FMO DATABASE

FMODB ID: N9Z1Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1039387.19038
FMO2-HF: Nuclear repulsion	987498.527583
FMO2-HF: Total energy	-51888.662797
FMO2-MP2: Total energy	-52044.120658

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.
-7.534	-3.734	1.16	-1.765	-3.194	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 : 0.014 / 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

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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	-0.814	-0.884	3.219	0.280	2.641	0.014	-0.979	-1.396	0.003
4	K	8	ILE	0	-0.009	0.000	2.602	-3.665	-2.441	1.147	-0.751	-1.619	0.005
5	K	9	TYR	0	-0.010	-0.017	4.469	-1.453	-1.238	-0.001	-0.035	-0.179	0.000
6	K	10	TYR	0	-0.002	-0.001	6.267	-0.367	-0.367	0.000	0.000	0.000	0.000
7	K	11	LYS	1	0.932	0.943	7.510	-2.043	-2.043	0.000	0.000	0.000	0.000
8	K	12	THR	0	-0.048	-0.030	8.307	-0.224	-0.224	0.000	0.000	0.000	0.000
9	K	13	LEU	0	-0.005	0.002	10.507	-0.149	-0.149	0.000	0.000	0.000	0.000
10	K	14	ASP	-1	-0.815	-0.903	12.216	0.372	0.372	0.000	0.000	0.000	0.000
11	K	15	ALA	0	-0.038	-0.016	14.112	-0.076	-0.076	0.000	0.000	0.000	0.000
12	K	16	ILE	0	-0.015	-0.001	14.609	-0.053	-0.053	0.000	0.000	0.000	0.000
13	K	17	PHE	0	0.014	-0.003	16.087	-0.053	-0.053	0.000	0.000	0.000	0.000
14	K	18	MET	0	0.031	0.010	17.589	-0.043	-0.043	0.000	0.000	0.000	0.000
15	K	19	PRO	0	-0.042	-0.019	19.829	-0.029	-0.029	0.000	0.000	0.000	0.000
16	K	20	ILE	0	-0.024	-0.010	20.793	-0.018	-0.018	0.000	0.000	0.000	0.000
17	K	21	ILE	0	-0.036	-0.008	17.774	-0.017	-0.017	0.000	0.000	0.000	0.000
18	K	22	LYS	1	0.948	0.974	22.360	-0.190	-0.190	0.000	0.000	0.000	0.000
19	K	23	VAL	0	-0.023	0.002	24.932	-0.011	-0.011	0.000	0.000	0.000	0.000
20	K	24	LEU	0	-0.019	0.009	24.814	-0.011	-0.011	0.000	0.000	0.000	0.000
21	K	25	HIS	0	0.070	0.034	26.235	0.003	0.003	0.000	0.000	0.000	0.000
22	K	26	PRO	0	0.065	0.017	23.411	-0.001	-0.001	0.000	0.000	0.000	0.000
23	K	27	ALA	0	-0.002	0.001	24.259	-0.006	-0.006	0.000	0.000	0.000	0.000
24	K	28	LEU	0	-0.014	-0.021	26.403	-0.004	-0.004	0.000	0.000	0.000	0.000
25	K	29	ALA	0	0.012	0.011	22.279	0.001	0.001	0.000	0.000	0.000	0.000
26	K	30	ILE	0	-0.003	-0.001	19.742	0.000	0.000	0.000	0.000	0.000	0.000
27	K	31	LEU	0	-0.001	0.006	22.645	-0.006	-0.006	0.000	0.000	0.000	0.000
28	K	32	ILE	0	0.022	0.005	23.522	-0.004	-0.004	0.000	0.000	0.000	0.000
29	K	33	ILE	0	0.010	0.002	18.140	-0.002	-0.002	0.000	0.000	0.000	0.000
30	K	34	ALA	0	-0.018	-0.003	20.956	-0.009	-0.009	0.000	0.000	0.000	0.000
31	K	35	ILE	0	0.026	0.001	22.683	-0.007	-0.007	0.000	0.000	0.000	0.000
32	K	36	ILE	0	0.007	0.008	21.671	-0.003	-0.003	0.000	0.000	0.000	0.000
33	K	37	VAL	0	0.023	0.004	18.317	-0.004	-0.004	0.000	0.000	0.000	0.000
34	K	38	SER	0	-0.048	-0.013	21.589	-0.011	-0.011	0.000	0.000	0.000	0.000
35	K	39	LEU	0	-0.009	-0.012	24.545	-0.005	-0.005	0.000	0.000	0.000	0.000
36	K	40	ILE	0	-0.019	-0.008	20.319	0.000	0.000	0.000	0.000	0.000	0.000
37	K	41	ILE	0	-0.053	-0.021	20.111	-0.006	-0.006	0.000	0.000	0.000	0.000
38	K	42	ASN	0	-0.036	-0.016	23.468	-0.009	-0.009	0.000	0.000	0.000	0.000
39	K	43	ILE	0	-0.038	-0.009	26.927	0.000	0.000	0.000	0.000	0.000	0.000
40	K	44	ALA	0	-0.052	-0.009	23.496	-0.006	-0.006	0.000	0.000	0.000	0.000
41	K	102	PRO	0	0.052	0.004	19.731	-0.006	-0.006	0.000	0.000	0.000	0.000
42	K	103	MET	0	0.064	0.038	19.698	0.001	0.001	0.000	0.000	0.000	0.000
43	K	104	ILE	0	0.013	-0.006	16.071	-0.004	-0.004	0.000	0.000	0.000	0.000
44	K	105	TYR	0	0.005	0.006	12.800	-0.016	-0.016	0.000	0.000	0.000	0.000
45	K	106	THR	0	0.054	0.014	15.259	0.000	0.000	0.000	0.000	0.000	0.000
46	K	107	TRP	0	-0.013	-0.008	16.330	0.015	0.015	0.000	0.000	0.000	0.000
47	K	108	VAL	0	0.009	0.009	10.492	-0.017	-0.017	0.000	0.000	0.000	0.000
48	K	109	PRO	0	0.020	0.003	12.072	-0.026	-0.026	0.000	0.000	0.000	0.000
49	K	110	ILE	0	0.058	0.036	13.357	0.007	0.007	0.000	0.000	0.000	0.000
50	K	111	ILE	0	0.008	0.008	10.637	0.001	0.001	0.000	0.000	0.000	0.000
51	K	112	LEU	0	-0.011	-0.007	8.487	-0.043	-0.043	0.000	0.000	0.000	0.000
52	K	113	ILE	0	0.004	0.020	9.916	0.039	0.039	0.000	0.000	0.000	0.000
53	K	114	PHE	0	-0.013	-0.009	12.806	0.021	0.021	0.000	0.000	0.000	0.000
54	K	115	ILE	0	-0.024	0.001	5.760	0.019	0.019	0.000	0.000	0.000	0.000
55	K	116	TYR	0	-0.008	-0.029	9.868	-0.006	-0.006	0.000	0.000	0.000	0.000
56	K	117	LEU	0	0.030	0.007	10.857	0.041	0.041	0.000	0.000	0.000	0.000
57	K	118	ARG	1	0.914	0.960	11.996	0.142	0.142	0.000	0.000	0.000	0.000
58	K	119	HIS	1	0.858	0.939	10.393	-0.249	-0.249	0.000	0.000	0.000	0.000
59	K	120	VAL	0	-0.006	0.007	12.494	0.034	0.034	0.000	0.000	0.000	0.000
60	K	121	TYR	0	0.032	-0.003	15.654	0.008	0.008	0.000	0.000	0.000	0.000
61	K	122	GLY	0	-0.030	-0.001	16.473	-0.010	-0.010	0.000	0.000	0.000	0.000
62	K	123	PHE	0	0.020	0.006	17.571	0.016	0.016	0.000	0.000	0.000	0.000
63	K	124	GLY	0	-0.026	-0.016	17.020	-0.016	-0.016	0.000	0.000	0.000	0.000
64	K	125	GLY	0	-0.031	-0.003	15.689	0.018	0.018	0.000	0.000	0.000	0.000
65	K	126	VAL	0	0.020	0.006	15.982	0.007	0.007	0.000	0.000	0.000	0.000
66	K	127	TYR	0	-0.002	0.013	17.689	-0.003	-0.003	0.000	0.000	0.000	0.000
67	K	128	GLN	0	0.018	0.007	20.555	-0.007	-0.007	0.000	0.000	0.000	0.000
68	K	129	GLU	-1	-1.000	-0.983	18.737	0.180	0.180	0.000	0.000	0.000	0.000
69	K	130	LEU	0	-0.007	-0.007	21.227	0.002	0.002	0.000	0.000	0.000	0.000
70	K	131	ASN	0	-0.076	-0.047	23.043	0.001	0.001	0.000	0.000	0.000	0.000
71	K	132	PRO	0	0.051	0.024	25.258	-0.007	-0.007	0.000	0.000	0.000	0.000
72	K	133	GLY	0	-0.028	-0.026	27.196	-0.003	-0.003	0.000	0.000	0.000	0.000
73	K	134	TRP	0	-0.001	0.003	21.722	-0.001	-0.001	0.000	0.000	0.000	0.000
74	K	135	ASN	0	-0.004	0.003	27.017	0.001	0.001	0.000	0.000	0.000	0.000
75	K	136	GLY	0	0.043	0.025	25.134	-0.007	-0.007	0.000	0.000	0.000	0.000
76	K	137	VAL	0	-0.070	-0.038	25.246	0.002	0.002	0.000	0.000	0.000	0.000
77	K	138	VAL	0	0.041	0.026	23.384	0.005	0.005	0.000	0.000	0.000	0.000
78	K	139	VAL	0	-0.001	-0.024	25.885	0.005	0.005	0.000	0.000	0.000	0.000
79	K	140	TYR	0	0.030	0.026	29.225	-0.005	-0.005	0.000	0.000	0.000	0.000
80	K	141	LEU	0	0.026	0.002	31.367	0.002	0.002	0.000	0.000	0.000	0.000
81	K	142	PRO	0	0.025	0.028	34.226	-0.003	-0.003	0.000	0.000	0.000	0.000
82	K	143	ILE	0	0.031	0.020	37.852	0.000	0.000	0.000	0.000	0.000	0.000
83	K	144	ILE	0	0.048	-0.007	33.247	-0.002	-0.002	0.000	0.000	0.000	0.000
84	K	145	LEU	0	0.017	-0.001	31.195	-0.003	-0.003	0.000	0.000	0.000	0.000
85	K	146	SER	0	-0.049	-0.023	35.158	-0.002	-0.002	0.000	0.000	0.000	0.000
86	K	147	LYS	1	0.915	0.954	38.458	0.008	0.008	0.000	0.000	0.000	0.000
87	K	148	ILE	0	-0.011	0.026	33.200	-0.001	-0.001	0.000	0.000	0.000	0.000
88	K	149	LEU	0	0.009	0.013	36.455	-0.001	-0.001	0.000	0.000	0.000	0.000
89	K	150	PHE	0	0.023	0.003	31.398	-0.002	-0.002	0.000	0.000	0.000	0.000
90	K	151	ILE	0	0.019	0.007	33.827	-0.003	-0.003	0.000	0.000	0.000	0.000
91	K	152	ASP	-1	-0.786	-0.904	35.156	-0.029	-0.029	0.000	0.000	0.000	0.000
92	K	153	PHE	0	-0.010	0.004	26.027	-0.002	-0.002	0.000	0.000	0.000	0.000
93	K	154	TRP	0	0.023	0.008	28.799	-0.005	-0.005	0.000	0.000	0.000	0.000
94	K	155	HIS	0	0.024	0.003	31.678	-0.001	-0.001	0.000	0.000	0.000	0.000
95	K	156	TRP	0	-0.007	0.003	24.707	-0.004	-0.004	0.000	0.000	0.000	0.000
96	K	157	LEU	0	-0.010	-0.012	25.542	-0.003	-0.003	0.000	0.000	0.000	0.000
97	K	158	GLY	0	0.000	-0.032	28.119	-0.006	-0.006	0.000	0.000	0.000	0.000
98	K	159	SER	0	-0.025	-0.015	30.611	-0.001	-0.001	0.000	0.000	0.000	0.000
99	K	160	ILE	0	-0.046	-0.013	24.440	-0.001	-0.001	0.000	0.000	0.000	0.000
100	K	161	PHE	0	-0.034	-0.017	21.624	-0.007	-0.007	0.000	0.000	0.000	0.000
101	K	162	TYR	0	-0.033	0.016	26.810	-0.004	-0.004	0.000	0.000	0.000	0.000
102	K	163	LYS	1	0.921	0.975	25.907	0.073	0.073	0.000	0.000	0.000	0.000
103	K	164	GLY	0	0.010	-0.001	31.588	0.005	0.005	0.000	0.000	0.000	0.000
104	K	165	GLY	0	0.014	0.000	33.415	-0.003	-0.003	0.000	0.000	0.000	0.000
105	K	166	PHE	0	-0.025	-0.027	35.006	0.004	0.004	0.000	0.000	0.000	0.000
106	K	167	LYS	1	0.947	0.978	36.867	0.043	0.043	0.000	0.000	0.000	0.000
107	K	168	ILE	0	0.019	0.011	36.325	-0.001	-0.001	0.000	0.000	0.000	0.000
108	K	169	VAL	0	-0.024	-0.005	38.809	0.000	0.000	0.000	0.000	0.000	0.000
109	K	170	SER	0	0.005	0.004	41.998	0.001	0.001	0.000	0.000	0.000	0.000
110	K	171	ASN	0	0.005	0.009	39.952	-0.001	-0.001	0.000	0.000	0.000	0.000
111	K	172	THR	0	-0.042	-0.025	41.379	0.001	0.001	0.000	0.000	0.000	0.000
112	K	173	ALA	0	0.038	0.025	41.492	-0.001	-0.001	0.000	0.000	0.000	0.000
113	K	174	LEU	0	-0.012	-0.013	36.528	-0.001	-0.001	0.000	0.000	0.000	0.000
114	K	175	GLY	0	0.016	0.020	36.652	0.001	0.001	0.000	0.000	0.000	0.000
115	K	176	TRP	0	0.073	0.015	31.477	0.003	0.003	0.000	0.000	0.000	0.000
116	K	177	LEU	0	0.007	0.015	28.861	0.001	0.001	0.000	0.000	0.000	0.000
117	K	178	GLY	0	0.057	0.021	33.511	0.000	0.000	0.000	0.000	0.000	0.000
118	K	179	TRP	0	0.048	0.021	34.636	0.002	0.002	0.000	0.000	0.000	0.000
119	K	180	TYR	0	0.025	0.009	31.964	0.000	0.000	0.000	0.000	0.000	0.000
120	K	181	ILE	0	0.015	0.005	29.406	0.000	0.000	0.000	0.000	0.000	0.000
121	K	182	LEU	0	-0.009	0.002	33.323	0.002	0.002	0.000	0.000	0.000	0.000
122	K	183	CYS	0	0.036	0.022	36.339	0.002	0.002	0.000	0.000	0.000	0.000
123	K	184	SER	0	0.014	0.009	33.828	0.002	0.002	0.000	0.000	0.000	0.000
124	K	185	PHE	0	-0.036	-0.009	33.603	0.000	0.000	0.000	0.000	0.000	0.000
125	K	186	ALA	0	0.000	0.002	35.216	0.003	0.003	0.000	0.000	0.000	0.000
126	K	187	THR	0	-0.031	-0.028	38.287	0.003	0.003	0.000	0.000	0.000	0.000
127	K	188	SER	0	-0.014	-0.035	35.244	0.000	0.000	0.000	0.000	0.000	0.000
128	K	189	THR	0	-0.042	-0.026	37.090	0.002	0.002	0.000	0.000	0.000	0.000
129	K	190	VAL	0	-0.035	-0.027	38.687	0.002	0.002	0.000	0.000	0.000	0.000
130	K	191	LEU	0	0.023	0.021	37.938	0.001	0.001	0.000	0.000	0.000	0.000
131	K	192	ARG	1	0.942	0.976	31.829	0.052	0.052	0.000	0.000	0.000	0.000
132	K	193	LYS	1	0.900	0.964	39.730	0.029	0.029	0.000	0.000	0.000	0.000
133	K	194	ILE	0	-0.014	0.020	42.712	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)