FMO DATABASE

FMODB ID: 39KQL

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	OptH
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	-1053852.589195
FMO2-HF: Nuclear repulsion	1001605.294804
FMO2-HF: Total energy	-52247.294392
FMO2-MP2: Total energy	-52403.974233

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.
-6.957	-3.742	1.722	-1.48	-3.457	0.006

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 : 0.016 / q_NPA : -0.004

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	-0.857	-0.925	3.295	0.370	2.709	0.015	-0.951	-1.403	0.002
4	J	8	ILE	0	-0.034	-0.007	2.583	-3.388	-2.731	1.708	-0.488	-1.877	0.004
5	J	9	TYR	0	0.017	0.011	4.424	-1.465	-1.246	-0.001	-0.041	-0.177	0.000
6	J	10	TYR	0	0.002	0.008	6.221	-0.369	-0.369	0.000	0.000	0.000	0.000
7	J	11	LYS	1	1.009	0.999	7.511	-1.951	-1.951	0.000	0.000	0.000	0.000
8	J	12	THR	0	-0.059	-0.046	8.212	-0.200	-0.200	0.000	0.000	0.000	0.000
9	J	13	LEU	0	-0.003	0.005	10.246	-0.146	-0.146	0.000	0.000	0.000	0.000
10	J	14	ASP	-1	-0.834	-0.934	12.133	0.352	0.352	0.000	0.000	0.000	0.000
11	J	15	ALA	0	-0.036	-0.016	14.067	-0.071	-0.071	0.000	0.000	0.000	0.000
12	J	16	ILE	0	-0.018	-0.003	14.798	-0.051	-0.051	0.000	0.000	0.000	0.000
13	J	17	PHE	0	0.007	-0.005	15.577	-0.051	-0.051	0.000	0.000	0.000	0.000
14	J	18	MET	0	0.034	0.009	17.498	-0.039	-0.039	0.000	0.000	0.000	0.000
15	J	19	PRO	0	-0.052	-0.027	19.836	-0.028	-0.028	0.000	0.000	0.000	0.000
16	J	20	ILE	0	-0.004	0.001	20.327	-0.017	-0.017	0.000	0.000	0.000	0.000
17	J	21	ILE	0	-0.040	-0.012	17.634	-0.017	-0.017	0.000	0.000	0.000	0.000
18	J	22	LYS	1	0.924	0.972	22.249	-0.180	-0.180	0.000	0.000	0.000	0.000
19	J	23	VAL	0	-0.022	0.001	24.773	-0.010	-0.010	0.000	0.000	0.000	0.000
20	J	24	LEU	0	-0.025	0.009	24.530	-0.010	-0.010	0.000	0.000	0.000	0.000
21	J	25	HIS	0	0.082	0.039	26.016	0.003	0.003	0.000	0.000	0.000	0.000
22	J	26	PRO	0	0.088	0.033	23.210	-0.002	-0.002	0.000	0.000	0.000	0.000
23	J	27	ALA	0	-0.025	-0.011	24.186	-0.007	-0.007	0.000	0.000	0.000	0.000
24	J	28	LEU	0	-0.007	-0.015	26.450	-0.004	-0.004	0.000	0.000	0.000	0.000
25	J	29	ALA	0	0.016	0.009	22.285	0.001	0.001	0.000	0.000	0.000	0.000
26	J	30	ILE	0	-0.015	-0.004	19.898	-0.001	-0.001	0.000	0.000	0.000	0.000
27	J	31	LEU	0	0.005	0.009	22.559	-0.006	-0.006	0.000	0.000	0.000	0.000
28	J	32	ILE	0	0.021	0.006	23.288	-0.004	-0.004	0.000	0.000	0.000	0.000
29	J	33	ILE	0	0.008	0.000	17.981	-0.002	-0.002	0.000	0.000	0.000	0.000
30	J	34	ALA	0	-0.017	-0.004	20.845	-0.009	-0.009	0.000	0.000	0.000	0.000
31	J	35	ILE	0	0.010	-0.010	22.565	-0.007	-0.007	0.000	0.000	0.000	0.000
32	J	36	ILE	0	0.016	0.012	21.436	-0.002	-0.002	0.000	0.000	0.000	0.000
33	J	37	VAL	0	0.013	0.000	18.452	-0.004	-0.004	0.000	0.000	0.000	0.000
34	J	38	SER	0	-0.056	-0.015	21.431	-0.010	-0.010	0.000	0.000	0.000	0.000
35	J	39	LEU	0	0.023	0.002	24.387	-0.004	-0.004	0.000	0.000	0.000	0.000
36	J	40	ILE	0	-0.027	-0.014	20.463	0.000	0.000	0.000	0.000	0.000	0.000
37	J	41	ILE	0	-0.022	-0.004	19.987	-0.006	-0.006	0.000	0.000	0.000	0.000
38	J	42	ASN	0	-0.034	0.000	23.477	-0.008	-0.008	0.000	0.000	0.000	0.000
39	J	43	ILE	0	-0.040	-0.012	26.967	0.000	0.000	0.000	0.000	0.000	0.000
40	J	44	ALA	0	-0.019	0.001	23.415	0.001	0.001	0.000	0.000	0.000	0.000
41	J	45	THR	0	-0.066	-0.035	21.362	-0.007	-0.007	0.000	0.000	0.000	0.000
42	J	102	PRO	0	0.091	0.026	21.221	-0.002	-0.002	0.000	0.000	0.000	0.000
43	J	103	MET	0	0.029	0.004	20.568	-0.005	-0.005	0.000	0.000	0.000	0.000
44	J	104	ILE	0	0.019	0.038	16.575	-0.006	-0.006	0.000	0.000	0.000	0.000
45	J	105	TYR	0	0.021	0.010	14.886	-0.026	-0.026	0.000	0.000	0.000	0.000
46	J	106	THR	0	-0.004	-0.030	16.023	-0.001	-0.001	0.000	0.000	0.000	0.000
47	J	107	TRP	0	0.023	0.000	15.833	0.005	0.005	0.000	0.000	0.000	0.000
48	J	108	VAL	0	0.001	0.013	10.596	-0.021	-0.021	0.000	0.000	0.000	0.000
49	J	109	PRO	0	0.029	0.001	11.994	-0.024	-0.024	0.000	0.000	0.000	0.000
50	J	110	ILE	0	0.059	0.021	13.638	0.007	0.007	0.000	0.000	0.000	0.000
51	J	111	ILE	0	-0.024	-0.008	10.492	0.001	0.001	0.000	0.000	0.000	0.000
52	J	112	LEU	0	0.003	-0.004	8.904	-0.048	-0.048	0.000	0.000	0.000	0.000
53	J	113	ILE	0	0.014	0.016	9.918	0.033	0.033	0.000	0.000	0.000	0.000
54	J	114	PHE	0	-0.012	-0.005	12.804	0.019	0.019	0.000	0.000	0.000	0.000
55	J	115	ILE	0	-0.036	0.005	6.187	0.018	0.018	0.000	0.000	0.000	0.000
56	J	116	TYR	0	-0.015	-0.014	9.937	-0.003	-0.003	0.000	0.000	0.000	0.000
57	J	117	LEU	0	0.034	0.002	10.972	0.041	0.041	0.000	0.000	0.000	0.000
58	J	118	ARG	1	0.960	0.984	11.516	0.200	0.200	0.000	0.000	0.000	0.000
59	J	119	HIS	1	0.855	0.939	10.321	-0.217	-0.217	0.000	0.000	0.000	0.000
60	J	120	VAL	0	0.003	0.004	12.428	0.039	0.039	0.000	0.000	0.000	0.000
61	J	121	TYR	0	0.041	-0.004	15.671	0.006	0.006	0.000	0.000	0.000	0.000
62	J	122	GLY	0	-0.004	0.013	16.358	-0.010	-0.010	0.000	0.000	0.000	0.000
63	J	123	PHE	0	0.021	-0.002	17.330	0.019	0.019	0.000	0.000	0.000	0.000
64	J	124	GLY	0	-0.023	-0.008	16.978	-0.014	-0.014	0.000	0.000	0.000	0.000
65	J	125	GLY	0	-0.018	0.003	15.550	0.018	0.018	0.000	0.000	0.000	0.000
66	J	126	VAL	0	0.007	0.020	15.773	0.007	0.007	0.000	0.000	0.000	0.000
67	J	127	TYR	0	0.004	-0.003	17.488	0.002	0.002	0.000	0.000	0.000	0.000
68	J	128	GLN	0	0.000	-0.003	20.328	-0.005	-0.005	0.000	0.000	0.000	0.000
69	J	129	GLU	-1	-1.002	-0.988	17.252	0.189	0.189	0.000	0.000	0.000	0.000
70	J	130	LEU	0	-0.046	-0.031	20.224	0.007	0.007	0.000	0.000	0.000	0.000
71	J	131	ASN	0	-0.061	-0.030	23.052	0.005	0.005	0.000	0.000	0.000	0.000
72	J	132	PRO	0	0.034	0.012	25.644	-0.010	-0.010	0.000	0.000	0.000	0.000
73	J	133	GLY	0	-0.031	-0.007	27.078	-0.002	-0.002	0.000	0.000	0.000	0.000
74	J	134	TRP	0	-0.034	-0.022	21.335	0.001	0.001	0.000	0.000	0.000	0.000
75	J	135	ASN	0	0.008	0.006	26.042	-0.001	-0.001	0.000	0.000	0.000	0.000
76	J	136	GLY	0	0.064	0.023	24.470	-0.007	-0.007	0.000	0.000	0.000	0.000
77	J	137	VAL	0	-0.059	-0.033	25.435	0.004	0.004	0.000	0.000	0.000	0.000
78	J	138	VAL	0	0.079	0.052	22.865	0.005	0.005	0.000	0.000	0.000	0.000
79	J	139	VAL	0	-0.023	-0.030	25.835	0.006	0.006	0.000	0.000	0.000	0.000
80	J	140	TYR	0	-0.002	0.015	29.199	-0.005	-0.005	0.000	0.000	0.000	0.000
81	J	141	LEU	0	0.040	0.006	30.930	0.002	0.002	0.000	0.000	0.000	0.000
82	J	142	PRO	0	0.016	0.027	34.230	-0.002	-0.002	0.000	0.000	0.000	0.000
83	J	143	ILE	0	0.026	0.019	37.981	-0.001	-0.001	0.000	0.000	0.000	0.000
84	J	144	ILE	0	0.086	-0.006	33.203	-0.002	-0.002	0.000	0.000	0.000	0.000
85	J	145	LEU	0	0.017	0.007	31.083	-0.002	-0.002	0.000	0.000	0.000	0.000
86	J	146	SER	0	-0.052	-0.020	35.151	-0.002	-0.002	0.000	0.000	0.000	0.000
87	J	147	LYS	1	0.902	0.950	38.411	0.011	0.011	0.000	0.000	0.000	0.000
88	J	148	ILE	0	-0.023	0.019	33.142	-0.001	-0.001	0.000	0.000	0.000	0.000
89	J	149	LEU	0	0.011	0.011	36.482	-0.001	-0.001	0.000	0.000	0.000	0.000
90	J	150	PHE	0	0.027	0.003	31.554	-0.002	-0.002	0.000	0.000	0.000	0.000
91	J	151	ILE	0	0.000	-0.002	33.969	-0.003	-0.003	0.000	0.000	0.000	0.000
92	J	152	ASP	-1	-0.825	-0.923	35.324	-0.032	-0.032	0.000	0.000	0.000	0.000
93	J	153	PHE	0	-0.029	-0.011	26.482	-0.002	-0.002	0.000	0.000	0.000	0.000
94	J	154	TRP	0	0.017	0.007	29.104	-0.005	-0.005	0.000	0.000	0.000	0.000
95	J	155	HIS	0	0.060	0.021	31.410	-0.003	-0.003	0.000	0.000	0.000	0.000
96	J	156	TRP	0	0.006	0.019	24.603	-0.004	-0.004	0.000	0.000	0.000	0.000
97	J	157	LEU	0	0.000	-0.010	25.218	-0.004	-0.004	0.000	0.000	0.000	0.000
98	J	158	GLY	0	-0.018	-0.021	27.548	-0.006	-0.006	0.000	0.000	0.000	0.000
99	J	159	SER	0	-0.041	-0.014	30.068	-0.003	-0.003	0.000	0.000	0.000	0.000
100	J	160	ILE	0	0.000	0.001	23.947	-0.001	-0.001	0.000	0.000	0.000	0.000
101	J	161	PHE	0	-0.064	-0.037	21.775	-0.008	-0.008	0.000	0.000	0.000	0.000
102	J	162	TYR	0	-0.045	-0.014	27.060	-0.003	-0.003	0.000	0.000	0.000	0.000
103	J	163	LYS	1	0.930	0.986	24.181	0.093	0.093	0.000	0.000	0.000	0.000
104	J	164	GLY	0	-0.012	-0.012	30.875	0.005	0.005	0.000	0.000	0.000	0.000
105	J	165	GLY	0	0.002	-0.005	33.214	-0.003	-0.003	0.000	0.000	0.000	0.000
106	J	166	PHE	0	-0.050	-0.033	35.672	0.000	0.000	0.000	0.000	0.000	0.000
107	J	167	LYS	1	0.977	0.986	37.315	0.038	0.038	0.000	0.000	0.000	0.000
108	J	168	ILE	0	0.028	0.022	36.245	0.000	0.000	0.000	0.000	0.000	0.000
109	J	169	VAL	0	0.020	0.019	39.099	0.000	0.000	0.000	0.000	0.000	0.000
110	J	170	SER	0	-0.017	-0.012	41.829	0.001	0.001	0.000	0.000	0.000	0.000
111	J	171	ASN	0	0.044	0.024	40.291	-0.001	-0.001	0.000	0.000	0.000	0.000
112	J	172	THR	0	-0.059	-0.026	41.621	0.001	0.001	0.000	0.000	0.000	0.000
113	J	173	ALA	0	0.047	0.027	42.360	-0.001	-0.001	0.000	0.000	0.000	0.000
114	J	174	LEU	0	-0.023	-0.007	36.833	-0.001	-0.001	0.000	0.000	0.000	0.000
115	J	175	GLY	0	0.023	0.016	36.789	0.001	0.001	0.000	0.000	0.000	0.000
116	J	176	TRP	0	0.096	0.025	31.653	0.003	0.003	0.000	0.000	0.000	0.000
117	J	177	LEU	0	0.007	0.022	28.608	0.001	0.001	0.000	0.000	0.000	0.000
118	J	178	GLY	0	0.069	0.025	33.291	-0.001	-0.001	0.000	0.000	0.000	0.000
119	J	179	TRP	0	0.074	0.032	34.476	0.002	0.002	0.000	0.000	0.000	0.000
120	J	180	TYR	0	-0.003	-0.003	32.609	0.000	0.000	0.000	0.000	0.000	0.000
121	J	181	ILE	0	0.039	0.005	29.686	0.000	0.000	0.000	0.000	0.000	0.000
122	J	182	LEU	0	-0.010	0.000	33.340	0.002	0.002	0.000	0.000	0.000	0.000
123	J	183	CYS	0	-0.015	0.010	36.333	0.001	0.001	0.000	0.000	0.000	0.000
124	J	184	SER	0	0.036	0.007	33.926	0.002	0.002	0.000	0.000	0.000	0.000
125	J	185	PHE	0	-0.031	-0.005	33.703	0.001	0.001	0.000	0.000	0.000	0.000
126	J	186	ALA	0	0.003	0.032	35.339	0.003	0.003	0.000	0.000	0.000	0.000
127	J	187	THR	0	-0.035	-0.024	38.381	0.003	0.003	0.000	0.000	0.000	0.000
128	J	188	SER	0	-0.016	-0.040	35.202	0.000	0.000	0.000	0.000	0.000	0.000
129	J	189	THR	0	-0.062	-0.068	37.253	0.001	0.001	0.000	0.000	0.000	0.000
130	J	190	VAL	0	-0.033	-0.025	38.796	0.002	0.002	0.000	0.000	0.000	0.000
131	J	191	LEU	0	0.030	0.031	37.888	0.001	0.001	0.000	0.000	0.000	0.000
132	J	192	ARG	1	0.928	0.968	31.764	0.055	0.055	0.000	0.000	0.000	0.000
133	J	193	LYS	1	0.905	0.964	39.838	0.031	0.031	0.000	0.000	0.000	0.000
134	J	194	ILE	0	-0.018	0.019	42.799	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)