FMO DATABASE

FMODB ID: Z6N4N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-624367.412712
FMO2-HF: Nuclear repulsion	588667.076305
FMO2-HF: Total energy	-35700.336407
FMO2-MP2: Total energy	-35802.37246

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.
-0.393	0.375	-0.005	-0.291	-0.472	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 : 0.019 / q_NPA : -0.001

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	-0.012	3.847	1.598	2.366	-0.005	-0.291	-0.472
4	A	3	ARG	1	0.937	0.989	6.227	-0.172	-0.172	0.000	0.000	0.000
5	A	4	THR	0	0.026	0.021	9.894	-0.011	-0.011	0.000	0.000	0.000
6	A	5	LYS	1	0.904	0.971	12.499	0.049	0.049	0.000	0.000	0.000
7	A	6	LEU	0	-0.007	-0.022	15.765	-0.003	-0.003	0.000	0.000	0.000
8	A	7	LYS	1	0.941	0.973	19.001	0.025	0.025	0.000	0.000	0.000
9	A	8	LEU	0	-0.008	0.013	22.559	-0.006	-0.006	0.000	0.000	0.000
10	A	9	PHE	0	0.008	0.004	24.908	0.011	0.011	0.000	0.000	0.000
11	A	10	VAL	0	0.005	-0.010	28.884	-0.004	-0.004	0.000	0.000	0.000
12	A	11	ILE	0	0.051	0.016	32.078	0.004	0.004	0.000	0.000	0.000
13	A	12	GLY	0	-0.009	-0.005	35.803	-0.001	-0.001	0.000	0.000	0.000
14	A	13	ASN	0	0.004	-0.012	35.618	-0.005	-0.005	0.000	0.000	0.000
15	A	14	SER	0	0.051	0.028	37.464	-0.001	-0.001	0.000	0.000	0.000
16	A	15	ALA	0	0.037	0.003	36.959	-0.002	-0.002	0.000	0.000	0.000
17	A	16	ILE	0	0.031	0.014	34.221	-0.003	-0.003	0.000	0.000	0.000
18	A	17	SER	0	0.023	0.013	32.978	-0.005	-0.005	0.000	0.000	0.000
19	A	18	LYS	1	0.908	0.953	31.930	0.025	0.025	0.000	0.000	0.000
20	A	19	ARG	1	0.882	0.943	31.897	0.048	0.048	0.000	0.000	0.000
21	A	20	ALA	0	0.055	0.029	29.047	-0.005	-0.005	0.000	0.000	0.000
22	A	21	ILE	0	-0.004	-0.003	27.551	-0.007	-0.007	0.000	0.000	0.000
23	A	22	ILE	0	0.000	0.006	26.840	-0.004	-0.004	0.000	0.000	0.000
24	A	23	ASN	0	-0.029	-0.027	27.136	-0.007	-0.007	0.000	0.000	0.000
25	A	24	LEU	0	-0.006	0.003	21.121	-0.011	-0.011	0.000	0.000	0.000
26	A	25	GLN	0	0.006	-0.011	22.340	-0.014	-0.014	0.000	0.000	0.000
27	A	26	SER	0	-0.003	0.012	22.731	-0.012	-0.012	0.000	0.000	0.000
28	A	27	ILE	0	-0.017	0.027	19.889	-0.012	-0.012	0.000	0.000	0.000
29	A	28	CYS	0	-0.051	-0.028	18.221	-0.026	-0.026	0.000	0.000	0.000
30	A	29	SER	0	-0.085	-0.068	18.068	-0.007	-0.007	0.000	0.000	0.000
31	A	30	ASP	-1	-0.882	-0.941	17.460	-0.269	-0.269	0.000	0.000	0.000
32	A	31	PRO	0	-0.019	-0.010	14.739	-0.028	-0.028	0.000	0.000	0.000
33	A	32	LYS	1	0.891	0.931	13.079	0.302	0.302	0.000	0.000	0.000
34	A	33	LEU	0	-0.038	0.007	12.974	-0.046	-0.046	0.000	0.000	0.000
35	A	34	ALA	0	0.025	-0.011	11.044	-0.052	-0.052	0.000	0.000	0.000
36	A	35	ASP	-1	-0.889	-0.928	6.377	-1.705	-1.705	0.000	0.000	0.000
37	A	36	LEU	0	-0.057	-0.037	8.930	0.062	0.062	0.000	0.000	0.000
38	A	37	CYS	0	0.020	0.010	11.046	-0.001	-0.001	0.000	0.000	0.000
39	A	38	ASP	-1	-0.902	-0.945	14.088	0.068	0.068	0.000	0.000	0.000
40	A	39	ILE	0	-0.021	-0.016	16.482	-0.012	-0.012	0.000	0.000	0.000
41	A	40	GLU	-1	-0.923	-0.958	19.987	0.018	0.018	0.000	0.000	0.000
42	A	41	VAL	0	-0.024	-0.021	23.077	-0.009	-0.009	0.000	0.000	0.000
43	A	42	VAL	0	0.002	0.000	26.364	0.008	0.008	0.000	0.000	0.000
44	A	43	ASP	-1	-0.837	-0.925	28.903	-0.020	-0.020	0.000	0.000	0.000
45	A	44	LEU	0	0.051	0.004	31.098	0.005	0.005	0.000	0.000	0.000
46	A	45	CYS	0	-0.065	-0.023	33.842	0.002	0.002	0.000	0.000	0.000
47	A	46	LYS	1	0.886	0.943	35.016	0.006	0.006	0.000	0.000	0.000
48	A	47	ASN	0	-0.021	-0.002	32.401	0.007	0.007	0.000	0.000	0.000
49	A	48	LYS	1	0.995	0.992	34.110	-0.002	-0.002	0.000	0.000	0.000
50	A	49	GLY	0	0.058	0.034	34.911	0.003	0.003	0.000	0.000	0.000
51	A	50	ILE	0	0.032	0.015	28.861	-0.001	-0.001	0.000	0.000	0.000
52	A	51	ALA	0	0.002	-0.004	30.524	-0.003	-0.003	0.000	0.000	0.000
53	A	52	GLU	-1	-0.915	-0.948	31.885	-0.010	-0.010	0.000	0.000	0.000
54	A	53	GLN	0	-0.025	-0.015	28.995	0.000	0.000	0.000	0.000	0.000
55	A	54	GLU	-1	-0.854	-0.899	25.154	-0.025	-0.025	0.000	0.000	0.000
56	A	55	LYS	1	0.932	0.971	28.172	0.018	0.018	0.000	0.000	0.000
57	A	56	ILE	0	-0.046	-0.020	28.252	-0.005	-0.005	0.000	0.000	0.000
58	A	57	LEU	0	0.018	-0.001	31.596	0.003	0.003	0.000	0.000	0.000
59	A	58	ALA	0	-0.016	-0.004	32.707	0.000	0.000	0.000	0.000	0.000
60	A	59	THR	0	-0.034	0.001	32.190	-0.002	-0.002	0.000	0.000	0.000
61	A	60	PRO	0	-0.003	-0.016	30.501	0.002	0.002	0.000	0.000	0.000
62	A	61	ILE	0	0.006	0.005	27.078	-0.003	-0.003	0.000	0.000	0.000
63	A	62	LEU	0	0.000	0.009	21.726	0.007	0.007	0.000	0.000	0.000
64	A	63	ILE	0	-0.007	-0.014	21.418	-0.006	-0.006	0.000	0.000	0.000
65	A	64	LYS	1	0.904	0.942	14.394	0.294	0.294	0.000	0.000	0.000
66	A	65	LYS	1	0.795	0.887	17.832	0.039	0.039	0.000	0.000	0.000
67	A	66	GLU	-1	-0.929	-0.945	12.605	0.038	0.038	0.000	0.000	0.000
68	A	67	PRO	0	0.091	0.028	10.107	0.012	0.012	0.000	0.000	0.000
69	A	68	LEU	0	-0.019	-0.004	12.266	0.010	0.010	0.000	0.000	0.000
70	A	69	PRO	0	0.015	-0.004	13.710	-0.027	-0.027	0.000	0.000	0.000
71	A	70	GLU	-1	-0.864	-0.939	17.195	-0.072	-0.072	0.000	0.000	0.000
72	A	71	ARG	1	0.850	0.950	18.608	0.146	0.146	0.000	0.000	0.000
73	A	72	ARG	1	0.821	0.889	20.775	0.065	0.065	0.000	0.000	0.000
74	A	73	ILE	0	0.025	0.021	23.688	-0.001	-0.001	0.000	0.000	0.000
75	A	74	ILE	0	0.012	0.006	26.145	0.005	0.005	0.000	0.000	0.000
76	A	75	GLY	0	0.020	0.011	29.642	-0.003	-0.003	0.000	0.000	0.000
77	A	76	ASP	-1	-0.854	-0.938	30.122	-0.068	-0.068	0.000	0.000	0.000
78	A	77	LEU	0	-0.005	0.002	24.982	-0.002	-0.002	0.000	0.000	0.000
79	A	78	SER	0	-0.008	-0.009	27.604	-0.007	-0.007	0.000	0.000	0.000
80	A	79	ASP	-1	-0.849	-0.920	27.632	-0.112	-0.112	0.000	0.000	0.000
81	A	80	LYS	1	1.014	0.997	21.851	0.161	0.161	0.000	0.000	0.000
82	A	81	GLN	0	0.053	0.013	21.200	-0.011	-0.011	0.000	0.000	0.000
83	A	82	LYS	1	0.899	0.957	23.043	0.096	0.096	0.000	0.000	0.000
84	A	83	VAL	0	0.010	0.007	21.606	-0.003	-0.003	0.000	0.000	0.000
85	A	84	ILE	0	0.004	0.003	17.470	0.002	0.002	0.000	0.000	0.000
86	A	85	SER	0	-0.048	-0.007	18.672	-0.017	-0.017	0.000	0.000	0.000
87	A	86	ALA	0	0.005	0.006	20.719	-0.001	-0.001	0.000	0.000	0.000
88	A	87	LEU	0	-0.038	-0.032	18.234	0.011	0.011	0.000	0.000	0.000
89	A	88	GLU	-1	-0.927	-0.952	16.561	-0.221	-0.221	0.000	0.000	0.000
90	A	89	MET	0	-0.038	-0.018	14.063	-0.023	-0.023	0.000	0.000	0.000
91	A	90	ASP	-1	-0.909	-0.945	12.865	-0.458	-0.458	0.000	0.000	0.000

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