FMO DATABASE

FMODB ID: 2J42R

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	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	-1055734.972582
FMO2-HF: Nuclear repulsion	1003486.124886
FMO2-HF: Total energy	-52248.847696
FMO2-MP2: Total energy	-52405.242661

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.
-6.041	-2.429	1.128	-1.605	-3.135	0.007

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 : 0.033 / 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

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	-0.801	-0.878	3.156	1.320	3.349	0.035	-0.769	-1.296	0.003
4	I	8	ILE	0	0.046	0.026	2.667	-3.687	-2.430	1.094	-0.750	-1.601	0.004
5	I	9	TYR	0	-0.039	-0.029	4.213	-1.412	-1.086	-0.001	-0.086	-0.238	0.000
6	I	10	TYR	0	-0.033	-0.029	5.963	-0.201	-0.201	0.000	0.000	0.000	0.000
7	I	11	LYS	1	0.892	0.933	7.841	-1.969	-1.969	0.000	0.000	0.000	0.000
8	I	12	THR	0	-0.038	-0.025	8.121	-0.184	-0.184	0.000	0.000	0.000	0.000
9	I	13	LEU	0	-0.004	0.007	10.256	-0.118	-0.118	0.000	0.000	0.000	0.000
10	I	14	ASP	-1	-0.789	-0.894	12.053	0.348	0.348	0.000	0.000	0.000	0.000
11	I	15	ALA	0	-0.027	-0.014	13.732	-0.059	-0.059	0.000	0.000	0.000	0.000
12	I	16	ILE	0	-0.013	0.005	14.318	-0.045	-0.045	0.000	0.000	0.000	0.000
13	I	17	PHE	0	0.009	-0.002	15.983	-0.046	-0.046	0.000	0.000	0.000	0.000
14	I	18	MET	0	0.011	0.004	17.398	-0.039	-0.039	0.000	0.000	0.000	0.000
15	I	19	PRO	0	-0.054	-0.030	19.611	-0.020	-0.020	0.000	0.000	0.000	0.000
16	I	20	ILE	0	0.007	0.002	20.702	-0.015	-0.015	0.000	0.000	0.000	0.000
17	I	21	ILE	0	-0.015	-0.005	17.119	-0.015	-0.015	0.000	0.000	0.000	0.000
18	I	22	LYS	1	0.940	0.966	21.752	-0.177	-0.177	0.000	0.000	0.000	0.000
19	I	23	VAL	0	-0.028	0.003	24.626	-0.007	-0.007	0.000	0.000	0.000	0.000
20	I	24	LEU	0	-0.030	0.000	24.120	-0.009	-0.009	0.000	0.000	0.000	0.000
21	I	25	HIS	0	0.043	0.023	25.818	0.002	0.002	0.000	0.000	0.000	0.000
22	I	26	PRO	0	0.068	0.026	23.355	-0.003	-0.003	0.000	0.000	0.000	0.000
23	I	27	ALA	0	-0.001	-0.003	23.940	-0.007	-0.007	0.000	0.000	0.000	0.000
24	I	28	LEU	0	-0.016	-0.014	26.035	-0.005	-0.005	0.000	0.000	0.000	0.000
25	I	29	ALA	0	0.021	0.018	21.620	-0.001	-0.001	0.000	0.000	0.000	0.000
26	I	30	ILE	0	-0.005	-0.005	19.602	-0.004	-0.004	0.000	0.000	0.000	0.000
27	I	31	LEU	0	-0.009	0.005	22.275	-0.007	-0.007	0.000	0.000	0.000	0.000
28	I	32	ILE	0	0.018	-0.001	23.019	-0.005	-0.005	0.000	0.000	0.000	0.000
29	I	33	ILE	0	0.012	0.007	17.746	-0.004	-0.004	0.000	0.000	0.000	0.000
30	I	34	ALA	0	-0.018	-0.010	21.006	-0.009	-0.009	0.000	0.000	0.000	0.000
31	I	35	ILE	0	0.012	0.002	22.436	-0.006	-0.006	0.000	0.000	0.000	0.000
32	I	36	ILE	0	0.017	0.009	20.661	-0.003	-0.003	0.000	0.000	0.000	0.000
33	I	37	VAL	0	-0.004	-0.006	17.787	-0.005	-0.005	0.000	0.000	0.000	0.000
34	I	38	SER	0	-0.012	0.001	20.902	-0.008	-0.008	0.000	0.000	0.000	0.000
35	I	39	LEU	0	-0.018	-0.010	24.111	-0.002	-0.002	0.000	0.000	0.000	0.000
36	I	40	ILE	0	0.002	0.003	19.535	-0.001	-0.001	0.000	0.000	0.000	0.000
37	I	41	ILE	0	-0.018	-0.014	19.817	-0.006	-0.006	0.000	0.000	0.000	0.000
38	I	42	ASN	0	-0.013	0.005	23.365	-0.006	-0.006	0.000	0.000	0.000	0.000
39	I	43	ILE	0	-0.017	-0.002	25.163	0.000	0.000	0.000	0.000	0.000	0.000
40	I	44	ALA	0	-0.045	-0.013	22.384	0.000	0.000	0.000	0.000	0.000	0.000
41	I	45	THR	0	-0.102	-0.054	24.412	-0.001	-0.001	0.000	0.000	0.000	0.000
42	I	102	PRO	0	0.072	0.011	21.292	-0.003	-0.003	0.000	0.000	0.000	0.000
43	I	103	MET	0	0.045	0.031	20.288	-0.003	-0.003	0.000	0.000	0.000	0.000
44	I	104	ILE	0	0.030	0.024	15.871	-0.005	-0.005	0.000	0.000	0.000	0.000
45	I	105	TYR	0	0.012	0.013	15.911	-0.023	-0.023	0.000	0.000	0.000	0.000
46	I	106	THR	0	0.023	-0.008	15.973	-0.001	-0.001	0.000	0.000	0.000	0.000
47	I	107	TRP	0	-0.021	-0.022	15.588	0.008	0.008	0.000	0.000	0.000	0.000
48	I	108	VAL	0	0.012	0.022	10.305	-0.017	-0.017	0.000	0.000	0.000	0.000
49	I	109	PRO	0	0.029	0.010	11.486	-0.026	-0.026	0.000	0.000	0.000	0.000
50	I	110	ILE	0	0.039	0.022	13.085	0.008	0.008	0.000	0.000	0.000	0.000
51	I	111	ILE	0	0.000	-0.003	9.841	0.006	0.006	0.000	0.000	0.000	0.000
52	I	112	LEU	0	0.019	0.011	8.003	-0.024	-0.024	0.000	0.000	0.000	0.000
53	I	113	ILE	0	0.032	0.039	9.213	0.030	0.030	0.000	0.000	0.000	0.000
54	I	114	PHE	0	-0.003	-0.006	12.295	0.026	0.026	0.000	0.000	0.000	0.000
55	I	115	ILE	0	-0.027	-0.010	5.695	0.027	0.027	0.000	0.000	0.000	0.000
56	I	116	TYR	0	-0.020	-0.024	9.878	-0.003	-0.003	0.000	0.000	0.000	0.000
57	I	117	LEU	0	0.029	0.000	10.815	0.046	0.046	0.000	0.000	0.000	0.000
58	I	118	ARG	1	0.923	0.964	11.664	0.147	0.147	0.000	0.000	0.000	0.000
59	I	119	HIS	1	0.881	0.955	10.499	-0.244	-0.244	0.000	0.000	0.000	0.000
60	I	120	VAL	0	-0.008	0.007	12.582	0.035	0.035	0.000	0.000	0.000	0.000
61	I	121	TYR	0	0.013	-0.010	15.754	0.007	0.007	0.000	0.000	0.000	0.000
62	I	122	GLY	0	0.004	0.012	16.509	-0.012	-0.012	0.000	0.000	0.000	0.000
63	I	123	PHE	0	-0.015	-0.013	17.482	0.016	0.016	0.000	0.000	0.000	0.000
64	I	124	GLY	0	-0.003	-0.003	17.420	-0.007	-0.007	0.000	0.000	0.000	0.000
65	I	125	GLY	0	-0.004	0.008	15.696	0.021	0.021	0.000	0.000	0.000	0.000
66	I	126	VAL	0	0.001	-0.007	15.763	-0.002	-0.002	0.000	0.000	0.000	0.000
67	I	127	TYR	0	0.000	-0.007	17.590	-0.002	-0.002	0.000	0.000	0.000	0.000
68	I	128	GLN	0	-0.020	-0.017	20.274	-0.007	-0.007	0.000	0.000	0.000	0.000
69	I	129	GLU	-1	-0.980	-0.979	16.857	0.235	0.235	0.000	0.000	0.000	0.000
70	I	130	LEU	0	-0.057	-0.030	20.090	0.003	0.003	0.000	0.000	0.000	0.000
71	I	131	ASN	0	-0.050	-0.010	23.010	-0.004	-0.004	0.000	0.000	0.000	0.000
72	I	132	PRO	0	0.065	0.030	25.670	-0.008	-0.008	0.000	0.000	0.000	0.000
73	I	133	GLY	0	-0.019	-0.013	27.099	-0.004	-0.004	0.000	0.000	0.000	0.000
74	I	134	TRP	0	-0.022	-0.013	21.518	-0.005	-0.005	0.000	0.000	0.000	0.000
75	I	135	ASN	0	0.016	0.003	26.157	0.002	0.002	0.000	0.000	0.000	0.000
76	I	136	GLY	0	0.017	0.022	24.333	-0.007	-0.007	0.000	0.000	0.000	0.000
77	I	137	VAL	0	-0.071	-0.042	25.279	0.003	0.003	0.000	0.000	0.000	0.000
78	I	138	VAL	0	0.045	0.020	22.244	0.003	0.003	0.000	0.000	0.000	0.000
79	I	139	VAL	0	0.005	-0.009	25.674	0.004	0.004	0.000	0.000	0.000	0.000
80	I	140	TYR	0	0.039	0.033	28.970	-0.004	-0.004	0.000	0.000	0.000	0.000
81	I	141	LEU	0	-0.001	-0.010	30.816	0.002	0.002	0.000	0.000	0.000	0.000
82	I	142	PRO	0	0.047	0.027	33.999	-0.002	-0.002	0.000	0.000	0.000	0.000
83	I	143	ILE	0	0.037	0.010	37.679	-0.001	-0.001	0.000	0.000	0.000	0.000
84	I	144	ILE	0	0.008	-0.010	33.633	-0.002	-0.002	0.000	0.000	0.000	0.000
85	I	145	LEU	0	0.030	0.013	31.727	-0.003	-0.003	0.000	0.000	0.000	0.000
86	I	146	SER	0	-0.044	-0.024	35.072	-0.001	-0.001	0.000	0.000	0.000	0.000
87	I	147	LYS	1	0.934	0.966	37.827	0.010	0.010	0.000	0.000	0.000	0.000
88	I	148	ILE	0	-0.001	0.024	32.725	-0.001	-0.001	0.000	0.000	0.000	0.000
89	I	149	LEU	0	0.010	0.016	36.087	-0.001	-0.001	0.000	0.000	0.000	0.000
90	I	150	PHE	0	0.015	-0.002	31.400	-0.002	-0.002	0.000	0.000	0.000	0.000
91	I	151	ILE	0	0.003	0.009	33.978	-0.003	-0.003	0.000	0.000	0.000	0.000
92	I	152	ASP	-1	-0.803	-0.918	35.347	-0.032	-0.032	0.000	0.000	0.000	0.000
93	I	153	PHE	0	-0.009	0.001	26.311	-0.002	-0.002	0.000	0.000	0.000	0.000
94	I	154	TRP	0	0.009	-0.002	29.613	-0.005	-0.005	0.000	0.000	0.000	0.000
95	I	155	HIS	0	-0.010	-0.008	31.601	-0.003	-0.003	0.000	0.000	0.000	0.000
96	I	156	TRP	0	-0.007	0.005	24.704	-0.004	-0.004	0.000	0.000	0.000	0.000
97	I	157	LEU	0	0.003	0.001	25.699	-0.004	-0.004	0.000	0.000	0.000	0.000
98	I	158	GLY	0	0.026	-0.004	27.687	-0.006	-0.006	0.000	0.000	0.000	0.000
99	I	159	SER	0	-0.009	-0.011	30.022	-0.001	-0.001	0.000	0.000	0.000	0.000
100	I	160	ILE	0	-0.038	0.006	23.984	-0.001	-0.001	0.000	0.000	0.000	0.000
101	I	161	PHE	0	-0.050	-0.032	20.904	-0.008	-0.008	0.000	0.000	0.000	0.000
102	I	162	TYR	0	-0.021	0.002	26.266	-0.002	-0.002	0.000	0.000	0.000	0.000
103	I	163	LYS	1	0.886	0.944	24.374	0.091	0.091	0.000	0.000	0.000	0.000
104	I	164	GLY	0	-0.004	-0.014	30.460	0.005	0.005	0.000	0.000	0.000	0.000
105	I	165	GLY	0	0.012	0.010	32.471	-0.004	-0.004	0.000	0.000	0.000	0.000
106	I	166	PHE	0	-0.031	-0.021	35.147	0.003	0.003	0.000	0.000	0.000	0.000
107	I	167	LYS	1	0.968	0.985	35.940	0.041	0.041	0.000	0.000	0.000	0.000
108	I	168	ILE	0	0.014	0.001	35.812	0.000	0.000	0.000	0.000	0.000	0.000
109	I	169	VAL	0	-0.012	0.007	38.167	0.001	0.001	0.000	0.000	0.000	0.000
110	I	170	SER	0	0.005	0.000	41.917	0.001	0.001	0.000	0.000	0.000	0.000
111	I	171	ASN	0	0.038	0.026	40.449	-0.002	-0.002	0.000	0.000	0.000	0.000
112	I	172	THR	0	-0.046	-0.026	41.365	0.001	0.001	0.000	0.000	0.000	0.000
113	I	173	ALA	0	0.039	0.026	41.664	-0.001	-0.001	0.000	0.000	0.000	0.000
114	I	174	LEU	0	-0.004	-0.009	35.842	-0.001	-0.001	0.000	0.000	0.000	0.000
115	I	175	GLY	0	0.042	0.038	36.012	0.000	0.000	0.000	0.000	0.000	0.000
116	I	176	TRP	0	0.053	0.003	31.010	0.001	0.001	0.000	0.000	0.000	0.000
117	I	177	LEU	0	0.005	0.017	28.259	0.001	0.001	0.000	0.000	0.000	0.000
118	I	178	GLY	0	0.076	0.029	32.812	0.000	0.000	0.000	0.000	0.000	0.000
119	I	179	TRP	0	0.045	0.010	33.843	0.002	0.002	0.000	0.000	0.000	0.000
120	I	180	TYR	0	0.031	0.024	30.963	0.001	0.001	0.000	0.000	0.000	0.000
121	I	181	ILE	0	0.024	0.014	28.990	0.001	0.001	0.000	0.000	0.000	0.000
122	I	182	LEU	0	-0.011	0.008	32.936	0.002	0.002	0.000	0.000	0.000	0.000
123	I	183	CYS	0	-0.029	-0.020	35.988	0.002	0.002	0.000	0.000	0.000	0.000
124	I	184	SER	0	0.028	0.016	33.787	0.002	0.002	0.000	0.000	0.000	0.000
125	I	185	PHE	0	-0.028	-0.013	33.571	0.001	0.001	0.000	0.000	0.000	0.000
126	I	186	ALA	0	0.012	0.012	35.168	0.003	0.003	0.000	0.000	0.000	0.000
127	I	187	THR	0	0.011	-0.015	38.442	0.003	0.003	0.000	0.000	0.000	0.000
128	I	188	SER	0	0.006	-0.014	35.003	0.001	0.001	0.000	0.000	0.000	0.000
129	I	189	THR	0	-0.053	-0.030	36.928	0.002	0.002	0.000	0.000	0.000	0.000
130	I	190	VAL	0	-0.022	-0.009	38.734	0.003	0.003	0.000	0.000	0.000	0.000
131	I	191	LEU	0	0.041	0.021	37.794	0.001	0.001	0.000	0.000	0.000	0.000
132	I	192	ARG	1	0.898	0.945	31.867	0.043	0.043	0.000	0.000	0.000	0.000
133	I	193	LYS	1	0.855	0.940	39.841	0.026	0.026	0.000	0.000	0.000	0.000
134	I	194	ILE	0	-0.011	0.020	43.176	0.001	0.001	0.000	0.000	0.000	0.000

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