FMO DATABASE

FMODB ID: LJMM9

Calculation Name: 3K5B-G-Xray317

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K5B

Chain ID: G

ChEMBL ID:

UniProt ID: P74901

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	101
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-466749.374828
FMO2-HF: Nuclear repulsion	427511.547522
FMO2-HF: Total energy	-39237.827305
FMO2-MP2: Total energy	-39354.058799

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(G:20:ACE )

Summations of interaction energy for fragment #1(G:20: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.
1.47	2.552	-0.005	-0.518	-0.559	-0.001

Interaction energy analysis for fragmet #1(G:20:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : -0.002

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	G	22	LEU	0	-0.010	-0.021	3.837	0.784	1.866	-0.005	-0.518	-0.559	-0.001
4	G	23	ILE	0	0.055	0.036	6.019	0.414	0.414	0.000	0.000	0.000	0.000
5	G	24	LYS	1	0.978	0.989	6.935	0.317	0.317	0.000	0.000	0.000	0.000
6	G	25	SER	0	-0.005	0.001	7.611	0.028	0.028	0.000	0.000	0.000	0.000
7	G	26	LEU	0	0.052	0.010	8.765	0.000	0.000	0.000	0.000	0.000	0.000
8	G	27	ALA	0	0.039	0.032	10.199	-0.016	-0.016	0.000	0.000	0.000	0.000
9	G	28	GLU	-1	-0.836	-0.917	12.064	-0.067	-0.067	0.000	0.000	0.000	0.000
10	G	29	LYS	1	0.911	0.979	13.730	-0.064	-0.064	0.000	0.000	0.000	0.000
11	G	30	GLU	-1	-0.863	-0.937	14.631	0.120	0.120	0.000	0.000	0.000	0.000
12	G	31	LYS	1	0.847	0.898	15.370	0.026	0.026	0.000	0.000	0.000	0.000
13	G	32	GLN	0	-0.038	-0.013	17.568	-0.006	-0.006	0.000	0.000	0.000	0.000
14	G	33	LEU	0	-0.041	-0.024	17.719	-0.002	-0.002	0.000	0.000	0.000	0.000
15	G	34	LEU	0	0.021	0.011	20.308	-0.001	-0.001	0.000	0.000	0.000	0.000
16	G	35	GLU	-1	-0.875	-0.938	22.179	0.003	0.003	0.000	0.000	0.000	0.000
17	G	36	ARG	1	0.905	0.949	23.815	-0.046	-0.046	0.000	0.000	0.000	0.000
18	G	37	LEU	0	-0.030	-0.019	23.251	-0.001	-0.001	0.000	0.000	0.000	0.000
19	G	38	GLU	-1	-0.918	-0.958	26.612	0.024	0.024	0.000	0.000	0.000	0.000
20	G	39	ALA	0	-0.035	-0.017	28.549	-0.003	-0.003	0.000	0.000	0.000	0.000
21	G	40	ALA	0	-0.005	0.001	29.753	-0.002	-0.002	0.000	0.000	0.000	0.000
22	G	41	LYS	1	0.951	0.970	29.853	-0.051	-0.051	0.000	0.000	0.000	0.000
23	G	42	LYS	1	1.011	1.006	30.804	-0.016	-0.016	0.000	0.000	0.000	0.000
24	G	43	GLU	-1	-0.961	-0.962	34.734	0.018	0.018	0.000	0.000	0.000	0.000
25	G	44	ALA	0	-0.015	-0.002	35.291	0.000	0.000	0.000	0.000	0.000	0.000
26	G	45	GLU	-1	-0.860	-0.951	37.011	0.019	0.019	0.000	0.000	0.000	0.000
27	G	46	GLU	-1	-0.976	-0.997	38.580	0.010	0.010	0.000	0.000	0.000	0.000
28	G	47	ARG	1	0.862	0.939	40.402	-0.020	-0.020	0.000	0.000	0.000	0.000
29	G	48	VAL	0	0.043	0.024	41.071	-0.001	-0.001	0.000	0.000	0.000	0.000
30	G	49	LYS	1	1.007	1.011	41.901	-0.014	-0.014	0.000	0.000	0.000	0.000
31	G	50	ARG	1	0.867	0.925	41.100	-0.016	-0.016	0.000	0.000	0.000	0.000
32	G	51	ALA	0	0.000	0.014	46.393	-0.001	-0.001	0.000	0.000	0.000	0.000
33	G	52	GLU	-1	-0.897	-0.946	46.319	0.018	0.018	0.000	0.000	0.000	0.000
34	G	53	ALA	0	-0.084	-0.049	48.982	-0.001	-0.001	0.000	0.000	0.000	0.000
35	G	54	GLU	-1	-0.933	-0.986	50.599	0.013	0.013	0.000	0.000	0.000	0.000
36	G	55	ALA	0	0.000	0.014	52.223	0.000	0.000	0.000	0.000	0.000	0.000
37	G	56	LYS	1	0.948	0.974	53.687	-0.009	-0.009	0.000	0.000	0.000	0.000
38	G	57	ALA	0	0.006	-0.008	55.183	0.000	0.000	0.000	0.000	0.000	0.000
39	G	58	LEU	0	0.015	0.025	56.720	0.000	0.000	0.000	0.000	0.000	0.000
40	G	59	LEU	0	-0.018	-0.028	57.927	0.000	0.000	0.000	0.000	0.000	0.000
41	G	60	GLU	-1	-0.958	-0.964	59.595	0.007	0.007	0.000	0.000	0.000	0.000
42	G	61	GLU	-1	-0.927	-0.956	61.343	0.007	0.007	0.000	0.000	0.000	0.000
43	G	62	ALA	0	-0.070	-0.044	62.606	0.000	0.000	0.000	0.000	0.000	0.000
44	G	63	GLU	-1	-0.896	-0.941	64.384	0.008	0.008	0.000	0.000	0.000	0.000
45	G	64	ALA	0	-0.018	-0.005	65.954	0.000	0.000	0.000	0.000	0.000	0.000
46	G	65	LYS	1	0.966	0.990	67.395	-0.008	-0.008	0.000	0.000	0.000	0.000
47	G	66	ALA	0	0.049	0.018	68.835	0.000	0.000	0.000	0.000	0.000	0.000
48	G	67	LYS	1	0.946	0.961	68.192	-0.007	-0.007	0.000	0.000	0.000	0.000
49	G	68	ALA	0	-0.021	-0.009	71.748	0.000	0.000	0.000	0.000	0.000	0.000
50	G	69	LEU	0	-0.062	-0.032	72.741	0.000	0.000	0.000	0.000	0.000	0.000
51	G	70	GLU	-1	-0.880	-0.957	74.003	0.006	0.006	0.000	0.000	0.000	0.000
52	G	71	ALA	0	-0.089	-0.022	76.423	0.000	0.000	0.000	0.000	0.000	0.000
53	G	72	GLN	0	-0.004	0.010	76.768	0.000	0.000	0.000	0.000	0.000	0.000
54	G	73	TYR	0	-0.012	-0.017	78.184	0.000	0.000	0.000	0.000	0.000	0.000
55	G	74	ARG	1	0.978	0.973	77.802	-0.005	-0.005	0.000	0.000	0.000	0.000
56	G	75	GLU	-1	-0.948	-0.981	82.616	0.004	0.004	0.000	0.000	0.000	0.000
57	G	76	ARG	1	0.901	0.966	79.811	-0.006	-0.006	0.000	0.000	0.000	0.000
58	G	77	GLU	-1	-0.860	-0.935	85.410	0.005	0.005	0.000	0.000	0.000	0.000
59	G	78	ARG	1	0.943	1.021	87.152	-0.004	-0.004	0.000	0.000	0.000	0.000
60	G	79	ALA	0	-0.001	0.000	88.544	0.000	0.000	0.000	0.000	0.000	0.000
61	G	80	GLU	-1	-0.937	-0.963	88.341	0.005	0.005	0.000	0.000	0.000	0.000
62	G	81	THR	0	-0.132	-0.103	90.520	0.000	0.000	0.000	0.000	0.000	0.000
63	G	82	GLU	-1	-0.903	-0.943	92.949	0.003	0.003	0.000	0.000	0.000	0.000
64	G	83	ALA	0	0.027	0.007	94.487	0.000	0.000	0.000	0.000	0.000	0.000
65	G	84	LEU	0	-0.011	-0.011	94.152	0.000	0.000	0.000	0.000	0.000	0.000
66	G	85	LEU	0	-0.009	-0.016	96.280	0.000	0.000	0.000	0.000	0.000	0.000
67	G	86	ALA	0	-0.001	-0.002	98.651	0.000	0.000	0.000	0.000	0.000	0.000
68	G	87	ARG	1	0.988	0.993	99.304	-0.004	-0.004	0.000	0.000	0.000	0.000
69	G	88	TYR	0	-0.008	-0.008	98.451	0.000	0.000	0.000	0.000	0.000	0.000
70	G	89	ARG	1	0.913	0.959	101.221	-0.003	-0.003	0.000	0.000	0.000	0.000
71	G	90	GLU	-1	-0.851	-0.913	104.313	0.003	0.003	0.000	0.000	0.000	0.000
72	G	91	ARG	1	0.912	0.958	104.436	-0.004	-0.004	0.000	0.000	0.000	0.000
73	G	92	ALA	0	-0.016	-0.016	106.765	0.000	0.000	0.000	0.000	0.000	0.000
74	G	93	GLU	-1	-0.927	-0.966	108.470	0.003	0.003	0.000	0.000	0.000	0.000
75	G	94	ALA	0	0.011	0.008	110.598	0.000	0.000	0.000	0.000	0.000	0.000
76	G	95	GLU	-1	-0.964	-0.997	109.737	0.004	0.004	0.000	0.000	0.000	0.000
77	G	96	ALA	0	-0.039	-0.009	112.774	0.000	0.000	0.000	0.000	0.000	0.000
78	G	97	LYS	1	0.925	0.947	114.521	-0.003	-0.003	0.000	0.000	0.000	0.000
79	G	98	ALA	0	0.005	0.015	115.236	0.000	0.000	0.000	0.000	0.000	0.000
80	G	99	VAL	0	0.004	0.004	115.366	0.000	0.000	0.000	0.000	0.000	0.000
81	G	100	ARG	1	0.948	0.976	115.805	-0.003	-0.003	0.000	0.000	0.000	0.000
82	G	101	GLU	-1	-0.882	-0.954	120.821	0.003	0.003	0.000	0.000	0.000	0.000
83	G	102	LYS	1	0.849	0.924	117.353	-0.003	-0.003	0.000	0.000	0.000	0.000
84	G	103	ALA	0	0.001	0.004	122.938	0.000	0.000	0.000	0.000	0.000	0.000
85	G	104	MET	0	-0.045	-0.018	124.707	0.000	0.000	0.000	0.000	0.000	0.000
86	G	105	ALA	0	0.002	0.012	126.865	0.000	0.000	0.000	0.000	0.000	0.000
87	G	106	ARG	1	0.871	0.955	127.990	-0.003	-0.003	0.000	0.000	0.000	0.000
88	G	107	LEU	0	0.045	0.030	127.627	0.000	0.000	0.000	0.000	0.000	0.000
89	G	108	ASP	-1	-0.845	-0.933	130.294	0.002	0.002	0.000	0.000	0.000	0.000
90	G	109	GLU	-1	-0.887	-0.960	132.113	0.003	0.003	0.000	0.000	0.000	0.000
91	G	110	ALA	0	-0.015	-0.003	129.614	0.000	0.000	0.000	0.000	0.000	0.000
92	G	111	VAL	0	0.008	-0.004	131.626	0.000	0.000	0.000	0.000	0.000	0.000
93	G	112	ALA	0	-0.054	-0.030	133.912	0.000	0.000	0.000	0.000	0.000	0.000
94	G	113	LEU	0	-0.022	-0.014	131.275	0.000	0.000	0.000	0.000	0.000	0.000
95	G	114	VAL	0	0.020	0.016	131.655	0.000	0.000	0.000	0.000	0.000	0.000
96	G	115	LEU	0	0.014	0.008	134.618	0.000	0.000	0.000	0.000	0.000	0.000
97	G	116	LYS	1	0.891	0.926	138.061	-0.002	-0.002	0.000	0.000	0.000	0.000
98	G	117	GLU	-1	-0.903	-0.951	135.375	0.003	0.003	0.000	0.000	0.000	0.000
99	G	118	VAL	0	-0.114	-0.050	136.385	0.000	0.000	0.000	0.000	0.000	0.000
100	G	119	LEU	0	-0.101	-0.057	138.923	0.000	0.000	0.000	0.000	0.000	0.000
101	G	120	PRO	-1	-0.961	-0.941	140.766	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:20:ACE )