FMO DATABASE

FMODB ID: 2MK3R

Calculation Name: 1N4Y-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1N4Y

Chain ID: A

ChEMBL ID:

UniProt ID: P30403

Base Structure: SolutionNMR

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	62
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-346907.363233
FMO2-HF: Nuclear repulsion	317739.347079
FMO2-HF: Total energy	-29168.016155
FMO2-MP2: Total energy	-29240.942204

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:1:GLY)

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

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.
-153.063	-146.834	16.385	-12.283	-10.329	-0.145

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.797 / q_NPA : 0.887

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

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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	3	GLU	-1	-0.851	-0.914	3.185	-25.524	-23.700	0.007	-0.817	-1.013	-0.003
4	A	4	CYS	0	-0.085	-0.045	1.940	-43.566	-41.499	7.397	-4.764	-4.700	-0.057
16	A	17	ALA	0	-0.017	0.000	3.773	-14.270	-13.227	0.003	-0.648	-0.397	-0.004
17	A	18	THR	0	0.017	-0.006	1.810	-43.632	-42.510	8.967	-6.016	-4.073	-0.080
18	A	20	LYS	1	0.912	0.948	3.421	49.551	49.724	0.011	-0.038	-0.146	-0.001
5	A	5	ASP	-1	-0.795	-0.891	5.953	-26.871	-26.871	0.000	0.000	0.000	0.000
6	A	6	CYS	0	-0.125	-0.023	6.875	4.672	4.672	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.006	-0.015	8.317	-3.047	-3.047	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.052	-0.038	9.885	-0.385	-0.385	0.000	0.000	0.000	0.000
9	A	9	PRO	0	-0.049	-0.024	6.757	-1.979	-1.979	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.895	-0.957	8.158	-26.916	-26.916	0.000	0.000	0.000	0.000
11	A	11	ASN	0	-0.023	-0.020	10.315	2.584	2.584	0.000	0.000	0.000	0.000
12	A	12	PRO	0	0.010	0.004	10.809	-1.633	-1.633	0.000	0.000	0.000	0.000
13	A	13	CYS	0	-0.028	-0.010	12.239	0.687	0.687	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.854	-0.911	6.135	-33.690	-33.690	0.000	0.000	0.000	0.000
15	A	16	ALA	0	0.071	0.040	5.431	-7.368	-7.368	0.000	0.000	0.000	0.000
19	A	21	LEU	0	0.014	-0.001	6.274	0.580	0.580	0.000	0.000	0.000	0.000
20	A	22	ARG	1	0.846	0.934	9.554	25.951	25.951	0.000	0.000	0.000	0.000
21	A	23	PRO	0	-0.025	-0.005	11.689	1.648	1.648	0.000	0.000	0.000	0.000
22	A	24	GLY	0	0.018	0.006	15.212	-0.373	-0.373	0.000	0.000	0.000	0.000
23	A	25	ALA	0	-0.075	-0.045	14.870	1.099	1.099	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.018	-0.004	16.409	0.223	0.223	0.000	0.000	0.000	0.000
25	A	27	CYS	0	-0.046	-0.007	13.896	-0.286	-0.286	0.000	0.000	0.000	0.000
26	A	28	GLY	0	0.072	0.010	11.615	0.280	0.280	0.000	0.000	0.000	0.000
27	A	29	GLU	-1	-0.783	-0.875	12.199	-23.520	-23.520	0.000	0.000	0.000	0.000
28	A	30	GLY	0	0.049	0.022	14.768	-0.144	-0.144	0.000	0.000	0.000	0.000
29	A	31	LEU	0	-0.026	-0.017	17.955	0.369	0.369	0.000	0.000	0.000	0.000
30	A	32	CYS	0	-0.057	0.003	21.070	0.654	0.654	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.869	-0.933	19.118	-14.303	-14.303	0.000	0.000	0.000	0.000
32	A	35	GLN	0	-0.035	-0.023	19.400	0.333	0.333	0.000	0.000	0.000	0.000
33	A	37	LYS	1	0.924	0.956	16.992	14.667	14.667	0.000	0.000	0.000	0.000
34	A	38	PHE	0	0.029	0.012	17.839	0.072	0.072	0.000	0.000	0.000	0.000
35	A	39	SER	0	0.003	0.001	21.916	0.776	0.776	0.000	0.000	0.000	0.000
36	A	40	ARG	1	0.919	0.945	24.767	10.112	10.112	0.000	0.000	0.000	0.000
37	A	41	ALA	0	0.079	0.029	28.397	0.045	0.045	0.000	0.000	0.000	0.000
38	A	42	GLY	0	-0.003	-0.010	30.604	0.329	0.329	0.000	0.000	0.000	0.000
39	A	43	LYS	1	0.867	0.945	27.835	11.086	11.086	0.000	0.000	0.000	0.000
40	A	44	ILE	0	-0.009	0.000	29.499	-0.252	-0.252	0.000	0.000	0.000	0.000
41	A	45	CYS	0	-0.106	-0.016	21.102	0.471	0.471	0.000	0.000	0.000	0.000
42	A	46	ARG	1	0.870	0.916	25.301	11.461	11.461	0.000	0.000	0.000	0.000
43	A	47	ILE	0	0.001	0.004	28.725	0.322	0.322	0.000	0.000	0.000	0.000
44	A	48	PRO	0	-0.005	0.014	31.779	-0.155	-0.155	0.000	0.000	0.000	0.000
45	A	49	ARG	1	0.948	0.953	31.526	9.667	9.667	0.000	0.000	0.000	0.000
46	A	50	GLY	0	-0.004	-0.005	36.887	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	51	ASP	-1	-0.884	-0.943	40.422	-7.769	-7.769	0.000	0.000	0.000	0.000
48	A	52	MET	0	-0.063	-0.014	35.926	-0.047	-0.047	0.000	0.000	0.000	0.000
49	A	53	PRO	0	0.006	0.003	36.115	0.023	0.023	0.000	0.000	0.000	0.000
50	A	54	ASP	-1	-0.831	-0.902	33.845	-9.148	-9.148	0.000	0.000	0.000	0.000
51	A	55	ASP	-1	-0.759	-0.873	28.463	-11.042	-11.042	0.000	0.000	0.000	0.000
52	A	56	ARG	1	0.829	0.872	30.313	8.872	8.872	0.000	0.000	0.000	0.000
53	A	58	THR	0	0.072	0.019	26.509	0.254	0.254	0.000	0.000	0.000	0.000
54	A	59	GLY	0	-0.060	-0.010	26.633	0.329	0.329	0.000	0.000	0.000	0.000
55	A	60	GLN	0	-0.041	-0.025	25.319	0.167	0.167	0.000	0.000	0.000	0.000
56	A	61	SER	0	-0.048	-0.048	21.998	-0.405	-0.405	0.000	0.000	0.000	0.000
57	A	62	ALA	0	0.072	0.044	17.605	0.265	0.265	0.000	0.000	0.000	0.000
58	A	63	ASP	-1	-0.857	-0.935	19.537	-14.821	-14.821	0.000	0.000	0.000	0.000
59	A	65	PRO	0	-0.007	0.015	24.855	-0.053	-0.053	0.000	0.000	0.000	0.000
60	A	66	ARG	1	0.928	0.945	27.253	10.181	10.181	0.000	0.000	0.000	0.000
61	A	67	TYR	0	-0.028	-0.026	30.622	0.273	0.273	0.000	0.000	0.000	0.000
62	A	68	HIS	-1	-0.878	-0.911	30.677	-9.861	-9.861	0.000	0.000	0.000	0.000

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