FMO DATABASE

FMODB ID: 7419K

Calculation Name: 1PP7-U-Xray549

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1PP7

Chain ID: U

ChEMBL ID:

UniProt ID: Q95VR4

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	114
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-984560.660586
FMO2-HF: Nuclear repulsion	938674.066926
FMO2-HF: Total energy	-45886.59366
FMO2-MP2: Total energy	-46021.534959

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(U:5:ASP)

Summations of interaction energy for fragment #1(U:5: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.
14.654	17.888	0.358	-1.259	-2.332	-0.006

Interaction energy analysis for fragmet #1(U:5:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.041 / q_NPA : -0.025

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	U	7	GLU	-1	-0.889	-0.933	3.819	-8.924	-7.197	-0.008	-0.642	-1.076	0.000
4	U	8	ALA	0	0.001	0.003	2.569	2.080	3.166	0.366	-0.459	-0.993	-0.006
5	U	9	SER	0	0.005	0.014	4.103	5.559	5.980	0.000	-0.158	-0.263	0.000
6	U	10	PHE	0	0.026	0.012	5.933	2.032	2.032	0.000	0.000	0.000	0.000
7	U	11	THR	0	-0.009	-0.025	7.300	1.249	1.249	0.000	0.000	0.000	0.000
8	U	12	SER	0	-0.058	-0.047	7.402	1.430	1.430	0.000	0.000	0.000	0.000
9	U	13	ARG	1	0.807	0.886	8.908	4.248	4.248	0.000	0.000	0.000	0.000
10	U	14	LEU	0	-0.027	0.008	12.047	0.447	0.447	0.000	0.000	0.000	0.000
11	U	15	PRO	0	0.047	0.020	14.128	-0.086	-0.086	0.000	0.000	0.000	0.000
12	U	16	PRO	0	0.042	0.003	15.519	-0.127	-0.127	0.000	0.000	0.000	0.000
13	U	17	GLU	-1	-0.911	-0.943	16.547	-1.304	-1.304	0.000	0.000	0.000	0.000
14	U	18	ILE	0	0.027	0.011	16.196	0.008	0.008	0.000	0.000	0.000	0.000
15	U	19	VAL	0	-0.004	-0.005	12.156	-0.126	-0.126	0.000	0.000	0.000	0.000
16	U	20	ALA	0	-0.025	-0.012	14.597	-0.077	-0.077	0.000	0.000	0.000	0.000
17	U	21	ALA	0	-0.016	-0.014	17.519	0.073	0.073	0.000	0.000	0.000	0.000
18	U	22	LEU	0	-0.012	-0.012	14.481	0.149	0.149	0.000	0.000	0.000	0.000
19	U	23	LYS	1	0.948	0.981	11.693	3.402	3.402	0.000	0.000	0.000	0.000
20	U	24	ARG	1	0.863	0.928	16.318	1.215	1.215	0.000	0.000	0.000	0.000
21	U	25	LYS	1	0.973	0.989	20.089	1.000	1.000	0.000	0.000	0.000	0.000
22	U	26	SER	0	0.024	0.003	22.091	0.020	0.020	0.000	0.000	0.000	0.000
23	U	27	SER	0	-0.060	-0.044	24.180	0.080	0.080	0.000	0.000	0.000	0.000
24	U	28	ARG	1	1.004	0.991	27.844	0.635	0.635	0.000	0.000	0.000	0.000
25	U	29	ASP	-1	-0.742	-0.824	28.244	-0.862	-0.862	0.000	0.000	0.000	0.000
26	U	30	PRO	0	0.093	0.046	28.171	-0.079	-0.079	0.000	0.000	0.000	0.000
27	U	31	ASN	0	0.002	-0.007	25.880	-0.056	-0.056	0.000	0.000	0.000	0.000
28	U	32	SER	0	-0.050	-0.022	23.622	-0.085	-0.085	0.000	0.000	0.000	0.000
29	U	33	ARG	1	0.875	0.932	23.442	0.689	0.689	0.000	0.000	0.000	0.000
30	U	34	PHE	0	0.042	0.017	19.622	-0.054	-0.054	0.000	0.000	0.000	0.000
31	U	35	PRO	0	0.061	0.033	23.046	-0.088	-0.088	0.000	0.000	0.000	0.000
32	U	36	ARG	1	0.970	0.977	25.184	0.799	0.799	0.000	0.000	0.000	0.000
33	U	37	LYS	1	0.833	0.931	19.384	1.596	1.596	0.000	0.000	0.000	0.000
34	U	38	LEU	0	0.015	0.005	20.272	-0.112	-0.112	0.000	0.000	0.000	0.000
35	U	39	HIS	1	0.879	0.940	21.414	0.913	0.913	0.000	0.000	0.000	0.000
36	U	40	MET	0	-0.044	-0.005	21.706	0.043	0.043	0.000	0.000	0.000	0.000
37	U	41	LEU	0	0.010	0.001	15.204	-0.009	-0.009	0.000	0.000	0.000	0.000
38	U	42	LEU	0	0.001	-0.003	19.332	-0.021	-0.021	0.000	0.000	0.000	0.000
39	U	43	THR	0	-0.047	-0.033	21.672	0.124	0.124	0.000	0.000	0.000	0.000
40	U	44	TYR	0	0.044	0.030	16.251	-0.043	-0.043	0.000	0.000	0.000	0.000
41	U	45	LEU	0	-0.001	-0.002	15.804	0.004	0.004	0.000	0.000	0.000	0.000
42	U	46	ALA	0	0.036	0.032	19.839	0.053	0.053	0.000	0.000	0.000	0.000
43	U	47	SER	0	-0.088	-0.050	21.882	0.104	0.104	0.000	0.000	0.000	0.000
44	U	48	ASN	0	-0.034	-0.031	15.612	0.105	0.105	0.000	0.000	0.000	0.000
45	U	49	PRO	0	0.099	0.033	18.330	-0.161	-0.161	0.000	0.000	0.000	0.000
46	U	50	GLN	0	0.054	0.044	14.310	-0.219	-0.219	0.000	0.000	0.000	0.000
47	U	51	LEU	0	0.003	-0.014	11.274	-0.235	-0.235	0.000	0.000	0.000	0.000
48	U	52	GLU	-1	-0.946	-0.965	14.752	-1.362	-1.362	0.000	0.000	0.000	0.000
49	U	53	GLU	-1	-0.954	-0.981	15.910	-1.000	-1.000	0.000	0.000	0.000	0.000
50	U	54	GLU	-1	-0.891	-0.929	10.773	-2.366	-2.366	0.000	0.000	0.000	0.000
51	U	55	ILE	0	-0.056	-0.030	11.642	-0.398	-0.398	0.000	0.000	0.000	0.000
52	U	56	GLY	0	0.032	0.014	13.239	0.124	0.124	0.000	0.000	0.000	0.000
53	U	57	LEU	0	-0.092	-0.059	16.742	0.017	0.017	0.000	0.000	0.000	0.000
54	U	58	SER	0	0.079	0.048	19.106	0.026	0.026	0.000	0.000	0.000	0.000
55	U	59	TRP	0	-0.019	-0.012	22.477	0.054	0.054	0.000	0.000	0.000	0.000
56	U	60	ILE	0	-0.064	-0.033	26.257	0.008	0.008	0.000	0.000	0.000	0.000
57	U	61	SER	0	0.035	0.019	28.600	0.046	0.046	0.000	0.000	0.000	0.000
58	U	62	ASP	-1	-0.810	-0.889	30.636	-0.604	-0.604	0.000	0.000	0.000	0.000
59	U	63	THR	0	-0.028	-0.022	32.219	-0.021	-0.021	0.000	0.000	0.000	0.000
60	U	64	GLU	-1	-0.906	-0.939	29.605	-0.579	-0.579	0.000	0.000	0.000	0.000
61	U	65	PHE	0	0.007	-0.010	22.376	-0.018	-0.018	0.000	0.000	0.000	0.000
62	U	66	LYS	1	0.946	0.985	22.407	0.884	0.884	0.000	0.000	0.000	0.000
63	U	67	MET	0	-0.016	-0.013	18.668	-0.158	-0.158	0.000	0.000	0.000	0.000
64	U	68	LYS	1	0.932	0.983	14.881	1.316	1.316	0.000	0.000	0.000	0.000
65	U	69	LYS	1	0.908	0.950	15.428	0.757	0.757	0.000	0.000	0.000	0.000
66	U	70	LYS	1	0.946	0.964	11.246	1.197	1.197	0.000	0.000	0.000	0.000
67	U	71	ASN	0	-0.007	0.004	10.826	-0.362	-0.362	0.000	0.000	0.000	0.000
68	U	72	VAL	0	0.054	0.014	11.433	-0.533	-0.533	0.000	0.000	0.000	0.000
69	U	73	ALA	0	-0.035	-0.020	12.943	-0.076	-0.076	0.000	0.000	0.000	0.000
70	U	74	LEU	0	-0.019	0.002	6.853	0.061	0.061	0.000	0.000	0.000	0.000
71	U	75	VAL	0	0.038	0.024	9.769	-0.307	-0.307	0.000	0.000	0.000	0.000
72	U	76	MET	0	-0.048	-0.013	11.160	0.353	0.353	0.000	0.000	0.000	0.000
73	U	77	GLY	0	0.023	0.028	11.534	0.345	0.345	0.000	0.000	0.000	0.000
74	U	78	ILE	0	-0.066	-0.025	12.583	0.380	0.380	0.000	0.000	0.000	0.000
75	U	79	LYS	1	0.951	0.964	12.060	2.255	2.255	0.000	0.000	0.000	0.000
76	U	80	LEU	0	0.075	0.015	14.876	0.103	0.103	0.000	0.000	0.000	0.000
77	U	81	ASN	0	-0.024	-0.004	16.379	0.080	0.080	0.000	0.000	0.000	0.000
78	U	82	THR	0	0.076	0.033	17.692	0.015	0.015	0.000	0.000	0.000	0.000
79	U	83	LEU	0	0.007	0.014	16.281	0.060	0.060	0.000	0.000	0.000	0.000
80	U	84	ASN	0	0.013	-0.002	19.342	0.060	0.060	0.000	0.000	0.000	0.000
81	U	85	VAL	0	0.010	0.015	22.183	0.068	0.068	0.000	0.000	0.000	0.000
82	U	86	ASN	0	-0.003	-0.004	20.351	0.133	0.133	0.000	0.000	0.000	0.000
83	U	87	LEU	0	-0.058	-0.023	21.522	0.029	0.029	0.000	0.000	0.000	0.000
84	U	88	ARG	1	0.956	0.985	24.966	0.668	0.668	0.000	0.000	0.000	0.000
85	U	89	ASP	-1	-0.867	-0.943	27.528	-0.670	-0.670	0.000	0.000	0.000	0.000
86	U	90	LEU	0	-0.077	-0.031	25.637	0.018	0.018	0.000	0.000	0.000	0.000
87	U	91	ALA	0	0.042	0.025	29.257	-0.003	-0.003	0.000	0.000	0.000	0.000
88	U	92	PHE	0	-0.033	-0.013	26.162	-0.009	-0.009	0.000	0.000	0.000	0.000
89	U	93	GLU	-1	-0.829	-0.905	28.626	-0.512	-0.512	0.000	0.000	0.000	0.000
90	U	94	GLN	0	-0.077	-0.060	25.728	-0.051	-0.051	0.000	0.000	0.000	0.000
91	U	95	LEU	0	0.016	0.003	28.566	0.047	0.047	0.000	0.000	0.000	0.000
92	U	96	GLN	0	-0.004	-0.003	24.779	0.070	0.070	0.000	0.000	0.000	0.000
93	U	97	HIS	0	0.049	0.040	26.016	-0.086	-0.086	0.000	0.000	0.000	0.000
94	U	98	ASP	-1	-0.860	-0.925	20.187	-0.834	-0.834	0.000	0.000	0.000	0.000
95	U	99	LYS	1	0.914	0.952	22.554	0.594	0.594	0.000	0.000	0.000	0.000
96	U	100	GLY	0	0.055	0.034	19.544	-0.020	-0.020	0.000	0.000	0.000	0.000
97	U	101	GLY	0	-0.060	-0.042	17.093	-0.107	-0.107	0.000	0.000	0.000	0.000
98	U	102	TRP	0	-0.020	-0.003	18.093	-0.179	-0.179	0.000	0.000	0.000	0.000
99	U	103	THR	0	-0.040	-0.012	20.661	0.097	0.097	0.000	0.000	0.000	0.000
100	U	104	GLN	0	0.037	0.006	23.298	-0.073	-0.073	0.000	0.000	0.000	0.000
101	U	105	TRP	0	0.008	-0.011	23.395	0.010	0.010	0.000	0.000	0.000	0.000
102	U	106	LYS	1	0.925	0.963	27.262	0.515	0.515	0.000	0.000	0.000	0.000
103	U	107	ARG	1	0.855	0.906	29.003	0.725	0.725	0.000	0.000	0.000	0.000
104	U	108	SER	0	0.044	0.032	31.424	0.009	0.009	0.000	0.000	0.000	0.000
105	U	109	GLY	0	0.050	0.005	33.461	-0.024	-0.024	0.000	0.000	0.000	0.000
106	U	110	PHE	0	-0.091	-0.017	24.825	-0.033	-0.033	0.000	0.000	0.000	0.000
107	U	111	THR	0	0.038	-0.009	31.076	0.004	0.004	0.000	0.000	0.000	0.000
108	U	112	ARG	1	0.864	0.919	28.944	0.621	0.621	0.000	0.000	0.000	0.000
109	U	113	ASN	0	-0.028	-0.016	29.616	-0.045	-0.045	0.000	0.000	0.000	0.000
110	U	114	SER	0	-0.013	0.007	31.791	0.028	0.028	0.000	0.000	0.000	0.000
111	U	115	VAL	0	-0.013	-0.026	28.186	-0.053	-0.053	0.000	0.000	0.000	0.000
112	U	116	PHE	0	-0.035	0.006	31.323	0.020	0.020	0.000	0.000	0.000	0.000
113	U	117	GLU	-1	-0.919	-0.960	32.806	-0.612	-0.612	0.000	0.000	0.000	0.000
114	U	118	ASP	-2	-1.773	-1.864	29.926	-1.437	-1.437	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(U:5:ASP)