FMO DATABASE

FMODB ID: 3M35L

Calculation Name: 1JM7-A-Other547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1JM7

Chain ID: A

ChEMBL ID:

UniProt ID: Q99728

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	103
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-733317.966204
FMO2-HF: Nuclear repulsion	690009.206383
FMO2-HF: Total energy	-43308.759822
FMO2-MP2: Total energy	-43427.240879

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:MET)

Summations of interaction energy for fragment #1(A:1: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.
-73.317	-67.398	1.326	-2.543	-4.704	-0.014

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.804 / q_NPA : 0.888

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

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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	0.035	0.008	2.430	12.415	15.375	1.074	-1.351	-2.684	0.000
4	A	4	SER	0	-0.048	-0.027	3.380	6.372	6.488	0.002	0.322	-0.440	0.000
96	A	96	ASP	-1	-0.922	-0.950	4.661	-36.569	-36.336	-0.001	-0.013	-0.220	0.000
97	A	97	THR	0	-0.103	-0.074	2.860	-13.551	-11.950	0.232	-0.828	-1.005	-0.009
98	A	98	GLY	0	0.005	0.002	3.256	-19.507	-18.633	0.020	-0.661	-0.233	-0.005
99	A	99	LEU	0	-0.040	-0.010	4.697	2.647	2.782	-0.001	-0.012	-0.122	0.000
5	A	5	ALA	0	0.024	0.013	5.515	4.966	4.966	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.051	-0.016	6.406	4.255	4.255	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.900	0.943	8.496	17.783	17.783	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.013	0.016	6.871	1.219	1.219	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.905	-0.955	10.063	-21.317	-21.317	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.890	-0.960	13.183	-17.674	-17.674	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.009	0.000	11.608	1.200	1.200	0.000	0.000	0.000	0.000
12	A	12	GLN	0	0.064	0.027	11.078	-0.552	-0.552	0.000	0.000	0.000	0.000
13	A	13	ASN	0	-0.035	-0.005	14.003	1.734	1.734	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.006	0.004	17.022	1.076	1.076	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.012	-0.003	14.271	0.980	0.980	0.000	0.000	0.000	0.000
16	A	16	ASN	0	-0.025	0.013	17.241	1.651	1.651	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.012	-0.006	18.907	0.954	0.954	0.000	0.000	0.000	0.000
18	A	18	MET	0	-0.031	-0.019	20.492	1.120	1.120	0.000	0.000	0.000	0.000
19	A	19	GLN	0	0.012	-0.008	20.931	0.417	0.417	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.949	0.981	22.915	13.218	13.218	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.068	-0.027	25.687	0.653	0.653	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.070	-0.039	24.801	0.570	0.570	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.793	-0.884	24.156	-13.215	-13.215	0.000	0.000	0.000	0.000
24	A	24	CYS	0	-0.079	-0.010	27.674	0.705	0.705	0.000	0.000	0.000	0.000
25	A	25	PRO	0	-0.012	-0.017	30.873	-0.030	-0.030	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.061	-0.075	33.699	0.297	0.297	0.000	0.000	0.000	0.000
27	A	27	CYS	0	-0.040	-0.033	32.137	0.124	0.124	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.019	0.026	27.529	-0.092	-0.092	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.875	-0.924	26.936	-12.101	-12.101	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.002	-0.006	22.497	0.405	0.405	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.033	-0.031	26.425	0.432	0.432	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.884	0.925	27.005	11.479	11.479	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.870	-0.931	30.354	-8.689	-8.689	0.000	0.000	0.000	0.000
34	A	34	PRO	0	-0.014	-0.009	32.062	0.211	0.211	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.050	-0.023	34.285	0.227	0.227	0.000	0.000	0.000	0.000
36	A	36	SER	0	0.031	0.016	37.808	-0.152	-0.152	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.067	-0.062	39.877	0.264	0.264	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.895	0.925	42.123	6.627	6.627	0.000	0.000	0.000	0.000
39	A	39	CYS	0	-0.025	-0.010	42.753	0.085	0.085	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.852	-0.912	39.467	-8.431	-8.431	0.000	0.000	0.000	0.000
41	A	41	HIS	1	0.888	0.950	37.585	8.203	8.203	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.064	0.053	33.312	0.228	0.228	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.009	-0.007	34.781	-0.027	-0.027	0.000	0.000	0.000	0.000
44	A	44	CYS	0	0.071	0.047	31.369	0.056	0.056	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.824	0.919	34.012	8.404	8.404	0.000	0.000	0.000	0.000
46	A	46	PHE	0	0.056	0.001	36.393	0.321	0.321	0.000	0.000	0.000	0.000
47	A	47	CYS	0	0.002	0.002	34.954	0.156	0.156	0.000	0.000	0.000	0.000
48	A	48	MET	0	0.008	0.026	38.104	0.295	0.295	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.013	-0.002	41.125	0.231	0.231	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.886	0.961	39.306	8.160	8.160	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.009	-0.004	40.884	0.189	0.189	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.024	-0.024	43.535	0.193	0.193	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.025	-0.004	45.800	0.178	0.178	0.000	0.000	0.000	0.000
54	A	54	GLN	0	-0.042	-0.006	46.130	0.152	0.152	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.986	0.993	48.226	6.353	6.353	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.940	0.954	48.149	6.808	6.808	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.021	0.031	51.859	0.029	0.029	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.032	-0.029	50.517	-0.116	-0.116	0.000	0.000	0.000	0.000
59	A	59	SER	0	0.019	0.021	44.042	-0.048	-0.048	0.000	0.000	0.000	0.000
60	A	60	GLN	0	-0.001	-0.017	45.667	0.006	0.006	0.000	0.000	0.000	0.000
61	A	61	CYS	0	-0.021	-0.007	41.789	-0.240	-0.240	0.000	0.000	0.000	0.000
62	A	62	PRO	0	0.046	0.023	38.553	0.088	0.088	0.000	0.000	0.000	0.000
63	A	63	LEU	0	0.022	0.010	35.825	-0.072	-0.072	0.000	0.000	0.000	0.000
64	A	64	CYS	0	-0.075	-0.019	39.074	0.019	0.019	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.984	0.984	42.487	6.853	6.853	0.000	0.000	0.000	0.000
66	A	66	ASN	0	-0.039	-0.027	45.307	0.078	0.078	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.825	-0.893	46.081	-6.802	-6.802	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.060	0.011	42.619	-0.121	-0.121	0.000	0.000	0.000	0.000
69	A	69	THR	0	0.011	0.015	46.998	0.072	0.072	0.000	0.000	0.000	0.000
70	A	70	LYS	1	1.030	0.995	47.054	6.672	6.672	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.916	0.966	48.164	6.356	6.356	0.000	0.000	0.000	0.000
72	A	72	SER	0	0.016	-0.002	47.623	0.113	0.113	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.026	0.005	42.327	-0.056	-0.056	0.000	0.000	0.000	0.000
74	A	74	GLN	0	0.012	0.004	42.857	0.026	0.026	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.777	-0.880	38.718	-8.459	-8.459	0.000	0.000	0.000	0.000
76	A	76	SER	0	-0.017	-0.030	38.674	0.049	0.049	0.000	0.000	0.000	0.000
77	A	77	THR	0	0.007	0.014	34.026	-0.105	-0.105	0.000	0.000	0.000	0.000
78	A	78	ARG	1	0.911	0.975	33.823	8.690	8.690	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.004	-0.009	30.664	-0.073	-0.073	0.000	0.000	0.000	0.000
80	A	80	SER	0	0.013	0.004	30.034	-0.272	-0.272	0.000	0.000	0.000	0.000
81	A	81	GLN	0	0.043	0.009	27.067	-0.494	-0.494	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.018	0.002	25.235	-0.408	-0.408	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.011	0.023	24.168	-0.483	-0.483	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.829	-0.909	23.019	-13.227	-13.227	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.907	-0.965	21.221	-14.458	-14.458	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.024	-0.003	18.718	-0.799	-0.799	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.031	0.018	18.253	-1.127	-1.127	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.918	0.959	15.455	16.654	16.654	0.000	0.000	0.000	0.000
89	A	89	ILE	0	-0.057	-0.018	15.063	-1.078	-1.078	0.000	0.000	0.000	0.000
90	A	90	ILE	0	0.020	0.014	13.505	-1.630	-1.630	0.000	0.000	0.000	0.000
91	A	91	CYS	0	-0.025	-0.016	12.376	-1.903	-1.903	0.000	0.000	0.000	0.000
92	A	92	ALA	0	-0.015	-0.006	10.998	-1.922	-1.922	0.000	0.000	0.000	0.000
93	A	93	PHE	0	0.024	0.012	8.951	-2.597	-2.597	0.000	0.000	0.000	0.000
94	A	94	GLN	0	-0.032	-0.006	7.698	-3.437	-3.437	0.000	0.000	0.000	0.000
95	A	95	LEU	0	-0.051	-0.017	6.778	-4.183	-4.183	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.903	-0.950	7.103	-22.072	-22.072	0.000	0.000	0.000	0.000
101	A	101	TYR	0	-0.056	-0.059	10.545	0.198	0.198	0.000	0.000	0.000	0.000
102	A	102	ALA	0	-0.042	-0.040	13.657	1.157	1.157	0.000	0.000	0.000	0.000
103	A	103	ASN	-1	-0.964	-0.960	14.504	-16.301	-16.301	0.000	0.000	0.000	0.000

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