FMO DATABASE

FMODB ID: MVR3Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1054496.030218
FMO2-HF: Nuclear repulsion	1002248.750274
FMO2-HF: Total energy	-52247.279944
FMO2-MP2: Total energy	-52403.96729

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.
-6.675	-3.24	1.199	-1.433	-3.201	0.006

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 : 0.013 / 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	-0.858	-0.927	3.353	0.399	2.718	0.011	-0.947	-1.383	0.002
4	I	8	ILE	0	-0.026	-0.006	2.659	-3.361	-2.437	1.189	-0.456	-1.658	0.004
5	I	9	TYR	0	0.009	0.013	4.538	-1.395	-1.203	-0.001	-0.030	-0.160	0.000
6	I	10	TYR	0	0.003	0.005	6.323	-0.354	-0.354	0.000	0.000	0.000	0.000
7	I	11	LYS	1	1.005	0.996	7.607	-1.852	-1.852	0.000	0.000	0.000	0.000
8	I	12	THR	0	-0.063	-0.056	8.251	-0.182	-0.182	0.000	0.000	0.000	0.000
9	I	13	LEU	0	-0.003	0.003	10.376	-0.138	-0.138	0.000	0.000	0.000	0.000
10	I	14	ASP	-1	-0.810	-0.912	12.330	0.325	0.325	0.000	0.000	0.000	0.000
11	I	15	ALA	0	-0.036	-0.014	14.164	-0.069	-0.069	0.000	0.000	0.000	0.000
12	I	16	ILE	0	-0.019	-0.005	14.824	-0.050	-0.050	0.000	0.000	0.000	0.000
13	I	17	PHE	0	0.005	-0.008	15.697	-0.050	-0.050	0.000	0.000	0.000	0.000
14	I	18	MET	0	0.030	0.008	17.531	-0.039	-0.039	0.000	0.000	0.000	0.000
15	I	19	PRO	0	-0.057	-0.030	19.865	-0.027	-0.027	0.000	0.000	0.000	0.000
16	I	20	ILE	0	-0.005	0.000	20.352	-0.017	-0.017	0.000	0.000	0.000	0.000
17	I	21	ILE	0	-0.031	-0.007	17.586	-0.016	-0.016	0.000	0.000	0.000	0.000
18	I	22	LYS	1	0.928	0.971	22.197	-0.176	-0.176	0.000	0.000	0.000	0.000
19	I	23	VAL	0	-0.030	0.000	24.702	-0.010	-0.010	0.000	0.000	0.000	0.000
20	I	24	LEU	0	-0.024	0.007	24.710	-0.010	-0.010	0.000	0.000	0.000	0.000
21	I	25	HIS	0	0.076	0.035	26.004	0.003	0.003	0.000	0.000	0.000	0.000
22	I	26	PRO	0	0.096	0.036	23.323	-0.002	-0.002	0.000	0.000	0.000	0.000
23	I	27	ALA	0	-0.026	-0.016	24.151	-0.006	-0.006	0.000	0.000	0.000	0.000
24	I	28	LEU	0	-0.014	-0.019	26.368	-0.004	-0.004	0.000	0.000	0.000	0.000
25	I	29	ALA	0	0.009	0.013	22.054	0.001	0.001	0.000	0.000	0.000	0.000
26	I	30	ILE	0	-0.006	-0.002	19.899	0.000	0.000	0.000	0.000	0.000	0.000
27	I	31	LEU	0	0.008	0.010	22.545	-0.005	-0.005	0.000	0.000	0.000	0.000
28	I	32	ILE	0	0.024	0.007	23.377	-0.004	-0.004	0.000	0.000	0.000	0.000
29	I	33	ILE	0	0.008	0.000	18.073	-0.001	-0.001	0.000	0.000	0.000	0.000
30	I	34	ALA	0	-0.028	-0.010	20.947	-0.009	-0.009	0.000	0.000	0.000	0.000
31	I	35	ILE	0	0.000	-0.015	22.706	-0.006	-0.006	0.000	0.000	0.000	0.000
32	I	36	ILE	0	0.024	0.018	21.378	-0.001	-0.001	0.000	0.000	0.000	0.000
33	I	37	VAL	0	0.014	0.004	18.623	-0.003	-0.003	0.000	0.000	0.000	0.000
34	I	38	SER	0	-0.045	-0.014	21.579	-0.009	-0.009	0.000	0.000	0.000	0.000
35	I	39	LEU	0	0.018	0.003	24.716	-0.003	-0.003	0.000	0.000	0.000	0.000
36	I	40	ILE	0	-0.029	-0.015	20.118	0.001	0.001	0.000	0.000	0.000	0.000
37	I	41	ILE	0	-0.016	-0.003	21.205	-0.006	-0.006	0.000	0.000	0.000	0.000
38	I	42	ASN	0	-0.008	0.019	24.021	-0.007	-0.007	0.000	0.000	0.000	0.000
39	I	43	ILE	0	-0.032	0.003	25.579	0.001	0.001	0.000	0.000	0.000	0.000
40	I	44	ALA	0	-0.032	-0.005	22.854	-0.001	-0.001	0.000	0.000	0.000	0.000
41	I	45	THR	0	-0.089	-0.066	24.687	-0.003	-0.003	0.000	0.000	0.000	0.000
42	I	102	PRO	0	0.129	0.028	21.166	-0.002	-0.002	0.000	0.000	0.000	0.000
43	I	103	MET	0	0.036	0.018	20.370	-0.001	-0.001	0.000	0.000	0.000	0.000
44	I	104	ILE	0	0.050	0.046	16.276	-0.005	-0.005	0.000	0.000	0.000	0.000
45	I	105	TYR	0	-0.010	0.006	16.198	-0.022	-0.022	0.000	0.000	0.000	0.000
46	I	106	THR	0	-0.006	-0.028	16.151	0.000	0.000	0.000	0.000	0.000	0.000
47	I	107	TRP	0	-0.018	-0.029	15.746	0.002	0.002	0.000	0.000	0.000	0.000
48	I	108	VAL	0	0.019	0.026	10.701	-0.024	-0.024	0.000	0.000	0.000	0.000
49	I	109	PRO	0	0.026	0.006	11.728	-0.027	-0.027	0.000	0.000	0.000	0.000
50	I	110	ILE	0	0.073	0.027	13.337	0.007	0.007	0.000	0.000	0.000	0.000
51	I	111	ILE	0	-0.023	0.001	10.267	0.002	0.002	0.000	0.000	0.000	0.000
52	I	112	LEU	0	0.016	-0.008	8.868	-0.052	-0.052	0.000	0.000	0.000	0.000
53	I	113	ILE	0	0.006	0.018	9.804	0.041	0.041	0.000	0.000	0.000	0.000
54	I	114	PHE	0	-0.018	-0.021	12.836	0.020	0.020	0.000	0.000	0.000	0.000
55	I	115	ILE	0	-0.051	0.015	6.340	0.019	0.019	0.000	0.000	0.000	0.000
56	I	116	TYR	0	-0.020	-0.021	10.044	-0.003	-0.003	0.000	0.000	0.000	0.000
57	I	117	LEU	0	0.040	0.010	11.062	0.039	0.039	0.000	0.000	0.000	0.000
58	I	118	ARG	1	0.962	0.986	11.665	0.199	0.199	0.000	0.000	0.000	0.000
59	I	119	HIS	1	0.856	0.939	10.401	-0.193	-0.193	0.000	0.000	0.000	0.000
60	I	120	VAL	0	0.004	0.006	12.513	0.039	0.039	0.000	0.000	0.000	0.000
61	I	121	TYR	0	0.019	-0.006	15.751	0.012	0.012	0.000	0.000	0.000	0.000
62	I	122	GLY	0	-0.016	0.004	16.472	-0.009	-0.009	0.000	0.000	0.000	0.000
63	I	123	PHE	0	0.029	0.005	17.435	0.017	0.017	0.000	0.000	0.000	0.000
64	I	124	GLY	0	-0.015	-0.007	16.855	-0.010	-0.010	0.000	0.000	0.000	0.000
65	I	125	GLY	0	-0.003	0.013	15.707	0.017	0.017	0.000	0.000	0.000	0.000
66	I	126	VAL	0	0.011	0.006	15.615	0.004	0.004	0.000	0.000	0.000	0.000
67	I	127	TYR	0	0.001	0.001	17.357	0.004	0.004	0.000	0.000	0.000	0.000
68	I	128	GLN	0	-0.026	-0.013	20.069	-0.006	-0.006	0.000	0.000	0.000	0.000
69	I	129	GLU	-1	-1.010	-0.993	17.266	0.179	0.179	0.000	0.000	0.000	0.000
70	I	130	LEU	0	-0.069	-0.037	19.893	0.007	0.007	0.000	0.000	0.000	0.000
71	I	131	ASN	0	-0.036	-0.018	23.027	0.003	0.003	0.000	0.000	0.000	0.000
72	I	132	PRO	0	0.046	0.025	25.164	-0.006	-0.006	0.000	0.000	0.000	0.000
73	I	133	GLY	0	-0.036	-0.027	27.252	-0.002	-0.002	0.000	0.000	0.000	0.000
74	I	134	TRP	0	-0.012	-0.008	21.681	-0.001	-0.001	0.000	0.000	0.000	0.000
75	I	135	ASN	0	0.022	0.013	26.651	0.000	0.000	0.000	0.000	0.000	0.000
76	I	136	GLY	0	0.057	0.025	24.731	-0.008	-0.008	0.000	0.000	0.000	0.000
77	I	137	VAL	0	-0.104	-0.044	25.674	0.005	0.005	0.000	0.000	0.000	0.000
78	I	138	VAL	0	0.092	0.054	22.945	0.005	0.005	0.000	0.000	0.000	0.000
79	I	139	VAL	0	-0.019	-0.031	26.049	0.005	0.005	0.000	0.000	0.000	0.000
80	I	140	TYR	0	0.007	0.018	29.392	-0.005	-0.005	0.000	0.000	0.000	0.000
81	I	141	LEU	0	0.039	0.003	31.551	0.002	0.002	0.000	0.000	0.000	0.000
82	I	142	PRO	0	0.015	0.023	34.323	-0.002	-0.002	0.000	0.000	0.000	0.000
83	I	143	ILE	0	0.041	0.030	38.076	0.000	0.000	0.000	0.000	0.000	0.000
84	I	144	ILE	0	0.022	-0.025	33.628	-0.002	-0.002	0.000	0.000	0.000	0.000
85	I	145	LEU	0	0.010	0.004	31.500	-0.002	-0.002	0.000	0.000	0.000	0.000
86	I	146	SER	0	-0.033	-0.022	35.111	-0.002	-0.002	0.000	0.000	0.000	0.000
87	I	147	LYS	1	0.939	0.970	38.288	0.010	0.010	0.000	0.000	0.000	0.000
88	I	148	ILE	0	-0.017	0.021	33.094	-0.001	-0.001	0.000	0.000	0.000	0.000
89	I	149	LEU	0	0.007	0.009	36.387	-0.001	-0.001	0.000	0.000	0.000	0.000
90	I	150	PHE	0	0.024	0.001	31.561	-0.002	-0.002	0.000	0.000	0.000	0.000
91	I	151	ILE	0	0.005	-0.002	34.004	-0.003	-0.003	0.000	0.000	0.000	0.000
92	I	152	ASP	-1	-0.827	-0.920	35.608	-0.031	-0.031	0.000	0.000	0.000	0.000
93	I	153	PHE	0	-0.042	-0.018	26.408	-0.002	-0.002	0.000	0.000	0.000	0.000
94	I	154	TRP	0	0.016	0.004	29.071	-0.005	-0.005	0.000	0.000	0.000	0.000
95	I	155	HIS	0	0.050	0.023	31.463	-0.003	-0.003	0.000	0.000	0.000	0.000
96	I	156	TRP	0	0.003	0.010	25.206	-0.004	-0.004	0.000	0.000	0.000	0.000
97	I	157	LEU	0	-0.019	-0.014	25.598	-0.003	-0.003	0.000	0.000	0.000	0.000
98	I	158	GLY	0	-0.002	-0.015	27.737	-0.006	-0.006	0.000	0.000	0.000	0.000
99	I	159	SER	0	-0.063	-0.031	30.168	-0.003	-0.003	0.000	0.000	0.000	0.000
100	I	160	ILE	0	-0.010	0.006	24.264	-0.001	-0.001	0.000	0.000	0.000	0.000
101	I	161	PHE	0	-0.057	-0.035	21.257	-0.008	-0.008	0.000	0.000	0.000	0.000
102	I	162	TYR	0	-0.037	-0.007	26.679	-0.002	-0.002	0.000	0.000	0.000	0.000
103	I	163	LYS	1	0.944	0.978	24.670	0.085	0.085	0.000	0.000	0.000	0.000
104	I	164	GLY	0	-0.011	-0.005	30.864	0.006	0.006	0.000	0.000	0.000	0.000
105	I	165	GLY	0	0.021	0.002	32.640	-0.004	-0.004	0.000	0.000	0.000	0.000
106	I	166	PHE	0	-0.032	-0.014	35.259	0.003	0.003	0.000	0.000	0.000	0.000
107	I	167	LYS	1	0.980	0.986	36.516	0.037	0.037	0.000	0.000	0.000	0.000
108	I	168	ILE	0	0.016	0.006	36.298	0.000	0.000	0.000	0.000	0.000	0.000
109	I	169	VAL	0	-0.005	0.011	38.455	0.000	0.000	0.000	0.000	0.000	0.000
110	I	170	SER	0	-0.001	-0.008	41.795	0.001	0.001	0.000	0.000	0.000	0.000
111	I	171	ASN	0	0.091	0.050	41.462	-0.003	-0.003	0.000	0.000	0.000	0.000
112	I	172	THR	0	-0.096	-0.045	41.312	0.001	0.001	0.000	0.000	0.000	0.000
113	I	173	ALA	0	0.037	0.022	41.685	-0.001	-0.001	0.000	0.000	0.000	0.000
114	I	174	LEU	0	-0.020	-0.013	36.658	-0.001	-0.001	0.000	0.000	0.000	0.000
115	I	175	GLY	0	0.034	0.024	36.279	0.001	0.001	0.000	0.000	0.000	0.000
116	I	176	TRP	0	0.071	0.015	30.917	0.002	0.002	0.000	0.000	0.000	0.000
117	I	177	LEU	0	-0.008	0.011	28.455	0.001	0.001	0.000	0.000	0.000	0.000
118	I	178	GLY	0	0.057	0.021	33.169	0.000	0.000	0.000	0.000	0.000	0.000
119	I	179	TRP	0	0.060	0.029	34.355	0.001	0.001	0.000	0.000	0.000	0.000
120	I	180	TYR	0	0.048	0.024	31.882	0.000	0.000	0.000	0.000	0.000	0.000
121	I	181	ILE	0	0.031	0.008	29.431	0.000	0.000	0.000	0.000	0.000	0.000
122	I	182	LEU	0	0.004	0.010	33.070	0.002	0.002	0.000	0.000	0.000	0.000
123	I	183	CYS	0	-0.028	-0.006	36.139	0.001	0.001	0.000	0.000	0.000	0.000
124	I	184	SER	0	0.037	0.007	33.672	0.002	0.002	0.000	0.000	0.000	0.000
125	I	185	PHE	0	-0.041	-0.012	33.478	0.001	0.001	0.000	0.000	0.000	0.000
126	I	186	ALA	0	0.000	0.015	35.111	0.003	0.003	0.000	0.000	0.000	0.000
127	I	187	THR	0	-0.028	-0.025	38.148	0.003	0.003	0.000	0.000	0.000	0.000
128	I	188	SER	0	-0.007	-0.034	35.017	0.000	0.000	0.000	0.000	0.000	0.000
129	I	189	THR	0	-0.054	-0.046	37.054	0.001	0.001	0.000	0.000	0.000	0.000
130	I	190	VAL	0	-0.033	-0.024	38.662	0.002	0.002	0.000	0.000	0.000	0.000
131	I	191	LEU	0	0.020	0.030	37.624	0.001	0.001	0.000	0.000	0.000	0.000
132	I	192	ARG	1	0.930	0.968	31.567	0.055	0.055	0.000	0.000	0.000	0.000
133	I	193	LYS	1	0.906	0.965	39.696	0.031	0.031	0.000	0.000	0.000	0.000
134	I	194	ILE	0	-0.016	0.019	42.719	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)