FMO DATABASE

FMODB ID: 5534Z

Calculation Name: 1R8D-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion

Ligand 3-letter code: SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1R8D

Chain ID: A

ChEMBL ID:

UniProt ID: P71039

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	109
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-807323.709909
FMO2-HF: Nuclear repulsion	761957.351345
FMO2-HF: Total energy	-45366.358564
FMO2-MP2: Total energy	-45497.315051

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:1:MET)

Summations of interaction energy for fragment #1(A: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.
-121.25	-114.8	0.249	-3.363	-3.338	-0.026

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.862 / q_NPA : 0.927

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	3	TYR	0	-0.084	-0.051	2.761	-12.649	-8.513	0.222	-2.082	-2.277	-0.015
43	A	43	ASP	-1	-0.784	-0.886	3.262	-74.483	-72.169	0.027	-1.281	-1.061	-0.011
4	A	4	GLN	0	0.070	0.037	6.235	4.467	4.467	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.004	-0.019	9.878	0.094	0.094	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.884	0.941	12.650	21.723	21.723	0.000	0.000	0.000	0.000
7	A	7	GLN	0	0.065	0.025	6.329	1.468	1.468	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.029	0.023	8.878	-0.008	-0.008	0.000	0.000	0.000	0.000
9	A	9	ALA	0	-0.003	0.014	10.871	1.071	1.071	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.933	-0.955	12.568	-21.277	-21.277	0.000	0.000	0.000	0.000
11	A	11	ILE	0	-0.030	-0.016	7.614	0.440	0.440	0.000	0.000	0.000	0.000
12	A	12	SER	0	0.007	-0.013	11.980	1.131	1.131	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.019	0.022	14.641	1.216	1.216	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.038	-0.006	16.125	1.223	1.223	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.036	0.019	17.653	-0.685	-0.685	0.000	0.000	0.000	0.000
16	A	16	ILE	0	0.074	0.016	16.159	-0.166	-0.166	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.908	0.965	18.350	12.695	12.695	0.000	0.000	0.000	0.000
18	A	18	THR	0	0.009	-0.009	19.559	0.643	0.643	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.009	0.013	13.729	0.123	0.123	0.000	0.000	0.000	0.000
20	A	20	HIS	0	0.019	0.009	17.356	-0.478	-0.478	0.000	0.000	0.000	0.000
21	A	21	HIS	0	-0.002	0.007	19.647	0.240	0.240	0.000	0.000	0.000	0.000
22	A	22	TYR	0	0.043	0.003	18.049	0.564	0.564	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.786	-0.865	17.137	-17.305	-17.305	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.058	-0.047	18.928	0.668	0.668	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.011	0.017	22.422	0.582	0.582	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.863	-0.917	20.514	-13.432	-13.432	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.057	-0.001	19.886	-0.060	-0.060	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.037	-0.045	13.391	-0.489	-0.489	0.000	0.000	0.000	0.000
29	A	29	ASN	0	-0.003	-0.010	15.789	-0.233	-0.233	0.000	0.000	0.000	0.000
30	A	30	PRO	0	-0.072	-0.028	11.164	-1.089	-1.089	0.000	0.000	0.000	0.000
31	A	31	SER	0	0.005	-0.019	7.797	-0.416	-0.416	0.000	0.000	0.000	0.000
32	A	32	ALA	0	-0.048	-0.026	7.460	-0.116	-0.116	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.026	0.012	9.504	-0.417	-0.417	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.020	0.000	10.135	-0.198	-0.198	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.851	-0.928	12.001	-17.829	-17.829	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.050	-0.021	14.934	1.022	1.022	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.011	0.006	15.556	0.480	0.480	0.000	0.000	0.000	0.000
38	A	38	TYR	0	-0.081	-0.040	12.354	-0.174	-0.174	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.860	0.911	11.806	16.631	16.631	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.041	-0.024	6.447	-1.628	-1.628	0.000	0.000	0.000	0.000
41	A	41	TYR	0	0.055	0.017	7.762	0.256	0.256	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.037	-0.041	4.916	-7.095	-7.095	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.075	0.047	5.956	4.334	4.334	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.776	-0.852	8.604	-27.569	-27.569	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.023	-0.012	6.159	2.675	2.675	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.918	-0.953	9.924	-23.197	-23.197	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.800	0.873	12.157	18.678	18.678	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.026	-0.014	12.351	1.561	1.561	0.000	0.000	0.000	0.000
50	A	50	GLN	0	0.029	-0.002	13.113	1.263	1.263	0.000	0.000	0.000	0.000
51	A	51	GLN	0	-0.006	0.006	15.585	1.770	1.770	0.000	0.000	0.000	0.000
52	A	52	ILE	0	-0.024	-0.024	17.447	1.096	1.096	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.040	-0.025	17.163	1.022	1.022	0.000	0.000	0.000	0.000
54	A	54	PHE	0	0.053	0.035	19.671	0.847	0.847	0.000	0.000	0.000	0.000
55	A	55	PHE	0	-0.001	-0.012	21.613	0.846	0.846	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.902	0.944	22.288	14.248	14.248	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.925	-0.950	22.814	-13.052	-13.052	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.058	-0.018	25.936	0.579	0.579	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.006	0.007	27.852	0.471	0.471	0.000	0.000	0.000	0.000
60	A	60	PHE	0	-0.043	-0.020	27.028	0.366	0.366	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.822	0.895	27.695	9.448	9.448	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.007	-0.015	23.477	-0.248	-0.248	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.837	-0.925	25.250	-10.980	-10.980	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.791	-0.886	27.624	-10.102	-10.102	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.048	-0.023	22.135	-0.170	-0.170	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.905	0.959	22.934	12.371	12.371	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.870	-0.931	23.803	-11.771	-11.771	0.000	0.000	0.000	0.000
68	A	68	MET	0	-0.059	-0.027	25.483	0.085	0.085	0.000	0.000	0.000	0.000
69	A	69	LEU	0	-0.044	-0.022	19.154	-0.246	-0.246	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.820	-0.888	20.677	-15.172	-15.172	0.000	0.000	0.000	0.000
71	A	71	HIS	0	-0.020	0.007	22.676	0.164	0.164	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.042	-0.028	21.916	0.359	0.359	0.000	0.000	0.000	0.000
73	A	73	ASN	0	0.004	-0.007	24.636	-0.148	-0.148	0.000	0.000	0.000	0.000
74	A	74	PHE	0	-0.002	0.005	27.958	0.509	0.509	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.797	-0.891	28.980	-9.860	-9.860	0.000	0.000	0.000	0.000
76	A	76	ARG	1	0.901	0.950	23.895	12.789	12.789	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.869	0.925	29.754	9.399	9.399	0.000	0.000	0.000	0.000
78	A	78	ALA	0	0.048	0.021	32.886	0.115	0.115	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.016	0.033	30.522	0.172	0.172	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.015	0.001	28.038	0.097	0.097	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.052	-0.026	32.044	0.040	0.040	0.000	0.000	0.000	0.000
82	A	82	SER	0	0.040	0.004	35.436	0.243	0.243	0.000	0.000	0.000	0.000
83	A	83	GLN	0	-0.029	-0.015	31.126	0.424	0.424	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.938	0.967	34.406	8.492	8.492	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.954	-0.992	36.027	-7.586	-7.586	0.000	0.000	0.000	0.000
86	A	86	ILE	0	-0.019	-0.004	35.947	0.242	0.242	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.024	-0.010	32.588	0.188	0.188	0.000	0.000	0.000	0.000
88	A	88	MET	0	-0.040	-0.015	37.256	0.161	0.161	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.983	0.997	40.518	7.566	7.566	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.939	0.972	35.083	9.020	9.020	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.962	0.983	40.024	7.708	7.708	0.000	0.000	0.000	0.000
92	A	92	GLN	0	0.004	0.011	41.645	0.014	0.014	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.887	0.932	44.419	6.664	6.664	0.000	0.000	0.000	0.000
94	A	94	MET	0	-0.009	-0.018	40.367	0.013	0.013	0.000	0.000	0.000	0.000
95	A	95	ASP	-1	-0.871	-0.929	44.703	-6.960	-6.960	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.861	-0.922	47.129	-6.362	-6.362	0.000	0.000	0.000	0.000
97	A	97	MET	0	-0.071	-0.028	45.200	0.101	0.101	0.000	0.000	0.000	0.000
98	A	98	ILE	0	0.014	0.016	44.767	0.078	0.078	0.000	0.000	0.000	0.000
99	A	99	GLN	0	0.029	0.011	49.175	0.048	0.048	0.000	0.000	0.000	0.000
100	A	100	THR	0	-0.080	-0.052	52.047	0.176	0.176	0.000	0.000	0.000	0.000
101	A	101	ILE	0	-0.012	0.011	48.778	0.097	0.097	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.851	-0.932	52.258	-6.084	-6.084	0.000	0.000	0.000	0.000
103	A	103	ARG	1	0.857	0.917	54.636	5.580	5.580	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.076	-0.054	55.905	0.127	0.127	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.014	-0.007	52.736	0.038	0.038	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.037	0.016	57.324	0.050	0.050	0.000	0.000	0.000	0.000
107	A	107	SER	0	-0.067	-0.053	60.570	0.107	0.107	0.000	0.000	0.000	0.000
108	A	108	VAL	0	-0.100	-0.044	62.013	-0.008	-0.008	0.000	0.000	0.000	0.000
109	A	109	ASP	-2	-1.832	-1.901	58.908	-10.686	-10.686	0.000	0.000	0.000	0.000

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