FMO DATABASE

FMODB ID: 97MV2

Calculation Name: 3OSJ-A-Xray547

Preferred Name:

Target Type:

Ligand Name: nitrate ion

Ligand 3-letter code: NO3

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3OSJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q55544

Base Structure: X-ray

Registration Date: 2025-10-04

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	135
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1273392.466235
FMO2-HF: Nuclear repulsion	1219921.629851
FMO2-HF: Total energy	-53470.836384
FMO2-MP2: Total energy	-53629.809526

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:265:GLN)

Summations of interaction energy for fragment #1(A:265:GLN)

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.
14.046	19.653	1.919	-2.383	-5.141	-0.015

Interaction energy analysis for fragmet #1(A:265:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.875 / q_NPA : 0.919

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	267	TYR	0	0.048	0.037	2.618	-3.581	2.023	1.920	-2.382	-5.141	-0.015
4	A	268	ALA	0	0.050	0.018	5.743	0.936	0.939	-0.001	-0.001	0.000	0.000
5	A	269	MET	0	-0.024	0.007	9.266	0.397	0.397	0.000	0.000	0.000	0.000
6	A	270	LYS	1	0.960	0.982	11.233	22.256	22.256	0.000	0.000	0.000	0.000
7	A	271	PRO	0	0.080	0.026	14.377	-0.238	-0.238	0.000	0.000	0.000	0.000
8	A	272	GLY	0	0.030	0.021	16.689	0.233	0.233	0.000	0.000	0.000	0.000
9	A	273	LEU	0	-0.046	0.003	9.966	-0.080	-0.080	0.000	0.000	0.000	0.000
10	A	274	SER	0	0.063	0.021	11.298	0.544	0.544	0.000	0.000	0.000	0.000
11	A	275	ALA	0	0.047	0.012	12.333	-0.832	-0.832	0.000	0.000	0.000	0.000
12	A	276	LEU	0	-0.011	-0.002	10.089	-0.432	-0.432	0.000	0.000	0.000	0.000
13	A	277	GLU	-1	-0.850	-0.926	5.718	-33.865	-33.865	0.000	0.000	0.000	0.000
14	A	278	LYS	1	0.824	0.900	8.447	14.939	14.939	0.000	0.000	0.000	0.000
15	A	279	ASN	0	0.016	0.008	11.067	0.226	0.226	0.000	0.000	0.000	0.000
16	A	280	ALA	0	-0.007	0.011	5.331	-0.382	-0.382	0.000	0.000	0.000	0.000
17	A	281	VAL	0	0.009	-0.005	7.427	-1.854	-1.854	0.000	0.000	0.000	0.000
18	A	282	ILE	0	0.007	0.013	8.370	-0.130	-0.130	0.000	0.000	0.000	0.000
19	A	283	LYS	1	0.880	0.945	9.201	24.243	24.243	0.000	0.000	0.000	0.000
20	A	284	ALA	0	-0.026	-0.010	5.947	-0.337	-0.337	0.000	0.000	0.000	0.000
21	A	285	ALA	0	0.041	0.014	7.656	0.427	0.427	0.000	0.000	0.000	0.000
22	A	286	TYR	0	-0.064	-0.068	10.628	1.104	1.104	0.000	0.000	0.000	0.000
23	A	287	ARG	1	0.834	0.914	6.364	32.540	32.540	0.000	0.000	0.000	0.000
24	A	288	GLN	0	-0.017	-0.001	8.703	-1.536	-1.536	0.000	0.000	0.000	0.000
25	A	289	ILE	0	-0.045	-0.023	10.521	1.459	1.459	0.000	0.000	0.000	0.000
26	A	290	PHE	0	-0.001	-0.032	14.149	1.263	1.263	0.000	0.000	0.000	0.000
27	A	291	GLU	-1	-0.864	-0.901	13.113	-17.501	-17.501	0.000	0.000	0.000	0.000
28	A	292	ARG	1	0.937	0.958	14.099	16.682	16.682	0.000	0.000	0.000	0.000
29	A	293	ASP	-1	-0.803	-0.883	11.983	-24.265	-24.265	0.000	0.000	0.000	0.000
30	A	294	ILE	0	-0.024	-0.004	14.402	1.204	1.204	0.000	0.000	0.000	0.000
31	A	295	THR	0	0.005	-0.012	15.641	-0.805	-0.805	0.000	0.000	0.000	0.000
32	A	296	LYS	1	0.953	0.986	18.067	14.346	14.346	0.000	0.000	0.000	0.000
33	A	297	ALA	0	0.015	-0.001	20.758	0.521	0.521	0.000	0.000	0.000	0.000
34	A	298	TYR	0	0.017	0.022	21.609	0.461	0.461	0.000	0.000	0.000	0.000
35	A	299	SER	0	0.013	-0.006	23.456	0.485	0.485	0.000	0.000	0.000	0.000
36	A	300	GLN	0	0.065	0.034	24.611	-0.342	-0.342	0.000	0.000	0.000	0.000
37	A	301	SER	0	-0.004	0.006	25.571	-0.270	-0.270	0.000	0.000	0.000	0.000
38	A	302	ILE	0	0.054	0.021	19.296	-0.181	-0.181	0.000	0.000	0.000	0.000
39	A	303	SER	0	-0.009	-0.008	20.977	-0.688	-0.688	0.000	0.000	0.000	0.000
40	A	304	TYR	0	-0.004	0.010	22.310	-0.232	-0.232	0.000	0.000	0.000	0.000
41	A	305	LEU	0	0.013	0.012	20.599	-0.199	-0.199	0.000	0.000	0.000	0.000
42	A	306	GLU	-1	-0.775	-0.870	16.626	-16.762	-16.762	0.000	0.000	0.000	0.000
43	A	307	SER	0	-0.103	-0.071	18.462	-0.211	-0.211	0.000	0.000	0.000	0.000
44	A	308	GLN	0	0.045	0.024	20.732	0.105	0.105	0.000	0.000	0.000	0.000
45	A	309	VAL	0	0.007	0.011	15.366	-0.116	-0.116	0.000	0.000	0.000	0.000
46	A	310	ARG	1	0.774	0.872	14.563	16.334	16.334	0.000	0.000	0.000	0.000
47	A	311	ASN	0	-0.073	-0.050	17.104	-0.215	-0.215	0.000	0.000	0.000	0.000
48	A	312	GLY	0	-0.002	0.006	19.077	0.102	0.102	0.000	0.000	0.000	0.000
49	A	313	ASP	-1	-0.859	-0.913	19.890	-11.829	-11.829	0.000	0.000	0.000	0.000
50	A	314	ILE	0	-0.076	-0.037	19.587	0.333	0.333	0.000	0.000	0.000	0.000
51	A	315	SER	0	0.013	-0.010	17.947	-0.567	-0.567	0.000	0.000	0.000	0.000
52	A	316	MET	0	-0.012	-0.001	11.768	0.139	0.139	0.000	0.000	0.000	0.000
53	A	317	LYS	1	0.873	0.955	15.233	14.879	14.879	0.000	0.000	0.000	0.000
54	A	318	GLU	-1	-0.769	-0.869	17.024	-12.619	-12.619	0.000	0.000	0.000	0.000
55	A	319	PHE	0	0.000	-0.019	14.461	0.413	0.413	0.000	0.000	0.000	0.000
56	A	320	VAL	0	-0.018	-0.009	13.694	0.131	0.131	0.000	0.000	0.000	0.000
57	A	321	ARG	1	0.818	0.883	16.453	13.504	13.504	0.000	0.000	0.000	0.000
58	A	322	ARG	1	0.831	0.898	20.156	13.149	13.149	0.000	0.000	0.000	0.000
59	A	323	LEU	0	-0.019	-0.002	15.402	0.592	0.592	0.000	0.000	0.000	0.000
60	A	324	ALA	0	0.022	0.018	18.235	0.422	0.422	0.000	0.000	0.000	0.000
61	A	325	LYS	1	0.833	0.898	19.938	12.622	12.622	0.000	0.000	0.000	0.000
62	A	326	SER	0	-0.050	-0.022	21.251	0.695	0.695	0.000	0.000	0.000	0.000
63	A	327	PRO	0	0.022	-0.015	23.869	-0.109	-0.109	0.000	0.000	0.000	0.000
64	A	328	LEU	0	-0.039	0.002	19.925	0.239	0.239	0.000	0.000	0.000	0.000
65	A	329	TYR	0	0.083	0.052	17.744	-0.381	-0.381	0.000	0.000	0.000	0.000
66	A	330	ARG	1	0.961	0.984	21.607	10.751	10.751	0.000	0.000	0.000	0.000
67	A	331	LYS	1	0.926	0.963	24.542	12.044	12.044	0.000	0.000	0.000	0.000
68	A	332	GLN	0	-0.057	-0.014	19.136	0.492	0.492	0.000	0.000	0.000	0.000
69	A	333	PHE	0	0.001	-0.013	17.915	-0.112	-0.112	0.000	0.000	0.000	0.000
70	A	334	PHE	0	-0.026	-0.025	22.754	-0.092	-0.092	0.000	0.000	0.000	0.000
71	A	335	GLU	-1	-0.889	-0.955	25.944	-9.785	-9.785	0.000	0.000	0.000	0.000
72	A	336	PRO	0	-0.039	-0.002	26.818	0.348	0.348	0.000	0.000	0.000	0.000
73	A	337	PHE	0	-0.044	-0.025	23.931	-0.035	-0.035	0.000	0.000	0.000	0.000
74	A	338	ILE	0	0.057	0.037	29.102	0.163	0.163	0.000	0.000	0.000	0.000
75	A	339	ASN	0	0.029	-0.004	28.624	-0.788	-0.788	0.000	0.000	0.000	0.000
76	A	340	SER	0	0.050	0.000	27.459	-0.311	-0.311	0.000	0.000	0.000	0.000
77	A	341	ARG	1	0.871	0.953	21.321	13.365	13.365	0.000	0.000	0.000	0.000
78	A	342	ALA	0	0.030	0.016	23.734	-0.639	-0.639	0.000	0.000	0.000	0.000
79	A	343	LEU	0	-0.012	-0.003	23.087	-0.668	-0.668	0.000	0.000	0.000	0.000
80	A	344	GLU	-1	-0.850	-0.932	21.019	-14.278	-14.278	0.000	0.000	0.000	0.000
81	A	345	LEU	0	-0.025	-0.001	19.042	-1.091	-1.091	0.000	0.000	0.000	0.000
82	A	346	ALA	0	-0.030	-0.006	18.076	-0.954	-0.954	0.000	0.000	0.000	0.000
83	A	347	PHE	0	0.011	-0.005	17.805	-0.644	-0.644	0.000	0.000	0.000	0.000
84	A	348	ARG	1	0.962	0.988	14.678	16.684	16.684	0.000	0.000	0.000	0.000
85	A	349	HIS	1	0.779	0.869	13.264	17.017	17.017	0.000	0.000	0.000	0.000
86	A	350	ILE	0	-0.013	0.002	13.457	-1.365	-1.365	0.000	0.000	0.000	0.000
87	A	351	LEU	0	0.026	0.003	14.347	-0.758	-0.758	0.000	0.000	0.000	0.000
88	A	352	GLY	0	0.016	0.027	10.966	-0.882	-0.882	0.000	0.000	0.000	0.000
89	A	353	ARG	1	0.765	0.829	11.533	15.705	15.705	0.000	0.000	0.000	0.000
90	A	354	GLY	0	-0.009	-0.015	14.251	0.680	0.680	0.000	0.000	0.000	0.000
91	A	355	PRO	0	-0.029	-0.018	17.738	-0.148	-0.148	0.000	0.000	0.000	0.000
92	A	356	SER	0	-0.032	-0.027	20.306	0.057	0.057	0.000	0.000	0.000	0.000
93	A	357	SER	0	0.012	-0.022	21.785	0.253	0.253	0.000	0.000	0.000	0.000
94	A	358	ARG	1	0.971	0.987	25.626	9.509	9.509	0.000	0.000	0.000	0.000
95	A	359	GLU	-1	-0.821	-0.897	28.614	-10.304	-10.304	0.000	0.000	0.000	0.000
96	A	360	GLU	-1	-0.740	-0.814	22.034	-14.234	-14.234	0.000	0.000	0.000	0.000
97	A	361	VAL	0	0.001	-0.012	25.079	-0.038	-0.038	0.000	0.000	0.000	0.000
98	A	362	GLN	0	0.023	0.016	26.859	0.055	0.055	0.000	0.000	0.000	0.000
99	A	363	LYS	1	0.959	0.993	26.071	11.805	11.805	0.000	0.000	0.000	0.000
100	A	364	TYR	0	0.016	-0.012	22.918	0.151	0.151	0.000	0.000	0.000	0.000
101	A	365	PHE	0	0.028	0.022	27.262	0.091	0.091	0.000	0.000	0.000	0.000
102	A	366	SER	0	0.029	0.006	29.853	0.359	0.359	0.000	0.000	0.000	0.000
103	A	367	ILE	0	-0.025	-0.006	27.699	0.191	0.191	0.000	0.000	0.000	0.000
104	A	368	VAL	0	-0.053	-0.022	27.441	0.104	0.104	0.000	0.000	0.000	0.000
105	A	369	SER	0	-0.026	-0.029	30.129	0.201	0.201	0.000	0.000	0.000	0.000
106	A	370	SER	0	-0.044	0.002	33.344	0.305	0.305	0.000	0.000	0.000	0.000
107	A	371	GLY	0	0.048	0.015	32.117	0.189	0.189	0.000	0.000	0.000	0.000
108	A	372	GLY	0	-0.015	-0.002	30.394	-0.219	-0.219	0.000	0.000	0.000	0.000
109	A	373	LEU	0	-0.033	-0.014	23.170	-0.194	-0.194	0.000	0.000	0.000	0.000
110	A	374	PRO	0	-0.031	-0.029	25.567	-0.468	-0.468	0.000	0.000	0.000	0.000
111	A	375	ALA	0	0.095	0.050	26.262	-0.343	-0.343	0.000	0.000	0.000	0.000
112	A	376	LEU	0	-0.029	-0.004	23.398	-0.222	-0.222	0.000	0.000	0.000	0.000
113	A	377	VAL	0	-0.011	-0.005	20.750	-0.569	-0.569	0.000	0.000	0.000	0.000
114	A	378	ASP	-1	-0.781	-0.854	22.030	-12.710	-12.710	0.000	0.000	0.000	0.000
115	A	379	ALA	0	-0.020	-0.006	23.839	-0.235	-0.235	0.000	0.000	0.000	0.000
116	A	380	LEU	0	-0.012	0.000	19.241	-0.193	-0.193	0.000	0.000	0.000	0.000
117	A	381	VAL	0	-0.001	0.003	18.293	-0.685	-0.685	0.000	0.000	0.000	0.000
118	A	382	ASP	-1	-0.850	-0.909	20.122	-13.455	-13.455	0.000	0.000	0.000	0.000
119	A	383	SER	0	-0.059	-0.028	19.463	0.282	0.282	0.000	0.000	0.000	0.000
120	A	384	GLN	0	-0.019	-0.031	20.194	0.002	0.002	0.000	0.000	0.000	0.000
121	A	385	GLU	-1	-0.717	-0.812	15.980	-18.595	-18.595	0.000	0.000	0.000	0.000
122	A	386	TYR	0	0.035	0.007	14.451	-1.579	-1.579	0.000	0.000	0.000	0.000
123	A	387	ALA	0	-0.022	-0.016	15.571	-1.140	-1.140	0.000	0.000	0.000	0.000
124	A	388	ASP	-1	-0.852	-0.913	16.340	-16.445	-16.445	0.000	0.000	0.000	0.000
125	A	389	TYR	0	-0.048	-0.022	10.784	-1.132	-1.132	0.000	0.000	0.000	0.000
126	A	390	PHE	0	-0.036	-0.025	9.211	-3.047	-3.047	0.000	0.000	0.000	0.000
127	A	391	GLY	0	0.044	0.036	12.604	-0.182	-0.182	0.000	0.000	0.000	0.000
128	A	392	GLU	-1	-0.810	-0.915	15.971	-15.197	-15.197	0.000	0.000	0.000	0.000
129	A	393	GLU	-1	-0.874	-0.954	12.853	-19.438	-19.438	0.000	0.000	0.000	0.000
130	A	394	THR	0	-0.078	-0.040	8.431	-1.473	-1.473	0.000	0.000	0.000	0.000
131	A	395	VAL	0	-0.029	-0.019	7.335	1.744	1.744	0.000	0.000	0.000	0.000
132	A	396	PRO	0	-0.038	-0.007	8.142	-3.455	-3.455	0.000	0.000	0.000	0.000
133	A	397	TYR	0	-0.051	-0.030	5.042	-4.327	-4.327	0.000	0.000	0.000	0.000
134	A	398	LEU	0	-0.028	-0.015	6.847	3.310	3.310	0.000	0.000	0.000	0.000
135	A	399	ARG	0	-0.125	-0.068	7.057	-6.748	-6.748	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:265:GLN)