FMO DATABASE

FMODB ID: 5346Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-466331.587368
FMO2-HF: Nuclear repulsion	427243.271267
FMO2-HF: Total energy	-39088.316101
FMO2-MP2: Total energy	-39204.093013

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.
0.007	1.131	-0.013	-0.536	-0.574	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 : 0.049 / q_NPA : 0.014

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	0.068	0.044	3.866	0.455	1.579	-0.013	-0.536	-0.574
4	G	24	LYS	1	0.974	0.987	6.296	-0.156	-0.156	0.000	0.000	0.000
5	G	25	SER	0	-0.034	-0.025	6.347	-0.014	-0.014	0.000	0.000	0.000
6	G	26	LEU	0	0.047	0.029	8.634	-0.106	-0.106	0.000	0.000	0.000
7	G	27	ALA	0	0.035	0.018	10.281	-0.145	-0.145	0.000	0.000	0.000
8	G	28	GLU	-1	-0.844	-0.929	12.297	0.093	0.093	0.000	0.000	0.000
9	G	29	LYS	1	0.863	0.937	13.362	-0.138	-0.138	0.000	0.000	0.000
10	G	30	GLU	-1	-0.915	-0.959	14.590	0.370	0.370	0.000	0.000	0.000
11	G	31	LYS	1	0.887	0.929	14.810	-0.243	-0.243	0.000	0.000	0.000
12	G	32	GLN	0	0.055	0.036	16.886	-0.025	-0.025	0.000	0.000	0.000
13	G	33	LEU	0	-0.045	-0.021	17.632	-0.022	-0.022	0.000	0.000	0.000
14	G	34	LEU	0	0.010	0.011	20.620	-0.016	-0.016	0.000	0.000	0.000
15	G	35	GLU	-1	-0.876	-0.951	22.016	0.082	0.082	0.000	0.000	0.000
16	G	36	ARG	1	0.930	0.967	23.715	-0.066	-0.066	0.000	0.000	0.000
17	G	37	LEU	0	-0.023	-0.013	23.747	-0.010	-0.010	0.000	0.000	0.000
18	G	38	GLU	-1	-0.829	-0.915	26.631	0.075	0.075	0.000	0.000	0.000
19	G	39	ALA	0	-0.033	-0.015	28.267	-0.007	-0.007	0.000	0.000	0.000
20	G	40	ALA	0	-0.024	-0.015	29.503	-0.005	-0.005	0.000	0.000	0.000
21	G	41	LYS	1	0.913	0.953	30.733	-0.084	-0.084	0.000	0.000	0.000
22	G	42	LYS	1	0.889	0.945	30.116	-0.072	-0.072	0.000	0.000	0.000
23	G	43	GLU	-1	-0.812	-0.882	34.665	0.025	0.025	0.000	0.000	0.000
24	G	44	ALA	0	-0.031	-0.006	35.915	-0.003	-0.003	0.000	0.000	0.000
25	G	45	GLU	-1	-0.825	-0.914	37.263	0.042	0.042	0.000	0.000	0.000
26	G	46	GLU	-1	-0.850	-0.918	38.685	0.032	0.032	0.000	0.000	0.000
27	G	47	ARG	1	0.748	0.860	40.373	-0.028	-0.028	0.000	0.000	0.000
28	G	48	VAL	0	0.002	0.003	41.689	-0.002	-0.002	0.000	0.000	0.000
29	G	49	LYS	1	0.859	0.915	41.202	-0.040	-0.040	0.000	0.000	0.000
30	G	50	ARG	1	0.759	0.850	40.612	-0.029	-0.029	0.000	0.000	0.000
31	G	51	ALA	0	0.051	0.031	46.555	-0.002	-0.002	0.000	0.000	0.000
32	G	52	GLU	-1	-0.941	-0.965	47.154	0.032	0.032	0.000	0.000	0.000
33	G	53	ALA	0	-0.033	-0.015	49.443	-0.001	-0.001	0.000	0.000	0.000
34	G	54	GLU	-1	-0.830	-0.902	48.822	0.021	0.021	0.000	0.000	0.000
35	G	55	ALA	0	0.000	0.004	52.438	-0.001	-0.001	0.000	0.000	0.000
36	G	56	LYS	1	0.794	0.874	53.900	-0.020	-0.020	0.000	0.000	0.000
37	G	57	ALA	0	0.023	0.010	55.364	-0.001	-0.001	0.000	0.000	0.000
38	G	58	LEU	0	-0.014	-0.003	56.868	-0.001	-0.001	0.000	0.000	0.000
39	G	59	LEU	0	-0.009	-0.013	57.612	-0.001	-0.001	0.000	0.000	0.000
40	G	60	GLU	-1	-0.812	-0.885	58.478	0.017	0.017	0.000	0.000	0.000
41	G	61	GLU	-1	-0.924	-0.955	61.443	0.012	0.012	0.000	0.000	0.000
42	G	62	ALA	0	-0.021	-0.008	62.867	-0.001	-0.001	0.000	0.000	0.000
43	G	63	GLU	-1	-0.809	-0.894	64.615	0.014	0.014	0.000	0.000	0.000
44	G	64	ALA	0	-0.019	0.005	65.915	-0.001	-0.001	0.000	0.000	0.000
45	G	65	LYS	1	0.921	0.958	67.271	-0.011	-0.011	0.000	0.000	0.000
46	G	66	ALA	0	0.014	0.002	68.771	-0.001	-0.001	0.000	0.000	0.000
47	G	67	LYS	1	0.857	0.902	69.290	-0.014	-0.014	0.000	0.000	0.000
48	G	68	ALA	0	-0.003	0.000	71.823	-0.001	-0.001	0.000	0.000	0.000
49	G	69	LEU	0	-0.070	-0.038	72.313	-0.001	-0.001	0.000	0.000	0.000
50	G	70	GLU	-1	-0.793	-0.880	74.667	0.011	0.011	0.000	0.000	0.000
51	G	71	ALA	0	-0.032	0.003	76.525	0.000	0.000	0.000	0.000	0.000
52	G	72	GLN	0	0.011	0.008	75.673	0.000	0.000	0.000	0.000	0.000
53	G	73	TYR	0	0.005	0.003	78.291	0.000	0.000	0.000	0.000	0.000
54	G	74	ARG	1	0.876	0.900	76.685	-0.011	-0.011	0.000	0.000	0.000
55	G	75	GLU	-1	-0.866	-0.919	82.726	0.007	0.007	0.000	0.000	0.000
56	G	76	ARG	1	0.849	0.933	80.247	-0.009	-0.009	0.000	0.000	0.000
57	G	77	GLU	-1	-0.880	-0.941	84.668	0.009	0.009	0.000	0.000	0.000
58	G	78	ARG	1	0.794	0.899	87.245	-0.007	-0.007	0.000	0.000	0.000
59	G	79	ALA	0	0.010	0.006	88.632	0.000	0.000	0.000	0.000	0.000
60	G	80	GLU	-1	-0.947	-0.980	87.794	0.008	0.008	0.000	0.000	0.000
61	G	81	THR	0	-0.053	-0.058	90.976	0.000	0.000	0.000	0.000	0.000
62	G	82	GLU	-1	-0.839	-0.902	93.123	0.006	0.006	0.000	0.000	0.000
63	G	83	ALA	0	-0.005	0.002	94.443	0.000	0.000	0.000	0.000	0.000
64	G	84	LEU	0	-0.028	-0.014	95.015	0.000	0.000	0.000	0.000	0.000
65	G	85	LEU	0	0.000	-0.011	96.429	0.000	0.000	0.000	0.000	0.000
66	G	86	ALA	0	-0.034	-0.014	98.883	0.000	0.000	0.000	0.000	0.000
67	G	87	ARG	1	0.997	0.992	99.095	-0.006	-0.006	0.000	0.000	0.000
68	G	88	TYR	0	-0.015	-0.009	99.242	0.000	0.000	0.000	0.000	0.000
69	G	89	ARG	1	0.915	0.974	101.078	-0.006	-0.006	0.000	0.000	0.000
70	G	90	GLU	-1	-0.857	-0.928	104.313	0.005	0.005	0.000	0.000	0.000
71	G	91	ARG	1	0.784	0.860	104.598	-0.006	-0.006	0.000	0.000	0.000
72	G	92	ALA	0	0.016	0.013	107.225	0.000	0.000	0.000	0.000	0.000
73	G	93	GLU	-1	-0.958	-0.983	108.949	0.005	0.005	0.000	0.000	0.000
74	G	94	ALA	0	0.016	0.016	110.919	0.000	0.000	0.000	0.000	0.000
75	G	95	GLU	-1	-0.811	-0.884	109.246	0.005	0.005	0.000	0.000	0.000
76	G	96	ALA	0	-0.010	-0.010	112.966	0.000	0.000	0.000	0.000	0.000
77	G	97	LYS	1	0.805	0.877	114.857	-0.004	-0.004	0.000	0.000	0.000
78	G	98	ALA	0	0.018	0.008	115.683	0.000	0.000	0.000	0.000	0.000
79	G	99	VAL	0	-0.027	-0.006	116.270	0.000	0.000	0.000	0.000	0.000
80	G	100	ARG	1	0.955	0.981	115.547	-0.005	-0.005	0.000	0.000	0.000
81	G	101	GLU	-1	-0.802	-0.891	120.304	0.004	0.004	0.000	0.000	0.000
82	G	102	LYS	1	0.868	0.929	118.227	-0.005	-0.005	0.000	0.000	0.000
83	G	103	ALA	0	0.010	0.015	123.372	0.000	0.000	0.000	0.000	0.000
84	G	104	MET	0	-0.013	-0.011	125.111	0.000	0.000	0.000	0.000	0.000
85	G	105	ALA	0	-0.007	0.008	127.241	0.000	0.000	0.000	0.000	0.000
86	G	106	ARG	1	0.758	0.860	128.247	-0.004	-0.004	0.000	0.000	0.000
87	G	107	LEU	0	0.040	0.036	128.091	0.000	0.000	0.000	0.000	0.000
88	G	108	ASP	-1	-0.865	-0.946	130.652	0.004	0.004	0.000	0.000	0.000
89	G	109	GLU	-1	-0.792	-0.882	132.921	0.004	0.004	0.000	0.000	0.000
90	G	110	ALA	0	0.003	0.007	130.256	0.000	0.000	0.000	0.000	0.000
91	G	111	VAL	0	0.002	-0.002	132.270	0.000	0.000	0.000	0.000	0.000
92	G	112	ALA	0	-0.011	-0.007	134.383	0.000	0.000	0.000	0.000	0.000
93	G	113	LEU	0	0.029	0.016	132.365	0.000	0.000	0.000	0.000	0.000
94	G	114	VAL	0	0.058	0.028	132.288	0.000	0.000	0.000	0.000	0.000
95	G	115	LEU	0	-0.040	-0.023	135.400	0.000	0.000	0.000	0.000	0.000
96	G	116	LYS	1	0.786	0.879	138.449	-0.004	-0.004	0.000	0.000	0.000
97	G	117	GLU	-1	-0.891	-0.937	135.692	0.004	0.004	0.000	0.000	0.000
98	G	118	VAL	0	-0.078	-0.045	136.687	0.000	0.000	0.000	0.000	0.000
99	G	119	LEU	0	-0.044	-0.017	139.286	0.000	0.000	0.000	0.000	0.000
100	G	120	PRO	0	-0.038	0.012	141.693	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)