FMO DATABASE

FMODB ID: 7KJ9K

Calculation Name: 1NT3-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1NT3

Chain ID: A

ChEMBL ID:

UniProt ID: P20783

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	105
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-761173.552881
FMO2-HF: Nuclear repulsion	716992.416746
FMO2-HF: Total energy	-44181.136135
FMO2-MP2: Total energy	-44306.958677

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:8:ARG)

Summations of interaction energy for fragment #1(A:8:ARG)

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.
-95.615	-95.106	20.566	-11.952	-9.122	-0.147

Interaction energy analysis for fragmet #1(A:8:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.703 / q_NPA : 1.824

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	10	GLU	-1	-0.782	-0.874	1.874	-184.401	-184.063	20.567	-11.938	-8.967	-0.147
4	A	11	TYR	0	0.061	0.033	5.056	7.029	7.200	-0.001	-0.014	-0.155	0.000
5	A	12	SER	0	-0.037	-0.015	6.395	5.643	5.643	0.000	0.000	0.000	0.000
6	A	13	VAL	0	0.101	0.043	7.873	4.221	4.221	0.000	0.000	0.000	0.000
7	A	14	CYS	0	-0.043	-0.009	10.198	4.343	4.343	0.000	0.000	0.000	0.000
8	A	15	ASP	-1	-0.771	-0.832	10.190	-47.331	-47.331	0.000	0.000	0.000	0.000
9	A	16	SER	0	-0.013	-0.017	8.670	2.000	2.000	0.000	0.000	0.000	0.000
10	A	17	GLU	-1	-0.804	-0.875	11.302	-32.574	-32.574	0.000	0.000	0.000	0.000
11	A	18	SER	0	0.002	-0.005	9.876	-1.711	-1.711	0.000	0.000	0.000	0.000
12	A	19	LEU	0	-0.039	-0.013	12.288	1.222	1.222	0.000	0.000	0.000	0.000
13	A	20	TRP	0	0.030	0.011	14.740	-0.873	-0.873	0.000	0.000	0.000	0.000
14	A	21	VAL	0	-0.031	0.000	18.183	1.115	1.115	0.000	0.000	0.000	0.000
15	A	22	THR	0	-0.013	-0.036	21.001	-0.086	-0.086	0.000	0.000	0.000	0.000
16	A	23	ASP	-1	-0.865	-0.926	24.122	-22.592	-22.592	0.000	0.000	0.000	0.000
17	A	24	LYS	1	0.804	0.880	20.928	27.743	27.743	0.000	0.000	0.000	0.000
18	A	25	SER	0	0.068	0.045	25.959	0.156	0.156	0.000	0.000	0.000	0.000
19	A	26	SER	0	-0.045	-0.028	28.169	0.632	0.632	0.000	0.000	0.000	0.000
20	A	27	ALA	0	0.006	0.001	24.659	-0.976	-0.976	0.000	0.000	0.000	0.000
21	A	28	ILE	0	-0.003	0.010	25.147	0.818	0.818	0.000	0.000	0.000	0.000
22	A	29	ASP	-1	-0.788	-0.896	24.969	-22.073	-22.073	0.000	0.000	0.000	0.000
23	A	30	ILE	0	-0.011	-0.016	23.311	-0.081	-0.081	0.000	0.000	0.000	0.000
24	A	31	ARG	1	0.753	0.858	26.002	19.079	19.079	0.000	0.000	0.000	0.000
25	A	32	GLY	0	0.021	0.012	28.227	0.567	0.567	0.000	0.000	0.000	0.000
26	A	33	HIS	0	-0.060	-0.034	29.309	0.400	0.400	0.000	0.000	0.000	0.000
27	A	34	GLN	0	0.030	0.025	28.790	-0.956	-0.956	0.000	0.000	0.000	0.000
28	A	35	VAL	0	-0.034	-0.016	28.715	0.671	0.671	0.000	0.000	0.000	0.000
29	A	36	THR	0	0.024	0.012	30.148	-0.292	-0.292	0.000	0.000	0.000	0.000
30	A	37	VAL	0	-0.075	-0.037	25.675	-0.198	-0.198	0.000	0.000	0.000	0.000
31	A	38	LEU	0	0.003	0.008	29.013	0.450	0.450	0.000	0.000	0.000	0.000
32	A	39	GLY	0	0.094	0.045	28.235	-0.774	-0.774	0.000	0.000	0.000	0.000
33	A	40	GLU	-1	-0.982	-0.979	28.532	-19.278	-19.278	0.000	0.000	0.000	0.000
34	A	41	ILE	0	-0.025	-0.033	25.188	0.042	0.042	0.000	0.000	0.000	0.000
35	A	42	LYS	0	-0.027	-0.007	29.499	-0.067	-0.067	0.000	0.000	0.000	0.000
36	A	43	THR	0	-0.010	-0.006	31.591	0.336	0.336	0.000	0.000	0.000	0.000
37	A	44	GLY	0	0.000	-0.007	34.685	-0.269	-0.269	0.000	0.000	0.000	0.000
38	A	45	ASN	0	-0.082	-0.036	32.667	0.267	0.267	0.000	0.000	0.000	0.000
39	A	46	SER	-1	-0.809	-0.896	32.961	-17.945	-17.945	0.000	0.000	0.000	0.000
40	A	47	PRO	0	-0.012	0.008	31.839	-0.567	-0.567	0.000	0.000	0.000	0.000
41	A	48	VAL	0	0.001	-0.007	25.280	-0.469	-0.469	0.000	0.000	0.000	0.000
42	A	49	LYS	1	0.950	0.973	25.006	22.564	22.564	0.000	0.000	0.000	0.000
43	A	50	GLN	0	-0.046	-0.039	24.071	-1.488	-1.488	0.000	0.000	0.000	0.000
44	A	51	TYR	0	-0.052	-0.027	19.456	0.798	0.798	0.000	0.000	0.000	0.000
45	A	52	PHE	0	0.016	0.004	18.490	-0.588	-0.588	0.000	0.000	0.000	0.000
46	A	53	TYR	0	-0.005	0.006	9.620	0.499	0.499	0.000	0.000	0.000	0.000
47	A	54	GLU	-1	-0.801	-0.886	14.734	-30.080	-30.080	0.000	0.000	0.000	0.000
48	A	55	THR	0	-0.095	-0.065	9.696	-1.402	-1.402	0.000	0.000	0.000	0.000
49	A	56	ARG	1	0.899	0.941	12.544	31.938	31.938	0.000	0.000	0.000	0.000
50	A	57	CYS	0	-0.002	0.004	9.472	2.942	2.942	0.000	0.000	0.000	0.000
51	A	58	LYS	1	0.854	0.924	13.833	36.569	36.569	0.000	0.000	0.000	0.000
52	A	59	GLU	-1	-0.820	-0.910	16.070	-24.083	-24.083	0.000	0.000	0.000	0.000
53	A	60	ALA	0	-0.024	-0.019	17.074	-1.577	-1.577	0.000	0.000	0.000	0.000
54	A	61	ARG	1	0.846	0.920	18.382	25.255	25.255	0.000	0.000	0.000	0.000
55	A	62	PRO	0	-0.007	0.021	14.416	1.028	1.028	0.000	0.000	0.000	0.000
56	A	63	VAL	0	-0.002	0.004	17.331	0.583	0.583	0.000	0.000	0.000	0.000
57	A	64	LYS	1	0.928	0.949	19.755	23.936	23.936	0.000	0.000	0.000	0.000
58	A	65	ASN	0	-0.038	-0.011	21.802	0.809	0.809	0.000	0.000	0.000	0.000
59	A	66	GLY	0	0.065	0.028	20.119	0.591	0.591	0.000	0.000	0.000	0.000
60	A	67	CYS	0	-0.008	-0.027	11.740	2.559	2.559	0.000	0.000	0.000	0.000
61	A	68	ARG	1	0.743	0.847	11.119	45.967	45.967	0.000	0.000	0.000	0.000
62	A	69	GLY	0	-0.013	-0.009	13.768	-2.583	-2.583	0.000	0.000	0.000	0.000
63	A	70	ILE	0	-0.002	-0.010	15.380	-1.140	-1.140	0.000	0.000	0.000	0.000
64	A	71	ASP	-1	-0.821	-0.913	17.977	-28.717	-28.717	0.000	0.000	0.000	0.000
65	A	72	ASP	-1	-0.909	-0.950	21.163	-24.597	-24.597	0.000	0.000	0.000	0.000
66	A	73	LYS	1	0.912	0.948	23.561	20.299	20.299	0.000	0.000	0.000	0.000
67	A	74	HIS	0	-0.072	-0.031	23.012	0.560	0.560	0.000	0.000	0.000	0.000
68	A	75	TRP	0	-0.022	-0.011	20.568	-0.067	-0.067	0.000	0.000	0.000	0.000
69	A	76	ASN	0	0.027	0.023	22.998	-0.072	-0.072	0.000	0.000	0.000	0.000
70	A	77	SER	0	0.006	-0.004	18.379	-1.275	-1.275	0.000	0.000	0.000	0.000
71	A	78	GLN	0	0.007	-0.001	18.790	1.185	1.185	0.000	0.000	0.000	0.000
72	A	80	LYS	1	0.948	0.963	15.020	29.390	29.390	0.000	0.000	0.000	0.000
73	A	81	THR	0	-0.019	-0.019	14.320	-2.156	-2.156	0.000	0.000	0.000	0.000
74	A	82	SER	0	-0.002	0.002	12.720	1.785	1.785	0.000	0.000	0.000	0.000
75	A	83	GLN	0	-0.044	-0.038	14.077	-0.589	-0.589	0.000	0.000	0.000	0.000
76	A	84	THR	0	-0.010	-0.003	13.862	0.543	0.543	0.000	0.000	0.000	0.000
77	A	85	TYR	0	0.015	0.002	16.372	1.681	1.681	0.000	0.000	0.000	0.000
78	A	86	VAL	0	0.012	0.006	16.843	-1.419	-1.419	0.000	0.000	0.000	0.000
79	A	87	ARG	1	0.871	0.946	19.429	25.232	25.232	0.000	0.000	0.000	0.000
80	A	88	ALA	0	0.056	0.025	22.304	-0.579	-0.579	0.000	0.000	0.000	0.000
81	A	89	LEU	0	-0.024	0.008	24.831	0.740	0.740	0.000	0.000	0.000	0.000
82	A	90	THR	0	0.059	0.025	27.618	0.143	0.143	0.000	0.000	0.000	0.000
83	A	91	SER	0	0.009	0.005	30.304	0.297	0.297	0.000	0.000	0.000	0.000
84	A	92	GLU	-1	-0.779	-0.871	33.783	-18.139	-18.139	0.000	0.000	0.000	0.000
85	A	93	ASN	0	-0.014	-0.024	36.008	0.324	0.324	0.000	0.000	0.000	0.000
86	A	94	ASN	0	0.031	0.021	36.655	-0.068	-0.068	0.000	0.000	0.000	0.000
87	A	95	LYS	1	0.937	0.987	37.917	14.378	14.378	0.000	0.000	0.000	0.000
88	A	96	LEU	0	0.016	-0.006	37.336	0.154	0.154	0.000	0.000	0.000	0.000
89	A	97	VAL	0	0.028	0.012	33.747	-0.385	-0.385	0.000	0.000	0.000	0.000
90	A	98	GLY	0	0.022	0.003	32.322	0.343	0.343	0.000	0.000	0.000	0.000
91	A	99	TRP	0	0.008	0.013	24.333	-0.481	-0.481	0.000	0.000	0.000	0.000
92	A	100	ARG	1	0.822	0.914	27.473	19.236	19.236	0.000	0.000	0.000	0.000
93	A	101	TRP	0	0.004	-0.002	19.287	-0.894	-0.894	0.000	0.000	0.000	0.000
94	A	102	ILE	0	0.025	0.012	22.197	0.777	0.777	0.000	0.000	0.000	0.000
95	A	103	ARG	1	0.910	0.957	19.704	26.537	26.537	0.000	0.000	0.000	0.000
96	A	104	ILE	0	0.004	0.007	16.663	0.851	0.851	0.000	0.000	0.000	0.000
97	A	105	ASP	-1	-0.857	-0.898	15.458	-32.690	-32.690	0.000	0.000	0.000	0.000
98	A	106	THR	0	0.040	0.007	10.560	-0.275	-0.275	0.000	0.000	0.000	0.000
99	A	107	SER	0	-0.003	0.007	8.772	-3.384	-3.384	0.000	0.000	0.000	0.000
100	A	109	VAL	0	-0.002	0.008	9.576	-4.521	-4.521	0.000	0.000	0.000	0.000
101	A	111	ALA	0	-0.028	-0.002	14.129	-0.177	-0.177	0.000	0.000	0.000	0.000
102	A	112	LEU	0	0.035	0.005	16.172	0.655	0.655	0.000	0.000	0.000	0.000
103	A	113	SER	0	-0.062	-0.040	19.607	0.983	0.983	0.000	0.000	0.000	0.000
104	A	114	ARG	1	0.943	0.973	23.000	23.619	23.619	0.000	0.000	0.000	0.000
105	A	115	LYS	0	0.101	0.060	25.651	-1.160	-1.160	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:ARG)