FMO DATABASE

FMODB ID: QM1RY

Calculation Name: 3BB9-B-Xray547

Preferred Name:

Target Type:

Ligand Name: 1,2-ethanediol

Ligand 3-letter code: EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3BB9

Chain ID: B

ChEMBL ID:

UniProt ID: Q082J6

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	125
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1024065.760673
FMO2-HF: Nuclear repulsion	975703.617341
FMO2-HF: Total energy	-48362.143333
FMO2-MP2: Total energy	-48502.187495

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:23:ALA)

Summations of interaction energy for fragment #1(A:23: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.
-132.86	-126.382	9.935	-8.155	-8.257	-0.085

Interaction energy analysis for fragmet #1(A:23:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.820 / q_NPA : 0.919

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	25	ILE	0	0.016	0.008	2.596	4.350	6.016	0.760	-0.849	-1.577	-0.003
72	A	94	GLU	-1	-0.936	-0.985	1.864	-121.090	-118.924	8.933	-5.979	-5.120	-0.070
73	A	95	HIS	0	-0.005	-0.008	3.617	12.601	13.111	0.001	-0.222	-0.288	-0.001
74	A	96	GLN	0	-0.009	-0.003	2.927	-15.445	-13.309	0.241	-1.105	-1.272	-0.011
4	A	26	GLY	0	0.098	0.056	5.470	0.631	0.631	0.000	0.000	0.000	0.000
5	A	27	VAL	0	-0.014	0.010	7.543	3.099	3.099	0.000	0.000	0.000	0.000
6	A	28	ASP	-1	-0.873	-0.942	9.865	-24.324	-24.324	0.000	0.000	0.000	0.000
7	A	29	SER	0	0.012	0.001	12.382	2.541	2.541	0.000	0.000	0.000	0.000
8	A	30	ALA	0	-0.009	-0.017	14.491	0.062	0.062	0.000	0.000	0.000	0.000
9	A	31	ALA	0	0.029	0.017	14.622	0.543	0.543	0.000	0.000	0.000	0.000
10	A	32	GLY	0	0.078	0.017	13.037	-0.198	-0.198	0.000	0.000	0.000	0.000
11	A	33	ASN	0	-0.035	-0.016	13.746	-0.767	-0.767	0.000	0.000	0.000	0.000
12	A	34	VAL	0	-0.010	0.002	17.026	0.437	0.437	0.000	0.000	0.000	0.000
13	A	35	VAL	0	-0.003	0.007	12.495	0.571	0.571	0.000	0.000	0.000	0.000
14	A	36	LYS	1	0.854	0.920	12.793	22.523	22.523	0.000	0.000	0.000	0.000
15	A	37	GLN	0	-0.060	-0.029	15.653	0.666	0.666	0.000	0.000	0.000	0.000
16	A	38	PHE	0	0.003	-0.003	16.989	0.976	0.976	0.000	0.000	0.000	0.000
17	A	39	HIS	0	-0.019	-0.028	11.863	0.564	0.564	0.000	0.000	0.000	0.000
18	A	40	ALA	0	0.020	0.011	17.134	0.688	0.688	0.000	0.000	0.000	0.000
19	A	41	ALA	0	-0.034	-0.027	19.291	0.764	0.764	0.000	0.000	0.000	0.000
20	A	42	LEU	0	0.002	-0.002	19.942	0.775	0.775	0.000	0.000	0.000	0.000
21	A	43	GLN	0	0.003	-0.009	16.428	-0.372	-0.372	0.000	0.000	0.000	0.000
22	A	44	MET	0	-0.052	-0.016	21.232	0.254	0.254	0.000	0.000	0.000	0.000
23	A	45	GLY	0	0.064	0.036	24.338	0.571	0.571	0.000	0.000	0.000	0.000
24	A	46	ASN	0	-0.045	-0.022	25.249	0.696	0.696	0.000	0.000	0.000	0.000
25	A	47	GLU	-1	-0.848	-0.937	26.259	-10.567	-10.567	0.000	0.000	0.000	0.000
26	A	48	ALA	0	-0.023	-0.011	28.256	-0.097	-0.097	0.000	0.000	0.000	0.000
27	A	49	ILE	0	-0.008	-0.011	23.005	0.021	0.021	0.000	0.000	0.000	0.000
28	A	50	VAL	0	0.054	0.046	23.042	-0.445	-0.445	0.000	0.000	0.000	0.000
29	A	51	ARG	1	0.964	0.976	24.651	9.940	9.940	0.000	0.000	0.000	0.000
30	A	52	GLN	0	-0.069	-0.029	25.650	-0.084	-0.084	0.000	0.000	0.000	0.000
31	A	53	SER	0	0.019	-0.008	20.937	-0.148	-0.148	0.000	0.000	0.000	0.000
32	A	54	LEU	0	0.023	0.032	21.435	-0.498	-0.498	0.000	0.000	0.000	0.000
33	A	55	ALA	0	0.003	-0.002	23.940	0.589	0.589	0.000	0.000	0.000	0.000
34	A	56	ALA	0	0.013	-0.006	26.159	0.021	0.021	0.000	0.000	0.000	0.000
35	A	57	ASN	0	-0.016	-0.012	28.838	0.313	0.313	0.000	0.000	0.000	0.000
36	A	58	VAL	0	-0.014	0.008	22.720	-0.110	-0.110	0.000	0.000	0.000	0.000
37	A	59	GLN	0	-0.031	-0.006	24.097	0.040	0.040	0.000	0.000	0.000	0.000
38	A	60	ILE	0	0.005	-0.011	21.302	-0.644	-0.644	0.000	0.000	0.000	0.000
39	A	61	TYR	0	-0.046	-0.022	20.503	0.759	0.759	0.000	0.000	0.000	0.000
40	A	62	GLU	-1	-0.768	-0.882	20.496	-15.112	-15.112	0.000	0.000	0.000	0.000
41	A	63	GLY	0	0.008	0.012	21.587	0.707	0.707	0.000	0.000	0.000	0.000
42	A	64	GLY	0	-0.038	-0.015	23.541	0.532	0.532	0.000	0.000	0.000	0.000
43	A	65	LYS	1	0.838	0.920	24.966	13.124	13.124	0.000	0.000	0.000	0.000
44	A	66	VAL	0	-0.019	-0.025	25.212	-0.485	-0.485	0.000	0.000	0.000	0.000
45	A	67	GLU	-1	-0.825	-0.888	26.172	-10.172	-10.172	0.000	0.000	0.000	0.000
46	A	68	ARG	1	0.937	0.945	26.835	10.124	10.124	0.000	0.000	0.000	0.000
47	A	69	SER	0	0.046	0.032	29.060	0.193	0.193	0.000	0.000	0.000	0.000
48	A	70	LEU	0	-0.004	0.011	26.650	-0.094	-0.094	0.000	0.000	0.000	0.000
49	A	71	THR	0	0.005	-0.005	28.761	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	72	GLU	-1	-0.929	-0.959	31.005	-9.253	-9.253	0.000	0.000	0.000	0.000
51	A	73	TYR	0	-0.025	-0.052	23.710	0.029	0.029	0.000	0.000	0.000	0.000
52	A	74	ALA	0	0.007	-0.006	28.599	-0.048	-0.048	0.000	0.000	0.000	0.000
53	A	75	ASN	0	-0.038	-0.021	30.378	0.181	0.181	0.000	0.000	0.000	0.000
54	A	76	HIS	1	0.749	0.878	30.792	10.079	10.079	0.000	0.000	0.000	0.000
55	A	77	HIS	0	-0.004	-0.009	26.754	0.153	0.153	0.000	0.000	0.000	0.000
56	A	78	MET	0	0.004	0.028	26.004	-0.254	-0.254	0.000	0.000	0.000	0.000
57	A	79	LEU	0	0.054	0.009	26.692	-0.274	-0.274	0.000	0.000	0.000	0.000
58	A	80	ALA	0	-0.030	-0.009	28.584	0.039	0.039	0.000	0.000	0.000	0.000
59	A	81	ASP	-1	-0.764	-0.871	22.984	-13.310	-13.310	0.000	0.000	0.000	0.000
60	A	82	MET	0	-0.075	-0.013	23.700	-0.208	-0.208	0.000	0.000	0.000	0.000
61	A	83	ALA	0	-0.018	-0.014	25.160	-0.143	-0.143	0.000	0.000	0.000	0.000
62	A	84	TYR	0	-0.030	-0.015	19.941	-0.088	-0.088	0.000	0.000	0.000	0.000
63	A	85	LEU	0	0.019	-0.006	18.728	-0.373	-0.373	0.000	0.000	0.000	0.000
64	A	86	LYS	0	-0.019	-0.008	21.936	-0.234	-0.234	0.000	0.000	0.000	0.000
65	A	87	GLY	0	-0.024	0.012	24.420	0.259	0.259	0.000	0.000	0.000	0.000
66	A	88	LEU	0	-0.053	-0.029	19.191	-0.147	-0.147	0.000	0.000	0.000	0.000
67	A	89	THR	0	-0.042	-0.029	17.960	-0.349	-0.349	0.000	0.000	0.000	0.000
68	A	90	ILE	0	0.026	0.012	13.361	-0.697	-0.697	0.000	0.000	0.000	0.000
69	A	91	THR	0	-0.033	-0.018	10.876	0.015	0.015	0.000	0.000	0.000	0.000
70	A	92	PRO	0	0.012	0.003	8.444	-1.539	-1.539	0.000	0.000	0.000	0.000
71	A	93	LYS	1	0.874	0.939	6.151	29.348	29.348	0.000	0.000	0.000	0.000
75	A	97	ILE	0	-0.007	0.012	5.847	4.987	4.987	0.000	0.000	0.000	0.000
76	A	98	THR	0	-0.010	0.002	8.993	-0.309	-0.309	0.000	0.000	0.000	0.000
77	A	99	ILE	0	-0.034	-0.019	10.980	1.253	1.253	0.000	0.000	0.000	0.000
78	A	100	THR	0	-0.011	-0.007	14.553	0.132	0.132	0.000	0.000	0.000	0.000
79	A	101	GLY	0	0.022	0.008	17.433	0.732	0.732	0.000	0.000	0.000	0.000
80	A	102	ASP	-1	-0.825	-0.907	20.303	-13.037	-13.037	0.000	0.000	0.000	0.000
81	A	103	ILE	0	-0.013	0.002	17.909	0.126	0.126	0.000	0.000	0.000	0.000
82	A	104	ALA	0	-0.015	-0.014	14.572	-0.444	-0.444	0.000	0.000	0.000	0.000
83	A	105	ILE	0	0.002	0.013	12.044	0.624	0.624	0.000	0.000	0.000	0.000
84	A	106	SER	0	0.050	0.026	10.548	-2.580	-2.580	0.000	0.000	0.000	0.000
85	A	107	THR	0	-0.010	-0.006	6.956	2.498	2.498	0.000	0.000	0.000	0.000
86	A	108	SER	0	-0.038	-0.029	6.938	-6.187	-6.187	0.000	0.000	0.000	0.000
87	A	109	ILE	0	0.038	0.021	6.120	3.087	3.087	0.000	0.000	0.000	0.000
88	A	110	SER	0	0.028	0.012	7.437	-3.913	-3.913	0.000	0.000	0.000	0.000
89	A	111	HIS	0	-0.073	-0.037	10.164	0.152	0.152	0.000	0.000	0.000	0.000
90	A	112	ALA	0	0.012	0.019	12.413	0.382	0.382	0.000	0.000	0.000	0.000
91	A	113	GLN	0	0.014	0.003	15.938	0.843	0.843	0.000	0.000	0.000	0.000
92	A	114	GLY	0	0.037	0.016	18.534	0.120	0.120	0.000	0.000	0.000	0.000
93	A	115	GLU	-1	-0.826	-0.909	22.210	-10.828	-10.828	0.000	0.000	0.000	0.000
94	A	116	TYR	0	0.051	0.040	25.142	0.036	0.036	0.000	0.000	0.000	0.000
95	A	117	LYS	1	0.902	0.952	26.909	9.943	9.943	0.000	0.000	0.000	0.000
96	A	118	GLY	0	0.013	-0.005	30.246	0.323	0.323	0.000	0.000	0.000	0.000
97	A	119	LYS	1	0.778	0.893	27.195	10.911	10.911	0.000	0.000	0.000	0.000
98	A	120	SER	0	0.033	0.014	24.594	-0.119	-0.119	0.000	0.000	0.000	0.000
99	A	121	ILE	0	-0.052	-0.020	19.503	0.085	0.085	0.000	0.000	0.000	0.000
100	A	122	ASP	-1	-0.841	-0.910	17.671	-17.408	-17.408	0.000	0.000	0.000	0.000
101	A	123	SER	0	-0.017	-0.006	16.561	0.227	0.227	0.000	0.000	0.000	0.000
102	A	124	MET	0	-0.035	-0.021	8.264	-0.650	-0.650	0.000	0.000	0.000	0.000
103	A	125	THR	0	0.002	0.012	12.800	0.767	0.767	0.000	0.000	0.000	0.000
104	A	126	MET	0	-0.016	-0.033	9.682	-2.663	-2.663	0.000	0.000	0.000	0.000
105	A	127	GLU	-1	-0.741	-0.849	10.879	-21.507	-21.507	0.000	0.000	0.000	0.000
106	A	128	THR	0	-0.069	-0.032	10.970	-2.757	-2.757	0.000	0.000	0.000	0.000
107	A	129	LEU	0	-0.010	-0.002	13.240	1.904	1.904	0.000	0.000	0.000	0.000
108	A	130	VAL	0	0.003	0.008	14.631	-1.054	-1.054	0.000	0.000	0.000	0.000
109	A	131	LEU	0	-0.008	-0.010	15.216	1.045	1.045	0.000	0.000	0.000	0.000
110	A	132	ILE	0	0.017	-0.003	18.623	-0.137	-0.137	0.000	0.000	0.000	0.000
111	A	133	LYS	1	0.816	0.919	21.539	13.847	13.847	0.000	0.000	0.000	0.000
112	A	134	GLN	0	-0.038	-0.030	23.148	0.833	0.833	0.000	0.000	0.000	0.000
113	A	135	ALA	0	0.022	-0.001	26.649	-0.036	-0.036	0.000	0.000	0.000	0.000
114	A	136	ASP	-1	-0.886	-0.938	28.168	-11.047	-11.047	0.000	0.000	0.000	0.000
115	A	137	GLY	0	-0.008	-0.001	25.787	0.009	0.009	0.000	0.000	0.000	0.000
116	A	138	ARG	1	0.874	0.943	24.012	11.428	11.428	0.000	0.000	0.000	0.000
117	A	139	TRP	0	0.007	-0.003	18.930	-0.068	-0.068	0.000	0.000	0.000	0.000
118	A	140	LYS	1	0.892	0.947	21.497	12.120	12.120	0.000	0.000	0.000	0.000
119	A	141	ILE	0	0.018	0.025	17.814	-0.139	-0.139	0.000	0.000	0.000	0.000
120	A	142	THR	0	-0.056	-0.044	20.461	0.896	0.896	0.000	0.000	0.000	0.000
121	A	143	HIS	0	-0.006	-0.004	19.054	0.120	0.120	0.000	0.000	0.000	0.000
122	A	144	VAL	0	0.039	0.026	17.525	-0.898	-0.898	0.000	0.000	0.000	0.000
123	A	145	HIS	0	-0.032	-0.017	16.377	1.173	1.173	0.000	0.000	0.000	0.000
124	A	146	TRP	0	0.015	-0.003	15.304	-0.908	-0.908	0.000	0.000	0.000	0.000
125	A	147	SER	-1	-0.860	-0.923	15.156	-18.976	-18.976	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:23:ALA)