FMO DATABASE

FMODB ID: LRR59

Calculation Name: 3E10-B-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin mononucleotide | 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid | 1,2-ethanediol

Ligand 3-letter code: FMN | EPE | EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3E10

Chain ID: B

ChEMBL ID:

UniProt ID: Q97IT9

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	167
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1735001.823353
FMO2-HF: Nuclear repulsion	1667159.56039
FMO2-HF: Total energy	-67842.262963
FMO2-MP2: Total energy	-68039.032707

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(B:1:MET)

Summations of interaction energy for fragment #1(B: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.
28.837	32.687	1.086	-1.293	-3.644	-0.005

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.862 / q_NPA : 0.920

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	B	3	ILE	0	0.044	0.039	2.630	2.530	5.677	1.085	-1.177	-3.056	-0.005
4	B	4	ILE	0	0.049	0.020	4.300	4.789	5.034	-0.001	-0.018	-0.226	0.000
105	B	105	TYR	0	-0.075	-0.034	4.037	-2.567	-2.109	0.002	-0.098	-0.362	0.000
5	B	5	ASN	0	-0.031	-0.016	6.375	6.395	6.395	0.000	0.000	0.000	0.000
6	B	6	ASN	0	-0.009	-0.030	6.365	7.528	7.528	0.000	0.000	0.000	0.000
7	B	7	ARG	1	0.921	0.981	8.067	23.933	23.933	0.000	0.000	0.000	0.000
8	B	8	ARG	1	0.753	0.867	9.819	24.492	24.492	0.000	0.000	0.000	0.000
9	B	9	SER	0	-0.024	-0.011	13.665	0.090	0.090	0.000	0.000	0.000	0.000
10	B	10	ILE	0	-0.022	0.003	14.476	0.919	0.919	0.000	0.000	0.000	0.000
11	B	11	ARG	1	0.932	0.959	17.662	13.800	13.800	0.000	0.000	0.000	0.000
12	B	12	ASN	0	0.049	0.027	20.776	0.862	0.862	0.000	0.000	0.000	0.000
13	B	13	TYR	0	-0.038	-0.020	17.750	-0.562	-0.562	0.000	0.000	0.000	0.000
14	B	14	LYS	1	0.920	0.962	20.118	15.208	15.208	0.000	0.000	0.000	0.000
15	B	15	GLY	0	0.026	0.009	22.849	-0.099	-0.099	0.000	0.000	0.000	0.000
16	B	16	LYS	1	0.813	0.910	19.242	14.623	14.623	0.000	0.000	0.000	0.000
17	B	17	LYS	1	0.946	0.969	21.517	10.626	10.626	0.000	0.000	0.000	0.000
18	B	18	VAL	0	0.030	0.017	16.106	-0.299	-0.299	0.000	0.000	0.000	0.000
19	B	19	GLU	-1	-0.753	-0.840	17.107	-15.152	-15.152	0.000	0.000	0.000	0.000
20	B	20	LYS	1	0.865	0.905	17.548	11.183	11.183	0.000	0.000	0.000	0.000
21	B	21	GLU	-1	-0.815	-0.899	14.818	-16.987	-16.987	0.000	0.000	0.000	0.000
22	B	22	LYS	1	0.825	0.885	12.267	19.670	19.670	0.000	0.000	0.000	0.000
23	B	23	ILE	0	-0.009	-0.009	13.704	-0.532	-0.532	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.820	-0.890	15.824	-14.293	-14.293	0.000	0.000	0.000	0.000
25	B	25	LYS	1	0.874	0.949	10.382	19.674	19.674	0.000	0.000	0.000	0.000
26	B	26	LEU	0	0.005	0.017	11.114	-0.507	-0.507	0.000	0.000	0.000	0.000
27	B	27	LEU	0	0.000	0.005	12.826	0.035	0.035	0.000	0.000	0.000	0.000
28	B	28	ARG	1	0.835	0.886	12.864	15.117	15.117	0.000	0.000	0.000	0.000
29	B	29	ALA	0	0.029	0.014	9.194	0.006	0.006	0.000	0.000	0.000	0.000
30	B	30	ALA	0	-0.009	-0.004	10.743	-0.039	-0.039	0.000	0.000	0.000	0.000
31	B	31	MET	0	-0.053	-0.021	13.698	0.370	0.370	0.000	0.000	0.000	0.000
32	B	32	GLN	0	-0.050	-0.020	10.660	-0.008	-0.008	0.000	0.000	0.000	0.000
33	B	33	ALA	0	-0.012	0.016	11.906	-0.755	-0.755	0.000	0.000	0.000	0.000
34	B	34	PRO	0	-0.013	-0.008	12.835	0.679	0.679	0.000	0.000	0.000	0.000
35	B	35	SER	0	-0.007	-0.009	15.711	0.355	0.355	0.000	0.000	0.000	0.000
36	B	36	ALA	0	0.017	0.002	19.371	0.106	0.106	0.000	0.000	0.000	0.000
37	B	37	GLY	0	0.014	0.000	22.580	0.276	0.276	0.000	0.000	0.000	0.000
38	B	38	ASN	0	-0.026	-0.004	20.513	-0.087	-0.087	0.000	0.000	0.000	0.000
39	B	39	GLN	0	-0.020	-0.027	22.188	0.619	0.619	0.000	0.000	0.000	0.000
40	B	40	GLN	0	-0.046	-0.028	19.574	0.193	0.193	0.000	0.000	0.000	0.000
41	B	41	PRO	0	-0.001	0.013	20.785	0.205	0.205	0.000	0.000	0.000	0.000
42	B	42	TRP	0	0.045	0.005	17.068	0.239	0.239	0.000	0.000	0.000	0.000
43	B	43	GLU	-1	-0.887	-0.944	21.987	-10.028	-10.028	0.000	0.000	0.000	0.000
44	B	44	PHE	0	-0.012	-0.018	17.746	-0.342	-0.342	0.000	0.000	0.000	0.000
45	B	45	ILE	0	-0.002	0.018	22.698	0.300	0.300	0.000	0.000	0.000	0.000
46	B	46	VAL	0	0.003	0.005	20.553	-0.348	-0.348	0.000	0.000	0.000	0.000
47	B	47	LEU	0	-0.023	-0.009	23.088	0.492	0.492	0.000	0.000	0.000	0.000
48	B	48	GLU	-1	-0.763	-0.886	22.713	-12.261	-12.261	0.000	0.000	0.000	0.000
49	B	49	ASP	-1	-0.843	-0.918	25.185	-9.029	-9.029	0.000	0.000	0.000	0.000
50	B	50	ARG	1	0.831	0.890	26.421	10.230	10.230	0.000	0.000	0.000	0.000
51	B	51	GLU	-1	-0.895	-0.919	29.732	-8.328	-8.328	0.000	0.000	0.000	0.000
52	B	52	ASN	0	-0.037	-0.044	30.251	0.102	0.102	0.000	0.000	0.000	0.000
53	B	53	ILE	0	-0.040	-0.011	24.722	-0.068	-0.068	0.000	0.000	0.000	0.000
54	B	54	ASP	-1	-0.838	-0.927	28.095	-9.480	-9.480	0.000	0.000	0.000	0.000
55	B	55	LYS	1	0.997	1.022	30.652	8.227	8.227	0.000	0.000	0.000	0.000
56	B	56	LEU	0	0.034	0.012	25.675	0.090	0.090	0.000	0.000	0.000	0.000
57	B	57	SER	0	-0.069	-0.058	28.495	-0.044	-0.044	0.000	0.000	0.000	0.000
58	B	58	ASN	0	-0.040	-0.022	29.417	0.066	0.066	0.000	0.000	0.000	0.000
59	B	59	PHE	0	-0.008	-0.007	25.518	0.168	0.168	0.000	0.000	0.000	0.000
60	B	60	SER	0	0.056	0.019	27.911	0.122	0.122	0.000	0.000	0.000	0.000
61	B	61	LYS	1	0.965	0.992	30.324	8.720	8.720	0.000	0.000	0.000	0.000
62	B	62	TYR	0	-0.036	-0.031	26.550	0.107	0.107	0.000	0.000	0.000	0.000
63	B	63	ALA	0	0.019	0.019	25.787	-0.481	-0.481	0.000	0.000	0.000	0.000
64	B	64	ASN	0	0.041	0.003	26.514	0.002	0.002	0.000	0.000	0.000	0.000
65	B	65	SER	0	-0.005	0.003	22.153	0.223	0.223	0.000	0.000	0.000	0.000
66	B	66	LEU	0	0.011	-0.001	23.420	-0.266	-0.266	0.000	0.000	0.000	0.000
67	B	67	LYS	1	0.865	0.938	25.251	9.312	9.312	0.000	0.000	0.000	0.000
68	B	68	THR	0	-0.016	-0.017	24.805	0.102	0.102	0.000	0.000	0.000	0.000
69	B	69	ALA	0	-0.028	0.007	22.003	-0.279	-0.279	0.000	0.000	0.000	0.000
70	B	70	PRO	0	-0.063	-0.012	20.592	0.535	0.535	0.000	0.000	0.000	0.000
71	B	71	LEU	0	0.002	-0.003	17.323	0.287	0.287	0.000	0.000	0.000	0.000
72	B	72	ALA	0	0.007	-0.002	20.917	-0.231	-0.231	0.000	0.000	0.000	0.000
73	B	73	ILE	0	0.009	0.005	16.611	0.183	0.183	0.000	0.000	0.000	0.000
74	B	74	VAL	0	-0.003	0.000	20.730	-0.171	-0.171	0.000	0.000	0.000	0.000
75	B	75	LEU	0	0.009	0.000	17.294	-0.085	-0.085	0.000	0.000	0.000	0.000
76	B	76	LEU	0	-0.013	-0.014	21.815	0.371	0.371	0.000	0.000	0.000	0.000
77	B	77	ALA	0	0.054	0.015	23.239	-0.427	-0.427	0.000	0.000	0.000	0.000
78	B	78	ASP	-1	-0.796	-0.882	25.337	-8.684	-8.684	0.000	0.000	0.000	0.000
79	B	79	GLU	-1	-0.830	-0.928	28.261	-8.453	-8.453	0.000	0.000	0.000	0.000
80	B	80	GLU	-1	-0.951	-0.980	30.709	-7.965	-7.965	0.000	0.000	0.000	0.000
81	B	81	LYS	1	0.791	0.898	25.457	9.855	9.855	0.000	0.000	0.000	0.000
82	B	82	MET	0	-0.114	-0.035	25.993	-0.196	-0.196	0.000	0.000	0.000	0.000
83	B	83	LYS	1	0.879	0.945	25.511	10.277	10.277	0.000	0.000	0.000	0.000
84	B	84	ILE	0	0.000	-0.009	25.747	0.180	0.180	0.000	0.000	0.000	0.000
85	B	85	SER	0	0.006	0.002	26.891	-0.246	-0.246	0.000	0.000	0.000	0.000
86	B	86	GLU	-1	-0.865	-0.934	28.177	-9.090	-9.090	0.000	0.000	0.000	0.000
87	B	87	MET	0	-0.037	-0.022	22.410	-0.093	-0.093	0.000	0.000	0.000	0.000
88	B	88	TRP	0	0.030	0.016	23.037	-0.620	-0.620	0.000	0.000	0.000	0.000
89	B	89	GLU	-1	-0.809	-0.915	22.447	-10.580	-10.580	0.000	0.000	0.000	0.000
90	B	90	GLN	0	-0.039	-0.023	20.211	-0.784	-0.784	0.000	0.000	0.000	0.000
91	B	91	ASP	-1	-0.734	-0.856	18.328	-12.735	-12.735	0.000	0.000	0.000	0.000
92	B	92	MET	0	-0.033	-0.005	17.516	-0.675	-0.675	0.000	0.000	0.000	0.000
93	B	93	ALA	0	-0.019	-0.009	17.666	-0.516	-0.516	0.000	0.000	0.000	0.000
94	B	94	ALA	0	-0.019	-0.004	13.971	-0.911	-0.911	0.000	0.000	0.000	0.000
95	B	95	ALA	0	0.026	0.010	12.856	-1.092	-1.092	0.000	0.000	0.000	0.000
96	B	96	ALA	0	-0.020	-0.013	13.738	-0.624	-0.624	0.000	0.000	0.000	0.000
97	B	97	GLU	-1	-0.829	-0.926	9.895	-22.078	-22.078	0.000	0.000	0.000	0.000
98	B	98	ASN	0	-0.017	-0.016	8.945	-2.444	-2.444	0.000	0.000	0.000	0.000
99	B	99	ILE	0	-0.007	0.009	9.319	-1.237	-1.237	0.000	0.000	0.000	0.000
100	B	100	LEU	0	-0.057	-0.031	10.950	-0.518	-0.518	0.000	0.000	0.000	0.000
101	B	101	LEU	0	-0.026	-0.011	5.419	-1.559	-1.559	0.000	0.000	0.000	0.000
102	B	102	GLU	-1	-0.822	-0.921	6.265	-29.051	-29.051	0.000	0.000	0.000	0.000
103	B	103	ALA	0	-0.025	-0.027	7.519	-0.268	-0.268	0.000	0.000	0.000	0.000
104	B	104	ALA	0	-0.031	-0.020	7.603	-0.126	-0.126	0.000	0.000	0.000	0.000
106	B	106	LEU	0	-0.024	0.005	5.868	0.241	0.241	0.000	0.000	0.000	0.000
107	B	107	ASP	-1	-0.919	-0.949	9.226	-23.780	-23.780	0.000	0.000	0.000	0.000
108	B	108	LEU	0	-0.066	-0.027	11.109	2.171	2.171	0.000	0.000	0.000	0.000
109	B	109	GLY	0	0.011	-0.008	12.154	-1.213	-1.213	0.000	0.000	0.000	0.000
110	B	110	ALA	0	0.036	0.007	13.711	0.708	0.708	0.000	0.000	0.000	0.000
111	B	111	VAL	0	-0.052	-0.029	15.548	-0.459	-0.459	0.000	0.000	0.000	0.000
112	B	112	TRP	0	0.059	0.035	15.483	0.275	0.275	0.000	0.000	0.000	0.000
113	B	113	LEU	0	-0.064	-0.024	18.648	0.284	0.284	0.000	0.000	0.000	0.000
114	B	114	GLY	0	0.029	0.012	22.479	0.188	0.188	0.000	0.000	0.000	0.000
115	B	115	ALA	0	-0.007	-0.006	23.698	0.345	0.345	0.000	0.000	0.000	0.000
116	B	116	GLN	0	0.014	0.012	25.652	0.489	0.489	0.000	0.000	0.000	0.000
117	B	117	PRO	0	-0.066	-0.032	26.121	-0.355	-0.355	0.000	0.000	0.000	0.000
118	B	118	ILE	0	-0.031	-0.032	28.877	0.318	0.318	0.000	0.000	0.000	0.000
119	B	119	GLU	-1	-0.885	-0.944	31.354	-7.674	-7.674	0.000	0.000	0.000	0.000
120	B	120	GLU	-1	-0.927	-0.961	33.695	-8.525	-8.525	0.000	0.000	0.000	0.000
121	B	121	ARG	1	0.891	0.953	26.967	9.945	9.945	0.000	0.000	0.000	0.000
122	B	122	VAL	0	0.003	0.004	29.435	-0.102	-0.102	0.000	0.000	0.000	0.000
123	B	123	LYS	1	0.894	0.928	31.435	7.459	7.459	0.000	0.000	0.000	0.000
124	B	124	ASN	0	-0.021	-0.023	32.624	0.231	0.231	0.000	0.000	0.000	0.000
125	B	125	LEU	0	-0.031	-0.020	27.097	0.003	0.003	0.000	0.000	0.000	0.000
126	B	126	LYS	1	0.809	0.906	31.236	8.329	8.329	0.000	0.000	0.000	0.000
127	B	127	GLU	-1	-0.845	-0.898	33.651	-7.388	-7.388	0.000	0.000	0.000	0.000
128	B	128	MET	0	-0.080	-0.029	31.873	0.031	0.031	0.000	0.000	0.000	0.000
129	B	129	PHE	0	-0.023	-0.027	28.432	-0.063	-0.063	0.000	0.000	0.000	0.000
130	B	130	ASN	0	-0.032	-0.003	33.157	0.074	0.074	0.000	0.000	0.000	0.000
131	B	131	LEU	0	-0.026	0.000	30.016	0.027	0.027	0.000	0.000	0.000	0.000
132	B	132	LYS	1	1.007	0.997	32.671	8.441	8.441	0.000	0.000	0.000	0.000
133	B	133	SER	0	0.020	0.000	34.175	-0.148	-0.148	0.000	0.000	0.000	0.000
134	B	134	ASN	0	0.017	0.007	32.140	-0.008	-0.008	0.000	0.000	0.000	0.000
135	B	135	ILE	0	-0.011	0.011	28.592	-0.272	-0.272	0.000	0.000	0.000	0.000
136	B	136	LYS	1	0.893	0.941	27.971	9.029	9.029	0.000	0.000	0.000	0.000
137	B	137	PRO	0	-0.015	-0.012	26.850	-0.380	-0.380	0.000	0.000	0.000	0.000
138	B	138	PHE	0	0.032	0.025	19.394	0.146	0.146	0.000	0.000	0.000	0.000
139	B	139	CYS	0	-0.073	-0.033	19.520	-0.026	-0.026	0.000	0.000	0.000	0.000
140	B	140	VAL	0	0.043	0.038	22.356	0.122	0.122	0.000	0.000	0.000	0.000
141	B	141	ILE	0	0.017	0.010	15.641	-0.297	-0.297	0.000	0.000	0.000	0.000
142	B	142	SER	0	0.004	0.015	19.234	0.396	0.396	0.000	0.000	0.000	0.000
143	B	143	VAL	0	-0.007	-0.017	15.118	-0.717	-0.717	0.000	0.000	0.000	0.000
144	B	144	GLY	0	0.060	0.012	16.947	0.867	0.867	0.000	0.000	0.000	0.000
145	B	145	TYR	0	0.016	-0.010	15.193	-1.089	-1.089	0.000	0.000	0.000	0.000
146	B	146	PRO	0	0.023	0.017	15.241	1.039	1.039	0.000	0.000	0.000	0.000
147	B	147	GLU	-1	-0.918	-0.943	18.276	-12.578	-12.578	0.000	0.000	0.000	0.000
148	B	148	ASN	0	0.025	0.012	21.798	-0.364	-0.364	0.000	0.000	0.000	0.000
149	B	149	SER	0	-0.047	-0.036	18.782	0.325	0.325	0.000	0.000	0.000	0.000
150	B	150	GLU	-1	-0.820	-0.899	14.357	-19.089	-19.089	0.000	0.000	0.000	0.000
151	B	151	ASN	0	-0.008	-0.012	10.276	0.985	0.985	0.000	0.000	0.000	0.000
152	B	152	LYS	1	0.905	0.957	11.077	16.474	16.474	0.000	0.000	0.000	0.000
153	B	153	PHE	0	0.036	0.026	10.974	1.003	1.003	0.000	0.000	0.000	0.000
154	B	154	ILE	0	-0.046	-0.025	12.447	1.739	1.739	0.000	0.000	0.000	0.000
155	B	155	ASP	-1	-0.838	-0.920	14.986	-20.400	-20.400	0.000	0.000	0.000	0.000
156	B	156	ARG	1	0.886	0.936	15.587	18.082	18.082	0.000	0.000	0.000	0.000
157	B	157	PHE	0	0.002	0.014	16.123	0.751	0.751	0.000	0.000	0.000	0.000
158	B	158	ASP	-1	-0.769	-0.863	17.802	-12.049	-12.049	0.000	0.000	0.000	0.000
159	B	159	ALA	0	0.056	0.021	21.450	0.100	0.100	0.000	0.000	0.000	0.000
160	B	160	LYS	1	0.872	0.918	22.788	12.258	12.258	0.000	0.000	0.000	0.000
161	B	161	ARG	1	0.835	0.906	21.232	13.279	13.279	0.000	0.000	0.000	0.000
162	B	162	ILE	0	0.000	0.010	19.764	-0.060	-0.060	0.000	0.000	0.000	0.000
163	B	163	HIS	1	0.774	0.876	23.224	11.516	11.516	0.000	0.000	0.000	0.000
164	B	164	ILE	0	0.040	0.019	24.663	-0.365	-0.365	0.000	0.000	0.000	0.000
165	B	165	GLU	-1	-0.908	-0.947	27.259	-10.750	-10.750	0.000	0.000	0.000	0.000
166	B	166	LYS	1	0.901	0.957	29.107	9.305	9.305	0.000	0.000	0.000	0.000
167	B	167	TYR	-1	-0.846	-0.908	27.865	-10.160	-10.160	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:MET)