FMO DATABASE

FMODB ID: 9LZ22

Calculation Name: 1OO0-B-Xray547

Preferred Name:

Target Type:

Ligand Name: (4s)-2-methyl-2,4-pentanediol | beta-mercaptoethanol | strontium ion

Ligand 3-letter code: MPD | BME | SR

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1OO0

Chain ID: B

ChEMBL ID:

UniProt ID: P49028

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	92
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-650876.976034
FMO2-HF: Nuclear repulsion	614146.786466
FMO2-HF: Total energy	-36730.189568
FMO2-MP2: Total energy	-36837.226391

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:64:PRO)

Summations of interaction energy for fragment #1(A:64: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.
-134.725	-123.531	7.541	-7.184	-11.548	-0.082

Interaction energy analysis for fragmet #1(A:64:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.835 / q_NPA : 0.910

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	66	PRO	0	0.040	0.031	3.589	-4.637	-3.166	0.000	-0.760	-0.711	-0.001
88	A	151	VAL	0	0.010	-0.001	2.291	-3.231	-2.128	1.316	-0.565	-1.853	-0.004
89	A	152	LYS	1	0.877	0.939	3.166	32.786	33.987	0.070	-0.469	-0.802	-0.004
90	A	153	GLY	0	-0.005	0.005	2.893	5.916	6.983	0.295	-0.333	-1.028	-0.003
91	A	154	PRO	0	-0.030	-0.014	2.526	-11.068	-9.796	2.028	-1.235	-2.064	-0.019
92	A	155	LYS	0	0.090	0.049	2.305	-68.022	-62.942	3.832	-3.822	-5.090	-0.051
4	A	67	GLN	0	-0.055	-0.060	6.323	0.442	0.442	0.000	0.000	0.000	0.000
5	A	68	ARG	1	0.856	0.960	7.644	18.655	18.655	0.000	0.000	0.000	0.000
6	A	69	SER	0	0.051	0.026	11.468	-1.109	-1.109	0.000	0.000	0.000	0.000
7	A	70	VAL	0	-0.004	-0.013	14.072	0.432	0.432	0.000	0.000	0.000	0.000
8	A	71	GLU	-1	-0.899	-0.958	17.083	-12.882	-12.882	0.000	0.000	0.000	0.000
9	A	72	GLY	0	0.035	0.034	17.075	0.838	0.838	0.000	0.000	0.000	0.000
10	A	73	TRP	0	-0.095	-0.054	10.025	-1.978	-1.978	0.000	0.000	0.000	0.000
11	A	74	ILE	0	0.019	0.022	13.491	0.538	0.538	0.000	0.000	0.000	0.000
12	A	75	LEU	0	-0.009	0.004	12.544	-2.655	-2.655	0.000	0.000	0.000	0.000
13	A	76	PHE	0	-0.027	-0.029	12.078	1.173	1.173	0.000	0.000	0.000	0.000
14	A	77	VAL	0	0.043	0.031	13.845	-0.781	-0.781	0.000	0.000	0.000	0.000
15	A	78	THR	0	-0.018	-0.024	15.055	0.382	0.382	0.000	0.000	0.000	0.000
16	A	79	SER	0	-0.022	-0.011	17.554	0.296	0.296	0.000	0.000	0.000	0.000
17	A	80	ILE	0	-0.010	0.000	20.252	0.356	0.356	0.000	0.000	0.000	0.000
18	A	81	HIS	0	0.059	0.037	22.920	-0.142	-0.142	0.000	0.000	0.000	0.000
19	A	82	GLU	-1	-0.914	-0.968	26.636	-10.589	-10.589	0.000	0.000	0.000	0.000
20	A	83	GLU	-1	-0.954	-0.989	28.217	-9.157	-9.157	0.000	0.000	0.000	0.000
21	A	84	ALA	0	-0.021	0.004	26.877	0.205	0.205	0.000	0.000	0.000	0.000
22	A	85	GLN	0	-0.023	-0.012	28.479	-0.099	-0.099	0.000	0.000	0.000	0.000
23	A	86	GLU	-1	-0.904	-0.980	26.540	-11.903	-11.903	0.000	0.000	0.000	0.000
24	A	87	ASP	-1	-0.900	-0.927	27.830	-9.989	-9.989	0.000	0.000	0.000	0.000
25	A	88	GLU	-1	-0.835	-0.929	27.496	-10.524	-10.524	0.000	0.000	0.000	0.000
26	A	89	ILE	0	-0.076	-0.035	22.560	-0.528	-0.528	0.000	0.000	0.000	0.000
27	A	90	GLN	0	0.055	0.008	25.086	-0.371	-0.371	0.000	0.000	0.000	0.000
28	A	91	GLU	-1	-0.895	-0.955	27.304	-10.237	-10.237	0.000	0.000	0.000	0.000
29	A	92	LYS	1	0.857	0.946	24.050	11.643	11.643	0.000	0.000	0.000	0.000
30	A	93	PHE	0	0.017	-0.007	18.259	-0.641	-0.641	0.000	0.000	0.000	0.000
31	A	94	CYS	0	-0.011	0.007	23.584	-0.282	-0.282	0.000	0.000	0.000	0.000
32	A	95	ASP	-1	-0.900	-0.942	26.101	-11.144	-11.144	0.000	0.000	0.000	0.000
33	A	96	TYR	0	-0.076	-0.033	21.585	-0.141	-0.141	0.000	0.000	0.000	0.000
34	A	97	GLY	0	-0.075	-0.060	22.916	-0.503	-0.503	0.000	0.000	0.000	0.000
35	A	98	GLU	-1	-0.928	-0.956	24.503	-11.166	-11.166	0.000	0.000	0.000	0.000
36	A	99	ILE	0	-0.029	-0.019	21.974	-0.687	-0.687	0.000	0.000	0.000	0.000
37	A	100	LYS	1	0.841	0.924	21.294	13.983	13.983	0.000	0.000	0.000	0.000
38	A	101	ASN	0	-0.021	-0.027	21.141	0.860	0.860	0.000	0.000	0.000	0.000
39	A	102	ILE	0	0.047	0.034	21.525	-0.824	-0.824	0.000	0.000	0.000	0.000
40	A	103	HIS	0	-0.106	-0.051	20.312	0.252	0.252	0.000	0.000	0.000	0.000
41	A	104	LEU	0	0.052	0.038	21.117	-0.868	-0.868	0.000	0.000	0.000	0.000
42	A	105	ASN	0	-0.041	-0.024	20.745	0.894	0.894	0.000	0.000	0.000	0.000
43	A	106	LEU	0	0.062	0.038	23.978	-0.078	-0.078	0.000	0.000	0.000	0.000
44	A	107	ASP	-1	-0.797	-0.888	26.730	-11.403	-11.403	0.000	0.000	0.000	0.000
45	A	108	ARG	1	0.902	0.939	26.899	11.147	11.147	0.000	0.000	0.000	0.000
46	A	109	ARG	1	0.895	0.955	29.526	10.146	10.146	0.000	0.000	0.000	0.000
47	A	110	THR	0	-0.060	-0.057	30.615	0.285	0.285	0.000	0.000	0.000	0.000
48	A	111	GLY	0	-0.004	0.011	31.507	0.241	0.241	0.000	0.000	0.000	0.000
49	A	112	PHE	0	0.039	0.035	29.830	0.045	0.045	0.000	0.000	0.000	0.000
50	A	113	SER	0	0.033	0.004	25.646	-0.321	-0.321	0.000	0.000	0.000	0.000
51	A	114	LYS	1	0.787	0.876	22.492	12.613	12.613	0.000	0.000	0.000	0.000
52	A	115	GLY	0	0.043	0.023	22.550	-0.447	-0.447	0.000	0.000	0.000	0.000
53	A	116	TYR	0	-0.075	-0.034	17.703	-0.605	-0.605	0.000	0.000	0.000	0.000
54	A	117	ALA	0	0.042	0.016	18.459	0.839	0.839	0.000	0.000	0.000	0.000
55	A	118	LEU	0	-0.050	-0.013	15.376	-1.278	-1.278	0.000	0.000	0.000	0.000
56	A	119	VAL	0	0.047	0.026	17.091	1.027	1.027	0.000	0.000	0.000	0.000
57	A	120	GLU	-1	-0.918	-0.948	17.244	-17.487	-17.487	0.000	0.000	0.000	0.000
58	A	121	TYR	0	0.031	0.001	17.883	0.395	0.395	0.000	0.000	0.000	0.000
59	A	122	GLU	-1	-0.851	-0.930	18.581	-13.453	-13.453	0.000	0.000	0.000	0.000
60	A	123	THR	0	-0.083	-0.073	18.232	-0.646	-0.646	0.000	0.000	0.000	0.000
61	A	124	HIS	0	-0.020	-0.025	10.964	0.008	0.008	0.000	0.000	0.000	0.000
62	A	125	LYS	1	0.942	0.962	15.699	14.303	14.303	0.000	0.000	0.000	0.000
63	A	126	GLN	0	0.117	0.088	18.647	-0.558	-0.558	0.000	0.000	0.000	0.000
64	A	127	ALA	0	0.038	0.027	14.994	-0.032	-0.032	0.000	0.000	0.000	0.000
65	A	128	LEU	0	-0.048	-0.021	12.632	-0.660	-0.660	0.000	0.000	0.000	0.000
66	A	129	ALA	0	0.017	0.005	15.391	0.028	0.028	0.000	0.000	0.000	0.000
67	A	130	ALA	0	0.062	0.034	18.060	0.311	0.311	0.000	0.000	0.000	0.000
68	A	131	LYS	1	0.783	0.885	9.647	27.001	27.001	0.000	0.000	0.000	0.000
69	A	132	GLU	-1	-0.979	-1.009	14.799	-19.915	-19.915	0.000	0.000	0.000	0.000
70	A	133	ALA	0	-0.025	0.005	16.890	0.512	0.512	0.000	0.000	0.000	0.000
71	A	134	LEU	0	-0.017	-0.004	18.837	0.663	0.663	0.000	0.000	0.000	0.000
72	A	135	ASN	0	-0.026	0.002	14.717	-0.548	-0.548	0.000	0.000	0.000	0.000
73	A	136	GLY	0	-0.008	-0.005	17.192	0.106	0.106	0.000	0.000	0.000	0.000
74	A	137	ALA	0	-0.026	0.007	19.891	0.850	0.850	0.000	0.000	0.000	0.000
75	A	138	GLU	-1	-0.899	-0.957	22.484	-12.007	-12.007	0.000	0.000	0.000	0.000
76	A	139	ILE	0	-0.023	-0.021	23.752	0.274	0.274	0.000	0.000	0.000	0.000
77	A	140	MET	0	-0.017	-0.002	26.777	-0.165	-0.165	0.000	0.000	0.000	0.000
78	A	141	GLY	0	0.004	0.012	29.366	0.201	0.201	0.000	0.000	0.000	0.000
79	A	142	GLN	0	-0.030	-0.014	23.159	0.449	0.449	0.000	0.000	0.000	0.000
80	A	143	THR	0	-0.024	-0.017	21.056	-0.124	-0.124	0.000	0.000	0.000	0.000
81	A	144	ILE	0	-0.007	0.013	19.567	-0.300	-0.300	0.000	0.000	0.000	0.000
82	A	145	GLN	0	-0.010	-0.003	14.354	0.580	0.580	0.000	0.000	0.000	0.000
83	A	146	VAL	0	-0.004	-0.006	14.572	0.131	0.131	0.000	0.000	0.000	0.000
84	A	147	ASP	-1	-0.840	-0.923	9.168	-29.669	-29.669	0.000	0.000	0.000	0.000
85	A	148	TRP	0	0.011	-0.010	7.595	1.612	1.612	0.000	0.000	0.000	0.000
86	A	149	CYS	0	-0.029	-0.006	8.818	-1.427	-1.427	0.000	0.000	0.000	0.000
87	A	150	PHE	0	0.014	0.012	7.507	-0.862	-0.862	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:64:PRO)