FMO DATABASE

FMODB ID: NN6YQ

Calculation Name: 5KUX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5KUX

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-23

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	92
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-505176.703166
FMO2-HF: Nuclear repulsion	469578.007804
FMO2-HF: Total energy	-35598.695362
FMO2-MP2: Total energy	-35703.092893

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:4:GLY)

Summations of interaction energy for fragment #1(A:4: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.
-13.84	-14.697	13.103	-6.691	-5.554	-0.067

Interaction energy analysis for fragmet #1(A:4:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : -0.006

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	A	6	VAL	0	-0.006	0.001	3.848	1.167	1.940	0.002	-0.333	-0.442	0.002
4	A	7	ASN	0	-0.019	-0.028	6.088	0.141	0.141	0.000	0.000	0.000	0.000
5	A	8	VAL	0	-0.019	-0.001	9.818	-0.033	-0.033	0.000	0.000	0.000	0.000
6	A	9	PRO	0	-0.005	0.005	12.370	0.072	0.072	0.000	0.000	0.000	0.000
7	A	10	ASN	0	0.038	0.001	14.991	0.032	0.032	0.000	0.000	0.000	0.000
8	A	11	CYS	0	0.001	0.008	16.371	-0.033	-0.033	0.000	0.000	0.000	0.000
9	A	12	ASN	0	0.091	0.040	17.650	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	13	THR	0	0.005	0.018	18.353	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	14	THR	0	0.034	-0.007	20.741	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.810	0.906	12.097	0.612	0.612	0.000	0.000	0.000	0.000
13	A	16	TYR	0	0.017	-0.027	12.554	0.026	0.026	0.000	0.000	0.000	0.000
14	A	17	GLN	0	0.012	0.013	18.201	0.012	0.012	0.000	0.000	0.000	0.000
15	A	18	GLN	0	0.045	0.037	21.737	0.021	0.021	0.000	0.000	0.000	0.000
16	A	19	LEU	0	-0.011	0.007	15.608	0.005	0.005	0.000	0.000	0.000	0.000
17	A	20	ALA	0	0.024	0.019	19.812	0.011	0.011	0.000	0.000	0.000	0.000
18	A	21	ARG	1	0.882	0.927	21.190	0.135	0.135	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.026	-0.019	21.937	0.011	0.011	0.000	0.000	0.000	0.000
20	A	23	ALA	0	0.007	0.005	20.355	0.008	0.008	0.000	0.000	0.000	0.000
21	A	24	VAL	0	-0.017	-0.006	22.469	0.014	0.014	0.000	0.000	0.000	0.000
22	A	25	ALA	0	-0.011	-0.002	25.747	0.010	0.010	0.000	0.000	0.000	0.000
23	A	26	ILE	0	-0.005	-0.007	22.674	0.005	0.005	0.000	0.000	0.000	0.000
24	A	27	TYR	0	0.008	0.007	25.297	0.009	0.009	0.000	0.000	0.000	0.000
25	A	28	ASN	0	-0.011	-0.028	26.974	0.012	0.012	0.000	0.000	0.000	0.000
26	A	29	TYR	0	-0.053	-0.005	29.463	0.005	0.005	0.000	0.000	0.000	0.000
27	A	30	HIS	0	0.000	-0.013	25.363	0.009	0.009	0.000	0.000	0.000	0.000
28	A	31	GLU	-1	-0.926	-0.965	28.654	-0.034	-0.034	0.000	0.000	0.000	0.000
29	A	32	GLN	0	-0.113	-0.052	31.511	0.010	0.010	0.000	0.000	0.000	0.000
30	A	33	ALA	0	-0.019	0.011	31.150	0.005	0.005	0.000	0.000	0.000	0.000
31	A	34	HIS	0	0.005	-0.013	33.308	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	35	LEU	0	-0.021	0.003	27.963	0.003	0.003	0.000	0.000	0.000	0.000
33	A	36	THR	0	-0.001	0.001	30.988	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	37	PHE	0	-0.021	-0.015	22.882	0.003	0.003	0.000	0.000	0.000	0.000
35	A	38	VAL	0	-0.007	0.001	27.016	0.002	0.002	0.000	0.000	0.000	0.000
36	A	39	GLU	-1	-0.951	-0.981	24.757	-0.022	-0.022	0.000	0.000	0.000	0.000
37	A	40	ASN	0	-0.067	-0.041	19.328	0.011	0.011	0.000	0.000	0.000	0.000
38	A	41	LEU	0	0.053	0.022	20.733	0.006	0.006	0.000	0.000	0.000	0.000
39	A	42	ASN	0	-0.019	-0.022	15.903	0.037	0.037	0.000	0.000	0.000	0.000
40	A	43	CYS	0	-0.021	-0.008	12.819	-0.024	-0.024	0.000	0.000	0.000	0.000
41	A	44	LYS	1	0.943	0.974	8.855	-0.466	-0.466	0.000	0.000	0.000	0.000
42	A	45	GLU	-1	-0.726	-0.833	8.106	-0.672	-0.672	0.000	0.000	0.000	0.000
43	A	46	GLN	0	0.017	-0.011	2.269	1.655	2.750	0.360	-0.667	-0.788	0.000
44	A	47	LEU	0	-0.030	-0.004	5.797	0.521	0.521	0.000	0.000	0.000	0.000
45	A	48	GLY	0	-0.005	-0.007	5.693	-0.561	-0.561	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.765	-0.841	1.865	-17.906	-21.192	12.682	-5.449	-3.947	-0.069
47	A	50	GLY	0	-0.013	0.007	6.291	0.258	0.258	0.000	0.000	0.000	0.000
48	A	51	ASP	-1	-0.835	-0.889	9.175	-0.484	-0.484	0.000	0.000	0.000	0.000
49	A	52	TYR	0	-0.128	-0.091	11.878	0.054	0.054	0.000	0.000	0.000	0.000
50	A	53	TYR	0	-0.059	-0.039	14.343	0.060	0.060	0.000	0.000	0.000	0.000
51	A	54	TYR	0	0.000	-0.017	18.675	0.017	0.017	0.000	0.000	0.000	0.000
52	A	55	ILE	0	-0.019	-0.013	20.889	0.003	0.003	0.000	0.000	0.000	0.000
53	A	56	THR	0	-0.005	-0.013	24.687	0.007	0.007	0.000	0.000	0.000	0.000
54	A	57	LEU	0	-0.053	-0.022	26.337	0.000	0.000	0.000	0.000	0.000	0.000
55	A	58	ALA	0	-0.007	-0.008	29.826	0.003	0.003	0.000	0.000	0.000	0.000
56	A	59	ALA	0	-0.012	0.001	31.607	0.001	0.001	0.000	0.000	0.000	0.000
57	A	60	THR	0	-0.022	-0.022	33.737	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	61	ASP	-1	-0.843	-0.915	35.685	-0.022	-0.022	0.000	0.000	0.000	0.000
59	A	62	ASP	-1	-0.923	-0.965	37.602	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	63	ALA	0	-0.026	0.004	39.644	0.002	0.002	0.000	0.000	0.000	0.000
61	A	64	GLY	0	-0.018	-0.014	40.470	0.000	0.000	0.000	0.000	0.000	0.000
62	A	65	LYS	1	0.763	0.870	41.078	0.022	0.022	0.000	0.000	0.000	0.000
63	A	66	LYS	1	0.880	0.928	37.711	0.036	0.036	0.000	0.000	0.000	0.000
64	A	67	ALA	0	-0.011	-0.014	36.122	0.000	0.000	0.000	0.000	0.000	0.000
65	A	68	ILE	0	0.018	0.006	32.656	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	69	TYR	0	0.014	-0.005	29.789	0.004	0.004	0.000	0.000	0.000	0.000
67	A	70	GLU	-1	-0.857	-0.908	27.694	-0.117	-0.117	0.000	0.000	0.000	0.000
68	A	71	ALA	0	-0.005	-0.003	23.371	0.007	0.007	0.000	0.000	0.000	0.000
69	A	72	LYS	1	0.821	0.923	17.293	0.292	0.292	0.000	0.000	0.000	0.000
70	A	73	ILE	0	-0.006	-0.015	16.335	0.023	0.023	0.000	0.000	0.000	0.000
71	A	74	GLY	0	0.039	0.023	14.130	-0.036	-0.036	0.000	0.000	0.000	0.000
72	A	75	VAL	0	-0.008	-0.014	10.849	0.083	0.083	0.000	0.000	0.000	0.000
73	A	76	VAL	0	-0.003	-0.004	5.469	-0.162	-0.162	0.000	0.000	0.000	0.000
74	A	77	GLU	-1	-0.863	-0.931	7.707	-0.144	-0.144	0.000	0.000	0.000	0.000
75	A	78	SER	0	-0.103	-0.076	2.902	0.890	1.413	0.060	-0.241	-0.342	0.000
76	A	79	ALA	0	-0.053	-0.027	5.304	1.018	1.056	-0.001	-0.001	-0.035	0.000
77	A	80	GLY	0	-0.015	-0.004	6.815	0.003	0.003	0.000	0.000	0.000	0.000
78	A	81	TRP	0	-0.025	-0.001	9.274	0.004	0.004	0.000	0.000	0.000	0.000
79	A	82	THR	0	0.016	-0.013	11.016	-0.136	-0.136	0.000	0.000	0.000	0.000
80	A	83	GLY	0	-0.020	0.003	13.871	0.062	0.062	0.000	0.000	0.000	0.000
81	A	84	VAL	0	-0.031	-0.013	16.231	-0.040	-0.040	0.000	0.000	0.000	0.000
82	A	85	GLU	-1	-0.802	-0.879	15.800	-0.290	-0.290	0.000	0.000	0.000	0.000
83	A	86	GLU	-1	-0.803	-0.885	19.832	-0.089	-0.089	0.000	0.000	0.000	0.000
84	A	87	PHE	0	-0.019	-0.015	23.434	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	88	LYS	1	0.808	0.892	26.161	0.094	0.094	0.000	0.000	0.000	0.000
86	A	89	LEU	0	0.015	0.014	29.841	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	90	VAL	0	-0.029	-0.018	31.501	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	91	GLY	0	0.014	0.007	34.481	0.001	0.001	0.000	0.000	0.000	0.000
89	A	92	SER	0	0.000	0.011	37.499	0.001	0.001	0.000	0.000	0.000	0.000
90	A	93	LEU	0	-0.002	-0.004	36.218	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	94	GLU	-1	-0.816	-0.873	40.625	-0.029	-0.029	0.000	0.000	0.000	0.000
92	A	95	HIS	0	-0.032	-0.019	43.982	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:GLY)