FMO DATABASE

FMODB ID: 7NYKK

Calculation Name: 3SWN-B-Xray547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3SWN

Chain ID: B

ChEMBL ID:

UniProt ID: O42978

Base Structure: X-ray

Registration Date: 2025-10-04

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	71
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-418597.436751
FMO2-HF: Nuclear repulsion	391142.576121
FMO2-HF: Total energy	-27454.86063
FMO2-MP2: Total energy	-27535.138769

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:3:SER)

Summations of interaction energy for fragment #1(A:3:SER)

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.
-84.62	-79.918	18.756	-12.804	-10.652	-0.122

Interaction energy analysis for fragmet #1(A:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.753 / q_NPA : 0.850

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	5	PRO	0	0.055	0.014	3.715	-1.324	-0.026	-0.002	-0.556	-0.740	0.000
5	A	7	GLU	-1	-0.720	-0.841	1.950	-144.442	-142.689	18.478	-11.487	-8.743	-0.131
6	A	8	PHE	0	-0.095	-0.045	4.087	4.029	4.303	-0.001	-0.023	-0.250	0.000
9	A	11	LYS	1	0.904	0.965	2.719	37.879	39.256	0.281	-0.738	-0.919	0.009
4	A	6	ASN	0	0.061	0.030	6.477	2.900	2.900	0.000	0.000	0.000	0.000
7	A	9	LEU	0	0.048	0.021	5.440	3.962	3.962	0.000	0.000	0.000	0.000
8	A	10	ASN	0	0.016	-0.006	7.041	0.320	0.320	0.000	0.000	0.000	0.000
10	A	12	VAL	0	-0.037	-0.022	7.967	1.802	1.802	0.000	0.000	0.000	0.000
11	A	13	ILE	0	0.050	0.041	11.026	1.519	1.519	0.000	0.000	0.000	0.000
12	A	14	GLY	0	0.003	0.013	13.704	0.100	0.100	0.000	0.000	0.000	0.000
13	A	15	LYS	1	0.870	0.932	11.980	19.883	19.883	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.921	0.968	15.873	14.625	14.625	0.000	0.000	0.000	0.000
15	A	17	VAL	0	0.018	0.014	13.869	-0.916	-0.916	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.041	-0.017	16.065	1.141	1.141	0.000	0.000	0.000	0.000
17	A	19	ILE	0	0.007	-0.006	15.980	-1.187	-1.187	0.000	0.000	0.000	0.000
18	A	20	ARG	1	0.857	0.947	17.642	14.360	14.360	0.000	0.000	0.000	0.000
19	A	21	LEU	0	0.065	0.017	19.024	-0.657	-0.657	0.000	0.000	0.000	0.000
20	A	22	SER	0	0.003	-0.014	21.737	0.082	0.082	0.000	0.000	0.000	0.000
21	A	23	SER	0	-0.001	0.007	22.998	0.182	0.182	0.000	0.000	0.000	0.000
22	A	24	GLY	0	0.001	0.005	24.508	0.419	0.419	0.000	0.000	0.000	0.000
23	A	25	VAL	0	-0.038	-0.008	25.460	0.262	0.262	0.000	0.000	0.000	0.000
24	A	26	ASP	-1	-0.843	-0.922	21.841	-13.466	-13.466	0.000	0.000	0.000	0.000
25	A	27	TYR	0	0.003	-0.017	21.199	0.381	0.381	0.000	0.000	0.000	0.000
26	A	28	LYS	1	0.928	0.957	20.373	11.532	11.532	0.000	0.000	0.000	0.000
27	A	29	GLY	0	0.066	0.040	20.136	0.787	0.787	0.000	0.000	0.000	0.000
28	A	30	ILE	0	-0.039	-0.008	18.427	-0.625	-0.625	0.000	0.000	0.000	0.000
29	A	31	LEU	0	0.010	0.012	12.878	0.287	0.287	0.000	0.000	0.000	0.000
30	A	32	SER	0	-0.039	-0.029	16.908	-0.252	-0.252	0.000	0.000	0.000	0.000
31	A	33	CYS	0	-0.032	-0.023	16.244	-0.396	-0.396	0.000	0.000	0.000	0.000
32	A	34	LEU	0	0.005	-0.007	10.443	-0.471	-0.471	0.000	0.000	0.000	0.000
33	A	35	ASP	-1	-0.758	-0.865	14.486	-17.539	-17.539	0.000	0.000	0.000	0.000
34	A	36	GLY	0	-0.017	-0.014	12.605	-1.520	-1.520	0.000	0.000	0.000	0.000
35	A	37	TYR	0	-0.065	-0.027	13.447	-0.899	-0.899	0.000	0.000	0.000	0.000
36	A	38	MET	0	-0.026	-0.010	11.218	-0.215	-0.215	0.000	0.000	0.000	0.000
37	A	39	ASN	0	-0.030	-0.024	13.800	1.216	1.216	0.000	0.000	0.000	0.000
38	A	40	LEU	0	-0.019	-0.007	13.820	-0.862	-0.862	0.000	0.000	0.000	0.000
39	A	41	ALA	0	0.022	0.018	16.766	0.988	0.988	0.000	0.000	0.000	0.000
40	A	42	LEU	0	-0.023	-0.022	18.320	-0.909	-0.909	0.000	0.000	0.000	0.000
41	A	43	GLU	-1	-0.777	-0.863	20.449	-12.626	-12.626	0.000	0.000	0.000	0.000
42	A	44	ARG	1	0.883	0.937	23.322	10.498	10.498	0.000	0.000	0.000	0.000
43	A	45	THR	0	-0.065	-0.034	23.099	-0.545	-0.545	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.832	-0.894	24.683	-10.102	-10.102	0.000	0.000	0.000	0.000
45	A	47	GLU	-1	-0.749	-0.838	24.922	-10.930	-10.930	0.000	0.000	0.000	0.000
46	A	48	TYR	0	-0.067	-0.066	25.740	0.562	0.562	0.000	0.000	0.000	0.000
47	A	49	VAL	0	0.047	0.026	26.982	-0.335	-0.335	0.000	0.000	0.000	0.000
48	A	50	ASN	0	0.022	0.008	27.424	0.062	0.062	0.000	0.000	0.000	0.000
49	A	51	GLY	0	0.018	0.015	27.568	0.311	0.311	0.000	0.000	0.000	0.000
50	A	52	LYS	1	0.938	0.975	29.007	8.716	8.716	0.000	0.000	0.000	0.000
51	A	53	LYS	1	0.867	0.940	29.143	9.874	9.874	0.000	0.000	0.000	0.000
52	A	54	THR	0	-0.101	-0.083	30.647	0.338	0.338	0.000	0.000	0.000	0.000
53	A	55	ASN	0	0.040	0.028	30.343	0.404	0.404	0.000	0.000	0.000	0.000
54	A	56	VAL	0	-0.070	-0.047	29.059	-0.299	-0.299	0.000	0.000	0.000	0.000
55	A	57	TYR	0	-0.037	-0.015	27.173	0.360	0.360	0.000	0.000	0.000	0.000
56	A	58	GLY	0	-0.014	-0.020	28.028	-0.211	-0.211	0.000	0.000	0.000	0.000
57	A	59	ASP	-1	-0.836	-0.910	25.237	-11.635	-11.635	0.000	0.000	0.000	0.000
58	A	60	ALA	0	-0.054	-0.036	23.237	0.373	0.373	0.000	0.000	0.000	0.000
59	A	61	PHE	0	0.012	0.011	21.496	-0.657	-0.657	0.000	0.000	0.000	0.000
60	A	62	ILE	0	0.003	-0.001	19.009	0.430	0.430	0.000	0.000	0.000	0.000
61	A	63	ARG	1	0.919	0.952	18.727	14.585	14.585	0.000	0.000	0.000	0.000
62	A	64	GLY	0	0.080	0.032	15.372	0.264	0.264	0.000	0.000	0.000	0.000
63	A	65	ASN	0	-0.084	-0.045	15.840	-1.037	-1.037	0.000	0.000	0.000	0.000
64	A	66	ASN	0	-0.030	-0.018	17.177	0.038	0.038	0.000	0.000	0.000	0.000
65	A	67	VAL	0	-0.037	-0.002	16.065	0.835	0.835	0.000	0.000	0.000	0.000
66	A	68	LEU	0	-0.033	-0.009	17.516	-0.386	-0.386	0.000	0.000	0.000	0.000
67	A	69	TYR	0	0.020	-0.001	13.400	-0.706	-0.706	0.000	0.000	0.000	0.000
68	A	70	VAL	0	0.018	0.005	11.813	0.975	0.975	0.000	0.000	0.000	0.000
69	A	71	SER	0	-0.020	-0.009	11.466	-1.964	-1.964	0.000	0.000	0.000	0.000
70	A	72	ALA	0	-0.015	-0.012	11.655	0.772	0.772	0.000	0.000	0.000	0.000
71	A	73	LEU	-1	-0.940	-0.968	13.445	-15.560	-15.560	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)