FMO DATABASE

FMODB ID: 94LG2

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	OptAll
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	-1054889.471486
FMO2-HF: Nuclear repulsion	1002640.615976
FMO2-HF: Total energy	-52248.85551
FMO2-MP2: Total energy	-52405.230643

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.
-6.002	-2.438	1.207	-1.623	-3.15	0.007

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 : 0.035 / 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	-0.797	-0.876	3.182	1.330	3.331	0.032	-0.757	-1.276	0.003
4	J	8	ILE	0	0.044	0.026	2.630	-3.632	-2.414	1.176	-0.770	-1.625	0.004
5	J	9	TYR	0	-0.038	-0.029	4.178	-1.405	-1.060	-0.001	-0.096	-0.249	0.000
6	J	10	TYR	0	-0.036	-0.034	5.935	-0.186	-0.186	0.000	0.000	0.000	0.000
7	J	11	LYS	1	0.888	0.931	7.818	-2.006	-2.006	0.000	0.000	0.000	0.000
8	J	12	THR	0	-0.038	-0.025	8.098	-0.180	-0.180	0.000	0.000	0.000	0.000
9	J	13	LEU	0	-0.003	0.007	10.195	-0.115	-0.115	0.000	0.000	0.000	0.000
10	J	14	ASP	-1	-0.787	-0.892	12.016	0.354	0.354	0.000	0.000	0.000	0.000
11	J	15	ALA	0	-0.025	-0.013	13.737	-0.057	-0.057	0.000	0.000	0.000	0.000
12	J	16	ILE	0	-0.015	0.005	14.302	-0.044	-0.044	0.000	0.000	0.000	0.000
13	J	17	PHE	0	0.007	-0.003	15.963	-0.044	-0.044	0.000	0.000	0.000	0.000
14	J	18	MET	0	0.019	0.007	17.402	-0.038	-0.038	0.000	0.000	0.000	0.000
15	J	19	PRO	0	-0.054	-0.029	19.631	-0.020	-0.020	0.000	0.000	0.000	0.000
16	J	20	ILE	0	0.007	0.002	20.765	-0.015	-0.015	0.000	0.000	0.000	0.000
17	J	21	ILE	0	-0.014	-0.005	17.165	-0.015	-0.015	0.000	0.000	0.000	0.000
18	J	22	LYS	1	0.929	0.964	21.807	-0.172	-0.172	0.000	0.000	0.000	0.000
19	J	23	VAL	0	-0.026	0.002	24.641	-0.006	-0.006	0.000	0.000	0.000	0.000
20	J	24	LEU	0	-0.032	0.000	24.268	-0.009	-0.009	0.000	0.000	0.000	0.000
21	J	25	HIS	0	0.048	0.024	25.858	0.003	0.003	0.000	0.000	0.000	0.000
22	J	26	PRO	0	0.069	0.026	23.346	-0.003	-0.003	0.000	0.000	0.000	0.000
23	J	27	ALA	0	-0.001	-0.002	23.935	-0.007	-0.007	0.000	0.000	0.000	0.000
24	J	28	LEU	0	-0.017	-0.014	26.025	-0.005	-0.005	0.000	0.000	0.000	0.000
25	J	29	ALA	0	0.017	0.016	21.702	-0.002	-0.002	0.000	0.000	0.000	0.000
26	J	30	ILE	0	-0.005	-0.004	19.590	-0.005	-0.005	0.000	0.000	0.000	0.000
27	J	31	LEU	0	-0.009	0.004	22.257	-0.007	-0.007	0.000	0.000	0.000	0.000
28	J	32	ILE	0	0.017	-0.001	23.083	-0.005	-0.005	0.000	0.000	0.000	0.000
29	J	33	ILE	0	0.011	0.006	17.770	-0.004	-0.004	0.000	0.000	0.000	0.000
30	J	34	ALA	0	-0.015	-0.008	20.978	-0.010	-0.010	0.000	0.000	0.000	0.000
31	J	35	ILE	0	0.013	0.003	22.312	-0.007	-0.007	0.000	0.000	0.000	0.000
32	J	36	ILE	0	0.017	0.011	20.768	-0.004	-0.004	0.000	0.000	0.000	0.000
33	J	37	VAL	0	-0.001	-0.006	17.695	-0.006	-0.006	0.000	0.000	0.000	0.000
34	J	38	SER	0	-0.023	-0.002	20.843	-0.009	-0.009	0.000	0.000	0.000	0.000
35	J	39	LEU	0	-0.016	-0.006	23.877	-0.003	-0.003	0.000	0.000	0.000	0.000
36	J	40	ILE	0	0.007	0.004	19.793	-0.001	-0.001	0.000	0.000	0.000	0.000
37	J	41	ILE	0	-0.024	-0.020	19.222	-0.006	-0.006	0.000	0.000	0.000	0.000
38	J	42	ASN	0	-0.030	-0.015	23.159	-0.006	-0.006	0.000	0.000	0.000	0.000
39	J	43	ILE	0	-0.030	-0.003	26.335	0.002	0.002	0.000	0.000	0.000	0.000
40	J	44	ALA	0	-0.020	0.000	23.275	0.002	0.002	0.000	0.000	0.000	0.000
41	J	45	THR	0	-0.096	-0.042	20.861	-0.009	-0.009	0.000	0.000	0.000	0.000
42	J	102	PRO	0	0.057	0.009	21.176	-0.004	-0.004	0.000	0.000	0.000	0.000
43	J	103	MET	0	0.044	0.014	20.175	-0.010	-0.010	0.000	0.000	0.000	0.000
44	J	104	ILE	0	0.016	0.018	16.272	-0.005	-0.005	0.000	0.000	0.000	0.000
45	J	105	TYR	0	0.016	0.011	14.543	-0.027	-0.027	0.000	0.000	0.000	0.000
46	J	106	THR	0	0.042	0.005	15.746	-0.005	-0.005	0.000	0.000	0.000	0.000
47	J	107	TRP	0	-0.017	-0.015	15.502	0.011	0.011	0.000	0.000	0.000	0.000
48	J	108	VAL	0	0.001	0.016	10.313	-0.017	-0.017	0.000	0.000	0.000	0.000
49	J	109	PRO	0	0.029	0.009	11.496	-0.026	-0.026	0.000	0.000	0.000	0.000
50	J	110	ILE	0	0.040	0.021	13.091	0.008	0.008	0.000	0.000	0.000	0.000
51	J	111	ILE	0	0.000	-0.004	9.886	0.006	0.006	0.000	0.000	0.000	0.000
52	J	112	LEU	0	0.019	0.010	7.996	-0.025	-0.025	0.000	0.000	0.000	0.000
53	J	113	ILE	0	0.031	0.038	9.211	0.028	0.028	0.000	0.000	0.000	0.000
54	J	114	PHE	0	-0.007	-0.006	12.269	0.027	0.027	0.000	0.000	0.000	0.000
55	J	115	ILE	0	-0.022	-0.007	5.663	0.028	0.028	0.000	0.000	0.000	0.000
56	J	116	TYR	0	-0.020	-0.020	9.843	-0.002	-0.002	0.000	0.000	0.000	0.000
57	J	117	LEU	0	0.029	0.001	10.749	0.049	0.049	0.000	0.000	0.000	0.000
58	J	118	ARG	1	0.927	0.967	11.661	0.141	0.141	0.000	0.000	0.000	0.000
59	J	119	HIS	1	0.875	0.951	10.479	-0.257	-0.257	0.000	0.000	0.000	0.000
60	J	120	VAL	0	-0.004	0.005	12.555	0.035	0.035	0.000	0.000	0.000	0.000
61	J	121	TYR	0	0.009	-0.011	15.700	0.007	0.007	0.000	0.000	0.000	0.000
62	J	122	GLY	0	0.000	0.013	16.403	-0.012	-0.012	0.000	0.000	0.000	0.000
63	J	123	PHE	0	-0.011	-0.012	17.415	0.017	0.017	0.000	0.000	0.000	0.000
64	J	124	GLY	0	-0.014	-0.002	17.490	-0.009	-0.009	0.000	0.000	0.000	0.000
65	J	125	GLY	0	-0.005	0.008	15.663	0.023	0.023	0.000	0.000	0.000	0.000
66	J	126	VAL	0	-0.006	-0.009	15.785	-0.004	-0.004	0.000	0.000	0.000	0.000
67	J	127	TYR	0	-0.005	-0.007	17.628	-0.003	-0.003	0.000	0.000	0.000	0.000
68	J	128	GLN	0	-0.017	-0.023	20.260	-0.004	-0.004	0.000	0.000	0.000	0.000
69	J	129	GLU	-1	-0.974	-0.979	16.958	0.241	0.241	0.000	0.000	0.000	0.000
70	J	130	LEU	0	-0.015	-0.019	20.119	0.002	0.002	0.000	0.000	0.000	0.000
71	J	131	ASN	0	-0.081	-0.016	23.060	-0.006	-0.006	0.000	0.000	0.000	0.000
72	J	132	PRO	0	0.041	0.005	25.430	-0.011	-0.011	0.000	0.000	0.000	0.000
73	J	133	GLY	0	0.001	0.004	26.794	-0.004	-0.004	0.000	0.000	0.000	0.000
74	J	134	TRP	0	-0.026	-0.007	21.333	-0.006	-0.006	0.000	0.000	0.000	0.000
75	J	135	ASN	0	0.027	0.007	25.700	0.002	0.002	0.000	0.000	0.000	0.000
76	J	136	GLY	0	0.037	0.015	24.277	-0.007	-0.007	0.000	0.000	0.000	0.000
77	J	137	VAL	0	-0.074	-0.034	25.316	0.003	0.003	0.000	0.000	0.000	0.000
78	J	138	VAL	0	0.047	0.026	22.105	0.004	0.004	0.000	0.000	0.000	0.000
79	J	139	VAL	0	-0.008	-0.012	25.538	0.004	0.004	0.000	0.000	0.000	0.000
80	J	140	TYR	0	0.039	0.027	28.825	-0.003	-0.003	0.000	0.000	0.000	0.000
81	J	141	LEU	0	0.000	-0.006	30.241	0.001	0.001	0.000	0.000	0.000	0.000
82	J	142	PRO	0	0.037	0.029	34.222	-0.002	-0.002	0.000	0.000	0.000	0.000
83	J	143	ILE	0	0.054	0.016	37.905	-0.001	-0.001	0.000	0.000	0.000	0.000
84	J	144	ILE	0	0.031	0.000	33.783	-0.002	-0.002	0.000	0.000	0.000	0.000
85	J	145	LEU	0	0.033	0.008	31.043	-0.003	-0.003	0.000	0.000	0.000	0.000
86	J	146	SER	0	-0.062	-0.018	35.053	-0.001	-0.001	0.000	0.000	0.000	0.000
87	J	147	LYS	1	0.906	0.944	37.902	0.011	0.011	0.000	0.000	0.000	0.000
88	J	148	ILE	0	0.008	0.024	32.965	-0.001	-0.001	0.000	0.000	0.000	0.000
89	J	149	LEU	0	0.015	0.022	36.365	-0.001	-0.001	0.000	0.000	0.000	0.000
90	J	150	PHE	0	0.011	-0.004	31.340	-0.002	-0.002	0.000	0.000	0.000	0.000
91	J	151	ILE	0	0.002	0.004	33.954	-0.004	-0.004	0.000	0.000	0.000	0.000
92	J	152	ASP	-1	-0.780	-0.892	35.323	-0.032	-0.032	0.000	0.000	0.000	0.000
93	J	153	PHE	0	-0.017	-0.007	26.189	-0.003	-0.003	0.000	0.000	0.000	0.000
94	J	154	TRP	0	0.013	-0.001	29.227	-0.005	-0.005	0.000	0.000	0.000	0.000
95	J	155	HIS	0	0.010	-0.002	31.702	-0.003	-0.003	0.000	0.000	0.000	0.000
96	J	156	TRP	0	-0.011	0.005	24.259	-0.004	-0.004	0.000	0.000	0.000	0.000
97	J	157	LEU	0	-0.002	-0.002	25.514	-0.004	-0.004	0.000	0.000	0.000	0.000
98	J	158	GLY	0	0.015	-0.005	27.639	-0.006	-0.006	0.000	0.000	0.000	0.000
99	J	159	SER	0	-0.006	-0.005	29.964	-0.002	-0.002	0.000	0.000	0.000	0.000
100	J	160	ILE	0	-0.007	0.011	23.842	-0.002	-0.002	0.000	0.000	0.000	0.000
101	J	161	PHE	0	-0.066	-0.025	21.678	-0.010	-0.010	0.000	0.000	0.000	0.000
102	J	162	TYR	0	-0.039	-0.020	26.536	-0.003	-0.003	0.000	0.000	0.000	0.000
103	J	163	LYS	1	0.880	0.945	24.125	0.098	0.098	0.000	0.000	0.000	0.000
104	J	164	GLY	0	0.007	-0.008	30.552	0.005	0.005	0.000	0.000	0.000	0.000
105	J	165	GLY	0	0.001	0.000	33.005	-0.003	-0.003	0.000	0.000	0.000	0.000
106	J	166	PHE	0	-0.034	-0.023	35.309	0.003	0.003	0.000	0.000	0.000	0.000
107	J	167	LYS	1	0.969	0.989	36.621	0.041	0.041	0.000	0.000	0.000	0.000
108	J	168	ILE	0	0.013	0.001	35.116	0.001	0.001	0.000	0.000	0.000	0.000
109	J	169	VAL	0	-0.004	0.017	38.614	0.001	0.001	0.000	0.000	0.000	0.000
110	J	170	SER	0	0.012	0.014	41.826	0.000	0.000	0.000	0.000	0.000	0.000
111	J	171	ASN	0	0.006	-0.007	39.514	-0.002	-0.002	0.000	0.000	0.000	0.000
112	J	172	THR	0	-0.056	-0.036	41.546	0.001	0.001	0.000	0.000	0.000	0.000
113	J	173	ALA	0	0.038	0.027	42.157	-0.001	-0.001	0.000	0.000	0.000	0.000
114	J	174	LEU	0	0.007	-0.006	36.237	-0.001	-0.001	0.000	0.000	0.000	0.000
115	J	175	GLY	0	0.032	0.027	36.482	0.001	0.001	0.000	0.000	0.000	0.000
116	J	176	TRP	0	0.075	0.011	31.787	0.002	0.002	0.000	0.000	0.000	0.000
117	J	177	LEU	0	-0.001	0.018	28.599	0.001	0.001	0.000	0.000	0.000	0.000
118	J	178	GLY	0	0.082	0.034	33.153	0.000	0.000	0.000	0.000	0.000	0.000
119	J	179	TRP	0	0.031	0.008	34.121	0.002	0.002	0.000	0.000	0.000	0.000
120	J	180	TYR	0	0.027	0.011	31.657	0.001	0.001	0.000	0.000	0.000	0.000
121	J	181	ILE	0	0.018	0.013	29.280	0.001	0.001	0.000	0.000	0.000	0.000
122	J	182	LEU	0	-0.010	0.010	33.210	0.002	0.002	0.000	0.000	0.000	0.000
123	J	183	CYS	0	0.031	0.011	36.264	0.002	0.002	0.000	0.000	0.000	0.000
124	J	184	SER	0	-0.011	0.004	34.044	0.002	0.002	0.000	0.000	0.000	0.000
125	J	185	PHE	0	-0.018	-0.008	33.701	0.002	0.002	0.000	0.000	0.000	0.000
126	J	186	ALA	0	0.012	0.011	35.410	0.003	0.003	0.000	0.000	0.000	0.000
127	J	187	THR	0	0.007	-0.018	38.727	0.003	0.003	0.000	0.000	0.000	0.000
128	J	188	SER	0	0.006	-0.014	35.254	0.001	0.001	0.000	0.000	0.000	0.000
129	J	189	THR	0	-0.051	-0.029	37.122	0.002	0.002	0.000	0.000	0.000	0.000
130	J	190	VAL	0	-0.021	-0.008	38.916	0.003	0.003	0.000	0.000	0.000	0.000
131	J	191	LEU	0	0.042	0.020	38.058	0.001	0.001	0.000	0.000	0.000	0.000
132	J	192	ARG	1	0.898	0.945	32.063	0.042	0.042	0.000	0.000	0.000	0.000
133	J	193	LYS	1	0.855	0.940	39.993	0.025	0.025	0.000	0.000	0.000	0.000
134	J	194	ILE	0	-0.013	0.019	43.283	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)