FMO DATABASE

FMODB ID: LZQJ9

Calculation Name: 5C8J-J-Xray372

Preferred Name:

Target Type:

Ligand Name: dodecyl-beta-d-maltoside

ligand 3-letter code: LMT

PDB ID: 5C8J

Chain ID: J

ChEMBL ID:

UniProt ID: Q57904

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1052207.986959
FMO2-HF: Nuclear repulsion	999959.64404
FMO2-HF: Total energy	-52248.342919
FMO2-MP2: Total energy	-52404.85557

3D Structure

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(J:5:ILE)

Summations of interaction energy for fragment #1(J:5:ILE)

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.
-7.556	-3.815	1.471	-1.866	-3.345	0.008

Interaction energy analysis for fragmet #1(J:5:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.005

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	J	7	ASP	-1	-0.809	-0.880	3.206	0.247	2.629	0.016	-0.984	-1.414	0.003
4	J	8	ILE	0	-0.016	-0.004	2.520	-3.693	-2.568	1.456	-0.839	-1.741	0.005
5	J	9	TYR	0	-0.012	-0.018	4.393	-1.462	-1.228	-0.001	-0.043	-0.190	0.000
6	J	10	TYR	0	-0.003	0.002	6.197	-0.366	-0.366	0.000	0.000	0.000	0.000
7	J	11	LYS	1	0.938	0.948	7.527	-2.073	-2.073	0.000	0.000	0.000	0.000
8	J	12	THR	0	-0.047	-0.030	8.256	-0.221	-0.221	0.000	0.000	0.000	0.000
9	J	13	LEU	0	-0.004	0.002	10.445	-0.147	-0.147	0.000	0.000	0.000	0.000
10	J	14	ASP	-1	-0.818	-0.906	12.150	0.372	0.372	0.000	0.000	0.000	0.000
11	J	15	ALA	0	-0.042	-0.018	14.027	-0.075	-0.075	0.000	0.000	0.000	0.000
12	J	16	ILE	0	-0.016	-0.001	14.562	-0.053	-0.053	0.000	0.000	0.000	0.000
13	J	17	PHE	0	0.016	-0.002	16.034	-0.052	-0.052	0.000	0.000	0.000	0.000
14	J	18	MET	0	0.038	0.015	17.641	-0.043	-0.043	0.000	0.000	0.000	0.000
15	J	19	PRO	0	-0.054	-0.027	19.836	-0.029	-0.029	0.000	0.000	0.000	0.000
16	J	20	ILE	0	-0.018	-0.009	20.806	-0.018	-0.018	0.000	0.000	0.000	0.000
17	J	21	ILE	0	-0.026	-0.002	17.768	-0.018	-0.018	0.000	0.000	0.000	0.000
18	J	22	LYS	1	0.934	0.971	22.340	-0.188	-0.188	0.000	0.000	0.000	0.000
19	J	23	VAL	0	-0.018	-0.001	24.864	-0.011	-0.011	0.000	0.000	0.000	0.000
20	J	24	LEU	0	-0.020	0.008	24.852	-0.011	-0.011	0.000	0.000	0.000	0.000
21	J	25	HIS	0	0.068	0.032	26.102	0.003	0.003	0.000	0.000	0.000	0.000
22	J	26	PRO	0	0.078	0.025	23.251	-0.001	-0.001	0.000	0.000	0.000	0.000
23	J	27	ALA	0	-0.019	-0.002	24.260	-0.006	-0.006	0.000	0.000	0.000	0.000
24	J	28	LEU	0	-0.008	-0.018	26.522	-0.004	-0.004	0.000	0.000	0.000	0.000
25	J	29	ALA	0	0.014	0.011	22.373	0.000	0.000	0.000	0.000	0.000	0.000
26	J	30	ILE	0	-0.005	-0.002	19.810	0.000	0.000	0.000	0.000	0.000	0.000
27	J	31	LEU	0	0.002	0.005	22.630	-0.006	-0.006	0.000	0.000	0.000	0.000
28	J	32	ILE	0	0.019	0.005	23.451	-0.004	-0.004	0.000	0.000	0.000	0.000
29	J	33	ILE	0	0.011	0.002	18.088	-0.002	-0.002	0.000	0.000	0.000	0.000
30	J	34	ALA	0	-0.021	-0.004	20.912	-0.009	-0.009	0.000	0.000	0.000	0.000
31	J	35	ILE	0	0.024	-0.002	22.626	-0.007	-0.007	0.000	0.000	0.000	0.000
32	J	36	ILE	0	0.005	0.008	21.574	-0.003	-0.003	0.000	0.000	0.000	0.000
33	J	37	VAL	0	0.021	0.002	18.226	-0.005	-0.005	0.000	0.000	0.000	0.000
34	J	38	SER	0	-0.044	-0.013	21.487	-0.010	-0.010	0.000	0.000	0.000	0.000
35	J	39	LEU	0	-0.017	-0.015	24.436	-0.005	-0.005	0.000	0.000	0.000	0.000
36	J	40	ILE	0	-0.011	-0.006	20.270	0.000	0.000	0.000	0.000	0.000	0.000
37	J	41	ILE	0	-0.018	-0.003	19.589	-0.007	-0.007	0.000	0.000	0.000	0.000
38	J	42	ASN	0	-0.037	-0.012	23.413	-0.009	-0.009	0.000	0.000	0.000	0.000
39	J	43	ILE	0	-0.029	-0.006	26.907	0.000	0.000	0.000	0.000	0.000	0.000
40	J	44	ALA	0	-0.021	0.001	23.402	0.000	0.000	0.000	0.000	0.000	0.000
41	J	45	THR	0	-0.072	-0.031	21.268	-0.005	-0.005	0.000	0.000	0.000	0.000
42	J	102	PRO	0	0.074	0.013	21.129	-0.004	-0.004	0.000	0.000	0.000	0.000
43	J	103	MET	0	0.039	0.015	20.509	-0.004	-0.004	0.000	0.000	0.000	0.000
44	J	104	ILE	0	0.017	0.019	16.496	-0.005	-0.005	0.000	0.000	0.000	0.000
45	J	105	TYR	0	0.016	0.009	14.777	-0.025	-0.025	0.000	0.000	0.000	0.000
46	J	106	THR	0	0.030	0.002	15.961	0.002	0.002	0.000	0.000	0.000	0.000
47	J	107	TRP	0	-0.012	-0.018	15.817	0.009	0.009	0.000	0.000	0.000	0.000
48	J	108	VAL	0	0.009	0.023	10.481	-0.019	-0.019	0.000	0.000	0.000	0.000
49	J	109	PRO	0	0.038	0.007	11.936	-0.019	-0.019	0.000	0.000	0.000	0.000
50	J	110	ILE	0	0.044	0.020	13.681	0.009	0.009	0.000	0.000	0.000	0.000
51	J	111	ILE	0	-0.016	-0.008	10.362	0.002	0.002	0.000	0.000	0.000	0.000
52	J	112	LEU	0	-0.004	0.000	8.735	-0.040	-0.040	0.000	0.000	0.000	0.000
53	J	113	ILE	0	0.021	0.028	9.960	0.038	0.038	0.000	0.000	0.000	0.000
54	J	114	PHE	0	-0.011	-0.005	12.860	0.020	0.020	0.000	0.000	0.000	0.000
55	J	115	ILE	0	-0.027	-0.003	5.866	0.017	0.017	0.000	0.000	0.000	0.000
56	J	116	TYR	0	-0.020	-0.035	9.981	-0.005	-0.005	0.000	0.000	0.000	0.000
57	J	117	LEU	0	0.044	0.005	11.044	0.039	0.039	0.000	0.000	0.000	0.000
58	J	118	ARG	1	0.942	0.978	11.827	0.170	0.170	0.000	0.000	0.000	0.000
59	J	119	HIS	1	0.862	0.946	10.383	-0.246	-0.246	0.000	0.000	0.000	0.000
60	J	120	VAL	0	-0.007	0.006	12.492	0.038	0.038	0.000	0.000	0.000	0.000
61	J	121	TYR	0	0.023	-0.002	15.744	0.007	0.007	0.000	0.000	0.000	0.000
62	J	122	GLY	0	-0.017	0.004	16.401	-0.012	-0.012	0.000	0.000	0.000	0.000
63	J	123	PHE	0	0.001	-0.005	17.376	0.018	0.018	0.000	0.000	0.000	0.000
64	J	124	GLY	0	-0.012	0.000	17.015	-0.013	-0.013	0.000	0.000	0.000	0.000
65	J	125	GLY	0	-0.029	-0.004	15.611	0.021	0.021	0.000	0.000	0.000	0.000
66	J	126	VAL	0	0.023	0.008	15.769	0.006	0.006	0.000	0.000	0.000	0.000
67	J	127	TYR	0	-0.014	-0.004	17.564	-0.003	-0.003	0.000	0.000	0.000	0.000
68	J	128	GLN	0	0.001	-0.007	20.387	-0.005	-0.005	0.000	0.000	0.000	0.000
69	J	129	GLU	-1	-0.977	-0.974	17.262	0.216	0.216	0.000	0.000	0.000	0.000
70	J	130	LEU	0	-0.048	-0.033	20.286	0.006	0.006	0.000	0.000	0.000	0.000
71	J	131	ASN	0	-0.061	-0.022	23.062	0.001	0.001	0.000	0.000	0.000	0.000
72	J	132	PRO	0	0.035	0.011	25.710	-0.010	-0.010	0.000	0.000	0.000	0.000
73	J	133	GLY	0	-0.027	-0.002	27.140	-0.003	-0.003	0.000	0.000	0.000	0.000
74	J	134	TRP	0	-0.008	-0.019	21.423	0.002	0.002	0.000	0.000	0.000	0.000
75	J	135	ASN	0	0.009	-0.004	26.095	0.001	0.001	0.000	0.000	0.000	0.000
76	J	136	GLY	0	0.069	0.023	24.521	-0.007	-0.007	0.000	0.000	0.000	0.000
77	J	137	VAL	0	-0.071	-0.032	25.485	0.004	0.004	0.000	0.000	0.000	0.000
78	J	138	VAL	0	0.066	0.046	22.495	0.005	0.005	0.000	0.000	0.000	0.000
79	J	139	VAL	0	-0.026	-0.028	25.896	0.006	0.006	0.000	0.000	0.000	0.000
80	J	140	TYR	0	0.022	0.024	29.260	-0.005	-0.005	0.000	0.000	0.000	0.000
81	J	141	LEU	0	0.031	0.004	30.802	0.002	0.002	0.000	0.000	0.000	0.000
82	J	142	PRO	0	0.025	0.028	34.283	-0.002	-0.002	0.000	0.000	0.000	0.000
83	J	143	ILE	0	0.033	0.021	38.032	-0.001	-0.001	0.000	0.000	0.000	0.000
84	J	144	ILE	0	0.064	-0.006	33.573	-0.002	-0.002	0.000	0.000	0.000	0.000
85	J	145	LEU	0	0.024	0.007	31.250	-0.003	-0.003	0.000	0.000	0.000	0.000
86	J	146	SER	0	-0.044	-0.019	35.190	-0.002	-0.002	0.000	0.000	0.000	0.000
87	J	147	LYS	1	0.904	0.949	38.452	0.008	0.008	0.000	0.000	0.000	0.000
88	J	148	ILE	0	-0.025	0.019	33.176	-0.001	-0.001	0.000	0.000	0.000	0.000
89	J	149	LEU	0	0.009	0.012	36.513	-0.001	-0.001	0.000	0.000	0.000	0.000
90	J	150	PHE	0	0.017	0.000	31.282	-0.002	-0.002	0.000	0.000	0.000	0.000
91	J	151	ILE	0	0.000	-0.002	33.979	-0.003	-0.003	0.000	0.000	0.000	0.000
92	J	152	ASP	-1	-0.790	-0.912	35.333	-0.030	-0.030	0.000	0.000	0.000	0.000
93	J	153	PHE	0	-0.023	-0.006	26.355	-0.002	-0.002	0.000	0.000	0.000	0.000
94	J	154	TRP	0	0.023	0.010	29.202	-0.005	-0.005	0.000	0.000	0.000	0.000
95	J	155	HIS	0	0.056	0.021	31.412	-0.003	-0.003	0.000	0.000	0.000	0.000
96	J	156	TRP	0	0.006	0.018	24.555	-0.004	-0.004	0.000	0.000	0.000	0.000
97	J	157	LEU	0	-0.012	-0.012	25.471	-0.004	-0.004	0.000	0.000	0.000	0.000
98	J	158	GLY	0	-0.014	-0.018	27.547	-0.007	-0.007	0.000	0.000	0.000	0.000
99	J	159	SER	0	-0.006	0.001	30.064	-0.001	-0.001	0.000	0.000	0.000	0.000
100	J	160	ILE	0	-0.026	-0.004	23.988	-0.001	-0.001	0.000	0.000	0.000	0.000
101	J	161	PHE	0	-0.063	-0.030	21.768	-0.009	-0.009	0.000	0.000	0.000	0.000
102	J	162	TYR	0	-0.035	-0.011	27.048	-0.003	-0.003	0.000	0.000	0.000	0.000
103	J	163	LYS	1	0.885	0.952	24.321	0.089	0.089	0.000	0.000	0.000	0.000
104	J	164	GLY	0	-0.006	-0.009	30.833	0.005	0.005	0.000	0.000	0.000	0.000
105	J	165	GLY	0	0.004	-0.003	33.175	-0.003	-0.003	0.000	0.000	0.000	0.000
106	J	166	PHE	0	-0.046	-0.034	35.655	0.000	0.000	0.000	0.000	0.000	0.000
107	J	167	LYS	1	0.975	0.987	37.309	0.037	0.037	0.000	0.000	0.000	0.000
108	J	168	ILE	0	0.018	0.016	35.904	0.000	0.000	0.000	0.000	0.000	0.000
109	J	169	VAL	0	0.011	0.015	39.093	0.000	0.000	0.000	0.000	0.000	0.000
110	J	170	SER	0	-0.002	0.001	41.830	0.000	0.000	0.000	0.000	0.000	0.000
111	J	171	ASN	0	-0.004	-0.004	39.964	-0.002	-0.002	0.000	0.000	0.000	0.000
112	J	172	THR	0	-0.044	-0.025	41.674	0.001	0.001	0.000	0.000	0.000	0.000
113	J	173	ALA	0	0.040	0.029	42.352	-0.001	-0.001	0.000	0.000	0.000	0.000
114	J	174	LEU	0	-0.005	-0.012	36.666	-0.001	-0.001	0.000	0.000	0.000	0.000
115	J	175	GLY	0	0.025	0.021	36.806	0.000	0.000	0.000	0.000	0.000	0.000
116	J	176	TRP	0	0.098	0.027	31.651	0.003	0.003	0.000	0.000	0.000	0.000
117	J	177	LEU	0	-0.001	0.013	28.700	0.001	0.001	0.000	0.000	0.000	0.000
118	J	178	GLY	0	0.078	0.032	33.322	0.000	0.000	0.000	0.000	0.000	0.000
119	J	179	TRP	0	0.064	0.035	34.460	0.002	0.002	0.000	0.000	0.000	0.000
120	J	180	TYR	0	0.018	0.004	32.018	0.000	0.000	0.000	0.000	0.000	0.000
121	J	181	ILE	0	0.014	0.006	29.409	0.000	0.000	0.000	0.000	0.000	0.000
122	J	182	LEU	0	-0.016	-0.004	33.321	0.002	0.002	0.000	0.000	0.000	0.000
123	J	183	CYS	0	0.030	0.019	36.321	0.002	0.002	0.000	0.000	0.000	0.000
124	J	184	SER	0	0.015	0.010	33.875	0.002	0.002	0.000	0.000	0.000	0.000
125	J	185	PHE	0	-0.042	-0.013	33.667	0.001	0.001	0.000	0.000	0.000	0.000
126	J	186	ALA	0	-0.002	0.001	35.327	0.003	0.003	0.000	0.000	0.000	0.000
127	J	187	THR	0	-0.037	-0.032	38.364	0.003	0.003	0.000	0.000	0.000	0.000
128	J	188	SER	0	-0.019	-0.038	35.278	0.000	0.000	0.000	0.000	0.000	0.000
129	J	189	THR	0	-0.043	-0.026	37.236	0.002	0.002	0.000	0.000	0.000	0.000
130	J	190	VAL	0	-0.034	-0.028	38.787	0.002	0.002	0.000	0.000	0.000	0.000
131	J	191	LEU	0	0.026	0.022	38.057	0.001	0.001	0.000	0.000	0.000	0.000
132	J	192	ARG	1	0.940	0.974	31.893	0.051	0.051	0.000	0.000	0.000	0.000
133	J	193	LYS	1	0.899	0.963	39.825	0.028	0.028	0.000	0.000	0.000	0.000
134	J	194	ILE	0	-0.013	0.021	42.792	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(J:5:ILE)