FMO DATABASE

FMODB ID: VY4R1

Calculation Name: 6EBQ-A-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin mononucleotide

Ligand 3-letter code: FMN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6EBQ

Chain ID: A

ChEMBL ID:

UniProt ID: F2I8Y0

Base Structure: X-ray

Registration Date: 2025-10-06

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	138
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1248253.869362
FMO2-HF: Nuclear repulsion	1195057.192166
FMO2-HF: Total energy	-53196.677196
FMO2-MP2: Total energy	-53355.292858

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:3:GLU)

Summations of interaction energy for fragment #1(A:3:GLU)

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.
-56.392	-54.588	32.192	-15.334	-18.662	0.061

Interaction energy analysis for fragmet #1(A:3:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.003

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 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	5	ILE	0	0.010	0.014	3.841	3.224	5.190	-0.021	-0.882	-1.063	0.000
21	A	23	ASP	-1	-0.881	-0.942	4.537	11.688	11.783	-0.001	-0.010	-0.083	0.000
22	A	24	ALA	0	-0.060	-0.018	2.729	-6.565	-4.626	1.293	-1.276	-1.957	0.012
23	A	25	GLU	-1	-0.913	-0.954	3.753	-14.038	-13.740	0.003	-0.020	-0.281	0.000
129	A	131	ASN	0	0.017	0.013	4.936	1.510	1.619	-0.001	-0.002	-0.106	0.000
130	A	132	ARG	1	0.799	0.885	4.629	0.093	0.254	-0.001	-0.002	-0.158	0.000
132	A	134	ILE	0	-0.040	-0.009	2.549	-6.986	-5.298	1.469	-1.316	-1.841	0.015
133	A	135	SER	0	0.013	-0.029	1.640	-23.440	-30.895	22.121	-8.954	-5.712	0.074
134	A	136	GLU	-1	-0.945	-0.967	3.210	0.255	-1.275	0.132	2.016	-0.619	0.007
136	A	138	PHE	0	-0.019	-0.018	2.263	-18.290	-13.948	7.199	-4.857	-6.683	-0.047
137	A	139	ASN	0	-0.076	-0.026	4.215	-4.166	-3.975	-0.001	-0.031	-0.159	0.000
4	A	6	VAL	0	0.009	0.017	6.564	-0.614	-0.614	0.000	0.000	0.000	0.000
5	A	7	TYR	0	0.028	-0.015	10.270	1.036	1.036	0.000	0.000	0.000	0.000
6	A	8	PHE	0	0.021	0.013	12.718	-0.207	-0.207	0.000	0.000	0.000	0.000
7	A	9	SER	0	0.012	-0.015	16.515	0.392	0.392	0.000	0.000	0.000	0.000
8	A	10	THR	0	0.024	0.034	18.961	-0.119	-0.119	0.000	0.000	0.000	0.000
9	A	11	GLN	0	0.103	0.029	22.149	0.085	0.085	0.000	0.000	0.000	0.000
10	A	12	SER	0	-0.039	-0.008	23.694	0.070	0.070	0.000	0.000	0.000	0.000
11	A	13	ASN	0	-0.009	-0.017	20.385	0.033	0.033	0.000	0.000	0.000	0.000
12	A	14	ASN	0	-0.009	0.013	19.585	0.133	0.133	0.000	0.000	0.000	0.000
13	A	15	THR	0	0.133	0.048	14.611	0.240	0.240	0.000	0.000	0.000	0.000
14	A	16	HIS	0	0.033	0.048	14.847	0.109	0.109	0.000	0.000	0.000	0.000
15	A	17	ARG	1	0.882	0.931	15.169	-0.682	-0.682	0.000	0.000	0.000	0.000
16	A	18	PHE	0	-0.004	0.006	11.334	0.027	0.027	0.000	0.000	0.000	0.000
17	A	19	VAL	0	0.047	0.011	9.447	0.532	0.532	0.000	0.000	0.000	0.000
18	A	20	GLN	0	-0.055	-0.034	10.516	0.013	0.013	0.000	0.000	0.000	0.000
19	A	21	LYS	1	0.734	0.883	11.861	-3.010	-3.010	0.000	0.000	0.000	0.000
20	A	22	LEU	0	-0.019	0.006	6.646	0.323	0.323	0.000	0.000	0.000	0.000
24	A	26	SER	0	0.006	-0.013	5.827	-0.414	-0.414	0.000	0.000	0.000	0.000
25	A	27	ILE	0	0.012	0.014	8.587	0.555	0.555	0.000	0.000	0.000	0.000
26	A	28	ARG	1	0.799	0.890	11.610	0.992	0.992	0.000	0.000	0.000	0.000
27	A	29	ILE	0	0.003	-0.007	14.706	-0.113	-0.113	0.000	0.000	0.000	0.000
28	A	30	PRO	0	0.006	0.010	17.032	0.259	0.259	0.000	0.000	0.000	0.000
29	A	31	ILE	0	-0.033	-0.029	20.543	0.127	0.127	0.000	0.000	0.000	0.000
30	A	32	ASP	-1	-0.846	-0.915	23.155	-0.709	-0.709	0.000	0.000	0.000	0.000
31	A	33	GLU	-1	-0.784	-0.877	24.559	-0.639	-0.639	0.000	0.000	0.000	0.000
32	A	34	GLU	-1	-0.920	-0.944	26.513	-0.824	-0.824	0.000	0.000	0.000	0.000
33	A	35	GLU	-1	-0.959	-0.966	22.906	-1.338	-1.338	0.000	0.000	0.000	0.000
34	A	36	ARG	1	0.787	0.864	21.291	1.202	1.202	0.000	0.000	0.000	0.000
35	A	37	ILE	0	-0.004	0.007	14.434	-0.013	-0.013	0.000	0.000	0.000	0.000
36	A	38	LYS	1	0.797	0.877	16.432	2.619	2.619	0.000	0.000	0.000	0.000
37	A	39	VAL	0	-0.016	-0.013	10.213	-0.089	-0.089	0.000	0.000	0.000	0.000
38	A	40	ASP	-1	-0.888	-0.945	11.809	-4.585	-4.585	0.000	0.000	0.000	0.000
39	A	41	GLU	-1	-0.910	-0.940	6.660	-10.117	-10.117	0.000	0.000	0.000	0.000
40	A	42	ASP	-1	-0.832	-0.903	6.444	-5.931	-5.931	0.000	0.000	0.000	0.000
41	A	43	TYR	0	-0.070	-0.071	5.412	-3.562	-3.562	0.000	0.000	0.000	0.000
42	A	44	VAL	0	0.035	0.032	5.929	1.943	1.943	0.000	0.000	0.000	0.000
43	A	45	LEU	0	-0.038	-0.021	7.596	-0.222	-0.222	0.000	0.000	0.000	0.000
44	A	46	ILE	0	0.035	0.010	8.059	0.690	0.690	0.000	0.000	0.000	0.000
45	A	47	VAL	0	-0.015	-0.027	12.129	-0.332	-0.332	0.000	0.000	0.000	0.000
46	A	48	PRO	0	-0.030	0.001	15.958	0.195	0.195	0.000	0.000	0.000	0.000
47	A	49	THR	0	-0.021	-0.019	19.301	-0.183	-0.183	0.000	0.000	0.000	0.000
48	A	50	TYR	0	-0.027	-0.019	22.268	0.046	0.046	0.000	0.000	0.000	0.000
49	A	51	SER	0	0.003	0.023	25.516	-0.025	-0.025	0.000	0.000	0.000	0.000
50	A	52	GLY	0	0.000	-0.004	28.125	-0.022	-0.022	0.000	0.000	0.000	0.000
51	A	53	GLY	0	0.008	0.002	29.725	0.007	0.007	0.000	0.000	0.000	0.000
52	A	54	LYS	1	0.797	0.910	31.128	-0.103	-0.103	0.000	0.000	0.000	0.000
53	A	55	VAL	0	0.025	0.010	33.267	0.027	0.027	0.000	0.000	0.000	0.000
54	A	56	THR	0	-0.004	-0.005	35.969	-0.023	-0.023	0.000	0.000	0.000	0.000
55	A	57	ASP	-1	-0.894	-0.951	38.315	0.108	0.108	0.000	0.000	0.000	0.000
56	A	58	ALA	0	-0.071	-0.032	40.238	0.006	0.006	0.000	0.000	0.000	0.000
57	A	59	GLY	0	-0.004	0.000	39.282	0.018	0.018	0.000	0.000	0.000	0.000
58	A	60	GLN	0	-0.031	-0.007	34.524	0.008	0.008	0.000	0.000	0.000	0.000
59	A	61	VAL	0	0.026	0.014	29.464	-0.027	-0.027	0.000	0.000	0.000	0.000
60	A	62	ASP	-1	-0.860	-0.930	32.730	0.032	0.032	0.000	0.000	0.000	0.000
61	A	63	ALA	0	0.009	-0.010	27.312	0.016	0.016	0.000	0.000	0.000	0.000
62	A	64	HIS	0	0.023	0.009	27.977	-0.045	-0.045	0.000	0.000	0.000	0.000
63	A	65	GLY	0	0.001	-0.008	27.679	0.041	0.041	0.000	0.000	0.000	0.000
64	A	66	ALA	0	-0.011	0.001	24.254	0.014	0.014	0.000	0.000	0.000	0.000
65	A	67	VAL	0	0.022	0.010	20.223	0.064	0.064	0.000	0.000	0.000	0.000
66	A	68	PRO	0	0.021	0.010	20.599	-0.050	-0.050	0.000	0.000	0.000	0.000
67	A	69	LYS	1	0.868	0.914	22.558	0.383	0.383	0.000	0.000	0.000	0.000
68	A	70	GLN	0	0.041	0.016	21.475	-0.026	-0.026	0.000	0.000	0.000	0.000
69	A	71	VAL	0	0.007	0.011	17.305	-0.185	-0.185	0.000	0.000	0.000	0.000
70	A	72	ILE	0	-0.041	-0.019	19.641	-0.131	-0.131	0.000	0.000	0.000	0.000
71	A	73	HIS	0	-0.060	-0.053	22.131	-0.137	-0.137	0.000	0.000	0.000	0.000
72	A	74	PHE	0	-0.002	0.011	12.929	0.026	0.026	0.000	0.000	0.000	0.000
73	A	75	LEU	0	0.050	0.019	15.417	-0.181	-0.181	0.000	0.000	0.000	0.000
74	A	76	ASN	0	-0.013	-0.010	18.913	0.057	0.057	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-0.801	-0.872	19.122	-2.139	-2.139	0.000	0.000	0.000	0.000
76	A	78	PRO	0	-0.030	-0.024	18.775	-0.105	-0.105	0.000	0.000	0.000	0.000
77	A	79	ASP	-1	-0.821	-0.907	17.126	-2.623	-2.623	0.000	0.000	0.000	0.000
78	A	80	ASN	0	0.039	0.017	14.358	-0.816	-0.816	0.000	0.000	0.000	0.000
79	A	81	ARG	1	0.843	0.929	13.783	1.153	1.153	0.000	0.000	0.000	0.000
80	A	82	LYS	1	0.795	0.898	14.627	3.126	3.126	0.000	0.000	0.000	0.000
81	A	83	HIS	1	0.812	0.894	10.199	6.168	6.168	0.000	0.000	0.000	0.000
82	A	84	CYS	0	-0.062	0.001	9.445	-0.712	-0.712	0.000	0.000	0.000	0.000
83	A	85	LEU	0	0.093	0.037	6.006	0.622	0.622	0.000	0.000	0.000	0.000
84	A	86	GLY	0	-0.005	-0.008	9.604	0.994	0.994	0.000	0.000	0.000	0.000
85	A	87	VAL	0	-0.074	-0.028	10.703	-0.439	-0.439	0.000	0.000	0.000	0.000
86	A	88	ILE	0	0.029	0.027	9.303	0.422	0.422	0.000	0.000	0.000	0.000
87	A	89	SER	0	-0.043	-0.039	13.123	-0.365	-0.365	0.000	0.000	0.000	0.000
88	A	90	SER	0	0.013	0.013	16.393	0.190	0.190	0.000	0.000	0.000	0.000
89	A	91	GLY	0	0.020	-0.009	18.502	-0.244	-0.244	0.000	0.000	0.000	0.000
90	A	92	ASN	0	-0.012	-0.009	22.237	0.083	0.083	0.000	0.000	0.000	0.000
91	A	93	THR	0	0.063	0.001	24.304	-0.107	-0.107	0.000	0.000	0.000	0.000
92	A	94	ASN	0	-0.050	-0.024	26.693	-0.053	-0.053	0.000	0.000	0.000	0.000
93	A	95	PHE	0	-0.057	-0.021	27.022	-0.068	-0.068	0.000	0.000	0.000	0.000
94	A	96	GLY	0	0.040	0.025	29.741	-0.048	-0.048	0.000	0.000	0.000	0.000
95	A	97	ASP	-1	-0.881	-0.944	28.171	0.645	0.645	0.000	0.000	0.000	0.000
96	A	98	SER	0	-0.051	-0.034	27.538	-0.055	-0.055	0.000	0.000	0.000	0.000
97	A	99	PHE	0	-0.041	-0.023	20.411	-0.048	-0.048	0.000	0.000	0.000	0.000
98	A	100	ALA	0	-0.007	0.010	19.654	0.009	0.009	0.000	0.000	0.000	0.000
99	A	101	ILE	0	0.057	0.036	20.502	-0.025	-0.025	0.000	0.000	0.000	0.000
100	A	102	ALA	0	-0.001	-0.007	19.676	-0.102	-0.102	0.000	0.000	0.000	0.000
101	A	103	GLY	0	0.036	0.018	17.436	-0.146	-0.146	0.000	0.000	0.000	0.000
102	A	104	PRO	0	0.030	0.011	18.247	-0.148	-0.148	0.000	0.000	0.000	0.000
103	A	105	VAL	0	-0.032	-0.003	21.050	-0.112	-0.112	0.000	0.000	0.000	0.000
104	A	106	ILE	0	-0.004	-0.005	16.268	-0.141	-0.141	0.000	0.000	0.000	0.000
105	A	107	SER	0	-0.038	-0.014	17.617	-0.123	-0.123	0.000	0.000	0.000	0.000
106	A	108	TYR	0	0.025	0.002	18.630	-0.140	-0.140	0.000	0.000	0.000	0.000
107	A	109	LYS	1	0.926	0.961	21.464	0.477	0.477	0.000	0.000	0.000	0.000
108	A	110	LEU	0	-0.019	-0.029	15.432	-0.061	-0.061	0.000	0.000	0.000	0.000
109	A	111	LYS	1	0.806	0.918	18.227	0.119	0.119	0.000	0.000	0.000	0.000
110	A	112	VAL	0	0.054	0.054	13.683	0.019	0.019	0.000	0.000	0.000	0.000
111	A	113	PRO	0	0.037	0.026	12.650	0.142	0.142	0.000	0.000	0.000	0.000
112	A	114	LEU	0	-0.022	-0.014	13.926	-0.099	-0.099	0.000	0.000	0.000	0.000
113	A	115	LEU	0	-0.014	0.004	9.002	0.018	0.018	0.000	0.000	0.000	0.000
114	A	116	TYR	0	0.011	-0.024	12.045	0.574	0.574	0.000	0.000	0.000	0.000
115	A	117	GLN	0	-0.037	-0.027	14.032	-0.680	-0.680	0.000	0.000	0.000	0.000
116	A	118	PHE	0	0.027	0.026	14.019	0.153	0.153	0.000	0.000	0.000	0.000
117	A	119	GLU	-1	-0.780	-0.880	17.557	0.939	0.939	0.000	0.000	0.000	0.000
118	A	120	LEU	0	-0.054	-0.042	19.321	0.126	0.126	0.000	0.000	0.000	0.000
119	A	121	ILE	0	-0.010	-0.001	17.924	-0.100	-0.100	0.000	0.000	0.000	0.000
120	A	122	GLY	0	0.026	0.032	15.780	0.257	0.257	0.000	0.000	0.000	0.000
121	A	123	THR	0	-0.053	-0.052	16.863	-0.045	-0.045	0.000	0.000	0.000	0.000
122	A	124	LYS	1	0.909	0.944	15.574	-2.535	-2.535	0.000	0.000	0.000	0.000
123	A	125	GLU	-1	-0.771	-0.897	14.116	3.515	3.515	0.000	0.000	0.000	0.000
124	A	126	ASP	-1	-0.769	-0.852	13.544	3.600	3.600	0.000	0.000	0.000	0.000
125	A	127	VAL	0	-0.050	-0.025	10.102	0.338	0.338	0.000	0.000	0.000	0.000
126	A	128	GLU	-1	-0.948	-0.961	9.223	7.135	7.135	0.000	0.000	0.000	0.000
127	A	129	GLU	-1	-0.839	-0.906	9.383	7.472	7.472	0.000	0.000	0.000	0.000
128	A	130	VAL	0	-0.036	-0.024	7.580	0.684	0.684	0.000	0.000	0.000	0.000
131	A	133	ILE	0	0.003	-0.002	6.539	1.226	1.226	0.000	0.000	0.000	0.000
135	A	137	THR	0	-0.080	-0.055	6.133	-3.249	-3.249	0.000	0.000	0.000	0.000
138	A	140	ALA	-1	-0.974	-0.960	6.613	-2.125	-2.125	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLU)