FMO DATABASE

FMODB ID: M82GZ

Calculation Name: 4YCS-D-Xray547

Preferred Name:

Target Type:

Ligand Name: acetate ion

Ligand 3-letter code: ACT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4YCS

Chain ID: D

ChEMBL ID:

UniProt ID: Q189B5

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	122
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1021646.532554
FMO2-HF: Nuclear repulsion	973782.168114
FMO2-HF: Total energy	-47864.364439
FMO2-MP2: Total energy	-48002.123104

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:48:LYS)

Summations of interaction energy for fragment #1(A:48: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.
-435.845	-425.771	20.464	-13.665	-16.874	-0.185

Interaction energy analysis for fragmet #1(A:48:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.648 / q_NPA : 1.819

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	50	SER	0	-0.010	-0.008	2.996	-11.529	-8.522	0.212	-1.452	-1.768	-0.009
34	A	81	ASN	0	0.002	-0.004	2.498	-29.972	-27.678	3.209	-2.007	-3.497	-0.029
35	A	82	ILE	0	-0.024	-0.019	2.570	-14.591	-12.643	3.406	-1.829	-3.525	-0.023
36	A	83	ASP	-1	-0.827	-0.898	1.756	-191.055	-188.362	13.634	-8.328	-7.998	-0.124
37	A	84	THR	0	-0.007	-0.025	3.901	12.111	12.243	0.003	-0.049	-0.086	0.000
4	A	51	VAL	0	0.029	0.014	5.763	6.907	6.907	0.000	0.000	0.000	0.000
5	A	52	SER	0	0.012	0.015	9.044	-1.100	-1.100	0.000	0.000	0.000	0.000
6	A	53	MET	0	-0.047	-0.010	11.956	1.906	1.906	0.000	0.000	0.000	0.000
7	A	54	ILE	0	0.001	0.006	15.124	0.085	0.085	0.000	0.000	0.000	0.000
8	A	55	LEU	0	-0.001	-0.016	17.614	0.658	0.658	0.000	0.000	0.000	0.000
9	A	56	ASP	-1	-0.742	-0.844	21.370	-21.791	-21.791	0.000	0.000	0.000	0.000
10	A	57	ILE	0	-0.008	-0.008	23.989	0.202	0.202	0.000	0.000	0.000	0.000
11	A	58	GLU	-1	-0.768	-0.850	26.782	-18.889	-18.889	0.000	0.000	0.000	0.000
12	A	59	GLY	0	-0.040	-0.004	30.317	0.393	0.393	0.000	0.000	0.000	0.000
13	A	60	THR	0	0.042	0.002	30.493	-0.431	-0.431	0.000	0.000	0.000	0.000
14	A	61	ASN	0	-0.041	-0.021	30.885	-0.280	-0.280	0.000	0.000	0.000	0.000
15	A	62	ASN	0	0.014	0.004	26.409	0.387	0.387	0.000	0.000	0.000	0.000
16	A	63	GLU	-1	-0.924	-0.942	26.334	-21.783	-21.783	0.000	0.000	0.000	0.000
17	A	64	ALA	0	0.018	-0.008	25.688	-0.900	-0.900	0.000	0.000	0.000	0.000
18	A	65	MET	0	-0.079	-0.019	24.245	-0.527	-0.527	0.000	0.000	0.000	0.000
19	A	66	ASN	0	0.070	0.009	21.900	-1.278	-1.278	0.000	0.000	0.000	0.000
20	A	67	ASN	0	0.023	0.006	20.760	-2.187	-2.187	0.000	0.000	0.000	0.000
21	A	68	SER	0	-0.043	-0.002	21.232	-0.201	-0.201	0.000	0.000	0.000	0.000
22	A	69	ALA	0	0.071	0.040	18.747	-1.295	-1.295	0.000	0.000	0.000	0.000
23	A	70	LEU	0	0.039	0.007	16.204	-2.646	-2.646	0.000	0.000	0.000	0.000
24	A	71	LEU	0	-0.031	-0.004	15.716	-2.412	-2.412	0.000	0.000	0.000	0.000
25	A	72	ALA	0	0.015	0.005	16.062	-1.498	-1.498	0.000	0.000	0.000	0.000
26	A	73	LEU	0	0.039	0.014	10.397	-2.213	-2.213	0.000	0.000	0.000	0.000
27	A	74	ASN	0	-0.011	-0.004	11.263	-6.535	-6.535	0.000	0.000	0.000	0.000
28	A	75	ASN	0	-0.019	-0.030	11.771	-2.570	-2.570	0.000	0.000	0.000	0.000
29	A	76	ALA	0	0.012	0.019	10.611	-0.612	-0.612	0.000	0.000	0.000	0.000
30	A	77	GLN	0	-0.025	-0.026	6.920	-6.948	-6.948	0.000	0.000	0.000	0.000
31	A	78	LYS	1	0.895	0.956	7.470	37.122	37.122	0.000	0.000	0.000	0.000
32	A	79	LYS	1	0.890	0.957	10.049	40.152	40.152	0.000	0.000	0.000	0.000
33	A	80	LEU	0	0.011	0.020	6.695	1.187	1.187	0.000	0.000	0.000	0.000
38	A	85	ASN	0	-0.016	-0.004	7.765	1.986	1.986	0.000	0.000	0.000	0.000
39	A	86	LYS	1	0.865	0.927	10.289	50.198	50.198	0.000	0.000	0.000	0.000
40	A	87	VAL	0	0.017	0.018	14.549	0.366	0.366	0.000	0.000	0.000	0.000
41	A	88	GLU	-1	-0.913	-0.962	17.913	-28.019	-28.019	0.000	0.000	0.000	0.000
42	A	89	SER	0	-0.020	-0.010	21.463	0.365	0.365	0.000	0.000	0.000	0.000
43	A	90	ASP	-1	-0.896	-0.943	24.872	-21.595	-21.595	0.000	0.000	0.000	0.000
44	A	91	ASP	-1	-0.738	-0.820	28.097	-19.645	-19.645	0.000	0.000	0.000	0.000
45	A	92	SER	0	-0.014	-0.024	28.357	-0.547	-0.547	0.000	0.000	0.000	0.000
46	A	93	SER	0	-0.154	-0.095	29.838	-0.124	-0.124	0.000	0.000	0.000	0.000
47	A	94	THR	0	-0.015	-0.035	27.008	-0.456	-0.456	0.000	0.000	0.000	0.000
48	A	95	PHE	0	0.005	0.015	25.040	-1.231	-1.231	0.000	0.000	0.000	0.000
49	A	96	SER	0	0.004	-0.005	23.998	-1.071	-1.071	0.000	0.000	0.000	0.000
50	A	97	ASN	0	0.007	-0.001	23.629	-0.756	-0.756	0.000	0.000	0.000	0.000
51	A	98	SER	0	0.007	-0.003	21.654	-1.076	-1.076	0.000	0.000	0.000	0.000
52	A	99	ILE	0	0.001	0.003	19.496	-1.737	-1.737	0.000	0.000	0.000	0.000
53	A	100	ASP	-1	-0.789	-0.863	18.829	-28.674	-28.674	0.000	0.000	0.000	0.000
54	A	101	ILE	0	0.037	0.023	17.468	-0.879	-0.879	0.000	0.000	0.000	0.000
55	A	102	LEU	0	0.003	0.013	14.312	-2.059	-2.059	0.000	0.000	0.000	0.000
56	A	103	CYS	0	-0.091	-0.046	14.121	-2.444	-2.444	0.000	0.000	0.000	0.000
57	A	104	ASN	0	-0.118	-0.065	14.937	-0.237	-0.237	0.000	0.000	0.000	0.000
58	A	105	ASP	-1	-0.850	-0.919	11.935	-41.944	-41.944	0.000	0.000	0.000	0.000
59	A	106	ASN	0	-0.132	-0.059	8.619	-2.969	-2.969	0.000	0.000	0.000	0.000
60	A	107	TYR	0	0.034	0.018	7.910	-7.810	-7.810	0.000	0.000	0.000	0.000
61	A	108	ASP	-1	-0.829	-0.910	6.334	-74.977	-74.977	0.000	0.000	0.000	0.000
62	A	109	LEU	0	-0.053	-0.031	9.516	4.541	4.541	0.000	0.000	0.000	0.000
63	A	110	ILE	0	0.011	0.018	11.893	-2.306	-2.306	0.000	0.000	0.000	0.000
64	A	111	ILE	0	-0.020	-0.018	13.370	2.122	2.122	0.000	0.000	0.000	0.000
65	A	112	ALA	0	0.020	0.013	16.722	-0.129	-0.129	0.000	0.000	0.000	0.000
66	A	113	VAL	0	-0.004	-0.013	19.410	0.451	0.451	0.000	0.000	0.000	0.000
67	A	114	GLY	0	0.085	0.024	22.042	0.721	0.721	0.000	0.000	0.000	0.000
68	A	115	ALA	0	0.028	0.017	25.821	-0.269	-0.269	0.000	0.000	0.000	0.000
69	A	116	ARG	1	0.720	0.803	28.529	20.662	20.662	0.000	0.000	0.000	0.000
70	A	117	PHE	0	0.033	0.016	23.104	0.114	0.114	0.000	0.000	0.000	0.000
71	A	118	ALA	0	0.022	0.029	26.095	-0.340	-0.340	0.000	0.000	0.000	0.000
72	A	119	LYS	1	0.987	0.996	27.546	19.391	19.391	0.000	0.000	0.000	0.000
73	A	120	PRO	0	-0.032	-0.017	26.063	0.056	0.056	0.000	0.000	0.000	0.000
74	A	121	LEU	0	0.057	0.030	20.653	-0.521	-0.521	0.000	0.000	0.000	0.000
75	A	122	GLU	-1	-0.824	-0.899	24.200	-21.389	-21.389	0.000	0.000	0.000	0.000
76	A	123	MET	0	-0.083	-0.048	26.616	0.163	0.163	0.000	0.000	0.000	0.000
77	A	124	VAL	0	-0.014	-0.004	21.143	0.189	0.189	0.000	0.000	0.000	0.000
78	A	125	ALA	0	0.033	0.015	21.449	-0.638	-0.638	0.000	0.000	0.000	0.000
79	A	126	LYS	1	0.798	0.884	22.465	21.236	21.236	0.000	0.000	0.000	0.000
80	A	127	LYS	1	0.826	0.905	23.013	25.384	25.384	0.000	0.000	0.000	0.000
81	A	128	TYR	0	-0.053	-0.035	18.074	-0.379	-0.379	0.000	0.000	0.000	0.000
82	A	129	PRO	0	0.028	0.009	19.082	-1.278	-1.278	0.000	0.000	0.000	0.000
83	A	130	LYS	1	0.910	0.944	15.483	31.497	31.497	0.000	0.000	0.000	0.000
84	A	131	GLN	0	-0.043	-0.015	12.616	-2.143	-2.143	0.000	0.000	0.000	0.000
85	A	132	GLN	0	-0.004	-0.003	13.845	2.857	2.857	0.000	0.000	0.000	0.000
86	A	133	PHE	0	0.049	0.010	15.133	-2.080	-2.080	0.000	0.000	0.000	0.000
87	A	134	ALA	0	-0.015	-0.013	16.995	0.474	0.474	0.000	0.000	0.000	0.000
88	A	135	ILE	0	-0.043	-0.007	18.523	-0.339	-0.339	0.000	0.000	0.000	0.000
89	A	136	ILE	0	-0.006	-0.006	19.031	0.304	0.304	0.000	0.000	0.000	0.000
90	A	137	ASP	-1	-0.895	-0.966	22.995	-20.959	-20.959	0.000	0.000	0.000	0.000
91	A	138	TYR	0	-0.005	-0.015	26.112	0.856	0.856	0.000	0.000	0.000	0.000
92	A	139	GLU	-1	-0.938	-0.942	26.209	-21.847	-21.847	0.000	0.000	0.000	0.000
93	A	140	TYR	0	-0.040	-0.039	25.446	0.272	0.272	0.000	0.000	0.000	0.000
94	A	141	ASP	-1	-0.878	-0.932	30.169	-17.973	-17.973	0.000	0.000	0.000	0.000
95	A	142	LYS	1	0.870	0.925	31.611	19.105	19.105	0.000	0.000	0.000	0.000
96	A	143	GLN	0	0.016	-0.003	23.937	0.600	0.600	0.000	0.000	0.000	0.000
97	A	144	PRO	0	-0.017	-0.007	24.883	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	145	SER	0	-0.005	-0.008	23.717	-0.755	-0.755	0.000	0.000	0.000	0.000
99	A	146	ASN	0	-0.035	-0.004	19.157	0.383	0.383	0.000	0.000	0.000	0.000
100	A	147	ILE	0	0.025	0.019	19.262	-1.744	-1.744	0.000	0.000	0.000	0.000
101	A	148	THR	0	-0.036	-0.014	18.682	0.549	0.549	0.000	0.000	0.000	0.000
102	A	149	SER	0	0.044	0.002	20.696	-0.872	-0.872	0.000	0.000	0.000	0.000
103	A	150	ILE	0	-0.066	-0.020	19.098	-0.420	-0.420	0.000	0.000	0.000	0.000
104	A	151	SER	0	0.072	0.022	23.293	-0.124	-0.124	0.000	0.000	0.000	0.000
105	A	152	TYR	0	0.017	0.000	25.398	-0.937	-0.937	0.000	0.000	0.000	0.000
106	A	153	GLU	-1	-0.857	-0.927	26.616	-21.521	-21.521	0.000	0.000	0.000	0.000
107	A	154	ASP	-1	-0.888	-0.942	23.564	-23.950	-23.950	0.000	0.000	0.000	0.000
108	A	155	ASN	0	-0.054	-0.049	21.484	-2.477	-2.477	0.000	0.000	0.000	0.000
109	A	156	LYS	1	0.826	0.922	22.324	22.636	22.636	0.000	0.000	0.000	0.000
110	A	157	SER	0	-0.003	0.011	24.121	-0.329	-0.329	0.000	0.000	0.000	0.000
111	A	158	GLY	0	-0.017	-0.020	20.307	-0.906	-0.906	0.000	0.000	0.000	0.000
112	A	159	TYR	0	0.015	0.014	19.203	-1.756	-1.756	0.000	0.000	0.000	0.000
113	A	160	LEU	0	0.062	0.037	17.010	-1.485	-1.485	0.000	0.000	0.000	0.000
114	A	161	ALA	0	-0.001	-0.004	14.916	-2.017	-2.017	0.000	0.000	0.000	0.000
115	A	162	GLY	0	-0.016	-0.003	14.323	-2.418	-2.418	0.000	0.000	0.000	0.000
116	A	163	LEU	0	-0.003	0.005	15.575	-1.148	-1.148	0.000	0.000	0.000	0.000
117	A	164	ILE	0	-0.011	-0.014	10.572	-1.674	-1.674	0.000	0.000	0.000	0.000
118	A	165	ALA	0	-0.027	-0.027	10.870	-2.974	-2.974	0.000	0.000	0.000	0.000
119	A	166	GLY	0	0.023	0.012	11.406	-1.878	-1.878	0.000	0.000	0.000	0.000
120	A	167	LYS	1	0.888	0.950	12.169	36.717	36.717	0.000	0.000	0.000	0.000
121	A	168	MET	0	-0.114	-0.049	7.013	-6.346	-6.346	0.000	0.000	0.000	0.000
122	A	169	THR	-1	-0.954	-0.958	7.790	-51.327	-51.327	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:48:LYS)