FMO DATABASE

FMODB ID: VVLR1

Calculation Name: 1TOP-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion | calcium ion

Ligand 3-letter code: SO4 | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1TOP

Chain ID: A

ChEMBL ID:

UniProt ID: P02588

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	162
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1397148.762595
FMO2-HF: Nuclear repulsion	1330449.398667
FMO2-HF: Total energy	-66699.363928
FMO2-MP2: Total energy	-66885.208557

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:ALA)

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

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.
-415.932	-410.287	9.906	-8.351	-7.202	-0.068

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.821 / q_NPA : 0.902

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	MET	0	0.104	0.046	3.260	-7.618	-5.789	0.047	-0.958	-0.918	-0.001
5	A	5	ASP	-1	-0.883	-0.912	2.147	-78.182	-77.185	8.627	-5.692	-3.934	-0.054
6	A	6	GLN	0	0.068	0.031	2.310	8.223	9.011	0.919	-0.603	-1.104	-0.003
7	A	7	GLN	0	0.038	0.025	3.969	4.008	4.089	0.003	-0.040	-0.044	0.000
9	A	9	GLU	-1	-0.984	-1.005	3.049	-57.714	-55.764	0.310	-1.058	-1.202	-0.010
4	A	4	THR	0	0.050	0.027	5.891	2.363	2.363	0.000	0.000	0.000	0.000
8	A	8	ALA	0	-0.035	-0.010	6.858	3.218	3.218	0.000	0.000	0.000	0.000
10	A	10	ALA	0	-0.028	-0.012	7.114	2.767	2.767	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.799	0.860	9.298	21.070	21.070	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.043	-0.024	10.101	1.532	1.532	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.045	-0.023	10.779	0.796	0.796	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.002	0.008	12.646	1.202	1.202	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.035	-0.029	15.688	-0.234	-0.234	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.889	-0.964	18.038	-15.636	-15.636	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.889	-0.933	19.743	-12.806	-12.806	0.000	0.000	0.000	0.000
18	A	18	MET	0	0.009	0.017	19.094	0.141	0.141	0.000	0.000	0.000	0.000
19	A	19	ILE	0	0.021	0.019	15.075	-0.115	-0.115	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.010	-0.016	18.646	0.153	0.153	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.984	-0.990	22.100	-11.948	-11.948	0.000	0.000	0.000	0.000
22	A	22	PHE	0	0.039	-0.010	16.447	0.114	0.114	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.819	0.897	20.172	13.547	13.547	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.048	-0.017	21.525	0.379	0.379	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.036	-0.014	23.348	0.413	0.413	0.000	0.000	0.000	0.000
26	A	26	PHE	0	0.011	0.007	18.545	0.301	0.301	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.752	-0.876	22.826	-12.464	-12.464	0.000	0.000	0.000	0.000
28	A	28	MET	0	-0.126	-0.055	25.143	0.536	0.536	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.051	-0.045	24.992	0.483	0.483	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.761	-0.842	24.117	-12.214	-12.214	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.094	-0.051	25.892	0.319	0.319	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-1.008	-1.006	27.437	-10.360	-10.360	0.000	0.000	0.000	0.000
33	A	33	GLY	0	-0.077	-0.040	26.829	0.254	0.254	0.000	0.000	0.000	0.000
34	A	34	GLY	0	-0.015	0.000	24.267	-0.109	-0.109	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.062	-0.037	20.776	-0.489	-0.489	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.960	-0.985	19.272	-14.664	-14.664	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.004	0.003	20.280	0.769	0.769	0.000	0.000	0.000	0.000
38	A	38	SER	0	0.032	0.008	21.670	-0.462	-0.462	0.000	0.000	0.000	0.000
39	A	39	THR	0	0.032	0.001	19.750	0.186	0.186	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.852	0.919	22.064	11.906	11.906	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.868	-0.929	24.539	-10.592	-10.592	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.039	0.045	17.214	0.099	0.099	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.015	-0.007	21.306	-0.156	-0.156	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.105	-0.060	23.066	0.265	0.265	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.039	0.017	21.557	0.171	0.171	0.000	0.000	0.000	0.000
46	A	46	MET	0	0.033	0.007	16.696	0.027	0.027	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.889	0.968	21.046	12.182	12.182	0.000	0.000	0.000	0.000
48	A	48	MET	0	-0.088	-0.037	24.462	0.387	0.387	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.038	0.001	20.239	0.287	0.287	0.000	0.000	0.000	0.000
50	A	50	GLY	0	-0.007	-0.005	21.900	-0.473	-0.473	0.000	0.000	0.000	0.000
51	A	51	GLN	0	-0.005	0.005	18.453	-0.457	-0.457	0.000	0.000	0.000	0.000
52	A	52	ASN	0	-0.117	-0.080	21.634	0.799	0.799	0.000	0.000	0.000	0.000
53	A	53	PRO	0	0.005	0.034	19.038	0.132	0.132	0.000	0.000	0.000	0.000
54	A	54	THR	0	-0.073	-0.077	20.909	0.904	0.904	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.890	0.919	21.936	10.901	10.901	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.899	-0.940	19.643	-15.355	-15.355	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.672	-0.779	17.446	-15.826	-15.826	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.050	-0.029	17.540	-0.552	-0.552	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.953	-0.970	19.088	-13.262	-13.262	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.033	0.014	16.062	-0.380	-0.380	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.012	-0.018	13.775	-1.024	-1.024	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.043	-0.029	15.260	-0.474	-0.474	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.995	-1.005	17.696	-15.019	-15.019	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.827	-0.867	9.341	-29.251	-29.251	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.033	-0.020	12.740	-1.209	-1.209	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.831	-0.909	14.919	-14.000	-14.000	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.990	-0.988	15.171	-19.760	-19.760	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.958	-0.971	18.364	-14.992	-14.992	0.000	0.000	0.000	0.000
69	A	69	GLY	0	-0.059	-0.022	20.606	0.815	0.815	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.077	-0.046	20.515	0.818	0.818	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.043	-0.025	22.572	0.625	0.625	0.000	0.000	0.000	0.000
72	A	72	THR	0	-0.098	-0.042	20.811	0.245	0.245	0.000	0.000	0.000	0.000
73	A	73	ILE	0	0.039	0.020	14.559	-0.488	-0.488	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.775	-0.889	14.209	-19.571	-19.571	0.000	0.000	0.000	0.000
75	A	75	PHE	0	-0.002	-0.016	15.645	-0.513	-0.513	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.801	-0.877	11.476	-20.462	-20.462	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.849	-0.946	10.858	-22.996	-22.996	0.000	0.000	0.000	0.000
78	A	78	PHE	0	-0.023	-0.008	11.916	-0.466	-0.466	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.010	0.002	11.929	0.147	0.147	0.000	0.000	0.000	0.000
80	A	80	VAL	0	-0.021	-0.015	7.344	-0.772	-0.772	0.000	0.000	0.000	0.000
81	A	81	MET	0	-0.025	0.000	9.666	-0.344	-0.344	0.000	0.000	0.000	0.000
82	A	82	MET	0	-0.018	0.008	12.525	0.887	0.887	0.000	0.000	0.000	0.000
83	A	83	VAL	0	-0.048	-0.018	9.957	0.425	0.425	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.701	0.806	6.815	30.040	30.040	0.000	0.000	0.000	0.000
85	A	85	GLN	0	-0.012	-0.012	11.781	0.082	0.082	0.000	0.000	0.000	0.000
86	A	86	MET	0	0.028	0.016	15.039	0.789	0.789	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.869	0.947	9.052	27.760	27.760	0.000	0.000	0.000	0.000
88	A	88	GLU	0	-0.079	-0.065	15.001	0.078	0.078	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.757	-0.879	16.629	-13.935	-13.935	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.033	-0.020	18.517	0.747	0.747	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.876	0.945	17.541	15.743	15.743	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.070	0.045	19.575	0.589	0.589	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.852	0.915	22.356	11.466	11.466	0.000	0.000	0.000	0.000
94	A	94	SER	0	-0.058	-0.048	22.102	0.395	0.395	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.808	-0.901	21.944	-13.465	-13.465	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.985	-0.986	25.407	-10.081	-10.081	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.853	-0.927	27.779	-9.602	-9.602	0.000	0.000	0.000	0.000
98	A	98	LEU	0	0.024	0.024	25.543	0.466	0.466	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.018	0.002	29.474	0.388	0.388	0.000	0.000	0.000	0.000
100	A	100	ASN	0	-0.105	-0.059	31.419	0.548	0.548	0.000	0.000	0.000	0.000
101	A	101	CYS	0	-0.043	-0.007	32.246	0.310	0.310	0.000	0.000	0.000	0.000
102	A	102	PHE	0	0.057	0.028	33.385	0.241	0.241	0.000	0.000	0.000	0.000
103	A	103	ARG	1	0.883	0.937	33.837	9.050	9.050	0.000	0.000	0.000	0.000
104	A	104	ILE	0	-0.071	-0.020	36.999	0.236	0.236	0.000	0.000	0.000	0.000
105	A	105	PHE	0	-0.020	-0.022	35.102	0.180	0.180	0.000	0.000	0.000	0.000
106	A	106	ASP	-1	-0.769	-0.871	39.240	-7.371	-7.371	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.745	0.882	41.117	7.253	7.253	0.000	0.000	0.000	0.000
108	A	108	ASN	0	-0.111	-0.070	44.322	0.306	0.306	0.000	0.000	0.000	0.000
109	A	109	ALA	0	-0.073	-0.029	42.860	0.126	0.126	0.000	0.000	0.000	0.000
110	A	110	ASP	-1	-0.950	-0.969	43.502	-7.214	-7.214	0.000	0.000	0.000	0.000
111	A	111	GLY	0	-0.065	-0.031	39.649	-0.038	-0.038	0.000	0.000	0.000	0.000
112	A	112	PHE	0	-0.080	-0.049	38.732	-0.247	-0.247	0.000	0.000	0.000	0.000
113	A	113	ILE	0	0.022	0.028	36.309	0.056	0.056	0.000	0.000	0.000	0.000
114	A	114	ASP	-1	-0.791	-0.885	40.322	-7.087	-7.087	0.000	0.000	0.000	0.000
115	A	115	ILE	0	0.044	-0.015	42.478	-0.111	-0.111	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.989	-0.981	44.058	-6.428	-6.428	0.000	0.000	0.000	0.000
117	A	117	GLU	-1	-0.824	-0.933	42.820	-7.309	-7.309	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.048	0.019	37.801	-0.077	-0.077	0.000	0.000	0.000	0.000
119	A	119	GLY	0	0.042	-0.001	41.362	-0.069	-0.069	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.962	-0.977	43.869	-6.686	-6.686	0.000	0.000	0.000	0.000
121	A	121	ILE	0	-0.038	-0.014	38.765	0.051	0.051	0.000	0.000	0.000	0.000
122	A	122	LEU	0	0.022	0.011	37.295	-0.052	-0.052	0.000	0.000	0.000	0.000
123	A	123	ARG	1	0.817	0.896	40.943	6.770	6.770	0.000	0.000	0.000	0.000
124	A	124	ALA	0	-0.053	-0.017	43.133	0.094	0.094	0.000	0.000	0.000	0.000
125	A	125	THR	0	-0.053	-0.037	38.462	-0.009	-0.009	0.000	0.000	0.000	0.000
126	A	126	GLY	0	-0.057	-0.021	41.502	-0.009	-0.009	0.000	0.000	0.000	0.000
127	A	127	GLU	-1	-0.907	-0.964	38.661	-7.739	-7.739	0.000	0.000	0.000	0.000
128	A	128	HIS	0	-0.164	-0.071	42.136	0.304	0.304	0.000	0.000	0.000	0.000
129	A	129	VAL	0	0.013	0.015	40.652	0.005	0.005	0.000	0.000	0.000	0.000
130	A	130	THR	0	-0.103	-0.078	43.493	0.238	0.238	0.000	0.000	0.000	0.000
131	A	131	GLU	-1	-0.815	-0.911	44.731	-6.825	-6.825	0.000	0.000	0.000	0.000
132	A	132	GLU	-1	-0.961	-0.964	44.150	-6.930	-6.930	0.000	0.000	0.000	0.000
133	A	133	ASP	-1	-0.769	-0.872	40.488	-7.600	-7.600	0.000	0.000	0.000	0.000
134	A	134	ILE	0	-0.038	0.001	40.011	-0.215	-0.215	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.911	-0.963	41.003	-6.967	-6.967	0.000	0.000	0.000	0.000
136	A	136	ASP	-1	-0.918	-0.958	39.124	-7.728	-7.728	0.000	0.000	0.000	0.000
137	A	137	LEU	0	0.016	0.013	33.858	-0.184	-0.184	0.000	0.000	0.000	0.000
138	A	138	MET	0	-0.006	0.039	36.472	-0.271	-0.271	0.000	0.000	0.000	0.000
139	A	139	LYS	1	0.770	0.885	37.888	7.215	7.215	0.000	0.000	0.000	0.000
140	A	140	ASP	-1	-0.920	-0.953	33.940	-9.001	-9.001	0.000	0.000	0.000	0.000
141	A	141	SER	0	-0.046	-0.031	33.200	-0.471	-0.471	0.000	0.000	0.000	0.000
142	A	142	ASP	-1	-0.781	-0.888	33.902	-8.324	-8.324	0.000	0.000	0.000	0.000
143	A	143	LYS	1	0.744	0.853	31.374	9.523	9.523	0.000	0.000	0.000	0.000
144	A	144	ASN	0	-0.109	-0.076	35.058	0.187	0.187	0.000	0.000	0.000	0.000
145	A	145	ASN	0	-0.115	-0.056	37.827	0.268	0.268	0.000	0.000	0.000	0.000
146	A	146	ASP	-1	-0.855	-0.903	40.664	-7.593	-7.593	0.000	0.000	0.000	0.000
147	A	147	GLY	0	-0.056	-0.025	41.903	0.186	0.186	0.000	0.000	0.000	0.000
148	A	148	ARG	1	0.778	0.863	40.758	7.590	7.590	0.000	0.000	0.000	0.000
149	A	149	ILE	0	0.036	0.023	34.662	-0.143	-0.143	0.000	0.000	0.000	0.000
150	A	150	ASP	-1	-0.815	-0.904	34.061	-9.148	-9.148	0.000	0.000	0.000	0.000
151	A	151	PHE	0	-0.014	-0.027	29.707	-0.198	-0.198	0.000	0.000	0.000	0.000
152	A	152	ASP	-1	-0.860	-0.916	28.789	-11.105	-11.105	0.000	0.000	0.000	0.000
153	A	153	GLU	-1	-0.787	-0.907	29.671	-9.231	-9.231	0.000	0.000	0.000	0.000
154	A	154	PHE	0	0.006	0.002	31.172	-0.118	-0.118	0.000	0.000	0.000	0.000
155	A	155	LEU	0	0.001	-0.004	26.436	-0.131	-0.131	0.000	0.000	0.000	0.000
156	A	156	LYS	1	0.815	0.912	26.476	10.309	10.309	0.000	0.000	0.000	0.000
157	A	157	MET	0	-0.044	-0.006	27.492	-0.055	-0.055	0.000	0.000	0.000	0.000
158	A	158	MET	0	-0.090	-0.039	28.215	0.084	0.084	0.000	0.000	0.000	0.000
159	A	159	GLU	-1	-0.881	-0.937	22.404	-13.464	-13.464	0.000	0.000	0.000	0.000
160	A	160	GLY	0	-0.022	0.014	23.376	-0.535	-0.535	0.000	0.000	0.000	0.000
161	A	161	VAL	0	-0.157	-0.102	19.022	-0.053	-0.053	0.000	0.000	0.000	0.000
162	A	162	GLN	-1	-0.968	-0.985	21.765	-13.173	-13.173	0.000	0.000	0.000	0.000

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