FMO DATABASE

FMODB ID: 159MZ

Calculation Name: 1BVY-F-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | flavin mononucleotide | 1,2-ethanediol

Ligand 3-letter code: HEM | FMN | EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1BVY

Chain ID: F

ChEMBL ID:

UniProt ID: P14779

Base Structure: X-ray

Registration Date: 2025-09-02

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	152
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1407641.85553
FMO2-HF: Nuclear repulsion	1349567.431277
FMO2-HF: Total energy	-58074.424253
FMO2-MP2: Total energy	-58244.014752

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:479:ASN)

Summations of interaction energy for fragment #1(A:479:ASN)

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.
-267.484	-261.5	10.222	-8.742	-7.464	-0.072

Interaction energy analysis for fragmet #1(A:479:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.815 / q_NPA : 0.899

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	481	PRO	0	0.051	0.007	3.847	-0.551	0.915	-0.013	-0.549	-0.905	0.001
30	A	508	GLY	0	-0.010	0.014	4.294	-3.926	-3.677	-0.001	-0.103	-0.145	0.000
31	A	509	PHE	0	-0.003	-0.016	2.081	-42.013	-39.333	9.100	-7.197	-4.582	-0.064
32	A	510	ALA	0	-0.070	-0.044	2.217	-2.826	-1.365	1.133	-0.836	-1.758	-0.009
33	A	511	PRO	0	0.009	0.012	3.963	4.222	4.302	0.004	-0.047	-0.037	0.000
151	A	629	ASN	0	-0.083	-0.052	4.400	-1.249	-1.201	-0.001	-0.010	-0.037	0.000
4	A	482	LEU	0	0.033	0.025	6.177	2.705	2.705	0.000	0.000	0.000	0.000
5	A	483	LEU	0	-0.052	-0.012	8.341	1.177	1.177	0.000	0.000	0.000	0.000
6	A	484	VAL	0	0.032	0.019	11.611	0.683	0.683	0.000	0.000	0.000	0.000
7	A	485	LEU	0	-0.030	-0.013	14.092	0.772	0.772	0.000	0.000	0.000	0.000
8	A	486	TYR	0	0.012	-0.003	17.634	0.283	0.283	0.000	0.000	0.000	0.000
9	A	487	GLY	0	0.028	0.021	20.589	0.324	0.324	0.000	0.000	0.000	0.000
10	A	488	SER	0	-0.030	-0.049	24.332	0.219	0.219	0.000	0.000	0.000	0.000
11	A	489	ASN	0	0.059	0.048	26.289	-0.314	-0.314	0.000	0.000	0.000	0.000
12	A	490	MET	0	-0.020	-0.006	28.916	0.247	0.247	0.000	0.000	0.000	0.000
13	A	491	GLY	0	0.051	0.043	25.482	0.065	0.065	0.000	0.000	0.000	0.000
14	A	492	THR	0	0.025	0.010	24.315	-0.490	-0.490	0.000	0.000	0.000	0.000
15	A	493	ALA	0	0.051	0.029	22.824	-0.401	-0.401	0.000	0.000	0.000	0.000
16	A	494	GLU	-1	-0.846	-0.893	20.633	-14.500	-14.500	0.000	0.000	0.000	0.000
17	A	495	GLY	0	-0.011	-0.016	19.580	-0.775	-0.775	0.000	0.000	0.000	0.000
18	A	496	THR	0	0.024	0.009	19.273	-0.572	-0.572	0.000	0.000	0.000	0.000
19	A	497	ALA	0	0.001	-0.002	16.643	-0.919	-0.919	0.000	0.000	0.000	0.000
20	A	498	ARG	1	0.790	0.863	14.999	14.739	14.739	0.000	0.000	0.000	0.000
21	A	499	ASP	-1	-0.806	-0.865	14.825	-18.279	-18.279	0.000	0.000	0.000	0.000
22	A	500	LEU	0	0.021	0.015	13.452	-1.306	-1.306	0.000	0.000	0.000	0.000
23	A	501	ALA	0	-0.020	-0.017	10.638	-2.280	-2.280	0.000	0.000	0.000	0.000
24	A	502	ASP	-1	-0.916	-0.952	10.016	-23.781	-23.781	0.000	0.000	0.000	0.000
25	A	503	ILE	0	0.045	0.016	11.053	-2.037	-2.037	0.000	0.000	0.000	0.000
26	A	504	ALA	0	0.005	0.005	7.449	-2.058	-2.058	0.000	0.000	0.000	0.000
27	A	505	MET	0	-0.084	-0.049	6.447	-5.536	-5.536	0.000	0.000	0.000	0.000
28	A	506	SER	0	-0.041	-0.018	7.267	-2.685	-2.685	0.000	0.000	0.000	0.000
29	A	507	LYS	1	0.898	0.970	7.733	26.060	26.060	0.000	0.000	0.000	0.000
34	A	512	GLN	0	-0.032	-0.013	7.802	3.345	3.345	0.000	0.000	0.000	0.000
35	A	513	VAL	0	0.028	0.012	10.778	0.442	0.442	0.000	0.000	0.000	0.000
36	A	514	ALA	0	-0.052	-0.017	14.463	0.677	0.677	0.000	0.000	0.000	0.000
37	A	515	THR	0	0.034	0.024	17.472	-0.146	-0.146	0.000	0.000	0.000	0.000
38	A	516	LEU	0	0.061	0.023	20.307	-0.365	-0.365	0.000	0.000	0.000	0.000
39	A	517	ASP	-1	-0.930	-0.959	21.702	-12.039	-12.039	0.000	0.000	0.000	0.000
40	A	518	SER	0	-0.055	-0.030	20.024	0.061	0.061	0.000	0.000	0.000	0.000
41	A	519	HIS	1	0.848	0.895	14.928	18.020	18.020	0.000	0.000	0.000	0.000
42	A	520	ALA	0	0.055	0.048	20.100	-0.320	-0.320	0.000	0.000	0.000	0.000
43	A	521	GLY	0	0.025	0.022	23.045	0.110	0.110	0.000	0.000	0.000	0.000
44	A	522	ASN	0	-0.137	-0.066	18.380	-0.564	-0.564	0.000	0.000	0.000	0.000
45	A	523	LEU	0	0.033	0.033	17.088	-0.927	-0.927	0.000	0.000	0.000	0.000
46	A	524	PRO	0	-0.007	-0.004	12.055	0.314	0.314	0.000	0.000	0.000	0.000
47	A	525	ARG	1	0.967	0.982	14.218	17.755	17.755	0.000	0.000	0.000	0.000
48	A	526	GLU	-1	-1.003	-1.001	8.777	-30.823	-30.823	0.000	0.000	0.000	0.000
49	A	527	GLY	0	-0.008	0.006	8.771	-0.523	-0.523	0.000	0.000	0.000	0.000
50	A	528	ALA	0	0.023	0.010	9.392	2.727	2.727	0.000	0.000	0.000	0.000
51	A	529	VAL	0	-0.064	-0.044	11.055	-1.141	-1.141	0.000	0.000	0.000	0.000
52	A	530	LEU	0	0.018	0.024	12.416	1.113	1.113	0.000	0.000	0.000	0.000
53	A	531	ILE	0	-0.014	-0.008	15.044	0.213	0.213	0.000	0.000	0.000	0.000
54	A	532	VAL	0	0.035	0.020	17.768	0.486	0.486	0.000	0.000	0.000	0.000
55	A	533	THR	0	0.006	-0.014	20.562	0.257	0.257	0.000	0.000	0.000	0.000
56	A	534	ALA	0	0.022	0.035	24.230	0.202	0.202	0.000	0.000	0.000	0.000
57	A	535	SER	0	0.012	-0.016	27.675	-0.056	-0.056	0.000	0.000	0.000	0.000
58	A	536	TYR	0	0.009	-0.010	30.051	0.058	0.058	0.000	0.000	0.000	0.000
59	A	537	ASN	0	-0.025	-0.017	34.270	0.225	0.225	0.000	0.000	0.000	0.000
60	A	538	GLY	0	0.019	0.005	34.626	0.178	0.178	0.000	0.000	0.000	0.000
61	A	539	HIS	0	0.007	0.013	34.170	-0.267	-0.267	0.000	0.000	0.000	0.000
62	A	540	PRO	0	0.070	0.020	29.222	-0.136	-0.136	0.000	0.000	0.000	0.000
63	A	541	PRO	0	-0.033	-0.011	27.193	0.333	0.333	0.000	0.000	0.000	0.000
64	A	542	ASP	-1	-0.890	-0.963	29.380	-9.692	-9.692	0.000	0.000	0.000	0.000
65	A	543	ASN	0	-0.034	-0.002	25.107	0.028	0.028	0.000	0.000	0.000	0.000
66	A	544	ALA	0	0.069	0.009	24.837	-0.674	-0.674	0.000	0.000	0.000	0.000
67	A	545	LYS	1	0.844	0.949	26.528	9.642	9.642	0.000	0.000	0.000	0.000
68	A	546	GLN	0	0.054	0.014	27.472	0.147	0.147	0.000	0.000	0.000	0.000
69	A	547	PHE	0	0.003	-0.006	20.904	-0.120	-0.120	0.000	0.000	0.000	0.000
70	A	548	VAL	0	0.012	0.001	25.979	-0.065	-0.065	0.000	0.000	0.000	0.000
71	A	549	ASP	-1	-0.909	-0.959	28.704	-9.750	-9.750	0.000	0.000	0.000	0.000
72	A	550	TRP	0	-0.098	-0.054	22.939	-0.036	-0.036	0.000	0.000	0.000	0.000
73	A	551	LEU	0	0.001	0.005	24.915	0.065	0.065	0.000	0.000	0.000	0.000
74	A	552	ASP	-1	-0.948	-0.973	28.052	-9.474	-9.474	0.000	0.000	0.000	0.000
75	A	553	GLN	0	-0.013	-0.009	31.647	0.060	0.060	0.000	0.000	0.000	0.000
76	A	554	ALA	0	-0.047	-0.019	29.417	0.174	0.174	0.000	0.000	0.000	0.000
77	A	555	SER	0	0.017	-0.020	29.034	-0.063	-0.063	0.000	0.000	0.000	0.000
78	A	556	ALA	0	0.001	0.004	28.953	-0.218	-0.218	0.000	0.000	0.000	0.000
79	A	557	ASP	-1	-0.917	-0.947	25.863	-11.712	-11.712	0.000	0.000	0.000	0.000
80	A	558	GLU	-1	-0.862	-0.926	25.525	-12.007	-12.007	0.000	0.000	0.000	0.000
81	A	559	VAL	0	0.005	0.005	21.740	-0.500	-0.500	0.000	0.000	0.000	0.000
82	A	560	LYS	1	0.869	0.936	21.101	11.780	11.780	0.000	0.000	0.000	0.000
83	A	561	GLY	0	-0.009	-0.022	18.124	-0.214	-0.214	0.000	0.000	0.000	0.000
84	A	562	VAL	0	-0.064	-0.023	16.317	-1.459	-1.459	0.000	0.000	0.000	0.000
85	A	563	ARG	1	0.912	0.954	12.097	24.982	24.982	0.000	0.000	0.000	0.000
86	A	564	TYR	0	-0.082	-0.060	14.555	-1.548	-1.548	0.000	0.000	0.000	0.000
87	A	565	SER	0	0.023	0.002	16.424	0.274	0.274	0.000	0.000	0.000	0.000
88	A	566	VAL	0	-0.033	-0.023	17.836	-0.307	-0.307	0.000	0.000	0.000	0.000
89	A	567	PHE	0	0.030	0.030	19.754	0.233	0.233	0.000	0.000	0.000	0.000
90	A	568	GLY	0	0.008	-0.023	21.534	0.089	0.089	0.000	0.000	0.000	0.000
91	A	569	CYS	0	-0.042	-0.020	24.022	0.072	0.072	0.000	0.000	0.000	0.000
92	A	570	GLY	0	0.028	-0.003	26.724	0.223	0.223	0.000	0.000	0.000	0.000
93	A	571	ASP	-1	-0.779	-0.864	30.514	-8.909	-8.909	0.000	0.000	0.000	0.000
94	A	572	LYS	1	0.931	0.955	33.460	9.509	9.509	0.000	0.000	0.000	0.000
95	A	573	ASN	0	-0.083	-0.041	36.587	0.440	0.440	0.000	0.000	0.000	0.000
96	A	574	TRP	0	-0.078	-0.030	36.060	0.182	0.182	0.000	0.000	0.000	0.000
97	A	575	ALA	0	0.049	0.014	37.805	-0.089	-0.089	0.000	0.000	0.000	0.000
98	A	576	THR	0	-0.039	-0.016	38.357	-0.190	-0.190	0.000	0.000	0.000	0.000
99	A	577	THR	0	-0.118	-0.076	36.097	-0.056	-0.056	0.000	0.000	0.000	0.000
100	A	578	TYR	0	0.015	0.026	30.721	-0.225	-0.225	0.000	0.000	0.000	0.000
101	A	579	GLN	0	0.041	0.013	28.346	-0.193	-0.193	0.000	0.000	0.000	0.000
102	A	580	LYS	1	0.919	0.972	29.938	8.636	8.636	0.000	0.000	0.000	0.000
103	A	581	VAL	0	0.006	0.012	27.396	-0.051	-0.051	0.000	0.000	0.000	0.000
104	A	582	PRO	0	-0.008	0.016	25.046	-0.264	-0.264	0.000	0.000	0.000	0.000
105	A	583	ALA	0	0.049	0.026	25.834	-0.373	-0.373	0.000	0.000	0.000	0.000
106	A	584	PHE	0	0.003	0.005	28.158	-0.165	-0.165	0.000	0.000	0.000	0.000
107	A	585	ILE	0	0.001	-0.005	22.982	-0.106	-0.106	0.000	0.000	0.000	0.000
108	A	586	ASP	-1	-0.752	-0.860	23.659	-13.659	-13.659	0.000	0.000	0.000	0.000
109	A	587	GLU	-1	-0.880	-0.933	24.690	-10.836	-10.836	0.000	0.000	0.000	0.000
110	A	588	THR	0	-0.071	-0.047	27.668	0.353	0.353	0.000	0.000	0.000	0.000
111	A	589	LEU	0	-0.020	-0.016	20.783	-0.055	-0.055	0.000	0.000	0.000	0.000
112	A	590	ALA	0	-0.014	-0.010	24.600	-0.119	-0.119	0.000	0.000	0.000	0.000
113	A	591	ALA	0	-0.068	-0.038	25.973	0.114	0.114	0.000	0.000	0.000	0.000
114	A	592	LYS	1	0.831	0.939	26.377	11.411	11.411	0.000	0.000	0.000	0.000
115	A	593	GLY	0	-0.035	-0.009	25.220	-0.259	-0.259	0.000	0.000	0.000	0.000
116	A	594	ALA	0	0.000	0.001	21.858	-0.622	-0.622	0.000	0.000	0.000	0.000
117	A	595	GLU	-1	-0.868	-0.896	17.474	-18.106	-18.106	0.000	0.000	0.000	0.000
118	A	596	ASN	0	-0.032	-0.016	17.957	-1.530	-1.530	0.000	0.000	0.000	0.000
119	A	597	ILE	0	-0.031	-0.005	13.157	0.026	0.026	0.000	0.000	0.000	0.000
120	A	598	ALA	0	0.029	0.018	16.522	0.011	0.011	0.000	0.000	0.000	0.000
121	A	599	ASP	-1	-0.856	-0.904	18.434	-13.205	-13.205	0.000	0.000	0.000	0.000
122	A	600	ARG	1	0.700	0.853	21.108	11.318	11.318	0.000	0.000	0.000	0.000
123	A	601	GLY	0	0.022	0.013	22.159	0.337	0.337	0.000	0.000	0.000	0.000
124	A	602	GLU	-1	-0.904	-0.968	23.315	-10.885	-10.885	0.000	0.000	0.000	0.000
125	A	603	ALA	0	0.065	0.031	25.602	-0.053	-0.053	0.000	0.000	0.000	0.000
126	A	604	ASP	-1	-0.799	-0.906	27.395	-9.150	-9.150	0.000	0.000	0.000	0.000
127	A	605	ALA	0	-0.003	-0.019	31.101	0.014	0.014	0.000	0.000	0.000	0.000
128	A	606	SER	0	-0.093	-0.072	32.138	0.246	0.246	0.000	0.000	0.000	0.000
129	A	607	ASP	-1	-0.979	-0.989	33.495	-8.879	-8.879	0.000	0.000	0.000	0.000
130	A	608	ASP	-1	-0.830	-0.893	29.744	-10.922	-10.922	0.000	0.000	0.000	0.000
131	A	609	PHE	0	-0.079	-0.041	27.220	-0.376	-0.376	0.000	0.000	0.000	0.000
132	A	610	GLU	-1	-0.968	-0.977	24.402	-12.795	-12.795	0.000	0.000	0.000	0.000
133	A	611	GLY	0	0.037	0.018	24.765	-0.580	-0.580	0.000	0.000	0.000	0.000
134	A	612	THR	0	-0.005	-0.015	25.361	-0.307	-0.307	0.000	0.000	0.000	0.000
135	A	613	TYR	0	-0.065	-0.075	17.806	-0.727	-0.727	0.000	0.000	0.000	0.000
136	A	614	GLU	-1	-0.876	-0.926	20.771	-15.743	-15.743	0.000	0.000	0.000	0.000
137	A	615	GLU	-1	-0.969	-0.983	20.873	-12.456	-12.456	0.000	0.000	0.000	0.000
138	A	616	TRP	0	0.028	0.006	16.492	-0.929	-0.929	0.000	0.000	0.000	0.000
139	A	617	ARG	1	0.804	0.891	16.266	15.369	15.369	0.000	0.000	0.000	0.000
140	A	618	GLU	-1	-0.859	-0.928	16.225	-20.233	-20.233	0.000	0.000	0.000	0.000
141	A	619	HIS	0	-0.088	-0.029	17.283	-0.102	-0.102	0.000	0.000	0.000	0.000
142	A	620	MET	0	0.033	0.037	13.342	-1.773	-1.773	0.000	0.000	0.000	0.000
143	A	621	TRP	0	-0.017	-0.040	9.684	-2.838	-2.838	0.000	0.000	0.000	0.000
144	A	622	SER	0	-0.062	-0.036	12.307	-1.948	-1.948	0.000	0.000	0.000	0.000
145	A	623	ASP	-1	-0.893	-0.945	14.404	-18.019	-18.019	0.000	0.000	0.000	0.000
146	A	624	VAL	0	-0.024	-0.032	9.543	-0.983	-0.983	0.000	0.000	0.000	0.000
147	A	625	ALA	0	-0.041	-0.016	9.688	-1.949	-1.949	0.000	0.000	0.000	0.000
148	A	626	ALA	0	-0.051	-0.029	10.765	-0.465	-0.465	0.000	0.000	0.000	0.000
149	A	627	TYR	0	-0.078	-0.056	11.904	0.038	0.038	0.000	0.000	0.000	0.000
150	A	628	PHE	0	-0.107	-0.044	8.022	-0.576	-0.576	0.000	0.000	0.000	0.000
152	A	630	LEU	-1	-0.884	-0.932	6.911	-37.925	-37.925	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:479:ASN)