FMO DATABASE

FMODB ID: 2MK8R

Calculation Name: 1MOG-A-Xray547

Preferred Name:

Target Type:

Ligand Name: riboflavin | magnesium ion | chloride ion

Ligand 3-letter code: RBF | MG | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1MOG

Chain ID: A

ChEMBL ID:

UniProt ID: B0R5M0

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	67
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-350799.619816
FMO2-HF: Nuclear repulsion	325418.083408
FMO2-HF: Total energy	-25381.536407
FMO2-MP2: Total energy	-25456.901343

3D Structure Molmil

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:2:VAL)

Summations of interaction energy for fragment #1(A:2:VAL)

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.
-300.623	-287.921	4.369	-8.355	-8.714	-0.097

Interaction energy analysis for fragmet #1(A:2:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.785 / q_NPA : 0.889

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

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

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].
3	A	4	LYS	1	0.770	0.884	2.909	29.331	31.996	0.339	-1.329	-1.674	-0.010
4	A	5	LYS	1	0.836	0.906	4.865	26.841	26.845	-0.001	-0.005	0.003	0.000
62	A	63	GLU	-1	-0.923	-0.967	2.197	-108.469	-101.994	2.374	-4.901	-3.948	-0.069
63	A	64	LEU	0	-0.052	-0.041	2.286	7.158	8.888	1.615	-0.951	-2.394	-0.006
64	A	65	ASP	-1	-0.924	-0.964	3.009	-57.021	-55.193	0.042	-1.169	-0.701	-0.012
5	A	6	VAL	0	-0.007	0.001	8.553	0.441	0.441	0.000	0.000	0.000	0.000
6	A	7	LEU	0	-0.058	-0.012	11.818	-0.018	-0.018	0.000	0.000	0.000	0.000
7	A	8	LEU	0	-0.007	-0.008	14.982	0.501	0.501	0.000	0.000	0.000	0.000
8	A	9	THR	0	-0.005	-0.008	17.768	0.154	0.154	0.000	0.000	0.000	0.000
9	A	10	GLY	0	0.021	0.035	21.410	0.077	0.077	0.000	0.000	0.000	0.000
10	A	11	THR	0	-0.072	-0.068	23.047	0.534	0.534	0.000	0.000	0.000	0.000
11	A	12	SER	0	0.043	0.008	26.846	0.003	0.003	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.909	-0.952	29.772	-9.011	-9.011	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.949	-0.962	32.117	-8.869	-8.869	0.000	0.000	0.000	0.000
14	A	15	SER	0	-0.060	-0.050	30.262	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	16	PHE	0	0.025	0.002	26.938	-0.069	-0.069	0.000	0.000	0.000	0.000
16	A	17	THR	0	-0.026	0.003	25.597	-0.306	-0.306	0.000	0.000	0.000	0.000
17	A	18	ALA	0	0.064	0.034	25.131	-0.469	-0.469	0.000	0.000	0.000	0.000
18	A	19	ALA	0	-0.032	0.001	25.711	-0.217	-0.217	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.038	-0.023	21.199	-0.426	-0.426	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.896	-0.957	20.934	-14.211	-14.211	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.819	-0.891	21.895	-13.238	-13.238	0.000	0.000	0.000	0.000
22	A	23	ALA	0	-0.021	-0.022	18.678	-0.310	-0.310	0.000	0.000	0.000	0.000
23	A	24	ILE	0	-0.051	-0.023	16.904	-1.177	-1.177	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.870	-0.928	18.088	-14.868	-14.868	0.000	0.000	0.000	0.000
25	A	26	ARG	1	0.888	0.952	18.906	14.814	14.814	0.000	0.000	0.000	0.000
26	A	27	ALA	0	-0.028	-0.017	14.370	-0.381	-0.381	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.913	-0.971	15.540	-19.808	-19.808	0.000	0.000	0.000	0.000
28	A	29	ASP	-1	-0.941	-0.960	16.858	-14.627	-14.627	0.000	0.000	0.000	0.000
29	A	30	THR	0	-0.193	-0.111	16.747	0.475	0.475	0.000	0.000	0.000	0.000
30	A	31	LEU	0	-0.081	-0.029	10.960	-0.658	-0.658	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.859	-0.931	10.615	-23.579	-23.579	0.000	0.000	0.000	0.000
32	A	33	ASN	0	-0.099	-0.055	6.920	0.146	0.146	0.000	0.000	0.000	0.000
33	A	34	VAL	0	0.049	0.026	8.714	-4.353	-4.353	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.062	-0.024	7.273	0.445	0.445	0.000	0.000	0.000	0.000
35	A	36	TRP	0	-0.109	-0.066	7.135	0.740	0.740	0.000	0.000	0.000	0.000
36	A	37	ALA	0	0.064	0.031	12.794	-0.870	-0.870	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.858	-0.890	12.482	-23.079	-23.079	0.000	0.000	0.000	0.000
38	A	39	VAL	0	0.007	0.003	16.037	0.009	0.009	0.000	0.000	0.000	0.000
39	A	40	VAL	0	-0.102	-0.057	16.503	-0.149	-0.149	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.869	-0.922	19.691	-11.517	-11.517	0.000	0.000	0.000	0.000
41	A	42	GLN	0	-0.070	-0.041	23.062	-0.243	-0.243	0.000	0.000	0.000	0.000
42	A	43	GLY	0	0.008	0.015	26.107	0.346	0.346	0.000	0.000	0.000	0.000
43	A	44	VAL	0	-0.057	-0.038	29.035	-0.075	-0.075	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.818	-0.892	31.509	-8.910	-8.910	0.000	0.000	0.000	0.000
45	A	46	ILE	0	-0.074	-0.064	33.173	0.164	0.164	0.000	0.000	0.000	0.000
46	A	47	GLY	0	-0.034	-0.008	37.004	0.217	0.217	0.000	0.000	0.000	0.000
47	A	48	ALA	0	-0.028	-0.021	35.518	0.062	0.062	0.000	0.000	0.000	0.000
48	A	49	VAL	0	-0.038	-0.002	34.367	-0.045	-0.045	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.976	-0.985	37.807	-7.442	-7.442	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.923	-0.955	37.660	-8.023	-8.023	0.000	0.000	0.000	0.000
51	A	52	ARG	1	0.866	0.924	35.786	7.948	7.948	0.000	0.000	0.000	0.000
52	A	53	THR	0	0.060	0.039	30.286	-0.104	-0.104	0.000	0.000	0.000	0.000
53	A	54	TYR	0	-0.072	-0.030	30.153	0.029	0.029	0.000	0.000	0.000	0.000
54	A	55	GLN	0	0.010	-0.004	26.112	-0.129	-0.129	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.037	-0.042	21.845	0.380	0.380	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.893	-0.934	18.823	-14.880	-14.880	0.000	0.000	0.000	0.000
57	A	58	VAL	0	0.029	-0.002	16.603	-0.083	-0.083	0.000	0.000	0.000	0.000
58	A	59	GLN	0	0.001	-0.002	12.336	-1.433	-1.433	0.000	0.000	0.000	0.000
59	A	60	VAL	0	0.032	0.015	12.696	-0.799	-0.799	0.000	0.000	0.000	0.000
60	A	61	ALA	0	-0.031	-0.019	8.568	-1.320	-1.320	0.000	0.000	0.000	0.000
61	A	62	PHE	0	0.078	0.021	7.612	1.382	1.382	0.000	0.000	0.000	0.000
65	A	66	GLY	0	-0.025	-0.017	5.581	5.889	5.889	0.000	0.000	0.000	0.000
66	A	67	SER	0	-0.036	-0.021	7.928	-1.324	-1.324	0.000	0.000	0.000	0.000
67	A	68	GLN	-1	-0.789	-0.849	6.277	-26.191	-26.191	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:VAL)