FMO DATABASE

FMODB ID: JL439

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1041369.596642
FMO2-HF: Nuclear repulsion	989480.432896
FMO2-HF: Total energy	-51889.163746
FMO2-MP2: Total energy	-52044.50401

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.
-6.177	-2.622	1.196	-1.594	-3.157	0.008

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 : 0.035 / 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

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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	-0.800	-0.878	3.163	1.390	3.372	0.033	-0.741	-1.274	0.003
4	K	8	ILE	0	0.049	0.028	2.666	-3.735	-2.490	1.164	-0.766	-1.643	0.005
5	K	9	TYR	0	-0.039	-0.027	4.212	-1.454	-1.126	-0.001	-0.087	-0.240	0.000
6	K	10	TYR	0	-0.029	-0.036	5.971	-0.199	-0.199	0.000	0.000	0.000	0.000
7	K	11	LYS	1	0.883	0.925	7.800	-1.993	-1.993	0.000	0.000	0.000	0.000
8	K	12	THR	0	-0.038	-0.026	8.080	-0.188	-0.188	0.000	0.000	0.000	0.000
9	K	13	LEU	0	0.000	0.009	10.219	-0.120	-0.120	0.000	0.000	0.000	0.000
10	K	14	ASP	-1	-0.756	-0.869	12.203	0.323	0.323	0.000	0.000	0.000	0.000
11	K	15	ALA	0	-0.030	-0.013	13.829	-0.058	-0.058	0.000	0.000	0.000	0.000
12	K	16	ILE	0	-0.015	0.002	14.397	-0.045	-0.045	0.000	0.000	0.000	0.000
13	K	17	PHE	0	0.003	-0.005	15.952	-0.047	-0.047	0.000	0.000	0.000	0.000
14	K	18	MET	0	0.019	0.008	17.368	-0.040	-0.040	0.000	0.000	0.000	0.000
15	K	19	PRO	0	-0.038	-0.020	19.649	-0.020	-0.020	0.000	0.000	0.000	0.000
16	K	20	ILE	0	0.002	-0.001	20.750	-0.016	-0.016	0.000	0.000	0.000	0.000
17	K	21	ILE	0	-0.023	-0.011	17.130	-0.015	-0.015	0.000	0.000	0.000	0.000
18	K	22	LYS	1	0.928	0.964	21.770	-0.179	-0.179	0.000	0.000	0.000	0.000
19	K	23	VAL	0	-0.025	0.005	24.552	-0.007	-0.007	0.000	0.000	0.000	0.000
20	K	24	LEU	0	-0.028	0.002	24.394	-0.009	-0.009	0.000	0.000	0.000	0.000
21	K	25	HIS	0	0.056	0.028	25.971	0.003	0.003	0.000	0.000	0.000	0.000
22	K	26	PRO	0	0.063	0.025	23.175	-0.003	-0.003	0.000	0.000	0.000	0.000
23	K	27	ALA	0	0.002	-0.005	23.824	-0.006	-0.006	0.000	0.000	0.000	0.000
24	K	28	LEU	0	-0.008	-0.009	25.915	-0.005	-0.005	0.000	0.000	0.000	0.000
25	K	29	ALA	0	0.018	0.017	21.700	-0.001	-0.001	0.000	0.000	0.000	0.000
26	K	30	ILE	0	-0.006	-0.006	19.367	-0.004	-0.004	0.000	0.000	0.000	0.000
27	K	31	LEU	0	-0.003	0.008	22.143	-0.007	-0.007	0.000	0.000	0.000	0.000
28	K	32	ILE	0	0.019	0.001	23.057	-0.005	-0.005	0.000	0.000	0.000	0.000
29	K	33	ILE	0	0.007	0.004	17.735	-0.004	-0.004	0.000	0.000	0.000	0.000
30	K	34	ALA	0	-0.018	-0.009	20.966	-0.009	-0.009	0.000	0.000	0.000	0.000
31	K	35	ILE	0	0.017	0.002	22.289	-0.007	-0.007	0.000	0.000	0.000	0.000
32	K	36	ILE	0	0.022	0.012	20.835	-0.004	-0.004	0.000	0.000	0.000	0.000
33	K	37	VAL	0	-0.006	-0.009	17.737	-0.006	-0.006	0.000	0.000	0.000	0.000
34	K	38	SER	0	-0.015	-0.001	20.995	-0.009	-0.009	0.000	0.000	0.000	0.000
35	K	39	LEU	0	-0.011	0.007	24.104	-0.002	-0.002	0.000	0.000	0.000	0.000
36	K	40	ILE	0	0.012	-0.002	19.972	-0.002	-0.002	0.000	0.000	0.000	0.000
37	K	41	ILE	0	-0.054	-0.029	19.911	-0.004	-0.004	0.000	0.000	0.000	0.000
38	K	42	ASN	0	-0.072	-0.042	23.038	-0.007	-0.007	0.000	0.000	0.000	0.000
39	K	43	ILE	0	-0.026	0.004	26.142	0.003	0.003	0.000	0.000	0.000	0.000
40	K	44	ALA	0	-0.075	-0.024	22.967	-0.005	-0.005	0.000	0.000	0.000	0.000
41	K	102	PRO	0	0.049	0.009	19.832	-0.005	-0.005	0.000	0.000	0.000	0.000
42	K	103	MET	0	0.054	0.030	19.341	-0.005	-0.005	0.000	0.000	0.000	0.000
43	K	104	ILE	0	0.029	0.011	15.925	-0.004	-0.004	0.000	0.000	0.000	0.000
44	K	105	TYR	0	0.018	0.012	12.683	-0.013	-0.013	0.000	0.000	0.000	0.000
45	K	106	THR	0	0.018	-0.012	15.060	-0.004	-0.004	0.000	0.000	0.000	0.000
46	K	107	TRP	0	0.008	0.001	15.829	0.017	0.017	0.000	0.000	0.000	0.000
47	K	108	VAL	0	-0.009	-0.001	10.134	-0.014	-0.014	0.000	0.000	0.000	0.000
48	K	109	PRO	0	0.012	0.000	11.670	-0.026	-0.026	0.000	0.000	0.000	0.000
49	K	110	ILE	0	0.040	0.030	12.982	0.010	0.010	0.000	0.000	0.000	0.000
50	K	111	ILE	0	0.017	0.011	10.095	0.006	0.006	0.000	0.000	0.000	0.000
51	K	112	LEU	0	0.017	0.003	7.855	-0.026	-0.026	0.000	0.000	0.000	0.000
52	K	113	ILE	0	0.030	0.037	9.252	0.029	0.029	0.000	0.000	0.000	0.000
53	K	114	PHE	0	-0.004	-0.002	12.272	0.027	0.027	0.000	0.000	0.000	0.000
54	K	115	ILE	0	-0.012	-0.003	5.603	0.029	0.029	0.000	0.000	0.000	0.000
55	K	116	TYR	0	-0.013	-0.012	9.693	-0.001	-0.001	0.000	0.000	0.000	0.000
56	K	117	LEU	0	0.052	0.022	10.473	0.052	0.052	0.000	0.000	0.000	0.000
57	K	118	ARG	1	0.870	0.940	11.912	0.098	0.098	0.000	0.000	0.000	0.000
58	K	119	HIS	1	0.784	0.884	10.738	-0.222	-0.222	0.000	0.000	0.000	0.000
59	K	120	VAL	0	-0.013	0.015	12.915	0.044	0.044	0.000	0.000	0.000	0.000
60	K	121	TYR	0	0.025	-0.008	15.785	0.008	0.008	0.000	0.000	0.000	0.000
61	K	122	GLY	0	-0.018	0.007	16.639	-0.010	-0.010	0.000	0.000	0.000	0.000
62	K	123	PHE	0	0.018	0.002	17.683	0.017	0.017	0.000	0.000	0.000	0.000
63	K	124	GLY	0	-0.003	-0.004	17.073	-0.017	-0.017	0.000	0.000	0.000	0.000
64	K	125	GLY	0	-0.012	0.006	15.630	0.022	0.022	0.000	0.000	0.000	0.000
65	K	126	VAL	0	0.027	0.000	16.079	-0.005	-0.005	0.000	0.000	0.000	0.000
66	K	127	TYR	0	-0.004	-0.004	17.829	-0.005	-0.005	0.000	0.000	0.000	0.000
67	K	128	GLN	0	-0.001	-0.009	20.340	-0.008	-0.008	0.000	0.000	0.000	0.000
68	K	129	GLU	-1	-0.994	-0.984	18.729	0.190	0.190	0.000	0.000	0.000	0.000
69	K	130	LEU	0	-0.005	0.000	21.220	-0.002	-0.002	0.000	0.000	0.000	0.000
70	K	131	ASN	0	-0.043	-0.019	23.172	-0.003	-0.003	0.000	0.000	0.000	0.000
71	K	132	PRO	0	0.072	0.035	25.791	-0.009	-0.009	0.000	0.000	0.000	0.000
72	K	133	GLY	0	-0.027	-0.017	26.966	-0.004	-0.004	0.000	0.000	0.000	0.000
73	K	134	TRP	0	-0.020	-0.008	21.705	-0.005	-0.005	0.000	0.000	0.000	0.000
74	K	135	ASN	0	-0.011	-0.002	26.636	0.002	0.002	0.000	0.000	0.000	0.000
75	K	136	GLY	0	0.011	0.007	24.715	-0.007	-0.007	0.000	0.000	0.000	0.000
76	K	137	VAL	0	-0.071	-0.044	25.560	0.002	0.002	0.000	0.000	0.000	0.000
77	K	138	VAL	0	0.033	0.022	22.937	0.004	0.004	0.000	0.000	0.000	0.000
78	K	139	VAL	0	0.009	-0.011	25.478	0.005	0.005	0.000	0.000	0.000	0.000
79	K	140	TYR	0	0.039	0.031	28.816	-0.004	-0.004	0.000	0.000	0.000	0.000
80	K	141	LEU	0	0.015	-0.009	31.239	0.002	0.002	0.000	0.000	0.000	0.000
81	K	142	PRO	0	0.029	0.026	34.117	-0.003	-0.003	0.000	0.000	0.000	0.000
82	K	143	ILE	0	0.049	0.016	37.783	-0.001	-0.001	0.000	0.000	0.000	0.000
83	K	144	ILE	0	0.034	0.007	33.301	-0.002	-0.002	0.000	0.000	0.000	0.000
84	K	145	LEU	0	0.022	0.004	30.925	-0.003	-0.003	0.000	0.000	0.000	0.000
85	K	146	SER	0	-0.059	-0.021	34.994	-0.001	-0.001	0.000	0.000	0.000	0.000
86	K	147	LYS	1	0.906	0.945	37.867	0.011	0.011	0.000	0.000	0.000	0.000
87	K	148	ILE	0	0.015	0.034	33.001	-0.001	-0.001	0.000	0.000	0.000	0.000
88	K	149	LEU	0	0.010	0.011	36.355	-0.001	-0.001	0.000	0.000	0.000	0.000
89	K	150	PHE	0	0.006	-0.005	31.216	-0.002	-0.002	0.000	0.000	0.000	0.000
90	K	151	ILE	0	0.025	0.012	33.719	-0.003	-0.003	0.000	0.000	0.000	0.000
91	K	152	ASP	-1	-0.768	-0.897	35.307	-0.032	-0.032	0.000	0.000	0.000	0.000
92	K	153	PHE	0	-0.012	-0.001	25.963	-0.002	-0.002	0.000	0.000	0.000	0.000
93	K	154	TRP	0	0.016	0.006	28.801	-0.006	-0.006	0.000	0.000	0.000	0.000
94	K	155	HIS	0	0.019	0.006	31.751	-0.002	-0.002	0.000	0.000	0.000	0.000
95	K	156	TRP	0	0.004	0.008	24.412	-0.004	-0.004	0.000	0.000	0.000	0.000
96	K	157	LEU	0	0.004	0.004	25.782	-0.003	-0.003	0.000	0.000	0.000	0.000
97	K	158	GLY	0	0.025	-0.010	27.939	-0.006	-0.006	0.000	0.000	0.000	0.000
98	K	159	SER	0	-0.003	-0.005	30.410	-0.001	-0.001	0.000	0.000	0.000	0.000
99	K	160	ILE	0	-0.051	-0.014	23.868	-0.001	-0.001	0.000	0.000	0.000	0.000
100	K	161	PHE	0	-0.044	-0.027	21.287	-0.007	-0.007	0.000	0.000	0.000	0.000
101	K	162	TYR	0	-0.037	0.003	26.543	-0.004	-0.004	0.000	0.000	0.000	0.000
102	K	163	LYS	1	0.900	0.958	25.781	0.081	0.081	0.000	0.000	0.000	0.000
103	K	164	GLY	0	0.008	0.000	31.433	0.005	0.005	0.000	0.000	0.000	0.000
104	K	165	GLY	0	0.032	0.007	33.265	-0.003	-0.003	0.000	0.000	0.000	0.000
105	K	166	PHE	0	-0.019	-0.003	34.467	0.004	0.004	0.000	0.000	0.000	0.000
106	K	167	LYS	1	0.914	0.956	36.389	0.047	0.047	0.000	0.000	0.000	0.000
107	K	168	ILE	0	0.019	0.003	35.763	-0.001	-0.001	0.000	0.000	0.000	0.000
108	K	169	VAL	0	-0.029	-0.009	38.456	0.001	0.001	0.000	0.000	0.000	0.000
109	K	170	SER	0	0.008	0.001	42.191	0.001	0.001	0.000	0.000	0.000	0.000
110	K	171	ASN	0	-0.009	0.000	39.670	-0.001	-0.001	0.000	0.000	0.000	0.000
111	K	172	THR	0	-0.048	-0.023	40.992	0.001	0.001	0.000	0.000	0.000	0.000
112	K	173	ALA	0	0.045	0.026	41.686	-0.001	-0.001	0.000	0.000	0.000	0.000
113	K	174	LEU	0	-0.012	-0.013	36.189	-0.001	-0.001	0.000	0.000	0.000	0.000
114	K	175	GLY	0	0.033	0.030	36.662	0.001	0.001	0.000	0.000	0.000	0.000
115	K	176	TRP	0	0.046	0.000	31.573	0.001	0.001	0.000	0.000	0.000	0.000
116	K	177	LEU	0	0.012	0.022	28.717	0.001	0.001	0.000	0.000	0.000	0.000
117	K	178	GLY	0	0.065	0.024	33.224	0.000	0.000	0.000	0.000	0.000	0.000
118	K	179	TRP	0	0.029	0.007	34.311	0.002	0.002	0.000	0.000	0.000	0.000
119	K	180	TYR	0	0.030	0.015	31.578	0.000	0.000	0.000	0.000	0.000	0.000
120	K	181	ILE	0	0.024	0.015	29.340	0.001	0.001	0.000	0.000	0.000	0.000
121	K	182	LEU	0	-0.008	0.008	33.292	0.002	0.002	0.000	0.000	0.000	0.000
122	K	183	CYS	0	0.029	0.011	36.292	0.002	0.002	0.000	0.000	0.000	0.000
123	K	184	SER	0	-0.010	0.004	34.055	0.002	0.002	0.000	0.000	0.000	0.000
124	K	185	PHE	0	-0.019	-0.008	33.522	0.001	0.001	0.000	0.000	0.000	0.000
125	K	186	ALA	0	0.012	0.010	35.330	0.003	0.003	0.000	0.000	0.000	0.000
126	K	187	THR	0	0.008	-0.017	38.669	0.003	0.003	0.000	0.000	0.000	0.000
127	K	188	SER	0	0.001	-0.018	35.199	0.001	0.001	0.000	0.000	0.000	0.000
128	K	189	THR	0	-0.048	-0.026	36.993	0.002	0.002	0.000	0.000	0.000	0.000
129	K	190	VAL	0	-0.020	-0.008	38.811	0.003	0.003	0.000	0.000	0.000	0.000
130	K	191	LEU	0	0.043	0.021	37.976	0.001	0.001	0.000	0.000	0.000	0.000
131	K	192	ARG	1	0.900	0.947	31.976	0.043	0.043	0.000	0.000	0.000	0.000
132	K	193	LYS	1	0.855	0.940	39.905	0.025	0.025	0.000	0.000	0.000	0.000
133	K	194	ILE	0	-0.012	0.020	43.199	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)