0000.0114.5305.3185.413-0.001-0.027-0.0670.000
111A115ASP-1-0.790-0.8843.431-89.753-89.1090.007-0.321-0.330-0.002
113A117ARG10.8070.8712.73392.75093.4260.138-0.252-0.562-0.001
9A9GLN00.0530.0225.181-1.875-1.8750.0000.0000.0000.000
12A12ALA00.011-0.0066.6814.6164.6160.0000.0000.0000.000
13A13ILE0-0.005-0.0016.2883.2713.2710.0000.0000.0000.000
14A14GLN0-0.008-0.0065.5933.1223.1220.0000.0000.0000.000
15A15HIS0-0.041-0.0238.8850.1630.1630.0000.0000.0000.000
16A16ILE0-0.0370.00212.0032.9612.9610.0000.0000.0000.000
17A17SER00.0220.00514.117-0.027-0.0270.0000.0000.0000.000
18A18LEU00.0390.03616.9720.6860.6860.0000.0000.0000.000
19A19ASN0-0.004-0.00920.5231.0531.0530.0000.0000.0000.000
20A20PRO0-0.0010.02718.194-0.065-0.0650.0000.0000.0000.000
21A21PRO00.0250.01519.0921.1511.1510.0000.0000.0000.000
22A22ARG11.0301.00620.43722.54422.5440.0000.0000.0000.000
23A23CYS00.0120.01315.8050.5440.5440.0000.0000.0000.000
24A24THR0-0.030-0.00717.409-1.615-1.6150.0000.0000.0000.000
25A25ILE0-0.050-0.02318.874-0.124-0.1240.0000.0000.0000.000
26A26ALA00.0420.02116.437-1.355-1.3550.0000.0000.0000.000
27A27MET00.0000.00811.291-2.425-2.4250.0000.0000.0000.000
28A28ARG10.9040.95612.23026.24426.2440.0000.0000.0000.000
29A29ALA00.0080.01512.379-1.704-1.7040.0000.0000.0000.000
30A30ILE0-0.0180.0006.998-4.049-4.0490.0000.0000.0000.000
31A31ASN0-0.008-0.0497.931-7.997-7.9970.0000.0000.0000.000
32A32ASN00.0380.01710.1550.0080.0080.0000.0000.0000.000
33A33TYR0-0.0060.0126.511-0.438-0.4380.0000.0000.0000.000
34A34ARG10.8020.8885.47854.13054.1300.0000.0000.0000.000
35A35TRP00.1010.0567.7065.1925.1920.0000.0000.0000.000
36A36ARG10.9310.9699.17241.83741.8370.0000.0000.0000.000
37A37CYS00.0150.0559.515-3.869-3.8690.0000.0000.0000.000
38A38LYS10.8000.9087.50154.68554.6850.0000.0000.0000.000
39A39ASN00.0830.03510.7002.6832.6830.0000.0000.0000.000
40A40GLN00.0300.02012.0493.0093.0090.0000.0000.0000.000
41A41ASN00.006-0.01510.867-7.661-7.6610.0000.0000.0000.000
42A42THR00.0190.00513.3862.1612.1610.0000.0000.0000.000
43A43PHE00.0060.01112.767-2.388-2.3880.0000.0000.0000.000
44A44LEU00.014-0.00714.7812.5842.5840.0000.0000.0000.000
45A45ARG10.8550.91617.29424.37624.3760.0000.0000.0000.000
46A46THR0-0.002-0.00116.7391.9001.9000.0000.0000.0000.000
47A47THR00.0430.02017.561-0.993-0.9930.0000.0000.0000.000
48A48PHE00.0430.00110.053-0.038-0.0380.0000.0000.0000.000
49A49ALA00.0600.03614.949-0.444-0.4440.0000.0000.0000.000
50A50ASN0-0.0050.00117.8860.8550.8550.0000.0000.0000.000
51A51VAL0-0.019-0.00513.1640.4780.4780.0000.0000.0000.000
52A52VAL00.0200.00013.875-0.319-0.3190.0000.0000.0000.000
53A53ASN0-0.032-0.02716.0251.2451.2450.0000.0000.0000.000
54A54VAL0-0.061-0.01417.5831.0841.0840.0000.0000.0000.000
55A55CYS0-0.102-0.04711.316-3.415-3.4150.0000.0000.0000.000
56A56GLY00.0350.03417.3150.2450.2450.0000.0000.0000.000
57A57ASN0-0.093-0.04720.7122.1652.1650.0000.0000.0000.000
58A58GLN00.0110.00421.631-0.809-0.8090.0000.0000.0000.000
59A59SER00.0070.00620.368-0.359-0.3590.0000.0000.0000.000
60A60ILE0-0.016-0.00920.2861.3181.3180.0000.0000.0000.000
61A61ARG10.9040.95219.89024.57724.5770.0000.0000.0000.000
62A62CYS0-0.062-0.00615.390-3.011-3.0110.0000.0000.0000.000
63A63PRO0-0.032-0.02718.3030.5080.5080.0000.0000.0000.000
64A64HIS0-0.009-0.01715.6762.7942.7940.0000.0000.0000.000
65A65ASN0-0.025-0.01312.935-1.445-1.4450.0000.0000.0000.000
66A66ARG10.9971.00416.61125.95425.9540.0000.0000.0000.000
67A67THR00.0490.02716.8091.2771.2770.0000.0000.0000.000
68A68LEU00.0050.01112.5100.5230.5230.0000.0000.0000.000
69A69ASN0-0.029-0.04216.8562.1242.1240.0000.0000.0000.000
70A70ASN00.0300.01812.5792.2992.2990.0000.0000.0000.000
71A72HIS00.0370.01915.9710.4620.4620.0000.0000.0000.000
72A73ARG10.9350.97817.93822.98422.9840.0000.0000.0000.000
73A74SER00.005-0.00120.2340.3390.3390.0000.0000.0000.000
74A75ARG10.9790.97821.55621.99121.9910.0000.0000.0000.000
75A76PHE00.0500.02824.5520.7810.7810.0000.0000.0000.000
76A77ARG10.9260.97724.05219.91419.9140.0000.0000.0000.000
77A78VAL00.0250.00920.0400.7440.7440.0000.0000.0000.000
78A79PRO00.013-0.01123.355-0.100-0.1000.0000.0000.0000.000
79A80LEU0-0.033-0.01519.575-1.190-1.1900.0000.0000.0000.000
80A81LEU00.002-0.00219.4671.4771.4770.0000.0000.0000.000
81A82HIS0-0.0090.01516.182-2.509-2.5090.0000.0000.0000.000
82A84ASP-1-0.762-0.88116.488-31.547-31.5470.0000.0000.0000.000
83A85LEU0-0.067-0.03314.5920.7960.7960.0000.0000.0000.000
84A86ILE00.0080.00017.9660.4910.4910.0000.0000.0000.000
85A87ASN0-0.008-0.02119.540-0.022-0.0220.0000.0000.0000.000
86A88PRO00.0280.00216.862-0.858-0.8580.0000.0000.0000.000
87A89GLY00.0160.02216.936-1.017-1.0170.0000.0000.0000.000
88A90ALA0-0.036-0.00917.0690.4320.4320.0000.0000.0000.000
89A91GLN00.0330.00715.988-2.424-2.4240.0000.0000.0000.000
90A92ASN0-0.008-0.01315.135-1.606-1.6060.0000.0000.0000.000
91A93ILE00.0380.00111.2251.0681.0680.0000.0000.0000.000
92A94SER0-0.006-0.00214.6210.3110.3110.0000.0000.0000.000
93A95ASN0-0.024-0.00717.7661.9301.9300.0000.0000.0000.000
94A97ARG10.9400.97317.61425.29125.2910.0000.0000.0000.000
95A98TYR00.007-0.02313.300-0.909-0.9090.0000.0000.0000.000
96A99ALA00.0300.01719.7411.1121.1120.0000.0000.0000.000
97A100ASP-1-0.803-0.91421.009-27.339-27.3390.0000.0000.0000.000
98A101ARG10.9190.95921.53326.19226.1920.0000.0000.0000.000
99A102PRO00.0260.01322.332-1.049-1.0490.0000.0000.0000.000
100A103GLY00.0350.01624.1230.6740.6740.0000.0000.0000.000
101A104ARG10.9260.96124.73220.56220.5620.0000.0000.0000.000
102A105ARG10.8500.92321.80726.43826.4380.0000.0000.0000.000
103A106PHE0-0.045-0.01922.677-0.114-0.1140.0000.0000.0000.000
104A107TYR00.0370.01216.662-0.746-0.7460.0000.0000.0000.000
105A108VAL0-0.006-0.00117.0601.1241.1240.0000.0000.0000.000
106A109VAL00.0160.00412.748-1.718-1.7180.0000.0000.0000.000
107A110ALA00.0720.03711.2022.4452.4450.0000.0000.0000.000
108A112ASP-1-0.752-0.8439.572-49.700-49.7000.0000.0000.0000.000
109A113ASN00.0180.00011.3821.7151.7150.0000.0000.0000.000
110A114ARG10.8350.9329.05636.52536.5250.0000.0000.0000.000
112A116PRO00.0400.0136.3864.7024.7020.0000.0000.0000.000
114A118ASP-1-0.799-0.8667.441-63.952-63.9520.0000.0000.0000.000
115A119SER00.015-0.0039.5703.4503.4500.0000.0000.0000.000
116A120PRO00.0360.00313.309-0.309-0.3090.0000.0000.0000.000
117A121ARG10.9360.97815.67429.14829.1480.0000.0000.0000.000
118A122TYR0-0.023-0.02114.0131.9681.9680.0000.0000.0000.000
119A123PRO00.0540.02513.504-2.855-2.8550.0000.0000.0000.000
120A124VAL00.0380.03213.388-1.896-1.8960.0000.0000.0000.000
121A125VAL0-0.026-0.0139.2120.8100.8100.0000.0000.0000.000
122A126PRO00.0430.01210.240-0.516-0.5160.0000.0000.0000.000
123A127VAL0-0.088-0.0506.768-5.196-5.1960.0000.0000.0000.000
124A128HIS0-0.068-0.0526.256-10.732-10.7320.0000.0000.0000.000
125A129LEU0-0.0020.0068.7554.4404.4400.0000.0000.0000.000
126A130ASP-1-0.770-0.86311.937-39.148-39.1480.0000.0000.0000.000
127A131THR00.001-0.00914.2000.8010.8010.0000.0000.0000.000
128A132THR00.017-0.00117.1720.2870.2870.0000.0000.0000.000
129A133ILE-1-0.833-0.88619.870-23.422-23.4220.0000.0000.0000.000