FMO DATABASE

FMODB ID: 72YGK

Calculation Name: 5C8J-I-Xray372

Preferred Name:

Target Type:

Ligand Name: dodecyl-beta-d-maltoside

ligand 3-letter code: LMT

PDB ID: 5C8J

Chain ID: I

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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1053309.313451
FMO2-HF: Nuclear repulsion	1001061.01388
FMO2-HF: Total energy	-52248.299571
FMO2-MP2: Total energy	-52404.826123

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(I:5:ILE)

Summations of interaction energy for fragment #1(I: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.
-7.21	-3.457	1.134	-1.736	-3.153	0.008

Interaction energy analysis for fragmet #1(I:5:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / 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	I	7	ASP	-1	-0.810	-0.882	3.250	0.293	2.638	0.011	-0.972	-1.385	0.003
4	I	8	ILE	0	-0.015	-0.005	2.594	-3.568	-2.367	1.124	-0.731	-1.594	0.005
5	I	9	TYR	0	-0.013	-0.020	4.507	-1.394	-1.187	-0.001	-0.033	-0.174	0.000
6	I	10	TYR	0	-0.001	0.001	6.300	-0.346	-0.346	0.000	0.000	0.000	0.000
7	I	11	LYS	1	0.937	0.946	7.588	-2.008	-2.008	0.000	0.000	0.000	0.000
8	I	12	THR	0	-0.048	-0.030	8.346	-0.215	-0.215	0.000	0.000	0.000	0.000
9	I	13	LEU	0	-0.002	0.001	10.549	-0.140	-0.140	0.000	0.000	0.000	0.000
10	I	14	ASP	-1	-0.808	-0.894	12.301	0.353	0.353	0.000	0.000	0.000	0.000
11	I	15	ALA	0	-0.037	-0.014	14.144	-0.073	-0.073	0.000	0.000	0.000	0.000
12	I	16	ILE	0	-0.015	-0.001	14.612	-0.052	-0.052	0.000	0.000	0.000	0.000
13	I	17	PHE	0	0.015	-0.003	16.123	-0.051	-0.051	0.000	0.000	0.000	0.000
14	I	18	MET	0	0.030	0.011	17.671	-0.043	-0.043	0.000	0.000	0.000	0.000
15	I	19	PRO	0	-0.060	-0.029	19.865	-0.028	-0.028	0.000	0.000	0.000	0.000
16	I	20	ILE	0	-0.016	-0.008	20.808	-0.018	-0.018	0.000	0.000	0.000	0.000
17	I	21	ILE	0	-0.026	-0.002	17.716	-0.017	-0.017	0.000	0.000	0.000	0.000
18	I	22	LYS	1	0.955	0.975	22.287	-0.190	-0.190	0.000	0.000	0.000	0.000
19	I	23	VAL	0	-0.024	0.001	24.790	-0.011	-0.011	0.000	0.000	0.000	0.000
20	I	24	LEU	0	-0.020	0.008	24.757	-0.011	-0.011	0.000	0.000	0.000	0.000
21	I	25	HIS	0	0.061	0.031	26.087	0.003	0.003	0.000	0.000	0.000	0.000
22	I	26	PRO	0	0.079	0.023	23.355	-0.001	-0.001	0.000	0.000	0.000	0.000
23	I	27	ALA	0	-0.013	0.002	24.221	-0.006	-0.006	0.000	0.000	0.000	0.000
24	I	28	LEU	0	-0.024	-0.029	26.437	-0.004	-0.004	0.000	0.000	0.000	0.000
25	I	29	ALA	0	0.015	0.015	22.165	0.001	0.001	0.000	0.000	0.000	0.000
26	I	30	ILE	0	-0.001	0.001	19.821	0.000	0.000	0.000	0.000	0.000	0.000
27	I	31	LEU	0	0.001	0.005	22.614	-0.005	-0.005	0.000	0.000	0.000	0.000
28	I	32	ILE	0	0.019	0.005	23.519	-0.004	-0.004	0.000	0.000	0.000	0.000
29	I	33	ILE	0	0.015	0.004	18.182	-0.001	-0.001	0.000	0.000	0.000	0.000
30	I	34	ALA	0	-0.034	-0.011	21.011	-0.009	-0.009	0.000	0.000	0.000	0.000
31	I	35	ILE	0	0.014	-0.008	22.765	-0.006	-0.006	0.000	0.000	0.000	0.000
32	I	36	ILE	0	0.013	0.014	21.483	-0.002	-0.002	0.000	0.000	0.000	0.000
33	I	37	VAL	0	0.017	0.005	18.399	-0.004	-0.004	0.000	0.000	0.000	0.000
34	I	38	SER	0	-0.024	-0.009	21.633	-0.010	-0.010	0.000	0.000	0.000	0.000
35	I	39	LEU	0	-0.021	-0.015	24.763	-0.004	-0.004	0.000	0.000	0.000	0.000
36	I	40	ILE	0	-0.014	-0.008	19.958	0.000	0.000	0.000	0.000	0.000	0.000
37	I	41	ILE	0	-0.025	-0.010	20.550	-0.007	-0.007	0.000	0.000	0.000	0.000
38	I	42	ASN	0	-0.020	-0.008	23.959	-0.008	-0.008	0.000	0.000	0.000	0.000
39	I	43	ILE	0	-0.020	0.011	25.577	0.001	0.001	0.000	0.000	0.000	0.000
40	I	44	ALA	0	-0.032	-0.007	22.800	-0.001	-0.001	0.000	0.000	0.000	0.000
41	I	45	THR	0	-0.076	-0.037	24.540	-0.001	-0.001	0.000	0.000	0.000	0.000
42	I	102	PRO	0	0.090	0.017	21.065	-0.004	-0.004	0.000	0.000	0.000	0.000
43	I	103	MET	0	0.054	0.027	20.311	0.000	0.000	0.000	0.000	0.000	0.000
44	I	104	ILE	0	0.031	0.024	16.351	-0.006	-0.006	0.000	0.000	0.000	0.000
45	I	105	TYR	0	0.000	0.009	16.143	-0.021	-0.021	0.000	0.000	0.000	0.000
46	I	106	THR	0	0.027	-0.001	16.090	0.002	0.002	0.000	0.000	0.000	0.000
47	I	107	TRP	0	-0.034	-0.033	15.778	0.007	0.007	0.000	0.000	0.000	0.000
48	I	108	VAL	0	0.019	0.028	10.561	-0.022	-0.022	0.000	0.000	0.000	0.000
49	I	109	PRO	0	0.030	0.009	11.671	-0.022	-0.022	0.000	0.000	0.000	0.000
50	I	110	ILE	0	0.054	0.024	13.379	0.009	0.009	0.000	0.000	0.000	0.000
51	I	111	ILE	0	-0.017	0.002	10.102	0.003	0.003	0.000	0.000	0.000	0.000
52	I	112	LEU	0	0.007	0.003	8.674	-0.043	-0.043	0.000	0.000	0.000	0.000
53	I	113	ILE	0	0.018	0.027	9.845	0.045	0.045	0.000	0.000	0.000	0.000
54	I	114	PHE	0	-0.017	-0.021	12.890	0.020	0.020	0.000	0.000	0.000	0.000
55	I	115	ILE	0	-0.039	-0.003	5.964	0.016	0.016	0.000	0.000	0.000	0.000
56	I	116	TYR	0	-0.020	-0.036	10.085	-0.007	-0.007	0.000	0.000	0.000	0.000
57	I	117	LEU	0	0.047	0.009	11.132	0.036	0.036	0.000	0.000	0.000	0.000
58	I	118	ARG	1	0.944	0.979	11.898	0.173	0.173	0.000	0.000	0.000	0.000
59	I	119	HIS	1	0.860	0.944	10.452	-0.229	-0.229	0.000	0.000	0.000	0.000
60	I	120	VAL	0	-0.010	0.009	12.574	0.038	0.038	0.000	0.000	0.000	0.000
61	I	121	TYR	0	0.018	-0.007	15.822	0.006	0.006	0.000	0.000	0.000	0.000
62	I	122	GLY	0	-0.015	0.000	16.520	-0.011	-0.011	0.000	0.000	0.000	0.000
63	I	123	PHE	0	0.010	0.001	17.478	0.016	0.016	0.000	0.000	0.000	0.000
64	I	124	GLY	0	-0.009	-0.004	16.893	-0.008	-0.008	0.000	0.000	0.000	0.000
65	I	125	GLY	0	-0.014	0.005	15.766	0.020	0.020	0.000	0.000	0.000	0.000
66	I	126	VAL	0	0.023	-0.003	15.623	0.002	0.002	0.000	0.000	0.000	0.000
67	I	127	TYR	0	-0.013	-0.001	17.430	0.000	0.000	0.000	0.000	0.000	0.000
68	I	128	GLN	0	0.001	-0.005	20.141	-0.008	-0.008	0.000	0.000	0.000	0.000
69	I	129	GLU	-1	-0.992	-0.982	17.173	0.206	0.206	0.000	0.000	0.000	0.000
70	I	130	LEU	0	-0.077	-0.037	20.218	0.006	0.006	0.000	0.000	0.000	0.000
71	I	131	ASN	0	-0.048	-0.019	23.035	0.001	0.001	0.000	0.000	0.000	0.000
72	I	132	PRO	0	0.049	0.023	25.228	-0.006	-0.006	0.000	0.000	0.000	0.000
73	I	133	GLY	0	-0.028	-0.021	27.312	-0.003	-0.003	0.000	0.000	0.000	0.000
74	I	134	TRP	0	-0.003	-0.010	21.590	0.000	0.000	0.000	0.000	0.000	0.000
75	I	135	ASN	0	0.004	0.002	26.701	0.001	0.001	0.000	0.000	0.000	0.000
76	I	136	GLY	0	0.050	0.024	24.780	-0.007	-0.007	0.000	0.000	0.000	0.000
77	I	137	VAL	0	-0.090	-0.045	25.723	0.004	0.004	0.000	0.000	0.000	0.000
78	I	138	VAL	0	0.080	0.051	22.675	0.005	0.005	0.000	0.000	0.000	0.000
79	I	139	VAL	0	-0.011	-0.025	26.108	0.005	0.005	0.000	0.000	0.000	0.000
80	I	140	TYR	0	0.020	0.024	29.449	-0.005	-0.005	0.000	0.000	0.000	0.000
81	I	141	LEU	0	0.015	-0.006	31.109	0.002	0.002	0.000	0.000	0.000	0.000
82	I	142	PRO	0	0.040	0.035	34.373	-0.002	-0.002	0.000	0.000	0.000	0.000
83	I	143	ILE	0	0.031	0.024	38.124	0.000	0.000	0.000	0.000	0.000	0.000
84	I	144	ILE	0	0.030	-0.025	33.595	-0.002	-0.002	0.000	0.000	0.000	0.000
85	I	145	LEU	0	0.011	0.005	31.855	-0.002	-0.002	0.000	0.000	0.000	0.000
86	I	146	SER	0	-0.026	-0.017	35.148	-0.002	-0.002	0.000	0.000	0.000	0.000
87	I	147	LYS	1	0.936	0.969	38.321	0.007	0.007	0.000	0.000	0.000	0.000
88	I	148	ILE	0	-0.023	0.019	33.141	-0.001	-0.001	0.000	0.000	0.000	0.000
89	I	149	LEU	0	0.003	0.009	36.415	-0.001	-0.001	0.000	0.000	0.000	0.000
90	I	150	PHE	0	0.022	0.001	31.270	-0.002	-0.002	0.000	0.000	0.000	0.000
91	I	151	ILE	0	0.003	-0.002	34.011	-0.003	-0.003	0.000	0.000	0.000	0.000
92	I	152	ASP	-1	-0.829	-0.927	35.614	-0.029	-0.029	0.000	0.000	0.000	0.000
93	I	153	PHE	0	-0.029	-0.010	26.301	-0.002	-0.002	0.000	0.000	0.000	0.000
94	I	154	TRP	0	0.009	-0.003	29.367	-0.005	-0.005	0.000	0.000	0.000	0.000
95	I	155	HIS	0	0.049	0.024	31.464	-0.003	-0.003	0.000	0.000	0.000	0.000
96	I	156	TRP	0	0.004	0.011	25.155	-0.004	-0.004	0.000	0.000	0.000	0.000
97	I	157	LEU	0	-0.017	-0.009	26.014	-0.003	-0.003	0.000	0.000	0.000	0.000
98	I	158	GLY	0	-0.008	-0.018	27.737	-0.006	-0.006	0.000	0.000	0.000	0.000
99	I	159	SER	0	-0.020	-0.015	30.163	-0.001	-0.001	0.000	0.000	0.000	0.000
100	I	160	ILE	0	-0.045	-0.010	24.253	0.000	0.000	0.000	0.000	0.000	0.000
101	I	161	PHE	0	-0.047	-0.035	21.196	-0.008	-0.008	0.000	0.000	0.000	0.000
102	I	162	TYR	0	-0.027	0.001	26.668	-0.002	-0.002	0.000	0.000	0.000	0.000
103	I	163	LYS	1	0.911	0.964	24.500	0.083	0.083	0.000	0.000	0.000	0.000
104	I	164	GLY	0	0.005	0.004	30.816	0.006	0.006	0.000	0.000	0.000	0.000
105	I	165	GLY	0	0.020	0.002	32.605	-0.005	-0.005	0.000	0.000	0.000	0.000
106	I	166	PHE	0	-0.036	-0.016	35.228	0.003	0.003	0.000	0.000	0.000	0.000
107	I	167	LYS	1	0.978	0.987	36.503	0.037	0.037	0.000	0.000	0.000	0.000
108	I	168	ILE	0	0.015	0.007	36.213	0.000	0.000	0.000	0.000	0.000	0.000
109	I	169	VAL	0	-0.012	0.003	38.448	0.000	0.000	0.000	0.000	0.000	0.000
110	I	170	SER	0	-0.001	0.001	41.794	0.002	0.002	0.000	0.000	0.000	0.000
111	I	171	ASN	0	0.057	0.033	41.463	-0.003	-0.003	0.000	0.000	0.000	0.000
112	I	172	THR	0	-0.065	-0.042	41.353	0.001	0.001	0.000	0.000	0.000	0.000
113	I	173	ALA	0	0.040	0.028	41.681	-0.001	-0.001	0.000	0.000	0.000	0.000
114	I	174	LEU	0	-0.002	-0.006	36.614	-0.001	-0.001	0.000	0.000	0.000	0.000
115	I	175	GLY	0	0.035	0.024	36.288	0.001	0.001	0.000	0.000	0.000	0.000
116	I	176	TRP	0	0.072	0.013	30.863	0.002	0.002	0.000	0.000	0.000	0.000
117	I	177	LEU	0	-0.008	0.006	28.514	0.001	0.001	0.000	0.000	0.000	0.000
118	I	178	GLY	0	0.063	0.026	33.188	0.000	0.000	0.000	0.000	0.000	0.000
119	I	179	TRP	0	0.062	0.031	34.337	0.002	0.002	0.000	0.000	0.000	0.000
120	I	180	TYR	0	0.044	0.028	31.355	0.000	0.000	0.000	0.000	0.000	0.000
121	I	181	ILE	0	0.021	0.010	29.190	0.000	0.000	0.000	0.000	0.000	0.000
122	I	182	LEU	0	-0.007	0.006	33.050	0.002	0.002	0.000	0.000	0.000	0.000
123	I	183	CYS	0	-0.020	-0.010	36.125	0.002	0.002	0.000	0.000	0.000	0.000
124	I	184	SER	0	0.046	0.021	33.616	0.002	0.002	0.000	0.000	0.000	0.000
125	I	185	PHE	0	-0.051	-0.017	33.509	0.001	0.001	0.000	0.000	0.000	0.000
126	I	186	ALA	0	-0.001	0.002	35.096	0.003	0.003	0.000	0.000	0.000	0.000
127	I	187	THR	0	-0.029	-0.033	38.130	0.003	0.003	0.000	0.000	0.000	0.000
128	I	188	SER	0	-0.013	-0.033	35.090	0.000	0.000	0.000	0.000	0.000	0.000
129	I	189	THR	0	-0.048	-0.027	37.035	0.002	0.002	0.000	0.000	0.000	0.000
130	I	190	VAL	0	-0.033	-0.026	38.651	0.002	0.002	0.000	0.000	0.000	0.000
131	I	191	LEU	0	0.019	0.020	37.793	0.001	0.001	0.000	0.000	0.000	0.000
132	I	192	ARG	1	0.941	0.974	31.686	0.051	0.051	0.000	0.000	0.000	0.000
133	I	193	LYS	1	0.901	0.964	39.682	0.029	0.029	0.000	0.000	0.000	0.000
134	I	194	ILE	0	-0.013	0.021	42.710	0.001	0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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