FMO DATABASE

FMODB ID: JV8N9

Calculation Name: 6J2U-A-Xray547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6J2U

Chain ID: A

ChEMBL ID:

UniProt ID: Q93HL1

Base Structure: X-ray

Registration Date: 2025-10-06

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	80
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-471770.637691
FMO2-HF: Nuclear repulsion	441936.508702
FMO2-HF: Total energy	-29834.128989
FMO2-MP2: Total energy	-29921.6302

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:38:GLY)

Summations of interaction energy for fragment #1(A:38: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.
-98.184	-94.15	1.35	-2.827	-2.556	-0.035

Interaction energy analysis for fragmet #1(A:38:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.840 / q_NPA : 0.912

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	40	GLN	0	0.007	-0.007	2.315	-36.873	-33.608	1.333	-2.463	-2.135	-0.032
4	A	41	PRO	0	0.015	0.018	4.745	4.900	5.007	-0.001	-0.009	-0.096	0.000
27	A	64	SER	0	-0.054	-0.043	3.433	-9.709	-9.047	0.018	-0.355	-0.325	-0.003
5	A	42	PHE	0	-0.023	-0.013	7.249	1.155	1.155	0.000	0.000	0.000	0.000
6	A	43	ASP	-1	-0.787	-0.856	10.862	-18.537	-18.537	0.000	0.000	0.000	0.000
7	A	44	GLU	-1	-0.825	-0.888	14.473	-19.524	-19.524	0.000	0.000	0.000	0.000
8	A	45	VAL	0	0.006	0.002	17.473	0.225	0.225	0.000	0.000	0.000	0.000
9	A	46	TYR	0	-0.028	-0.018	19.653	0.034	0.034	0.000	0.000	0.000	0.000
10	A	47	GLN	0	0.006	-0.012	21.651	0.154	0.154	0.000	0.000	0.000	0.000
11	A	48	GLY	0	0.015	0.011	25.175	0.285	0.285	0.000	0.000	0.000	0.000
12	A	49	ARG	1	0.795	0.895	21.905	13.210	13.210	0.000	0.000	0.000	0.000
13	A	50	ARG	1	0.816	0.877	17.513	16.724	16.724	0.000	0.000	0.000	0.000
14	A	51	ILE	0	-0.031	-0.013	16.076	-0.101	-0.101	0.000	0.000	0.000	0.000
15	A	52	GLU	-1	-0.822	-0.893	13.554	-19.388	-19.388	0.000	0.000	0.000	0.000
16	A	53	GLY	0	0.008	0.009	9.442	0.207	0.207	0.000	0.000	0.000	0.000
17	A	54	ARG	1	0.770	0.858	9.144	17.668	17.668	0.000	0.000	0.000	0.000
18	A	55	ALA	0	0.048	0.011	5.511	-1.121	-1.121	0.000	0.000	0.000	0.000
19	A	56	THR	0	0.051	0.005	6.754	3.542	3.542	0.000	0.000	0.000	0.000
20	A	57	GLY	0	-0.042	-0.013	9.052	2.768	2.768	0.000	0.000	0.000	0.000
21	A	58	GLY	0	-0.016	-0.005	11.165	2.012	2.012	0.000	0.000	0.000	0.000
22	A	59	GLY	0	0.018	0.014	13.126	1.192	1.192	0.000	0.000	0.000	0.000
23	A	60	HIS	0	-0.015	0.021	9.847	0.892	0.892	0.000	0.000	0.000	0.000
24	A	61	HIS	0	-0.019	-0.020	10.553	-2.106	-2.106	0.000	0.000	0.000	0.000
25	A	62	HIS	0	-0.005	-0.007	11.891	-0.198	-0.198	0.000	0.000	0.000	0.000
26	A	63	GLY	0	0.011	0.004	9.180	-1.179	-1.179	0.000	0.000	0.000	0.000
28	A	65	GLY	0	0.010	0.027	5.688	-3.066	-3.066	0.000	0.000	0.000	0.000
29	A	66	TYR	0	-0.040	-0.065	5.600	-3.405	-3.405	0.000	0.000	0.000	0.000
30	A	67	GLY	0	0.082	0.046	8.160	2.958	2.958	0.000	0.000	0.000	0.000
31	A	68	VAL	0	-0.030	-0.012	10.355	-2.189	-2.189	0.000	0.000	0.000	0.000
32	A	69	PHE	0	0.016	0.013	12.797	1.197	1.197	0.000	0.000	0.000	0.000
33	A	70	ILE	0	0.037	0.011	16.053	-0.433	-0.433	0.000	0.000	0.000	0.000
34	A	71	ASP	-1	-0.801	-0.886	19.262	-13.086	-13.086	0.000	0.000	0.000	0.000
35	A	72	GLY	0	-0.056	-0.025	19.148	0.504	0.504	0.000	0.000	0.000	0.000
36	A	73	MET	0	0.001	0.014	19.807	-0.211	-0.211	0.000	0.000	0.000	0.000
37	A	74	GLU	-1	-0.929	-0.976	14.436	-21.129	-21.129	0.000	0.000	0.000	0.000
38	A	75	LEU	0	-0.033	-0.016	15.922	0.926	0.926	0.000	0.000	0.000	0.000
39	A	76	HIS	0	0.035	0.023	15.238	-1.340	-1.340	0.000	0.000	0.000	0.000
40	A	77	VAL	0	-0.007	-0.023	11.116	0.243	0.243	0.000	0.000	0.000	0.000
41	A	78	MET	0	-0.027	-0.011	11.618	-0.357	-0.357	0.000	0.000	0.000	0.000
42	A	79	GLN	0	-0.018	-0.003	6.366	-2.442	-2.442	0.000	0.000	0.000	0.000
43	A	80	ASN	0	-0.011	-0.004	10.897	1.283	1.283	0.000	0.000	0.000	0.000
44	A	81	VAL	0	-0.003	-0.022	11.808	-1.765	-1.765	0.000	0.000	0.000	0.000
45	A	82	ASP	-1	-0.845	-0.895	12.792	-20.875	-20.875	0.000	0.000	0.000	0.000
46	A	83	GLY	0	-0.027	-0.007	9.684	-0.697	-0.697	0.000	0.000	0.000	0.000
47	A	84	SER	0	-0.064	-0.047	10.456	-1.359	-1.359	0.000	0.000	0.000	0.000
48	A	85	TRP	0	-0.031	-0.036	6.309	-1.580	-1.580	0.000	0.000	0.000	0.000
49	A	86	ILE	0	0.012	0.026	12.948	1.269	1.269	0.000	0.000	0.000	0.000
50	A	87	SER	0	0.001	-0.017	14.698	-1.055	-1.055	0.000	0.000	0.000	0.000
51	A	88	VAL	0	-0.006	-0.005	17.144	0.749	0.749	0.000	0.000	0.000	0.000
52	A	89	VAL	0	-0.028	0.010	19.956	0.590	0.590	0.000	0.000	0.000	0.000
53	A	90	SER	0	0.001	-0.002	19.600	0.845	0.845	0.000	0.000	0.000	0.000
54	A	91	HIS	0	0.017	0.007	19.170	-1.194	-1.194	0.000	0.000	0.000	0.000
55	A	92	TYR	0	-0.027	-0.030	20.503	-0.200	-0.200	0.000	0.000	0.000	0.000
56	A	93	ASP	-1	-0.923	-0.944	21.019	-13.879	-13.879	0.000	0.000	0.000	0.000
57	A	94	PRO	0	-0.016	-0.007	16.633	-0.683	-0.683	0.000	0.000	0.000	0.000
58	A	95	VAL	0	0.006	0.013	14.855	0.134	0.134	0.000	0.000	0.000	0.000
59	A	96	ALA	0	0.011	-0.009	13.271	-1.305	-1.305	0.000	0.000	0.000	0.000
60	A	97	THR	0	-0.024	-0.007	9.764	-2.275	-2.275	0.000	0.000	0.000	0.000
61	A	98	PRO	0	0.072	0.031	7.618	2.405	2.405	0.000	0.000	0.000	0.000
62	A	99	ARG	1	0.858	0.923	10.887	24.985	24.985	0.000	0.000	0.000	0.000
63	A	100	ALA	0	-0.033	-0.016	12.682	1.947	1.947	0.000	0.000	0.000	0.000
64	A	101	ALA	0	0.058	0.026	13.882	1.441	1.441	0.000	0.000	0.000	0.000
65	A	102	ALA	0	0.025	0.011	14.455	1.278	1.278	0.000	0.000	0.000	0.000
66	A	103	ARG	1	0.884	0.945	16.326	18.602	18.602	0.000	0.000	0.000	0.000
67	A	104	ALA	0	0.014	0.007	18.590	0.973	0.973	0.000	0.000	0.000	0.000
68	A	105	ALA	0	0.043	0.014	19.179	0.813	0.813	0.000	0.000	0.000	0.000
69	A	106	VAL	0	-0.046	-0.020	20.116	0.677	0.677	0.000	0.000	0.000	0.000
70	A	107	VAL	0	-0.059	-0.031	22.502	0.634	0.634	0.000	0.000	0.000	0.000
71	A	108	GLU	-1	-0.957	-0.972	24.182	-11.664	-11.664	0.000	0.000	0.000	0.000
72	A	109	LEU	0	0.053	0.019	22.535	0.430	0.430	0.000	0.000	0.000	0.000
73	A	110	GLN	0	-0.072	-0.022	26.358	0.697	0.697	0.000	0.000	0.000	0.000
74	A	111	GLY	0	-0.007	-0.005	27.101	0.390	0.390	0.000	0.000	0.000	0.000
75	A	112	ALA	0	0.003	0.007	27.896	0.036	0.036	0.000	0.000	0.000	0.000
76	A	113	PRO	0	-0.015	-0.009	25.407	-0.585	-0.585	0.000	0.000	0.000	0.000
77	A	114	LEU	0	0.030	0.017	19.932	0.126	0.126	0.000	0.000	0.000	0.000
78	A	115	VAL	0	-0.029	-0.025	24.011	0.379	0.379	0.000	0.000	0.000	0.000
79	A	116	PRO	0	-0.039	-0.035	23.084	-0.470	-0.470	0.000	0.000	0.000	0.000
80	A	117	PHE	-1	-0.919	-0.938	17.179	-13.683	-13.683	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:38:GLY)