FMO DATABASE

FMODB ID: Q5ZMY

Calculation Name: 1A79-A-Xray549

Preferred Name:

Target Type:

Ligand Name: gold ion

Ligand 3-letter code: AU

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1A79

Chain ID: A

ChEMBL ID:

UniProt ID: Q58819

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	171
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1793574.359381
FMO2-HF: Nuclear repulsion	1725897.739704
FMO2-HF: Total energy	-67676.619678
FMO2-MP2: Total energy	-67878.779726

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:9:LYS)

Summations of interaction energy for fragment #1(A:9:LYS)

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.
-183.724	-173.094	20.038	-14.047	-16.621	-0.172

Interaction energy analysis for fragmet #1(A:9:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.686 / q_NPA : 1.841

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	11	THR	0	-0.007	-0.018	3.220	-2.767	-0.727	0.053	-0.859	-1.234	-0.003
4	A	12	GLY	0	-0.003	-0.004	4.981	6.147	6.206	-0.001	-0.005	-0.052	0.000
46	A	54	ILE	0	-0.013	0.002	3.769	-14.461	-14.238	-0.001	-0.028	-0.194	0.000
47	A	55	ASN	0	0.007	0.007	4.650	-4.638	-4.553	-0.001	-0.004	-0.079	0.000
49	A	57	GLY	0	-0.004	0.004	2.679	0.249	0.746	0.242	-0.265	-0.475	-0.002
50	A	58	TRP	0	-0.059	-0.037	1.901	-40.817	-40.382	9.150	-4.936	-4.649	-0.067
51	A	59	LEU	0	-0.054	-0.016	2.708	-20.438	-16.973	1.283	-2.020	-2.728	-0.023
52	A	60	GLU	-1	-0.865	-0.931	1.920	-148.382	-144.744	9.308	-5.870	-7.076	-0.077
53	A	61	VAL	0	0.044	0.019	3.980	7.491	7.679	0.005	-0.060	-0.134	0.000
5	A	13	LEU	0	-0.019	-0.013	8.332	-1.439	-1.439	0.000	0.000	0.000	0.000
6	A	14	LEU	0	-0.025	-0.011	11.581	0.518	0.518	0.000	0.000	0.000	0.000
7	A	15	ASP	-1	-0.928	-0.968	13.587	-29.465	-29.465	0.000	0.000	0.000	0.000
8	A	16	GLY	0	0.034	0.025	17.183	0.314	0.314	0.000	0.000	0.000	0.000
9	A	17	ASP	-1	-0.828	-0.905	17.996	-29.457	-29.457	0.000	0.000	0.000	0.000
10	A	18	ARG	1	0.789	0.865	16.030	33.053	33.053	0.000	0.000	0.000	0.000
11	A	19	VAL	0	0.014	0.016	9.504	-1.226	-1.226	0.000	0.000	0.000	0.000
12	A	20	ILE	0	-0.011	0.000	12.789	-0.368	-0.368	0.000	0.000	0.000	0.000
13	A	21	VAL	0	-0.007	-0.013	8.689	-4.070	-4.070	0.000	0.000	0.000	0.000
14	A	22	PHE	0	0.101	0.029	11.002	2.480	2.480	0.000	0.000	0.000	0.000
15	A	23	ASP	-1	-0.836	-0.898	6.741	-62.882	-62.882	0.000	0.000	0.000	0.000
16	A	24	LYS	1	1.030	1.010	10.034	33.272	33.272	0.000	0.000	0.000	0.000
17	A	25	ASN	0	-0.002	0.003	7.367	2.295	2.295	0.000	0.000	0.000	0.000
18	A	26	GLY	0	0.012	-0.005	7.192	0.256	0.256	0.000	0.000	0.000	0.000
19	A	27	ILE	0	0.037	0.013	7.878	1.466	1.466	0.000	0.000	0.000	0.000
20	A	28	SER	0	-0.011	-0.013	11.093	3.311	3.311	0.000	0.000	0.000	0.000
21	A	29	LYS	1	0.860	0.921	6.008	66.674	66.674	0.000	0.000	0.000	0.000
22	A	30	LEU	0	0.012	0.010	8.272	0.382	0.382	0.000	0.000	0.000	0.000
23	A	31	SER	0	0.073	0.029	11.443	3.033	3.033	0.000	0.000	0.000	0.000
24	A	32	ALA	0	-0.045	-0.014	13.371	1.915	1.915	0.000	0.000	0.000	0.000
25	A	33	ARG	1	0.888	0.959	9.913	48.181	48.181	0.000	0.000	0.000	0.000
26	A	34	HIS	0	0.047	0.031	15.042	-0.208	-0.208	0.000	0.000	0.000	0.000
27	A	35	TYR	0	-0.040	-0.017	11.498	1.195	1.195	0.000	0.000	0.000	0.000
28	A	36	GLY	0	0.012	0.004	14.512	-0.838	-0.838	0.000	0.000	0.000	0.000
29	A	37	ASN	0	-0.083	-0.047	15.709	1.980	1.980	0.000	0.000	0.000	0.000
30	A	38	VAL	0	0.000	0.000	16.133	-1.683	-1.683	0.000	0.000	0.000	0.000
31	A	39	GLU	-1	-0.797	-0.869	18.511	-27.341	-27.341	0.000	0.000	0.000	0.000
32	A	40	GLY	0	-0.009	-0.006	18.962	1.459	1.459	0.000	0.000	0.000	0.000
33	A	41	ASN	0	-0.118	-0.076	18.608	-0.585	-0.585	0.000	0.000	0.000	0.000
34	A	42	PHE	0	-0.004	-0.005	15.156	-2.156	-2.156	0.000	0.000	0.000	0.000
35	A	43	LEU	0	-0.034	0.002	12.029	1.328	1.328	0.000	0.000	0.000	0.000
36	A	44	SER	0	-0.008	0.008	14.059	-1.228	-1.228	0.000	0.000	0.000	0.000
37	A	45	LEU	0	-0.011	-0.005	9.499	1.355	1.355	0.000	0.000	0.000	0.000
38	A	46	SER	0	0.001	-0.027	13.994	1.320	1.320	0.000	0.000	0.000	0.000
39	A	47	LEU	0	0.086	0.050	13.264	-3.706	-3.706	0.000	0.000	0.000	0.000
40	A	48	VAL	0	0.034	0.027	12.601	-2.598	-2.598	0.000	0.000	0.000	0.000
41	A	49	GLU	-1	-0.822	-0.900	12.740	-39.428	-39.428	0.000	0.000	0.000	0.000
42	A	50	ALA	0	0.001	-0.006	9.212	-4.332	-4.332	0.000	0.000	0.000	0.000
43	A	51	LEU	0	0.043	0.027	7.930	-6.872	-6.872	0.000	0.000	0.000	0.000
44	A	52	TYR	0	0.024	0.017	8.566	-3.913	-3.913	0.000	0.000	0.000	0.000
45	A	53	LEU	0	0.015	-0.011	6.917	-3.222	-3.222	0.000	0.000	0.000	0.000
48	A	56	LEU	0	-0.044	-0.007	6.922	1.793	1.793	0.000	0.000	0.000	0.000
54	A	62	LYS	1	0.953	1.003	7.586	59.524	59.524	0.000	0.000	0.000	0.000
55	A	63	TYR	0	0.042	0.017	10.166	1.933	1.933	0.000	0.000	0.000	0.000
56	A	64	LYS	1	0.943	0.969	13.962	31.931	31.931	0.000	0.000	0.000	0.000
57	A	65	ASP	-1	-0.801	-0.886	14.003	-38.700	-38.700	0.000	0.000	0.000	0.000
58	A	66	ASN	0	-0.067	-0.048	9.876	-4.006	-4.006	0.000	0.000	0.000	0.000
59	A	67	LYS	1	0.854	0.921	9.663	43.443	43.443	0.000	0.000	0.000	0.000
60	A	68	PRO	0	-0.043	-0.023	5.420	0.689	0.689	0.000	0.000	0.000	0.000
61	A	69	LEU	0	-0.026	0.001	7.498	3.434	3.434	0.000	0.000	0.000	0.000
62	A	70	SER	0	-0.033	-0.048	7.071	-7.391	-7.391	0.000	0.000	0.000	0.000
63	A	71	PHE	0	-0.021	-0.018	7.604	0.525	0.525	0.000	0.000	0.000	0.000
64	A	72	GLU	-1	-0.828	-0.928	8.797	-45.026	-45.026	0.000	0.000	0.000	0.000
65	A	73	GLU	-1	-0.804	-0.873	11.046	-44.122	-44.122	0.000	0.000	0.000	0.000
66	A	74	LEU	0	-0.022	-0.014	9.151	1.768	1.768	0.000	0.000	0.000	0.000
67	A	75	TYR	0	-0.043	-0.063	11.934	2.341	2.341	0.000	0.000	0.000	0.000
68	A	76	GLU	-1	-0.849	-0.930	13.797	-27.402	-27.402	0.000	0.000	0.000	0.000
69	A	77	TYR	0	-0.057	-0.033	15.007	1.892	1.892	0.000	0.000	0.000	0.000
70	A	78	ALA	0	0.002	-0.019	14.867	1.512	1.512	0.000	0.000	0.000	0.000
71	A	79	ARG	1	0.863	0.901	16.873	29.255	29.255	0.000	0.000	0.000	0.000
72	A	80	ASN	0	-0.083	-0.034	19.643	2.378	2.378	0.000	0.000	0.000	0.000
73	A	81	VAL	0	-0.047	-0.005	18.984	0.976	0.976	0.000	0.000	0.000	0.000
74	A	82	GLU	-1	-0.943	-0.982	18.387	-30.348	-30.348	0.000	0.000	0.000	0.000
75	A	83	GLU	-1	-0.951	-0.974	21.808	-21.413	-21.413	0.000	0.000	0.000	0.000
76	A	84	ARG	1	0.868	0.909	23.730	22.360	22.360	0.000	0.000	0.000	0.000
77	A	85	LEU	0	0.002	0.000	15.704	-0.493	-0.493	0.000	0.000	0.000	0.000
78	A	86	CYS	-1	-0.832	-0.840	18.586	-29.433	-29.433	0.000	0.000	0.000	0.000
79	A	87	LEU	0	0.107	0.052	19.372	-0.781	-0.781	0.000	0.000	0.000	0.000
80	A	88	LYS	1	0.788	0.893	20.056	25.549	25.549	0.000	0.000	0.000	0.000
81	A	89	TYR	0	0.018	-0.009	11.975	-2.157	-2.157	0.000	0.000	0.000	0.000
82	A	90	LEU	0	0.066	0.040	16.537	-1.793	-1.793	0.000	0.000	0.000	0.000
83	A	91	VAL	0	0.033	0.018	18.564	-0.318	-0.318	0.000	0.000	0.000	0.000
84	A	92	TYR	0	-0.036	-0.020	13.758	0.406	0.406	0.000	0.000	0.000	0.000
85	A	93	LYS	1	0.941	0.958	12.690	39.654	39.654	0.000	0.000	0.000	0.000
86	A	94	ASP	-1	-0.727	-0.775	15.898	-27.516	-27.516	0.000	0.000	0.000	0.000
87	A	95	LEU	0	0.004	-0.008	19.056	0.198	0.198	0.000	0.000	0.000	0.000
88	A	96	ARG	1	0.830	0.908	14.939	37.123	37.123	0.000	0.000	0.000	0.000
89	A	97	THR	0	-0.045	-0.034	15.967	-1.515	-1.515	0.000	0.000	0.000	0.000
90	A	98	ARG	1	0.794	0.867	17.225	26.099	26.099	0.000	0.000	0.000	0.000
91	A	99	GLY	0	-0.021	0.001	19.104	1.017	1.017	0.000	0.000	0.000	0.000
92	A	100	TYR	0	-0.019	-0.007	20.113	0.666	0.666	0.000	0.000	0.000	0.000
93	A	101	ILE	0	-0.023	-0.012	20.013	-1.927	-1.927	0.000	0.000	0.000	0.000
94	A	102	VAL	0	0.000	0.005	19.017	1.482	1.482	0.000	0.000	0.000	0.000
95	A	103	LYS	1	0.843	0.924	17.857	32.052	32.052	0.000	0.000	0.000	0.000
96	A	104	THR	0	0.066	0.029	22.028	1.098	1.098	0.000	0.000	0.000	0.000
97	A	105	GLY	0	0.032	0.022	23.991	0.475	0.475	0.000	0.000	0.000	0.000
98	A	106	LEU	0	0.062	0.032	26.974	0.835	0.835	0.000	0.000	0.000	0.000
99	A	107	LYS	1	0.934	0.955	28.760	21.318	21.318	0.000	0.000	0.000	0.000
100	A	108	TYR	0	-0.001	-0.004	30.137	0.708	0.708	0.000	0.000	0.000	0.000
101	A	109	GLY	0	0.027	0.022	32.034	0.368	0.368	0.000	0.000	0.000	0.000
102	A	110	ALA	0	-0.041	-0.007	29.339	0.150	0.150	0.000	0.000	0.000	0.000
103	A	111	ASP	-1	-0.750	-0.857	24.432	-23.642	-23.642	0.000	0.000	0.000	0.000
104	A	112	PHE	0	-0.022	-0.032	20.034	-1.083	-1.083	0.000	0.000	0.000	0.000
105	A	113	ARG	1	0.820	0.908	24.821	25.343	25.343	0.000	0.000	0.000	0.000
106	A	114	LEU	0	0.002	0.013	23.170	-1.213	-1.213	0.000	0.000	0.000	0.000
107	A	115	TYR	0	0.020	0.003	24.588	1.097	1.097	0.000	0.000	0.000	0.000
108	A	116	GLU	-1	-0.805	-0.927	24.821	-22.526	-22.526	0.000	0.000	0.000	0.000
109	A	117	ARG	1	0.881	0.937	20.429	27.745	27.745	0.000	0.000	0.000	0.000
110	A	118	GLY	0	-0.010	-0.001	22.064	-1.451	-1.451	0.000	0.000	0.000	0.000
111	A	119	ALA	0	0.003	0.025	23.581	0.978	0.978	0.000	0.000	0.000	0.000
112	A	120	ASN	0	-0.070	-0.064	23.679	-0.553	-0.553	0.000	0.000	0.000	0.000
113	A	121	ILE	0	-0.030	-0.032	21.420	0.771	0.771	0.000	0.000	0.000	0.000
114	A	122	ASP	-1	-0.881	-0.916	25.479	-23.841	-23.841	0.000	0.000	0.000	0.000
115	A	123	LYS	1	0.922	0.958	27.833	20.683	20.683	0.000	0.000	0.000	0.000
116	A	124	GLU	-1	-0.834	-0.898	28.574	-21.490	-21.490	0.000	0.000	0.000	0.000
117	A	125	HIS	0	-0.042	-0.034	30.134	-0.051	-0.051	0.000	0.000	0.000	0.000
118	A	126	SER	0	-0.017	0.002	28.248	0.058	0.058	0.000	0.000	0.000	0.000
119	A	127	VAL	0	-0.009	-0.003	28.941	0.762	0.762	0.000	0.000	0.000	0.000
120	A	128	TYR	0	0.039	0.008	28.201	0.680	0.680	0.000	0.000	0.000	0.000
121	A	129	LEU	0	-0.023	-0.014	28.865	-0.677	-0.677	0.000	0.000	0.000	0.000
122	A	130	VAL	0	0.007	-0.003	25.142	0.272	0.272	0.000	0.000	0.000	0.000
123	A	131	LYS	1	0.867	0.927	27.713	18.192	18.192	0.000	0.000	0.000	0.000
124	A	132	VAL	0	0.009	0.012	23.685	0.276	0.276	0.000	0.000	0.000	0.000
125	A	133	PHE	0	-0.033	-0.018	27.090	0.364	0.364	0.000	0.000	0.000	0.000
126	A	134	PRO	0	0.046	0.035	27.997	-0.438	-0.438	0.000	0.000	0.000	0.000
127	A	135	GLU	-1	-0.915	-0.972	29.044	-17.981	-17.981	0.000	0.000	0.000	0.000
128	A	136	ASP	-1	-0.861	-0.917	30.647	-18.452	-18.452	0.000	0.000	0.000	0.000
129	A	137	SER	0	-0.094	-0.065	32.253	-0.151	-0.151	0.000	0.000	0.000	0.000
130	A	138	SER	0	-0.047	-0.013	34.374	0.328	0.328	0.000	0.000	0.000	0.000
131	A	139	PHE	0	0.014	0.010	35.398	-0.257	-0.257	0.000	0.000	0.000	0.000
132	A	140	LEU	0	0.016	0.000	37.232	0.567	0.567	0.000	0.000	0.000	0.000
133	A	141	LEU	0	0.056	0.020	39.037	-0.277	-0.277	0.000	0.000	0.000	0.000
134	A	142	SER	0	-0.002	-0.009	40.538	-0.181	-0.181	0.000	0.000	0.000	0.000
135	A	143	GLU	-1	-0.827	-0.911	34.704	-17.398	-17.398	0.000	0.000	0.000	0.000
136	A	144	LEU	0	0.045	0.035	34.722	-0.480	-0.480	0.000	0.000	0.000	0.000
137	A	145	THR	0	-0.009	-0.010	37.439	-0.056	-0.056	0.000	0.000	0.000	0.000
138	A	146	GLY	0	-0.002	-0.006	39.180	0.136	0.136	0.000	0.000	0.000	0.000
139	A	147	PHE	0	-0.016	-0.002	30.870	-0.126	-0.126	0.000	0.000	0.000	0.000
140	A	148	VAL	0	0.053	0.014	36.245	-0.141	-0.141	0.000	0.000	0.000	0.000
141	A	149	ARG	1	0.918	0.968	38.501	14.068	14.068	0.000	0.000	0.000	0.000
142	A	150	VAL	0	0.004	0.000	35.294	0.171	0.171	0.000	0.000	0.000	0.000
143	A	151	ALA	0	0.037	0.026	35.074	0.005	0.005	0.000	0.000	0.000	0.000
144	A	152	HIS	0	0.015	0.013	36.581	-0.120	-0.120	0.000	0.000	0.000	0.000
145	A	153	SER	0	-0.092	-0.047	39.616	0.129	0.129	0.000	0.000	0.000	0.000
146	A	154	VAL	0	-0.050	-0.031	34.999	0.110	0.110	0.000	0.000	0.000	0.000
147	A	155	ARG	1	0.914	0.960	37.349	15.720	15.720	0.000	0.000	0.000	0.000
148	A	156	LYS	1	0.832	0.935	31.913	19.029	19.029	0.000	0.000	0.000	0.000
149	A	157	LYS	1	0.945	0.990	32.194	19.650	19.650	0.000	0.000	0.000	0.000
150	A	158	LEU	0	-0.050	-0.021	32.013	-0.439	-0.439	0.000	0.000	0.000	0.000
151	A	159	LEU	0	-0.025	-0.006	27.238	0.095	0.095	0.000	0.000	0.000	0.000
152	A	160	ILE	0	-0.002	-0.007	29.687	-0.412	-0.412	0.000	0.000	0.000	0.000
153	A	161	ALA	0	-0.009	-0.006	25.807	0.117	0.117	0.000	0.000	0.000	0.000
154	A	162	ILE	0	0.011	0.006	27.766	-0.208	-0.208	0.000	0.000	0.000	0.000
155	A	163	VAL	0	-0.043	-0.020	23.452	-0.540	-0.540	0.000	0.000	0.000	0.000
156	A	164	ASP	-1	-0.760	-0.873	26.620	-21.399	-21.399	0.000	0.000	0.000	0.000
157	A	165	ALA	0	-0.008	-0.020	26.245	-0.840	-0.840	0.000	0.000	0.000	0.000
158	A	166	ASP	-1	-0.955	-0.954	25.134	-21.884	-21.884	0.000	0.000	0.000	0.000
159	A	167	GLY	0	-0.081	-0.034	22.220	-1.298	-1.298	0.000	0.000	0.000	0.000
160	A	168	ASP	-1	-0.961	-0.974	22.334	-25.582	-25.582	0.000	0.000	0.000	0.000
161	A	169	ILE	0	-0.058	-0.050	20.912	0.421	0.421	0.000	0.000	0.000	0.000
162	A	170	VAL	0	0.008	0.011	25.435	0.131	0.131	0.000	0.000	0.000	0.000
163	A	171	TYR	0	-0.076	-0.078	22.868	0.222	0.222	0.000	0.000	0.000	0.000
164	A	172	TYR	0	0.059	0.035	29.643	0.732	0.732	0.000	0.000	0.000	0.000
165	A	173	ASN	0	-0.018	-0.023	32.856	-0.415	-0.415	0.000	0.000	0.000	0.000
166	A	174	MET	0	0.015	0.003	35.426	0.208	0.208	0.000	0.000	0.000	0.000
167	A	175	THR	0	0.022	0.009	38.518	-0.176	-0.176	0.000	0.000	0.000	0.000
168	A	176	TYR	0	-0.016	-0.012	41.598	0.247	0.247	0.000	0.000	0.000	0.000
169	A	177	VAL	0	0.006	-0.008	44.805	-0.046	-0.046	0.000	0.000	0.000	0.000
170	A	178	LYS	1	0.880	0.939	47.884	12.577	12.577	0.000	0.000	0.000	0.000
171	A	179	PRO	-1	-0.879	-0.916	51.411	-11.549	-11.549	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:LYS)