FMO DATABASE

FMODB ID: Z944N

Calculation Name: 1PG5-B-Xray549

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1PG5

Chain ID: B

ChEMBL ID:

UniProt ID: Q55338

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	150
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1350014.771008
FMO2-HF: Nuclear repulsion	1291030.860926
FMO2-HF: Total energy	-58983.910082
FMO2-MP2: Total energy	-59152.990692

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(B:11:MET)

Summations of interaction energy for fragment #1(B:11: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.
67.501	71.162	2.156	-1.792	-4.025	-0.006

Interaction energy analysis for fragmet #1(B:11:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.863 / q_NPA : 0.922

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	B	13	SER	0	0.018	0.010	3.893	-5.326	-3.624	-0.015	-0.883	-0.803	-0.001
39	B	49	VAL	0	-0.097	-0.046	2.201	-6.847	-5.985	1.814	-0.613	-2.064	-0.004
40	B	50	ILE	0	0.036	0.017	5.096	0.886	0.938	-0.001	-0.012	-0.038	0.000
42	B	52	VAL	0	-0.020	0.000	2.969	-2.390	-1.484	0.359	-0.256	-1.010	-0.001
52	B	62	ILE	0	-0.115	-0.064	3.944	-1.852	-1.713	-0.001	-0.028	-0.110	0.000
4	B	14	LYS	1	0.927	0.951	5.602	37.359	37.359	0.000	0.000	0.000	0.000
5	B	15	ILE	0	0.017	0.033	8.612	0.047	0.047	0.000	0.000	0.000	0.000
6	B	16	LYS	1	0.918	0.959	11.726	16.122	16.122	0.000	0.000	0.000	0.000
7	B	17	ASN	0	0.045	0.008	15.287	0.844	0.844	0.000	0.000	0.000	0.000
8	B	18	GLY	0	0.054	0.048	16.348	-0.483	-0.483	0.000	0.000	0.000	0.000
9	B	19	THR	0	0.000	-0.017	14.584	0.486	0.486	0.000	0.000	0.000	0.000
10	B	20	VAL	0	-0.071	-0.040	8.827	-2.183	-2.183	0.000	0.000	0.000	0.000
11	B	21	ILE	0	0.035	0.023	11.014	1.620	1.620	0.000	0.000	0.000	0.000
12	B	22	ASP	-1	-0.815	-0.892	8.178	-37.096	-37.096	0.000	0.000	0.000	0.000
13	B	23	HIS	0	-0.010	-0.034	10.115	1.991	1.991	0.000	0.000	0.000	0.000
14	B	24	ILE	0	0.049	0.048	11.176	2.053	2.053	0.000	0.000	0.000	0.000
15	B	25	PRO	0	0.011	-0.003	12.302	-1.580	-1.580	0.000	0.000	0.000	0.000
16	B	26	ALA	0	0.000	-0.010	11.662	-0.158	-0.158	0.000	0.000	0.000	0.000
17	B	27	GLY	0	0.013	0.005	11.812	1.441	1.441	0.000	0.000	0.000	0.000
18	B	28	ARG	1	0.876	0.926	13.355	16.188	16.188	0.000	0.000	0.000	0.000
19	B	29	ALA	0	-0.001	-0.003	10.933	0.614	0.614	0.000	0.000	0.000	0.000
20	B	30	PHE	0	0.031	-0.004	11.447	0.277	0.277	0.000	0.000	0.000	0.000
21	B	31	ALA	0	0.038	0.041	15.777	0.777	0.777	0.000	0.000	0.000	0.000
22	B	32	VAL	0	-0.005	-0.011	15.106	0.601	0.601	0.000	0.000	0.000	0.000
23	B	33	LEU	0	-0.001	-0.005	14.207	0.284	0.284	0.000	0.000	0.000	0.000
24	B	34	ASN	0	0.033	0.016	17.618	0.774	0.774	0.000	0.000	0.000	0.000
25	B	35	VAL	0	-0.014	-0.002	20.478	0.591	0.591	0.000	0.000	0.000	0.000
26	B	36	LEU	0	-0.065	-0.034	17.358	0.343	0.343	0.000	0.000	0.000	0.000
27	B	37	GLY	0	0.023	0.020	21.369	0.227	0.227	0.000	0.000	0.000	0.000
28	B	38	ILE	0	-0.050	-0.017	18.341	0.170	0.170	0.000	0.000	0.000	0.000
29	B	39	LYS	1	0.891	0.948	19.113	12.002	12.002	0.000	0.000	0.000	0.000
30	B	40	GLY	0	-0.008	-0.008	19.460	0.409	0.409	0.000	0.000	0.000	0.000
31	B	41	HIS	0	-0.034	-0.033	20.416	-0.268	-0.268	0.000	0.000	0.000	0.000
32	B	42	GLU	-1	-0.864	-0.931	21.521	-12.441	-12.441	0.000	0.000	0.000	0.000
33	B	43	GLY	0	-0.016	0.002	23.035	-0.033	-0.033	0.000	0.000	0.000	0.000
34	B	44	PHE	0	-0.015	-0.015	17.341	-0.363	-0.363	0.000	0.000	0.000	0.000
35	B	45	ARG	1	0.855	0.919	14.164	18.661	18.661	0.000	0.000	0.000	0.000
36	B	46	ILE	0	0.035	0.014	12.461	-0.339	-0.339	0.000	0.000	0.000	0.000
37	B	47	ALA	0	-0.037	-0.014	8.289	-0.718	-0.718	0.000	0.000	0.000	0.000
38	B	48	LEU	0	0.028	0.007	7.924	-0.558	-0.558	0.000	0.000	0.000	0.000
41	B	51	ASN	0	0.005	0.007	6.340	-0.191	-0.191	0.000	0.000	0.000	0.000
43	B	53	ASP	-1	-0.809	-0.895	6.033	-26.817	-26.817	0.000	0.000	0.000	0.000
44	B	54	SER	0	-0.048	-0.042	7.643	-3.448	-3.448	0.000	0.000	0.000	0.000
45	B	55	LYS	1	0.944	0.959	9.801	28.822	28.822	0.000	0.000	0.000	0.000
46	B	56	LYS	1	0.914	0.962	12.706	22.339	22.339	0.000	0.000	0.000	0.000
47	B	57	MET	0	-0.002	0.029	13.344	0.269	0.269	0.000	0.000	0.000	0.000
48	B	58	GLY	0	0.060	0.056	13.754	0.661	0.661	0.000	0.000	0.000	0.000
49	B	59	LYS	1	0.830	0.891	9.145	24.110	24.110	0.000	0.000	0.000	0.000
50	B	60	LYS	1	0.804	0.882	6.483	38.053	38.053	0.000	0.000	0.000	0.000
51	B	61	ASP	-1	-0.728	-0.853	7.986	-27.350	-27.350	0.000	0.000	0.000	0.000
53	B	63	VAL	0	0.035	0.015	7.635	-1.162	-1.162	0.000	0.000	0.000	0.000
54	B	64	LYS	1	0.819	0.916	5.300	46.605	46.605	0.000	0.000	0.000	0.000
55	B	65	ILE	0	0.054	0.023	10.729	0.219	0.219	0.000	0.000	0.000	0.000
56	B	66	GLU	-1	-0.760	-0.880	13.903	-21.051	-21.051	0.000	0.000	0.000	0.000
57	B	67	ASP	-1	-0.913	-0.964	15.853	-15.712	-15.712	0.000	0.000	0.000	0.000
58	B	68	LYS	1	0.897	0.954	18.453	15.358	15.358	0.000	0.000	0.000	0.000
59	B	69	GLU	-1	-0.866	-0.910	18.329	-15.249	-15.249	0.000	0.000	0.000	0.000
60	B	70	ILE	0	-0.053	-0.020	17.763	0.609	0.609	0.000	0.000	0.000	0.000
61	B	71	SER	0	0.014	-0.026	20.493	0.223	0.223	0.000	0.000	0.000	0.000
62	B	72	ASP	-1	-0.787	-0.901	23.093	-13.251	-13.251	0.000	0.000	0.000	0.000
63	B	73	THR	0	-0.017	-0.003	24.512	0.205	0.205	0.000	0.000	0.000	0.000
64	B	74	GLU	-1	-0.781	-0.855	22.221	-13.528	-13.528	0.000	0.000	0.000	0.000
65	B	75	ALA	0	0.008	-0.006	20.389	-0.386	-0.386	0.000	0.000	0.000	0.000
66	B	76	ASN	0	0.047	0.019	21.344	-0.680	-0.680	0.000	0.000	0.000	0.000
67	B	77	LEU	0	0.023	0.030	23.625	0.138	0.138	0.000	0.000	0.000	0.000
68	B	78	ILE	0	-0.003	0.004	17.111	-0.185	-0.185	0.000	0.000	0.000	0.000
69	B	79	THR	0	-0.049	-0.047	20.597	-0.163	-0.163	0.000	0.000	0.000	0.000
70	B	80	LEU	0	0.025	0.022	22.474	0.065	0.065	0.000	0.000	0.000	0.000
71	B	81	ILE	0	0.034	0.027	18.497	0.042	0.042	0.000	0.000	0.000	0.000
72	B	82	ALA	0	-0.060	-0.031	16.553	-0.742	-0.742	0.000	0.000	0.000	0.000
73	B	83	PRO	0	0.043	0.031	18.517	-0.520	-0.520	0.000	0.000	0.000	0.000
74	B	84	THR	0	-0.048	-0.030	15.934	0.471	0.471	0.000	0.000	0.000	0.000
75	B	85	ALA	0	-0.036	-0.009	14.763	-0.930	-0.930	0.000	0.000	0.000	0.000
76	B	86	THR	0	-0.028	-0.012	12.655	0.554	0.554	0.000	0.000	0.000	0.000
77	B	87	ILE	0	0.043	0.017	13.524	-1.685	-1.685	0.000	0.000	0.000	0.000
78	B	88	ASN	0	-0.028	-0.021	11.963	2.116	2.116	0.000	0.000	0.000	0.000
79	B	89	ILE	0	0.023	0.013	14.687	-0.944	-0.944	0.000	0.000	0.000	0.000
80	B	90	VAL	0	-0.057	-0.034	12.650	-0.129	-0.129	0.000	0.000	0.000	0.000
81	B	91	ARG	1	0.872	0.907	16.110	14.280	14.280	0.000	0.000	0.000	0.000
82	B	92	GLU	-1	-0.811	-0.896	18.648	-14.827	-14.827	0.000	0.000	0.000	0.000
83	B	93	TYR	0	-0.067	-0.044	12.795	-0.532	-0.532	0.000	0.000	0.000	0.000
84	B	94	GLU	-1	-0.911	-0.931	14.127	-18.925	-18.925	0.000	0.000	0.000	0.000
85	B	95	VAL	0	-0.095	-0.060	13.771	-0.101	-0.101	0.000	0.000	0.000	0.000
86	B	96	VAL	0	0.003	0.010	16.532	0.783	0.783	0.000	0.000	0.000	0.000
87	B	97	LYS	1	0.849	0.905	18.845	14.338	14.338	0.000	0.000	0.000	0.000
88	B	98	LYS	1	0.931	0.974	15.473	17.271	17.271	0.000	0.000	0.000	0.000
89	B	99	THR	0	-0.018	-0.011	18.716	0.692	0.692	0.000	0.000	0.000	0.000
90	B	100	LYS	1	0.849	0.927	20.044	10.731	10.731	0.000	0.000	0.000	0.000
91	B	101	LEU	0	0.005	0.006	18.697	0.430	0.430	0.000	0.000	0.000	0.000
92	B	102	GLU	-1	-0.884	-0.940	22.752	-10.678	-10.678	0.000	0.000	0.000	0.000
93	B	103	VAL	0	0.034	0.016	26.053	-0.247	-0.247	0.000	0.000	0.000	0.000
94	B	104	PRO	0	-0.003	0.018	26.540	0.336	0.336	0.000	0.000	0.000	0.000
95	B	105	LYS	1	0.984	0.983	29.236	9.384	9.384	0.000	0.000	0.000	0.000
96	B	106	VAL	0	-0.005	-0.009	32.297	0.324	0.324	0.000	0.000	0.000	0.000
97	B	107	VAL	0	0.017	0.021	28.820	-0.348	-0.348	0.000	0.000	0.000	0.000
98	B	108	LYS	1	0.919	0.941	30.871	8.914	8.914	0.000	0.000	0.000	0.000
99	B	109	GLY	0	0.009	0.015	30.500	-0.338	-0.338	0.000	0.000	0.000	0.000
100	B	110	ILE	0	-0.056	-0.036	25.371	0.015	0.015	0.000	0.000	0.000	0.000
101	B	111	LEU	0	0.002	0.017	28.291	-0.153	-0.153	0.000	0.000	0.000	0.000
102	B	112	LYS	1	0.998	0.988	30.760	9.908	9.908	0.000	0.000	0.000	0.000
103	B	113	CYS	0	-0.018	-0.005	33.751	-0.002	-0.002	0.000	0.000	0.000	0.000
104	B	114	PRO	0	0.035	0.030	35.771	0.112	0.112	0.000	0.000	0.000	0.000
105	B	115	ASN	0	0.017	-0.002	37.692	0.232	0.232	0.000	0.000	0.000	0.000
106	B	116	PRO	0	0.027	0.016	41.339	-0.055	-0.055	0.000	0.000	0.000	0.000
107	B	117	TYR	0	0.033	0.011	42.545	0.060	0.060	0.000	0.000	0.000	0.000
108	B	118	CYS	0	-0.064	0.014	40.713	0.110	0.110	0.000	0.000	0.000	0.000
109	B	119	ILE	0	0.080	0.038	42.988	-0.071	-0.071	0.000	0.000	0.000	0.000
110	B	120	THR	0	-0.018	-0.047	38.418	-0.109	-0.109	0.000	0.000	0.000	0.000
111	B	121	SER	0	-0.067	-0.037	38.508	-0.289	-0.289	0.000	0.000	0.000	0.000
112	B	122	ASN	0	-0.111	-0.065	39.969	0.093	0.093	0.000	0.000	0.000	0.000
113	B	123	ASP	-1	-0.868	-0.928	42.275	-7.176	-7.176	0.000	0.000	0.000	0.000
114	B	124	VAL	0	-0.011	-0.015	38.668	-0.179	-0.179	0.000	0.000	0.000	0.000
115	B	125	GLU	-1	-0.935	-0.961	38.602	-7.566	-7.566	0.000	0.000	0.000	0.000
116	B	126	ALA	0	-0.046	-0.002	40.439	-0.065	-0.065	0.000	0.000	0.000	0.000
117	B	127	ILE	0	-0.014	-0.021	34.584	-0.161	-0.161	0.000	0.000	0.000	0.000
118	B	128	PRO	0	0.024	0.018	34.106	0.072	0.072	0.000	0.000	0.000	0.000
119	B	129	THR	0	-0.022	-0.012	34.765	-0.263	-0.263	0.000	0.000	0.000	0.000
120	B	130	PHE	0	0.050	0.028	33.547	0.267	0.267	0.000	0.000	0.000	0.000
121	B	131	LYS	1	0.868	0.938	34.590	7.942	7.942	0.000	0.000	0.000	0.000
122	B	132	THR	0	-0.014	-0.023	31.976	0.055	0.055	0.000	0.000	0.000	0.000
123	B	133	LEU	0	-0.067	-0.030	34.843	0.233	0.233	0.000	0.000	0.000	0.000
124	B	134	THR	0	-0.053	-0.048	35.382	0.266	0.266	0.000	0.000	0.000	0.000
125	B	135	GLU	-1	-0.897	-0.953	31.411	-9.797	-9.797	0.000	0.000	0.000	0.000
126	B	136	LYS	1	0.911	0.957	31.182	8.265	8.265	0.000	0.000	0.000	0.000
127	B	137	PRO	0	0.008	0.030	31.592	-0.220	-0.220	0.000	0.000	0.000	0.000
128	B	138	LEU	0	0.050	0.019	28.424	0.328	0.328	0.000	0.000	0.000	0.000
129	B	139	LYS	1	0.917	0.966	31.834	8.587	8.587	0.000	0.000	0.000	0.000
130	B	140	MET	0	0.012	0.011	31.515	-0.109	-0.109	0.000	0.000	0.000	0.000
131	B	141	ARG	1	0.860	0.932	35.040	7.610	7.610	0.000	0.000	0.000	0.000
132	B	142	CYS	0	-0.003	0.026	38.025	-0.022	-0.022	0.000	0.000	0.000	0.000
133	B	143	GLU	-1	-0.884	-0.960	38.536	-7.979	-7.979	0.000	0.000	0.000	0.000
134	B	144	TYR	0	0.038	0.011	39.724	0.199	0.199	0.000	0.000	0.000	0.000
135	B	145	CYS	0	-0.058	-0.018	41.943	0.107	0.107	0.000	0.000	0.000	0.000
136	B	146	GLU	-1	-0.830	-0.920	42.879	-7.223	-7.223	0.000	0.000	0.000	0.000
137	B	147	THR	0	0.011	0.000	39.248	-0.016	-0.016	0.000	0.000	0.000	0.000
138	B	148	ILE	0	-0.055	-0.029	37.756	-0.161	-0.161	0.000	0.000	0.000	0.000
139	B	149	ILE	0	0.022	0.028	32.140	0.053	0.053	0.000	0.000	0.000	0.000
140	B	150	ASP	-1	-0.864	-0.949	32.539	-9.380	-9.380	0.000	0.000	0.000	0.000
141	B	151	GLU	-1	-0.854	-0.948	26.710	-11.656	-11.656	0.000	0.000	0.000	0.000
142	B	152	ASN	0	-0.044	-0.010	27.712	-0.681	-0.681	0.000	0.000	0.000	0.000
143	B	153	GLU	-1	-0.819	-0.908	28.899	-9.526	-9.526	0.000	0.000	0.000	0.000
144	B	154	ILE	0	-0.014	-0.002	26.433	-0.200	-0.200	0.000	0.000	0.000	0.000
145	B	155	MET	0	-0.011	-0.010	23.222	-0.749	-0.749	0.000	0.000	0.000	0.000
146	B	156	SER	0	-0.068	-0.048	24.548	-0.292	-0.292	0.000	0.000	0.000	0.000
147	B	157	GLN	0	-0.022	-0.016	26.802	-0.146	-0.146	0.000	0.000	0.000	0.000
148	B	158	ILE	0	-0.035	-0.010	21.937	-0.205	-0.205	0.000	0.000	0.000	0.000
149	B	159	LEU	0	-0.127	-0.080	19.373	-0.760	-0.760	0.000	0.000	0.000	0.000
150	B	160	GLY	-1	-0.946	-0.947	22.300	-12.157	-12.157	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:11:MET)