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: 7K2JK

Calculation Name: 1T5B-A-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin mononucleotide

Ligand 3-letter code: FMN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1T5B

Chain ID: A

ChEMBL ID:

UniProt ID: P63462

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 201
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2105675.834859
FMO2-HF: Nuclear repulsion 2030980.389739
FMO2-HF: Total energy -74695.44512
FMO2-MP2: Total energy -74917.257864


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:1:MET)


Summations of interaction energy for fragment #1(A:1: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.
-144.837-137.52414.483-7.845-13.954-0.082
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.748 / q_NPA : 0.886
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].
3A3LYS10.8720.9442.91234.57836.9332.540-0.869-4.027-0.012
4A4VAL00.0040.0024.6361.9582.0100.007-0.001-0.0590.000
35A35ALA0-0.042-0.0184.0262.1872.4800.001-0.082-0.2120.000
36A36ASP-1-0.791-0.8762.061-94.139-91.3519.271-6.015-6.044-0.055
37A37GLU-1-0.912-0.9512.415-35.263-33.5822.665-0.875-3.471-0.015
38A38ILE0-0.053-0.0325.0130.9971.0840.000-0.001-0.0870.000
88A88ASP-1-0.834-0.9095.762-37.480-37.423-0.001-0.002-0.0540.000
5A5LEU0-0.0060.0078.0370.7500.7500.0000.0000.0000.000
6A6VAL0-0.025-0.01811.1250.6040.6040.0000.0000.0000.000
7A7LEU00.0270.02114.2040.6610.6610.0000.0000.0000.000
8A8LYS10.8290.89517.58414.99914.9990.0000.0000.0000.000
9A9SER00.007-0.02220.4470.2970.2970.0000.0000.0000.000
10A10SER0-0.031-0.02223.8610.6020.6020.0000.0000.0000.000
11A11ILE00.0530.01026.658-0.126-0.1260.0000.0000.0000.000
12A12LEU0-0.025-0.00829.1390.2280.2280.0000.0000.0000.000
13A13ALA00.0410.01426.7210.0770.0770.0000.0000.0000.000
14A14GLY00.0350.02026.558-0.284-0.2840.0000.0000.0000.000
15A15TYR00.0100.00527.628-0.103-0.1030.0000.0000.0000.000
16A16SER0-0.043-0.00525.3220.2040.2040.0000.0000.0000.000
17A17GLN00.0810.04025.949-0.459-0.4590.0000.0000.0000.000
18A18SER00.0230.01423.551-0.303-0.3030.0000.0000.0000.000
19A19GLY00.0150.01722.034-0.611-0.6110.0000.0000.0000.000
20A20GLN00.0300.01821.092-0.608-0.6080.0000.0000.0000.000
21A21LEU0-0.0210.00021.311-0.331-0.3310.0000.0000.0000.000
22A22THR0-0.015-0.03517.586-0.681-0.6810.0000.0000.0000.000
23A23ASP-1-0.838-0.90816.505-15.656-15.6560.0000.0000.0000.000
24A24TYR0-0.032-0.04316.792-0.441-0.4410.0000.0000.0000.000
25A25PHE00.0610.01911.514-0.601-0.6010.0000.0000.0000.000
26A26ILE0-0.040-0.01812.147-1.677-1.6770.0000.0000.0000.000
27A27GLU-1-0.934-0.95712.144-17.189-17.1890.0000.0000.0000.000
28A28GLN00.0360.00113.303-1.898-1.8980.0000.0000.0000.000
29A29TRP0-0.031-0.0315.8631.0711.0710.0000.0000.0000.000
30A30ARG10.9330.9598.75221.27421.2740.0000.0000.0000.000
31A31GLU-1-0.849-0.9099.808-19.453-19.4530.0000.0000.0000.000
32A32LYS10.8020.89110.26619.69919.6990.0000.0000.0000.000
33A33HIS10.8130.9145.03135.77835.7780.0000.0000.0000.000
34A34VAL00.0310.0196.028-2.786-2.7860.0000.0000.0000.000
39A39THR0-0.001-0.0158.1331.3061.3060.0000.0000.0000.000
40A40VAL0-0.032-0.02610.2000.2070.2070.0000.0000.0000.000
41A41ARG10.7710.84814.01915.62315.6230.0000.0000.0000.000
42A42ASP-1-0.859-0.92816.686-12.482-12.4820.0000.0000.0000.000
43A43LEU00.007-0.00719.7190.3710.3710.0000.0000.0000.000
44A44ALA0-0.058-0.03722.5040.5450.5450.0000.0000.0000.000
45A45ALA0-0.040-0.02523.0420.3830.3830.0000.0000.0000.000
46A46ASN0-0.041-0.01519.4920.6020.6020.0000.0000.0000.000
47A47PRO0-0.037-0.00222.910-0.271-0.2710.0000.0000.0000.000
48A48VAL00.0510.02522.6830.0780.0780.0000.0000.0000.000
49A49PRO0-0.018-0.00125.4450.2940.2940.0000.0000.0000.000
50A50VAL0-0.006-0.01528.640-0.176-0.1760.0000.0000.0000.000
51A51LEU00.0100.01529.6900.1370.1370.0000.0000.0000.000
52A52ASP-1-0.793-0.89431.717-8.096-8.0960.0000.0000.0000.000
53A53GLY00.015-0.00735.076-0.092-0.0920.0000.0000.0000.000
54A54GLU-1-0.813-0.87134.956-7.917-7.9170.0000.0000.0000.000
55A55LEU0-0.011-0.01729.651-0.112-0.1120.0000.0000.0000.000
56A56VAL0-0.028-0.01431.380-0.249-0.2490.0000.0000.0000.000
57A57GLY00.0150.01033.314-0.024-0.0240.0000.0000.0000.000
58A58ALA00.0340.01429.6740.0060.0060.0000.0000.0000.000
59A59MET0-0.044-0.01329.606-0.233-0.2330.0000.0000.0000.000
60A60ARG10.8700.92129.6309.3379.3370.0000.0000.0000.000
61A61PRO00.0330.03831.2990.1420.1420.0000.0000.0000.000
62A62GLY0-0.028-0.03033.3920.1080.1080.0000.0000.0000.000
63A63ASP-1-0.967-0.96934.080-7.285-7.2850.0000.0000.0000.000
64A64ALA00.0050.00536.7590.1590.1590.0000.0000.0000.000
65A65PRO0-0.055-0.02436.023-0.215-0.2150.0000.0000.0000.000
66A66LEU00.0130.00730.7830.0780.0780.0000.0000.0000.000
67A67THR0-0.014-0.03535.0310.0090.0090.0000.0000.0000.000
68A68PRO00.025-0.00333.321-0.201-0.2010.0000.0000.0000.000
69A69ARG10.9130.96431.6898.1848.1840.0000.0000.0000.000
70A70GLN0-0.034-0.02631.016-0.203-0.2030.0000.0000.0000.000
71A71GLN0-0.051-0.02629.404-0.366-0.3660.0000.0000.0000.000
72A72ASP-1-0.887-0.94127.226-9.696-9.6960.0000.0000.0000.000
73A73ALA0-0.024-0.01725.917-0.417-0.4170.0000.0000.0000.000
74A74LEU0-0.024-0.00325.603-0.355-0.3550.0000.0000.0000.000
75A75ALA00.0300.01923.176-0.461-0.4610.0000.0000.0000.000
76A76LEU00.0290.01220.812-0.538-0.5380.0000.0000.0000.000
77A77SER0-0.032-0.02520.889-0.555-0.5550.0000.0000.0000.000
78A78ASP-1-0.820-0.89920.115-12.489-12.4890.0000.0000.0000.000
79A79GLU-1-0.861-0.90716.885-14.476-14.4760.0000.0000.0000.000
80A80LEU0-0.013-0.01316.010-0.963-0.9630.0000.0000.0000.000
81A81ILE0-0.023-0.00816.463-0.780-0.7800.0000.0000.0000.000
82A82ALA0-0.028-0.01214.235-0.861-0.8610.0000.0000.0000.000
83A83GLU-1-0.827-0.88711.828-18.352-18.3520.0000.0000.0000.000
84A84LEU0-0.0130.00111.391-1.502-1.5020.0000.0000.0000.000
85A85LYS10.8760.92712.60614.65314.6530.0000.0000.0000.000
86A86ALA0-0.0320.0008.371-1.342-1.3420.0000.0000.0000.000
87A87HIS0-0.023-0.0057.080-3.343-3.3430.0000.0000.0000.000
89A89VAL0-0.0130.0018.2981.8481.8480.0000.0000.0000.000
90A90ILE00.000-0.00210.4100.5110.5110.0000.0000.0000.000
91A91VAL00.0110.00712.7771.2191.2190.0000.0000.0000.000
92A92ILE00.006-0.00315.2870.4940.4940.0000.0000.0000.000
93A93ALA00.0120.02118.7770.4090.4090.0000.0000.0000.000
94A94ALA00.0210.01621.5710.3260.3260.0000.0000.0000.000
95A95PRO0-0.0340.00924.7590.2000.2000.0000.0000.0000.000
96A96MET0-0.0140.00527.8360.1970.1970.0000.0000.0000.000
97A97TYR00.0030.00629.5330.2300.2300.0000.0000.0000.000
98A98ASN0-0.011-0.01433.1120.0630.0630.0000.0000.0000.000
99A99PHE0-0.003-0.01835.0530.1200.1200.0000.0000.0000.000
100A100ASN00.0170.02731.863-0.360-0.3600.0000.0000.0000.000
101A101ILE00.0210.00626.481-0.116-0.1160.0000.0000.0000.000
102A102PRO0-0.019-0.00526.8070.3310.3310.0000.0000.0000.000
103A103THR00.014-0.00528.097-0.255-0.2550.0000.0000.0000.000
104A104GLN00.0300.02925.402-0.028-0.0280.0000.0000.0000.000
105A105LEU00.0330.01621.660-0.284-0.2840.0000.0000.0000.000
106A106LYS10.8300.91824.7749.4269.4260.0000.0000.0000.000
107A107ASN00.020-0.00726.9160.1190.1190.0000.0000.0000.000
108A108TYR00.0590.02716.763-0.049-0.0490.0000.0000.0000.000
109A109PHE0-0.003-0.01921.239-0.243-0.2430.0000.0000.0000.000
110A110ASP-1-0.857-0.93624.462-9.955-9.9550.0000.0000.0000.000
111A111LEU00.0100.01423.9700.2020.2020.0000.0000.0000.000
112A112ILE00.0110.02619.371-0.125-0.1250.0000.0000.0000.000
113A113ALA00.0010.02422.340-0.294-0.2940.0000.0000.0000.000
114A114ARG10.8110.86622.93212.17612.1760.0000.0000.0000.000
115A115ALA00.0160.01325.052-0.328-0.3280.0000.0000.0000.000
116A116GLY0-0.038-0.02126.4670.1550.1550.0000.0000.0000.000
117A117ILE0-0.0280.00120.897-0.297-0.2970.0000.0000.0000.000
118A118THR0-0.029-0.04819.571-0.602-0.6020.0000.0000.0000.000
119A119PHE00.0290.02521.810-0.250-0.2500.0000.0000.0000.000
120A120ARG10.8610.92824.87212.37612.3760.0000.0000.0000.000
121A121TYR00.0240.00427.6200.0060.0060.0000.0000.0000.000
122A122THR0-0.0040.01128.2810.0770.0770.0000.0000.0000.000
123A123GLU-1-0.845-0.92330.926-10.051-10.0510.0000.0000.0000.000
124A124LYS10.8490.91329.52810.50110.5010.0000.0000.0000.000
125A125GLY00.0160.02832.0490.0310.0310.0000.0000.0000.000
126A126PRO0-0.041-0.02729.810-0.131-0.1310.0000.0000.0000.000
127A127GLU-1-0.841-0.92124.980-12.242-12.2420.0000.0000.0000.000
128A128GLY00.0530.02322.8290.1110.1110.0000.0000.0000.000
129A129LEU0-0.063-0.04320.572-0.164-0.1640.0000.0000.0000.000
130A130VAL0-0.042-0.02515.715-0.598-0.5980.0000.0000.0000.000
131A131THR00.0020.00217.200-0.420-0.4200.0000.0000.0000.000
132A132GLY0-0.007-0.00813.673-0.877-0.8770.0000.0000.0000.000
133A133LYS10.8080.91810.52422.89022.8900.0000.0000.0000.000
134A134ARG10.8820.94110.04226.42626.4260.0000.0000.0000.000
135A135ALA00.0060.00313.596-0.565-0.5650.0000.0000.0000.000
136A136VAL0-0.012-0.01014.4150.3160.3160.0000.0000.0000.000
137A137VAL0-0.0130.00417.2910.2390.2390.0000.0000.0000.000
138A138LEU00.0260.01017.7390.3650.3650.0000.0000.0000.000
139A139SER0-0.018-0.01521.8950.5340.5340.0000.0000.0000.000
140A140SER00.023-0.00725.6250.2020.2020.0000.0000.0000.000
141A141ARG10.7330.81728.19310.71610.7160.0000.0000.0000.000
142A142GLY00.0310.02132.0120.0330.0330.0000.0000.0000.000
143A143GLY00.0450.02035.1360.1580.1580.0000.0000.0000.000
144A144ILE00.010-0.00834.973-0.284-0.2840.0000.0000.0000.000
145A145HIS10.8410.90133.9558.9558.9550.0000.0000.0000.000
146A146LYS10.8810.95128.52710.62610.6260.0000.0000.0000.000
147A147ASP-1-0.851-0.91131.956-9.838-9.8380.0000.0000.0000.000
148A148THR0-0.0010.00234.3880.3530.3530.0000.0000.0000.000
149A149PRO00.002-0.02136.655-0.179-0.1790.0000.0000.0000.000
150A150THR0-0.033-0.00737.8990.0530.0530.0000.0000.0000.000
151A151ASP-1-0.774-0.88631.051-10.451-10.4510.0000.0000.0000.000
152A152LEU00.0430.02033.499-0.107-0.1070.0000.0000.0000.000
153A153ILE0-0.017-0.00728.411-0.164-0.1640.0000.0000.0000.000
154A154ALA00.0210.01627.485-0.385-0.3850.0000.0000.0000.000
155A155PRO0-0.018-0.00727.548-0.375-0.3750.0000.0000.0000.000
156A156TYR00.0100.00428.680-0.223-0.2230.0000.0000.0000.000
157A157LEU00.0290.01323.398-0.198-0.1980.0000.0000.0000.000
158A158LYS10.9840.99524.34711.59511.5950.0000.0000.0000.000
159A159VAL0-0.027-0.00925.237-0.247-0.2470.0000.0000.0000.000
160A160PHE0-0.018-0.00822.642-0.056-0.0560.0000.0000.0000.000
161A161LEU00.0100.00119.352-0.191-0.1910.0000.0000.0000.000
162A162GLY00.0350.01421.752-0.422-0.4220.0000.0000.0000.000
163A163PHE0-0.061-0.02423.725-0.043-0.0430.0000.0000.0000.000
164A164ILE00.0020.00519.7970.0790.0790.0000.0000.0000.000
165A165GLY00.0100.00120.629-0.470-0.4700.0000.0000.0000.000
166A166ILE0-0.028-0.00416.398-0.718-0.7180.0000.0000.0000.000
167A167THR0-0.016-0.02619.0250.3310.3310.0000.0000.0000.000
168A168ASP-1-0.942-0.94515.211-18.667-18.6670.0000.0000.0000.000
169A169VAL0-0.001-0.00617.468-0.611-0.6110.0000.0000.0000.000
170A170ASN0-0.0010.00216.212-0.108-0.1080.0000.0000.0000.000
171A171PHE0-0.022-0.02019.4710.0880.0880.0000.0000.0000.000
172A172VAL00.0000.01719.9500.1520.1520.0000.0000.0000.000
173A173PHE0-0.012-0.01722.9960.2320.2320.0000.0000.0000.000
174A174ALA00.0510.03326.5400.0220.0220.0000.0000.0000.000
175A175GLU-1-0.749-0.86728.252-9.503-9.5030.0000.0000.0000.000
176A176GLY00.0130.00331.9730.0360.0360.0000.0000.0000.000
177A177ILE00.0070.00630.1530.1790.1790.0000.0000.0000.000
178A178ALA0-0.045-0.03034.1640.1150.1150.0000.0000.0000.000
179A179TYR0-0.037-0.01237.5740.1800.1800.0000.0000.0000.000
180A180GLY00.0530.03738.0450.1540.1540.0000.0000.0000.000
181A181PRO00.009-0.00735.428-0.204-0.2040.0000.0000.0000.000
182A182GLU-1-0.845-0.90934.816-8.255-8.2550.0000.0000.0000.000
183A183VAL0-0.005-0.00235.308-0.160-0.1600.0000.0000.0000.000
184A184ALA0-0.007-0.00632.258-0.283-0.2830.0000.0000.0000.000
185A185ALA00.0180.00930.689-0.354-0.3540.0000.0000.0000.000
186A186LYS10.8510.92630.1038.2268.2260.0000.0000.0000.000
187A187ALA00.0570.03429.715-0.338-0.3380.0000.0000.0000.000
188A188GLN0-0.059-0.05126.752-0.427-0.4270.0000.0000.0000.000
189A189ALA0-0.0170.00125.453-0.557-0.5570.0000.0000.0000.000
190A190ASP-1-0.893-0.94525.341-11.046-11.0460.0000.0000.0000.000
191A191ALA0-0.049-0.03724.007-0.491-0.4910.0000.0000.0000.000
192A192LYS10.9120.96721.27612.20412.2040.0000.0000.0000.000
193A193ALA00.0870.05620.480-0.736-0.7360.0000.0000.0000.000
194A194ALA0-0.026-0.00620.961-0.525-0.5250.0000.0000.0000.000
195A195ILE0-0.025-0.01616.283-0.746-0.7460.0000.0000.0000.000
196A196ASP-1-0.811-0.89416.344-17.056-17.0560.0000.0000.0000.000
197A197SER0-0.055-0.04216.125-0.890-0.8900.0000.0000.0000.000
198A198VAL0-0.052-0.01914.223-0.548-0.5480.0000.0000.0000.000
199A199VAL0-0.035-0.01911.384-1.767-1.7670.0000.0000.0000.000
200A200ALA0-0.032-0.01411.264-2.537-2.5370.0000.0000.0000.000
201A201ALA-1-0.901-0.91010.992-27.075-27.0750.0000.0000.0000.000