FMO DATABASE

FMODB ID: GVVR1

Calculation Name: 2PC6-A-Xray547

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PC6

Chain ID: A

ChEMBL ID:

UniProt ID: Q82UZ2

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	164
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1513152.656572
FMO2-HF: Nuclear repulsion	1448949.327531
FMO2-HF: Total energy	-64203.329042
FMO2-MP2: Total energy	-64389.596372

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:0:HIS)

Summations of interaction energy for fragment #1(A:0:HIS)

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.
-48.773	-42.121	7.002	-5.378	-8.276	-0.031

Interaction energy analysis for fragmet #1(A:0:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.809 / q_NPA : 0.897

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	2	ARG	1	0.901	0.937	3.821	30.070	31.903	-0.027	-0.758	-1.048	0.000
30	A	29	ASN	0	0.043	0.013	4.688	0.245	0.309	-0.001	-0.005	-0.058	0.000
52	A	51	ASN	0	-0.018	-0.012	2.416	-2.239	-1.847	1.824	-0.809	-1.406	0.005
53	A	52	GLY	0	0.064	0.021	2.703	-0.926	1.976	2.591	-2.293	-3.201	-0.009
54	A	53	PRO	0	-0.043	-0.023	2.540	-21.626	-20.296	2.610	-1.457	-2.484	-0.027
55	A	54	ASP	-1	-0.791	-0.913	3.933	-32.347	-32.216	0.005	-0.056	-0.079	0.000
4	A	3	HIS	1	0.820	0.904	5.801	36.228	36.228	0.000	0.000	0.000	0.000
5	A	4	ILE	0	0.010	0.008	8.857	0.689	0.689	0.000	0.000	0.000	0.000
6	A	5	ILE	0	0.037	0.022	11.125	0.618	0.618	0.000	0.000	0.000	0.000
7	A	6	SER	0	-0.014	-0.005	14.182	0.884	0.884	0.000	0.000	0.000	0.000
8	A	7	LEU	0	0.006	-0.002	17.224	-0.001	-0.001	0.000	0.000	0.000	0.000
9	A	8	LEU	0	-0.013	0.000	20.256	0.222	0.222	0.000	0.000	0.000	0.000
10	A	9	MET	0	-0.017	-0.013	22.334	-0.434	-0.434	0.000	0.000	0.000	0.000
11	A	10	GLU	-1	-0.811	-0.903	24.565	-9.825	-9.825	0.000	0.000	0.000	0.000
12	A	11	ASN	0	-0.103	-0.047	26.631	-0.571	-0.571	0.000	0.000	0.000	0.000
13	A	12	GLU	-1	-0.902	-0.951	27.914	-9.339	-9.339	0.000	0.000	0.000	0.000
14	A	13	ALA	0	-0.010	-0.019	27.570	-0.360	-0.360	0.000	0.000	0.000	0.000
15	A	14	GLY	0	0.010	0.012	25.646	0.091	0.091	0.000	0.000	0.000	0.000
16	A	15	ALA	0	0.086	0.076	24.190	-0.456	-0.456	0.000	0.000	0.000	0.000
17	A	16	LEU	0	0.023	-0.001	18.558	-0.541	-0.541	0.000	0.000	0.000	0.000
18	A	17	SER	0	-0.081	-0.055	19.701	-0.488	-0.488	0.000	0.000	0.000	0.000
19	A	18	ARG	1	0.830	0.871	20.504	10.424	10.424	0.000	0.000	0.000	0.000
20	A	19	VAL	0	0.021	0.008	16.440	-0.569	-0.569	0.000	0.000	0.000	0.000
21	A	20	ALA	0	0.001	-0.007	15.741	-0.875	-0.875	0.000	0.000	0.000	0.000
22	A	21	GLY	0	0.009	-0.002	15.809	-0.648	-0.648	0.000	0.000	0.000	0.000
23	A	22	LEU	0	-0.049	-0.012	14.737	-0.358	-0.358	0.000	0.000	0.000	0.000
24	A	23	PHE	0	-0.007	-0.023	9.622	-0.675	-0.675	0.000	0.000	0.000	0.000
25	A	24	SER	0	-0.010	0.000	12.743	-0.813	-0.813	0.000	0.000	0.000	0.000
26	A	25	ALA	0	0.001	-0.001	14.533	-0.257	-0.257	0.000	0.000	0.000	0.000
27	A	26	ARG	1	0.884	0.943	12.904	17.335	17.335	0.000	0.000	0.000	0.000
28	A	27	GLY	0	0.013	0.022	11.113	-1.111	-1.111	0.000	0.000	0.000	0.000
29	A	28	TYR	0	-0.058	-0.034	8.275	-2.234	-2.234	0.000	0.000	0.000	0.000
31	A	30	ILE	0	0.044	0.038	6.586	-0.044	-0.044	0.000	0.000	0.000	0.000
32	A	31	GLU	-1	-0.839	-0.902	6.689	-28.229	-28.229	0.000	0.000	0.000	0.000
33	A	32	SER	0	0.000	-0.010	8.493	1.806	1.806	0.000	0.000	0.000	0.000
34	A	33	LEU	0	0.010	-0.003	12.137	-0.754	-0.754	0.000	0.000	0.000	0.000
35	A	34	SER	0	0.009	0.009	14.963	0.860	0.860	0.000	0.000	0.000	0.000
36	A	35	VAL	0	-0.042	-0.034	18.367	-0.310	-0.310	0.000	0.000	0.000	0.000
37	A	36	ALA	0	-0.005	0.011	21.315	0.306	0.306	0.000	0.000	0.000	0.000
38	A	37	PRO	0	0.036	0.017	25.098	-0.190	-0.190	0.000	0.000	0.000	0.000
39	A	38	THR	0	-0.061	-0.028	26.785	-0.141	-0.141	0.000	0.000	0.000	0.000
40	A	39	GLU	-1	-0.863	-0.937	29.218	-10.029	-10.029	0.000	0.000	0.000	0.000
41	A	40	ASP	-1	-0.861	-0.886	31.736	-8.739	-8.739	0.000	0.000	0.000	0.000
42	A	41	PRO	0	0.010	-0.009	31.437	-0.264	-0.264	0.000	0.000	0.000	0.000
43	A	42	THR	0	-0.045	-0.036	32.083	-0.126	-0.126	0.000	0.000	0.000	0.000
44	A	43	LEU	0	0.020	0.023	27.947	-0.287	-0.287	0.000	0.000	0.000	0.000
45	A	44	SER	0	-0.003	-0.017	24.448	0.126	0.126	0.000	0.000	0.000	0.000
46	A	45	ARG	1	0.836	0.924	20.796	13.340	13.340	0.000	0.000	0.000	0.000
47	A	46	MET	0	0.002	-0.005	17.268	-0.269	-0.269	0.000	0.000	0.000	0.000
48	A	47	THR	0	-0.061	-0.031	15.448	-0.219	-0.219	0.000	0.000	0.000	0.000
49	A	48	LEU	0	0.009	0.011	10.833	0.247	0.247	0.000	0.000	0.000	0.000
50	A	49	VAL	0	-0.039	-0.009	8.369	-0.867	-0.867	0.000	0.000	0.000	0.000
51	A	50	THR	0	-0.015	-0.021	6.675	-0.583	-0.583	0.000	0.000	0.000	0.000
56	A	55	GLU	-1	-0.918	-0.941	6.891	-22.105	-22.105	0.000	0.000	0.000	0.000
57	A	56	ILE	0	-0.019	-0.020	6.549	2.533	2.533	0.000	0.000	0.000	0.000
58	A	57	VAL	0	-0.011	-0.009	7.504	2.722	2.722	0.000	0.000	0.000	0.000
59	A	58	GLU	-1	-0.841	-0.926	8.952	-19.969	-19.969	0.000	0.000	0.000	0.000
60	A	59	GLN	0	-0.052	-0.009	11.648	2.255	2.255	0.000	0.000	0.000	0.000
61	A	60	ILE	0	0.007	0.004	9.087	1.761	1.761	0.000	0.000	0.000	0.000
62	A	61	THR	0	-0.015	-0.006	12.762	1.766	1.766	0.000	0.000	0.000	0.000
63	A	62	LYS	1	0.898	0.937	14.805	20.425	20.425	0.000	0.000	0.000	0.000
64	A	63	GLN	0	-0.059	-0.020	15.701	0.427	0.427	0.000	0.000	0.000	0.000
65	A	64	LEU	0	0.032	0.008	14.430	0.841	0.841	0.000	0.000	0.000	0.000
66	A	65	ASN	0	0.008	-0.005	18.426	1.083	1.083	0.000	0.000	0.000	0.000
67	A	66	LYS	1	0.924	0.975	21.201	14.162	14.162	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.027	-0.010	19.742	0.442	0.442	0.000	0.000	0.000	0.000
69	A	68	ILE	0	0.021	0.004	23.413	-0.043	-0.043	0.000	0.000	0.000	0.000
70	A	69	GLU	-1	-0.742	-0.833	24.684	-11.058	-11.058	0.000	0.000	0.000	0.000
71	A	70	VAL	0	-0.068	-0.027	20.465	-0.142	-0.142	0.000	0.000	0.000	0.000
72	A	71	VAL	0	0.028	0.027	23.657	0.008	0.008	0.000	0.000	0.000	0.000
73	A	72	LYS	1	0.810	0.896	24.018	11.474	11.474	0.000	0.000	0.000	0.000
74	A	73	LEU	0	-0.013	-0.004	16.095	-0.319	-0.319	0.000	0.000	0.000	0.000
75	A	74	ILE	0	-0.012	-0.001	17.684	0.190	0.190	0.000	0.000	0.000	0.000
76	A	75	ASP	-1	-0.753	-0.869	11.348	-25.917	-25.917	0.000	0.000	0.000	0.000
77	A	76	LEU	0	-0.017	-0.010	14.650	0.490	0.490	0.000	0.000	0.000	0.000
78	A	77	SER	0	-0.032	-0.024	11.193	0.185	0.185	0.000	0.000	0.000	0.000
79	A	78	SER	0	-0.077	-0.031	12.882	-0.220	-0.220	0.000	0.000	0.000	0.000
80	A	79	GLU	-1	-0.823	-0.901	13.767	-14.260	-14.260	0.000	0.000	0.000	0.000
81	A	80	GLY	0	0.011	0.006	17.014	-0.429	-0.429	0.000	0.000	0.000	0.000
82	A	81	TYR	0	-0.033	-0.008	14.337	0.303	0.303	0.000	0.000	0.000	0.000
83	A	82	VAL	0	-0.062	-0.035	19.655	0.183	0.183	0.000	0.000	0.000	0.000
84	A	83	GLU	-1	-0.824	-0.911	16.362	-17.810	-17.810	0.000	0.000	0.000	0.000
85	A	84	ARG	1	0.865	0.921	19.213	14.061	14.061	0.000	0.000	0.000	0.000
86	A	85	GLU	-1	-0.783	-0.868	15.899	-17.767	-17.767	0.000	0.000	0.000	0.000
87	A	86	LEU	0	0.023	0.012	19.521	0.343	0.343	0.000	0.000	0.000	0.000
88	A	87	MET	0	-0.029	-0.017	19.862	-0.710	-0.710	0.000	0.000	0.000	0.000
89	A	88	LEU	0	0.034	0.025	22.037	0.402	0.402	0.000	0.000	0.000	0.000
90	A	89	VAL	0	0.012	-0.001	22.337	-0.454	-0.454	0.000	0.000	0.000	0.000
91	A	90	LYS	1	0.866	0.941	24.855	9.991	9.991	0.000	0.000	0.000	0.000
92	A	91	VAL	0	0.030	0.003	26.264	-0.294	-0.294	0.000	0.000	0.000	0.000
93	A	92	ARG	1	0.906	0.935	28.594	9.185	9.185	0.000	0.000	0.000	0.000
94	A	93	ALA	0	0.030	0.010	31.130	-0.126	-0.126	0.000	0.000	0.000	0.000
95	A	94	VAL	0	0.035	0.015	33.752	0.271	0.271	0.000	0.000	0.000	0.000
96	A	95	GLY	0	0.017	0.006	36.544	-0.083	-0.083	0.000	0.000	0.000	0.000
97	A	96	LYS	1	0.867	0.915	36.823	7.608	7.608	0.000	0.000	0.000	0.000
98	A	97	ASP	-1	-0.824	-0.908	32.438	-9.098	-9.098	0.000	0.000	0.000	0.000
99	A	98	ARG	1	0.789	0.903	33.451	7.712	7.712	0.000	0.000	0.000	0.000
100	A	99	GLU	-1	-0.835	-0.915	35.761	-7.661	-7.661	0.000	0.000	0.000	0.000
101	A	100	GLU	-1	-0.812	-0.881	30.395	-9.673	-9.673	0.000	0.000	0.000	0.000
102	A	101	MET	0	0.019	0.003	27.902	-0.332	-0.332	0.000	0.000	0.000	0.000
103	A	102	LYS	1	0.816	0.906	30.920	8.371	8.371	0.000	0.000	0.000	0.000
104	A	103	ARG	1	0.849	0.907	32.579	8.769	8.769	0.000	0.000	0.000	0.000
105	A	104	LEU	0	0.023	0.015	26.273	-0.157	-0.157	0.000	0.000	0.000	0.000
106	A	105	ALA	0	0.021	0.009	28.354	-0.334	-0.334	0.000	0.000	0.000	0.000
107	A	106	ASP	-1	-0.796	-0.879	29.999	-8.927	-8.927	0.000	0.000	0.000	0.000
108	A	107	ILE	0	-0.065	-0.035	28.009	-0.046	-0.046	0.000	0.000	0.000	0.000
109	A	108	PHE	0	-0.038	-0.015	22.527	-0.237	-0.237	0.000	0.000	0.000	0.000
110	A	109	ARG	1	0.841	0.922	27.038	9.591	9.591	0.000	0.000	0.000	0.000
111	A	110	GLY	0	0.021	0.016	28.471	-0.210	-0.210	0.000	0.000	0.000	0.000
112	A	111	ASN	0	-0.048	-0.021	29.138	0.535	0.535	0.000	0.000	0.000	0.000
113	A	112	ILE	0	-0.015	-0.007	30.978	-0.214	-0.214	0.000	0.000	0.000	0.000
114	A	113	ILE	0	-0.016	-0.011	29.810	0.225	0.225	0.000	0.000	0.000	0.000
115	A	114	ASP	-1	-0.855	-0.924	33.126	-8.449	-8.449	0.000	0.000	0.000	0.000
116	A	115	VAL	0	-0.033	-0.013	34.284	-0.195	-0.195	0.000	0.000	0.000	0.000
117	A	116	THR	0	0.021	0.020	36.638	0.142	0.142	0.000	0.000	0.000	0.000
118	A	117	ASN	0	0.025	0.000	38.248	-0.118	-0.118	0.000	0.000	0.000	0.000
119	A	118	GLU	-1	-0.891	-0.946	36.665	-7.531	-7.531	0.000	0.000	0.000	0.000
120	A	119	LEU	0	-0.030	0.000	32.370	-0.260	-0.260	0.000	0.000	0.000	0.000
121	A	120	TYR	0	-0.016	-0.017	31.525	0.336	0.336	0.000	0.000	0.000	0.000
122	A	121	THR	0	-0.032	-0.026	28.553	-0.370	-0.370	0.000	0.000	0.000	0.000
123	A	122	ILE	0	-0.027	-0.018	27.574	0.288	0.288	0.000	0.000	0.000	0.000
124	A	123	GLU	-1	-0.896	-0.941	26.782	-10.514	-10.514	0.000	0.000	0.000	0.000
125	A	124	LEU	0	0.023	0.007	22.975	0.118	0.118	0.000	0.000	0.000	0.000
126	A	125	THR	0	0.053	0.025	23.457	-0.318	-0.318	0.000	0.000	0.000	0.000
127	A	126	GLY	0	-0.043	-0.027	22.263	0.371	0.371	0.000	0.000	0.000	0.000
128	A	127	THR	0	0.002	0.009	18.220	0.190	0.190	0.000	0.000	0.000	0.000
129	A	128	ARG	1	0.884	0.923	9.441	23.918	23.918	0.000	0.000	0.000	0.000
130	A	129	SER	0	-0.024	-0.017	15.949	0.280	0.280	0.000	0.000	0.000	0.000
131	A	130	LYS	1	0.832	0.924	17.086	12.518	12.518	0.000	0.000	0.000	0.000
132	A	131	LEU	0	0.027	0.014	18.173	0.565	0.565	0.000	0.000	0.000	0.000
133	A	132	ASP	-1	-0.753	-0.877	13.234	-20.026	-20.026	0.000	0.000	0.000	0.000
134	A	133	GLY	0	-0.008	-0.004	16.795	0.184	0.184	0.000	0.000	0.000	0.000
135	A	134	PHE	0	0.011	0.003	19.525	0.488	0.488	0.000	0.000	0.000	0.000
136	A	135	LEU	0	-0.020	-0.030	16.631	0.321	0.321	0.000	0.000	0.000	0.000
137	A	136	GLN	0	-0.076	-0.028	16.839	-0.676	-0.676	0.000	0.000	0.000	0.000
138	A	137	ALA	0	-0.015	-0.005	19.317	0.287	0.287	0.000	0.000	0.000	0.000
139	A	138	VAL	0	-0.027	-0.009	22.675	0.602	0.602	0.000	0.000	0.000	0.000
140	A	139	ASP	-1	-0.874	-0.918	22.670	-11.409	-11.409	0.000	0.000	0.000	0.000
141	A	140	CYS	0	-0.014	-0.024	20.408	0.333	0.333	0.000	0.000	0.000	0.000
142	A	141	ASN	0	0.006	-0.003	22.533	-0.163	-0.163	0.000	0.000	0.000	0.000
143	A	142	LEU	0	-0.015	-0.001	25.610	0.387	0.387	0.000	0.000	0.000	0.000
144	A	143	ILE	0	-0.029	-0.007	21.110	0.204	0.204	0.000	0.000	0.000	0.000
145	A	144	LEU	0	-0.076	-0.032	24.837	0.109	0.109	0.000	0.000	0.000	0.000
146	A	145	GLU	-1	-0.857	-0.922	23.447	-10.352	-10.352	0.000	0.000	0.000	0.000
147	A	146	ILE	0	-0.018	-0.017	19.115	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	147	ALA	0	-0.006	0.016	21.412	-0.148	-0.148	0.000	0.000	0.000	0.000
149	A	148	ARG	1	0.751	0.844	14.971	17.629	17.629	0.000	0.000	0.000	0.000
150	A	149	THR	0	0.006	-0.003	18.649	-0.137	-0.137	0.000	0.000	0.000	0.000
151	A	150	GLY	0	0.048	0.040	15.189	-0.093	-0.093	0.000	0.000	0.000	0.000
152	A	151	VAL	0	-0.062	-0.026	13.837	0.641	0.641	0.000	0.000	0.000	0.000
153	A	152	SER	0	0.052	0.030	16.316	0.077	0.077	0.000	0.000	0.000	0.000
154	A	153	GLY	0	0.031	-0.011	19.084	-0.289	-0.289	0.000	0.000	0.000	0.000
155	A	154	LEU	0	-0.030	-0.003	20.019	0.309	0.309	0.000	0.000	0.000	0.000
156	A	155	SER	0	0.055	0.019	20.225	-0.552	-0.552	0.000	0.000	0.000	0.000
157	A	156	ARG	1	0.878	0.936	21.554	14.277	14.277	0.000	0.000	0.000	0.000
158	A	157	GLY	0	0.000	0.003	24.360	-0.035	-0.035	0.000	0.000	0.000	0.000
159	A	158	GLU	-1	-0.883	-0.952	27.774	-9.925	-9.925	0.000	0.000	0.000	0.000
160	A	159	ARG	1	0.825	0.931	21.244	14.012	14.012	0.000	0.000	0.000	0.000
161	A	160	VAL	0	0.024	0.001	25.210	-0.420	-0.420	0.000	0.000	0.000	0.000
162	A	161	LEU	0	-0.011	-0.007	21.664	0.063	0.063	0.000	0.000	0.000	0.000
163	A	162	LYS	1	0.911	0.931	24.929	10.098	10.098	0.000	0.000	0.000	0.000
164	A	163	LEU	-1	-0.855	-0.898	27.220	-11.003	-11.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:HIS)