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: LGRG9

Calculation Name: 4MO2-A-Xray547

Preferred Name:

Target Type:

Ligand Name: dihydroflavine-adenine dinucleotide | flavin-adenine dinucleotide | ammonium ion

Ligand 3-letter code: FDA | FAD | NH4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4MO2

Chain ID: A

ChEMBL ID:

UniProt ID: Q0P8H5

Base Structure: X-ray

Registration Date: 2025-10-04

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 363
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -6389319.090426
FMO2-HF: Nuclear repulsion 6239511.734342
FMO2-HF: Total energy -149807.356084
FMO2-MP2: Total energy -150246.788441


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.
-15.104-5.87611.783-7.006-14.006-0.091
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 : 0.750 / q_NPA : 0.884
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].
3A3ASP-1-0.773-0.8502.442-46.897-43.8831.387-1.897-2.504-0.024
4A4TYR00.016-0.0315.0760.8861.054-0.001-0.005-0.1620.000
221A221ASN00.011-0.0082.350-4.089-3.5210.633-0.277-0.9250.001
222A222LYS10.8740.9462.53324.54427.0501.878-1.839-2.545-0.025
223A223ALA0-0.015-0.0042.297-21.764-19.4715.140-3.551-3.881-0.035
224A224LYS10.8560.9182.69044.03245.0012.6980.094-3.762-0.008
225A225LYS10.8250.9234.13925.02524.7350.0480.469-0.2270.000
5A5LEU0-0.048-0.0226.858-2.377-2.3770.0000.0000.0000.000
6A6ILE0-0.0070.0098.3492.1352.1350.0000.0000.0000.000
7A7VAL0-0.011-0.00512.063-0.167-0.1670.0000.0000.0000.000
8A8GLY00.0290.03414.6041.0791.0790.0000.0000.0000.000
9A9SER0-0.023-0.05817.455-0.270-0.2700.0000.0000.0000.000
10A10GLY00.0020.01419.1040.5250.5250.0000.0000.0000.000
11A11LEU00.0280.00120.816-0.582-0.5820.0000.0000.0000.000
12A12PHE00.0360.02317.267-0.264-0.2640.0000.0000.0000.000
13A13GLY00.0400.02416.595-0.485-0.4850.0000.0000.0000.000
14A14SER0-0.024-0.03116.427-1.129-1.1290.0000.0000.0000.000
15A15ILE00.0260.00918.474-0.302-0.3020.0000.0000.0000.000
16A16PHE00.0290.00611.484-0.246-0.2460.0000.0000.0000.000
17A17ALA00.002-0.00713.717-0.867-0.8670.0000.0000.0000.000
18A18TYR00.0080.03614.792-0.835-0.8350.0000.0000.0000.000
19A19GLU-1-0.817-0.90517.145-14.735-14.7350.0000.0000.0000.000
20A20ALA00.0140.00511.858-0.237-0.2370.0000.0000.0000.000
21A21THR0-0.074-0.06712.427-0.491-0.4910.0000.0000.0000.000
22A22GLU-1-0.868-0.91914.384-16.019-16.0190.0000.0000.0000.000
23A23LYS10.8210.90815.55815.99715.9970.0000.0000.0000.000
24A24GLY0-0.0060.01213.868-0.180-0.1800.0000.0000.0000.000
25A25TYR0-0.0100.0019.423-2.209-2.2090.0000.0000.0000.000
26A26THR0-0.027-0.0466.334-3.075-3.0750.0000.0000.0000.000
27A27CYS0-0.0070.0067.233-2.515-2.5150.0000.0000.0000.000
28A28LEU0-0.066-0.0266.2190.2540.2540.0000.0000.0000.000
29A29VAL00.0260.0088.7931.0721.0720.0000.0000.0000.000
30A30VAL0-0.022-0.01210.9480.0880.0880.0000.0000.0000.000
31A31GLU-1-0.783-0.85913.694-14.505-14.5050.0000.0000.0000.000
32A32GLN00.0230.01017.521-0.365-0.3650.0000.0000.0000.000
33A33ARG10.7800.87420.05312.42812.4280.0000.0000.0000.000
34A34GLU-1-0.899-0.95321.437-12.260-12.2600.0000.0000.0000.000
35A35HIS0-0.0120.01423.1070.0080.0080.0000.0000.0000.000
36A36ILE00.0360.01919.573-0.294-0.2940.0000.0000.0000.000
37A37GLY00.0700.02321.7440.6590.6590.0000.0000.0000.000
38A38GLY0-0.035-0.01423.1480.3750.3750.0000.0000.0000.000
39A39ASN0-0.005-0.02524.344-0.068-0.0680.0000.0000.0000.000
40A40CYS0-0.0100.00227.1680.3170.3170.0000.0000.0000.000
41A41TYR00.0070.01926.5640.1020.1020.0000.0000.0000.000
42A42THR0-0.017-0.00928.2960.3860.3860.0000.0000.0000.000
43A43GLU-1-0.824-0.89330.510-10.113-10.1130.0000.0000.0000.000
44A44ASN0-0.019-0.01732.1690.4350.4350.0000.0000.0000.000
45A45ILE00.0220.01234.6470.0170.0170.0000.0000.0000.000
46A46LYS10.9410.96037.5437.5417.5410.0000.0000.0000.000
47A47ASN0-0.006-0.00138.7310.0590.0590.0000.0000.0000.000
48A48ILE0-0.0040.01739.1970.0720.0720.0000.0000.0000.000
49A49ASN0-0.035-0.02134.500-0.341-0.3410.0000.0000.0000.000
50A50VAL00.0130.00135.6190.0990.0990.0000.0000.0000.000
51A51HIS00.0520.02233.446-0.407-0.4070.0000.0000.0000.000
52A52LYS10.8360.90931.1229.9029.9020.0000.0000.0000.000
53A53TYR0-0.067-0.04727.6240.1280.1280.0000.0000.0000.000
54A54GLY00.0670.03032.8720.0260.0260.0000.0000.0000.000
55A55ALA0-0.016-0.00835.057-0.206-0.2060.0000.0000.0000.000
56A56HIS0-0.029-0.02231.203-0.264-0.2640.0000.0000.0000.000
57A57ILE00.0100.01234.8370.0080.0080.0000.0000.0000.000
58A58PHE0-0.002-0.00630.103-0.094-0.0940.0000.0000.0000.000
59A59ARG10.8550.92435.1488.7568.7560.0000.0000.0000.000
60A60THR0-0.047-0.03434.170-0.249-0.2490.0000.0000.0000.000
61A61SER00.033-0.01036.5760.2540.2540.0000.0000.0000.000
62A62ASP-1-0.864-0.91532.999-9.138-9.1380.0000.0000.0000.000
63A63GLN00.001-0.01034.550-0.035-0.0350.0000.0000.0000.000
64A64ASN0-0.033-0.01631.099-0.196-0.1960.0000.0000.0000.000
65A65ILE0-0.028-0.01029.449-0.344-0.3440.0000.0000.0000.000
66A66TRP00.0110.00530.733-0.299-0.2990.0000.0000.0000.000
67A67ASP-1-0.820-0.90932.655-8.985-8.9850.0000.0000.0000.000
68A68TYR0-0.067-0.05122.235-0.142-0.1420.0000.0000.0000.000
69A69MET0-0.015-0.01627.605-0.466-0.4660.0000.0000.0000.000
70A70ASN0-0.026-0.02929.6080.0400.0400.0000.0000.0000.000
71A71GLN0-0.0180.00926.1160.1150.1150.0000.0000.0000.000
72A72PHE0-0.033-0.00823.023-0.232-0.2320.0000.0000.0000.000
73A73CYS0-0.121-0.05528.3690.0320.0320.0000.0000.0000.000
74A74GLU-1-0.732-0.84931.875-8.129-8.1290.0000.0000.0000.000
75A75PHE0-0.023-0.01032.337-0.053-0.0530.0000.0000.0000.000
76A76ASN0-0.017-0.01537.1870.1780.1780.0000.0000.0000.000
77A77HIS00.0540.01340.619-0.118-0.1180.0000.0000.0000.000
78A78PHE0-0.017-0.00141.0780.1640.1640.0000.0000.0000.000
79A79ILE0-0.014-0.00742.531-0.089-0.0890.0000.0000.0000.000
80A80ASN0-0.006-0.00642.4050.1120.1120.0000.0000.0000.000
81A81SER00.009-0.02444.5010.0990.0990.0000.0000.0000.000
82A82PRO0-0.0350.00044.9770.0730.0730.0000.0000.0000.000
83A83ILE00.0310.02347.7180.1370.1370.0000.0000.0000.000
84A84ALA0-0.031-0.01649.785-0.136-0.1360.0000.0000.0000.000
85A85ILE00.0340.01751.9860.1310.1310.0000.0000.0000.000
86A86TYR00.006-0.00353.567-0.042-0.0420.0000.0000.0000.000
87A87LYS10.9150.94056.2105.4935.4930.0000.0000.0000.000
88A88ASP-1-0.891-0.92958.206-5.192-5.1920.0000.0000.0000.000
89A89GLU-1-0.833-0.85459.209-5.237-5.2370.0000.0000.0000.000
90A90ILE00.0190.00255.395-0.104-0.1040.0000.0000.0000.000
91A91TYR0-0.068-0.06955.1300.1310.1310.0000.0000.0000.000
92A92ASN00.0310.01853.139-0.161-0.1610.0000.0000.0000.000
93A93LEU0-0.0160.01948.1140.0410.0410.0000.0000.0000.000
94A94PRO00.0280.01747.904-0.051-0.0510.0000.0000.0000.000
95A95PHE0-0.001-0.00949.7960.1130.1130.0000.0000.0000.000
96A96ASN00.0520.01752.9310.0970.0970.0000.0000.0000.000
97A97MET00.0150.02755.1630.0580.0580.0000.0000.0000.000
98A98ASN0-0.021-0.00255.8620.1840.1840.0000.0000.0000.000
99A99THR0-0.046-0.02154.4850.0160.0160.0000.0000.0000.000
100A100PHE00.014-0.01455.4880.0710.0710.0000.0000.0000.000
101A101SER0-0.033-0.02760.2500.0780.0780.0000.0000.0000.000
102A102LYS10.8740.93659.9735.3915.3910.0000.0000.0000.000
103A103LEU0-0.038-0.00657.9320.0230.0230.0000.0000.0000.000
104A104TRP0-0.031-0.04259.7160.0290.0290.0000.0000.0000.000
105A105GLY00.0250.02965.4860.0850.0850.0000.0000.0000.000
106A106ILE0-0.083-0.02863.0850.0680.0680.0000.0000.0000.000
107A107LYS10.9610.95865.7144.5834.5830.0000.0000.0000.000
108A108THR0-0.019-0.01165.224-0.064-0.0640.0000.0000.0000.000
109A109PRO00.050-0.00261.624-0.015-0.0150.0000.0000.0000.000
110A110ASN00.0110.00062.787-0.080-0.0800.0000.0000.0000.000
111A111GLU-1-0.814-0.88465.449-4.667-4.6670.0000.0000.0000.000
112A112ALA00.0410.02360.895-0.004-0.0040.0000.0000.0000.000
113A113ARG10.8630.92558.8665.2155.2150.0000.0000.0000.000
114A114LYS10.9490.97462.3464.5424.5420.0000.0000.0000.000
115A115ILE00.0050.01763.2040.0260.0260.0000.0000.0000.000
116A116ILE0-0.0020.00557.414-0.017-0.0170.0000.0000.0000.000
117A117GLU-1-0.875-0.94760.287-5.223-5.2230.0000.0000.0000.000
118A118MET0-0.0050.00461.9430.0140.0140.0000.0000.0000.000
119A119GLN0-0.018-0.02061.697-0.080-0.0800.0000.0000.0000.000
120A120LYS10.8860.95856.3395.5335.5330.0000.0000.0000.000
121A121GLN0-0.037-0.00960.1500.0270.0270.0000.0000.0000.000
122A122ILE00.0040.00461.5600.0680.0680.0000.0000.0000.000
123A123ILE0-0.086-0.03556.9220.0040.0040.0000.0000.0000.000
124A124GLN0-0.0050.00059.833-0.061-0.0610.0000.0000.0000.000
125A125HIS0-0.0070.00557.8880.0930.0930.0000.0000.0000.000
126A126PRO00.014-0.00953.943-0.054-0.0540.0000.0000.0000.000
127A127PRO0-0.024-0.00252.3920.0400.0400.0000.0000.0000.000
128A128LYS10.8380.90752.4845.2975.2970.0000.0000.0000.000
129A129ASN0-0.027-0.00250.884-0.095-0.0950.0000.0000.0000.000
130A130LEU00.003-0.00346.6350.0350.0350.0000.0000.0000.000
131A131GLU-1-0.772-0.85250.409-5.548-5.5480.0000.0000.0000.000
132A132GLU-1-0.775-0.88853.872-5.471-5.4710.0000.0000.0000.000
133A133GLN0-0.006-0.00748.1280.1520.1520.0000.0000.0000.000
134A134ALA0-0.016-0.00451.2850.0160.0160.0000.0000.0000.000
135A135ILE00.0210.01352.5750.0370.0370.0000.0000.0000.000
136A136SER0-0.009-0.01353.8670.0530.0530.0000.0000.0000.000
137A137LEU0-0.064-0.02949.7670.0110.0110.0000.0000.0000.000
138A138VAL0-0.049-0.04552.8800.0210.0210.0000.0000.0000.000
139A139GLY00.0490.03255.6740.0770.0770.0000.0000.0000.000
140A140THR00.024-0.00657.439-0.100-0.1000.0000.0000.0000.000
141A141ASP-1-0.798-0.86858.494-5.169-5.1690.0000.0000.0000.000
142A142VAL0-0.002-0.00954.098-0.059-0.0590.0000.0000.0000.000
143A143TYR00.012-0.04152.554-0.163-0.1630.0000.0000.0000.000
144A144GLU-1-0.877-0.94554.427-5.420-5.4200.0000.0000.0000.000
145A145LYS10.8220.90756.5125.2185.2180.0000.0000.0000.000
146A146LEU0-0.018-0.00752.302-0.084-0.0840.0000.0000.0000.000
147A147ILE0-0.041-0.00949.049-0.147-0.1470.0000.0000.0000.000
148A148LYS10.8670.94650.1305.4085.4080.0000.0000.0000.000
149A149GLY00.0890.03451.081-0.086-0.0860.0000.0000.0000.000
150A150TYR0-0.022-0.00843.150-0.118-0.1180.0000.0000.0000.000
151A151THR0-0.039-0.04546.191-0.206-0.2060.0000.0000.0000.000
152A152GLU-1-0.877-0.96246.715-6.050-6.0500.0000.0000.0000.000
153A153LYS10.7840.90846.6406.4166.4160.0000.0000.0000.000
154A154GLN0-0.053-0.02141.923-0.122-0.1220.0000.0000.0000.000
155A155TRP0-0.028-0.02539.864-0.287-0.2870.0000.0000.0000.000
156A156GLY00.0280.02844.292-0.023-0.0230.0000.0000.0000.000
157A157ARG10.8730.93843.6676.9546.9540.0000.0000.0000.000
158A158SER00.030-0.01149.553-0.019-0.0190.0000.0000.0000.000
159A159CYS0-0.003-0.00250.445-0.117-0.1170.0000.0000.0000.000
160A160LYS10.8550.92551.4905.4355.4350.0000.0000.0000.000
161A161ASP-1-0.839-0.87250.521-5.933-5.9330.0000.0000.0000.000
162A162LEU0-0.034-0.01245.449-0.194-0.1940.0000.0000.0000.000
163A163PRO00.0430.02244.4030.1370.1370.0000.0000.0000.000
164A164ALA00.0820.02646.495-0.103-0.1030.0000.0000.0000.000
165A165SER0-0.007-0.00643.093-0.024-0.0240.0000.0000.0000.000
166A166ILE00.0200.02642.239-0.193-0.1930.0000.0000.0000.000
167A167ILE00.0070.01142.999-0.118-0.1180.0000.0000.0000.000
168A168ARG10.8890.93939.4137.6817.6810.0000.0000.0000.000
169A169ARG10.9850.98242.7017.1407.1400.0000.0000.0000.000
170A170LEU00.0300.02746.442-0.131-0.1310.0000.0000.0000.000
171A171PRO0-0.057-0.01946.3620.1150.1150.0000.0000.0000.000
172A172VAL00.0520.02149.4420.0160.0160.0000.0000.0000.000
173A173ARG10.7710.87748.3216.3676.3670.0000.0000.0000.000
174A174TYR00.0140.00354.2770.0230.0230.0000.0000.0000.000
175A175ILE00.019-0.00955.4640.0950.0950.0000.0000.0000.000
176A176TYR0-0.026-0.02956.583-0.056-0.0560.0000.0000.0000.000
177A177ASP-1-0.839-0.92051.349-6.259-6.2590.0000.0000.0000.000
178A178ASN00.0550.02551.3560.0240.0240.0000.0000.0000.000
179A179ASN00.0720.06345.768-0.230-0.2300.0000.0000.0000.000
180A180TYR0-0.025-0.02142.3950.0080.0080.0000.0000.0000.000
181A181PHE0-0.031-0.02039.759-0.095-0.0950.0000.0000.0000.000
182A182ASN0-0.017-0.01243.6070.1350.1350.0000.0000.0000.000
183A183ASP-1-0.859-0.91639.295-7.868-7.8680.0000.0000.0000.000
184A184PRO0-0.018-0.00341.0010.0570.0570.0000.0000.0000.000
185A185TYR00.0120.01937.9200.0380.0380.0000.0000.0000.000
186A186GLN00.023-0.01638.820-0.140-0.1400.0000.0000.0000.000
187A187GLY00.0320.02938.4670.1310.1310.0000.0000.0000.000
188A188ILE0-0.063-0.02836.311-0.205-0.2050.0000.0000.0000.000
189A189PRO0-0.0140.00832.1590.1580.1580.0000.0000.0000.000
190A190LYS10.8280.89334.8198.1198.1190.0000.0000.0000.000
191A191GLY0-0.040-0.02334.056-0.225-0.2250.0000.0000.0000.000
192A192GLY0-0.0010.00632.699-0.246-0.2460.0000.0000.0000.000
193A193TYR0-0.007-0.04428.921-0.180-0.1800.0000.0000.0000.000
194A194THR0-0.036-0.02825.921-0.432-0.4320.0000.0000.0000.000
195A195ALA00.0820.04925.886-0.516-0.5160.0000.0000.0000.000
196A196ILE0-0.015-0.01025.354-0.168-0.1680.0000.0000.0000.000
197A197PHE00.0200.00222.265-0.479-0.4790.0000.0000.0000.000
198A198ASP-1-0.858-0.94021.450-13.756-13.7560.0000.0000.0000.000
199A199LYS10.7930.89821.69510.80610.8060.0000.0000.0000.000
200A200MET0-0.065-0.01820.216-0.641-0.6410.0000.0000.0000.000
201A201LEU00.0280.00116.312-1.038-1.0380.0000.0000.0000.000
202A202LYS10.9420.98516.47813.04813.0480.0000.0000.0000.000
203A203LYS10.8350.90014.80616.88016.8800.0000.0000.0000.000
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