FMO DATABASE

FMODB ID: J4JN9

Calculation Name: 2D4R-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion

Ligand 3-letter code: SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2D4R

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SK03

Base Structure: X-ray

Registration Date: 2025-10-03

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	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1457038.793817
FMO2-HF: Nuclear repulsion	1398549.992291
FMO2-HF: Total energy	-58488.801526
FMO2-MP2: Total energy	-58662.813773

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:2:PRO)

Summations of interaction energy for fragment #1(A:2:PRO)

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.
-114.018	-103.167	12.722	-10.495	-13.077	-0.113

Interaction energy analysis for fragmet #1(A:2:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.759 / q_NPA : 0.866

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	4	VAL	0	-0.024	0.002	3.855	0.409	2.304	-0.012	-0.881	-1.002	-0.002
85	A	86	ARG	1	0.782	0.857	4.568	47.120	47.242	-0.001	-0.005	-0.115	0.000
106	A	107	THR	0	0.009	0.000	3.534	-9.043	-8.686	0.004	-0.113	-0.247	0.000
107	A	108	TYR	0	-0.007	-0.019	2.527	2.973	7.129	1.772	-2.060	-3.868	-0.019
108	A	109	GLU	-1	-0.936	-0.969	1.824	-110.444	-108.895	10.408	-6.454	-5.504	-0.083
109	A	110	LEU	0	0.052	0.010	3.966	8.113	8.319	0.001	-0.064	-0.143	0.000
119	A	120	ARG	1	0.930	0.988	3.056	47.151	48.313	0.264	-0.290	-1.136	-0.002
123	A	124	GLN	0	-0.024	-0.004	2.898	-9.328	-7.924	0.286	-0.628	-1.062	-0.007
4	A	5	ARG	1	0.888	0.936	6.118	22.755	22.755	0.000	0.000	0.000	0.000
5	A	6	ALA	0	0.026	0.030	9.925	1.010	1.010	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.813	-0.895	13.271	-16.946	-16.946	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.814	0.896	16.728	14.182	14.182	0.000	0.000	0.000	0.000
8	A	9	TYR	0	0.000	0.013	20.125	0.109	0.109	0.000	0.000	0.000	0.000
9	A	10	ILE	0	0.028	0.006	22.298	-0.021	-0.021	0.000	0.000	0.000	0.000
10	A	11	PRO	0	0.013	0.025	25.947	0.129	0.129	0.000	0.000	0.000	0.000
11	A	12	ALA	0	0.011	-0.008	29.145	0.383	0.383	0.000	0.000	0.000	0.000
12	A	13	PRO	0	0.026	0.033	29.104	-0.364	-0.364	0.000	0.000	0.000	0.000
13	A	14	PRO	0	0.026	0.006	26.760	-0.037	-0.037	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.901	-0.945	27.301	-10.338	-10.338	0.000	0.000	0.000	0.000
15	A	16	ARG	1	0.933	0.966	29.220	9.372	9.372	0.000	0.000	0.000	0.000
16	A	17	VAL	0	0.005	0.001	24.088	-0.139	-0.139	0.000	0.000	0.000	0.000
17	A	18	TYR	0	-0.008	-0.028	22.913	-0.506	-0.506	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.945	0.957	25.145	10.280	10.280	0.000	0.000	0.000	0.000
19	A	20	LEU	0	-0.036	-0.020	27.388	0.042	0.042	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.008	0.008	21.610	-0.169	-0.169	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.823	0.906	22.706	11.598	11.598	0.000	0.000	0.000	0.000
22	A	23	ASP	-1	-0.872	-0.919	24.461	-11.143	-11.143	0.000	0.000	0.000	0.000
23	A	24	LEU	0	0.054	0.021	20.076	0.075	0.075	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.853	-0.928	23.615	-11.766	-11.766	0.000	0.000	0.000	0.000
25	A	26	GLY	0	-0.016	-0.011	26.336	0.169	0.169	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.003	-0.009	21.321	0.154	0.154	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.914	0.960	22.779	12.459	12.459	0.000	0.000	0.000	0.000
28	A	29	PRO	0	-0.051	-0.017	24.370	-0.127	-0.127	0.000	0.000	0.000	0.000
29	A	30	TYR	0	0.013	0.013	24.693	0.259	0.259	0.000	0.000	0.000	0.000
30	A	31	LEU	0	-0.021	0.001	19.385	-0.334	-0.334	0.000	0.000	0.000	0.000
31	A	32	LYS	1	0.862	0.914	21.390	12.154	12.154	0.000	0.000	0.000	0.000
32	A	33	GLU	-1	-0.830	-0.884	15.678	-18.448	-18.448	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.015	-0.012	17.803	-0.729	-0.729	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.866	-0.912	20.048	-12.683	-12.683	0.000	0.000	0.000	0.000
35	A	36	SER	0	-0.050	-0.041	21.772	0.648	0.648	0.000	0.000	0.000	0.000
36	A	37	LEU	0	0.025	0.008	20.086	-0.695	-0.695	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.904	-0.923	22.431	-11.879	-11.879	0.000	0.000	0.000	0.000
38	A	39	VAL	0	-0.017	-0.028	23.344	-0.632	-0.632	0.000	0.000	0.000	0.000
39	A	40	VAL	0	-0.043	-0.012	22.912	0.542	0.542	0.000	0.000	0.000	0.000
40	A	41	ALA	0	-0.013	-0.001	24.977	0.458	0.458	0.000	0.000	0.000	0.000
41	A	42	ARG	1	0.909	0.943	25.276	11.043	11.043	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.876	-0.926	25.842	-11.832	-11.832	0.000	0.000	0.000	0.000
43	A	44	GLY	0	-0.014	-0.008	27.071	-0.278	-0.278	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.003	0.003	26.012	0.039	0.039	0.000	0.000	0.000	0.000
45	A	46	ARG	1	0.874	0.926	22.082	13.042	13.042	0.000	0.000	0.000	0.000
46	A	47	THR	0	-0.076	-0.074	21.581	0.891	0.891	0.000	0.000	0.000	0.000
47	A	48	ARG	1	0.808	0.896	20.340	13.390	13.390	0.000	0.000	0.000	0.000
48	A	49	SER	0	-0.027	-0.040	19.035	0.656	0.656	0.000	0.000	0.000	0.000
49	A	50	ARG	1	0.881	0.944	19.332	12.996	12.996	0.000	0.000	0.000	0.000
50	A	51	TRP	0	0.048	0.023	16.423	0.673	0.673	0.000	0.000	0.000	0.000
51	A	52	VAL	0	-0.051	-0.033	18.025	-0.450	-0.450	0.000	0.000	0.000	0.000
52	A	53	ALA	0	0.081	0.047	14.789	0.734	0.734	0.000	0.000	0.000	0.000
53	A	54	VAL	0	-0.049	-0.035	16.942	0.136	0.136	0.000	0.000	0.000	0.000
54	A	55	ALA	0	0.061	0.034	13.277	-0.375	-0.375	0.000	0.000	0.000	0.000
55	A	56	MET	0	-0.039	-0.035	15.088	0.013	0.013	0.000	0.000	0.000	0.000
56	A	57	GLY	0	0.020	0.023	17.381	0.506	0.506	0.000	0.000	0.000	0.000
57	A	58	LYS	1	0.864	0.949	17.057	16.527	16.527	0.000	0.000	0.000	0.000
58	A	59	LYS	1	0.845	0.911	17.064	13.035	13.035	0.000	0.000	0.000	0.000
59	A	60	VAL	0	-0.017	-0.006	11.696	0.191	0.191	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.911	0.943	15.167	16.392	16.392	0.000	0.000	0.000	0.000
61	A	62	TRP	0	-0.035	-0.026	13.588	-1.137	-1.137	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.019	0.004	15.696	1.327	1.327	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.862	-0.926	14.152	-23.266	-23.266	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.820	-0.893	16.079	-14.540	-14.540	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.796	-0.853	16.505	-17.565	-17.565	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.885	-0.931	18.452	-14.188	-14.188	0.000	0.000	0.000	0.000
67	A	68	TRP	0	0.001	-0.015	20.224	-0.525	-0.525	0.000	0.000	0.000	0.000
68	A	69	ASP	-1	-0.803	-0.898	22.495	-12.718	-12.718	0.000	0.000	0.000	0.000
69	A	70	ASP	-1	-0.798	-0.901	24.128	-11.792	-11.792	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.966	-0.953	27.333	-9.982	-9.982	0.000	0.000	0.000	0.000
71	A	72	ASN	0	-0.115	-0.075	24.611	0.431	0.431	0.000	0.000	0.000	0.000
72	A	73	LEU	0	-0.009	0.010	24.729	-0.422	-0.422	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.882	0.933	19.789	13.549	13.549	0.000	0.000	0.000	0.000
74	A	75	ASN	0	0.043	0.017	17.043	0.702	0.702	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.931	0.976	14.682	18.320	18.320	0.000	0.000	0.000	0.000
76	A	77	PHE	0	0.017	0.020	10.451	1.099	1.099	0.000	0.000	0.000	0.000
77	A	78	PHE	0	0.020	0.000	10.645	-2.386	-2.386	0.000	0.000	0.000	0.000
78	A	79	SER	0	-0.032	-0.011	11.271	1.703	1.703	0.000	0.000	0.000	0.000
79	A	80	PRO	0	-0.029	-0.014	12.680	-1.102	-1.102	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.921	-0.961	15.240	-15.510	-15.510	0.000	0.000	0.000	0.000
81	A	82	GLY	0	0.024	-0.005	14.485	0.229	0.229	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.877	-0.935	13.319	-19.148	-19.148	0.000	0.000	0.000	0.000
83	A	84	PHE	0	-0.072	-0.038	7.024	-1.677	-1.677	0.000	0.000	0.000	0.000
84	A	85	ASP	-1	-0.816	-0.878	7.182	-29.897	-29.897	0.000	0.000	0.000	0.000
86	A	87	TYR	0	0.029	0.005	6.417	-6.288	-6.288	0.000	0.000	0.000	0.000
87	A	88	GLU	-1	-0.825	-0.893	7.376	-30.597	-30.597	0.000	0.000	0.000	0.000
88	A	89	GLY	0	0.028	0.013	8.360	-4.155	-4.155	0.000	0.000	0.000	0.000
89	A	90	THR	0	-0.074	-0.037	10.677	2.791	2.791	0.000	0.000	0.000	0.000
90	A	91	TRP	0	0.042	0.027	13.971	-0.433	-0.433	0.000	0.000	0.000	0.000
91	A	92	VAL	0	-0.029	-0.019	16.777	0.702	0.702	0.000	0.000	0.000	0.000
92	A	93	PHE	0	0.012	0.004	19.473	-0.229	-0.229	0.000	0.000	0.000	0.000
93	A	94	LEU	0	0.034	0.021	20.310	0.520	0.520	0.000	0.000	0.000	0.000
94	A	95	PRO	0	0.023	0.007	24.229	0.099	0.099	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.835	-0.912	25.074	-12.803	-12.803	0.000	0.000	0.000	0.000
96	A	97	GLY	0	-0.003	-0.005	28.059	0.195	0.195	0.000	0.000	0.000	0.000
97	A	98	GLU	-1	-0.943	-0.978	31.790	-8.755	-8.755	0.000	0.000	0.000	0.000
98	A	99	GLY	0	-0.043	-0.008	29.368	0.045	0.045	0.000	0.000	0.000	0.000
99	A	100	THR	0	-0.025	-0.030	23.814	-0.072	-0.072	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.775	0.863	19.974	14.164	14.164	0.000	0.000	0.000	0.000
101	A	102	VAL	0	-0.008	-0.002	18.583	-0.165	-0.165	0.000	0.000	0.000	0.000
102	A	103	VAL	0	-0.017	-0.012	14.510	-0.338	-0.338	0.000	0.000	0.000	0.000
103	A	104	LEU	0	-0.007	0.006	12.389	0.316	0.316	0.000	0.000	0.000	0.000
104	A	105	THR	0	-0.012	-0.004	9.238	-0.699	-0.699	0.000	0.000	0.000	0.000
105	A	106	LEU	0	0.003	0.006	6.721	1.158	1.158	0.000	0.000	0.000	0.000
110	A	111	THR	0	-0.068	-0.040	6.505	-0.201	-0.201	0.000	0.000	0.000	0.000
111	A	112	ILE	0	-0.006	0.005	8.069	2.427	2.427	0.000	0.000	0.000	0.000
112	A	113	PRO	0	0.029	0.002	11.015	-0.080	-0.080	0.000	0.000	0.000	0.000
113	A	114	ILE	0	0.008	0.018	13.913	0.489	0.489	0.000	0.000	0.000	0.000
114	A	115	PHE	0	0.020	-0.014	12.552	-0.410	-0.410	0.000	0.000	0.000	0.000
115	A	116	GLY	0	0.003	0.023	8.659	-0.643	-0.643	0.000	0.000	0.000	0.000
116	A	117	GLY	0	-0.003	-0.007	6.897	-3.739	-3.739	0.000	0.000	0.000	0.000
117	A	118	LEU	0	-0.024	-0.015	8.660	-0.281	-0.281	0.000	0.000	0.000	0.000
118	A	119	LEU	0	0.023	0.003	10.037	0.326	0.326	0.000	0.000	0.000	0.000
120	A	121	LYS	1	0.984	0.974	5.499	19.361	19.361	0.000	0.000	0.000	0.000
121	A	122	LEU	0	0.025	0.021	7.942	0.548	0.548	0.000	0.000	0.000	0.000
122	A	123	VAL	0	0.027	0.003	5.297	0.441	0.441	0.000	0.000	0.000	0.000
124	A	125	LYS	1	0.865	0.917	5.819	21.574	21.574	0.000	0.000	0.000	0.000
125	A	126	LEU	0	0.019	-0.001	9.399	1.164	1.164	0.000	0.000	0.000	0.000
126	A	127	MET	0	0.005	0.005	5.739	0.968	0.968	0.000	0.000	0.000	0.000
127	A	128	GLN	0	-0.045	-0.033	7.945	-1.983	-1.983	0.000	0.000	0.000	0.000
128	A	129	GLU	-1	-0.815	-0.902	9.667	-18.641	-18.641	0.000	0.000	0.000	0.000
129	A	130	ASN	0	-0.001	0.014	11.036	0.895	0.895	0.000	0.000	0.000	0.000
130	A	131	VAL	0	0.013	0.008	10.042	1.124	1.124	0.000	0.000	0.000	0.000
131	A	132	GLU	-1	-0.900	-0.955	12.561	-19.100	-19.100	0.000	0.000	0.000	0.000
132	A	133	SER	0	-0.099	-0.071	15.039	1.454	1.454	0.000	0.000	0.000	0.000
133	A	134	LEU	0	0.004	0.004	13.726	1.222	1.222	0.000	0.000	0.000	0.000
134	A	135	LEU	0	0.000	-0.001	16.059	1.137	1.137	0.000	0.000	0.000	0.000
135	A	136	LYS	1	0.816	0.912	18.590	13.595	13.595	0.000	0.000	0.000	0.000
136	A	137	GLY	0	0.024	0.012	20.379	0.758	0.758	0.000	0.000	0.000	0.000
137	A	138	LEU	0	-0.011	-0.009	21.196	0.611	0.611	0.000	0.000	0.000	0.000
138	A	139	GLU	-1	-0.828	-0.906	22.911	-11.544	-11.544	0.000	0.000	0.000	0.000
139	A	140	GLU	-1	-0.880	-0.937	24.952	-11.466	-11.466	0.000	0.000	0.000	0.000
140	A	141	ARG	1	0.866	0.942	25.732	11.350	11.350	0.000	0.000	0.000	0.000
141	A	142	VAL	0	-0.011	-0.017	26.328	0.437	0.437	0.000	0.000	0.000	0.000
142	A	143	LEU	0	-0.014	0.006	28.740	0.401	0.401	0.000	0.000	0.000	0.000
143	A	144	ALA	0	-0.030	-0.020	30.604	0.360	0.360	0.000	0.000	0.000	0.000
144	A	145	ALA	0	-0.063	-0.027	31.398	0.264	0.264	0.000	0.000	0.000	0.000
145	A	146	SER	0	-0.103	-0.062	32.221	0.119	0.119	0.000	0.000	0.000	0.000
146	A	147	SER	-1	-0.960	-0.959	34.838	-8.018	-8.018	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:2:PRO)