FMO DATABASE

FMODB ID: 3ZGML

Calculation Name: 4N4R-D-Xray547

Preferred Name:

Target Type:

Ligand Name: cacodylate ion | zinc ion

Ligand 3-letter code: CAC | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4N4R

Chain ID: D

ChEMBL ID:

UniProt ID: Q8ZRW0

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	151
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1295666.131478
FMO2-HF: Nuclear repulsion	1235586.209178
FMO2-HF: Total energy	-60079.9223
FMO2-MP2: Total energy	-60251.176912

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:19:CYS)

Summations of interaction energy for fragment #1(A:19:CYS)

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.
-2.392	1.827	1.316	-2.168	-3.367	-0.001

Interaction energy analysis for fragmet #1(A:19:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.022

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	21	TRP	0	-0.012	0.002	2.332	-3.055	1.155	1.317	-2.135	-3.393	-0.001
4	A	22	HIS	0	-0.024	-0.013	4.615	-2.086	-2.077	-0.001	-0.033	0.026	0.000
5	A	23	LEU	0	0.024	0.010	7.508	1.081	1.081	0.000	0.000	0.000	0.000
6	A	24	ARG	1	0.871	0.935	10.929	0.769	0.769	0.000	0.000	0.000	0.000
7	A	25	SER	0	0.064	0.033	13.474	0.162	0.162	0.000	0.000	0.000	0.000
8	A	26	THR	0	-0.010	0.003	15.674	0.128	0.128	0.000	0.000	0.000	0.000
9	A	27	THR	0	-0.018	-0.013	18.254	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	28	GLN	0	0.031	0.020	20.193	0.005	0.005	0.000	0.000	0.000	0.000
11	A	29	VAL	0	0.035	0.026	21.800	0.058	0.058	0.000	0.000	0.000	0.000
12	A	30	PRO	0	0.020	0.009	24.495	-0.064	-0.064	0.000	0.000	0.000	0.000
13	A	31	ALA	0	0.039	0.002	25.434	0.031	0.031	0.000	0.000	0.000	0.000
14	A	32	SER	0	0.008	0.005	27.566	0.008	0.008	0.000	0.000	0.000	0.000
15	A	33	MET	0	0.017	0.009	29.000	0.035	0.035	0.000	0.000	0.000	0.000
16	A	34	LYS	1	0.881	0.957	27.985	0.434	0.434	0.000	0.000	0.000	0.000
17	A	35	THR	0	-0.063	-0.028	30.327	0.002	0.002	0.000	0.000	0.000	0.000
18	A	36	MET	0	0.029	0.012	31.928	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	37	ILE	0	0.018	0.025	35.696	0.002	0.002	0.000	0.000	0.000	0.000
20	A	38	LEU	0	-0.031	-0.021	35.089	0.003	0.003	0.000	0.000	0.000	0.000
21	A	39	ASP	-1	-0.817	-0.909	38.072	-0.081	-0.081	0.000	0.000	0.000	0.000
22	A	40	SER	0	-0.008	-0.026	39.970	0.010	0.010	0.000	0.000	0.000	0.000
23	A	41	GLY	0	0.014	0.017	42.171	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	42	ASP	-1	-0.798	-0.897	43.705	-0.028	-0.028	0.000	0.000	0.000	0.000
25	A	43	PRO	0	-0.013	-0.017	42.529	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	44	ASN	0	-0.029	0.001	42.466	-0.013	-0.013	0.000	0.000	0.000	0.000
27	A	45	GLY	0	0.094	0.063	42.749	0.002	0.002	0.000	0.000	0.000	0.000
28	A	46	PRO	0	-0.005	-0.004	38.382	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	47	LEU	0	0.043	0.017	34.383	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	48	SER	0	-0.031	-0.018	36.162	-0.018	-0.018	0.000	0.000	0.000	0.000
31	A	49	ARG	1	0.906	0.952	37.284	0.041	0.041	0.000	0.000	0.000	0.000
32	A	50	ALA	0	0.056	0.037	33.070	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	51	VAL	0	0.002	-0.010	32.380	-0.020	-0.020	0.000	0.000	0.000	0.000
34	A	52	ARG	1	0.980	0.986	32.774	0.124	0.124	0.000	0.000	0.000	0.000
35	A	53	ASN	0	0.012	0.019	32.284	-0.046	-0.046	0.000	0.000	0.000	0.000
36	A	54	GLN	0	0.035	0.015	27.241	-0.051	-0.051	0.000	0.000	0.000	0.000
37	A	55	LEU	0	0.012	0.004	28.667	-0.038	-0.038	0.000	0.000	0.000	0.000
38	A	56	ARG	1	0.905	0.954	30.211	0.186	0.186	0.000	0.000	0.000	0.000
39	A	57	LEU	0	-0.010	-0.008	26.989	-0.031	-0.031	0.000	0.000	0.000	0.000
40	A	58	ASN	0	-0.088	-0.054	24.211	-0.078	-0.078	0.000	0.000	0.000	0.000
41	A	59	ASN	0	-0.029	-0.008	25.486	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	60	VAL	0	0.005	0.004	28.817	-0.016	-0.016	0.000	0.000	0.000	0.000
43	A	61	ASN	0	-0.034	-0.021	31.245	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	62	LEU	0	-0.016	-0.022	34.521	0.003	0.003	0.000	0.000	0.000	0.000
45	A	63	LEU	0	-0.035	-0.015	37.061	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	64	ASP	-1	-0.844	-0.918	40.441	-0.139	-0.139	0.000	0.000	0.000	0.000
47	A	65	LYS	1	0.806	0.869	43.765	0.087	0.087	0.000	0.000	0.000	0.000
48	A	66	ASP	-1	-0.921	-0.950	45.068	-0.131	-0.131	0.000	0.000	0.000	0.000
49	A	67	THR	0	-0.025	0.004	42.481	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	68	THR	0	0.029	0.004	45.830	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	69	ARG	1	0.827	0.918	37.314	0.262	0.262	0.000	0.000	0.000	0.000
52	A	70	LYS	1	0.972	0.970	43.247	0.163	0.163	0.000	0.000	0.000	0.000
53	A	71	ASP	-1	-0.828	-0.908	38.108	-0.245	-0.245	0.000	0.000	0.000	0.000
54	A	72	VAL	0	-0.048	-0.011	37.130	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	73	PRO	0	0.032	0.026	33.590	0.018	0.018	0.000	0.000	0.000	0.000
56	A	74	SER	0	0.003	-0.013	36.650	0.003	0.003	0.000	0.000	0.000	0.000
57	A	75	LEU	0	-0.054	0.000	31.937	0.003	0.003	0.000	0.000	0.000	0.000
58	A	76	ARG	1	0.964	0.985	35.542	0.053	0.053	0.000	0.000	0.000	0.000
59	A	77	LEU	0	0.000	-0.016	35.237	0.011	0.011	0.000	0.000	0.000	0.000
60	A	78	GLY	0	-0.005	-0.006	38.205	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	79	THR	0	0.011	0.007	40.091	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	80	VAL	0	0.031	0.010	37.726	0.003	0.003	0.000	0.000	0.000	0.000
63	A	81	THR	0	-0.045	-0.026	38.545	0.000	0.000	0.000	0.000	0.000	0.000
64	A	82	ILE	0	-0.001	-0.007	38.232	0.005	0.005	0.000	0.000	0.000	0.000
65	A	83	LEU	0	-0.005	0.015	39.096	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	84	GLN	0	0.011	-0.015	39.487	0.001	0.001	0.000	0.000	0.000	0.000
67	A	85	ASP	-1	-0.869	-0.920	40.685	0.150	0.150	0.000	0.000	0.000	0.000
68	A	86	THR	0	-0.028	-0.025	41.055	0.007	0.007	0.000	0.000	0.000	0.000
69	A	87	ALA	0	-0.047	-0.022	37.794	0.003	0.003	0.000	0.000	0.000	0.000
70	A	88	SER	0	-0.042	-0.048	39.059	0.009	0.009	0.000	0.000	0.000	0.000
71	A	89	VAL	0	-0.007	0.004	41.074	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	90	PHE	0	0.011	0.008	44.115	0.015	0.015	0.000	0.000	0.000	0.000
73	A	91	GLN	0	-0.026	-0.033	46.296	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	92	ASP	-1	-0.859	-0.927	49.199	0.168	0.168	0.000	0.000	0.000	0.000
75	A	93	GLY	0	-0.019	-0.002	49.644	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	94	GLN	0	-0.048	-0.020	49.269	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	95	THR	0	-0.024	-0.013	44.848	0.016	0.016	0.000	0.000	0.000	0.000
78	A	96	ALA	0	-0.003	0.007	42.405	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	97	GLU	-1	-0.855	-0.899	36.027	0.297	0.297	0.000	0.000	0.000	0.000
80	A	98	TYR	0	-0.011	-0.015	40.210	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	99	GLN	0	-0.006	-0.015	33.094	0.011	0.011	0.000	0.000	0.000	0.000
82	A	100	MET	0	-0.006	0.000	36.306	-0.016	-0.016	0.000	0.000	0.000	0.000
83	A	101	VAL	0	-0.050	-0.031	33.579	0.019	0.019	0.000	0.000	0.000	0.000
84	A	102	MET	0	0.007	0.030	33.803	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	103	THR	0	-0.039	-0.033	33.702	0.022	0.022	0.000	0.000	0.000	0.000
86	A	104	VAL	0	0.011	0.012	33.454	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	105	ASN	0	-0.018	-0.018	34.000	0.010	0.010	0.000	0.000	0.000	0.000
88	A	106	ALA	0	-0.017	-0.005	33.934	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	107	SER	0	-0.014	-0.001	35.210	0.010	0.010	0.000	0.000	0.000	0.000
90	A	108	VAL	0	-0.014	-0.006	31.261	-0.009	-0.009	0.000	0.000	0.000	0.000
91	A	109	LEU	0	0.016	0.008	34.697	0.009	0.009	0.000	0.000	0.000	0.000
92	A	110	ILE	0	0.067	0.022	32.755	-0.018	-0.018	0.000	0.000	0.000	0.000
93	A	111	PRO	0	-0.001	0.000	36.676	0.012	0.012	0.000	0.000	0.000	0.000
94	A	112	GLY	0	-0.002	-0.002	39.476	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	113	HIS	1	0.835	0.927	34.531	0.198	0.198	0.000	0.000	0.000	0.000
96	A	114	ASP	-1	-0.872	-0.923	37.970	-0.079	-0.079	0.000	0.000	0.000	0.000
97	A	115	ILE	0	-0.068	-0.033	37.174	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	116	TYR	0	0.068	0.025	32.429	0.005	0.005	0.000	0.000	0.000	0.000
99	A	117	PRO	0	-0.017	-0.004	34.082	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	118	ILE	0	-0.014	-0.013	29.570	0.004	0.004	0.000	0.000	0.000	0.000
101	A	119	SER	0	0.034	0.025	31.222	0.002	0.002	0.000	0.000	0.000	0.000
102	A	120	THR	0	-0.046	-0.026	28.160	0.015	0.015	0.000	0.000	0.000	0.000
103	A	121	LYS	1	0.943	0.972	29.308	-0.165	-0.165	0.000	0.000	0.000	0.000
104	A	122	VAL	0	-0.040	-0.001	28.971	0.014	0.014	0.000	0.000	0.000	0.000
105	A	123	TYR	0	0.030	0.010	29.506	-0.014	-0.014	0.000	0.000	0.000	0.000
106	A	124	ARG	1	0.815	0.880	30.447	-0.181	-0.181	0.000	0.000	0.000	0.000
107	A	125	SER	0	0.005	0.026	32.747	-0.011	-0.011	0.000	0.000	0.000	0.000
108	A	126	PHE	0	0.006	-0.002	34.763	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	127	PHE	0	0.047	0.026	36.626	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	128	ASP	-1	-0.794	-0.886	40.188	0.132	0.132	0.000	0.000	0.000	0.000
111	A	129	ASN	0	-0.056	-0.055	43.813	0.004	0.004	0.000	0.000	0.000	0.000
112	A	130	PRO	0	0.061	0.031	46.429	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	131	GLN	0	0.017	0.008	50.038	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	132	MET	0	-0.048	-0.019	46.775	-0.009	-0.009	0.000	0.000	0.000	0.000
115	A	133	ALA	0	0.049	0.035	47.375	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	134	LEU	0	0.032	0.017	47.667	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	135	ALA	0	0.003	-0.001	44.894	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	136	LYS	1	0.803	0.879	40.470	-0.170	-0.170	0.000	0.000	0.000	0.000
119	A	137	ASP	-1	-0.914	-0.941	43.145	0.079	0.079	0.000	0.000	0.000	0.000
120	A	138	ASN	0	-0.030	-0.030	43.342	-0.009	-0.009	0.000	0.000	0.000	0.000
121	A	139	GLU	-1	-0.856	-0.905	38.545	0.164	0.164	0.000	0.000	0.000	0.000
122	A	140	GLN	0	0.015	0.006	38.840	0.003	0.003	0.000	0.000	0.000	0.000
123	A	141	ALA	0	0.008	0.000	39.746	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	142	MET	0	-0.034	-0.016	34.738	-0.012	-0.012	0.000	0.000	0.000	0.000
125	A	143	ILE	0	0.003	0.002	34.844	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	144	VAL	0	0.024	0.000	35.000	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	145	GLN	0	-0.071	-0.038	35.032	-0.009	-0.009	0.000	0.000	0.000	0.000
128	A	146	GLU	-1	-0.772	-0.874	31.432	0.121	0.121	0.000	0.000	0.000	0.000
129	A	147	MET	0	-0.081	-0.037	31.240	0.000	0.000	0.000	0.000	0.000	0.000
130	A	148	TYR	0	0.040	0.003	32.123	-0.009	-0.009	0.000	0.000	0.000	0.000
131	A	149	ASP	-1	-0.873	-0.924	30.458	-0.042	-0.042	0.000	0.000	0.000	0.000
132	A	150	LYS	1	0.941	0.972	24.913	-0.254	-0.254	0.000	0.000	0.000	0.000
133	A	151	ALA	0	0.010	0.000	27.755	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	152	ALA	0	0.014	0.004	29.534	-0.015	-0.015	0.000	0.000	0.000	0.000
135	A	153	GLU	-1	-0.875	-0.926	23.426	-0.013	-0.013	0.000	0.000	0.000	0.000
136	A	154	GLN	0	-0.065	-0.053	24.594	-0.006	-0.006	0.000	0.000	0.000	0.000
137	A	155	LEU	0	-0.026	-0.004	25.878	0.002	0.002	0.000	0.000	0.000	0.000
138	A	156	ILE	0	0.003	-0.004	25.430	-0.021	-0.021	0.000	0.000	0.000	0.000
139	A	157	ARG	1	0.834	0.913	19.436	-0.047	-0.047	0.000	0.000	0.000	0.000
140	A	158	LYS	1	0.883	0.934	22.834	-0.058	-0.058	0.000	0.000	0.000	0.000
141	A	159	LEU	0	0.007	0.002	25.528	-0.006	-0.006	0.000	0.000	0.000	0.000
142	A	160	THR	0	0.002	-0.012	20.369	-0.036	-0.036	0.000	0.000	0.000	0.000
143	A	161	SER	0	-0.024	-0.005	23.845	-0.013	-0.013	0.000	0.000	0.000	0.000
144	A	162	VAL	0	0.034	0.009	24.797	0.002	0.002	0.000	0.000	0.000	0.000
145	A	163	ARG	1	0.931	0.973	23.079	0.454	0.454	0.000	0.000	0.000	0.000
146	A	164	ALA	0	-0.035	-0.017	23.658	-0.031	-0.031	0.000	0.000	0.000	0.000
147	A	165	ALA	0	0.006	-0.007	25.695	0.006	0.006	0.000	0.000	0.000	0.000
148	A	166	ASP	-1	-0.900	-0.950	29.037	-0.222	-0.222	0.000	0.000	0.000	0.000
149	A	167	ILE	0	-0.081	-0.036	25.903	-0.016	-0.016	0.000	0.000	0.000	0.000
150	A	168	GLN	0	-0.088	-0.027	28.295	-0.008	-0.008	0.000	0.000	0.000	0.000
151	A	169	ALA	-1	-0.898	-0.938	30.225	-0.156	-0.156	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:19:CYS)