FMO DATABASE

FMODB ID: 4993N

Calculation Name: 4D2K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4D2K

Chain ID: A

ChEMBL ID:

UniProt ID: Q7K304

Base Structure: X-ray

Registration Date: 2023-06-21

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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-563304.07864
FMO2-HF: Nuclear repulsion	531151.068892
FMO2-HF: Total energy	-32153.009748
FMO2-MP2: Total energy	-32248.908297

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:7:ARG)

Summations of interaction energy for fragment #1(A:7:ARG)

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.
31.869	34.783	0.237	-1.523	-1.629	0.007

Interaction energy analysis for fragmet #1(A:7:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.977 / q_NPA : 0.971

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	9	LYS	1	0.818	0.902	3.859	29.047	30.797	-0.017	-0.886	-0.848	0.001
4	A	10	ARG	1	0.855	0.927	2.990	19.848	21.012	0.254	-0.637	-0.781	0.006
5	A	11	PRO	0	-0.014	0.005	6.210	2.437	2.437	0.000	0.000	0.000	0.000
6	A	12	LEU	0	0.013	0.007	9.286	-0.493	-0.493	0.000	0.000	0.000	0.000
7	A	13	LYS	1	0.871	0.936	11.791	16.866	16.866	0.000	0.000	0.000	0.000
8	A	14	ILE	0	-0.007	0.004	15.608	0.002	0.002	0.000	0.000	0.000	0.000
9	A	15	TRP	0	0.028	-0.002	17.971	0.296	0.296	0.000	0.000	0.000	0.000
10	A	16	ASP	-1	-0.721	-0.848	21.666	-10.181	-10.181	0.000	0.000	0.000	0.000
11	A	17	SER	0	0.017	-0.019	24.784	-0.067	-0.067	0.000	0.000	0.000	0.000
12	A	18	TRP	0	-0.022	0.006	26.472	0.230	0.230	0.000	0.000	0.000	0.000
13	A	19	ARG	1	0.732	0.859	24.540	10.642	10.642	0.000	0.000	0.000	0.000
14	A	20	ASN	0	-0.014	-0.008	26.098	0.099	0.099	0.000	0.000	0.000	0.000
15	A	21	VAL	0	-0.043	-0.021	24.147	-0.174	-0.174	0.000	0.000	0.000	0.000
16	A	22	ARG	1	0.864	0.923	22.320	10.670	10.670	0.000	0.000	0.000	0.000
17	A	23	LYS	1	0.879	0.929	19.941	11.732	11.732	0.000	0.000	0.000	0.000
18	A	24	GLY	0	0.027	0.018	16.127	-0.276	-0.276	0.000	0.000	0.000	0.000
19	A	25	VAL	0	-0.041	-0.013	12.709	0.460	0.460	0.000	0.000	0.000	0.000
20	A	26	VAL	0	0.031	0.002	9.550	-1.043	-1.043	0.000	0.000	0.000	0.000
21	A	27	VAL	0	-0.022	-0.012	9.299	0.416	0.416	0.000	0.000	0.000	0.000
22	A	28	GLY	0	0.010	-0.001	6.925	-2.203	-2.203	0.000	0.000	0.000	0.000
23	A	29	THR	0	-0.048	-0.043	7.190	-0.627	-0.627	0.000	0.000	0.000	0.000
24	A	30	PHE	0	0.069	0.049	9.804	0.143	0.143	0.000	0.000	0.000	0.000
25	A	31	GLU	-1	-0.769	-0.885	12.512	-16.930	-16.930	0.000	0.000	0.000	0.000
26	A	32	GLU	-1	-0.765	-0.860	11.658	-19.845	-19.845	0.000	0.000	0.000	0.000
27	A	33	LEU	0	-0.019	-0.008	12.298	0.385	0.385	0.000	0.000	0.000	0.000
28	A	34	LEU	0	0.028	0.020	14.118	0.698	0.698	0.000	0.000	0.000	0.000
29	A	35	VAL	0	-0.033	-0.010	17.048	0.661	0.661	0.000	0.000	0.000	0.000
30	A	36	ARG	1	0.839	0.896	14.776	16.664	16.664	0.000	0.000	0.000	0.000
31	A	37	GLY	0	0.018	0.014	17.201	0.308	0.308	0.000	0.000	0.000	0.000
32	A	38	LYS	1	0.844	0.911	18.615	12.016	12.016	0.000	0.000	0.000	0.000
33	A	39	ASP	-1	-0.812	-0.895	19.557	-13.298	-13.298	0.000	0.000	0.000	0.000
34	A	40	LYS	1	0.808	0.890	18.380	14.507	14.507	0.000	0.000	0.000	0.000
35	A	41	LEU	0	-0.015	-0.010	21.246	0.266	0.266	0.000	0.000	0.000	0.000
36	A	42	GLY	0	-0.018	0.018	24.251	0.403	0.403	0.000	0.000	0.000	0.000
37	A	43	VAL	0	-0.044	-0.019	24.723	0.411	0.411	0.000	0.000	0.000	0.000
38	A	44	PRO	0	0.029	0.012	25.872	-0.282	-0.282	0.000	0.000	0.000	0.000
39	A	45	ALA	0	0.051	0.020	24.186	-0.131	-0.131	0.000	0.000	0.000	0.000
40	A	46	SER	0	0.005	0.008	24.403	-0.345	-0.345	0.000	0.000	0.000	0.000
41	A	47	GLU	-1	-0.767	-0.843	27.004	-9.292	-9.292	0.000	0.000	0.000	0.000
42	A	48	PRO	0	0.008	0.011	25.376	-0.461	-0.461	0.000	0.000	0.000	0.000
43	A	49	VAL	0	-0.024	-0.021	21.635	0.226	0.226	0.000	0.000	0.000	0.000
44	A	50	ARG	1	0.837	0.924	21.636	9.869	9.869	0.000	0.000	0.000	0.000
45	A	51	VAL	0	0.001	-0.008	16.293	0.002	0.002	0.000	0.000	0.000	0.000
46	A	52	VAL	0	0.016	0.013	19.180	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	53	LEU	0	0.014	-0.001	15.093	-0.542	-0.542	0.000	0.000	0.000	0.000
48	A	54	GLU	-1	-0.869	-0.930	18.589	-11.248	-11.248	0.000	0.000	0.000	0.000
49	A	55	CYS	0	-0.021	-0.012	19.555	0.284	0.284	0.000	0.000	0.000	0.000
50	A	56	ASP	-1	-0.810	-0.878	20.509	-12.173	-12.173	0.000	0.000	0.000	0.000
51	A	57	GLY	0	0.037	0.013	22.126	0.360	0.360	0.000	0.000	0.000	0.000
52	A	58	THR	0	-0.074	-0.057	18.622	0.232	0.232	0.000	0.000	0.000	0.000
53	A	59	GLN	0	-0.084	-0.061	19.168	-0.276	-0.276	0.000	0.000	0.000	0.000
54	A	60	ILE	0	-0.024	-0.015	13.520	-0.480	-0.480	0.000	0.000	0.000	0.000
55	A	61	GLU	-1	-0.893	-0.940	16.820	-11.217	-11.217	0.000	0.000	0.000	0.000
56	A	62	ASP	-1	-0.821	-0.901	14.264	-15.121	-15.121	0.000	0.000	0.000	0.000
57	A	63	GLY	0	0.049	0.006	11.545	-0.564	-0.564	0.000	0.000	0.000	0.000
58	A	64	GLU	-1	-0.846	-0.909	9.768	-19.347	-19.347	0.000	0.000	0.000	0.000
59	A	65	TYR	0	0.073	0.033	9.980	-1.280	-1.280	0.000	0.000	0.000	0.000
60	A	66	PHE	0	-0.001	0.021	7.296	-0.848	-0.848	0.000	0.000	0.000	0.000
61	A	67	ARG	1	0.785	0.870	5.564	20.334	20.334	0.000	0.000	0.000	0.000
62	A	68	THR	0	-0.059	-0.031	5.750	-2.556	-2.556	0.000	0.000	0.000	0.000
63	A	69	LEU	0	-0.012	0.014	8.420	-0.326	-0.326	0.000	0.000	0.000	0.000
64	A	70	ALA	0	0.060	0.037	7.648	-2.134	-2.134	0.000	0.000	0.000	0.000
65	A	71	ASN	0	0.029	0.007	5.675	1.206	1.206	0.000	0.000	0.000	0.000
66	A	72	ASN	0	-0.057	-0.046	8.550	2.129	2.129	0.000	0.000	0.000	0.000
67	A	73	THR	0	0.045	0.015	11.159	1.445	1.445	0.000	0.000	0.000	0.000
68	A	74	VAL	0	-0.038	-0.014	13.335	-0.183	-0.183	0.000	0.000	0.000	0.000
69	A	75	LEU	0	0.019	0.019	13.140	0.074	0.074	0.000	0.000	0.000	0.000
70	A	76	LEU	0	-0.009	0.001	17.549	0.191	0.191	0.000	0.000	0.000	0.000
71	A	77	LEU	0	-0.017	-0.010	20.536	-0.193	-0.193	0.000	0.000	0.000	0.000
72	A	78	LEU	0	-0.018	-0.004	21.807	0.420	0.420	0.000	0.000	0.000	0.000
73	A	79	ARG	1	0.834	0.886	25.029	9.521	9.521	0.000	0.000	0.000	0.000
74	A	80	GLN	0	-0.022	-0.049	27.328	0.289	0.289	0.000	0.000	0.000	0.000
75	A	81	GLY	0	0.014	0.024	30.795	0.159	0.159	0.000	0.000	0.000	0.000
76	A	82	GLU	-1	-0.840	-0.888	27.773	-9.616	-9.616	0.000	0.000	0.000	0.000
77	A	83	ARG	1	0.950	0.959	28.114	8.345	8.345	0.000	0.000	0.000	0.000
78	A	84	TRP	0	0.023	0.028	23.619	0.204	0.204	0.000	0.000	0.000	0.000
79	A	85	LEU	0	0.005	0.004	26.854	0.355	0.355	0.000	0.000	0.000	0.000
80	A	86	GLU	-1	-0.830	-0.895	27.519	-9.150	-9.150	0.000	0.000	0.000	0.000
81	A	87	HIS	0	-0.094	-0.054	27.833	-0.070	-0.070	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ARG)