FMO DATABASE

FMODB ID: M8V8Z

Calculation Name: 3DMO-B-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphate ion | (4r)-2-methylpentane-2,4-diol | zinc ion

Ligand 3-letter code: PO4 | MRD | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3DMO

Chain ID: B

ChEMBL ID:

UniProt ID: Q3JJN0

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

Total energy (hartree)

FMO2-HF: Electronic energy	-984944.283338
FMO2-HF: Nuclear repulsion	937135.371541
FMO2-HF: Total energy	-47808.911797
FMO2-MP2: Total energy	-47944.111143

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:MET)

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

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.
-54.212	-48.131	10.105	-3.843	-12.345	-0.03

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.851 / q_NPA : 0.928

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

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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	HIS	0	0.056	0.001	2.802	-6.803	-3.725	0.353	-1.561	-1.871	-0.012
4	A	4	HIS	0	0.042	0.031	5.366	1.890	2.034	-0.001	-0.007	-0.136	0.000
5	A	5	ALA	0	0.016	0.006	2.695	1.687	2.652	0.934	-0.542	-1.357	0.001
6	A	6	LEU	0	-0.011	-0.008	2.552	-1.798	-0.756	5.534	-1.760	-4.817	-0.013
7	A	7	ILE	0	0.050	0.018	3.024	5.443	4.634	0.112	1.020	-0.323	-0.001
9	A	9	ALA	0	-0.057	-0.020	2.929	2.236	2.571	0.105	-0.091	-0.349	0.000
10	A	10	ALA	0	0.025	0.013	4.972	2.469	2.513	-0.001	-0.001	-0.042	0.000
29	A	29	ALA	0	-0.022	-0.016	4.641	0.071	0.120	-0.001	-0.003	-0.045	0.000
31	A	31	VAL	0	-0.038	-0.025	3.363	-2.437	-1.424	0.299	-0.260	-1.052	-0.001
32	A	32	THR	0	-0.001	-0.032	5.977	0.272	0.261	-0.001	-0.007	0.019	0.000
36	A	36	LYS	1	0.926	0.979	4.815	19.666	19.927	-0.001	-0.018	-0.242	0.000
37	A	37	VAL	0	-0.015	-0.015	2.324	-1.056	-1.086	2.773	-0.613	-2.130	-0.004
8	A	8	GLU	-1	-0.883	-0.957	5.695	-20.749	-20.749	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.914	0.965	7.803	22.081	22.081	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.008	-0.010	7.770	1.503	1.503	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.066	-0.026	8.581	1.315	1.315	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.938	0.963	10.347	15.629	15.629	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.865	-0.934	13.264	-13.352	-13.352	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.832	0.918	10.418	19.049	19.049	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.014	0.021	15.943	0.255	0.255	0.000	0.000	0.000	0.000
18	A	18	TYR	0	-0.040	-0.008	17.749	0.446	0.446	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.020	0.000	20.923	0.156	0.156	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.011	0.006	22.817	0.092	0.092	0.000	0.000	0.000	0.000
21	A	21	TYR	0	-0.025	-0.016	26.344	0.301	0.301	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.053	-0.067	24.040	0.144	0.144	0.000	0.000	0.000	0.000
23	A	23	ASN	0	-0.061	-0.027	24.945	0.080	0.080	0.000	0.000	0.000	0.000
24	A	24	PHE	0	0.004	0.011	20.143	-0.356	-0.356	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.836	0.920	17.345	12.873	12.873	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.014	-0.014	15.194	-0.329	-0.329	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.023	0.002	11.981	0.274	0.274	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.043	-0.020	9.966	-0.099	-0.099	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.009	0.024	6.734	-1.074	-1.074	0.000	0.000	0.000	0.000
33	A	33	ASN	0	0.023	0.000	7.061	-6.093	-6.093	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.825	-0.857	8.471	-28.038	-28.038	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.029	-0.013	4.831	-1.692	-1.692	0.000	0.000	0.000	0.000
38	A	38	PHE	0	-0.004	-0.002	5.494	2.629	2.629	0.000	0.000	0.000	0.000
39	A	39	HIS	0	0.049	0.028	5.539	1.224	1.224	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.012	0.013	8.844	0.931	0.931	0.000	0.000	0.000	0.000
41	A	41	CYS	0	-0.046	-0.021	11.879	-0.480	-0.480	0.000	0.000	0.000	0.000
42	A	42	ASN	0	0.024	0.009	14.662	-0.191	-0.191	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.002	0.000	18.247	0.121	0.121	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.762	-0.862	21.004	-10.627	-10.627	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.007	-0.026	24.533	0.340	0.340	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.050	0.028	28.057	0.034	0.034	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.012	0.001	31.444	0.193	0.193	0.000	0.000	0.000	0.000
48	A	48	TYR	0	0.070	0.005	29.085	-0.232	-0.232	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.012	-0.003	28.221	-0.287	-0.287	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.050	-0.024	27.699	-0.131	-0.131	0.000	0.000	0.000	0.000
51	A	51	CYS	0	-0.064	0.026	24.150	-0.191	-0.191	0.000	0.000	0.000	0.000
52	A	52	ASN	0	-0.009	-0.006	18.679	0.149	0.149	0.000	0.000	0.000	0.000
53	A	53	CYS	0	0.026	0.024	18.423	0.190	0.190	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.026	0.036	13.215	-0.148	-0.148	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.738	-0.903	13.266	-15.953	-15.953	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.877	0.922	14.330	12.108	12.108	0.000	0.000	0.000	0.000
57	A	57	THR	0	-0.023	-0.008	14.577	0.117	0.117	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.007	0.020	10.307	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.016	0.007	12.277	-0.351	-0.351	0.000	0.000	0.000	0.000
60	A	60	PHE	0	0.004	-0.008	14.367	0.293	0.293	0.000	0.000	0.000	0.000
61	A	61	SER	0	-0.023	-0.018	13.096	0.558	0.558	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.010	-0.001	11.993	0.053	0.053	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.011	-0.011	13.909	0.282	0.282	0.000	0.000	0.000	0.000
64	A	64	ALA	0	-0.045	-0.025	17.607	0.561	0.561	0.000	0.000	0.000	0.000
65	A	65	ALA	0	-0.071	-0.033	14.823	0.392	0.392	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.015	0.018	16.903	-0.252	-0.252	0.000	0.000	0.000	0.000
67	A	67	TYR	0	-0.037	-0.034	11.782	0.417	0.417	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.828	0.901	16.174	15.670	15.670	0.000	0.000	0.000	0.000
69	A	69	PRO	0	-0.011	-0.016	16.695	-0.937	-0.937	0.000	0.000	0.000	0.000
70	A	70	GLY	0	-0.014	0.003	15.691	0.599	0.599	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.891	-0.927	13.773	-18.896	-18.896	0.000	0.000	0.000	0.000
72	A	72	PHE	0	-0.043	-0.041	10.137	-1.777	-1.777	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.029	0.037	6.471	0.837	0.837	0.000	0.000	0.000	0.000
74	A	74	ALA	0	0.020	-0.001	6.114	1.159	1.159	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.031	-0.017	7.933	-0.178	-0.178	0.000	0.000	0.000	0.000
76	A	76	ALA	0	-0.001	0.025	7.250	0.838	0.838	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.016	-0.020	9.004	0.905	0.905	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.018	-0.002	11.117	0.101	0.101	0.000	0.000	0.000	0.000
79	A	79	GLY	0	0.072	0.019	13.306	0.453	0.453	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.947	-0.969	16.756	-12.832	-12.832	0.000	0.000	0.000	0.000
81	A	81	THR	0	-0.015	-0.025	19.254	0.526	0.526	0.000	0.000	0.000	0.000
82	A	82	HIS	0	0.024	0.007	20.606	-0.319	-0.319	0.000	0.000	0.000	0.000
83	A	83	GLY	0	0.067	0.041	20.632	-0.037	-0.037	0.000	0.000	0.000	0.000
84	A	84	PRO	0	-0.038	-0.017	16.287	-0.035	-0.035	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.018	0.018	15.484	0.755	0.755	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.033	0.001	17.520	-0.594	-0.594	0.000	0.000	0.000	0.000
87	A	87	PRO	0	0.031	0.027	16.564	0.501	0.501	0.000	0.000	0.000	0.000
88	A	88	CYS	0	0.006	0.019	19.198	0.471	0.471	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.055	0.014	21.876	-0.346	-0.346	0.000	0.000	0.000	0.000
90	A	90	ALA	0	0.049	0.017	23.503	-0.160	-0.160	0.000	0.000	0.000	0.000
91	A	91	CYS	0	-0.084	-0.053	18.048	0.001	0.001	0.000	0.000	0.000	0.000
92	A	92	ARG	1	0.823	0.905	19.127	12.516	12.516	0.000	0.000	0.000	0.000
93	A	93	GLN	0	0.025	0.006	20.890	-0.270	-0.270	0.000	0.000	0.000	0.000
94	A	94	VAL	0	-0.019	-0.012	18.150	-0.148	-0.148	0.000	0.000	0.000	0.000
95	A	95	MET	0	-0.027	-0.022	15.512	-0.817	-0.817	0.000	0.000	0.000	0.000
96	A	96	ILE	0	0.022	0.021	17.610	-0.722	-0.722	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.938	-0.949	20.038	-12.377	-12.377	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.044	-0.046	17.362	-0.303	-0.303	0.000	0.000	0.000	0.000
99	A	99	GLY	0	0.017	-0.002	14.931	-0.853	-0.853	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.931	0.977	15.453	14.263	14.263	0.000	0.000	0.000	0.000
101	A	101	PRO	0	0.062	0.012	17.078	-0.721	-0.721	0.000	0.000	0.000	0.000
102	A	102	THR	0	0.002	-0.007	15.631	0.255	0.255	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.047	0.016	10.955	-1.296	-1.296	0.000	0.000	0.000	0.000
104	A	104	GLU	-1	-0.817	-0.901	8.478	-31.403	-31.403	0.000	0.000	0.000	0.000
105	A	105	VAL	0	0.000	-0.015	10.871	-0.916	-0.916	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.025	-0.022	8.286	0.641	0.641	0.000	0.000	0.000	0.000
107	A	107	LEU	0	-0.007	0.007	11.144	-0.044	-0.044	0.000	0.000	0.000	0.000
108	A	108	THR	0	0.001	-0.031	10.608	-0.266	-0.266	0.000	0.000	0.000	0.000
109	A	109	ASN	0	-0.035	-0.039	13.821	0.001	0.001	0.000	0.000	0.000	0.000
110	A	110	MET	0	-0.008	-0.022	14.347	-1.295	-1.295	0.000	0.000	0.000	0.000
111	A	111	GLN	0	-0.032	-0.002	16.513	-0.075	-0.075	0.000	0.000	0.000	0.000
112	A	112	GLY	0	-0.005	0.009	14.248	-0.083	-0.083	0.000	0.000	0.000	0.000
113	A	113	ASP	-1	-0.847	-0.899	15.262	-14.950	-14.950	0.000	0.000	0.000	0.000
114	A	114	VAL	0	-0.033	-0.024	12.035	-0.849	-0.849	0.000	0.000	0.000	0.000
115	A	115	ARG	1	0.899	0.950	14.933	15.931	15.931	0.000	0.000	0.000	0.000
116	A	116	VAL	0	0.013	0.016	11.589	-0.388	-0.388	0.000	0.000	0.000	0.000
117	A	117	THR	0	-0.036	-0.021	14.213	1.716	1.716	0.000	0.000	0.000	0.000
118	A	118	SER	0	-0.003	-0.012	14.531	-1.204	-1.204	0.000	0.000	0.000	0.000
119	A	119	ALA	0	0.011	-0.014	16.016	0.779	0.779	0.000	0.000	0.000	0.000
120	A	120	GLY	0	0.016	0.003	17.647	0.815	0.815	0.000	0.000	0.000	0.000
121	A	121	ASP	-1	-0.865	-0.897	19.103	-14.989	-14.989	0.000	0.000	0.000	0.000
122	A	122	LEU	0	-0.083	-0.040	17.626	0.612	0.612	0.000	0.000	0.000	0.000
123	A	123	LEU	0	-0.047	-0.020	21.483	0.467	0.467	0.000	0.000	0.000	0.000
124	A	124	PRO	0	0.039	0.017	24.066	-0.038	-0.038	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.968	-0.981	26.532	-10.115	-10.115	0.000	0.000	0.000	0.000
126	A	126	ALA	0	-0.053	-0.019	25.435	0.254	0.254	0.000	0.000	0.000	0.000
127	A	127	PHE	-1	-0.896	-0.921	27.106	-10.846	-10.846	0.000	0.000	0.000	0.000

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