FMO DATABASE

FMODB ID: 85G2Y

Calculation Name: 5C8J-K-Xray372

Preferred Name:

Target Type:

Ligand Name: dodecyl-beta-d-maltoside

ligand 3-letter code: LMT

PDB ID: 5C8J

Chain ID: K

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1040659.186421
FMO2-HF: Nuclear repulsion	988771.532403
FMO2-HF: Total energy	-51887.654018
FMO2-MP2: Total energy	-52043.259597

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(K:5:ILE)

Summations of interaction energy for fragment #1(K: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.
-7.118	-3.684	1.339	-1.489	-3.286	0.007

Interaction energy analysis for fragmet #1(K: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 : -0.003

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	K	7	ASP	-1	-0.864	-0.929	3.345	0.431	2.765	0.013	-0.959	-1.389	0.003
4	K	8	ILE	0	-0.019	-0.001	2.670	-3.512	-2.610	1.327	-0.498	-1.732	0.004
5	K	9	TYR	0	0.029	0.029	4.498	-1.469	-1.271	-0.001	-0.032	-0.165	0.000
6	K	10	TYR	0	-0.004	0.002	6.289	-0.379	-0.379	0.000	0.000	0.000	0.000
7	K	11	LYS	1	1.004	0.995	7.476	-1.988	-1.988	0.000	0.000	0.000	0.000
8	K	12	THR	0	-0.066	-0.059	8.204	-0.191	-0.191	0.000	0.000	0.000	0.000
9	K	13	LEU	0	-0.004	0.004	10.332	-0.150	-0.150	0.000	0.000	0.000	0.000
10	K	14	ASP	-1	-0.828	-0.934	12.151	0.382	0.382	0.000	0.000	0.000	0.000
11	K	15	ALA	0	-0.030	-0.013	14.111	-0.074	-0.074	0.000	0.000	0.000	0.000
12	K	16	ILE	0	-0.015	-0.002	14.867	-0.052	-0.052	0.000	0.000	0.000	0.000
13	K	17	PHE	0	0.003	-0.007	15.605	-0.053	-0.053	0.000	0.000	0.000	0.000
14	K	18	MET	0	0.025	0.005	17.476	-0.039	-0.039	0.000	0.000	0.000	0.000
15	K	19	PRO	0	-0.048	-0.025	19.829	-0.028	-0.028	0.000	0.000	0.000	0.000
16	K	20	ILE	0	-0.009	-0.001	20.354	-0.017	-0.017	0.000	0.000	0.000	0.000
17	K	21	ILE	0	-0.043	-0.015	17.633	-0.016	-0.016	0.000	0.000	0.000	0.000
18	K	22	LYS	1	0.938	0.978	22.269	-0.190	-0.190	0.000	0.000	0.000	0.000
19	K	23	VAL	0	-0.028	0.001	24.841	-0.011	-0.011	0.000	0.000	0.000	0.000
20	K	24	LEU	0	-0.025	0.010	24.589	-0.011	-0.011	0.000	0.000	0.000	0.000
21	K	25	HIS	0	0.085	0.036	26.149	0.003	0.003	0.000	0.000	0.000	0.000
22	K	26	PRO	0	0.078	0.025	23.503	-0.002	-0.002	0.000	0.000	0.000	0.000
23	K	27	ALA	0	-0.015	-0.004	24.185	-0.006	-0.006	0.000	0.000	0.000	0.000
24	K	28	LEU	0	-0.003	-0.015	26.331	-0.004	-0.004	0.000	0.000	0.000	0.000
25	K	29	ALA	0	0.019	0.011	22.190	0.001	0.001	0.000	0.000	0.000	0.000
26	K	30	ILE	0	-0.004	-0.003	19.921	-0.001	-0.001	0.000	0.000	0.000	0.000
27	K	31	LEU	0	-0.002	0.007	22.574	-0.006	-0.006	0.000	0.000	0.000	0.000
28	K	32	ILE	0	0.025	0.006	23.346	-0.004	-0.004	0.000	0.000	0.000	0.000
29	K	33	ILE	0	0.003	-0.002	18.026	-0.002	-0.002	0.000	0.000	0.000	0.000
30	K	34	ALA	0	-0.012	-0.003	20.892	-0.009	-0.009	0.000	0.000	0.000	0.000
31	K	35	ILE	0	0.011	-0.008	22.623	-0.007	-0.007	0.000	0.000	0.000	0.000
32	K	36	ILE	0	0.018	0.012	21.540	-0.003	-0.003	0.000	0.000	0.000	0.000
33	K	37	VAL	0	0.014	0.002	18.469	-0.004	-0.004	0.000	0.000	0.000	0.000
34	K	38	SER	0	-0.055	-0.014	21.536	-0.011	-0.011	0.000	0.000	0.000	0.000
35	K	39	LEU	0	0.020	0.001	24.499	-0.004	-0.004	0.000	0.000	0.000	0.000
36	K	40	ILE	0	-0.034	-0.016	20.445	0.000	0.000	0.000	0.000	0.000	0.000
37	K	41	ILE	0	-0.052	-0.019	20.267	-0.006	-0.006	0.000	0.000	0.000	0.000
38	K	42	ASN	0	-0.043	-0.019	23.524	-0.008	-0.008	0.000	0.000	0.000	0.000
39	K	43	ILE	0	-0.054	-0.013	26.964	0.000	0.000	0.000	0.000	0.000	0.000
40	K	44	ALA	0	-0.034	-0.003	23.528	-0.002	-0.002	0.000	0.000	0.000	0.000
41	K	102	PRO	0	0.090	0.020	19.841	-0.003	-0.003	0.000	0.000	0.000	0.000
42	K	103	MET	0	0.041	0.025	19.758	0.000	0.000	0.000	0.000	0.000	0.000
43	K	104	ILE	0	0.012	0.005	16.113	-0.004	-0.004	0.000	0.000	0.000	0.000
44	K	105	TYR	0	0.017	0.004	12.695	-0.014	-0.014	0.000	0.000	0.000	0.000
45	K	106	THR	0	0.008	-0.012	15.318	0.000	0.000	0.000	0.000	0.000	0.000
46	K	107	TRP	0	0.023	0.007	16.373	0.013	0.013	0.000	0.000	0.000	0.000
47	K	108	VAL	0	-0.014	0.004	10.727	-0.018	-0.018	0.000	0.000	0.000	0.000
48	K	109	PRO	0	0.025	-0.021	12.123	-0.032	-0.032	0.000	0.000	0.000	0.000
49	K	110	ILE	0	0.086	0.040	13.316	0.005	0.005	0.000	0.000	0.000	0.000
50	K	111	ILE	0	0.012	0.010	10.644	0.002	0.002	0.000	0.000	0.000	0.000
51	K	112	LEU	0	-0.017	0.004	8.778	-0.048	-0.048	0.000	0.000	0.000	0.000
52	K	113	ILE	0	-0.006	0.002	9.877	0.037	0.037	0.000	0.000	0.000	0.000
53	K	114	PHE	0	-0.015	-0.008	12.751	0.021	0.021	0.000	0.000	0.000	0.000
54	K	115	ILE	0	-0.040	0.014	6.117	0.022	0.022	0.000	0.000	0.000	0.000
55	K	116	TYR	0	0.002	0.000	9.822	-0.004	-0.004	0.000	0.000	0.000	0.000
56	K	117	LEU	0	0.024	0.003	10.784	0.044	0.044	0.000	0.000	0.000	0.000
57	K	118	ARG	1	0.926	0.963	11.901	0.173	0.173	0.000	0.000	0.000	0.000
58	K	119	HIS	1	0.859	0.942	10.317	-0.238	-0.238	0.000	0.000	0.000	0.000
59	K	120	VAL	0	-0.021	-0.005	12.427	0.034	0.034	0.000	0.000	0.000	0.000
60	K	121	TYR	0	0.058	0.004	15.578	0.008	0.008	0.000	0.000	0.000	0.000
61	K	122	GLY	0	-0.024	0.006	16.411	-0.009	-0.009	0.000	0.000	0.000	0.000
62	K	123	PHE	0	0.029	0.003	17.520	0.017	0.017	0.000	0.000	0.000	0.000
63	K	124	GLY	0	-0.019	-0.008	16.977	-0.015	-0.015	0.000	0.000	0.000	0.000
64	K	125	GLY	0	-0.022	0.000	15.624	0.017	0.017	0.000	0.000	0.000	0.000
65	K	126	VAL	0	-0.004	0.008	15.943	0.007	0.007	0.000	0.000	0.000	0.000
66	K	127	TYR	0	-0.006	0.011	17.612	0.000	0.000	0.000	0.000	0.000	0.000
67	K	128	GLN	0	-0.013	-0.005	20.447	-0.005	-0.005	0.000	0.000	0.000	0.000
68	K	129	GLU	-1	-0.998	-0.990	18.744	0.168	0.168	0.000	0.000	0.000	0.000
69	K	130	LEU	0	0.014	0.002	21.252	0.002	0.002	0.000	0.000	0.000	0.000
70	K	131	ASN	0	-0.081	-0.056	23.070	0.003	0.003	0.000	0.000	0.000	0.000
71	K	132	PRO	0	0.053	0.029	25.189	-0.007	-0.007	0.000	0.000	0.000	0.000
72	K	133	GLY	0	-0.033	-0.031	27.130	-0.003	-0.003	0.000	0.000	0.000	0.000
73	K	134	TRP	0	0.006	0.005	21.750	-0.002	-0.002	0.000	0.000	0.000	0.000
74	K	135	ASN	0	0.004	0.003	26.960	0.000	0.000	0.000	0.000	0.000	0.000
75	K	136	GLY	0	0.040	0.030	25.081	-0.007	-0.007	0.000	0.000	0.000	0.000
76	K	137	VAL	0	-0.075	-0.034	25.204	0.001	0.001	0.000	0.000	0.000	0.000
77	K	138	VAL	0	0.044	0.021	23.040	0.005	0.005	0.000	0.000	0.000	0.000
78	K	139	VAL	0	0.000	-0.024	25.821	0.005	0.005	0.000	0.000	0.000	0.000
79	K	140	TYR	0	0.015	0.021	29.163	-0.005	-0.005	0.000	0.000	0.000	0.000
80	K	141	LEU	0	0.025	0.001	31.510	0.002	0.002	0.000	0.000	0.000	0.000
81	K	142	PRO	0	0.023	0.029	34.171	-0.003	-0.003	0.000	0.000	0.000	0.000
82	K	143	ILE	0	0.027	0.015	37.799	0.000	0.000	0.000	0.000	0.000	0.000
83	K	144	ILE	0	0.067	-0.002	33.180	-0.002	-0.002	0.000	0.000	0.000	0.000
84	K	145	LEU	0	0.017	-0.002	31.013	-0.003	-0.003	0.000	0.000	0.000	0.000
85	K	146	SER	0	-0.063	-0.024	35.117	-0.002	-0.002	0.000	0.000	0.000	0.000
86	K	147	LYS	1	0.905	0.951	38.421	0.010	0.010	0.000	0.000	0.000	0.000
87	K	148	ILE	0	-0.006	0.030	33.118	-0.001	-0.001	0.000	0.000	0.000	0.000
88	K	149	LEU	0	0.009	0.011	36.422	-0.001	-0.001	0.000	0.000	0.000	0.000
89	K	150	PHE	0	0.029	0.004	31.662	-0.002	-0.002	0.000	0.000	0.000	0.000
90	K	151	ILE	0	0.019	0.008	33.815	-0.003	-0.003	0.000	0.000	0.000	0.000
91	K	152	ASP	-1	-0.813	-0.911	35.146	-0.030	-0.030	0.000	0.000	0.000	0.000
92	K	153	PHE	0	-0.011	0.003	26.180	-0.002	-0.002	0.000	0.000	0.000	0.000
93	K	154	TRP	0	0.024	0.009	29.023	-0.005	-0.005	0.000	0.000	0.000	0.000
94	K	155	HIS	0	0.018	-0.012	31.675	-0.001	-0.001	0.000	0.000	0.000	0.000
95	K	156	TRP	0	-0.006	0.006	24.836	-0.003	-0.003	0.000	0.000	0.000	0.000
96	K	157	LEU	0	-0.004	-0.016	25.733	-0.003	-0.003	0.000	0.000	0.000	0.000
97	K	158	GLY	0	-0.007	-0.034	28.118	-0.006	-0.006	0.000	0.000	0.000	0.000
98	K	159	SER	0	-0.064	-0.032	30.615	-0.003	-0.003	0.000	0.000	0.000	0.000
99	K	160	ILE	0	-0.025	-0.007	24.902	-0.001	-0.001	0.000	0.000	0.000	0.000
100	K	161	PHE	0	-0.056	-0.027	21.798	-0.008	-0.008	0.000	0.000	0.000	0.000
101	K	162	TYR	0	-0.041	0.017	26.820	-0.004	-0.004	0.000	0.000	0.000	0.000
102	K	163	LYS	1	0.990	1.008	26.242	0.073	0.073	0.000	0.000	0.000	0.000
103	K	164	GLY	0	-0.006	-0.009	31.629	0.005	0.005	0.000	0.000	0.000	0.000
104	K	165	GLY	0	0.013	-0.001	33.444	-0.003	-0.003	0.000	0.000	0.000	0.000
105	K	166	PHE	0	-0.044	-0.029	35.216	0.004	0.004	0.000	0.000	0.000	0.000
106	K	167	LYS	1	0.975	0.987	36.882	0.042	0.042	0.000	0.000	0.000	0.000
107	K	168	ILE	0	0.021	0.012	36.433	-0.001	-0.001	0.000	0.000	0.000	0.000
108	K	169	VAL	0	-0.017	0.003	38.813	0.001	0.001	0.000	0.000	0.000	0.000
109	K	170	SER	0	0.009	-0.003	41.997	0.001	0.001	0.000	0.000	0.000	0.000
110	K	171	ASN	0	0.046	0.036	40.078	-0.001	-0.001	0.000	0.000	0.000	0.000
111	K	172	THR	0	-0.068	-0.035	41.359	0.001	0.001	0.000	0.000	0.000	0.000
112	K	173	ALA	0	0.042	0.023	41.493	-0.001	-0.001	0.000	0.000	0.000	0.000
113	K	174	LEU	0	-0.015	-0.022	36.180	-0.002	-0.002	0.000	0.000	0.000	0.000
114	K	175	GLY	0	0.017	0.028	36.642	0.001	0.001	0.000	0.000	0.000	0.000
115	K	176	TRP	0	0.079	0.017	31.507	0.003	0.003	0.000	0.000	0.000	0.000
116	K	177	LEU	0	0.010	0.020	28.784	0.001	0.001	0.000	0.000	0.000	0.000
117	K	178	GLY	0	0.044	0.011	33.485	0.000	0.000	0.000	0.000	0.000	0.000
118	K	179	TRP	0	0.059	0.034	34.649	0.002	0.002	0.000	0.000	0.000	0.000
119	K	180	TYR	0	0.022	0.011	32.572	0.000	0.000	0.000	0.000	0.000	0.000
120	K	181	ILE	0	0.033	0.005	29.667	0.000	0.000	0.000	0.000	0.000	0.000
121	K	182	LEU	0	-0.001	0.007	33.338	0.002	0.002	0.000	0.000	0.000	0.000
122	K	183	CYS	0	-0.014	0.004	36.348	0.002	0.002	0.000	0.000	0.000	0.000
123	K	184	SER	0	0.027	0.006	33.870	0.002	0.002	0.000	0.000	0.000	0.000
124	K	185	PHE	0	-0.026	-0.003	33.557	0.000	0.000	0.000	0.000	0.000	0.000
125	K	186	ALA	0	-0.001	0.026	35.223	0.003	0.003	0.000	0.000	0.000	0.000
126	K	187	THR	0	-0.033	-0.028	38.280	0.003	0.003	0.000	0.000	0.000	0.000
127	K	188	SER	0	-0.007	-0.037	35.185	0.000	0.000	0.000	0.000	0.000	0.000
128	K	189	THR	0	-0.056	-0.059	37.195	0.001	0.001	0.000	0.000	0.000	0.000
129	K	190	VAL	0	-0.032	-0.024	38.690	0.002	0.002	0.000	0.000	0.000	0.000
130	K	191	LEU	0	0.025	0.033	37.734	0.001	0.001	0.000	0.000	0.000	0.000
131	K	192	ARG	1	0.929	0.969	31.682	0.053	0.053	0.000	0.000	0.000	0.000
132	K	193	LYS	1	0.904	0.963	39.737	0.029	0.029	0.000	0.000	0.000	0.000
133	K	194	ILE	0	-0.018	0.018	42.713	0.001	0.001	0.000	0.000	0.000	0.000

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