FMO DATABASE

FMODB ID: 4J88N

Calculation Name: 3KXE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KXE

Chain ID: A

ChEMBL ID:

UniProt ID: P58091

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	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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-680742.189422
FMO2-HF: Nuclear repulsion	642321.887599
FMO2-HF: Total energy	-38420.301823
FMO2-MP2: Total energy	-38531.544584

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:2:LYS)

Summations of interaction energy for fragment #1(A:2:LYS)

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.
-53.283	-47.595	0.193	-2.721	-3.16	-0.019

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.021 / q_NPA : 1.001

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	4	TYR	0	0.026	0.012	3.792	4.902	6.359	-0.008	-0.604	-0.846	0.002
4	A	5	ARG	1	0.851	0.913	6.691	19.742	19.742	0.000	0.000	0.000	0.000
5	A	6	LEU	0	0.053	0.020	10.273	-0.392	-0.392	0.000	0.000	0.000	0.000
6	A	7	SER	0	-0.070	-0.024	12.670	1.144	1.144	0.000	0.000	0.000	0.000
7	A	8	ARG	1	1.045	1.001	16.379	14.767	14.767	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.892	0.950	18.543	13.164	13.164	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.068	0.040	16.140	0.268	0.268	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.874	0.916	15.827	16.243	16.243	0.000	0.000	0.000	0.000
11	A	12	ALA	0	-0.017	-0.018	17.326	0.175	0.175	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.740	-0.870	19.186	-14.036	-14.036	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.001	0.005	14.238	0.162	0.162	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.813	-0.880	18.591	-15.026	-15.026	0.000	0.000	0.000	0.000
15	A	16	ASP	-1	-0.929	-0.952	21.192	-12.001	-12.001	0.000	0.000	0.000	0.000
16	A	17	ILE	0	-0.079	-0.054	19.683	0.390	0.390	0.000	0.000	0.000	0.000
17	A	18	TRP	0	-0.019	-0.003	18.097	-0.172	-0.172	0.000	0.000	0.000	0.000
18	A	19	THR	0	0.000	-0.003	22.293	0.546	0.546	0.000	0.000	0.000	0.000
19	A	20	TYR	0	-0.020	-0.008	25.833	0.584	0.584	0.000	0.000	0.000	0.000
20	A	21	SER	0	-0.012	-0.029	23.396	0.349	0.349	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.863	-0.919	25.029	-11.991	-11.991	0.000	0.000	0.000	0.000
22	A	23	GLN	0	-0.057	-0.017	26.299	0.213	0.213	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.816	0.903	28.957	10.524	10.524	0.000	0.000	0.000	0.000
24	A	25	TRP	0	-0.072	-0.053	26.006	0.224	0.224	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.081	0.068	27.678	0.013	0.013	0.000	0.000	0.000	0.000
26	A	27	VAL	0	0.043	-0.002	23.563	-0.416	-0.416	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.925	-0.954	22.430	-13.257	-13.257	0.000	0.000	0.000	0.000
28	A	29	GLN	0	0.067	0.029	21.481	-0.929	-0.929	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.020	0.000	21.528	-0.588	-0.588	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.021	-0.017	18.142	-0.842	-0.842	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.922	-0.973	17.036	-17.164	-17.164	0.000	0.000	0.000	0.000
32	A	33	TYR	0	-0.008	-0.014	17.046	-0.851	-0.851	0.000	0.000	0.000	0.000
33	A	34	ALA	0	0.014	0.001	15.918	-0.746	-0.746	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.942	0.983	12.685	17.593	17.593	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.880	-0.923	12.286	-22.282	-22.282	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.032	-0.001	13.764	-0.989	-0.989	0.000	0.000	0.000	0.000
37	A	38	GLN	0	-0.076	-0.039	7.179	2.367	2.367	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.035	0.023	9.107	-3.529	-3.529	0.000	0.000	0.000	0.000
39	A	40	THR	0	-0.021	-0.036	9.662	-1.237	-1.237	0.000	0.000	0.000	0.000
40	A	41	ILE	0	-0.047	-0.026	8.192	-0.147	-0.147	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.900	-0.969	4.444	-49.031	-48.869	-0.001	-0.008	-0.152	0.000
42	A	43	MET	0	-0.007	-0.001	5.737	-4.876	-4.876	0.000	0.000	0.000	0.000
43	A	44	ILE	0	-0.064	-0.020	7.868	1.617	1.617	0.000	0.000	0.000	0.000
44	A	45	ALA	0	-0.074	-0.052	3.334	1.487	1.727	0.007	-0.073	-0.174	0.000
45	A	46	GLU	-1	-0.957	-0.964	2.843	-69.291	-65.525	0.196	-2.031	-1.931	-0.021
46	A	47	HIS	0	0.031	0.012	4.441	5.106	5.169	-0.001	-0.005	-0.057	0.000
47	A	48	PRO	0	0.015	0.018	6.327	2.851	2.851	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.052	-0.036	8.803	1.698	1.698	0.000	0.000	0.000	0.000
49	A	50	MET	0	-0.003	0.009	11.472	1.147	1.147	0.000	0.000	0.000	0.000
50	A	51	GLY	0	0.029	0.035	12.652	0.693	0.693	0.000	0.000	0.000	0.000
51	A	52	GLN	0	0.038	0.018	14.330	0.443	0.443	0.000	0.000	0.000	0.000
52	A	53	PRO	0	-0.041	-0.033	17.911	-0.239	-0.239	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.848	-0.934	18.891	-11.487	-11.487	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.851	-0.940	21.237	-12.328	-12.328	0.000	0.000	0.000	0.000
55	A	56	ASN	0	0.021	0.007	22.830	0.383	0.383	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.078	-0.001	21.995	0.230	0.230	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.924	0.938	21.930	12.210	12.210	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.065	0.037	21.588	-0.410	-0.410	0.000	0.000	0.000	0.000
59	A	60	GLY	0	-0.024	-0.008	18.205	-0.330	-0.330	0.000	0.000	0.000	0.000
60	A	61	TYR	0	-0.069	-0.046	16.379	-0.825	-0.825	0.000	0.000	0.000	0.000
61	A	62	ARG	1	0.910	0.968	13.159	17.556	17.556	0.000	0.000	0.000	0.000
62	A	63	ARG	1	0.801	0.901	15.876	12.603	12.603	0.000	0.000	0.000	0.000
63	A	64	CYS	0	-0.018	-0.010	12.603	0.259	0.259	0.000	0.000	0.000	0.000
64	A	65	ALA	0	-0.016	-0.003	15.788	-0.260	-0.260	0.000	0.000	0.000	0.000
65	A	66	SER	0	0.038	0.021	16.156	-0.404	-0.404	0.000	0.000	0.000	0.000
66	A	67	GLY	0	0.055	0.028	18.414	0.454	0.454	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.046	-0.029	21.376	0.762	0.762	0.000	0.000	0.000	0.000
68	A	69	HIS	0	0.007	0.013	20.186	0.379	0.379	0.000	0.000	0.000	0.000
69	A	70	VAL	0	0.010	0.006	19.001	-0.328	-0.328	0.000	0.000	0.000	0.000
70	A	71	VAL	0	0.008	0.013	12.866	0.268	0.268	0.000	0.000	0.000	0.000
71	A	72	PHE	0	0.005	-0.004	15.857	0.057	0.057	0.000	0.000	0.000	0.000
72	A	73	TYR	0	-0.047	-0.053	10.723	-0.415	-0.415	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.947	0.993	13.182	16.209	16.209	0.000	0.000	0.000	0.000
74	A	75	VAL	0	0.001	-0.002	10.044	-1.389	-1.389	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.033	0.038	11.843	1.231	1.231	0.000	0.000	0.000	0.000
76	A	77	VAL	0	-0.002	-0.014	11.874	-0.540	-0.540	0.000	0.000	0.000	0.000
77	A	78	ARG	1	0.933	0.961	6.496	24.867	24.867	0.000	0.000	0.000	0.000
78	A	79	VAL	0	0.066	0.039	6.417	2.012	2.012	0.000	0.000	0.000	0.000
79	A	80	GLU	-1	-0.870	-0.941	8.364	-18.643	-18.643	0.000	0.000	0.000	0.000
80	A	81	ILE	0	0.058	0.032	9.310	1.349	1.349	0.000	0.000	0.000	0.000
81	A	82	ILE	0	-0.054	-0.025	12.580	0.790	0.790	0.000	0.000	0.000	0.000
82	A	83	ARG	1	0.853	0.922	16.279	14.134	14.134	0.000	0.000	0.000	0.000
83	A	84	VAL	0	0.036	0.033	16.004	-0.652	-0.652	0.000	0.000	0.000	0.000
84	A	85	LEU	0	-0.019	-0.010	18.585	0.648	0.648	0.000	0.000	0.000	0.000
85	A	86	HIS	0	0.097	0.051	21.968	-0.210	-0.210	0.000	0.000	0.000	0.000
86	A	87	GLN	0	0.041	0.016	24.405	-0.174	-0.174	0.000	0.000	0.000	0.000
87	A	88	SER	0	-0.033	-0.027	25.291	0.352	0.352	0.000	0.000	0.000	0.000
88	A	89	MET	0	-0.040	-0.023	25.574	0.383	0.383	0.000	0.000	0.000	0.000
89	A	90	ASN	0	-0.037	-0.008	23.771	-0.407	-0.407	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.042	0.018	26.580	0.393	0.393	0.000	0.000	0.000	0.000
91	A	92	ARG	1	0.919	0.963	27.531	9.377	9.377	0.000	0.000	0.000	0.000
92	A	93	ALA	0	0.040	0.027	26.850	0.262	0.262	0.000	0.000	0.000	0.000
93	A	94	HIS	0	-0.020	-0.014	28.810	0.080	0.080	0.000	0.000	0.000	0.000
94	A	95	LEU	0	0.004	0.016	29.141	-0.109	-0.109	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)