FMO DATABASE

FMODB ID: JV559

Calculation Name: 4WHC-B-Xray547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4WHC

Chain ID: B

ChEMBL ID:

UniProt ID: P40199

Base Structure: X-ray

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	108
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-824499.366784
FMO2-HF: Nuclear repulsion	783614.26301
FMO2-HF: Total energy	-40885.103773
FMO2-MP2: Total energy	-41007.800236

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:0:ALA)

Summations of interaction energy for fragment #1(A:0: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.
-94.247	-90.94	1.857	-2.276	-2.887	-0.018

Interaction energy analysis for fragmet #1(A:0:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.830 / 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

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	2	LEU	0	0.053	0.049	3.735	-2.343	-0.635	-0.009	-0.878	-0.821	-0.002
4	A	3	THR	0	-0.026	-0.021	4.441	-0.920	-0.814	-0.001	-0.009	-0.095	0.000
24	A	23	ASN	0	-0.068	-0.059	2.624	-9.151	-7.658	1.867	-1.389	-1.971	-0.016
5	A	4	ILE	0	-0.027	-0.008	6.702	0.998	0.998	0.000	0.000	0.000	0.000
6	A	5	GLU	-1	-0.910	-0.944	8.797	-25.748	-25.748	0.000	0.000	0.000	0.000
7	A	6	SER	0	-0.051	-0.042	11.407	0.695	0.695	0.000	0.000	0.000	0.000
8	A	7	THR	0	-0.069	-0.004	15.251	0.289	0.289	0.000	0.000	0.000	0.000
9	A	8	PRO	0	0.034	0.003	17.461	0.261	0.261	0.000	0.000	0.000	0.000
10	A	9	PHE	0	0.060	0.015	16.185	0.271	0.271	0.000	0.000	0.000	0.000
11	A	10	ASN	0	-0.032	-0.016	18.649	0.493	0.493	0.000	0.000	0.000	0.000
12	A	11	VAL	0	-0.009	-0.007	22.164	0.078	0.078	0.000	0.000	0.000	0.000
13	A	12	ALA	0	0.029	0.022	24.526	0.250	0.250	0.000	0.000	0.000	0.000
14	A	13	GLU	-1	-0.852	-0.945	28.310	-9.305	-9.305	0.000	0.000	0.000	0.000
15	A	14	GLY	0	-0.027	-0.007	30.487	0.205	0.205	0.000	0.000	0.000	0.000
16	A	15	LYS	1	0.825	0.922	27.290	9.627	9.627	0.000	0.000	0.000	0.000
17	A	16	GLU	-1	-0.876	-0.931	24.943	-11.015	-11.015	0.000	0.000	0.000	0.000
18	A	17	VAL	0	-0.010	-0.005	19.047	-0.204	-0.204	0.000	0.000	0.000	0.000
19	A	18	LEU	0	-0.018	0.001	16.945	0.106	0.106	0.000	0.000	0.000	0.000
20	A	19	LEU	0	-0.005	-0.001	15.318	-0.859	-0.859	0.000	0.000	0.000	0.000
21	A	20	LEU	0	-0.006	-0.013	12.058	0.073	0.073	0.000	0.000	0.000	0.000
22	A	21	ALA	0	0.042	0.018	10.189	-1.053	-1.053	0.000	0.000	0.000	0.000
23	A	22	HIS	0	0.000	-0.001	5.737	-1.631	-1.631	0.000	0.000	0.000	0.000
25	A	24	LEU	0	0.026	0.019	5.576	0.124	0.124	0.000	0.000	0.000	0.000
26	A	25	PRO	0	0.017	0.037	9.286	-0.388	-0.388	0.000	0.000	0.000	0.000
27	A	26	GLN	0	0.036	0.001	9.373	2.014	2.014	0.000	0.000	0.000	0.000
28	A	27	ASN	0	0.011	-0.010	13.200	0.882	0.882	0.000	0.000	0.000	0.000
29	A	28	ARG	1	0.901	0.971	13.042	22.436	22.436	0.000	0.000	0.000	0.000
30	A	29	ILE	0	-0.006	-0.015	16.615	0.603	0.603	0.000	0.000	0.000	0.000
31	A	30	GLY	0	0.019	0.010	18.868	0.948	0.948	0.000	0.000	0.000	0.000
32	A	31	TYR	0	-0.031	-0.020	14.913	-1.684	-1.684	0.000	0.000	0.000	0.000
33	A	32	SER	0	-0.039	-0.020	17.981	1.280	1.280	0.000	0.000	0.000	0.000
34	A	33	TRP	0	0.025	0.012	14.246	-0.956	-0.956	0.000	0.000	0.000	0.000
35	A	34	TYR	0	0.014	0.005	18.704	1.108	1.108	0.000	0.000	0.000	0.000
36	A	35	LYS	1	0.901	0.953	20.045	11.059	11.059	0.000	0.000	0.000	0.000
37	A	36	GLY	0	0.023	0.007	21.355	0.307	0.307	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.958	-0.975	18.053	-15.151	-15.151	0.000	0.000	0.000	0.000
39	A	38	ARG	1	0.921	0.952	18.126	13.065	13.065	0.000	0.000	0.000	0.000
40	A	39	VAL	0	0.016	0.023	18.012	0.296	0.296	0.000	0.000	0.000	0.000
41	A	40	ASP	-1	-0.804	-0.895	20.518	-11.127	-11.127	0.000	0.000	0.000	0.000
42	A	41	GLY	0	-0.015	-0.001	24.271	-0.034	-0.034	0.000	0.000	0.000	0.000
43	A	42	ASN	0	-0.076	-0.059	26.777	0.528	0.528	0.000	0.000	0.000	0.000
44	A	43	SER	0	0.009	-0.004	24.384	0.314	0.314	0.000	0.000	0.000	0.000
45	A	44	LEU	0	-0.049	-0.012	22.755	-0.425	-0.425	0.000	0.000	0.000	0.000
46	A	45	ILE	0	0.003	0.009	21.679	0.439	0.439	0.000	0.000	0.000	0.000
47	A	46	VAL	0	0.015	-0.011	22.183	0.471	0.471	0.000	0.000	0.000	0.000
48	A	47	GLY	0	0.039	0.038	22.212	-0.747	-0.747	0.000	0.000	0.000	0.000
49	A	48	TYR	0	-0.015	-0.023	20.709	0.222	0.222	0.000	0.000	0.000	0.000
50	A	49	VAL	0	0.025	0.017	22.040	-0.636	-0.636	0.000	0.000	0.000	0.000
51	A	50	ILE	0	-0.008	-0.009	17.754	0.359	0.359	0.000	0.000	0.000	0.000
52	A	51	GLY	0	-0.024	-0.012	22.204	0.308	0.308	0.000	0.000	0.000	0.000
53	A	52	THR	0	-0.018	-0.023	24.895	0.257	0.257	0.000	0.000	0.000	0.000
54	A	53	GLN	0	-0.033	-0.008	24.618	0.228	0.228	0.000	0.000	0.000	0.000
55	A	54	GLN	0	-0.029	0.003	25.979	0.302	0.302	0.000	0.000	0.000	0.000
56	A	55	ALA	0	0.025	0.010	25.723	-0.454	-0.454	0.000	0.000	0.000	0.000
57	A	56	THR	0	-0.013	-0.012	26.328	0.648	0.648	0.000	0.000	0.000	0.000
58	A	57	PRO	0	-0.005	0.010	26.840	-0.456	-0.456	0.000	0.000	0.000	0.000
59	A	58	GLY	0	0.021	0.002	27.519	0.154	0.154	0.000	0.000	0.000	0.000
60	A	59	PRO	0	-0.032	-0.025	28.399	0.195	0.195	0.000	0.000	0.000	0.000
61	A	60	ALA	0	-0.016	-0.001	26.139	0.238	0.238	0.000	0.000	0.000	0.000
62	A	61	TYR	0	-0.075	-0.019	27.007	-0.044	-0.044	0.000	0.000	0.000	0.000
63	A	62	SER	0	-0.039	-0.056	28.556	0.409	0.409	0.000	0.000	0.000	0.000
64	A	63	GLY	0	-0.008	-0.002	30.041	0.301	0.301	0.000	0.000	0.000	0.000
65	A	64	ARG	1	0.702	0.814	28.029	10.634	10.634	0.000	0.000	0.000	0.000
66	A	65	GLU	-1	-0.785	-0.850	24.008	-11.276	-11.276	0.000	0.000	0.000	0.000
67	A	66	THR	0	-0.023	-0.015	23.813	0.402	0.402	0.000	0.000	0.000	0.000
68	A	67	ILE	0	-0.048	-0.004	18.224	-0.536	-0.536	0.000	0.000	0.000	0.000
69	A	68	TYR	0	0.024	0.017	19.156	0.649	0.649	0.000	0.000	0.000	0.000
70	A	69	PRO	0	0.043	0.006	18.825	-0.783	-0.783	0.000	0.000	0.000	0.000
71	A	70	ASN	0	-0.031	0.011	14.559	-0.143	-0.143	0.000	0.000	0.000	0.000
72	A	71	ALA	0	0.044	0.016	13.667	-1.368	-1.368	0.000	0.000	0.000	0.000
73	A	72	SER	0	-0.046	-0.023	15.135	0.203	0.203	0.000	0.000	0.000	0.000
74	A	73	LEU	0	0.040	0.010	16.187	0.854	0.854	0.000	0.000	0.000	0.000
75	A	74	LEU	0	0.007	0.006	18.934	-0.299	-0.299	0.000	0.000	0.000	0.000
76	A	75	ILE	0	-0.002	0.000	21.542	0.311	0.311	0.000	0.000	0.000	0.000
77	A	76	GLN	0	-0.019	-0.032	23.852	0.002	0.002	0.000	0.000	0.000	0.000
78	A	77	ASN	0	-0.012	-0.014	27.066	0.166	0.166	0.000	0.000	0.000	0.000
79	A	78	VAL	0	-0.005	0.013	24.844	0.132	0.132	0.000	0.000	0.000	0.000
80	A	79	THR	0	0.068	0.032	28.217	0.350	0.350	0.000	0.000	0.000	0.000
81	A	80	GLN	0	0.035	-0.004	28.530	-0.628	-0.628	0.000	0.000	0.000	0.000
82	A	81	ASN	0	-0.064	-0.040	28.684	-0.093	-0.093	0.000	0.000	0.000	0.000
83	A	82	ASP	-1	-0.782	-0.862	24.956	-11.114	-11.114	0.000	0.000	0.000	0.000
84	A	83	THR	0	0.015	0.046	23.896	-0.835	-0.835	0.000	0.000	0.000	0.000
85	A	84	GLY	0	0.007	0.002	22.025	0.245	0.245	0.000	0.000	0.000	0.000
86	A	85	PHE	0	-0.021	-0.022	17.055	-0.498	-0.498	0.000	0.000	0.000	0.000
87	A	86	TYR	0	-0.010	-0.027	17.475	0.850	0.850	0.000	0.000	0.000	0.000
88	A	87	THR	0	-0.023	-0.017	15.112	-1.365	-1.365	0.000	0.000	0.000	0.000
89	A	88	LEU	0	-0.024	0.008	11.838	0.879	0.879	0.000	0.000	0.000	0.000
90	A	89	GLN	0	-0.025	-0.038	14.335	-0.069	-0.069	0.000	0.000	0.000	0.000
91	A	90	VAL	0	-0.039	-0.031	12.118	0.789	0.789	0.000	0.000	0.000	0.000
92	A	91	ILE	0	-0.001	0.004	15.059	-0.367	-0.367	0.000	0.000	0.000	0.000
93	A	92	LYS	1	0.806	0.889	12.333	24.117	24.117	0.000	0.000	0.000	0.000
94	A	93	SER	0	-0.011	-0.022	17.896	0.820	0.820	0.000	0.000	0.000	0.000
95	A	94	ASP	-1	-0.856	-0.938	16.560	-18.564	-18.564	0.000	0.000	0.000	0.000
96	A	95	LEU	0	-0.038	-0.017	19.750	0.442	0.442	0.000	0.000	0.000	0.000
97	A	96	VAL	0	-0.038	0.004	14.988	0.130	0.130	0.000	0.000	0.000	0.000
98	A	97	ASN	0	-0.027	-0.035	14.838	-1.932	-1.932	0.000	0.000	0.000	0.000
99	A	98	GLU	-1	-0.816	-0.891	9.098	-33.383	-33.383	0.000	0.000	0.000	0.000
100	A	99	GLU	-1	-0.847	-0.925	12.583	-19.273	-19.273	0.000	0.000	0.000	0.000
101	A	100	ALA	0	-0.074	-0.029	9.278	-2.336	-2.336	0.000	0.000	0.000	0.000
102	A	101	THR	0	0.026	0.013	11.192	1.244	1.244	0.000	0.000	0.000	0.000
103	A	102	GLY	0	-0.009	0.003	11.659	-1.413	-1.413	0.000	0.000	0.000	0.000
104	A	103	GLN	0	0.008	-0.014	13.982	0.342	0.342	0.000	0.000	0.000	0.000
105	A	104	PHE	0	-0.004	0.020	16.697	-0.673	-0.673	0.000	0.000	0.000	0.000
106	A	105	HIS	0	0.019	0.020	19.492	0.294	0.294	0.000	0.000	0.000	0.000
107	A	106	VAL	0	0.008	0.004	22.909	-0.155	-0.155	0.000	0.000	0.000	0.000
108	A	107	TYR	-1	-0.889	-0.923	25.556	-9.509	-9.509	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:ALA)