FMO DATABASE

FMODB ID: 6638Z

Calculation Name: 5B3D-A-Xray323

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5B3D

Chain ID: A

ChEMBL ID:

UniProt ID: P0A1J7

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	116
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-738319.911373
FMO2-HF: Nuclear repulsion	691907.151694
FMO2-HF: Total energy	-46412.759678
FMO2-MP2: Total energy	-46548.863948

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(A:1:ACE )

Summations of interaction energy for fragment #1(A:1:ACE )

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.
-0.075	1.372	-0.006	-0.677	-0.763	-0.002

Interaction energy analysis for fragmet #1(A:1:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.010

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	A	3	ARG	1	0.996	1.011	3.807	0.449	1.753	-0.007	-0.655	-0.642	-0.002
4	A	4	LEU	0	-0.009	-0.004	4.104	0.030	0.173	0.001	-0.022	-0.121	0.000
5	A	5	SER	0	0.027	0.002	5.199	0.064	0.064	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.904	-0.946	6.924	-0.468	-0.468	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.035	-0.020	8.780	0.144	0.144	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.003	-0.009	9.020	0.065	0.065	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.857	-0.921	11.200	-0.494	-0.494	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.062	-0.039	13.125	0.034	0.034	0.000	0.000	0.000	0.000
11	A	11	MET	0	-0.014	-0.008	14.200	0.040	0.040	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.001	0.004	15.392	0.024	0.024	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.006	0.006	17.505	0.015	0.015	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.017	0.011	19.025	0.016	0.016	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.023	-0.019	18.417	0.013	0.013	0.000	0.000	0.000	0.000
16	A	16	ASN	0	-0.028	-0.012	20.866	0.018	0.018	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.898	-0.947	23.421	-0.090	-0.090	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.031	-0.033	23.250	0.009	0.009	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.860	0.942	25.859	0.058	0.058	0.000	0.000	0.000	0.000
20	A	20	THR	0	0.002	0.010	27.681	0.004	0.004	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.025	-0.015	29.348	0.005	0.005	0.000	0.000	0.000	0.000
22	A	22	MET	0	0.008	-0.006	28.947	0.004	0.004	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.812	-0.893	31.780	-0.038	-0.038	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.034	-0.021	33.701	0.003	0.003	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.948	-0.980	34.146	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	26	GLN	0	0.042	0.021	35.922	0.001	0.001	0.000	0.000	0.000	0.000
27	A	27	GLN	0	-0.039	-0.004	37.470	0.000	0.000	0.000	0.000	0.000	0.000
28	A	28	GLN	0	-0.071	-0.047	39.497	0.003	0.003	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.012	-0.002	38.551	0.002	0.002	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.075	-0.034	41.051	0.002	0.002	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.001	-0.016	43.577	0.000	0.000	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.009	0.020	47.269	0.000	0.000	0.000	0.000	0.000	0.000
33	A	33	GLN	0	-0.070	-0.038	43.535	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	34	ILE	0	0.027	0.011	46.768	0.000	0.000	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.032	-0.014	44.561	0.001	0.001	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.032	0.030	44.760	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.023	0.010	43.261	0.000	0.000	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.006	-0.035	45.205	0.002	0.002	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.068	0.046	44.155	0.001	0.001	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.036	0.044	46.702	0.001	0.001	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.921	0.958	47.441	0.021	0.021	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.019	0.021	49.240	0.001	0.001	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.046	-0.031	48.895	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.886	-0.964	51.257	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.925	-0.952	53.932	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.926	0.966	52.988	0.007	0.007	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.039	-0.030	54.962	0.001	0.001	0.000	0.000	0.000	0.000
48	A	48	SER	0	0.003	0.005	57.137	0.001	0.001	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.012	-0.002	59.468	0.001	0.001	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.038	-0.027	57.668	0.001	0.001	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.021	0.025	61.391	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.017	-0.004	63.067	0.000	0.000	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.033	-0.019	64.072	0.000	0.000	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.914	-0.958	64.551	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	55	TYR	0	0.016	0.009	66.587	0.000	0.000	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.012	-0.024	69.121	0.000	0.000	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.803	-0.865	69.280	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.032	-0.024	68.425	0.000	0.000	0.000	0.000	0.000	0.000
59	A	59	GLN	0	-0.011	-0.010	72.618	0.000	0.000	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.848	0.911	73.209	0.003	0.003	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.870	0.929	71.301	0.002	0.002	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.055	-0.025	76.675	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.945	-0.960	79.093	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	64	GLN	0	-0.064	-0.031	78.518	0.000	0.000	0.000	0.000	0.000	0.000
65	A	65	ASN	0	-0.034	-0.020	82.264	0.000	0.000	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.005	0.026	84.491	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	GLN	0	-0.024	-0.021	86.263	0.000	0.000	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.975	0.993	87.129	0.002	0.002	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.015	-0.020	87.531	0.000	0.000	0.000	0.000	0.000	0.000
70	A	70	ALA	0	-0.070	0.023	88.738	0.000	0.000	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.024	-0.033	86.577	0.000	0.000	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.801	-0.943	83.953	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.845	-0.899	80.478	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.000	-0.009	79.894	0.000	0.000	0.000	0.000	0.000	0.000
75	A	75	ALA	0	-0.017	-0.019	78.909	0.000	0.000	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.931	-0.953	78.077	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.898	0.939	75.933	0.004	0.004	0.000	0.000	0.000	0.000
78	A	78	TRP	0	-0.027	-0.018	72.407	0.000	0.000	0.000	0.000	0.000	0.000
79	A	79	GLN	0	0.004	-0.006	72.603	0.000	0.000	0.000	0.000	0.000	0.000
80	A	80	ALA	0	0.038	0.018	71.890	0.000	0.000	0.000	0.000	0.000	0.000
81	A	81	ILE	0	-0.032	-0.011	69.803	0.000	0.000	0.000	0.000	0.000	0.000
82	A	82	THR	0	-0.046	-0.033	68.735	0.000	0.000	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.859	-0.909	68.035	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.930	0.960	65.520	0.005	0.005	0.000	0.000	0.000	0.000
85	A	85	THR	0	-0.033	-0.016	64.007	0.000	0.000	0.000	0.000	0.000	0.000
86	A	86	GLN	0	-0.012	0.001	62.810	0.000	0.000	0.000	0.000	0.000	0.000
87	A	87	HIS	0	0.039	0.018	59.434	0.001	0.001	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.019	-0.016	59.347	0.000	0.000	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.893	0.959	58.520	0.001	0.001	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.838	-0.920	57.943	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.024	-0.006	53.881	0.000	0.000	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.028	-0.025	53.892	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	93	GLN	0	-0.002	0.002	53.188	0.000	0.000	0.000	0.000	0.000	0.000
94	A	94	HIS	0	0.027	0.023	49.632	0.001	0.001	0.000	0.000	0.000	0.000
95	A	95	ASN	0	0.010	-0.020	49.456	0.000	0.000	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.006	0.011	48.332	0.000	0.000	0.000	0.000	0.000	0.000
97	A	97	TRP	0	0.039	0.015	47.641	0.000	0.000	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.069	-0.032	45.367	0.000	0.000	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.049	-0.025	43.762	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.888	-0.946	42.913	0.003	0.003	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.038	0.026	41.380	0.001	0.001	0.000	0.000	0.000	0.000
102	A	102	GLN	0	-0.087	-0.056	39.292	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	103	ILE	0	0.010	0.009	38.089	0.000	0.000	0.000	0.000	0.000	0.000
104	A	104	GLU	-1	-0.929	-0.951	37.257	0.007	0.007	0.000	0.000	0.000	0.000
105	A	105	ARG	1	0.938	0.956	34.780	0.007	0.007	0.000	0.000	0.000	0.000
106	A	106	ASN	0	-0.008	0.008	33.349	0.002	0.002	0.000	0.000	0.000	0.000
107	A	107	GLN	0	0.030	0.000	32.946	0.001	0.001	0.000	0.000	0.000	0.000
108	A	108	GLN	0	-0.039	-0.018	31.568	0.001	0.001	0.000	0.000	0.000	0.000
109	A	109	ALA	0	-0.010	-0.007	29.167	0.002	0.002	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.015	-0.004	28.079	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.928	-0.976	27.769	0.029	0.029	0.000	0.000	0.000	0.000
112	A	112	VAL	0	-0.094	-0.035	23.380	0.006	0.006	0.000	0.000	0.000	0.000
113	A	113	LEU	0	-0.023	-0.011	23.215	0.000	0.000	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.920	0.991	24.121	-0.048	-0.048	0.000	0.000	0.000	0.000
115	A	115	PRO	0	-0.019	-0.018	21.187	0.004	0.004	0.000	0.000	0.000	0.000
116	A	116	NME	0	-0.020	-0.003	19.897	0.008	0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:ACE )