FMO DATABASE

FMODB ID: QYN2Y

Calculation Name: 4KUN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KUN

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-22

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	91
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-626637.303925
FMO2-HF: Nuclear repulsion	590936.168608
FMO2-HF: Total energy	-35701.135317
FMO2-MP2: Total energy	-35803.203495

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:0:GLY)

Summations of interaction energy for fragment #1(A:0: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.
-0.053999999999999	0.868	-0.001	-0.352	-0.569	0.001

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : -0.005

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	2	THR	0	-0.027	-0.016	3.859	1.200	2.077	0.000	-0.350	-0.527	0.001
4	A	3	ARG	1	0.818	0.896	5.924	0.276	0.321	-0.001	-0.002	-0.042	0.000
5	A	4	THR	0	0.006	0.005	9.560	-0.050	-0.050	0.000	0.000	0.000	0.000
6	A	5	LYS	1	0.771	0.882	12.382	0.173	0.173	0.000	0.000	0.000	0.000
7	A	6	LEU	0	0.005	-0.005	15.666	0.005	0.005	0.000	0.000	0.000	0.000
8	A	7	LYS	1	0.824	0.904	19.071	0.089	0.089	0.000	0.000	0.000	0.000
9	A	8	LEU	0	-0.019	-0.001	22.534	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	9	PHE	0	-0.006	-0.006	24.814	0.014	0.014	0.000	0.000	0.000	0.000
11	A	10	VAL	0	0.010	-0.011	28.877	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	11	ILE	0	0.053	0.023	32.157	0.004	0.004	0.000	0.000	0.000	0.000
13	A	12	GLY	0	0.050	0.025	35.932	0.001	0.001	0.000	0.000	0.000	0.000
14	A	13	ASN	0	0.014	0.012	35.979	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	14	SER	0	0.008	0.004	37.354	0.000	0.000	0.000	0.000	0.000	0.000
16	A	15	ALA	0	0.029	0.000	36.739	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	16	ILE	0	0.031	0.018	34.241	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	17	SER	0	0.045	0.008	32.746	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	18	LYS	1	0.873	0.928	31.882	0.034	0.034	0.000	0.000	0.000	0.000
20	A	19	ARG	1	0.848	0.915	31.959	0.063	0.063	0.000	0.000	0.000	0.000
21	A	20	ALA	0	0.059	0.032	28.923	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	21	ILE	0	0.002	0.000	27.567	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	22	ILE	0	0.010	0.009	26.990	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	23	ASN	0	-0.025	-0.020	27.318	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	24	LEU	0	0.011	0.011	21.171	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	25	GLN	0	-0.020	-0.018	22.568	-0.012	-0.012	0.000	0.000	0.000	0.000
27	A	26	SER	0	-0.019	0.002	23.059	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	27	ILE	0	-0.021	-0.007	20.128	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	28	CYS	0	-0.029	-0.026	17.803	-0.023	-0.023	0.000	0.000	0.000	0.000
30	A	29	SER	0	-0.073	-0.030	18.300	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	30	ASP	-1	-0.806	-0.890	17.563	-0.244	-0.244	0.000	0.000	0.000	0.000
32	A	31	PRO	0	0.002	-0.003	15.041	-0.038	-0.038	0.000	0.000	0.000	0.000
33	A	32	LYS	1	0.844	0.908	12.346	0.312	0.312	0.000	0.000	0.000	0.000
34	A	33	LEU	0	-0.017	0.018	13.635	-0.052	-0.052	0.000	0.000	0.000	0.000
35	A	34	ALA	0	0.028	-0.009	11.197	-0.073	-0.073	0.000	0.000	0.000	0.000
36	A	35	ASP	-1	-0.877	-0.925	6.434	-1.333	-1.333	0.000	0.000	0.000	0.000
37	A	36	LEU	0	-0.062	-0.051	9.413	0.015	0.015	0.000	0.000	0.000	0.000
38	A	37	CYS	0	0.040	0.027	11.207	-0.031	-0.031	0.000	0.000	0.000	0.000
39	A	38	ASP	-1	-0.812	-0.865	14.075	-0.028	-0.028	0.000	0.000	0.000	0.000
40	A	39	ILE	0	0.011	-0.015	16.370	-0.025	-0.025	0.000	0.000	0.000	0.000
41	A	40	GLU	-1	-0.824	-0.887	19.900	-0.033	-0.033	0.000	0.000	0.000	0.000
42	A	41	VAL	0	-0.009	-0.012	23.006	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	42	VAL	0	0.004	0.008	26.290	0.010	0.010	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.750	-0.876	29.038	-0.036	-0.036	0.000	0.000	0.000	0.000
45	A	44	LEU	0	0.064	0.023	30.951	0.005	0.005	0.000	0.000	0.000	0.000
46	A	45	CYS	0	-0.093	-0.028	33.901	0.003	0.003	0.000	0.000	0.000	0.000
47	A	46	LYS	1	0.840	0.902	34.735	0.026	0.026	0.000	0.000	0.000	0.000
48	A	47	ASN	0	-0.043	-0.012	31.513	0.005	0.005	0.000	0.000	0.000	0.000
49	A	48	LYS	1	0.965	0.971	33.498	0.017	0.017	0.000	0.000	0.000	0.000
50	A	49	GLY	0	0.063	0.040	34.741	0.002	0.002	0.000	0.000	0.000	0.000
51	A	50	ILE	0	0.035	0.010	28.395	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	51	ALA	0	0.005	0.000	30.121	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	52	GLU	-1	-0.929	-0.949	31.794	-0.040	-0.040	0.000	0.000	0.000	0.000
54	A	53	GLN	0	-0.058	-0.033	28.536	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	54	GLU	-1	-0.781	-0.883	24.220	-0.098	-0.098	0.000	0.000	0.000	0.000
56	A	55	LYS	1	0.914	0.975	27.703	0.053	0.053	0.000	0.000	0.000	0.000
57	A	56	ILE	0	-0.029	-0.006	28.149	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	57	LEU	0	0.016	-0.003	31.526	0.006	0.006	0.000	0.000	0.000	0.000
59	A	58	ALA	0	-0.006	0.002	33.263	0.002	0.002	0.000	0.000	0.000	0.000
60	A	59	THR	0	-0.010	0.005	32.178	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	60	PRO	0	-0.027	-0.028	30.405	0.004	0.004	0.000	0.000	0.000	0.000
62	A	61	ILE	0	-0.017	-0.002	26.900	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	62	LEU	0	-0.004	0.013	21.518	0.007	0.007	0.000	0.000	0.000	0.000
64	A	63	ILE	0	-0.006	-0.015	21.381	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	64	LYS	1	0.895	0.965	14.443	0.394	0.394	0.000	0.000	0.000	0.000
66	A	65	LYS	1	0.746	0.830	17.790	0.120	0.120	0.000	0.000	0.000	0.000
67	A	66	GLU	-1	-0.783	-0.873	12.170	-0.120	-0.120	0.000	0.000	0.000	0.000
68	A	67	PRO	0	0.082	0.040	9.792	0.038	0.038	0.000	0.000	0.000	0.000
69	A	68	LEU	0	-0.028	-0.008	11.906	0.052	0.052	0.000	0.000	0.000	0.000
70	A	69	PRO	0	0.004	0.000	13.354	-0.046	-0.046	0.000	0.000	0.000	0.000
71	A	70	GLU	-1	-0.776	-0.867	16.925	-0.151	-0.151	0.000	0.000	0.000	0.000
72	A	71	ARG	1	0.770	0.886	18.639	0.239	0.239	0.000	0.000	0.000	0.000
73	A	72	ARG	1	0.805	0.872	20.587	0.117	0.117	0.000	0.000	0.000	0.000
74	A	73	ILE	0	0.023	0.021	23.487	0.001	0.001	0.000	0.000	0.000	0.000
75	A	74	ILE	0	0.015	0.006	25.987	0.005	0.005	0.000	0.000	0.000	0.000
76	A	75	GLY	0	0.022	0.009	29.509	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	76	ASP	-1	-0.810	-0.879	30.152	-0.085	-0.085	0.000	0.000	0.000	0.000
78	A	77	LEU	0	-0.004	-0.005	24.917	0.001	0.001	0.000	0.000	0.000	0.000
79	A	78	SER	0	-0.011	-0.025	27.394	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	79	ASP	-1	-0.850	-0.902	27.245	-0.136	-0.136	0.000	0.000	0.000	0.000
81	A	80	LYS	1	0.957	0.958	20.627	0.198	0.198	0.000	0.000	0.000	0.000
82	A	81	GLN	0	0.060	0.025	20.918	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	82	LYS	1	0.885	0.949	22.912	0.116	0.116	0.000	0.000	0.000	0.000
84	A	83	VAL	0	-0.014	0.000	21.671	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	84	ILE	0	0.004	0.001	17.560	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	85	SER	0	-0.024	-0.026	18.651	-0.022	-0.022	0.000	0.000	0.000	0.000
87	A	86	ALA	0	-0.011	-0.005	20.329	-0.010	-0.010	0.000	0.000	0.000	0.000
88	A	87	LEU	0	-0.019	-0.026	18.001	0.008	0.008	0.000	0.000	0.000	0.000
89	A	88	GLU	-1	-0.851	-0.909	15.846	-0.321	-0.321	0.000	0.000	0.000	0.000
90	A	89	MET	0	-0.015	0.003	13.943	-0.047	-0.047	0.000	0.000	0.000	0.000
91	A	90	ASP	-1	-0.962	-0.979	13.434	-0.465	-0.465	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)