FMO DATABASE

FMODB ID: K3J53

Calculation Name: 3K5B-G-Xray372

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: 2023-06-19

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	100
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-464964.854024
FMO2-HF: Nuclear repulsion	425878.081207
FMO2-HF: Total energy	-39086.772817
FMO2-MP2: Total energy	-39202.576473

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:21:GLY)

Summations of interaction energy for fragment #1(G:21:GLY)

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.
0.492	1.556	-0.016	-0.494	-0.554	0

Interaction energy analysis for fragmet #1(G:21:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.008

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].
3	G	23	ILE	0	0.062	0.039	3.815	0.627	1.691	-0.016	-0.494	-0.554
4	G	24	LYS	1	0.974	0.987	6.538	-0.096	-0.096	0.000	0.000	0.000
5	G	25	SER	0	-0.005	0.001	7.062	0.050	0.050	0.000	0.000	0.000
6	G	26	LEU	0	0.053	0.011	8.814	-0.074	-0.074	0.000	0.000	0.000
7	G	27	ALA	0	0.039	0.032	10.351	-0.074	-0.074	0.000	0.000	0.000
8	G	28	GLU	-1	-0.837	-0.918	12.258	0.122	0.122	0.000	0.000	0.000
9	G	29	LYS	1	0.911	0.979	13.620	-0.082	-0.082	0.000	0.000	0.000
10	G	30	GLU	-1	-0.863	-0.938	14.915	0.322	0.322	0.000	0.000	0.000
11	G	31	LYS	1	0.846	0.897	14.726	-0.249	-0.249	0.000	0.000	0.000
12	G	32	GLN	0	-0.039	-0.013	16.891	-0.040	-0.040	0.000	0.000	0.000
13	G	33	LEU	0	-0.040	-0.023	18.057	-0.017	-0.017	0.000	0.000	0.000
14	G	34	LEU	0	0.022	0.011	20.805	-0.010	-0.010	0.000	0.000	0.000
15	G	35	GLU	-1	-0.875	-0.938	22.528	0.069	0.069	0.000	0.000	0.000
16	G	36	ARG	1	0.903	0.949	23.899	-0.032	-0.032	0.000	0.000	0.000
17	G	37	LEU	0	-0.030	-0.018	23.941	-0.007	-0.007	0.000	0.000	0.000
18	G	38	GLU	-1	-0.919	-0.957	27.024	0.082	0.082	0.000	0.000	0.000
19	G	39	ALA	0	-0.035	-0.017	28.743	-0.005	-0.005	0.000	0.000	0.000
20	G	40	ALA	0	-0.004	0.001	29.996	-0.005	-0.005	0.000	0.000	0.000
21	G	41	LYS	1	0.950	0.970	30.676	-0.071	-0.071	0.000	0.000	0.000
22	G	42	LYS	1	1.010	1.006	30.997	-0.052	-0.052	0.000	0.000	0.000
23	G	43	GLU	-1	-0.961	-0.963	34.920	0.016	0.016	0.000	0.000	0.000
24	G	44	ALA	0	-0.015	-0.002	35.775	-0.003	-0.003	0.000	0.000	0.000
25	G	45	GLU	-1	-0.859	-0.950	37.487	0.035	0.035	0.000	0.000	0.000
26	G	46	GLU	-1	-0.973	-0.996	38.939	0.025	0.025	0.000	0.000	0.000
27	G	47	ARG	1	0.861	0.938	40.734	-0.021	-0.021	0.000	0.000	0.000
28	G	48	VAL	0	0.043	0.024	41.641	-0.002	-0.002	0.000	0.000	0.000
29	G	49	LYS	1	1.005	1.011	42.288	-0.030	-0.030	0.000	0.000	0.000
30	G	50	ARG	1	0.868	0.925	41.076	-0.019	-0.019	0.000	0.000	0.000
31	G	51	ALA	0	-0.001	0.013	46.782	-0.002	-0.002	0.000	0.000	0.000
32	G	52	GLU	-1	-0.898	-0.946	47.025	0.028	0.028	0.000	0.000	0.000
33	G	53	ALA	0	-0.083	-0.049	49.416	-0.001	-0.001	0.000	0.000	0.000
34	G	54	GLU	-1	-0.935	-0.986	50.937	0.013	0.013	0.000	0.000	0.000
35	G	55	ALA	0	-0.001	0.014	52.669	-0.001	-0.001	0.000	0.000	0.000
36	G	56	LYS	1	0.949	0.974	54.185	-0.018	-0.018	0.000	0.000	0.000
37	G	57	ALA	0	0.007	-0.008	55.554	-0.001	-0.001	0.000	0.000	0.000
38	G	58	LEU	0	0.017	0.026	57.101	-0.001	-0.001	0.000	0.000	0.000
39	G	59	LEU	0	-0.018	-0.028	58.541	-0.001	-0.001	0.000	0.000	0.000
40	G	60	GLU	-1	-0.958	-0.964	60.014	0.013	0.013	0.000	0.000	0.000
41	G	61	GLU	-1	-0.928	-0.957	61.685	0.008	0.008	0.000	0.000	0.000
42	G	62	ALA	0	-0.069	-0.044	63.026	-0.001	-0.001	0.000	0.000	0.000
43	G	63	GLU	-1	-0.891	-0.934	64.846	0.012	0.012	0.000	0.000	0.000
44	G	64	ALA	0	-0.018	-0.005	66.329	0.000	0.000	0.000	0.000	0.000
45	G	65	LYS	1	0.966	0.991	67.747	-0.008	-0.008	0.000	0.000	0.000
46	G	66	ALA	0	0.048	0.017	69.282	0.000	0.000	0.000	0.000	0.000
47	G	67	LYS	1	0.940	0.955	68.623	-0.012	-0.012	0.000	0.000	0.000
48	G	68	ALA	0	-0.021	-0.009	72.107	0.000	0.000	0.000	0.000	0.000
49	G	69	LEU	0	-0.062	-0.031	73.247	-0.001	-0.001	0.000	0.000	0.000
50	G	70	GLU	-1	-0.879	-0.956	74.567	0.010	0.010	0.000	0.000	0.000
51	G	71	ALA	0	-0.091	-0.023	76.813	0.000	0.000	0.000	0.000	0.000
52	G	72	GLN	0	-0.003	0.010	77.082	0.000	0.000	0.000	0.000	0.000
53	G	73	TYR	0	-0.012	-0.017	78.637	0.000	0.000	0.000	0.000	0.000
54	G	74	ARG	1	0.980	0.974	78.239	-0.008	-0.008	0.000	0.000	0.000
55	G	75	GLU	-1	-0.948	-0.981	82.997	0.005	0.005	0.000	0.000	0.000
56	G	76	ARG	1	0.899	0.966	80.209	-0.007	-0.007	0.000	0.000	0.000
57	G	77	GLU	-1	-0.859	-0.934	85.834	0.007	0.007	0.000	0.000	0.000
58	G	78	ARG	1	0.942	1.020	87.597	-0.005	-0.005	0.000	0.000	0.000
59	G	79	ALA	0	-0.001	0.000	88.915	0.000	0.000	0.000	0.000	0.000
60	G	80	GLU	-1	-0.937	-0.962	88.769	0.005	0.005	0.000	0.000	0.000
61	G	81	THR	0	-0.132	-0.103	91.019	0.000	0.000	0.000	0.000	0.000
62	G	82	GLU	-1	-0.901	-0.942	93.452	0.005	0.005	0.000	0.000	0.000
63	G	83	ALA	0	0.027	0.007	94.867	0.000	0.000	0.000	0.000	0.000
64	G	84	LEU	0	-0.011	-0.012	94.716	0.000	0.000	0.000	0.000	0.000
65	G	85	LEU	0	-0.011	-0.016	96.851	0.000	0.000	0.000	0.000	0.000
66	G	86	ALA	0	-0.001	-0.002	99.089	0.000	0.000	0.000	0.000	0.000
67	G	87	ARG	1	0.988	0.993	99.716	-0.004	-0.004	0.000	0.000	0.000
68	G	88	TYR	0	-0.006	-0.007	99.057	0.000	0.000	0.000	0.000	0.000
69	G	89	ARG	1	0.912	0.959	101.690	-0.005	-0.005	0.000	0.000	0.000
70	G	90	GLU	-1	-0.850	-0.913	104.675	0.004	0.004	0.000	0.000	0.000
71	G	91	ARG	1	0.911	0.958	105.120	-0.005	-0.005	0.000	0.000	0.000
72	G	92	ALA	0	-0.016	-0.016	107.350	0.000	0.000	0.000	0.000	0.000
73	G	93	GLU	-1	-0.925	-0.965	109.034	0.004	0.004	0.000	0.000	0.000
74	G	94	ALA	0	0.007	0.006	111.078	0.000	0.000	0.000	0.000	0.000
75	G	95	GLU	-1	-0.963	-0.997	110.374	0.004	0.004	0.000	0.000	0.000
76	G	96	ALA	0	-0.040	-0.009	113.335	0.000	0.000	0.000	0.000	0.000
77	G	97	LYS	1	0.928	0.947	115.106	-0.003	-0.003	0.000	0.000	0.000
78	G	98	ALA	0	0.006	0.016	115.815	0.000	0.000	0.000	0.000	0.000
79	G	99	VAL	0	0.005	0.006	116.031	0.000	0.000	0.000	0.000	0.000
80	G	100	ARG	1	0.947	0.976	116.345	-0.004	-0.004	0.000	0.000	0.000
81	G	101	GLU	-1	-0.880	-0.953	121.287	0.003	0.003	0.000	0.000	0.000
82	G	102	LYS	1	0.845	0.920	117.908	-0.004	-0.004	0.000	0.000	0.000
83	G	103	ALA	0	-0.001	0.003	123.572	0.000	0.000	0.000	0.000	0.000
84	G	104	MET	0	-0.043	-0.018	125.365	0.000	0.000	0.000	0.000	0.000
85	G	105	ALA	0	0.003	0.013	127.466	0.000	0.000	0.000	0.000	0.000
86	G	106	ARG	1	0.873	0.956	128.667	-0.003	-0.003	0.000	0.000	0.000
87	G	107	LEU	0	0.045	0.031	128.274	0.000	0.000	0.000	0.000	0.000
88	G	108	ASP	-1	-0.843	-0.932	130.979	0.003	0.003	0.000	0.000	0.000
89	G	109	GLU	-1	-0.886	-0.960	132.852	0.003	0.003	0.000	0.000	0.000
90	G	110	ALA	0	-0.012	-0.001	130.393	0.000	0.000	0.000	0.000	0.000
91	G	111	VAL	0	0.010	-0.002	132.419	0.000	0.000	0.000	0.000	0.000
92	G	112	ALA	0	-0.054	-0.030	134.693	0.000	0.000	0.000	0.000	0.000
93	G	113	LEU	0	-0.019	-0.013	132.164	0.000	0.000	0.000	0.000	0.000
94	G	114	VAL	0	0.026	0.020	132.516	0.000	0.000	0.000	0.000	0.000
95	G	115	LEU	0	0.017	0.011	135.505	0.000	0.000	0.000	0.000	0.000
96	G	116	LYS	1	0.903	0.931	138.928	-0.003	-0.003	0.000	0.000	0.000
97	G	117	GLU	-1	-0.904	-0.954	136.345	0.004	0.004	0.000	0.000	0.000
98	G	118	VAL	0	-0.097	-0.040	137.332	0.000	0.000	0.000	0.000	0.000
99	G	119	LEU	0	-0.068	-0.034	139.884	0.000	0.000	0.000	0.000	0.000
100	G	120	PRO	0	-0.043	0.012	141.740	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:21:GLY)