FMO DATABASE

FMODB ID: VNV91

Calculation Name: 3TRF-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion

Ligand 3-letter code: SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3TRF

Chain ID: A

ChEMBL ID:

UniProt ID: Q83AJ3

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	170
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1748735.621785
FMO2-HF: Nuclear repulsion	1681198.034132
FMO2-HF: Total energy	-67537.587653
FMO2-MP2: Total energy	-67734.113185

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:5:LEU)

Summations of interaction energy for fragment #1(A:5:LEU)

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.
-107.446	-99.443	9.375	-8.281	-9.096	-0.084

Interaction energy analysis for fragmet #1(A:5:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.868 / q_NPA : 0.931

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	7	ASN	0	0.018	0.003	3.429	11.831	13.801	0.002	-0.897	-1.076	-0.001
4	A	8	ILE	0	-0.012	0.002	4.905	-1.105	-0.974	-0.001	-0.008	-0.122	0.000
71	A	75	ASP	-1	-0.856	-0.912	4.315	-63.233	-63.166	-0.001	-0.031	-0.034	0.000
93	A	97	GLU	-1	-0.906	-0.949	4.294	-36.973	-36.700	0.000	-0.047	-0.226	0.000
94	A	98	THR	0	-0.044	-0.040	2.464	-21.012	-17.385	1.111	-2.307	-2.431	-0.020
95	A	99	GLY	0	-0.083	-0.049	2.308	-29.537	-27.748	8.230	-5.404	-4.614	-0.062
96	A	100	VAL	0	0.049	0.046	3.185	4.115	4.250	0.035	0.415	-0.585	-0.001
97	A	101	VAL	0	-0.030	-0.020	5.054	1.933	1.944	-0.001	-0.002	-0.008	0.000
5	A	9	TYR	0	0.018	-0.003	5.364	5.482	5.482	0.000	0.000	0.000	0.000
6	A	10	LEU	0	-0.014	0.004	9.487	1.472	1.472	0.000	0.000	0.000	0.000
7	A	11	ILE	0	0.033	0.017	12.201	1.078	1.078	0.000	0.000	0.000	0.000
8	A	12	GLY	0	0.089	0.044	14.891	0.621	0.621	0.000	0.000	0.000	0.000
9	A	13	LEU	0	-0.041	-0.002	18.485	-0.090	-0.090	0.000	0.000	0.000	0.000
10	A	14	MET	0	0.027	0.013	21.866	-0.233	-0.233	0.000	0.000	0.000	0.000
11	A	15	GLY	0	0.029	0.003	24.214	0.282	0.282	0.000	0.000	0.000	0.000
12	A	16	ALA	0	-0.011	0.001	20.678	0.301	0.301	0.000	0.000	0.000	0.000
13	A	17	GLY	0	0.042	0.019	20.729	-0.395	-0.395	0.000	0.000	0.000	0.000
14	A	18	LYS	1	0.877	0.946	16.661	16.111	16.111	0.000	0.000	0.000	0.000
15	A	19	THR	0	0.087	0.040	17.933	-0.467	-0.467	0.000	0.000	0.000	0.000
16	A	20	SER	0	-0.081	-0.012	20.005	0.033	0.033	0.000	0.000	0.000	0.000
17	A	21	VAL	0	0.070	0.022	16.286	0.128	0.128	0.000	0.000	0.000	0.000
18	A	22	GLY	0	0.071	0.027	15.508	-0.496	-0.496	0.000	0.000	0.000	0.000
19	A	23	SER	0	-0.016	-0.021	16.468	-0.275	-0.275	0.000	0.000	0.000	0.000
20	A	24	GLN	0	-0.069	-0.034	19.421	0.333	0.333	0.000	0.000	0.000	0.000
21	A	25	LEU	0	0.063	0.029	13.073	0.245	0.245	0.000	0.000	0.000	0.000
22	A	26	ALA	0	0.029	0.045	15.755	-0.483	-0.483	0.000	0.000	0.000	0.000
23	A	27	LYS	1	0.904	0.943	16.654	13.098	13.098	0.000	0.000	0.000	0.000
24	A	28	LEU	0	-0.056	-0.028	17.370	0.497	0.497	0.000	0.000	0.000	0.000
25	A	29	THR	0	-0.023	-0.032	12.926	-0.516	-0.516	0.000	0.000	0.000	0.000
26	A	30	LYS	1	0.905	0.954	15.285	14.871	14.871	0.000	0.000	0.000	0.000
27	A	31	ARG	1	0.904	0.980	7.553	32.162	32.162	0.000	0.000	0.000	0.000
28	A	32	ILE	0	0.014	0.006	13.827	1.315	1.315	0.000	0.000	0.000	0.000
29	A	33	LEU	0	-0.035	-0.008	13.321	-1.607	-1.607	0.000	0.000	0.000	0.000
30	A	34	TYR	0	0.012	0.001	12.577	0.908	0.908	0.000	0.000	0.000	0.000
31	A	35	ASP	-1	-0.850	-0.949	15.297	-16.347	-16.347	0.000	0.000	0.000	0.000
32	A	36	SER	0	0.072	0.027	15.466	0.142	0.142	0.000	0.000	0.000	0.000
33	A	37	ASP	-1	-0.915	-0.945	17.142	-14.423	-14.423	0.000	0.000	0.000	0.000
34	A	38	LYS	1	0.820	0.889	20.502	13.229	13.229	0.000	0.000	0.000	0.000
35	A	39	GLU	-1	-0.804	-0.905	16.337	-16.468	-16.468	0.000	0.000	0.000	0.000
36	A	40	ILE	0	-0.025	0.008	19.089	0.299	0.299	0.000	0.000	0.000	0.000
37	A	41	GLU	-1	-0.792	-0.872	21.238	-11.643	-11.643	0.000	0.000	0.000	0.000
38	A	42	LYS	1	0.834	0.906	19.224	16.180	16.180	0.000	0.000	0.000	0.000
39	A	43	ARG	1	0.909	0.953	16.945	16.931	16.931	0.000	0.000	0.000	0.000
40	A	44	THR	0	-0.050	-0.034	22.892	0.291	0.291	0.000	0.000	0.000	0.000
41	A	45	GLY	0	-0.016	0.010	25.969	0.411	0.411	0.000	0.000	0.000	0.000
42	A	46	ALA	0	-0.032	-0.014	28.023	0.466	0.466	0.000	0.000	0.000	0.000
43	A	47	ASP	-1	-0.821	-0.921	27.762	-10.598	-10.598	0.000	0.000	0.000	0.000
44	A	48	ILE	0	0.002	-0.016	23.938	0.014	0.014	0.000	0.000	0.000	0.000
45	A	49	ALA	0	-0.038	-0.006	28.093	0.058	0.058	0.000	0.000	0.000	0.000
46	A	50	TRP	0	0.066	0.027	29.540	0.035	0.035	0.000	0.000	0.000	0.000
47	A	51	ILE	0	-0.020	-0.005	25.411	0.023	0.023	0.000	0.000	0.000	0.000
48	A	52	PHE	0	-0.067	-0.049	26.564	0.025	0.025	0.000	0.000	0.000	0.000
49	A	53	GLU	-1	-0.974	-0.973	31.177	-8.355	-8.355	0.000	0.000	0.000	0.000
50	A	54	MET	0	-0.028	-0.007	32.861	0.292	0.292	0.000	0.000	0.000	0.000
51	A	55	GLU	-1	-0.846	-0.895	28.255	-11.269	-11.269	0.000	0.000	0.000	0.000
52	A	56	GLY	0	0.015	0.022	30.812	-0.132	-0.132	0.000	0.000	0.000	0.000
53	A	57	GLU	-1	-0.846	-0.919	26.078	-12.272	-12.272	0.000	0.000	0.000	0.000
54	A	58	ALA	0	-0.025	-0.020	26.448	-0.522	-0.522	0.000	0.000	0.000	0.000
55	A	59	GLY	0	0.028	0.006	26.273	-0.372	-0.372	0.000	0.000	0.000	0.000
56	A	60	PHE	0	-0.008	0.001	22.109	-0.478	-0.478	0.000	0.000	0.000	0.000
57	A	61	ARG	1	0.760	0.838	21.617	13.064	13.064	0.000	0.000	0.000	0.000
58	A	62	ARG	1	0.932	0.984	21.007	10.968	10.968	0.000	0.000	0.000	0.000
59	A	63	ARG	1	0.869	0.904	20.579	11.245	11.245	0.000	0.000	0.000	0.000
60	A	64	GLU	-1	-0.812	-0.909	17.955	-16.588	-16.588	0.000	0.000	0.000	0.000
61	A	65	ARG	1	0.844	0.913	16.506	14.905	14.905	0.000	0.000	0.000	0.000
62	A	66	GLU	-1	-0.927	-0.961	15.738	-16.044	-16.044	0.000	0.000	0.000	0.000
63	A	67	MET	0	-0.066	-0.014	15.778	-1.306	-1.306	0.000	0.000	0.000	0.000
64	A	68	ILE	0	-0.015	-0.014	11.749	-1.440	-1.440	0.000	0.000	0.000	0.000
65	A	69	GLU	-1	-0.832	-0.896	11.174	-23.877	-23.877	0.000	0.000	0.000	0.000
66	A	70	ALA	0	-0.039	-0.035	11.130	-1.716	-1.716	0.000	0.000	0.000	0.000
67	A	71	LEU	0	-0.006	-0.016	10.854	-1.206	-1.206	0.000	0.000	0.000	0.000
68	A	72	CYS	0	-0.064	-0.027	7.104	-1.927	-1.927	0.000	0.000	0.000	0.000
69	A	73	LYS	1	0.798	0.890	5.915	19.776	19.776	0.000	0.000	0.000	0.000
70	A	74	LEU	0	-0.039	0.003	7.713	0.602	0.602	0.000	0.000	0.000	0.000
72	A	76	ASN	0	-0.078	-0.057	5.806	5.600	5.600	0.000	0.000	0.000	0.000
73	A	77	ILE	0	-0.020	0.003	7.543	5.366	5.366	0.000	0.000	0.000	0.000
74	A	78	ILE	0	-0.021	-0.017	8.544	-2.046	-2.046	0.000	0.000	0.000	0.000
75	A	79	LEU	0	0.001	0.006	10.660	1.588	1.588	0.000	0.000	0.000	0.000
76	A	80	ALA	0	-0.033	-0.010	12.247	-0.062	-0.062	0.000	0.000	0.000	0.000
77	A	81	THR	0	0.015	-0.008	12.931	-0.274	-0.274	0.000	0.000	0.000	0.000
78	A	82	GLY	0	0.076	0.039	15.196	0.986	0.986	0.000	0.000	0.000	0.000
79	A	83	GLY	0	-0.020	-0.021	17.967	-0.397	-0.397	0.000	0.000	0.000	0.000
80	A	84	GLY	0	-0.028	-0.023	20.186	0.301	0.301	0.000	0.000	0.000	0.000
81	A	85	VAL	0	0.049	0.047	14.185	0.051	0.051	0.000	0.000	0.000	0.000
82	A	86	VAL	0	0.050	0.012	13.883	-0.243	-0.243	0.000	0.000	0.000	0.000
83	A	87	LEU	0	-0.009	0.004	16.055	0.225	0.225	0.000	0.000	0.000	0.000
84	A	88	ASP	-1	-0.812	-0.885	17.463	-16.704	-16.704	0.000	0.000	0.000	0.000
85	A	89	GLU	-1	-0.848	-0.923	15.647	-17.869	-17.869	0.000	0.000	0.000	0.000
86	A	90	LYS	1	0.973	0.994	14.067	19.704	19.704	0.000	0.000	0.000	0.000
87	A	91	ASN	0	-0.031	-0.018	12.598	-2.540	-2.540	0.000	0.000	0.000	0.000
88	A	92	ARG	1	0.818	0.888	11.238	15.758	15.758	0.000	0.000	0.000	0.000
89	A	93	GLN	0	-0.037	0.016	9.810	-0.815	-0.815	0.000	0.000	0.000	0.000
90	A	94	GLN	0	0.061	0.012	8.162	-0.660	-0.660	0.000	0.000	0.000	0.000
91	A	95	ILE	0	0.002	0.020	6.987	-5.622	-5.622	0.000	0.000	0.000	0.000
92	A	96	SER	0	-0.019	-0.028	5.439	-5.115	-5.115	0.000	0.000	0.000	0.000
98	A	102	ILE	0	0.012	0.003	8.419	2.120	2.120	0.000	0.000	0.000	0.000
99	A	103	TYR	0	0.002	-0.008	11.591	0.939	0.939	0.000	0.000	0.000	0.000
100	A	104	LEU	0	-0.011	0.001	14.845	0.751	0.751	0.000	0.000	0.000	0.000
101	A	105	THR	0	-0.014	-0.026	17.782	0.550	0.550	0.000	0.000	0.000	0.000
102	A	106	ALA	0	-0.027	-0.018	21.284	0.043	0.043	0.000	0.000	0.000	0.000
103	A	107	SER	0	0.017	-0.001	24.923	0.163	0.163	0.000	0.000	0.000	0.000
104	A	108	ILE	0	0.023	-0.002	28.491	-0.108	-0.108	0.000	0.000	0.000	0.000
105	A	109	ASP	-1	-0.898	-0.958	30.315	-9.084	-9.084	0.000	0.000	0.000	0.000
106	A	110	THR	0	-0.047	-0.048	26.740	0.190	0.190	0.000	0.000	0.000	0.000
107	A	111	GLN	0	-0.044	-0.017	25.601	0.149	0.149	0.000	0.000	0.000	0.000
108	A	112	LEU	0	0.003	-0.012	28.223	-0.006	-0.006	0.000	0.000	0.000	0.000
109	A	113	LYS	1	0.939	0.978	31.065	9.322	9.322	0.000	0.000	0.000	0.000
110	A	114	ARG	1	0.798	0.884	24.334	12.280	12.280	0.000	0.000	0.000	0.000
111	A	115	ILE	0	-0.007	0.006	27.987	-0.083	-0.083	0.000	0.000	0.000	0.000
112	A	116	GLY	0	0.054	0.030	29.772	0.119	0.119	0.000	0.000	0.000	0.000
113	A	117	GLN	0	-0.064	-0.036	31.560	0.270	0.270	0.000	0.000	0.000	0.000
114	A	118	LYS	1	0.872	0.932	31.599	9.583	9.583	0.000	0.000	0.000	0.000
115	A	119	GLY	0	0.028	0.013	33.626	0.110	0.110	0.000	0.000	0.000	0.000
116	A	120	GLU	-1	-0.916	-0.948	34.629	-8.530	-8.530	0.000	0.000	0.000	0.000
117	A	121	MET	0	-0.015	-0.002	37.498	0.279	0.279	0.000	0.000	0.000	0.000
118	A	122	ARG	1	0.982	0.985	37.997	7.120	7.120	0.000	0.000	0.000	0.000
119	A	123	ARG	1	0.906	0.956	39.078	7.423	7.423	0.000	0.000	0.000	0.000
120	A	124	PRO	0	0.033	0.023	34.883	-0.031	-0.031	0.000	0.000	0.000	0.000
121	A	125	LEU	0	0.013	0.007	35.405	0.254	0.254	0.000	0.000	0.000	0.000
122	A	126	PHE	0	-0.021	-0.020	36.123	-0.196	-0.196	0.000	0.000	0.000	0.000
123	A	127	ILE	0	0.008	0.011	33.215	0.124	0.124	0.000	0.000	0.000	0.000
124	A	128	LYS	1	0.999	0.991	37.338	7.506	7.506	0.000	0.000	0.000	0.000
125	A	129	ASN	0	0.047	0.014	38.109	-0.169	-0.169	0.000	0.000	0.000	0.000
126	A	130	ASN	0	0.100	0.058	37.884	-0.297	-0.297	0.000	0.000	0.000	0.000
127	A	131	SER	0	0.001	0.000	34.861	-0.124	-0.124	0.000	0.000	0.000	0.000
128	A	132	LYS	1	0.927	0.979	33.557	8.380	8.380	0.000	0.000	0.000	0.000
129	A	133	GLU	-1	-0.887	-0.948	33.378	-8.310	-8.310	0.000	0.000	0.000	0.000
130	A	134	LYS	1	0.895	0.953	32.448	9.094	9.094	0.000	0.000	0.000	0.000
131	A	135	LEU	0	0.008	0.003	27.164	-0.308	-0.308	0.000	0.000	0.000	0.000
132	A	136	GLN	0	0.007	-0.016	28.795	-0.182	-0.182	0.000	0.000	0.000	0.000
133	A	137	GLN	0	0.084	0.038	29.736	-0.277	-0.277	0.000	0.000	0.000	0.000
134	A	138	LEU	0	-0.026	-0.008	25.761	-0.309	-0.309	0.000	0.000	0.000	0.000
135	A	139	ASN	0	-0.011	-0.038	25.142	-0.758	-0.758	0.000	0.000	0.000	0.000
136	A	140	GLU	-1	-0.990	-0.984	25.268	-10.164	-10.164	0.000	0.000	0.000	0.000
137	A	141	ILE	0	0.016	-0.003	25.360	-0.324	-0.324	0.000	0.000	0.000	0.000
138	A	142	ARG	1	0.928	0.968	21.164	12.850	12.850	0.000	0.000	0.000	0.000
139	A	143	LYS	1	0.967	1.005	20.412	10.786	10.786	0.000	0.000	0.000	0.000
140	A	144	PRO	0	0.001	-0.002	19.921	-0.598	-0.598	0.000	0.000	0.000	0.000
141	A	145	LEU	0	0.006	0.011	17.073	-0.432	-0.432	0.000	0.000	0.000	0.000
142	A	146	TYR	0	-0.022	-0.044	15.746	-0.508	-0.508	0.000	0.000	0.000	0.000
143	A	147	GLN	0	-0.015	-0.018	14.931	-0.410	-0.410	0.000	0.000	0.000	0.000
144	A	148	ALA	0	-0.019	-0.007	15.470	-0.311	-0.311	0.000	0.000	0.000	0.000
145	A	149	MET	0	-0.039	-0.013	10.502	-0.014	-0.014	0.000	0.000	0.000	0.000
146	A	150	ALA	0	-0.061	-0.020	10.548	-1.719	-1.719	0.000	0.000	0.000	0.000
147	A	151	ASP	-1	-0.787	-0.866	6.449	-31.603	-31.603	0.000	0.000	0.000	0.000
148	A	152	LEU	0	-0.026	-0.010	9.873	1.443	1.443	0.000	0.000	0.000	0.000
149	A	153	VAL	0	-0.021	-0.017	12.529	-0.154	-0.154	0.000	0.000	0.000	0.000
150	A	154	TYR	0	-0.011	-0.038	13.738	0.375	0.375	0.000	0.000	0.000	0.000
151	A	155	PRO	0	0.005	0.029	18.627	-0.040	-0.040	0.000	0.000	0.000	0.000
152	A	156	THR	0	-0.026	-0.030	20.578	-0.125	-0.125	0.000	0.000	0.000	0.000
153	A	157	ASP	-1	-0.738	-0.837	23.214	-10.980	-10.980	0.000	0.000	0.000	0.000
154	A	158	ASP	-1	-0.921	-0.953	26.540	-10.014	-10.014	0.000	0.000	0.000	0.000
155	A	159	LEU	0	-0.056	-0.014	21.962	-0.073	-0.073	0.000	0.000	0.000	0.000
156	A	160	ASN	0	0.057	0.034	25.774	-0.029	-0.029	0.000	0.000	0.000	0.000
157	A	161	PRO	0	-0.002	-0.018	22.622	-0.449	-0.449	0.000	0.000	0.000	0.000
158	A	162	ARG	1	0.975	0.986	21.335	11.659	11.659	0.000	0.000	0.000	0.000
159	A	163	GLN	0	0.034	0.036	21.488	-0.240	-0.240	0.000	0.000	0.000	0.000
160	A	164	LEU	0	0.036	0.024	18.266	-0.266	-0.266	0.000	0.000	0.000	0.000
161	A	165	ALA	0	-0.013	-0.011	17.122	-0.718	-0.718	0.000	0.000	0.000	0.000
162	A	166	THR	0	-0.051	-0.054	16.441	-0.699	-0.699	0.000	0.000	0.000	0.000
163	A	167	GLN	0	-0.014	0.001	17.096	0.004	0.004	0.000	0.000	0.000	0.000
164	A	168	ILE	0	-0.001	-0.005	12.276	-0.558	-0.558	0.000	0.000	0.000	0.000
165	A	169	LEU	0	-0.071	-0.050	11.924	-1.337	-1.337	0.000	0.000	0.000	0.000
166	A	170	VAL	0	-0.061	-0.017	13.112	-0.396	-0.396	0.000	0.000	0.000	0.000
167	A	171	ASP	-1	-0.799	-0.871	13.460	-16.836	-16.836	0.000	0.000	0.000	0.000
168	A	172	ILE	0	-0.019	0.004	7.488	-1.593	-1.593	0.000	0.000	0.000	0.000
169	A	173	LYS	1	0.838	0.909	8.532	23.518	23.518	0.000	0.000	0.000	0.000
170	A	174	GLN	-1	-0.845	-0.905	7.635	-25.087	-25.087	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LEU)