FMO DATABASE

FMODB ID: RL788

Calculation Name: 4PH2-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion | glycerol

Ligand 3-letter code: SO4 | GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4PH2

Chain ID: A

ChEMBL ID:

UniProt ID: L0PI28

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	127
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1057314.371252
FMO2-HF: Nuclear repulsion	1008222.821675
FMO2-HF: Total energy	-49091.549578
FMO2-MP2: Total energy	-49236.571545

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:PRO)

Summations of interaction energy for fragment #1(A:1: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.
-120.32	-106.927	34.957	-20.536	-27.815	-0.209

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.749 / q_NPA : 0.858

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	ILE	0	0.007	0.009	2.859	1.804	3.683	0.094	-0.670	-1.304	0.000
11	A	11	HIS	0	0.005	-0.017	2.597	3.980	5.294	0.320	-0.580	-1.054	-0.004
12	A	12	ARG	1	0.765	0.842	2.670	65.861	68.130	1.312	-1.060	-2.521	-0.004
13	A	13	ALA	0	0.044	0.023	1.865	-33.834	-33.965	8.168	-4.407	-3.631	-0.056
14	A	14	TRP	0	0.008	-0.012	2.661	-15.474	-10.510	3.915	-2.213	-6.665	-0.026
15	A	15	ALA	0	0.007	0.007	3.224	8.593	8.350	0.065	0.377	-0.199	0.000
18	A	18	GLU	-1	-0.744	-0.819	3.216	-57.626	-56.155	0.193	-0.695	-0.970	-0.005
47	A	47	ALA	0	-0.008	0.003	2.401	-2.217	-1.604	0.979	-0.420	-1.171	-0.002
48	A	48	ASP	-1	-0.754	-0.836	2.373	-58.134	-56.269	4.105	-2.879	-3.092	-0.037
49	A	49	PRO	0	-0.055	-0.008	2.373	-9.772	-8.545	0.804	-1.004	-1.027	-0.001
50	A	50	THR	0	0.026	-0.014	3.300	16.405	17.154	0.020	-0.216	-0.553	-0.001
51	A	51	PRO	0	0.015	-0.006	5.343	-0.966	-0.878	-0.001	-0.001	-0.085	0.000
53	A	53	ASP	-1	-0.771	-0.831	1.804	-114.291	-117.113	14.984	-6.736	-5.426	-0.073
54	A	54	LEU	0	0.034	0.014	4.617	3.408	3.558	-0.001	-0.032	-0.117	0.000
4	A	4	SER	0	0.025	0.007	5.492	2.134	2.134	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.870	-0.924	9.077	-27.866	-27.866	0.000	0.000	0.000	0.000
6	A	6	GLY	0	-0.012	-0.002	10.852	0.845	0.845	0.000	0.000	0.000	0.000
7	A	7	ASN	0	-0.021	-0.016	14.623	-0.792	-0.792	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.966	0.997	12.420	23.387	23.387	0.000	0.000	0.000	0.000
9	A	9	ASN	0	0.028	0.012	8.868	-0.029	-0.029	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.814	0.879	7.900	31.554	31.554	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.023	0.003	5.848	-0.178	-0.178	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.909	0.935	9.163	22.483	22.483	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.013	0.012	5.970	1.227	1.227	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.024	-0.013	8.121	1.928	1.928	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.832	-0.912	9.622	-21.041	-21.041	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.006	-0.004	6.242	1.362	1.362	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.922	0.968	10.555	19.620	19.620	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.817	0.888	13.100	16.455	16.455	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.856	-0.906	13.897	-15.109	-15.109	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.022	-0.025	13.236	1.077	1.077	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.869	-0.908	16.002	-14.548	-14.548	0.000	0.000	0.000	0.000
28	A	28	ASN	0	-0.002	0.005	18.308	0.176	0.176	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.765	0.879	18.366	16.059	16.059	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.041	0.023	19.734	-0.344	-0.344	0.000	0.000	0.000	0.000
31	A	31	PRO	0	0.091	0.041	18.775	-0.350	-0.350	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.037	0.025	18.750	0.649	0.649	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.085	-0.047	20.426	0.410	0.410	0.000	0.000	0.000	0.000
34	A	34	GLN	0	0.013	-0.015	19.969	-0.839	-0.839	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.042	0.018	19.318	-0.609	-0.609	0.000	0.000	0.000	0.000
36	A	36	TRP	0	0.039	0.050	15.401	-0.993	-0.993	0.000	0.000	0.000	0.000
37	A	37	ILE	0	0.010	-0.004	15.265	-1.246	-1.246	0.000	0.000	0.000	0.000
38	A	38	GLN	0	0.014	0.004	15.106	-1.837	-1.837	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.004	-0.009	13.066	-0.707	-0.707	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.016	0.002	10.301	-2.026	-2.026	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.877	0.941	10.328	16.309	16.309	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.017	0.002	11.159	-1.190	-1.190	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.046	0.018	7.485	-1.480	-1.480	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.047	-0.035	6.629	-5.283	-5.283	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.033	-0.028	6.785	-2.811	-2.811	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.039	-0.011	6.922	-0.716	-0.716	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.090	0.049	6.618	0.843	0.843	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.882	-0.934	7.272	-21.562	-21.562	0.000	0.000	0.000	0.000
56	A	56	GLN	0	-0.046	-0.033	5.642	1.167	1.167	0.000	0.000	0.000	0.000
57	A	57	LEU	0	0.005	0.000	6.242	2.666	2.666	0.000	0.000	0.000	0.000
58	A	58	CYS	0	-0.041	-0.031	8.117	3.100	3.100	0.000	0.000	0.000	0.000
59	A	59	GLN	0	-0.028	-0.016	11.339	3.145	3.145	0.000	0.000	0.000	0.000
60	A	60	TYR	0	-0.036	-0.011	9.211	1.840	1.840	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.036	-0.026	11.200	1.170	1.170	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.010	0.016	14.604	1.037	1.037	0.000	0.000	0.000	0.000
63	A	63	SER	0	-0.004	-0.012	16.544	-0.058	-0.058	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.073	0.013	19.178	-0.344	-0.344	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.012	0.029	20.400	-0.078	-0.078	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.794	-0.876	19.242	-14.163	-14.163	0.000	0.000	0.000	0.000
67	A	67	GLN	0	-0.044	-0.036	15.114	-1.078	-1.078	0.000	0.000	0.000	0.000
68	A	68	THR	0	0.005	0.001	17.713	-0.382	-0.382	0.000	0.000	0.000	0.000
69	A	69	ALA	0	-0.009	0.008	20.603	0.122	0.122	0.000	0.000	0.000	0.000
70	A	70	HIS	1	0.847	0.915	13.643	19.554	19.554	0.000	0.000	0.000	0.000
71	A	71	MET	0	0.032	0.014	13.294	-0.139	-0.139	0.000	0.000	0.000	0.000
72	A	72	THR	0	-0.032	-0.012	18.097	0.279	0.279	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.017	-0.006	20.638	0.267	0.267	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.018	-0.013	14.258	0.077	0.077	0.000	0.000	0.000	0.000
75	A	75	THR	0	-0.027	-0.022	18.858	-0.176	-0.176	0.000	0.000	0.000	0.000
76	A	76	ALA	0	-0.008	-0.002	20.201	0.339	0.339	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.004	-0.001	20.265	0.331	0.331	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.019	-0.017	15.827	0.019	0.019	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.027	0.019	20.349	0.287	0.287	0.000	0.000	0.000	0.000
80	A	80	ALA	0	-0.008	-0.005	23.593	0.468	0.468	0.000	0.000	0.000	0.000
81	A	81	ALA	0	0.006	0.005	21.547	0.360	0.360	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.899	-0.963	22.839	-13.069	-13.069	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.015	-0.007	24.453	0.410	0.410	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.041	-0.018	27.144	0.444	0.444	0.000	0.000	0.000	0.000
85	A	85	ASN	0	-0.063	-0.028	26.798	-0.048	-0.048	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.060	-0.036	24.256	-0.023	-0.023	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.031	-0.005	18.737	-0.533	-0.533	0.000	0.000	0.000	0.000
88	A	88	GLN	0	0.051	0.022	20.501	0.450	0.450	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.021	0.004	19.761	-0.835	-0.835	0.000	0.000	0.000	0.000
90	A	90	PHE	0	-0.042	-0.013	18.344	-0.604	-0.604	0.000	0.000	0.000	0.000
91	A	91	ASN	0	0.047	0.016	20.962	0.853	0.853	0.000	0.000	0.000	0.000
92	A	92	PRO	0	0.050	0.041	21.843	-0.539	-0.539	0.000	0.000	0.000	0.000
93	A	93	GLN	0	-0.040	-0.024	22.918	0.027	0.027	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.049	-0.011	20.144	0.557	0.557	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.012	0.017	19.059	-0.954	-0.954	0.000	0.000	0.000	0.000
96	A	96	THR	0	0.037	-0.008	16.958	-0.414	-0.414	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.050	0.028	14.956	-0.910	-0.910	0.000	0.000	0.000	0.000
98	A	98	THR	0	0.000	0.000	12.321	-1.424	-1.424	0.000	0.000	0.000	0.000
99	A	99	GLN	0	0.043	0.038	11.810	-1.543	-1.543	0.000	0.000	0.000	0.000
100	A	100	GLN	0	-0.018	-0.017	12.664	-1.680	-1.680	0.000	0.000	0.000	0.000
101	A	101	SER	0	0.015	-0.008	10.358	-0.645	-0.645	0.000	0.000	0.000	0.000
102	A	102	ALA	0	-0.016	-0.007	8.018	-3.786	-3.786	0.000	0.000	0.000	0.000
103	A	103	GLN	0	-0.042	-0.008	8.437	-1.826	-1.826	0.000	0.000	0.000	0.000
104	A	104	PRO	0	0.025	0.012	8.118	0.241	0.241	0.000	0.000	0.000	0.000
105	A	105	ASN	0	0.029	0.008	9.171	-1.517	-1.517	0.000	0.000	0.000	0.000
106	A	106	ALA	0	0.025	0.032	11.931	1.458	1.458	0.000	0.000	0.000	0.000
107	A	107	GLY	0	0.027	0.011	10.426	-0.625	-0.625	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.858	-0.931	11.452	-18.921	-18.921	0.000	0.000	0.000	0.000
109	A	109	LEU	0	-0.043	-0.003	14.036	0.462	0.462	0.000	0.000	0.000	0.000
110	A	110	ARG	1	0.769	0.839	6.187	36.593	36.593	0.000	0.000	0.000	0.000
111	A	111	SER	0	0.029	0.023	10.795	-0.410	-0.410	0.000	0.000	0.000	0.000
112	A	112	GLN	0	-0.035	-0.033	12.112	1.440	1.440	0.000	0.000	0.000	0.000
113	A	113	TYR	0	0.050	0.019	10.684	-0.147	-0.147	0.000	0.000	0.000	0.000
114	A	114	GLN	0	-0.015	-0.038	6.378	3.463	3.463	0.000	0.000	0.000	0.000
115	A	115	ASN	0	-0.018	-0.020	11.323	1.212	1.212	0.000	0.000	0.000	0.000
116	A	116	LEU	0	0.018	0.011	14.764	0.946	0.946	0.000	0.000	0.000	0.000
117	A	117	TRP	0	0.014	0.013	10.535	0.922	0.922	0.000	0.000	0.000	0.000
118	A	118	LEU	0	-0.027	-0.022	12.554	0.656	0.656	0.000	0.000	0.000	0.000
119	A	119	GLN	0	-0.030	-0.012	15.243	1.777	1.777	0.000	0.000	0.000	0.000
120	A	120	ALA	0	0.040	0.027	17.405	0.710	0.710	0.000	0.000	0.000	0.000
121	A	121	TRP	0	0.001	0.004	13.073	0.728	0.728	0.000	0.000	0.000	0.000
122	A	122	LYS	1	0.881	0.937	18.604	14.354	14.354	0.000	0.000	0.000	0.000
123	A	123	ASN	0	-0.052	-0.030	22.144	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	124	LEU	0	0.030	0.031	20.249	0.032	0.032	0.000	0.000	0.000	0.000
125	A	125	PRO	0	-0.004	-0.016	24.377	0.369	0.369	0.000	0.000	0.000	0.000
126	A	126	THR	0	-0.048	-0.023	27.705	0.006	0.006	0.000	0.000	0.000	0.000
127	A	127	ARG	0	0.050	0.046	30.277	-0.483	-0.483	0.000	0.000	0.000	0.000

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