FMO DATABASE

FMODB ID: QL85Y

Calculation Name: 1M3V-A-Other547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1M3V

Chain ID: A

ChEMBL ID:

UniProt ID: P70662

Base Structure: SolutionNMR

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	-895670.427924
FMO2-HF: Nuclear repulsion	847522.759996
FMO2-HF: Total energy	-48147.667927
FMO2-MP2: Total energy	-48279.598921

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:1:GLY)

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

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.
-169.473	-169.438	20.69	-10.679	-10.047	-0.131

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.815 / q_NPA : 0.901

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	3	LEU	0	0.026	0.031	2.724	14.571	15.992	0.029	-0.608	-0.842	-0.001
4	A	4	SER	0	0.005	-0.012	2.021	-34.904	-35.043	4.457	-2.373	-1.946	-0.034
5	A	5	TRP	0	-0.026	-0.017	2.537	8.854	9.792	0.293	-0.451	-0.780	-0.003
6	A	6	LYS	1	0.833	0.924	4.918	40.277	40.297	-0.001	-0.002	-0.016	0.000
27	A	27	TYR	0	-0.076	-0.075	3.507	4.824	4.968	-0.001	-0.049	-0.095	0.000
114	A	114	ASP	-1	-0.765	-0.862	1.945	-130.056	-132.438	15.914	-7.157	-6.376	-0.093
115	A	115	ALA	0	0.014	0.016	3.963	-0.091	-0.082	0.000	-0.024	0.015	0.000
116	A	116	ALA	0	-0.021	-0.007	4.434	3.734	3.758	-0.001	-0.015	-0.007	0.000
7	A	7	ARG	1	0.857	0.931	7.994	24.824	24.824	0.000	0.000	0.000	0.000
8	A	8	CYS	-1	-0.787	-0.732	10.033	-20.904	-20.904	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.008	0.004	12.521	1.123	1.123	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.031	0.009	15.406	1.269	1.269	0.000	0.000	0.000	0.000
11	A	11	CYS	0	-0.071	-0.095	15.075	0.732	0.732	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.014	0.008	16.922	0.031	0.031	0.000	0.000	0.000	0.000
13	A	13	GLY	0	-0.001	-0.003	13.246	0.186	0.186	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.941	0.966	9.640	25.178	25.178	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.004	-0.002	8.299	2.425	2.425	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.014	0.009	8.799	-3.036	-3.036	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.805	-0.868	10.852	-19.215	-19.215	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.917	0.949	10.702	17.287	17.287	0.000	0.000	0.000	0.000
19	A	19	PHE	0	-0.038	-0.032	11.634	-0.717	-0.717	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.017	-0.008	6.780	0.468	0.468	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.026	-0.018	11.254	0.733	0.733	0.000	0.000	0.000	0.000
22	A	22	TYR	0	0.013	-0.003	5.697	-3.321	-3.321	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.067	0.017	11.537	1.874	1.874	0.000	0.000	0.000	0.000
24	A	24	MET	0	0.025	0.016	14.120	-0.500	-0.500	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.834	-0.904	11.313	-25.952	-25.952	0.000	0.000	0.000	0.000
26	A	26	SER	0	-0.042	-0.004	10.575	-2.351	-2.351	0.000	0.000	0.000	0.000
28	A	28	TRP	0	0.049	-0.005	10.474	2.732	2.732	0.000	0.000	0.000	0.000
29	A	29	HIS	1	0.839	0.820	12.545	20.603	20.603	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.002	-0.033	14.762	0.812	0.812	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.957	0.971	17.414	13.470	13.470	0.000	0.000	0.000	0.000
32	A	32	CYS	0	-0.040	0.011	16.598	0.515	0.515	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.022	0.021	16.247	0.461	0.461	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.817	0.911	18.696	15.348	15.348	0.000	0.000	0.000	0.000
35	A	35	CYS	0	-0.045	0.011	22.168	-0.174	-0.174	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.011	-0.023	25.136	-0.028	-0.028	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.052	-0.053	27.350	0.230	0.230	0.000	0.000	0.000	0.000
38	A	38	CYS	0	-0.085	-0.068	28.523	0.307	0.307	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.018	-0.011	26.143	-0.216	-0.216	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.032	0.027	26.247	-0.147	-0.147	0.000	0.000	0.000	0.000
41	A	41	GLN	0	0.058	0.009	20.732	-0.471	-0.471	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.029	0.001	19.556	0.074	0.074	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.013	0.006	18.103	-0.075	-0.075	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.992	-0.990	19.022	-13.467	-13.467	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.002	0.002	22.202	0.443	0.443	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.047	0.042	22.304	0.496	0.496	0.000	0.000	0.000	0.000
47	A	47	THR	0	-0.087	-0.058	17.318	-0.651	-0.651	0.000	0.000	0.000	0.000
48	A	48	SER	0	0.009	-0.030	19.962	0.245	0.245	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.035	-0.025	18.185	0.046	0.046	0.000	0.000	0.000	0.000
50	A	50	TYR	0	-0.001	0.002	21.381	-0.230	-0.230	0.000	0.000	0.000	0.000
51	A	51	THR	0	0.006	-0.006	20.628	-0.400	-0.400	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.871	0.917	23.046	11.700	11.700	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.013	-0.010	26.508	0.157	0.157	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.017	-0.002	23.961	0.116	0.116	0.000	0.000	0.000	0.000
55	A	55	MET	0	-0.042	-0.008	23.587	-0.350	-0.350	0.000	0.000	0.000	0.000
56	A	56	ILE	0	0.049	0.021	19.601	-0.202	-0.202	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.042	0.006	22.951	0.463	0.463	0.000	0.000	0.000	0.000
58	A	58	CYS	0	-0.068	-0.002	24.439	-0.198	-0.198	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.952	0.975	25.552	10.975	10.975	0.000	0.000	0.000	0.000
60	A	60	ASN	0	0.090	0.038	27.790	0.673	0.673	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.692	-0.859	27.576	-11.054	-11.054	0.000	0.000	0.000	0.000
62	A	62	TYR	0	-0.024	-0.023	28.057	0.185	0.185	0.000	0.000	0.000	0.000
63	A	63	ILE	0	0.033	0.009	30.052	0.243	0.243	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.865	0.923	33.120	9.590	9.590	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.032	-0.007	31.139	0.220	0.220	0.000	0.000	0.000	0.000
66	A	66	PHE	0	-0.010	-0.019	28.872	0.114	0.114	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.031	0.039	33.488	-0.053	-0.053	0.000	0.000	0.000	0.000
68	A	68	ASN	0	-0.042	-0.019	35.347	0.499	0.499	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.005	0.009	37.202	-0.079	-0.079	0.000	0.000	0.000	0.000
70	A	70	GLY	0	-0.037	-0.016	37.021	0.168	0.168	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.035	0.007	37.368	-0.188	-0.188	0.000	0.000	0.000	0.000
72	A	72	GLY	0	-0.011	0.009	39.784	0.195	0.195	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.018	-0.011	42.175	0.148	0.148	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.042	-0.028	37.509	0.076	0.076	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.018	0.013	39.367	0.043	0.043	0.000	0.000	0.000	0.000
76	A	76	GLY	0	-0.012	-0.018	36.309	0.025	0.025	0.000	0.000	0.000	0.000
77	A	77	HIS	0	-0.097	-0.049	31.134	0.250	0.250	0.000	0.000	0.000	0.000
78	A	78	MET	0	0.072	0.038	31.563	-0.054	-0.054	0.000	0.000	0.000	0.000
79	A	79	GLY	0	-0.031	-0.006	28.508	-0.103	-0.103	0.000	0.000	0.000	0.000
80	A	80	SER	0	-0.056	-0.052	25.917	-0.531	-0.531	0.000	0.000	0.000	0.000
81	A	81	GLY	0	-0.009	-0.009	25.476	0.411	0.411	0.000	0.000	0.000	0.000
82	A	82	GLY	0	0.001	-0.001	22.575	0.178	0.178	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.796	-0.895	23.255	-11.574	-11.574	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.007	-0.025	24.954	0.191	0.191	0.000	0.000	0.000	0.000
85	A	85	MET	0	-0.095	-0.050	27.286	0.191	0.191	0.000	0.000	0.000	0.000
86	A	86	VAL	0	-0.051	-0.019	30.000	0.333	0.333	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.016	-0.014	28.225	0.290	0.290	0.000	0.000	0.000	0.000
88	A	88	GLY	0	-0.044	-0.007	28.289	-0.017	-0.017	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.926	-0.969	28.941	-8.970	-8.970	0.000	0.000	0.000	0.000
90	A	90	PRO	0	-0.033	-0.007	32.608	0.053	0.053	0.000	0.000	0.000	0.000
91	A	91	THR	0	-0.018	0.005	35.011	0.326	0.326	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.007	-0.021	36.209	0.301	0.301	0.000	0.000	0.000	0.000
93	A	93	MET	0	0.009	0.014	33.617	-0.267	-0.267	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.006	-0.020	36.132	0.035	0.035	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.025	0.034	34.188	0.097	0.097	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.909	-0.977	34.435	-9.078	-9.078	0.000	0.000	0.000	0.000
97	A	97	PHE	0	0.000	-0.012	32.544	-0.216	-0.216	0.000	0.000	0.000	0.000
98	A	98	GLY	0	0.005	0.024	30.783	-0.321	-0.321	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.832	-0.891	28.553	-11.171	-11.171	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.801	-0.902	25.895	-11.290	-11.290	0.000	0.000	0.000	0.000
101	A	101	ASP	-1	-0.918	-0.928	24.292	-13.245	-13.245	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.733	-0.820	22.450	-14.255	-14.255	0.000	0.000	0.000	0.000
103	A	103	ARG	1	0.786	0.863	18.454	13.675	13.675	0.000	0.000	0.000	0.000
104	A	104	LEU	0	0.006	0.017	16.560	-1.101	-1.101	0.000	0.000	0.000	0.000
105	A	105	ILE	0	-0.065	-0.016	15.019	-1.542	-1.542	0.000	0.000	0.000	0.000
106	A	106	THR	0	0.003	0.002	10.498	-0.437	-0.437	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.815	0.888	11.758	16.576	16.576	0.000	0.000	0.000	0.000
108	A	108	LEU	0	0.038	0.014	9.965	1.431	1.431	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.788	-0.837	10.362	-20.663	-20.663	0.000	0.000	0.000	0.000
110	A	110	ASN	0	0.003	-0.023	10.814	2.296	2.296	0.000	0.000	0.000	0.000
111	A	111	THR	0	0.052	0.031	8.166	-1.783	-1.783	0.000	0.000	0.000	0.000
112	A	112	GLN	0	0.002	0.012	8.211	-0.750	-0.750	0.000	0.000	0.000	0.000
113	A	113	PHE	0	0.006	-0.004	5.641	-1.530	-1.530	0.000	0.000	0.000	0.000
117	A	117	ASN	0	-0.058	-0.029	5.376	-6.392	-6.392	0.000	0.000	0.000	0.000
118	A	118	GLY	0	-0.016	-0.012	6.966	-0.157	-0.157	0.000	0.000	0.000	0.000
119	A	119	ILE	0	-0.094	-0.048	9.446	0.268	0.268	0.000	0.000	0.000	0.000
120	A	120	ASP	-1	-0.939	-0.973	11.993	-17.937	-17.937	0.000	0.000	0.000	0.000
121	A	121	ASP	-1	-0.974	-0.979	15.434	-15.641	-15.641	0.000	0.000	0.000	0.000
122	A	122	GLU	-2	-1.961	-1.961	18.893	-28.082	-28.082	0.000	0.000	0.000	0.000

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