FMO DATABASE

FMODB ID: 4G1LN

Calculation Name: 1NN7-A-Xray549

Preferred Name: Potassium voltage-gated channel subfamily D member 2

Target Type: SINGLE PROTEIN

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1NN7

Chain ID: A

ChEMBL ID: CHEMBL1075227

UniProt ID: Q63881

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

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	-898914.993117
FMO2-HF: Nuclear repulsion	854215.741455
FMO2-HF: Total energy	-44699.251662
FMO2-MP2: Total energy	-44830.464485

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:42:LEU)

Summations of interaction energy for fragment #1(A:42:LEU)

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.
-186.349	-174.275	12.884	-9.066	-15.888	-0.101

Interaction energy analysis for fragmet #1(A:42:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.751 / q_NPA : 0.877

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	44	VAL	0	-0.027	-0.023	3.180	-2.778	-0.740	0.087	-0.967	-1.157	-0.005
4	A	45	LEU	0	0.026	0.009	5.241	1.949	2.009	-0.001	-0.003	-0.056	0.000
12	A	53	GLN	0	-0.056	-0.047	2.560	-0.576	0.963	1.779	-0.743	-2.575	-0.004
13	A	54	THR	0	0.054	0.038	3.153	2.609	3.926	0.250	-0.468	-1.099	-0.004
14	A	55	TRP	0	0.015	-0.010	2.256	-47.061	-40.074	10.766	-6.842	-10.910	-0.088
15	A	56	GLN	0	0.088	0.027	3.939	5.126	5.259	0.003	-0.043	-0.091	0.000
5	A	46	ASN	0	-0.039	-0.028	8.328	1.440	1.440	0.000	0.000	0.000	0.000
6	A	47	VAL	0	0.050	0.025	11.024	0.722	0.722	0.000	0.000	0.000	0.000
7	A	48	SER	0	0.030	-0.004	14.044	0.467	0.467	0.000	0.000	0.000	0.000
8	A	49	GLY	0	-0.033	-0.007	15.113	0.786	0.786	0.000	0.000	0.000	0.000
9	A	50	THR	0	-0.035	-0.010	12.189	-0.417	-0.417	0.000	0.000	0.000	0.000
10	A	51	ARG	1	0.907	0.959	6.629	29.140	29.140	0.000	0.000	0.000	0.000
11	A	52	PHE	0	0.059	0.037	7.781	-1.024	-1.024	0.000	0.000	0.000	0.000
16	A	57	ASP	-1	-0.858	-0.922	6.623	-33.142	-33.142	0.000	0.000	0.000	0.000
17	A	58	THR	0	-0.133	-0.065	6.678	3.421	3.421	0.000	0.000	0.000	0.000
18	A	59	LEU	0	0.001	-0.006	7.752	1.961	1.961	0.000	0.000	0.000	0.000
19	A	60	GLU	-1	-0.869	-0.937	10.176	-24.372	-24.372	0.000	0.000	0.000	0.000
20	A	61	ARG	1	0.805	0.912	9.624	26.731	26.731	0.000	0.000	0.000	0.000
21	A	62	TYR	0	-0.026	0.000	14.036	1.603	1.603	0.000	0.000	0.000	0.000
22	A	63	PRO	0	0.009	0.022	15.878	-0.386	-0.386	0.000	0.000	0.000	0.000
23	A	64	ASP	-1	-0.956	-0.986	17.152	-13.060	-13.060	0.000	0.000	0.000	0.000
24	A	65	THR	0	0.016	0.021	16.001	-0.247	-0.247	0.000	0.000	0.000	0.000
25	A	66	LEU	0	0.030	0.036	15.385	-1.170	-1.170	0.000	0.000	0.000	0.000
26	A	67	LEU	0	-0.037	-0.041	11.244	-1.267	-1.267	0.000	0.000	0.000	0.000
27	A	68	GLY	0	0.027	0.016	11.651	-2.655	-2.655	0.000	0.000	0.000	0.000
28	A	69	SER	0	-0.042	-0.029	13.604	0.338	0.338	0.000	0.000	0.000	0.000
29	A	70	SER	0	0.011	-0.005	14.891	-0.957	-0.957	0.000	0.000	0.000	0.000
30	A	71	GLU	-1	-0.876	-0.916	16.870	-15.533	-15.533	0.000	0.000	0.000	0.000
31	A	72	ARG	1	0.838	0.911	9.365	29.597	29.597	0.000	0.000	0.000	0.000
32	A	73	ASP	-1	-0.918	-0.973	13.925	-22.594	-22.594	0.000	0.000	0.000	0.000
33	A	74	PHE	0	-0.074	-0.026	15.637	0.360	0.360	0.000	0.000	0.000	0.000
34	A	75	PHE	0	0.063	0.029	14.599	0.487	0.487	0.000	0.000	0.000	0.000
35	A	76	TYR	0	-0.037	-0.007	10.030	-1.769	-1.769	0.000	0.000	0.000	0.000
36	A	77	HIS	0	-0.007	-0.008	13.167	2.462	2.462	0.000	0.000	0.000	0.000
37	A	78	PRO	0	-0.001	-0.015	13.520	-1.236	-1.236	0.000	0.000	0.000	0.000
38	A	79	GLU	-1	-0.952	-0.966	13.919	-17.023	-17.023	0.000	0.000	0.000	0.000
39	A	80	THR	0	-0.032	-0.023	12.369	-0.306	-0.306	0.000	0.000	0.000	0.000
40	A	81	GLN	0	-0.103	-0.051	8.788	-2.646	-2.646	0.000	0.000	0.000	0.000
41	A	82	GLN	0	-0.023	0.000	8.210	-3.823	-3.823	0.000	0.000	0.000	0.000
42	A	83	TYR	0	0.006	0.018	8.529	0.374	0.374	0.000	0.000	0.000	0.000
43	A	84	PHE	0	-0.041	-0.012	10.989	-0.946	-0.946	0.000	0.000	0.000	0.000
44	A	85	PHE	0	0.025	0.000	11.198	0.251	0.251	0.000	0.000	0.000	0.000
45	A	86	ASP	-1	-0.935	-0.963	16.005	-14.623	-14.623	0.000	0.000	0.000	0.000
46	A	87	ARG	1	0.799	0.870	17.357	14.357	14.357	0.000	0.000	0.000	0.000
47	A	88	ASP	-1	-0.791	-0.884	18.500	-14.343	-14.343	0.000	0.000	0.000	0.000
48	A	89	PRO	0	-0.043	-0.024	15.687	-0.818	-0.818	0.000	0.000	0.000	0.000
49	A	90	ASP	-1	-0.920	-0.967	15.364	-15.637	-15.637	0.000	0.000	0.000	0.000
50	A	91	ILE	0	0.001	-0.012	17.282	-0.398	-0.398	0.000	0.000	0.000	0.000
51	A	92	PHE	0	0.014	0.011	10.100	-0.889	-0.889	0.000	0.000	0.000	0.000
52	A	93	ARG	1	0.936	0.973	12.752	14.573	14.573	0.000	0.000	0.000	0.000
53	A	94	HIS	0	-0.015	-0.007	13.619	-0.978	-0.978	0.000	0.000	0.000	0.000
54	A	95	ILE	0	0.027	0.034	13.931	-0.254	-0.254	0.000	0.000	0.000	0.000
55	A	96	LEU	0	-0.009	-0.011	6.978	-1.146	-1.146	0.000	0.000	0.000	0.000
56	A	97	ASN	0	-0.090	-0.070	11.063	-1.490	-1.490	0.000	0.000	0.000	0.000
57	A	98	PHE	0	0.058	0.058	12.792	-0.237	-0.237	0.000	0.000	0.000	0.000
58	A	99	TYR	0	0.033	-0.001	10.786	-0.328	-0.328	0.000	0.000	0.000	0.000
59	A	100	ARG	1	0.843	0.923	10.477	18.998	18.998	0.000	0.000	0.000	0.000
60	A	101	THR	0	-0.047	-0.034	12.135	0.151	0.151	0.000	0.000	0.000	0.000
61	A	102	GLY	0	0.036	0.037	15.979	0.740	0.740	0.000	0.000	0.000	0.000
62	A	103	LYS	0	-0.071	-0.026	17.831	0.942	0.942	0.000	0.000	0.000	0.000
63	A	104	LEU	0	0.006	0.008	18.047	-0.926	-0.926	0.000	0.000	0.000	0.000
64	A	105	HIS	0	-0.055	-0.082	18.041	0.082	0.082	0.000	0.000	0.000	0.000
65	A	106	TYR	0	0.012	-0.002	20.808	-0.272	-0.272	0.000	0.000	0.000	0.000
66	A	107	PRO	0	-0.057	-0.007	21.132	0.304	0.304	0.000	0.000	0.000	0.000
67	A	108	ARG	0	0.084	0.064	23.535	0.358	0.358	0.000	0.000	0.000	0.000
68	A	109	HIS	0	-0.098	-0.046	22.070	0.579	0.579	0.000	0.000	0.000	0.000
69	A	110	GLU	-1	-0.870	-0.933	22.079	-12.545	-12.545	0.000	0.000	0.000	0.000
70	A	111	CYS	-1	-0.851	-0.846	25.957	-9.959	-9.959	0.000	0.000	0.000	0.000
71	A	112	ILE	0	-0.007	-0.013	26.325	-0.466	-0.466	0.000	0.000	0.000	0.000
72	A	113	SER	0	0.026	-0.020	27.543	-0.087	-0.087	0.000	0.000	0.000	0.000
73	A	114	ALA	0	0.004	-0.042	25.033	-0.205	-0.205	0.000	0.000	0.000	0.000
74	A	115	TYR	0	-0.028	-0.046	20.757	-0.520	-0.520	0.000	0.000	0.000	0.000
75	A	116	ASP	-1	-0.766	-0.872	22.871	-11.498	-11.498	0.000	0.000	0.000	0.000
76	A	117	GLU	-1	-0.912	-0.925	24.815	-11.859	-11.859	0.000	0.000	0.000	0.000
77	A	118	GLU	-1	-0.788	-0.884	19.255	-14.940	-14.940	0.000	0.000	0.000	0.000
78	A	119	LEU	0	-0.054	-0.024	20.142	-0.770	-0.770	0.000	0.000	0.000	0.000
79	A	120	ALA	0	-0.011	-0.005	21.547	-0.267	-0.267	0.000	0.000	0.000	0.000
80	A	121	PHE	0	-0.032	-0.013	18.236	-0.156	-0.156	0.000	0.000	0.000	0.000
81	A	122	PHE	0	-0.002	-0.032	15.118	-0.799	-0.799	0.000	0.000	0.000	0.000
82	A	123	GLY	0	0.035	0.021	18.278	-0.708	-0.708	0.000	0.000	0.000	0.000
83	A	124	LEU	0	-0.071	-0.029	16.773	-0.124	-0.124	0.000	0.000	0.000	0.000
84	A	125	ILE	0	-0.024	0.009	20.835	0.619	0.619	0.000	0.000	0.000	0.000
85	A	126	PRO	0	-0.030	-0.029	24.582	0.013	0.013	0.000	0.000	0.000	0.000
86	A	127	GLU	-1	-0.838	-0.933	23.526	-11.488	-11.488	0.000	0.000	0.000	0.000
87	A	128	ILE	0	-0.041	-0.011	21.554	0.387	0.387	0.000	0.000	0.000	0.000
88	A	129	ILE	0	-0.030	-0.012	22.348	-0.554	-0.554	0.000	0.000	0.000	0.000
89	A	130	GLY	0	0.040	0.013	23.261	0.288	0.288	0.000	0.000	0.000	0.000
90	A	131	ASP	-1	-0.917	-0.976	24.526	-10.245	-10.245	0.000	0.000	0.000	0.000
91	A	132	CYS	0	-0.170	-0.121	24.333	0.152	0.152	0.000	0.000	0.000	0.000
92	A	133	CYS	-1	-0.755	-0.770	23.886	-12.024	-12.024	0.000	0.000	0.000	0.000
93	A	134	TYR	0	-0.009	0.002	26.426	0.356	0.356	0.000	0.000	0.000	0.000
94	A	135	GLU	-1	-0.789	-0.898	28.748	-8.623	-8.623	0.000	0.000	0.000	0.000
95	A	136	GLU	0	-0.046	-0.048	28.645	0.258	0.258	0.000	0.000	0.000	0.000
96	A	137	TYR	0	-0.028	-0.050	26.337	0.188	0.188	0.000	0.000	0.000	0.000
97	A	138	LYS	1	0.853	0.917	29.050	8.731	8.731	0.000	0.000	0.000	0.000
98	A	139	ASP	-1	-0.926	-0.963	32.253	-8.200	-8.200	0.000	0.000	0.000	0.000
99	A	140	ARG	1	0.849	0.929	29.665	9.746	9.746	0.000	0.000	0.000	0.000
100	A	141	ARG	1	0.872	0.931	29.181	10.140	10.140	0.000	0.000	0.000	0.000
101	A	142	ARG	1	0.787	0.880	32.740	7.612	7.612	0.000	0.000	0.000	0.000
102	A	143	GLU	-1	-0.935	-0.975	35.211	-8.232	-8.232	0.000	0.000	0.000	0.000
103	A	144	ASN	0	-0.060	-0.032	32.964	0.173	0.173	0.000	0.000	0.000	0.000
104	A	145	ALA	0	-0.072	-0.034	35.603	-0.033	-0.033	0.000	0.000	0.000	0.000
105	A	146	GLU	-2	-1.833	-1.880	38.114	-14.291	-14.291	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:42:LEU)