FMO DATABASE

FMODB ID: M8Z2Z

Calculation Name: 4NPD-A-Xray547

Preferred Name:

Target Type:

Ligand Name: thiocyanate ion | zinc ion

Ligand 3-letter code: SCN | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4NPD

Chain ID: A

ChEMBL ID:

UniProt ID: P38507

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	58
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-312503.840815
FMO2-HF: Nuclear repulsion	289654.436345
FMO2-HF: Total energy	-22849.40447
FMO2-MP2: Total energy	-22917.67322

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:ALA)

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

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.
-7.228	-4.948	0.061	-0.979	-1.363	-0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.841 / q_NPA : 0.909

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	ASN	0	0.018	0.005	3.464	-5.665	-3.385	0.061	-0.979	-1.363	-0.004
4	A	4	LYS	1	0.929	0.972	5.405	34.804	34.804	0.000	0.000	0.000	0.000
5	A	5	PHE	0	0.009	0.019	8.538	-0.466	-0.466	0.000	0.000	0.000	0.000
6	A	6	ASN	0	0.011	0.020	10.822	1.342	1.342	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.982	0.957	12.283	16.527	16.527	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.868	-0.921	14.636	-17.435	-17.435	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.062	0.026	9.979	-0.487	-0.487	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.027	-0.010	14.795	-0.095	-0.095	0.000	0.000	0.000	0.000
11	A	11	ASN	0	-0.037	-0.029	16.152	0.481	0.481	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.047	0.032	17.664	0.615	0.615	0.000	0.000	0.000	0.000
13	A	13	PHE	0	0.027	0.006	15.626	0.486	0.486	0.000	0.000	0.000	0.000
14	A	14	TYR	0	-0.021	-0.026	18.079	0.745	0.745	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.809	-0.891	21.276	-11.017	-11.017	0.000	0.000	0.000	0.000
16	A	16	ILE	0	0.004	-0.012	19.788	0.507	0.507	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.052	-0.023	20.333	0.357	0.357	0.000	0.000	0.000	0.000
18	A	18	HIS	0	-0.016	-0.010	23.729	0.660	0.660	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.040	-0.002	25.923	0.479	0.479	0.000	0.000	0.000	0.000
20	A	20	PRO	0	-0.018	0.002	28.643	-0.065	-0.065	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.035	-0.024	31.921	0.235	0.235	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.053	-0.005	26.672	0.101	0.101	0.000	0.000	0.000	0.000
23	A	23	THR	0	0.046	0.016	30.590	-0.054	-0.054	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.782	-0.882	27.862	-11.311	-11.311	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.987	-0.978	26.572	-10.588	-10.588	0.000	0.000	0.000	0.000
26	A	26	GLN	0	0.031	0.015	26.040	-0.528	-0.528	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.770	0.864	23.938	10.730	10.730	0.000	0.000	0.000	0.000
28	A	28	ASN	0	0.013	-0.004	22.253	-0.962	-0.962	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.028	0.026	21.152	-0.727	-0.727	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.027	0.012	20.758	-0.614	-0.614	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.009	-0.012	17.893	-0.897	-0.897	0.000	0.000	0.000	0.000
32	A	32	GLN	0	-0.076	-0.049	16.021	-1.002	-1.002	0.000	0.000	0.000	0.000
33	A	33	SER	0	0.003	-0.014	15.862	-0.979	-0.979	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.038	-0.018	14.751	-0.866	-0.866	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.879	0.952	11.816	21.209	21.209	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.922	-0.947	11.267	-21.480	-21.480	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.835	-0.897	10.969	-24.422	-24.422	0.000	0.000	0.000	0.000
38	A	38	PRO	0	0.019	0.004	8.882	1.339	1.339	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.107	-0.071	11.175	1.597	1.597	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.018	0.015	12.797	1.229	1.229	0.000	0.000	0.000	0.000
41	A	41	SER	0	-0.012	-0.018	14.510	1.313	1.313	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.856	0.927	16.853	16.536	16.536	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.831	-0.920	18.969	-14.194	-14.194	0.000	0.000	0.000	0.000
44	A	44	ILE	0	0.048	0.028	18.826	0.608	0.608	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.016	0.004	20.904	0.493	0.493	0.000	0.000	0.000	0.000
46	A	46	ALA	0	-0.022	-0.011	22.595	0.670	0.670	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.973	-0.977	24.628	-11.394	-11.394	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.020	0.011	24.272	0.475	0.475	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.851	0.905	26.207	11.172	11.172	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.914	0.955	28.462	10.834	10.834	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.005	0.009	28.723	0.348	0.348	0.000	0.000	0.000	0.000
52	A	52	ASN	0	0.009	-0.007	29.884	0.184	0.184	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.889	-0.946	31.726	-9.269	-9.269	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.074	-0.039	34.207	0.312	0.312	0.000	0.000	0.000	0.000
55	A	55	GLN	0	-0.061	-0.033	32.035	0.328	0.328	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.001	0.009	36.458	0.024	0.024	0.000	0.000	0.000	0.000
57	A	57	PRO	0	-0.051	-0.032	37.820	0.193	0.193	0.000	0.000	0.000	0.000
58	A	58	LYS	0	0.010	0.025	41.013	0.356	0.356	0.000	0.000	0.000	0.000

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