FMO DATABASE

FMODB ID: RMNK8

Calculation Name: 2NT3-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2NT3

Chain ID: A

ChEMBL ID:

UniProt ID: O68522

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	122
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-973679.025586
FMO2-HF: Nuclear repulsion	928663.610541
FMO2-HF: Total energy	-45015.415045
FMO2-MP2: Total energy	-45149.367186

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:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-156.039	-152.564	0.394	-1.398	-2.47	-0.008

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.825 / q_NPA : 0.900

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	4	LYS	1	0.827	0.912	3.850	35.043	36.512	-0.010	-0.562	-0.897	-0.001
4	A	5	ILE	0	0.012	0.002	5.243	2.291	2.316	-0.001	-0.003	-0.020	0.000
26	A	27	PHE	0	-0.025	-0.024	4.998	-6.401	-6.285	-0.001	-0.005	-0.110	0.000
27	A	28	THR	0	-0.047	-0.029	2.831	-2.397	-1.033	0.394	-0.696	-1.062	-0.006
28	A	29	VAL	0	0.003	0.002	5.013	0.093	0.086	-0.001	-0.001	0.009	0.000
122	A	123	PRO	-1	-0.974	-0.964	3.593	-56.439	-55.931	0.013	-0.131	-0.390	-0.001
5	A	6	LEU	0	-0.020	-0.003	8.824	0.376	0.376	0.000	0.000	0.000	0.000
6	A	7	ILE	0	0.000	0.001	11.695	0.656	0.656	0.000	0.000	0.000	0.000
7	A	8	VAL	0	-0.011	-0.013	14.771	0.414	0.414	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.719	-0.855	18.024	-12.336	-12.336	0.000	0.000	0.000	0.000
9	A	10	SER	0	0.000	-0.016	20.619	0.010	0.010	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.905	-0.939	23.621	-11.493	-11.493	0.000	0.000	0.000	0.000
11	A	12	THR	0	0.022	-0.012	21.088	-0.454	-0.454	0.000	0.000	0.000	0.000
12	A	13	ALA	0	0.024	0.028	20.887	-0.475	-0.475	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.012	0.003	20.986	-0.427	-0.427	0.000	0.000	0.000	0.000
14	A	15	SER	0	-0.062	-0.068	16.927	-0.677	-0.677	0.000	0.000	0.000	0.000
15	A	16	ALA	0	0.078	0.040	16.771	-0.874	-0.874	0.000	0.000	0.000	0.000
16	A	17	THR	0	-0.045	-0.018	17.087	-0.508	-0.508	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.024	-0.029	16.381	-0.528	-0.528	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.791	0.877	10.615	20.076	20.076	0.000	0.000	0.000	0.000
19	A	20	SER	0	-0.016	-0.013	12.654	-1.269	-1.269	0.000	0.000	0.000	0.000
20	A	21	ALA	0	-0.014	0.001	14.260	-0.590	-0.590	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.025	-0.013	10.268	-0.995	-0.995	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.824	-0.910	8.917	-25.085	-25.085	0.000	0.000	0.000	0.000
23	A	24	GLY	0	-0.022	-0.002	10.031	-1.128	-1.128	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.758	0.869	10.262	21.942	21.942	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.032	0.016	6.808	-1.948	-1.948	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.871	-0.933	8.469	-19.994	-19.994	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.801	-0.872	10.748	-16.917	-16.917	0.000	0.000	0.000	0.000
31	A	32	THR	0	-0.025	-0.013	14.521	0.767	0.767	0.000	0.000	0.000	0.000
32	A	33	THR	0	0.034	0.015	17.718	0.012	0.012	0.000	0.000	0.000	0.000
33	A	34	ASP	-1	-0.861	-0.926	20.767	-11.743	-11.743	0.000	0.000	0.000	0.000
34	A	35	GLY	0	0.038	0.006	21.033	-0.541	-0.541	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.876	0.954	22.722	10.217	10.217	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.022	0.014	21.449	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.045	-0.034	18.257	-0.609	-0.609	0.000	0.000	0.000	0.000
38	A	39	VAL	0	-0.021	-0.018	17.674	-0.696	-0.696	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.771	-0.862	18.711	-14.276	-14.276	0.000	0.000	0.000	0.000
40	A	41	GLN	0	-0.047	-0.006	13.551	0.523	0.523	0.000	0.000	0.000	0.000
41	A	42	ILE	0	0.039	0.010	13.942	-1.044	-1.044	0.000	0.000	0.000	0.000
42	A	43	ARG	1	0.744	0.826	14.318	13.130	13.130	0.000	0.000	0.000	0.000
43	A	44	ARG	1	0.899	0.952	13.810	17.307	17.307	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.866	-0.918	9.806	-26.140	-26.140	0.000	0.000	0.000	0.000
45	A	46	ARG	1	0.856	0.938	9.992	20.388	20.388	0.000	0.000	0.000	0.000
46	A	47	PRO	0	-0.038	-0.010	8.120	-2.725	-2.725	0.000	0.000	0.000	0.000
47	A	48	ASP	-1	-0.818	-0.906	5.255	-48.128	-48.128	0.000	0.000	0.000	0.000
48	A	49	LEU	0	-0.021	-0.008	8.558	2.440	2.440	0.000	0.000	0.000	0.000
49	A	50	VAL	0	-0.028	-0.018	11.189	-0.246	-0.246	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.022	0.018	13.612	0.665	0.665	0.000	0.000	0.000	0.000
51	A	52	LEU	0	-0.023	-0.013	15.904	0.378	0.378	0.000	0.000	0.000	0.000
52	A	53	ALA	0	0.036	0.019	19.202	0.479	0.479	0.000	0.000	0.000	0.000
53	A	54	VAL	0	-0.070	-0.037	22.317	0.180	0.180	0.000	0.000	0.000	0.000
54	A	55	ASP	-1	-0.894	-0.959	25.788	-10.482	-10.482	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.006	0.005	22.154	-0.118	-0.118	0.000	0.000	0.000	0.000
56	A	57	SER	0	0.012	0.011	25.615	0.550	0.550	0.000	0.000	0.000	0.000
57	A	58	ALA	0	0.002	-0.014	27.905	-0.102	-0.102	0.000	0.000	0.000	0.000
58	A	59	GLY	0	0.003	-0.001	30.428	0.026	0.026	0.000	0.000	0.000	0.000
59	A	60	GLN	0	-0.051	-0.022	25.642	-0.161	-0.161	0.000	0.000	0.000	0.000
60	A	61	ASN	0	0.051	0.010	27.315	-0.112	-0.112	0.000	0.000	0.000	0.000
61	A	62	GLY	0	0.091	0.044	23.878	-0.091	-0.091	0.000	0.000	0.000	0.000
62	A	63	TYR	0	0.015	-0.005	24.142	-0.437	-0.437	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.038	-0.014	26.637	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	65	ILE	0	-0.018	0.006	21.106	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	66	CYS	0	-0.009	0.011	21.873	-0.433	-0.433	0.000	0.000	0.000	0.000
66	A	67	GLY	0	0.003	0.001	22.908	-0.109	-0.109	0.000	0.000	0.000	0.000
67	A	68	LYS	1	0.895	0.944	23.973	12.262	12.262	0.000	0.000	0.000	0.000
68	A	69	LEU	0	0.051	0.023	17.939	0.066	0.066	0.000	0.000	0.000	0.000
69	A	70	LYS	1	0.829	0.907	18.571	16.328	16.328	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.849	0.924	22.618	11.241	11.241	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.803	-0.870	21.517	-13.665	-13.665	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.854	-0.924	21.522	-12.952	-12.952	0.000	0.000	0.000	0.000
73	A	74	ASP	-1	-0.878	-0.926	18.441	-15.294	-15.294	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.105	-0.060	16.457	-1.271	-1.271	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.834	0.921	17.100	12.690	12.690	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.027	-0.030	16.058	0.659	0.659	0.000	0.000	0.000	0.000
77	A	78	VAL	0	0.011	0.026	12.304	-0.924	-0.924	0.000	0.000	0.000	0.000
78	A	79	PRO	0	-0.020	-0.005	12.855	1.573	1.573	0.000	0.000	0.000	0.000
79	A	80	ILE	0	-0.029	-0.027	14.771	-0.529	-0.529	0.000	0.000	0.000	0.000
80	A	81	VAL	0	0.025	0.013	15.973	0.697	0.697	0.000	0.000	0.000	0.000
81	A	82	ILE	0	-0.042	-0.027	18.359	0.051	0.051	0.000	0.000	0.000	0.000
82	A	83	ILE	0	0.043	0.028	19.335	0.112	0.112	0.000	0.000	0.000	0.000
83	A	84	GLY	0	0.049	-0.002	22.492	0.232	0.232	0.000	0.000	0.000	0.000
84	A	85	ASN	0	0.018	0.010	26.272	-0.141	-0.141	0.000	0.000	0.000	0.000
85	A	86	PRO	0	0.058	0.010	29.062	-0.086	-0.086	0.000	0.000	0.000	0.000
86	A	87	ASP	-1	-0.865	-0.909	30.017	-8.954	-8.954	0.000	0.000	0.000	0.000
87	A	88	GLY	0	-0.052	-0.021	31.062	0.183	0.183	0.000	0.000	0.000	0.000
88	A	89	PHE	0	-0.005	-0.006	25.926	-0.024	-0.024	0.000	0.000	0.000	0.000
89	A	90	ALA	0	-0.022	-0.017	29.476	-0.137	-0.137	0.000	0.000	0.000	0.000
90	A	91	GLN	0	0.017	-0.002	32.523	0.067	0.067	0.000	0.000	0.000	0.000
91	A	92	HIS	0	0.059	0.041	25.505	-0.433	-0.433	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.990	0.984	27.796	10.631	10.631	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.898	0.965	29.672	8.929	8.929	0.000	0.000	0.000	0.000
94	A	95	LEU	0	-0.016	0.011	29.079	0.215	0.215	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.955	0.969	29.545	9.405	9.405	0.000	0.000	0.000	0.000
96	A	97	ALA	0	0.014	0.026	25.733	-0.254	-0.254	0.000	0.000	0.000	0.000
97	A	98	HIS	1	0.830	0.900	24.719	12.371	12.371	0.000	0.000	0.000	0.000
98	A	99	ALA	0	0.056	0.012	21.259	-0.336	-0.336	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.833	-0.890	18.751	-16.306	-16.306	0.000	0.000	0.000	0.000
100	A	101	GLU	-1	-0.786	-0.856	19.255	-16.075	-16.075	0.000	0.000	0.000	0.000
101	A	102	ALA	0	-0.058	-0.031	21.464	-0.043	-0.043	0.000	0.000	0.000	0.000
102	A	103	VAL	0	0.003	0.010	20.333	0.254	0.254	0.000	0.000	0.000	0.000
103	A	104	ALA	0	-0.001	-0.011	23.315	0.095	0.095	0.000	0.000	0.000	0.000
104	A	105	LYS	1	0.840	0.928	23.732	11.839	11.839	0.000	0.000	0.000	0.000
105	A	106	PRO	0	-0.017	-0.022	26.616	0.370	0.370	0.000	0.000	0.000	0.000
106	A	107	VAL	0	0.001	-0.007	20.331	0.061	0.061	0.000	0.000	0.000	0.000
107	A	108	ASP	-1	-0.887	-0.923	22.125	-13.475	-13.475	0.000	0.000	0.000	0.000
108	A	109	ALA	0	0.033	-0.003	18.715	-0.583	-0.583	0.000	0.000	0.000	0.000
109	A	110	ASP	-1	-0.860	-0.916	17.588	-16.460	-16.460	0.000	0.000	0.000	0.000
110	A	111	GLN	0	0.003	-0.008	17.608	-1.065	-1.065	0.000	0.000	0.000	0.000
111	A	112	LEU	0	-0.029	-0.027	15.915	-0.432	-0.432	0.000	0.000	0.000	0.000
112	A	113	VAL	0	0.011	0.008	12.447	-1.327	-1.327	0.000	0.000	0.000	0.000
113	A	114	GLU	-1	-0.813	-0.893	13.406	-20.777	-20.777	0.000	0.000	0.000	0.000
114	A	115	ARG	1	0.733	0.835	15.664	16.392	16.392	0.000	0.000	0.000	0.000
115	A	116	ALA	0	0.013	0.008	11.002	-0.515	-0.515	0.000	0.000	0.000	0.000
116	A	117	GLY	0	0.017	-0.001	10.981	-1.953	-1.953	0.000	0.000	0.000	0.000
117	A	118	ALA	0	-0.083	-0.042	12.029	-0.651	-0.651	0.000	0.000	0.000	0.000
118	A	119	LEU	0	-0.051	-0.022	13.889	0.191	0.191	0.000	0.000	0.000	0.000
119	A	120	ILE	0	-0.013	-0.003	7.532	-0.093	-0.093	0.000	0.000	0.000	0.000
120	A	121	GLY	0	0.010	0.026	8.430	-4.180	-4.180	0.000	0.000	0.000	0.000
121	A	122	PHE	0	0.004	-0.017	7.922	-2.818	-2.818	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)