FMO DATABASE

FMODB ID: RMJJ8

Calculation Name: 1A2X-A-Xray547

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1A2X

Chain ID: A

ChEMBL ID:

UniProt ID: P02586

Base Structure: X-ray

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	158
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1448903.828014
FMO2-HF: Nuclear repulsion	1383782.440971
FMO2-HF: Total energy	-65121.387043
FMO2-MP2: Total energy	-65303.519702

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:ASP)

Summations of interaction energy for fragment #1(A:2:ASP)

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.
-16.353	-12.662	1.673	-1.954	-3.41	-0.007

Interaction energy analysis for fragmet #1(A:2:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.081 / q_NPA : -0.056

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	GLN	0	0.057	0.017	2.144	2.036	5.370	1.674	-1.867	-3.141	-0.007
4	A	5	ALA	0	-0.019	-0.015	4.183	4.383	4.740	-0.001	-0.087	-0.269	0.000
5	A	6	GLU	-1	-0.914	-0.941	6.164	-0.906	-0.906	0.000	0.000	0.000	0.000
6	A	7	ALA	0	0.026	0.019	7.987	1.264	1.264	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.785	0.846	7.937	6.612	6.612	0.000	0.000	0.000	0.000
8	A	9	SER	0	-0.015	-0.001	10.180	0.974	0.974	0.000	0.000	0.000	0.000
9	A	10	TYR	0	-0.057	-0.046	12.091	0.537	0.537	0.000	0.000	0.000	0.000
10	A	11	LEU	0	0.005	0.007	13.158	0.408	0.408	0.000	0.000	0.000	0.000
11	A	12	SER	0	0.042	0.002	15.678	-0.060	-0.060	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.944	-0.975	17.179	-2.189	-2.189	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.861	-0.926	18.396	-1.599	-1.599	0.000	0.000	0.000	0.000
14	A	15	MET	0	0.022	0.020	18.125	-0.036	-0.036	0.000	0.000	0.000	0.000
15	A	16	ILE	0	0.003	0.011	13.042	-0.154	-0.154	0.000	0.000	0.000	0.000
16	A	17	ALA	0	-0.036	-0.023	16.411	-0.021	-0.021	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.959	-0.979	19.399	-1.379	-1.379	0.000	0.000	0.000	0.000
18	A	19	PHE	0	0.036	-0.016	15.352	0.041	0.041	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.798	0.889	15.320	2.371	2.371	0.000	0.000	0.000	0.000
20	A	21	ALA	0	-0.045	-0.014	18.173	0.126	0.126	0.000	0.000	0.000	0.000
21	A	22	ALA	0	-0.016	-0.015	21.234	0.124	0.124	0.000	0.000	0.000	0.000
22	A	23	PHE	0	0.006	0.003	15.013	0.085	0.085	0.000	0.000	0.000	0.000
23	A	24	ASP	-1	-0.771	-0.888	18.595	-1.933	-1.933	0.000	0.000	0.000	0.000
24	A	25	MET	0	-0.128	-0.044	20.927	0.155	0.155	0.000	0.000	0.000	0.000
25	A	26	PHE	0	-0.074	-0.056	22.067	0.173	0.173	0.000	0.000	0.000	0.000
26	A	27	ASP	-1	-0.780	-0.857	19.209	-1.627	-1.627	0.000	0.000	0.000	0.000
27	A	28	ALA	0	-0.081	-0.045	21.637	0.087	0.087	0.000	0.000	0.000	0.000
28	A	29	ASP	-1	-0.953	-0.990	20.296	-1.234	-1.234	0.000	0.000	0.000	0.000
29	A	30	GLY	0	-0.049	-0.019	21.811	0.084	0.084	0.000	0.000	0.000	0.000
30	A	31	GLY	0	-0.066	-0.029	18.665	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	32	GLY	0	-0.067	-0.034	15.477	-0.186	-0.186	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.852	-0.918	14.624	-2.317	-2.317	0.000	0.000	0.000	0.000
33	A	34	ILE	0	0.002	0.006	16.620	0.252	0.252	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.014	-0.008	18.246	0.002	0.002	0.000	0.000	0.000	0.000
35	A	36	VAL	0	0.061	0.027	17.701	-0.028	-0.028	0.000	0.000	0.000	0.000
36	A	37	LYS	1	0.809	0.892	20.101	0.774	0.774	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.869	-0.941	22.354	-0.897	-0.897	0.000	0.000	0.000	0.000
38	A	39	LEU	0	0.043	0.045	16.653	0.014	0.014	0.000	0.000	0.000	0.000
39	A	40	GLY	0	0.021	-0.005	20.135	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	41	THR	0	-0.105	-0.048	22.939	0.045	0.045	0.000	0.000	0.000	0.000
41	A	42	VAL	0	0.074	0.027	19.360	0.043	0.043	0.000	0.000	0.000	0.000
42	A	43	MET	0	0.004	0.001	18.431	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	44	ARG	1	0.840	0.936	21.594	0.983	0.983	0.000	0.000	0.000	0.000
44	A	45	MET	0	-0.094	-0.039	24.180	0.060	0.060	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.005	0.026	19.164	0.038	0.038	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.017	0.011	22.532	-0.061	-0.061	0.000	0.000	0.000	0.000
47	A	48	GLN	0	0.016	0.011	19.906	0.080	0.080	0.000	0.000	0.000	0.000
48	A	49	THR	0	-0.089	-0.063	23.362	0.054	0.054	0.000	0.000	0.000	0.000
49	A	50	PRO	0	0.066	0.054	21.599	0.088	0.088	0.000	0.000	0.000	0.000
50	A	51	THR	0	-0.079	-0.075	24.292	0.060	0.060	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.777	0.860	24.973	0.715	0.715	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.936	-0.970	25.092	-0.479	-0.479	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.791	-0.878	22.042	-0.834	-0.834	0.000	0.000	0.000	0.000
54	A	55	LEU	0	-0.015	0.000	20.265	-0.073	-0.073	0.000	0.000	0.000	0.000
55	A	56	ASP	-1	-0.825	-0.908	20.394	-0.828	-0.828	0.000	0.000	0.000	0.000
56	A	57	ALA	0	-0.013	-0.006	19.689	0.006	0.006	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.012	-0.007	15.915	-0.049	-0.049	0.000	0.000	0.000	0.000
58	A	59	ILE	0	-0.052	-0.030	15.785	-0.188	-0.188	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.968	-0.988	16.614	-0.584	-0.584	0.000	0.000	0.000	0.000
60	A	61	GLU	-1	-0.891	-0.926	11.277	-1.494	-1.494	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.026	-0.014	10.701	-0.187	-0.187	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.756	-0.849	11.915	-1.279	-1.279	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.956	-0.968	11.580	0.021	0.021	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-1.039	-1.027	14.207	-0.601	-0.601	0.000	0.000	0.000	0.000
65	A	66	GLY	0	-0.045	-0.010	16.385	0.129	0.129	0.000	0.000	0.000	0.000
66	A	67	SER	0	-0.093	-0.061	15.966	0.080	0.080	0.000	0.000	0.000	0.000
67	A	68	GLY	0	-0.095	-0.063	18.410	0.075	0.075	0.000	0.000	0.000	0.000
68	A	69	THR	0	-0.155	-0.105	16.938	0.107	0.107	0.000	0.000	0.000	0.000
69	A	70	ILE	0	0.032	0.023	12.932	0.025	0.025	0.000	0.000	0.000	0.000
70	A	71	ASP	-1	-0.760	-0.876	9.332	-5.723	-5.723	0.000	0.000	0.000	0.000
71	A	72	PHE	0	-0.019	-0.020	12.063	-0.143	-0.143	0.000	0.000	0.000	0.000
72	A	73	GLU	-1	-0.835	-0.892	6.828	-7.120	-7.120	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.855	-0.931	8.060	-4.698	-4.698	0.000	0.000	0.000	0.000
74	A	75	PHE	0	-0.022	-0.010	8.904	0.567	0.567	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.003	-0.001	9.703	0.389	0.389	0.000	0.000	0.000	0.000
76	A	77	VAL	0	-0.036	-0.025	5.896	0.172	0.172	0.000	0.000	0.000	0.000
77	A	78	MET	0	-0.062	-0.007	9.308	0.910	0.910	0.000	0.000	0.000	0.000
78	A	79	MET	0	0.007	0.010	12.349	0.552	0.552	0.000	0.000	0.000	0.000
79	A	80	VAL	0	-0.003	0.003	11.954	0.352	0.352	0.000	0.000	0.000	0.000
80	A	81	ARG	1	0.756	0.884	10.783	2.290	2.290	0.000	0.000	0.000	0.000
81	A	82	GLN	0	-0.024	-0.031	14.383	0.247	0.247	0.000	0.000	0.000	0.000
82	A	83	MET	0	0.026	0.013	17.360	0.136	0.136	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.844	0.921	14.504	1.667	1.667	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.895	-0.949	16.249	-1.205	-1.205	0.000	0.000	0.000	0.000
85	A	86	ASP	-1	-0.933	-0.957	19.890	-0.855	-0.855	0.000	0.000	0.000	0.000
86	A	87	ALA	0	-0.002	0.024	21.762	0.068	0.068	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.835	0.908	23.609	0.752	0.752	0.000	0.000	0.000	0.000
88	A	89	GLY	0	0.048	0.036	26.581	0.034	0.034	0.000	0.000	0.000	0.000
89	A	90	LYS	1	0.805	0.906	28.138	0.479	0.479	0.000	0.000	0.000	0.000
90	A	91	SER	0	-0.017	-0.027	27.396	-0.020	-0.020	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.826	-0.946	23.505	-0.488	-0.488	0.000	0.000	0.000	0.000
92	A	93	GLU	-1	-1.041	-1.001	27.796	-0.220	-0.220	0.000	0.000	0.000	0.000
93	A	94	GLU	-1	-0.751	-0.865	31.508	-0.391	-0.391	0.000	0.000	0.000	0.000
94	A	95	LEU	0	0.047	0.030	26.419	0.003	0.003	0.000	0.000	0.000	0.000
95	A	96	ALA	0	0.019	0.012	29.949	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	97	GLU	-1	-0.899	-0.940	31.004	-0.215	-0.215	0.000	0.000	0.000	0.000
97	A	98	CYS	0	-0.077	-0.044	31.712	0.004	0.004	0.000	0.000	0.000	0.000
98	A	99	PHE	0	0.033	0.035	27.684	0.019	0.019	0.000	0.000	0.000	0.000
99	A	100	ARG	1	0.811	0.891	31.597	0.249	0.249	0.000	0.000	0.000	0.000
100	A	101	ILE	0	-0.104	-0.046	34.697	0.031	0.031	0.000	0.000	0.000	0.000
101	A	102	PHE	0	-0.010	-0.018	31.541	0.011	0.011	0.000	0.000	0.000	0.000
102	A	103	ASP	0	0.057	0.031	32.572	0.019	0.019	0.000	0.000	0.000	0.000
103	A	104	ARG	1	0.751	0.887	34.484	0.325	0.325	0.000	0.000	0.000	0.000
104	A	105	ASN	0	-0.060	-0.033	34.257	0.035	0.035	0.000	0.000	0.000	0.000
105	A	106	ALA	0	-0.073	-0.032	35.476	0.026	0.026	0.000	0.000	0.000	0.000
106	A	107	ASP	-1	-0.882	-0.945	32.440	-0.238	-0.238	0.000	0.000	0.000	0.000
107	A	108	GLY	0	-0.053	-0.023	30.118	0.023	0.023	0.000	0.000	0.000	0.000
108	A	109	TYR	0	-0.075	-0.039	25.279	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	110	ILE	0	0.002	0.009	28.556	0.020	0.020	0.000	0.000	0.000	0.000
110	A	111	ASP	-1	-0.824	-0.916	28.919	-0.380	-0.380	0.000	0.000	0.000	0.000
111	A	112	ALA	0	0.094	0.035	30.256	-0.018	-0.018	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.954	-0.987	31.637	-0.380	-0.380	0.000	0.000	0.000	0.000
113	A	114	GLU	-1	-0.830	-0.928	33.544	-0.307	-0.307	0.000	0.000	0.000	0.000
114	A	115	LEU	0	0.003	0.001	29.413	0.008	0.008	0.000	0.000	0.000	0.000
115	A	116	ALA	0	0.012	0.003	33.115	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.970	-0.998	36.056	-0.265	-0.265	0.000	0.000	0.000	0.000
117	A	118	ILE	0	-0.042	0.001	33.001	0.021	0.021	0.000	0.000	0.000	0.000
118	A	119	PHE	0	0.080	0.034	32.338	0.024	0.024	0.000	0.000	0.000	0.000
119	A	120	ARG	1	0.881	0.967	38.166	0.343	0.343	0.000	0.000	0.000	0.000
120	A	121	ALA	0	-0.067	-0.023	40.846	0.020	0.020	0.000	0.000	0.000	0.000
121	A	122	SER	0	-0.028	-0.021	39.550	0.000	0.000	0.000	0.000	0.000	0.000
122	A	123	GLY	0	-0.067	-0.045	41.686	0.013	0.013	0.000	0.000	0.000	0.000
123	A	124	GLU	-1	-0.977	-0.987	37.681	-0.488	-0.488	0.000	0.000	0.000	0.000
124	A	125	HIS	0	-0.095	-0.054	40.285	0.014	0.014	0.000	0.000	0.000	0.000
125	A	126	VAL	0	0.039	0.037	34.082	-0.013	-0.013	0.000	0.000	0.000	0.000
126	A	127	THR	0	-0.091	-0.050	33.690	0.041	0.041	0.000	0.000	0.000	0.000
127	A	128	ASP	-1	-0.874	-0.954	34.223	-0.493	-0.493	0.000	0.000	0.000	0.000
128	A	129	GLU	-1	-0.903	-0.960	29.491	-0.722	-0.722	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.887	-0.926	29.551	-0.683	-0.683	0.000	0.000	0.000	0.000
130	A	131	ILE	0	-0.028	-0.003	29.633	-0.035	-0.035	0.000	0.000	0.000	0.000
131	A	132	GLU	-1	-0.912	-0.958	28.459	-0.622	-0.622	0.000	0.000	0.000	0.000
132	A	133	SER	0	-0.075	-0.055	25.566	-0.081	-0.081	0.000	0.000	0.000	0.000
133	A	134	LEU	0	-0.035	-0.017	24.790	-0.070	-0.070	0.000	0.000	0.000	0.000
134	A	135	MET	0	-0.018	-0.002	25.517	-0.023	-0.023	0.000	0.000	0.000	0.000
135	A	136	LYS	1	0.890	0.947	20.471	1.129	1.129	0.000	0.000	0.000	0.000
136	A	137	ASP	-1	-0.922	-0.963	20.193	-1.345	-1.345	0.000	0.000	0.000	0.000
137	A	138	GLY	0	0.028	0.011	19.925	-0.127	-0.127	0.000	0.000	0.000	0.000
138	A	139	ASP	-1	-0.834	-0.930	20.627	-0.875	-0.875	0.000	0.000	0.000	0.000
139	A	140	LYS	1	0.771	0.884	15.526	1.862	1.862	0.000	0.000	0.000	0.000
140	A	141	ASN	0	-0.083	-0.032	16.046	-0.034	-0.034	0.000	0.000	0.000	0.000
141	A	142	ASN	0	-0.130	-0.062	17.523	0.012	0.012	0.000	0.000	0.000	0.000
142	A	143	ASP	-1	-0.849	-0.905	20.487	-0.380	-0.380	0.000	0.000	0.000	0.000
143	A	144	GLY	0	-0.045	-0.021	23.580	0.065	0.065	0.000	0.000	0.000	0.000
144	A	145	ARG	1	0.754	0.861	25.101	0.374	0.374	0.000	0.000	0.000	0.000
145	A	146	ILE	0	0.032	0.036	23.620	-0.058	-0.058	0.000	0.000	0.000	0.000
146	A	147	ASP	-1	-0.838	-0.932	22.200	-0.435	-0.435	0.000	0.000	0.000	0.000
147	A	148	PHE	0	-0.025	-0.019	24.996	-0.050	-0.050	0.000	0.000	0.000	0.000
148	A	149	ASP	-1	-0.915	-0.964	19.905	-0.412	-0.412	0.000	0.000	0.000	0.000
149	A	150	GLU	-1	-0.790	-0.897	19.797	-0.914	-0.914	0.000	0.000	0.000	0.000
150	A	151	PHE	0	0.015	-0.003	21.431	-0.081	-0.081	0.000	0.000	0.000	0.000
151	A	152	LEU	0	-0.056	-0.033	21.981	-0.034	-0.034	0.000	0.000	0.000	0.000
152	A	153	LYS	1	0.826	0.911	16.988	0.925	0.925	0.000	0.000	0.000	0.000
153	A	154	MET	0	0.008	0.020	20.404	-0.051	-0.051	0.000	0.000	0.000	0.000
154	A	155	MET	0	-0.046	-0.022	22.981	0.000	0.000	0.000	0.000	0.000	0.000
155	A	156	GLU	-1	-0.813	-0.873	18.604	-1.192	-1.192	0.000	0.000	0.000	0.000
156	A	157	GLY	0	-0.029	-0.022	23.104	-0.059	-0.059	0.000	0.000	0.000	0.000
157	A	158	VAL	0	-0.031	-0.002	25.223	0.018	0.018	0.000	0.000	0.000	0.000
158	A	159	GLN	-1	-1.032	-1.026	27.940	-0.516	-0.516	0.000	0.000	0.000	0.000

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