FMO DATABASE

FMODB ID: 8QQ6Y

Calculation Name: 2PY2-A-Xray547

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PY2

Chain ID: A

ChEMBL ID:

UniProt ID: Q91992

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	122
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1138716.580684
FMO2-HF: Nuclear repulsion	1085278.570951
FMO2-HF: Total energy	-53438.009733
FMO2-MP2: Total energy	-53582.711489

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:4:CYS)

Summations of interaction energy for fragment #1(A:4:CYS)

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.
-184.03	-174.634	34.613	-15.871	-28.136	-0.046

Interaction energy analysis for fragmet #1(A:4:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.768 / q_NPA : 0.893

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	6	THR	0	0.050	0.004	3.799	-0.787	0.480	-0.004	-0.519	-0.744	0.000
5	A	8	TRP	0	-0.028	-0.019	2.296	-0.959	1.233	1.729	-1.189	-2.732	-0.010
6	A	9	LYS	1	0.896	0.955	2.950	22.851	24.878	0.502	-1.126	-1.403	-0.011
7	A	10	MET	0	-0.002	-0.021	2.460	-12.972	-7.773	8.197	-5.656	-7.741	-0.001
8	A	11	PHE	0	0.032	0.021	1.959	-6.828	-10.287	5.951	0.207	-2.699	0.032
9	A	12	ASN	0	-0.009	-0.006	3.186	-3.148	-2.843	0.365	0.215	-0.885	-0.001
10	A	13	GLY	0	0.051	0.036	3.881	-1.814	-0.575	-0.013	-0.748	-0.477	-0.002
13	A	17	LEU	0	-0.003	-0.002	3.852	-3.136	-1.082	-0.024	-1.001	-1.029	0.004
118	A	126	ALA	0	0.009	-0.012	4.474	-2.754	-2.570	-0.002	-0.055	-0.127	0.000
119	A	127	LYS	1	0.871	0.938	2.414	43.697	45.576	0.527	-0.709	-1.696	-0.002
120	A	128	PRO	0	-0.004	0.001	1.789	-19.293	-23.981	11.658	-3.989	-2.980	-0.046
121	A	129	LEU	0	-0.007	-0.016	2.395	-5.950	-4.381	5.714	-2.098	-5.185	-0.008
122	A	130	LYS	0	-0.033	-0.012	4.007	-6.169	-6.541	0.013	0.797	-0.438	-0.001
4	A	7	ASP	-1	-0.866	-0.920	5.549	-31.124	-31.124	0.000	0.000	0.000	0.000
14	A	18	PHE	0	0.047	0.030	6.780	1.525	1.525	0.000	0.000	0.000	0.000
15	A	19	ASN	0	0.006	-0.002	10.559	0.002	0.002	0.000	0.000	0.000	0.000
16	A	20	PRO	0	0.027	0.007	12.778	0.841	0.841	0.000	0.000	0.000	0.000
17	A	21	LEU	0	-0.034	-0.009	16.044	1.037	1.037	0.000	0.000	0.000	0.000
18	A	22	GLN	0	-0.009	0.001	17.926	-0.680	-0.680	0.000	0.000	0.000	0.000
19	A	23	LEU	0	-0.007	0.000	16.733	0.385	0.385	0.000	0.000	0.000	0.000
20	A	24	HIS	0	0.030	0.033	20.469	-0.102	-0.102	0.000	0.000	0.000	0.000
21	A	25	TRP	0	0.015	-0.010	16.454	-0.569	-0.569	0.000	0.000	0.000	0.000
22	A	26	ALA	0	0.009	0.002	17.980	-0.745	-0.745	0.000	0.000	0.000	0.000
23	A	27	ASP	-1	-0.812	-0.917	18.271	-13.606	-13.606	0.000	0.000	0.000	0.000
24	A	28	ALA	0	-0.047	-0.026	15.616	-0.845	-0.845	0.000	0.000	0.000	0.000
25	A	29	GLN	0	0.027	-0.011	13.189	-1.946	-1.946	0.000	0.000	0.000	0.000
26	A	30	GLU	-1	-0.912	-0.972	13.815	-15.067	-15.067	0.000	0.000	0.000	0.000
27	A	31	SER	0	-0.069	-0.060	13.825	-0.268	-0.268	0.000	0.000	0.000	0.000
28	A	32	CYS	0	-0.062	0.004	7.871	-0.024	-0.024	0.000	0.000	0.000	0.000
29	A	33	MET	0	0.023	0.021	10.016	-1.292	-1.292	0.000	0.000	0.000	0.000
30	A	34	LYS	1	0.886	0.965	12.225	17.239	17.239	0.000	0.000	0.000	0.000
31	A	35	GLU	-1	-0.932	-0.948	7.919	-28.520	-28.520	0.000	0.000	0.000	0.000
32	A	36	GLY	0	-0.022	-0.003	7.748	-3.370	-3.370	0.000	0.000	0.000	0.000
33	A	37	ALA	0	-0.096	-0.047	6.114	-2.861	-2.861	0.000	0.000	0.000	0.000
34	A	38	ASN	0	0.043	0.034	7.751	3.987	3.987	0.000	0.000	0.000	0.000
35	A	39	LEU	0	0.030	0.017	8.895	-2.189	-2.189	0.000	0.000	0.000	0.000
36	A	40	ALA	0	-0.058	-0.035	8.231	-0.142	-0.142	0.000	0.000	0.000	0.000
37	A	41	SER	0	0.010	-0.006	8.793	1.613	1.613	0.000	0.000	0.000	0.000
38	A	42	ILE	0	-0.048	-0.020	8.984	-1.868	-1.868	0.000	0.000	0.000	0.000
39	A	43	HIS	1	0.829	0.872	8.672	20.864	20.864	0.000	0.000	0.000	0.000
40	A	44	SER	0	-0.036	-0.035	11.884	0.390	0.390	0.000	0.000	0.000	0.000
41	A	45	LEU	0	0.073	0.044	13.284	-0.414	-0.414	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.844	-0.900	12.098	-15.508	-15.508	0.000	0.000	0.000	0.000
43	A	47	GLU	-1	-0.769	-0.880	6.528	-25.653	-25.653	0.000	0.000	0.000	0.000
44	A	48	SER	0	0.001	-0.006	10.127	-0.797	-0.797	0.000	0.000	0.000	0.000
45	A	49	THR	0	-0.037	-0.029	13.070	0.312	0.312	0.000	0.000	0.000	0.000
46	A	50	PHE	0	0.020	0.010	5.245	-0.102	-0.102	0.000	0.000	0.000	0.000
47	A	51	VAL	0	-0.016	-0.026	8.107	-0.766	-0.766	0.000	0.000	0.000	0.000
48	A	52	LYS	1	0.843	0.939	10.317	14.187	14.187	0.000	0.000	0.000	0.000
49	A	53	GLU	-1	-0.914	-0.947	11.780	-17.605	-17.605	0.000	0.000	0.000	0.000
50	A	54	LEU	0	-0.085	-0.035	6.659	-0.651	-0.651	0.000	0.000	0.000	0.000
51	A	55	THR	0	-0.055	-0.026	11.158	0.388	0.388	0.000	0.000	0.000	0.000
52	A	56	SER	0	-0.027	-0.022	14.461	1.318	1.318	0.000	0.000	0.000	0.000
53	A	57	ALA	0	0.040	0.006	16.817	0.165	0.165	0.000	0.000	0.000	0.000
54	A	58	ASP	-1	-0.912	-0.946	19.971	-12.127	-12.127	0.000	0.000	0.000	0.000
55	A	59	LEU	0	-0.064	-0.028	17.002	0.526	0.526	0.000	0.000	0.000	0.000
56	A	60	ILE	0	0.048	0.029	17.432	0.559	0.559	0.000	0.000	0.000	0.000
57	A	61	PRO	0	-0.003	0.002	17.722	-0.682	-0.682	0.000	0.000	0.000	0.000
58	A	62	SER	0	-0.025	-0.020	15.100	-0.304	-0.304	0.000	0.000	0.000	0.000
59	A	63	TRP	0	-0.059	-0.026	16.409	-0.075	-0.075	0.000	0.000	0.000	0.000
60	A	64	ILE	0	0.013	-0.004	12.405	-1.394	-1.394	0.000	0.000	0.000	0.000
61	A	65	GLY	0	0.027	0.015	12.644	0.920	0.920	0.000	0.000	0.000	0.000
62	A	66	GLY	0	-0.007	-0.006	13.800	-0.060	-0.060	0.000	0.000	0.000	0.000
63	A	67	THR	0	-0.004	-0.025	16.701	0.368	0.368	0.000	0.000	0.000	0.000
64	A	68	ASP	-1	-0.793	-0.895	20.245	-10.892	-10.892	0.000	0.000	0.000	0.000
65	A	69	CYS	0	0.038	0.030	23.197	0.101	0.101	0.000	0.000	0.000	0.000
66	A	70	GLN	0	-0.047	-0.005	21.777	0.339	0.339	0.000	0.000	0.000	0.000
67	A	71	VAL	0	-0.033	-0.032	26.437	0.444	0.444	0.000	0.000	0.000	0.000
68	A	72	SER	0	0.059	0.032	27.028	-0.205	-0.205	0.000	0.000	0.000	0.000
69	A	73	THR	0	-0.036	-0.034	26.641	0.186	0.186	0.000	0.000	0.000	0.000
70	A	74	ARG	1	0.818	0.912	24.834	9.997	9.997	0.000	0.000	0.000	0.000
71	A	75	TRP	0	0.040	0.019	20.156	-0.437	-0.437	0.000	0.000	0.000	0.000
72	A	76	PHE	0	-0.027	-0.007	18.328	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	77	TRP	0	0.033	0.014	12.785	-0.482	-0.482	0.000	0.000	0.000	0.000
74	A	78	MET	0	0.001	0.004	13.082	0.320	0.320	0.000	0.000	0.000	0.000
75	A	79	ASP	-1	-0.806	-0.847	8.597	-24.214	-24.214	0.000	0.000	0.000	0.000
76	A	80	SER	0	-0.083	-0.045	11.088	-0.252	-0.252	0.000	0.000	0.000	0.000
77	A	81	THR	0	-0.052	-0.039	9.072	0.935	0.935	0.000	0.000	0.000	0.000
78	A	82	SER	0	0.009	-0.003	12.547	0.978	0.978	0.000	0.000	0.000	0.000
79	A	83	MET	0	-0.027	-0.011	14.398	-0.664	-0.664	0.000	0.000	0.000	0.000
80	A	84	ASP	-1	-0.861	-0.915	13.979	-15.771	-15.771	0.000	0.000	0.000	0.000
81	A	85	TYR	0	0.004	0.004	14.536	0.338	0.338	0.000	0.000	0.000	0.000
82	A	86	ALA	0	-0.010	-0.015	16.699	-0.273	-0.273	0.000	0.000	0.000	0.000
83	A	87	ASP	-1	-0.864	-0.922	17.884	-12.877	-12.877	0.000	0.000	0.000	0.000
84	A	88	TRP	0	0.009	0.010	19.778	-0.035	-0.035	0.000	0.000	0.000	0.000
85	A	89	CYS	0	-0.009	0.013	20.096	-0.281	-0.281	0.000	0.000	0.000	0.000
86	A	90	ALA	0	-0.001	-0.016	25.769	0.147	0.147	0.000	0.000	0.000	0.000
87	A	91	ALA	0	-0.048	-0.034	29.327	0.018	0.018	0.000	0.000	0.000	0.000
88	A	92	GLN	0	-0.032	0.019	25.565	-0.314	-0.314	0.000	0.000	0.000	0.000
89	A	93	PRO	0	-0.047	-0.033	24.689	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	94	ASP	-1	-0.828	-0.915	26.592	-8.931	-8.931	0.000	0.000	0.000	0.000
91	A	95	THR	0	-0.143	-0.074	26.881	0.312	0.312	0.000	0.000	0.000	0.000
92	A	96	THR	0	-0.010	-0.004	28.348	0.201	0.201	0.000	0.000	0.000	0.000
93	A	97	LEU	0	-0.026	-0.022	28.044	-0.218	-0.218	0.000	0.000	0.000	0.000
94	A	98	THR	0	-0.027	-0.019	28.762	-0.088	-0.088	0.000	0.000	0.000	0.000
95	A	99	GLU	-1	-0.939	-0.961	26.987	-9.433	-9.433	0.000	0.000	0.000	0.000
96	A	101	CYS	0	-0.011	-0.001	20.377	-0.559	-0.559	0.000	0.000	0.000	0.000
97	A	102	ILE	0	0.007	0.013	17.673	0.264	0.264	0.000	0.000	0.000	0.000
98	A	103	GLN	0	-0.031	-0.007	18.035	-0.353	-0.353	0.000	0.000	0.000	0.000
99	A	104	MET	0	0.010	0.000	14.052	0.058	0.058	0.000	0.000	0.000	0.000
100	A	105	ASN	0	-0.006	-0.029	16.315	0.256	0.256	0.000	0.000	0.000	0.000
101	A	106	VAL	0	0.008	0.011	19.612	0.434	0.434	0.000	0.000	0.000	0.000
102	A	107	GLY	0	0.030	0.009	23.103	0.174	0.174	0.000	0.000	0.000	0.000
103	A	108	ILE	0	-0.019	-0.032	24.930	-0.300	-0.300	0.000	0.000	0.000	0.000
104	A	109	GLY	0	-0.005	0.001	25.330	-0.055	-0.055	0.000	0.000	0.000	0.000
105	A	110	LYS	1	0.787	0.911	20.228	12.041	12.041	0.000	0.000	0.000	0.000
106	A	112	TRP	0	-0.005	-0.017	14.798	-0.372	-0.372	0.000	0.000	0.000	0.000
107	A	113	ASN	0	0.010	-0.011	21.096	0.439	0.439	0.000	0.000	0.000	0.000
108	A	114	ASP	-1	-0.773	-0.869	22.236	-11.155	-11.155	0.000	0.000	0.000	0.000
109	A	115	THR	0	0.060	0.037	22.760	0.245	0.245	0.000	0.000	0.000	0.000
110	A	116	PRO	0	0.015	-0.005	24.530	-0.250	-0.250	0.000	0.000	0.000	0.000
111	A	118	THR	0	-0.001	-0.005	23.223	-0.412	-0.412	0.000	0.000	0.000	0.000
112	A	119	HIS	0	-0.033	-0.018	24.405	0.248	0.248	0.000	0.000	0.000	0.000
113	A	120	LEU	0	-0.007	-0.005	22.918	-0.459	-0.459	0.000	0.000	0.000	0.000
114	A	121	HIS	0	0.010	0.004	19.734	0.201	0.201	0.000	0.000	0.000	0.000
115	A	122	SER	0	0.042	0.034	16.292	-0.461	-0.461	0.000	0.000	0.000	0.000
116	A	123	SER	0	-0.006	-0.009	13.575	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	124	ILE	0	0.005	0.018	8.289	-0.953	-0.953	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:CYS)