FMO DATABASE

FMODB ID: ZLNGN

Calculation Name: 3NX6-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3NX6

Chain ID: A

ChEMBL ID:

UniProt ID: Q5GUT0

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	75
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-419993.116271
FMO2-HF: Nuclear repulsion	392835.968295
FMO2-HF: Total energy	-27157.147976
FMO2-MP2: Total energy	-27238.738263

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.
-32.98	-30.343	0.09	-1.265	-1.462	-0.006

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 : 0.875 / q_NPA : 0.926

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	1.005	1.010	3.845	24.700	25.852	-0.006	-0.591	-0.555	0.000
55	A	75	TYR	0	-0.031	-0.017	4.044	0.623	0.798	-0.001	-0.042	-0.132	0.000
57	A	77	SER	0	-0.041	-0.028	2.920	-8.595	-7.417	0.098	-0.624	-0.652	-0.006
58	A	78	GLU	-1	-0.870	-0.928	4.497	-45.191	-45.059	-0.001	-0.008	-0.123	0.000
4	A	5	PRO	0	0.011	0.018	6.409	3.297	3.297	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.013	-0.023	9.557	0.685	0.685	0.000	0.000	0.000	0.000
6	A	7	HIS	0	0.017	-0.010	13.070	-0.277	-0.277	0.000	0.000	0.000	0.000
7	A	8	ASP	-1	-0.739	-0.832	15.692	-17.000	-17.000	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.889	0.954	12.792	19.451	19.451	0.000	0.000	0.000	0.000
9	A	10	VAL	0	0.053	0.025	12.301	-1.079	-1.079	0.000	0.000	0.000	0.000
10	A	11	VAL	0	-0.047	-0.023	6.634	0.005	0.005	0.000	0.000	0.000	0.000
11	A	12	VAL	0	0.038	0.021	9.938	0.031	0.031	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.931	0.974	9.959	22.652	22.652	0.000	0.000	0.000	0.000
13	A	14	PRO	0	-0.007	0.004	11.610	1.184	1.184	0.000	0.000	0.000	0.000
14	A	15	ILE	-1	-0.942	-0.959	14.867	-16.715	-16.715	0.000	0.000	0.000	0.000
15	A	35	SER	0	-0.023	-0.029	23.486	0.063	0.063	0.000	0.000	0.000	0.000
16	A	36	THR	0	-0.071	-0.045	19.941	0.232	0.232	0.000	0.000	0.000	0.000
17	A	37	LYS	1	0.997	0.997	20.072	13.060	13.060	0.000	0.000	0.000	0.000
18	A	38	GLY	0	0.031	0.005	15.856	-0.454	-0.454	0.000	0.000	0.000	0.000
19	A	39	GLU	-1	-0.937	-0.955	13.376	-20.587	-20.587	0.000	0.000	0.000	0.000
20	A	40	VAL	0	-0.018	-0.006	11.990	-2.051	-2.051	0.000	0.000	0.000	0.000
21	A	41	VAL	0	0.002	0.001	6.231	-0.611	-0.611	0.000	0.000	0.000	0.000
22	A	42	ALA	0	-0.028	-0.028	6.244	-3.201	-3.201	0.000	0.000	0.000	0.000
23	A	43	ILE	0	0.025	0.023	8.410	1.758	1.758	0.000	0.000	0.000	0.000
24	A	44	GLY	0	-0.032	-0.006	10.734	-1.768	-1.768	0.000	0.000	0.000	0.000
25	A	45	ALA	0	-0.036	-0.035	12.581	0.784	0.784	0.000	0.000	0.000	0.000
26	A	46	GLY	0	0.096	0.064	14.978	1.059	1.059	0.000	0.000	0.000	0.000
27	A	47	LYS	1	0.888	0.940	17.912	13.247	13.247	0.000	0.000	0.000	0.000
28	A	48	PRO	0	-0.019	-0.012	19.317	0.537	0.537	0.000	0.000	0.000	0.000
29	A	49	LEU	0	-0.002	0.007	22.441	0.178	0.178	0.000	0.000	0.000	0.000
30	A	50	ASP	-1	-0.893	-0.954	26.049	-10.828	-10.828	0.000	0.000	0.000	0.000
31	A	51	ASN	0	-0.044	-0.003	28.644	-0.124	-0.124	0.000	0.000	0.000	0.000
32	A	52	GLY	0	0.020	0.020	27.159	0.180	0.180	0.000	0.000	0.000	0.000
33	A	53	SER	0	-0.052	-0.032	25.268	-0.307	-0.307	0.000	0.000	0.000	0.000
34	A	54	LEU	0	-0.034	-0.027	18.486	-0.216	-0.216	0.000	0.000	0.000	0.000
35	A	55	HIS	0	0.010	-0.002	21.976	0.490	0.490	0.000	0.000	0.000	0.000
36	A	56	ALA	0	-0.006	-0.006	19.799	-0.821	-0.821	0.000	0.000	0.000	0.000
37	A	57	PRO	0	-0.015	-0.009	15.755	0.470	0.470	0.000	0.000	0.000	0.000
38	A	58	VAL	0	-0.032	-0.012	18.802	0.366	0.366	0.000	0.000	0.000	0.000
39	A	59	VAL	0	-0.048	-0.007	15.558	0.185	0.185	0.000	0.000	0.000	0.000
40	A	60	LYS	1	0.835	0.881	15.099	15.017	15.017	0.000	0.000	0.000	0.000
41	A	61	VAL	0	-0.019	-0.024	9.955	-0.137	-0.137	0.000	0.000	0.000	0.000
42	A	62	GLY	0	0.013	0.010	12.684	1.034	1.034	0.000	0.000	0.000	0.000
43	A	63	ASP	-1	-0.794	-0.855	14.584	-15.386	-15.386	0.000	0.000	0.000	0.000
44	A	64	LYS	1	0.876	0.930	16.253	13.430	13.430	0.000	0.000	0.000	0.000
45	A	65	VAL	0	-0.003	-0.008	16.421	0.692	0.692	0.000	0.000	0.000	0.000
46	A	66	ILE	0	-0.032	-0.014	19.384	-0.036	-0.036	0.000	0.000	0.000	0.000
47	A	67	TYR	0	0.076	0.036	16.500	-0.286	-0.286	0.000	0.000	0.000	0.000
48	A	68	GLY	0	0.070	0.028	20.882	0.509	0.509	0.000	0.000	0.000	0.000
49	A	69	GLN	0	0.044	0.042	19.990	-1.067	-1.067	0.000	0.000	0.000	0.000
50	A	70	TYR	0	-0.059	-0.048	20.023	-0.744	-0.744	0.000	0.000	0.000	0.000
51	A	71	ALA	0	0.025	0.035	19.697	0.255	0.255	0.000	0.000	0.000	0.000
52	A	72	GLY	0	0.025	0.004	16.564	-0.756	-0.756	0.000	0.000	0.000	0.000
53	A	73	SER	0	-0.065	-0.034	13.784	0.739	0.739	0.000	0.000	0.000	0.000
54	A	74	SER	0	-0.022	-0.013	12.709	-1.029	-1.029	0.000	0.000	0.000	0.000
56	A	76	LYS	1	0.977	0.976	7.959	21.345	21.345	0.000	0.000	0.000	0.000
59	A	79	GLY	0	-0.013	0.001	7.516	2.766	2.766	0.000	0.000	0.000	0.000
60	A	80	VAL	0	-0.046	-0.014	8.536	2.644	2.644	0.000	0.000	0.000	0.000
61	A	81	GLU	-1	-0.920	-0.963	8.833	-21.883	-21.883	0.000	0.000	0.000	0.000
62	A	82	TYR	0	-0.017	-0.012	6.591	-0.643	-0.643	0.000	0.000	0.000	0.000
63	A	83	LYS	1	0.928	0.972	10.019	18.557	18.557	0.000	0.000	0.000	0.000
64	A	84	VAL	0	-0.045	-0.025	9.338	-2.073	-2.073	0.000	0.000	0.000	0.000
65	A	85	LEU	0	0.007	0.011	11.879	1.570	1.570	0.000	0.000	0.000	0.000
66	A	86	ARG	1	0.762	0.829	14.790	14.668	14.668	0.000	0.000	0.000	0.000
67	A	87	GLU	-1	-0.790	-0.913	17.549	-15.877	-15.877	0.000	0.000	0.000	0.000
68	A	88	ASP	-1	-0.931	-0.962	18.817	-12.501	-12.501	0.000	0.000	0.000	0.000
69	A	89	ASP	-1	-0.856	-0.920	18.604	-15.776	-15.776	0.000	0.000	0.000	0.000
70	A	90	ILE	0	-0.086	-0.049	16.706	-0.078	-0.078	0.000	0.000	0.000	0.000
71	A	91	LEU	0	-0.024	-0.007	20.840	0.530	0.530	0.000	0.000	0.000	0.000
72	A	92	ALA	0	0.008	-0.004	22.945	0.529	0.529	0.000	0.000	0.000	0.000
73	A	93	VAL	0	0.022	0.015	19.856	-0.654	-0.654	0.000	0.000	0.000	0.000
74	A	94	ILE	0	-0.084	-0.051	21.710	0.675	0.675	0.000	0.000	0.000	0.000
75	A	95	GLY	-1	-0.830	-0.894	20.458	-14.426	-14.426	0.000	0.000	0.000	0.000

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