FMO DATABASE

FMODB ID: 9RMQ2

Calculation Name: 2BYC-A-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin mononucleotide

Ligand 3-letter code: FMN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2BYC

Chain ID: A

ChEMBL ID:

UniProt ID:

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	137
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1274932.312179
FMO2-HF: Nuclear repulsion	1220670.888083
FMO2-HF: Total energy	-54261.424096
FMO2-MP2: Total energy	-54420.440849

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:0:PHE)

Summations of interaction energy for fragment #1(A:0:PHE)

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.
-71.622	-61.806	2.43	-4.485	-7.76	-0.014

Interaction energy analysis for fragmet #1(A:0:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.877 / q_NPA : 0.929

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	2	ASP	-1	-0.851	-0.926	2.902	-73.636	-67.983	0.194	-2.813	-3.034	-0.019
4	A	3	GLU	-1	-0.873	-0.920	3.470	-37.639	-36.687	0.029	-0.260	-0.721	-0.001
5	A	4	LEU	0	-0.006	0.023	5.034	1.681	1.706	-0.001	-0.008	-0.015	0.000
58	A	57	ARG	1	0.830	0.921	2.939	48.519	51.705	2.208	-1.404	-3.990	0.006
6	A	5	VAL	0	0.024	-0.002	6.693	0.492	0.492	0.000	0.000	0.000	0.000
7	A	6	SER	0	0.063	0.028	9.579	1.711	1.711	0.000	0.000	0.000	0.000
8	A	7	LEU	0	-0.042	-0.015	10.356	-0.768	-0.768	0.000	0.000	0.000	0.000
9	A	8	THR	0	0.015	0.020	12.767	1.060	1.060	0.000	0.000	0.000	0.000
10	A	9	TYR	0	-0.045	-0.032	15.723	0.051	0.051	0.000	0.000	0.000	0.000
11	A	10	ARG	1	0.937	0.981	17.675	11.327	11.327	0.000	0.000	0.000	0.000
12	A	11	SER	0	-0.012	-0.025	21.008	-0.161	-0.161	0.000	0.000	0.000	0.000
13	A	12	ARG	1	0.935	0.967	23.507	9.559	9.559	0.000	0.000	0.000	0.000
14	A	13	VAL	0	-0.052	-0.024	27.242	-0.143	-0.143	0.000	0.000	0.000	0.000
15	A	14	ARG	1	0.880	0.943	29.347	9.733	9.733	0.000	0.000	0.000	0.000
16	A	15	LEU	0	-0.046	-0.012	29.502	-0.051	-0.051	0.000	0.000	0.000	0.000
17	A	16	ALA	0	-0.011	0.005	32.691	0.218	0.218	0.000	0.000	0.000	0.000
18	A	17	ASP	-1	-0.830	-0.925	35.365	-7.752	-7.752	0.000	0.000	0.000	0.000
19	A	18	PRO	0	-0.006	-0.018	34.137	-0.241	-0.241	0.000	0.000	0.000	0.000
20	A	19	VAL	0	0.005	0.007	34.036	-0.272	-0.272	0.000	0.000	0.000	0.000
21	A	20	ALA	0	0.030	0.020	35.184	-0.213	-0.213	0.000	0.000	0.000	0.000
22	A	21	ASP	-1	-0.831	-0.923	31.071	-9.453	-9.453	0.000	0.000	0.000	0.000
23	A	22	ILE	0	0.014	0.006	29.960	-0.409	-0.409	0.000	0.000	0.000	0.000
24	A	23	VAL	0	-0.019	-0.002	30.421	-0.338	-0.338	0.000	0.000	0.000	0.000
25	A	24	GLN	0	-0.069	-0.051	30.102	-0.340	-0.340	0.000	0.000	0.000	0.000
26	A	25	ILE	0	0.035	0.024	25.054	-0.355	-0.355	0.000	0.000	0.000	0.000
27	A	26	MET	0	0.003	0.024	26.050	-0.583	-0.583	0.000	0.000	0.000	0.000
28	A	27	ARG	1	0.914	0.961	27.452	9.324	9.324	0.000	0.000	0.000	0.000
29	A	28	ALA	0	-0.022	-0.011	25.112	-0.219	-0.219	0.000	0.000	0.000	0.000
30	A	29	SER	0	0.003	-0.018	22.592	-0.503	-0.503	0.000	0.000	0.000	0.000
31	A	30	ARG	1	0.983	1.004	22.825	10.592	10.592	0.000	0.000	0.000	0.000
32	A	31	VAL	0	0.015	-0.003	23.709	-0.307	-0.307	0.000	0.000	0.000	0.000
33	A	32	ARG	1	0.881	0.953	18.995	14.320	14.320	0.000	0.000	0.000	0.000
34	A	33	ASN	0	0.040	-0.006	18.425	-0.759	-0.759	0.000	0.000	0.000	0.000
35	A	34	LEU	0	0.028	0.026	17.738	-0.872	-0.872	0.000	0.000	0.000	0.000
36	A	35	ARG	1	0.927	0.964	18.320	14.799	14.799	0.000	0.000	0.000	0.000
37	A	36	LEU	0	-0.023	-0.002	14.865	-0.398	-0.398	0.000	0.000	0.000	0.000
38	A	37	GLY	0	0.025	0.028	13.480	-1.780	-1.780	0.000	0.000	0.000	0.000
39	A	38	ILE	0	-0.073	-0.037	13.282	-1.213	-1.213	0.000	0.000	0.000	0.000
40	A	39	THR	0	-0.026	0.000	15.874	0.592	0.592	0.000	0.000	0.000	0.000
41	A	40	GLY	0	0.032	-0.005	17.881	-0.831	-0.831	0.000	0.000	0.000	0.000
42	A	41	ILE	0	-0.027	-0.004	20.154	0.782	0.782	0.000	0.000	0.000	0.000
43	A	42	LEU	0	0.000	-0.008	21.739	-0.357	-0.357	0.000	0.000	0.000	0.000
44	A	43	LEU	0	0.025	0.021	23.400	0.554	0.554	0.000	0.000	0.000	0.000
45	A	44	TYR	0	0.029	0.006	26.294	0.093	0.093	0.000	0.000	0.000	0.000
46	A	45	ASN	0	0.061	0.019	29.057	0.316	0.316	0.000	0.000	0.000	0.000
47	A	46	GLY	0	-0.086	-0.036	31.386	0.379	0.379	0.000	0.000	0.000	0.000
48	A	47	VAL	0	-0.002	0.011	31.344	0.167	0.167	0.000	0.000	0.000	0.000
49	A	48	HIS	0	0.007	-0.006	26.545	-0.077	-0.077	0.000	0.000	0.000	0.000
50	A	49	PHE	0	0.007	-0.002	24.290	0.272	0.272	0.000	0.000	0.000	0.000
51	A	50	VAL	0	0.021	0.012	21.100	-0.109	-0.109	0.000	0.000	0.000	0.000
52	A	51	GLN	0	-0.006	-0.010	19.606	0.164	0.164	0.000	0.000	0.000	0.000
53	A	52	THR	0	0.022	0.030	16.416	-0.061	-0.061	0.000	0.000	0.000	0.000
54	A	53	ILE	0	-0.036	-0.017	13.723	0.603	0.603	0.000	0.000	0.000	0.000
55	A	54	GLU	-1	-0.698	-0.840	13.556	-19.053	-19.053	0.000	0.000	0.000	0.000
56	A	55	GLY	0	0.042	0.004	11.955	1.537	1.537	0.000	0.000	0.000	0.000
57	A	56	PRO	0	0.022	0.028	7.512	-1.759	-1.759	0.000	0.000	0.000	0.000
59	A	58	SER	0	-0.010	-0.014	6.432	2.833	2.833	0.000	0.000	0.000	0.000
60	A	59	ALA	0	0.059	0.035	7.641	2.946	2.946	0.000	0.000	0.000	0.000
61	A	60	CYS	0	-0.036	-0.013	9.586	2.889	2.889	0.000	0.000	0.000	0.000
62	A	61	ASP	-1	-0.846	-0.897	7.304	-23.789	-23.789	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.948	-0.980	9.436	-18.992	-18.992	0.000	0.000	0.000	0.000
64	A	63	LEU	0	-0.023	-0.015	12.132	1.748	1.748	0.000	0.000	0.000	0.000
65	A	64	PHE	0	0.032	0.015	12.330	1.343	1.343	0.000	0.000	0.000	0.000
66	A	65	ARG	1	0.839	0.911	8.454	23.603	23.603	0.000	0.000	0.000	0.000
67	A	66	LEU	0	-0.028	-0.023	14.814	1.158	1.158	0.000	0.000	0.000	0.000
68	A	67	ILE	0	-0.009	0.002	17.410	0.877	0.877	0.000	0.000	0.000	0.000
69	A	68	SER	0	-0.029	-0.025	16.280	0.814	0.814	0.000	0.000	0.000	0.000
70	A	69	ALA	0	-0.037	-0.006	18.746	0.454	0.454	0.000	0.000	0.000	0.000
71	A	70	ASP	-1	-0.810	-0.866	21.107	-10.842	-10.842	0.000	0.000	0.000	0.000
72	A	71	PRO	0	-0.015	-0.019	23.850	0.140	0.140	0.000	0.000	0.000	0.000
73	A	72	ARG	1	0.818	0.884	26.269	11.041	11.041	0.000	0.000	0.000	0.000
74	A	73	HIS	0	-0.020	0.002	21.316	0.402	0.402	0.000	0.000	0.000	0.000
75	A	74	GLN	0	-0.013	-0.011	24.974	0.103	0.103	0.000	0.000	0.000	0.000
76	A	75	GLU	-1	-0.924	-0.977	23.901	-10.021	-10.021	0.000	0.000	0.000	0.000
77	A	76	ILE	0	-0.006	0.010	18.238	-0.057	-0.057	0.000	0.000	0.000	0.000
78	A	77	LEU	0	-0.014	-0.001	17.383	-0.208	-0.208	0.000	0.000	0.000	0.000
79	A	78	ALA	0	-0.014	-0.012	13.574	0.139	0.139	0.000	0.000	0.000	0.000
80	A	79	PHE	0	-0.027	-0.009	15.621	0.494	0.494	0.000	0.000	0.000	0.000
81	A	80	ASP	-1	-0.841	-0.943	13.075	-17.709	-17.709	0.000	0.000	0.000	0.000
82	A	81	LEU	0	-0.025	-0.029	5.974	-0.497	-0.497	0.000	0.000	0.000	0.000
83	A	82	GLU	-1	-0.827	-0.887	9.020	-20.184	-20.184	0.000	0.000	0.000	0.000
84	A	83	PRO	0	-0.035	-0.029	5.757	-0.627	-0.627	0.000	0.000	0.000	0.000
85	A	84	ILE	0	-0.022	0.004	8.338	2.332	2.332	0.000	0.000	0.000	0.000
86	A	85	THR	0	-0.017	-0.015	10.972	-1.139	-1.139	0.000	0.000	0.000	0.000
87	A	86	ALA	0	-0.005	-0.016	12.963	-0.254	-0.254	0.000	0.000	0.000	0.000
88	A	87	ARG	1	0.792	0.887	13.157	20.988	20.988	0.000	0.000	0.000	0.000
89	A	88	ARG	1	0.859	0.906	15.302	18.189	18.189	0.000	0.000	0.000	0.000
90	A	89	PHE	0	-0.044	-0.039	19.052	1.060	1.060	0.000	0.000	0.000	0.000
91	A	90	PRO	0	0.004	-0.007	18.933	-0.260	-0.260	0.000	0.000	0.000	0.000
92	A	91	ASP	-1	-0.864	-0.922	19.954	-13.572	-13.572	0.000	0.000	0.000	0.000
93	A	92	TRP	0	-0.017	-0.017	22.020	0.644	0.644	0.000	0.000	0.000	0.000
94	A	93	SER	0	-0.033	-0.021	20.619	-0.690	-0.690	0.000	0.000	0.000	0.000
95	A	94	MET	0	0.005	0.029	20.221	-0.405	-0.405	0.000	0.000	0.000	0.000
96	A	95	ARG	1	0.769	0.871	23.652	11.193	11.193	0.000	0.000	0.000	0.000
97	A	96	ILE	0	-0.007	-0.003	25.722	-0.162	-0.162	0.000	0.000	0.000	0.000
98	A	97	VAL	0	0.037	0.029	27.317	0.181	0.181	0.000	0.000	0.000	0.000
99	A	98	SER	0	0.009	0.002	29.362	0.070	0.070	0.000	0.000	0.000	0.000
100	A	99	ARG	1	0.990	0.963	32.111	8.529	8.529	0.000	0.000	0.000	0.000
101	A	100	LYS	1	0.893	0.956	34.243	7.784	7.784	0.000	0.000	0.000	0.000
102	A	101	GLU	-1	-0.757	-0.839	31.798	-9.813	-9.813	0.000	0.000	0.000	0.000
103	A	102	LEU	0	0.049	0.020	29.025	0.019	0.019	0.000	0.000	0.000	0.000
104	A	103	ARG	1	0.881	0.932	32.318	8.025	8.025	0.000	0.000	0.000	0.000
105	A	104	ALA	0	-0.040	-0.013	35.655	0.151	0.151	0.000	0.000	0.000	0.000
106	A	105	LEU	0	-0.041	-0.014	29.988	0.050	0.050	0.000	0.000	0.000	0.000
107	A	106	ALA	0	0.020	0.009	29.888	-0.111	-0.111	0.000	0.000	0.000	0.000
108	A	107	PRO	0	0.008	0.012	31.890	-0.049	-0.049	0.000	0.000	0.000	0.000
109	A	108	ASP	-1	-0.904	-0.953	33.025	-8.437	-8.437	0.000	0.000	0.000	0.000
110	A	109	LEU	0	0.001	0.004	27.505	-0.077	-0.077	0.000	0.000	0.000	0.000
111	A	110	GLU	-1	-0.943	-0.969	29.740	-8.544	-8.544	0.000	0.000	0.000	0.000
112	A	111	ARG	1	0.989	0.982	31.380	8.130	8.130	0.000	0.000	0.000	0.000
113	A	112	LEU	0	-0.057	-0.027	26.025	-0.090	-0.090	0.000	0.000	0.000	0.000
114	A	113	ASP	-1	-0.871	-0.965	26.224	-9.768	-9.768	0.000	0.000	0.000	0.000
115	A	114	LEU	0	-0.084	-0.032	20.828	-0.113	-0.113	0.000	0.000	0.000	0.000
116	A	115	SER	0	-0.016	0.003	23.892	-0.068	-0.068	0.000	0.000	0.000	0.000
117	A	116	GLY	0	0.008	0.011	26.544	0.159	0.159	0.000	0.000	0.000	0.000
118	A	117	PRO	0	-0.035	-0.035	23.042	-0.335	-0.335	0.000	0.000	0.000	0.000
119	A	118	GLU	-1	-0.901	-0.947	21.809	-12.317	-12.317	0.000	0.000	0.000	0.000
120	A	119	ASP	-1	-0.826	-0.907	23.581	-10.673	-10.673	0.000	0.000	0.000	0.000
121	A	120	VAL	0	0.002	-0.008	18.416	0.154	0.154	0.000	0.000	0.000	0.000
122	A	121	ALA	0	0.041	0.029	20.752	-0.212	-0.212	0.000	0.000	0.000	0.000
123	A	122	GLU	-1	-0.812	-0.873	21.906	-10.238	-10.238	0.000	0.000	0.000	0.000
124	A	123	LEU	0	-0.017	-0.005	23.932	0.203	0.203	0.000	0.000	0.000	0.000
125	A	124	HIS	0	-0.013	-0.026	17.323	-0.024	-0.024	0.000	0.000	0.000	0.000
126	A	125	ARG	1	0.847	0.899	22.839	10.807	10.807	0.000	0.000	0.000	0.000
127	A	126	THR	0	-0.048	-0.041	25.231	0.219	0.219	0.000	0.000	0.000	0.000
128	A	127	ILE	0	-0.015	-0.013	25.420	0.280	0.280	0.000	0.000	0.000	0.000
129	A	128	ALA	0	0.021	0.005	23.371	0.156	0.156	0.000	0.000	0.000	0.000
130	A	129	ALA	0	0.036	0.042	25.491	0.074	0.074	0.000	0.000	0.000	0.000
131	A	130	SER	0	-0.090	-0.023	28.719	0.552	0.552	0.000	0.000	0.000	0.000
132	A	131	LEU	0	-0.004	-0.009	25.747	0.222	0.222	0.000	0.000	0.000	0.000
133	A	132	SER	0	0.036	0.018	26.669	-0.028	-0.028	0.000	0.000	0.000	0.000
134	A	133	ARG	1	0.779	0.855	28.645	9.751	9.751	0.000	0.000	0.000	0.000
135	A	134	GLY	0	-0.055	-0.025	31.822	0.356	0.356	0.000	0.000	0.000	0.000
136	A	135	ASP	-1	-0.919	-0.945	27.980	-11.237	-11.237	0.000	0.000	0.000	0.000
137	A	136	ALA	-1	-0.964	-0.974	29.330	-9.535	-9.535	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:PHE)