FMO DATABASE

FMODB ID: R9Y78

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	OptHSide
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	-625326.045939
FMO2-HF: Nuclear repulsion	589625.09453
FMO2-HF: Total energy	-35700.951409
FMO2-MP2: Total energy	-35803.000826

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.
0.053000000000001	0.785	-0.003	-0.271	-0.458	0

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 : 0.023 / q_NPA : 0.000

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].
3	A	2	THR	0	-0.012	-0.009	3.837	1.724	2.456	-0.003	-0.271	-0.458
4	A	3	ARG	1	0.841	0.929	6.225	-0.114	-0.114	0.000	0.000	0.000
5	A	4	THR	0	0.020	0.018	9.894	-0.009	-0.009	0.000	0.000	0.000
6	A	5	LYS	1	0.836	0.930	12.499	0.027	0.027	0.000	0.000	0.000
7	A	6	LEU	0	-0.002	-0.020	15.763	-0.002	-0.002	0.000	0.000	0.000
8	A	7	LYS	1	0.847	0.910	19.001	0.027	0.027	0.000	0.000	0.000
9	A	8	LEU	0	-0.026	0.005	22.557	-0.006	-0.006	0.000	0.000	0.000
10	A	9	PHE	0	0.009	0.006	24.823	0.011	0.011	0.000	0.000	0.000
11	A	10	VAL	0	0.008	-0.012	28.884	-0.004	-0.004	0.000	0.000	0.000
12	A	11	ILE	0	0.046	0.014	32.078	0.005	0.005	0.000	0.000	0.000
13	A	12	GLY	0	0.018	0.010	35.803	-0.001	-0.001	0.000	0.000	0.000
14	A	13	ASN	0	0.000	-0.004	35.618	-0.005	-0.005	0.000	0.000	0.000
15	A	14	SER	0	0.032	0.012	36.999	-0.001	-0.001	0.000	0.000	0.000
16	A	15	ALA	0	0.055	0.010	36.959	-0.002	-0.002	0.000	0.000	0.000
17	A	16	ILE	0	0.041	0.019	34.247	-0.003	-0.003	0.000	0.000	0.000
18	A	17	SER	0	0.016	0.015	32.985	-0.005	-0.005	0.000	0.000	0.000
19	A	18	LYS	1	0.903	0.945	31.930	0.028	0.028	0.000	0.000	0.000
20	A	19	ARG	1	0.837	0.905	31.897	0.052	0.052	0.000	0.000	0.000
21	A	20	ALA	0	0.051	0.027	29.088	-0.005	-0.005	0.000	0.000	0.000
22	A	21	ILE	0	-0.010	-0.007	27.551	-0.007	-0.007	0.000	0.000	0.000
23	A	22	ILE	0	0.009	0.008	26.840	-0.005	-0.005	0.000	0.000	0.000
24	A	23	ASN	0	-0.027	-0.025	27.136	-0.007	-0.007	0.000	0.000	0.000
25	A	24	LEU	0	0.001	0.009	21.126	-0.011	-0.011	0.000	0.000	0.000
26	A	25	GLN	0	-0.012	-0.018	22.340	-0.014	-0.014	0.000	0.000	0.000
27	A	26	SER	0	-0.010	0.010	22.731	-0.011	-0.011	0.000	0.000	0.000
28	A	27	ILE	0	-0.014	0.002	20.000	-0.014	-0.014	0.000	0.000	0.000
29	A	28	CYS	0	-0.040	-0.019	17.840	-0.021	-0.021	0.000	0.000	0.000
30	A	29	SER	0	-0.074	-0.037	18.068	-0.008	-0.008	0.000	0.000	0.000
31	A	30	ASP	-1	-0.853	-0.927	17.465	-0.274	-0.274	0.000	0.000	0.000
32	A	31	PRO	0	0.012	0.001	14.643	-0.030	-0.030	0.000	0.000	0.000
33	A	32	LYS	1	0.888	0.939	12.825	0.378	0.378	0.000	0.000	0.000
34	A	33	LEU	0	-0.032	0.007	12.977	-0.047	-0.047	0.000	0.000	0.000
35	A	34	ALA	0	0.026	-0.007	11.049	-0.049	-0.049	0.000	0.000	0.000
36	A	35	ASP	-1	-0.909	-0.934	6.654	-1.570	-1.570	0.000	0.000	0.000
37	A	36	LEU	0	-0.056	-0.045	9.230	0.056	0.056	0.000	0.000	0.000
38	A	37	CYS	0	0.018	0.010	11.046	0.014	0.014	0.000	0.000	0.000
39	A	38	ASP	-1	-0.810	-0.885	14.088	0.062	0.062	0.000	0.000	0.000
40	A	39	ILE	0	-0.015	-0.024	16.482	-0.009	-0.009	0.000	0.000	0.000
41	A	40	GLU	-1	-0.825	-0.887	19.987	0.013	0.013	0.000	0.000	0.000
42	A	41	VAL	0	-0.009	-0.017	23.077	-0.008	-0.008	0.000	0.000	0.000
43	A	42	VAL	0	0.006	0.006	26.295	0.008	0.008	0.000	0.000	0.000
44	A	43	ASP	-1	-0.763	-0.880	28.903	-0.021	-0.021	0.000	0.000	0.000
45	A	44	LEU	0	0.060	0.015	30.994	0.005	0.005	0.000	0.000	0.000
46	A	45	CYS	0	-0.094	-0.028	33.840	0.003	0.003	0.000	0.000	0.000
47	A	46	LYS	1	0.809	0.887	34.971	0.011	0.011	0.000	0.000	0.000
48	A	47	ASN	0	-0.037	-0.014	32.213	0.007	0.007	0.000	0.000	0.000
49	A	48	LYS	1	0.987	0.989	34.108	0.000	0.000	0.000	0.000	0.000
50	A	49	GLY	0	0.067	0.038	34.909	0.003	0.003	0.000	0.000	0.000
51	A	50	ILE	0	0.031	0.012	28.848	-0.001	-0.001	0.000	0.000	0.000
52	A	51	ALA	0	0.005	-0.002	30.522	-0.003	-0.003	0.000	0.000	0.000
53	A	52	GLU	-1	-0.917	-0.950	31.883	-0.009	-0.009	0.000	0.000	0.000
54	A	53	GLN	0	-0.035	-0.017	29.059	0.001	0.001	0.000	0.000	0.000
55	A	54	GLU	-1	-0.817	-0.876	24.737	-0.031	-0.031	0.000	0.000	0.000
56	A	55	LYS	1	0.931	0.974	28.170	0.013	0.013	0.000	0.000	0.000
57	A	56	ILE	0	-0.040	-0.015	28.132	-0.005	-0.005	0.000	0.000	0.000
58	A	57	LEU	0	0.014	-0.001	31.594	0.004	0.004	0.000	0.000	0.000
59	A	58	ALA	0	-0.017	-0.003	32.699	0.000	0.000	0.000	0.000	0.000
60	A	59	THR	0	-0.008	0.015	32.189	0.000	0.000	0.000	0.000	0.000
61	A	60	PRO	0	-0.023	-0.032	30.405	0.002	0.002	0.000	0.000	0.000
62	A	61	ILE	0	0.005	0.004	27.040	-0.003	-0.003	0.000	0.000	0.000
63	A	62	LEU	0	-0.003	0.008	21.644	0.006	0.006	0.000	0.000	0.000
64	A	63	ILE	0	-0.008	-0.015	21.571	-0.006	-0.006	0.000	0.000	0.000
65	A	64	LYS	1	0.915	0.966	14.468	0.274	0.274	0.000	0.000	0.000
66	A	65	LYS	1	0.754	0.834	17.887	0.043	0.043	0.000	0.000	0.000
67	A	66	GLU	-1	-0.867	-0.914	12.584	0.042	0.042	0.000	0.000	0.000
68	A	67	PRO	0	0.100	0.032	10.109	0.008	0.008	0.000	0.000	0.000
69	A	68	LEU	0	-0.016	-0.002	12.265	0.009	0.009	0.000	0.000	0.000
70	A	69	PRO	0	0.012	-0.004	13.710	-0.025	-0.025	0.000	0.000	0.000
71	A	70	GLU	-1	-0.782	-0.873	17.194	-0.075	-0.075	0.000	0.000	0.000
72	A	71	ARG	1	0.789	0.897	18.921	0.147	0.147	0.000	0.000	0.000
73	A	72	ARG	1	0.790	0.860	20.775	0.063	0.063	0.000	0.000	0.000
74	A	73	ILE	0	0.025	0.019	23.687	-0.001	-0.001	0.000	0.000	0.000
75	A	74	ILE	0	0.010	0.007	26.144	0.004	0.004	0.000	0.000	0.000
76	A	75	GLY	0	0.031	0.015	29.641	-0.003	-0.003	0.000	0.000	0.000
77	A	76	ASP	-1	-0.815	-0.887	30.122	-0.070	-0.070	0.000	0.000	0.000
78	A	77	LEU	0	-0.006	0.000	24.998	-0.002	-0.002	0.000	0.000	0.000
79	A	78	SER	0	-0.011	-0.027	27.606	-0.007	-0.007	0.000	0.000	0.000
80	A	79	ASP	-1	-0.854	-0.901	27.376	-0.117	-0.117	0.000	0.000	0.000
81	A	80	LYS	1	0.956	0.966	20.396	0.202	0.202	0.000	0.000	0.000
82	A	81	GLN	0	0.059	0.016	21.087	-0.011	-0.011	0.000	0.000	0.000
83	A	82	LYS	1	0.887	0.941	23.044	0.099	0.099	0.000	0.000	0.000
84	A	83	VAL	0	0.003	0.006	21.667	-0.002	-0.002	0.000	0.000	0.000
85	A	84	ILE	0	0.001	-0.002	17.733	-0.001	-0.001	0.000	0.000	0.000
86	A	85	SER	0	-0.013	-0.005	18.673	-0.016	-0.016	0.000	0.000	0.000
87	A	86	ALA	0	-0.017	0.002	20.719	0.000	0.000	0.000	0.000	0.000
88	A	87	LEU	0	-0.038	-0.035	18.314	0.010	0.010	0.000	0.000	0.000
89	A	88	GLU	-1	-0.858	-0.904	16.481	-0.207	-0.207	0.000	0.000	0.000
90	A	89	MET	0	-0.007	0.006	14.086	-0.030	-0.030	0.000	0.000	0.000
91	A	90	ASP	-1	-0.974	-0.985	13.148	-0.420	-0.420	0.000	0.000	0.000

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