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: 7Y5RK

Calculation Name: 1MO9-A-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin-adenine dinucleotide | (2-[2-ketopropylthio]ethanesulfonate

Ligand 3-letter code: FAD | KPC

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1MO9

Chain ID: A

ChEMBL ID:

UniProt ID: Q56839

Base Structure: X-ray

Registration Date: 2025-10-03

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 521
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -10070373.3102
FMO2-HF: Nuclear repulsion 9867904.799561
FMO2-HF: Total energy -202468.510639
FMO2-MP2: Total energy -203053.495072


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:LYS)


Summations of interaction energy for fragment #1(A:2:LYS)
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.
-381.704-378.79419.091-11.318-10.684-0.13
Interaction energy analysis for fragmet #1(A:2:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.753 / q_NPA : 1.855
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].
3A4TRP00.0080.0012.857-6.592-3.0060.502-1.703-2.386-0.015
4A5ASN0-0.019-0.0244.2759.6709.7620.001-0.025-0.0670.000
30A31GLU-1-0.908-0.9561.647-187.966-189.51118.577-9.427-7.605-0.114
31A32VAL0-0.035-0.0153.47115.52416.2480.012-0.156-0.581-0.001
32A33ILE0-0.0120.0065.189-6.373-6.320-0.001-0.007-0.0450.000
5A6ALA00.0600.0357.6123.0263.0260.0000.0000.0000.000
6A7ARG10.8310.9199.37938.56538.5650.0000.0000.0000.000
7A8ASN0-0.010-0.02411.9643.7243.7240.0000.0000.0000.000
8A9ASP-1-0.846-0.8938.745-53.262-53.2620.0000.0000.0000.000
9A10HIS0-0.089-0.07612.2990.3680.3680.0000.0000.0000.000
10A11LEU0-0.0280.00510.1391.3501.3500.0000.0000.0000.000
11A12THR00.028-0.01414.5361.7121.7120.0000.0000.0000.000
12A13ILE00.0170.00316.333-1.740-1.7400.0000.0000.0000.000
13A14ASN00.0480.01417.314-1.102-1.1020.0000.0000.0000.000
14A15GLN00.0580.06013.363-0.712-0.7120.0000.0000.0000.000
15A16TRP00.0330.01510.380-4.160-4.1600.0000.0000.0000.000
16A17ALA00.006-0.00113.044-1.898-1.8980.0000.0000.0000.000
17A18THR0-0.026-0.01512.3270.0800.0800.0000.0000.0000.000
18A19ARG10.8620.9406.07966.12966.1290.0000.0000.0000.000
19A20ILE0-0.060-0.0429.256-3.779-3.7790.0000.0000.0000.000
20A21ASP-1-0.882-0.93411.804-38.432-38.4320.0000.0000.0000.000
21A22GLU-1-0.864-0.9358.227-57.893-57.8930.0000.0000.0000.000
22A23ILE0-0.083-0.0466.098-4.506-4.5060.0000.0000.0000.000
23A24LEU0-0.076-0.0388.806-0.395-0.3950.0000.0000.0000.000
24A25GLU-1-0.913-0.94612.385-36.161-36.1610.0000.0000.0000.000
25A26ALA0-0.0250.0057.8050.0740.0740.0000.0000.0000.000
26A27PRO0-0.018-0.0259.938-0.339-0.3390.0000.0000.0000.000
27A28ASP-1-0.926-0.9565.370-84.062-84.0620.0000.0000.0000.000
28A29GLY0-0.027-0.0017.063-3.220-3.2200.0000.0000.0000.000
29A30GLY00.0490.0255.4621.3551.3550.0000.0000.0000.000
33A34TYR0-0.079-0.0867.5704.7504.7500.0000.0000.0000.000
34A35ASN00.012-0.0039.4930.7770.7770.0000.0000.0000.000
35A36VAL00.0600.02812.9232.6632.6630.0000.0000.0000.000
36A37ASP-1-0.838-0.92014.849-31.044-31.0440.0000.0000.0000.000
37A38GLU-1-0.842-0.90513.301-40.843-40.8430.0000.0000.0000.000
38A39ASN0-0.042-0.01617.1421.2361.2360.0000.0000.0000.000
39A40ASP-1-0.823-0.88020.647-23.755-23.7550.0000.0000.0000.000
40A41PRO0-0.010-0.00122.268-0.712-0.7120.0000.0000.0000.000
41A42ARG10.7610.86824.74124.11824.1180.0000.0000.0000.000
42A43GLU-1-0.892-0.95224.190-22.583-22.5830.0000.0000.0000.000
43A44TYR0-0.048-0.02818.5250.0170.0170.0000.0000.0000.000
44A45ASP-1-0.777-0.87923.979-21.318-21.3180.0000.0000.0000.000
45A46ALA00.007-0.01624.9930.7260.7260.0000.0000.0000.000
46A47ILE0-0.0030.01318.340-0.781-0.7810.0000.0000.0000.000
47A48PHE0-0.036-0.01920.7311.2731.2730.0000.0000.0000.000
48A49ILE00.0230.00918.358-1.892-1.8920.0000.0000.0000.000
49A50GLY00.0380.02018.2071.3821.3820.0000.0000.0000.000
50A51GLY00.024-0.03018.3311.0741.0740.0000.0000.0000.000
51A52GLY00.0140.00019.3800.1770.1770.0000.0000.0000.000
52A53ALA0-0.031-0.02122.1280.3360.3360.0000.0000.0000.000
53A54ALA00.0240.01125.6890.4980.4980.0000.0000.0000.000
54A55GLY00.0660.03122.8590.4820.4820.0000.0000.0000.000
55A56ARG10.8430.92320.93327.05827.0580.0000.0000.0000.000
56A57PHE00.007-0.01023.1380.3430.3430.0000.0000.0000.000
57A58GLY00.0390.01926.8030.6160.6160.0000.0000.0000.000
58A59SER00.002-0.00522.6590.0350.0350.0000.0000.0000.000
59A60ALA00.002-0.00124.6880.1900.1900.0000.0000.0000.000
60A61TYR00.016-0.01026.2420.5770.5770.0000.0000.0000.000
61A62LEU00.0060.00426.3240.4710.4710.0000.0000.0000.000
62A63ARG10.8860.95422.17027.03227.0320.0000.0000.0000.000
63A64ALA0-0.020-0.00627.1150.3860.3860.0000.0000.0000.000
64A65MET0-0.071-0.01830.2910.5050.5050.0000.0000.0000.000
65A66GLY00.0180.02130.0060.4390.4390.0000.0000.0000.000
66A67GLY00.0310.00828.967-0.101-0.1010.0000.0000.0000.000
67A68ARG10.7120.81419.49328.47328.4730.0000.0000.0000.000
68A69GLN0-0.004-0.00720.0320.5110.5110.0000.0000.0000.000
69A70LEU00.0340.02515.427-0.745-0.7450.0000.0000.0000.000
70A71ILE0-0.052-0.00416.9801.1231.1230.0000.0000.0000.000
71A72VAL00.0320.01212.867-2.244-2.2440.0000.0000.0000.000
72A73ASP-1-0.820-0.90113.809-33.333-33.3330.0000.0000.0000.000
73A74ARG10.9760.98511.63130.62830.6280.0000.0000.0000.000
74A75TRP00.0500.03111.730-0.725-0.7250.0000.0000.0000.000
75A76PRO00.0380.02710.056-0.240-0.2400.0000.0000.0000.000
76A77PHE00.012-0.00411.7770.5520.5520.0000.0000.0000.000
77A78LEU00.0130.02015.0891.3261.3260.0000.0000.0000.000
78A79GLY0-0.029-0.02518.0210.7570.7570.0000.0000.0000.000
79A80GLY0-0.019-0.01620.0771.4401.4400.0000.0000.0000.000
80A81SER00.0750.02621.099-0.260-0.2600.0000.0000.0000.000
81A82CYS0-0.018-0.00723.3560.5580.5580.0000.0000.0000.000
82A83PRO00.031-0.00721.8590.5970.5970.0000.0000.0000.000
83A84HIS00.0120.02518.094-0.282-0.2820.0000.0000.0000.000
84A85ASN00.0300.00522.1590.4710.4710.0000.0000.0000.000
85A86ALA00.0560.03624.9250.7220.7220.0000.0000.0000.000
86A88VAL0-0.0130.01226.1200.5420.5420.0000.0000.0000.000
87A89PRO00.0080.02126.5600.4780.4780.0000.0000.0000.000
88A90HIS00.0080.00129.1720.0480.0480.0000.0000.0000.000
89A91HIS0-0.013-0.01531.9941.0571.0570.0000.0000.0000.000
90A92LEU00.0400.03829.1470.3770.3770.0000.0000.0000.000
91A93PHE00.0120.00129.6360.3270.3270.0000.0000.0000.000
92A94SER00.018-0.00734.6460.4340.4340.0000.0000.0000.000
93A95ASP-1-0.908-0.94735.592-16.921-16.9210.0000.0000.0000.000
94A96CYS0-0.082-0.04734.9410.3830.3830.0000.0000.0000.000
95A97ALA00.008-0.00537.8840.4170.4170.0000.0000.0000.000
96A98ALA0-0.0070.00740.6680.4610.4610.0000.0000.0000.000
97A99GLU-1-0.867-0.93039.801-14.618-14.6180.0000.0000.0000.000
98A100LEU0-0.036-0.01839.4280.3110.3110.0000.0000.0000.000
99A101MET0-0.0020.01643.2610.3380.3380.0000.0000.0000.000
100A102LEU0-0.0480.00345.6730.4220.4220.0000.0000.0000.000
101A103ALA00.009-0.01245.1160.3090.3090.0000.0000.0000.000
102A104ARG10.7730.88543.49914.39114.3910.0000.0000.0000.000
103A105THR0-0.033-0.02748.8790.3290.3290.0000.0000.0000.000
104A106PHE0-0.066-0.03450.5700.3400.3400.0000.0000.0000.000
105A107SER00.0560.04750.677-0.138-0.1380.0000.0000.0000.000
106A108GLY0-0.014-0.01151.2340.2720.2720.0000.0000.0000.000
107A109GLN0-0.049-0.02052.8530.2420.2420.0000.0000.0000.000
108A110TYR0-0.035-0.03252.310-0.146-0.1460.0000.0000.0000.000
109A111TRP0-0.0010.00746.7490.2310.2310.0000.0000.0000.000
110A112PHE0-0.0110.00046.053-0.349-0.3490.0000.0000.0000.000
111A113PRO00.0080.00445.3590.2360.2360.0000.0000.0000.000
112A114ASP-1-0.818-0.89248.693-12.189-12.1890.0000.0000.0000.000
113A115MET0-0.042-0.03443.528-0.370-0.3700.0000.0000.0000.000
114A116THR0-0.060-0.04948.306-0.134-0.1340.0000.0000.0000.000
115A117GLU-1-0.944-0.97149.303-12.395-12.3950.0000.0000.0000.000
116A118LYS10.8460.94140.34915.06515.0650.0000.0000.0000.000
117A119VAL00.0450.02840.987-0.073-0.0730.0000.0000.0000.000
118A120VAL0-0.070-0.04437.419-0.100-0.1000.0000.0000.0000.000
119A121GLY00.0680.03235.5910.0230.0230.0000.0000.0000.000
120A122ILE0-0.038-0.03333.194-0.329-0.3290.0000.0000.0000.000
121A123LYS10.8390.91027.62221.71121.7110.0000.0000.0000.000
122A124GLU-1-0.935-0.95630.062-18.677-18.6770.0000.0000.0000.000
123A125VAL0-0.010-0.00630.195-0.616-0.6160.0000.0000.0000.000
124A126VAL0-0.0030.00427.147-0.658-0.6580.0000.0000.0000.000
125A127ASP-1-0.839-0.91925.871-23.891-23.8910.0000.0000.0000.000
126A128LEU0-0.016-0.00325.215-0.990-0.9900.0000.0000.0000.000
127A129PHE0-0.003-0.01624.338-0.749-0.7490.0000.0000.0000.000
128A130ARG10.8440.91019.63128.23928.2390.0000.0000.0000.000
129A131ALA00.0110.01320.923-1.472-1.4720.0000.0000.0000.000
130A132GLY00.0010.01421.339-0.628-0.6280.0000.0000.0000.000
131A133ARG10.7570.84619.45629.72329.7230.0000.0000.0000.000
132A134ASN00.0490.00116.327-0.617-0.6170.0000.0000.0000.000
133A135GLY00.0260.02017.921-0.998-0.9980.0000.0000.0000.000
134A136PRO0-0.014-0.02120.119-0.439-0.4390.0000.0000.0000.000
135A137HIS10.8290.91816.62432.86832.8680.0000.0000.0000.000
136A138GLY00.0880.04416.250-1.308-1.3080.0000.0000.0000.000
137A139ILE0-0.037-0.02017.292-0.240-0.2400.0000.0000.0000.000
138A140MET0-0.055-0.01819.1470.6950.6950.0000.0000.0000.000
139A141ASN00.0580.04012.7552.3642.3640.0000.0000.0000.000
140A142PHE00.0390.02816.5690.0410.0410.0000.0000.0000.000
141A143GLN00.0530.04118.1220.2520.2520.0000.0000.0000.000
142A144SER0-0.018-0.04018.5411.4601.4600.0000.0000.0000.000
143A145LYS10.8310.94713.62138.05838.0580.0000.0000.0000.000
144A146GLU-1-0.796-0.89516.694-33.060-33.0600.0000.0000.0000.000
145A147GLN0-0.050-0.02520.5620.8810.8810.0000.0000.0000.000
146A148LEU0-0.051-0.02622.9800.9420.9420.0000.0000.0000.000
147A149ASN0-0.033-0.00421.6530.1340.1340.0000.0000.0000.000
148A150LEU0-0.041-0.01519.777-0.006-0.0060.0000.0000.0000.000
149A151GLU-1-0.735-0.82917.149-32.802-32.8020.0000.0000.0000.000
150A152TYR0-0.055-0.05412.6300.9240.9240.0000.0000.0000.000
151A153ILE0-0.0020.0059.974-2.922-2.9220.0000.0000.0000.000
152A154LEU0-0.034-0.01510.6263.5463.5460.0000.0000.0000.000
153A155ASN0-0.019-0.0206.5730.2220.2220.0000.0000.0000.000
154A156CYS00.0160.0167.670-6.544-6.5440.0000.0000.0000.000
155A157PRO0-0.041-0.0279.2944.4064.4060.0000.0000.0000.000
156A158ALA00.0070.01911.967-1.287-1.2870.0000.0000.0000.000
157A159LYS10.9460.98411.76441.59241.5920.0000.0000.0000.000
158A160VAL0-0.0040.00315.7040.0210.0210.0000.0000.0000.000
159A161ILE0-0.016-0.00516.7370.1710.1710.0000.0000.0000.000
160A162ASP-1-0.757-0.85620.524-23.198-23.1980.0000.0000.0000.000
161A163ASN0-0.004-0.02723.406-1.062-1.0620.0000.0000.0000.000
162A164HIS10.7760.90124.75721.86121.8610.0000.0000.0000.000
163A165THR0-0.013-0.02819.212-0.437-0.4370.0000.0000.0000.000
164A166VAL00.0060.00115.7260.3520.3520.0000.0000.0000.000
165A167GLU-1-0.914-0.95311.038-43.597-43.5970.0000.0000.0000.000
166A168ALA00.017-0.00811.0260.0430.0430.0000.0000.0000.000
167A169ALA0-0.005-0.0286.964-0.098-0.0980.0000.0000.0000.000
168A170GLY0-0.0190.0007.637-2.791-2.7910.0000.0000.0000.000
169A171LYS10.8810.9608.39556.55256.5520.0000.0000.0000.000
170A172VAL00.0130.00411.8670.1670.1670.0000.0000.0000.000
171A173PHE00.0160.01012.6190.8530.8530.0000.0000.0000.000
172A174LYS10.8900.92417.66625.82625.8260.0000.0000.0000.000
173A175ALA00.0090.00621.492-0.449-0.4490.0000.0000.0000.000
174A176LYS10.8780.94723.90021.73721.7370.0000.0000.0000.000
175A177ASN0-0.026-0.02426.3191.3671.3670.0000.0000.0000.000
176A178LEU00.0030.01921.799-1.158-1.1580.0000.0000.0000.000
177A179ILE0-0.006-0.00324.0401.1511.1510.0000.0000.0000.000
178A180LEU0-0.0040.00123.152-1.411-1.4110.0000.0000.0000.000
179A181ALA00.004-0.01222.6541.1511.1510.0000.0000.0000.000
180A182VAL00.0000.00719.696-0.471-0.4710.0000.0000.0000.000
181A183GLY0-0.026-0.00222.119-0.244-0.2440.0000.0000.0000.000
182A184ALA00.0340.01325.3620.1200.1200.0000.0000.0000.000
183A185GLY0-0.041-0.03425.065-1.103-1.1030.0000.0000.0000.000
184A186PRO00.0500.02925.3280.7620.7620.0000.0000.0000.000
185A187GLY00.0050.02128.290-0.011-0.0110.0000.0000.0000.000
186A188THR00.021-0.00430.7020.1680.1680.0000.0000.0000.000
187A189LEU0-0.021-0.01632.7440.4850.4850.0000.0000.0000.000
188A190ASP-1-0.924-0.95635.285-16.653-16.6530.0000.0000.0000.000
189A191VAL0-0.002-0.00336.9750.5290.5290.0000.0000.0000.000
190A192PRO0-0.037-0.03437.231-0.417-0.4170.0000.0000.0000.000
191A193GLY00.1040.05336.6420.2320.2320.0000.0000.0000.000
192A194VAL0-0.081-0.02832.833-0.241-0.2410.0000.0000.0000.000
193A195ASN0-0.024-0.02130.285-0.682-0.6820.0000.0000.0000.000
194A196ALA00.0290.03931.120-0.429-0.4290.0000.0000.0000.000
195A197LYS10.8930.93530.10719.03119.0310.0000.0000.0000.000
196A198GLY00.0810.03431.7860.6260.6260.0000.0000.0000.000
197A199VAL0-0.054-0.01332.6680.5070.5070.0000.0000.0000.000
198A200PHE00.0140.01328.268-0.657-0.6570.0000.0000.0000.000
199A201ASP-1-0.788-0.88527.353-22.038-22.0380.0000.0000.0000.000
200A202HIS10.8010.84926.32322.21322.2130.0000.0000.0000.000
201A203ALA0-0.098-0.04423.517-0.579-0.5790.0000.0000.0000.000
202A204THR00.0900.03024.592-0.383-0.3830.0000.0000.0000.000
203A205LEU0-0.0170.00725.689-0.277-0.2770.0000.0000.0000.000
204A206VAL0-0.046-0.03023.5650.1330.1330.0000.0000.0000.000
205A207GLU-1-0.800-0.87020.199-32.073-32.0730.0000.0000.0000.000
206A208GLU-1-0.911-0.96122.802-25.842-25.8420.0000.0000.0000.000
207A209LEU0-0.047-0.00225.1990.8260.8260.0000.0000.0000.000
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