FMO DATABASE

FMODB ID: RMQL8

Calculation Name: 3SWF-B-Xray547

Preferred Name: cGMP-gated cation channel alpha 1

Target Type: SINGLE PROTEIN

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3SWF

Chain ID: B

ChEMBL ID: CHEMBL4907

UniProt ID: Q00194

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	58
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-253197.416097
FMO2-HF: Nuclear repulsion	228955.790347
FMO2-HF: Total energy	-24241.62575
FMO2-MP2: Total energy	-24311.09251

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:3:MET)

Summations of interaction energy for fragment #1(A:3:MET)

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.
-62.781	-56.748	12.612	-10.672	-7.974	-0.125

Interaction energy analysis for fragmet #1(A:3:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.842 / 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

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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	5	LEU	0	0.012	0.013	3.553	7.655	9.940	-0.001	-0.962	-1.322	-0.001
4	A	6	GLU	-1	-0.756	-0.879	1.770	-120.313	-117.223	12.611	-9.568	-6.134	-0.124
5	A	7	GLU	-1	-0.831	-0.876	3.822	-30.964	-30.306	0.002	-0.142	-0.518	0.000
6	A	8	LYS	1	0.943	0.963	5.695	40.181	40.181	0.000	0.000	0.000	0.000
7	A	9	VAL	0	0.018	0.013	7.945	3.678	3.678	0.000	0.000	0.000	0.000
8	A	10	THR	0	0.020	0.003	7.485	3.838	3.838	0.000	0.000	0.000	0.000
9	A	11	ARG	1	0.811	0.879	7.400	31.408	31.408	0.000	0.000	0.000	0.000
10	A	12	MET	0	-0.016	0.007	11.769	2.679	2.679	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.879	-0.932	13.247	-18.212	-18.212	0.000	0.000	0.000	0.000
12	A	14	SER	0	0.024	0.011	14.411	1.895	1.895	0.000	0.000	0.000	0.000
13	A	15	SER	0	-0.048	-0.044	15.450	1.472	1.472	0.000	0.000	0.000	0.000
14	A	16	VAL	0	-0.023	-0.012	17.790	1.226	1.226	0.000	0.000	0.000	0.000
15	A	17	ASP	-1	-0.817	-0.896	18.566	-15.601	-15.601	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.039	-0.026	19.042	1.224	1.224	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.083	-0.024	22.038	0.823	0.823	0.000	0.000	0.000	0.000
18	A	20	GLN	0	0.031	0.005	23.239	0.276	0.276	0.000	0.000	0.000	0.000
19	A	21	THR	0	-0.019	-0.019	24.172	0.769	0.769	0.000	0.000	0.000	0.000
20	A	22	ARG	1	0.896	0.948	22.011	13.578	13.578	0.000	0.000	0.000	0.000
21	A	23	PHE	0	0.024	0.002	27.133	0.442	0.442	0.000	0.000	0.000	0.000
22	A	24	ALA	0	0.030	0.021	29.633	0.405	0.405	0.000	0.000	0.000	0.000
23	A	25	ARG	1	0.895	0.958	28.685	10.909	10.909	0.000	0.000	0.000	0.000
24	A	26	ILE	0	0.041	0.016	30.939	0.291	0.291	0.000	0.000	0.000	0.000
25	A	27	LEU	0	0.010	0.012	34.143	0.324	0.324	0.000	0.000	0.000	0.000
26	A	28	ALA	0	0.016	0.011	35.821	0.307	0.307	0.000	0.000	0.000	0.000
27	A	29	GLU	-1	-0.942	-0.983	35.098	-8.778	-8.778	0.000	0.000	0.000	0.000
28	A	30	TYR	0	-0.014	-0.013	36.481	0.256	0.256	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.838	-0.915	40.292	-7.157	-7.157	0.000	0.000	0.000	0.000
30	A	32	SER	0	-0.015	0.009	41.653	0.349	0.349	0.000	0.000	0.000	0.000
31	A	33	MET	0	-0.012	-0.011	43.046	0.310	0.310	0.000	0.000	0.000	0.000
32	A	34	GLN	0	-0.005	-0.007	44.188	0.261	0.261	0.000	0.000	0.000	0.000
33	A	35	GLN	0	0.047	0.021	46.179	0.205	0.205	0.000	0.000	0.000	0.000
34	A	36	LYS	1	0.892	0.937	45.061	7.253	7.253	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.019	-0.009	47.276	0.179	0.179	0.000	0.000	0.000	0.000
36	A	38	LYS	1	0.968	0.987	48.808	6.792	6.792	0.000	0.000	0.000	0.000
37	A	39	GLN	0	-0.032	-0.005	50.779	0.051	0.051	0.000	0.000	0.000	0.000
38	A	40	ARG	1	0.929	0.959	50.678	6.303	6.303	0.000	0.000	0.000	0.000
39	A	41	LEU	0	0.038	0.032	54.793	0.102	0.102	0.000	0.000	0.000	0.000
40	A	42	THR	0	0.023	-0.003	55.901	0.124	0.124	0.000	0.000	0.000	0.000
41	A	43	LYS	1	0.875	0.924	58.315	5.490	5.490	0.000	0.000	0.000	0.000
42	A	44	VAL	0	0.012	0.021	59.126	0.092	0.092	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.887	-0.952	59.145	-5.465	-5.465	0.000	0.000	0.000	0.000
44	A	46	LYS	1	0.904	0.943	60.067	5.466	5.466	0.000	0.000	0.000	0.000
45	A	47	PHE	0	-0.031	0.004	64.433	0.062	0.062	0.000	0.000	0.000	0.000
46	A	48	LEU	0	0.030	0.001	64.426	0.067	0.067	0.000	0.000	0.000	0.000
47	A	49	LYS	1	0.802	0.883	66.662	4.672	4.672	0.000	0.000	0.000	0.000
48	A	50	PRO	0	0.019	0.010	68.025	0.063	0.063	0.000	0.000	0.000	0.000
49	A	51	LEU	0	0.004	0.023	69.455	0.065	0.065	0.000	0.000	0.000	0.000
50	A	52	ILE	0	0.010	0.004	68.516	0.062	0.062	0.000	0.000	0.000	0.000
51	A	53	ASP	-1	-0.868	-0.930	72.321	-4.465	-4.465	0.000	0.000	0.000	0.000
52	A	54	THR	0	-0.113	-0.076	74.551	0.073	0.073	0.000	0.000	0.000	0.000
53	A	55	GLU	-1	-0.958	-0.972	74.982	-4.277	-4.277	0.000	0.000	0.000	0.000
54	A	56	PHE	0	-0.080	-0.046	72.891	0.038	0.038	0.000	0.000	0.000	0.000
55	A	57	SER	0	0.012	0.012	74.381	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	58	ALA	0	-0.037	-0.029	75.092	-0.023	-0.023	0.000	0.000	0.000	0.000
57	A	59	ILE	0	-0.061	-0.024	69.745	-0.014	-0.014	0.000	0.000	0.000	0.000
58	A	60	GLU	-2	-1.818	-1.868	69.895	-9.211	-9.211	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:MET)