FMO DATABASE

FMODB ID: YVJM2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-682877.284528
FMO2-HF: Nuclear repulsion	644456.075125
FMO2-HF: Total energy	-38421.209404
FMO2-MP2: Total energy	-38532.386471

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.
-185.326	-185.782	34.635	-17.824	-16.356	-0.217

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 : 0.876 / q_NPA : 0.925

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	0.003	-0.007	3.917	6.344	7.860	-0.010	-0.611	-0.895	0.003
4	A	5	ARG	1	0.846	0.912	6.702	20.445	20.445	0.000	0.000	0.000	0.000
5	A	6	LEU	0	0.046	0.022	10.373	-0.743	-0.743	0.000	0.000	0.000	0.000
6	A	7	SER	0	-0.041	-0.029	12.222	1.358	1.358	0.000	0.000	0.000	0.000
7	A	8	ARG	1	1.005	0.979	16.061	14.771	14.771	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.793	0.885	18.540	13.868	13.868	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.042	0.025	15.074	0.211	0.211	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.812	0.883	14.929	17.037	17.037	0.000	0.000	0.000	0.000
11	A	12	ALA	0	0.046	0.018	16.560	0.079	0.079	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.742	-0.825	18.095	-15.301	-15.301	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.029	0.007	12.631	0.173	0.173	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.779	-0.855	17.295	-16.345	-16.345	0.000	0.000	0.000	0.000
15	A	16	ASP	-1	-0.821	-0.881	20.170	-12.714	-12.714	0.000	0.000	0.000	0.000
16	A	17	ILE	0	-0.050	-0.029	18.019	0.488	0.488	0.000	0.000	0.000	0.000
17	A	18	TRP	0	-0.007	0.005	16.413	-0.314	-0.314	0.000	0.000	0.000	0.000
18	A	19	THR	0	-0.010	-0.019	20.512	0.575	0.575	0.000	0.000	0.000	0.000
19	A	20	TYR	0	-0.039	-0.020	23.956	0.733	0.733	0.000	0.000	0.000	0.000
20	A	21	SER	0	-0.016	-0.032	21.363	0.345	0.345	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.878	-0.938	23.374	-12.684	-12.684	0.000	0.000	0.000	0.000
22	A	23	GLN	0	-0.061	-0.025	24.760	0.502	0.502	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.861	0.941	26.844	11.279	11.279	0.000	0.000	0.000	0.000
24	A	25	TRP	0	-0.059	-0.039	23.792	0.203	0.203	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.078	0.058	25.849	0.287	0.287	0.000	0.000	0.000	0.000
26	A	27	VAL	0	0.012	-0.001	22.492	-0.496	-0.496	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.909	-0.947	20.872	-14.068	-14.068	0.000	0.000	0.000	0.000
28	A	29	GLN	0	0.069	0.021	19.827	-1.084	-1.084	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.019	-0.002	19.778	-0.702	-0.702	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.001	-0.008	16.715	-1.119	-1.119	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.854	-0.909	15.270	-18.937	-18.937	0.000	0.000	0.000	0.000
32	A	33	TYR	0	-0.006	-0.023	15.160	-1.349	-1.349	0.000	0.000	0.000	0.000
33	A	34	ALA	0	-0.016	-0.009	14.356	-1.077	-1.077	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.855	0.910	11.058	18.644	18.644	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.885	-0.927	10.415	-25.967	-25.967	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.021	-0.002	11.404	-1.794	-1.794	0.000	0.000	0.000	0.000
37	A	38	GLN	0	-0.073	-0.039	5.602	3.194	3.194	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.034	0.017	6.808	-5.886	-5.886	0.000	0.000	0.000	0.000
39	A	40	THR	0	-0.021	-0.024	7.502	-2.214	-2.214	0.000	0.000	0.000	0.000
40	A	41	ILE	0	-0.027	-0.022	7.115	-0.263	-0.263	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.852	-0.919	1.731	-112.876	-115.008	12.467	-5.846	-4.488	-0.082
42	A	43	MET	0	0.005	0.012	4.084	-6.236	-6.031	-0.001	-0.049	-0.156	0.000
43	A	44	ILE	0	-0.045	-0.026	6.395	2.246	2.246	0.000	0.000	0.000	0.000
44	A	45	ALA	0	-0.058	-0.035	3.519	2.986	3.320	0.020	-0.082	-0.273	0.000
45	A	46	GLU	-1	-0.828	-0.910	1.770	-139.529	-140.011	22.160	-11.227	-10.451	-0.138
46	A	47	HIS	0	-0.007	0.004	4.270	8.917	9.020	-0.001	-0.009	-0.093	0.000
47	A	48	PRO	0	0.027	0.010	5.818	3.791	3.791	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.037	-0.015	8.602	2.191	2.191	0.000	0.000	0.000	0.000
49	A	50	MET	0	0.008	0.008	11.283	1.397	1.397	0.000	0.000	0.000	0.000
50	A	51	GLY	0	0.035	0.037	12.486	1.030	1.030	0.000	0.000	0.000	0.000
51	A	52	GLN	0	-0.007	0.002	14.338	0.669	0.669	0.000	0.000	0.000	0.000
52	A	53	PRO	0	0.016	-0.003	17.590	-0.259	-0.259	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.813	-0.924	18.697	-12.496	-12.496	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.833	-0.905	20.377	-13.381	-13.381	0.000	0.000	0.000	0.000
55	A	56	ASN	0	-0.005	-0.004	22.529	0.403	0.403	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.041	-0.001	22.588	0.360	0.360	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.885	0.929	21.446	13.054	13.054	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.056	0.037	21.256	-0.523	-0.523	0.000	0.000	0.000	0.000
59	A	60	GLY	0	0.003	-0.006	17.983	-0.255	-0.255	0.000	0.000	0.000	0.000
60	A	61	TYR	0	-0.070	-0.047	16.192	-0.902	-0.902	0.000	0.000	0.000	0.000
61	A	62	ARG	1	0.854	0.928	13.159	19.482	19.482	0.000	0.000	0.000	0.000
62	A	63	ARG	1	0.797	0.892	16.301	14.017	14.017	0.000	0.000	0.000	0.000
63	A	64	CYS	0	-0.001	-0.009	13.609	-0.336	-0.336	0.000	0.000	0.000	0.000
64	A	65	ALA	0	-0.017	0.002	15.728	-0.161	-0.161	0.000	0.000	0.000	0.000
65	A	66	SER	0	0.022	-0.007	13.693	-0.957	-0.957	0.000	0.000	0.000	0.000
66	A	67	GLY	0	0.085	0.051	16.397	0.607	0.607	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.064	-0.032	19.228	1.229	1.229	0.000	0.000	0.000	0.000
68	A	69	HIS	0	0.011	0.023	18.348	0.629	0.629	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.025	-0.015	17.989	-0.370	-0.370	0.000	0.000	0.000	0.000
70	A	71	VAL	0	0.020	0.022	12.298	0.518	0.518	0.000	0.000	0.000	0.000
71	A	72	PHE	0	0.008	-0.005	15.663	0.236	0.236	0.000	0.000	0.000	0.000
72	A	73	TYR	0	-0.057	-0.048	10.790	-0.337	-0.337	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.892	0.940	13.060	17.422	17.422	0.000	0.000	0.000	0.000
74	A	75	VAL	0	-0.007	-0.010	9.174	-1.934	-1.934	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.042	0.023	11.176	1.498	1.498	0.000	0.000	0.000	0.000
76	A	77	VAL	0	-0.013	-0.003	11.242	-0.598	-0.598	0.000	0.000	0.000	0.000
77	A	78	ARG	1	0.934	0.963	6.470	23.023	23.023	0.000	0.000	0.000	0.000
78	A	79	VAL	0	0.066	0.044	6.132	2.227	2.227	0.000	0.000	0.000	0.000
79	A	80	GLU	-1	-0.820	-0.887	8.242	-18.459	-18.459	0.000	0.000	0.000	0.000
80	A	81	ILE	0	0.076	0.034	9.359	1.537	1.537	0.000	0.000	0.000	0.000
81	A	82	ILE	0	-0.039	-0.019	12.675	0.942	0.942	0.000	0.000	0.000	0.000
82	A	83	ARG	1	0.791	0.863	16.378	15.609	15.609	0.000	0.000	0.000	0.000
83	A	84	VAL	0	0.024	0.020	14.667	-0.985	-0.985	0.000	0.000	0.000	0.000
84	A	85	LEU	0	0.003	0.016	17.796	0.741	0.741	0.000	0.000	0.000	0.000
85	A	86	HIS	0	0.092	0.063	20.929	-0.257	-0.257	0.000	0.000	0.000	0.000
86	A	87	GLN	0	0.020	-0.001	22.870	-0.093	-0.093	0.000	0.000	0.000	0.000
87	A	88	SER	0	-0.017	-0.034	24.251	0.347	0.347	0.000	0.000	0.000	0.000
88	A	89	MET	0	-0.053	-0.022	25.029	0.425	0.425	0.000	0.000	0.000	0.000
89	A	90	ASN	0	-0.039	-0.003	23.319	-0.439	-0.439	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.043	0.018	26.720	0.455	0.455	0.000	0.000	0.000	0.000
91	A	92	ARG	1	0.913	0.960	27.879	10.107	10.107	0.000	0.000	0.000	0.000
92	A	93	ALA	0	0.039	0.032	26.551	0.292	0.292	0.000	0.000	0.000	0.000
93	A	94	HIS	0	0.010	0.000	28.623	0.064	0.064	0.000	0.000	0.000	0.000
94	A	95	LEU	0	-0.033	-0.009	29.386	0.127	0.127	0.000	0.000	0.000	0.000

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