FMO DATABASE

FMODB ID: VZMV1

Calculation Name: 1S4C-B-Xray549

Preferred Name:

Target Type:

Ligand Name: acetate ion | copper (ii) ion

Ligand 3-letter code: ACT | CU

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1S4C

Chain ID: B

ChEMBL ID:

UniProt ID: P44583

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	155
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1569206.384619
FMO2-HF: Nuclear repulsion	1506163.366104
FMO2-HF: Total energy	-63043.018515
FMO2-MP2: Total energy	-63223.003959

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(B:1:MET)

Summations of interaction energy for fragment #1(B:1:MET)

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.
-204.778	-198.323	35.783	-18.89	-23.349	-0.184

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.775 / q_NPA : 0.881

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	B	3	ILE	0	0.014	0.018	2.915	2.661	5.127	0.257	-0.782	-1.941	0.001
4	B	4	SER	0	0.006	0.002	5.185	2.919	2.927	-0.001	-0.002	-0.005	0.000
83	B	83	VAL	0	-0.008	-0.022	2.327	-2.595	-1.922	2.145	-0.499	-2.319	-0.002
84	B	84	GLY	0	0.071	0.035	3.473	3.245	3.758	0.044	-0.161	-0.398	-0.001
85	B	85	ALA	0	-0.037	-0.029	2.540	-11.006	-9.538	1.917	-1.186	-2.199	-0.012
86	B	86	THR	0	-0.055	-0.039	3.233	-0.684	-1.052	0.060	0.496	-0.189	-0.001
112	B	112	PHE	0	0.006	0.001	3.057	0.044	0.791	1.561	-0.634	-1.673	-0.003
114	B	114	VAL	0	-0.002	0.000	4.794	0.107	0.272	0.001	-0.025	-0.141	0.000
122	B	122	ALA	0	0.023	0.002	4.455	-1.564	-1.491	-0.001	-0.012	-0.060	0.000
123	B	123	VAL	0	-0.034	-0.002	3.612	3.252	3.720	0.005	-0.148	-0.326	0.000
124	B	124	PHE	0	-0.019	-0.021	2.251	-23.030	-20.067	6.191	-3.987	-5.167	-0.037
125	B	125	TYR	0	0.026	0.003	2.663	12.288	13.633	0.255	-0.568	-1.031	-0.005
126	B	126	PRO	0	0.019	0.003	5.361	-0.058	-0.006	-0.001	-0.001	-0.050	0.000
128	B	128	GLU	-1	-0.723	-0.832	1.724	-142.157	-146.520	23.352	-11.371	-7.618	-0.124
129	B	129	PRO	0	-0.013	0.022	4.798	2.818	2.927	-0.001	-0.004	-0.103	0.000
130	B	130	HIS	1	0.821	0.869	4.926	31.910	32.046	-0.001	-0.006	-0.129	0.000
5	B	5	SER	0	0.031	0.008	8.927	0.923	0.923	0.000	0.000	0.000	0.000
6	B	6	LEU	0	0.008	0.015	12.435	0.287	0.287	0.000	0.000	0.000	0.000
7	B	7	THR	0	-0.005	0.005	14.895	1.124	1.124	0.000	0.000	0.000	0.000
8	B	8	ASN	0	-0.022	-0.003	12.792	1.591	1.591	0.000	0.000	0.000	0.000
9	B	9	PRO	0	0.012	-0.006	16.484	-0.390	-0.390	0.000	0.000	0.000	0.000
10	B	10	ASN	0	0.011	0.004	16.435	0.597	0.597	0.000	0.000	0.000	0.000
11	B	11	PHE	0	-0.013	-0.007	13.015	-1.078	-1.078	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.866	0.909	12.455	14.767	14.767	0.000	0.000	0.000	0.000
13	B	13	VAL	0	-0.044	-0.016	13.764	-0.316	-0.316	0.000	0.000	0.000	0.000
14	B	14	GLY	0	0.013	0.009	10.815	-1.434	-1.434	0.000	0.000	0.000	0.000
15	B	15	LEU	0	-0.038	-0.004	8.672	-2.934	-2.934	0.000	0.000	0.000	0.000
16	B	16	PRO	0	0.039	0.021	8.120	2.748	2.748	0.000	0.000	0.000	0.000
17	B	17	LYS	1	0.954	0.977	11.135	17.578	17.578	0.000	0.000	0.000	0.000
18	B	18	VAL	0	0.111	0.060	13.148	0.235	0.235	0.000	0.000	0.000	0.000
19	B	19	ILE	0	-0.004	-0.003	7.198	0.045	0.045	0.000	0.000	0.000	0.000
20	B	20	ALA	0	-0.010	-0.003	11.337	0.515	0.515	0.000	0.000	0.000	0.000
21	B	21	GLU	-1	-0.884	-0.948	13.870	-16.144	-16.144	0.000	0.000	0.000	0.000
22	B	22	VAL	0	0.008	0.005	12.663	0.922	0.922	0.000	0.000	0.000	0.000
23	B	23	CYS	0	-0.051	-0.030	11.981	0.249	0.249	0.000	0.000	0.000	0.000
24	B	24	ASP	-1	-0.819	-0.900	14.794	-15.541	-15.541	0.000	0.000	0.000	0.000
25	B	25	TYR	0	0.013	0.008	18.132	0.710	0.710	0.000	0.000	0.000	0.000
26	B	26	LEU	0	0.011	-0.013	14.110	0.534	0.534	0.000	0.000	0.000	0.000
27	B	27	ASN	0	-0.070	-0.056	17.562	0.657	0.657	0.000	0.000	0.000	0.000
28	B	28	THR	0	-0.059	-0.014	20.090	0.797	0.797	0.000	0.000	0.000	0.000
29	B	29	LEU	0	-0.024	-0.005	20.660	0.617	0.617	0.000	0.000	0.000	0.000
30	B	30	ASP	-1	-0.863	-0.927	22.482	-12.014	-12.014	0.000	0.000	0.000	0.000
31	B	31	LEU	0	0.008	-0.024	17.292	-0.010	-0.010	0.000	0.000	0.000	0.000
32	B	32	ASN	0	-0.038	-0.030	21.116	-0.251	-0.251	0.000	0.000	0.000	0.000
33	B	33	ALA	0	-0.007	0.007	23.236	0.190	0.190	0.000	0.000	0.000	0.000
34	B	34	LEU	0	-0.021	0.014	20.206	0.201	0.201	0.000	0.000	0.000	0.000
35	B	35	GLU	-1	-0.909	-0.941	24.200	-10.448	-10.448	0.000	0.000	0.000	0.000
36	B	36	ASN	0	-0.072	-0.064	22.971	-0.826	-0.826	0.000	0.000	0.000	0.000
37	B	37	GLY	0	0.015	0.008	22.338	0.535	0.535	0.000	0.000	0.000	0.000
38	B	38	ARG	1	0.834	0.905	20.845	13.505	13.505	0.000	0.000	0.000	0.000
39	B	39	HIS	0	-0.001	-0.007	20.987	0.589	0.589	0.000	0.000	0.000	0.000
40	B	40	ASP	-1	-0.818	-0.908	20.505	-14.224	-14.224	0.000	0.000	0.000	0.000
41	B	41	ILE	0	-0.061	-0.032	17.107	0.244	0.244	0.000	0.000	0.000	0.000
42	B	42	ASN	0	-0.011	-0.018	19.207	0.136	0.136	0.000	0.000	0.000	0.000
43	B	43	ASP	-1	-0.879	-0.935	21.845	-12.260	-12.260	0.000	0.000	0.000	0.000
44	B	44	GLN	0	-0.066	-0.023	18.436	0.335	0.335	0.000	0.000	0.000	0.000
45	B	45	ILE	0	-0.033	-0.019	15.101	-0.997	-0.997	0.000	0.000	0.000	0.000
46	B	46	TYR	0	0.032	0.032	16.820	0.802	0.802	0.000	0.000	0.000	0.000
47	B	47	MET	0	-0.029	-0.009	16.059	-1.746	-1.746	0.000	0.000	0.000	0.000
48	B	48	ASN	0	0.006	0.013	16.417	1.489	1.489	0.000	0.000	0.000	0.000
49	B	49	VAL	0	0.044	0.013	16.712	-1.098	-1.098	0.000	0.000	0.000	0.000
50	B	50	MET	0	-0.027	-0.011	15.212	0.680	0.680	0.000	0.000	0.000	0.000
51	B	51	GLU	-1	-0.852	-0.922	19.376	-12.317	-12.317	0.000	0.000	0.000	0.000
52	B	52	PRO	0	-0.022	0.008	17.477	0.491	0.491	0.000	0.000	0.000	0.000
53	B	53	GLU	-1	-0.934	-0.990	20.499	-11.460	-11.460	0.000	0.000	0.000	0.000
54	B	54	THR	0	-0.040	-0.012	16.897	-0.005	-0.005	0.000	0.000	0.000	0.000
55	B	55	ALA	0	0.063	0.031	17.895	0.771	0.771	0.000	0.000	0.000	0.000
56	B	56	GLU	-1	-0.855	-0.940	17.393	-13.997	-13.997	0.000	0.000	0.000	0.000
57	B	57	PRO	0	0.051	0.037	13.384	-0.055	-0.055	0.000	0.000	0.000	0.000
58	B	58	SER	0	-0.015	-0.015	15.347	-0.358	-0.358	0.000	0.000	0.000	0.000
59	B	59	SER	0	-0.094	-0.050	18.028	0.398	0.398	0.000	0.000	0.000	0.000
60	B	60	LYS	1	0.944	0.972	15.941	16.290	16.290	0.000	0.000	0.000	0.000
61	B	61	LYS	1	0.823	0.893	15.490	14.339	14.339	0.000	0.000	0.000	0.000
62	B	62	ALA	0	0.002	0.015	9.984	-0.300	-0.300	0.000	0.000	0.000	0.000
63	B	63	GLU	-1	-0.885	-0.950	10.371	-21.773	-21.773	0.000	0.000	0.000	0.000
64	B	64	LEU	0	-0.058	-0.010	8.753	-2.984	-2.984	0.000	0.000	0.000	0.000
65	B	65	HIS	1	0.821	0.886	9.640	27.618	27.618	0.000	0.000	0.000	0.000
66	B	66	HIS	1	0.845	0.920	10.960	18.824	18.824	0.000	0.000	0.000	0.000
67	B	67	GLU	-1	-0.818	-0.889	12.767	-19.718	-19.718	0.000	0.000	0.000	0.000
68	B	68	TYR	0	-0.025	-0.023	12.097	0.218	0.218	0.000	0.000	0.000	0.000
69	B	69	LEU	0	-0.041	-0.011	6.658	-2.152	-2.152	0.000	0.000	0.000	0.000
70	B	70	ASP	-1	-0.773	-0.866	7.208	-24.730	-24.730	0.000	0.000	0.000	0.000
71	B	71	VAL	0	0.012	-0.008	6.643	-5.189	-5.189	0.000	0.000	0.000	0.000
72	B	72	GLN	0	-0.017	-0.006	7.693	4.625	4.625	0.000	0.000	0.000	0.000
73	B	73	VAL	0	0.024	0.002	8.992	-1.520	-1.520	0.000	0.000	0.000	0.000
74	B	74	LEU	0	-0.020	0.011	11.743	1.121	1.121	0.000	0.000	0.000	0.000
75	B	75	ILE	0	-0.048	-0.014	14.224	0.124	0.124	0.000	0.000	0.000	0.000
76	B	76	ARG	1	0.948	0.955	17.866	12.364	12.364	0.000	0.000	0.000	0.000
77	B	77	GLY	0	0.067	0.043	19.175	-0.156	-0.156	0.000	0.000	0.000	0.000
78	B	78	THR	0	-0.104	-0.072	15.706	-0.399	-0.399	0.000	0.000	0.000	0.000
79	B	79	GLU	-1	-0.684	-0.818	12.229	-20.434	-20.434	0.000	0.000	0.000	0.000
80	B	80	ASN	0	-0.017	0.004	11.535	-1.332	-1.332	0.000	0.000	0.000	0.000
81	B	81	ILE	0	-0.021	-0.005	7.195	0.306	0.306	0.000	0.000	0.000	0.000
82	B	82	GLU	-1	-0.847	-0.906	7.396	-21.192	-21.192	0.000	0.000	0.000	0.000
87	B	87	TYR	0	0.015	0.002	6.938	-1.398	-1.398	0.000	0.000	0.000	0.000
88	B	88	PRO	0	-0.004	0.013	7.988	2.698	2.698	0.000	0.000	0.000	0.000
89	B	89	ASN	0	0.056	0.034	10.539	1.260	1.260	0.000	0.000	0.000	0.000
90	B	90	LEU	0	0.027	0.000	12.695	0.578	0.578	0.000	0.000	0.000	0.000
91	B	91	SER	0	-0.046	-0.031	15.439	0.852	0.852	0.000	0.000	0.000	0.000
92	B	92	LYS	1	0.804	0.882	14.090	19.011	19.011	0.000	0.000	0.000	0.000
93	B	93	TYR	0	-0.049	-0.031	10.393	-0.925	-0.925	0.000	0.000	0.000	0.000
94	B	94	GLU	-1	-0.815	-0.893	16.359	-14.147	-14.147	0.000	0.000	0.000	0.000
95	B	95	ASP	-1	-0.879	-0.941	18.341	-14.055	-14.055	0.000	0.000	0.000	0.000
96	B	96	TYR	0	-0.090	-0.083	16.319	-0.278	-0.278	0.000	0.000	0.000	0.000
97	B	97	ASN	0	0.006	0.007	19.070	1.022	1.022	0.000	0.000	0.000	0.000
98	B	98	GLU	-1	-0.899	-0.974	19.437	-14.385	-14.385	0.000	0.000	0.000	0.000
99	B	99	ALA	0	-0.058	-0.010	21.054	-0.122	-0.122	0.000	0.000	0.000	0.000
100	B	100	ASP	-1	-0.891	-0.950	18.534	-14.993	-14.993	0.000	0.000	0.000	0.000
101	B	101	ASP	-1	-0.728	-0.833	14.005	-23.335	-23.335	0.000	0.000	0.000	0.000
102	B	102	TYR	0	-0.038	-0.008	14.645	-1.804	-1.804	0.000	0.000	0.000	0.000
103	B	103	GLN	0	0.011	0.023	14.216	0.191	0.191	0.000	0.000	0.000	0.000
104	B	104	LEU	0	-0.019	-0.010	13.754	-1.343	-1.343	0.000	0.000	0.000	0.000
105	B	105	CYS	0	0.004	0.030	12.938	1.077	1.077	0.000	0.000	0.000	0.000
106	B	106	ALA	0	0.003	0.000	14.450	-0.284	-0.284	0.000	0.000	0.000	0.000
107	B	107	ASP	-1	-0.839	-0.945	12.625	-17.805	-17.805	0.000	0.000	0.000	0.000
108	B	108	ILE	0	-0.064	-0.012	6.102	-0.567	-0.567	0.000	0.000	0.000	0.000
109	B	109	ASP	-1	-0.798	-0.886	9.427	-18.861	-18.861	0.000	0.000	0.000	0.000
110	B	110	ASP	-1	-0.862	-0.915	7.623	-26.314	-26.314	0.000	0.000	0.000	0.000
111	B	111	LYS	1	0.767	0.895	6.181	18.318	18.318	0.000	0.000	0.000	0.000
113	B	113	THR	0	-0.013	-0.010	6.296	-0.779	-0.779	0.000	0.000	0.000	0.000
115	B	115	THR	0	-0.021	-0.024	7.648	0.503	0.503	0.000	0.000	0.000	0.000
116	B	116	MET	0	-0.033	-0.008	8.853	-1.126	-1.126	0.000	0.000	0.000	0.000
117	B	117	LYS	1	0.935	0.930	11.906	16.627	16.627	0.000	0.000	0.000	0.000
118	B	118	PRO	0	0.012	-0.004	14.178	-0.865	-0.865	0.000	0.000	0.000	0.000
119	B	119	LYS	1	0.928	0.971	15.281	15.548	15.548	0.000	0.000	0.000	0.000
120	B	120	MET	0	-0.008	0.043	9.758	-0.086	-0.086	0.000	0.000	0.000	0.000
121	B	121	PHE	0	-0.001	-0.020	7.783	0.787	0.787	0.000	0.000	0.000	0.000
127	B	127	TYR	0	-0.030	-0.027	7.146	-2.924	-2.924	0.000	0.000	0.000	0.000
131	B	131	LYS	1	0.880	0.944	6.877	20.740	20.740	0.000	0.000	0.000	0.000
132	B	132	PRO	0	-0.010	-0.013	9.779	0.086	0.086	0.000	0.000	0.000	0.000
133	B	133	CYS	0	-0.054	-0.037	11.524	1.194	1.194	0.000	0.000	0.000	0.000
134	B	134	CYS	0	0.019	0.030	12.760	1.080	1.080	0.000	0.000	0.000	0.000
135	B	135	VAL	0	0.011	0.006	14.719	-0.170	-0.170	0.000	0.000	0.000	0.000
136	B	136	VAL	0	0.010	0.001	15.390	-0.646	-0.646	0.000	0.000	0.000	0.000
137	B	137	ASN	0	-0.066	-0.043	17.854	0.377	0.377	0.000	0.000	0.000	0.000
138	B	138	GLY	0	0.030	0.013	20.140	0.532	0.532	0.000	0.000	0.000	0.000
139	B	139	LYS	1	0.904	0.962	21.627	12.209	12.209	0.000	0.000	0.000	0.000
140	B	140	THR	0	0.039	0.031	20.814	-0.483	-0.483	0.000	0.000	0.000	0.000
141	B	141	GLU	-1	-0.953	-0.993	20.569	-12.600	-12.600	0.000	0.000	0.000	0.000
142	B	142	LYS	1	0.979	0.992	21.022	10.579	10.579	0.000	0.000	0.000	0.000
143	B	143	ILE	0	-0.047	-0.004	15.826	0.256	0.256	0.000	0.000	0.000	0.000
144	B	144	LYS	1	0.875	0.936	19.348	12.686	12.686	0.000	0.000	0.000	0.000
145	B	145	LYS	1	0.795	0.876	11.140	21.032	21.032	0.000	0.000	0.000	0.000
146	B	146	LEU	0	0.028	0.017	13.760	0.856	0.856	0.000	0.000	0.000	0.000
147	B	147	VAL	0	-0.017	-0.012	10.961	-1.642	-1.642	0.000	0.000	0.000	0.000
148	B	148	VAL	0	0.014	0.006	12.036	1.372	1.372	0.000	0.000	0.000	0.000
149	B	149	LYS	1	0.877	0.946	11.380	21.096	21.096	0.000	0.000	0.000	0.000
150	B	150	VAL	0	0.058	0.017	10.998	1.591	1.591	0.000	0.000	0.000	0.000
151	B	151	PRO	0	0.014	0.007	11.824	-1.857	-1.857	0.000	0.000	0.000	0.000
152	B	152	VAL	0	-0.008	-0.014	9.329	-0.079	-0.079	0.000	0.000	0.000	0.000
153	B	153	LYS	1	0.793	0.878	12.083	19.715	19.715	0.000	0.000	0.000	0.000
154	B	154	LEU	0	-0.051	-0.017	14.273	1.288	1.288	0.000	0.000	0.000	0.000
155	B	155	ILE	-1	-0.933	-0.956	8.500	-23.525	-23.525	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:MET)