FMO DATABASE

FMODB ID: JVYK9

Calculation Name: 2K1W-A-Other547

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2K1W

Chain ID: A

ChEMBL ID:

UniProt ID: Q8TMX3

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	85
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-545283.674467
FMO2-HF: Nuclear repulsion	512602.589703
FMO2-HF: Total energy	-32681.084764
FMO2-MP2: Total energy	-32777.537851

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:MET)

Summations of interaction energy for fragment #1(A:1: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.
-61.116	-59.562	-0.021	-0.681	-0.852	-0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.815 / q_NPA : 0.898

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	3	ALA	0	0.033	0.019	3.828	1.061	2.615	-0.021	-0.681	-0.852	-0.002
4	A	4	ALA	0	0.018	0.012	6.731	4.066	4.066	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.935	-0.961	9.877	-28.627	-28.627	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.038	-0.010	12.268	1.866	1.866	0.000	0.000	0.000	0.000
7	A	7	ILE	0	0.008	0.012	15.642	0.036	0.036	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.028	-0.011	17.995	0.618	0.618	0.000	0.000	0.000	0.000
9	A	9	TYR	0	0.025	0.013	21.652	-0.402	-0.402	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.860	-0.914	24.682	-12.511	-12.511	0.000	0.000	0.000	0.000
11	A	11	HIS	1	0.876	0.926	27.376	10.427	10.427	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.002	0.027	29.054	-0.299	-0.299	0.000	0.000	0.000	0.000
13	A	13	ASN	0	0.008	0.003	26.570	0.045	0.045	0.000	0.000	0.000	0.000
14	A	14	PHE	0	0.009	0.003	28.682	-0.222	-0.222	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.008	-0.014	30.661	0.351	0.351	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.010	0.002	28.744	0.255	0.255	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.842	0.930	22.024	13.986	13.986	0.000	0.000	0.000	0.000
18	A	18	SER	0	0.032	0.022	19.930	0.366	0.366	0.000	0.000	0.000	0.000
19	A	19	PHE	0	-0.042	-0.029	19.382	0.129	0.129	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.847	-0.922	15.319	-18.444	-18.444	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.010	0.016	12.835	-0.973	-0.973	0.000	0.000	0.000	0.000
22	A	22	THR	0	0.000	-0.009	8.848	-0.990	-0.990	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.019	-0.022	11.570	1.214	1.214	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.972	-0.976	12.763	-21.669	-21.669	0.000	0.000	0.000	0.000
25	A	25	GLN	0	0.074	0.045	14.840	1.437	1.437	0.000	0.000	0.000	0.000
26	A	26	PRO	0	-0.055	-0.042	17.988	0.004	0.004	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.004	0.006	20.285	0.663	0.663	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.015	-0.017	21.758	-0.338	-0.338	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.016	0.000	24.684	0.105	0.105	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.955	-0.966	27.356	-10.835	-10.835	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.023	-0.012	30.056	0.004	0.004	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.013	-0.006	32.819	0.267	0.267	0.000	0.000	0.000	0.000
33	A	33	ASN	0	0.059	0.028	35.056	-0.075	-0.075	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.748	-0.861	33.550	-9.775	-9.775	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.833	0.910	34.601	8.598	8.598	0.000	0.000	0.000	0.000
36	A	36	ILE	0	0.007	0.005	31.945	-0.170	-0.170	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.026	-0.008	27.839	0.056	0.056	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.040	-0.029	24.824	0.248	0.248	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.002	0.019	22.674	-0.590	-0.590	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.976	0.985	18.186	16.921	16.921	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.017	0.024	16.775	-0.891	-0.891	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.835	0.890	16.629	16.003	16.003	0.000	0.000	0.000	0.000
43	A	43	SER	0	0.042	0.014	13.294	-1.180	-1.180	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.018	0.037	15.113	0.387	0.387	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.048	-0.034	16.744	1.035	1.035	0.000	0.000	0.000	0.000
46	A	46	TRP	0	-0.013	-0.027	17.583	-0.370	-0.370	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.914	0.976	21.080	13.779	13.779	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.043	0.006	22.806	-0.569	-0.569	0.000	0.000	0.000	0.000
49	A	49	TYR	0	-0.024	-0.033	24.713	0.131	0.131	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.850	-0.925	29.143	-11.052	-11.052	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.024	-0.008	30.953	0.511	0.511	0.000	0.000	0.000	0.000
52	A	52	ILE	0	0.014	0.029	30.512	-0.371	-0.371	0.000	0.000	0.000	0.000
53	A	53	ASN	0	0.008	-0.001	26.046	-0.244	-0.244	0.000	0.000	0.000	0.000
54	A	54	TYR	0	-0.049	-0.031	29.117	-0.018	-0.018	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.013	-0.001	32.226	0.311	0.311	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.054	0.019	32.805	0.104	0.104	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.785	0.908	31.555	9.900	9.900	0.000	0.000	0.000	0.000
58	A	58	TYR	0	-0.096	-0.078	26.835	-0.119	-0.119	0.000	0.000	0.000	0.000
59	A	59	TRP	0	0.016	0.014	28.099	0.351	0.351	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.839	-0.896	24.652	-11.872	-11.872	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.036	-0.001	23.716	0.435	0.435	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.056	0.031	21.571	-0.536	-0.536	0.000	0.000	0.000	0.000
63	A	63	PRO	0	-0.008	0.002	18.824	0.034	0.034	0.000	0.000	0.000	0.000
64	A	64	GLY	0	-0.029	-0.012	20.837	0.244	0.244	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.983	-1.005	22.966	-12.600	-12.600	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.019	0.009	24.934	0.451	0.451	0.000	0.000	0.000	0.000
67	A	67	SER	0	0.051	0.022	27.698	-0.285	-0.285	0.000	0.000	0.000	0.000
68	A	68	SER	0	-0.034	-0.008	30.222	0.412	0.412	0.000	0.000	0.000	0.000
69	A	69	VAL	0	0.003	-0.020	33.565	-0.158	-0.158	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.942	-0.967	36.355	-7.789	-7.789	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.025	-0.018	36.074	0.212	0.212	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.008	0.003	32.526	-0.164	-0.164	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.003	0.013	34.144	-0.144	-0.144	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.017	-0.015	35.904	-0.177	-0.177	0.000	0.000	0.000	0.000
75	A	75	PRO	0	-0.070	-0.021	36.833	0.250	0.250	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.915	-0.984	37.400	-8.266	-8.266	0.000	0.000	0.000	0.000
77	A	77	ASN	0	-0.035	0.007	30.031	-0.193	-0.193	0.000	0.000	0.000	0.000
78	A	78	SER	0	-0.001	-0.006	33.297	-0.186	-0.186	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.061	-0.041	31.388	0.050	0.050	0.000	0.000	0.000	0.000
80	A	80	SER	0	0.031	0.022	29.099	0.046	0.046	0.000	0.000	0.000	0.000
81	A	81	SER	0	-0.033	-0.015	25.405	-0.416	-0.416	0.000	0.000	0.000	0.000
82	A	82	PHE	0	0.033	0.025	19.954	0.044	0.044	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.876	0.948	19.130	14.591	14.591	0.000	0.000	0.000	0.000
84	A	84	GLN	0	-0.015	-0.018	15.936	-0.393	-0.393	0.000	0.000	0.000	0.000
85	A	85	ILE	-1	-0.878	-0.928	14.335	-19.207	-19.207	0.000	0.000	0.000	0.000

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