FMO DATABASE

FMODB ID: Q1RMY

Calculation Name: 4R8O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R8O

Chain ID: A

ChEMBL ID:

UniProt ID: A6KZN2

Base Structure: X-ray

Registration Date: 2023-06-20

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	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-744980.821098
FMO2-HF: Nuclear repulsion	702255.115523
FMO2-HF: Total energy	-42725.705575
FMO2-MP2: Total energy	-42846.010549

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:30:ASP)

Summations of interaction energy for fragment #1(A:30:ASP)

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.
-29.714	-25.605	0.325	-1.669	-2.767	0.008

Interaction energy analysis for fragmet #1(A:30:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.949 / q_NPA : -0.981

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

Sort

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	32	LEU	0	-0.082	-0.045	2.631	-13.009	-9.227	0.327	-1.636	-2.474	0.008
4	A	33	ILE	0	0.032	0.019	4.076	0.463	0.624	-0.001	-0.012	-0.149	0.000
5	A	34	TYR	0	0.015	0.003	3.687	-3.067	-2.901	-0.001	-0.021	-0.144	0.000
6	A	35	ASN	0	-0.043	-0.022	9.303	-1.164	-1.164	0.000	0.000	0.000	0.000
7	A	36	ALA	0	0.029	0.017	13.086	-0.249	-0.249	0.000	0.000	0.000	0.000
8	A	37	GLU	-1	-0.874	-0.894	15.373	12.613	12.613	0.000	0.000	0.000	0.000
9	A	38	GLU	-1	-0.924	-0.981	19.007	13.203	13.203	0.000	0.000	0.000	0.000
10	A	39	VAL	0	-0.001	-0.014	21.310	-0.411	-0.411	0.000	0.000	0.000	0.000
11	A	40	ASN	0	-0.039	-0.029	24.919	0.004	0.004	0.000	0.000	0.000	0.000
12	A	41	GLY	0	0.037	0.034	24.326	-0.209	-0.209	0.000	0.000	0.000	0.000
13	A	42	VAL	0	-0.020	0.001	21.828	0.472	0.472	0.000	0.000	0.000	0.000
14	A	43	VAL	0	0.027	0.011	16.502	-0.160	-0.160	0.000	0.000	0.000	0.000
15	A	44	VAL	0	0.022	0.030	19.407	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	45	SER	0	-0.064	-0.068	17.721	0.144	0.144	0.000	0.000	0.000	0.000
17	A	46	GLU	-1	-0.826	-0.897	10.960	21.309	21.309	0.000	0.000	0.000	0.000
18	A	47	THR	0	-0.043	-0.013	12.888	-0.482	-0.482	0.000	0.000	0.000	0.000
19	A	48	ILE	0	0.009	0.003	6.637	0.910	0.910	0.000	0.000	0.000	0.000
20	A	49	PHE	0	-0.016	-0.021	8.580	-1.815	-1.815	0.000	0.000	0.000	0.000
21	A	50	LYS	1	0.952	0.986	7.474	-24.569	-24.569	0.000	0.000	0.000	0.000
22	A	51	MET	0	-0.008	-0.015	8.917	-2.980	-2.980	0.000	0.000	0.000	0.000
23	A	52	GLU	-1	-0.921	-0.928	10.770	24.549	24.549	0.000	0.000	0.000	0.000
24	A	53	GLY	0	0.032	0.005	12.460	-1.917	-1.917	0.000	0.000	0.000	0.000
25	A	54	THR	0	-0.002	-0.023	13.742	0.491	0.491	0.000	0.000	0.000	0.000
26	A	55	MET	0	-0.044	-0.005	15.861	-0.639	-0.639	0.000	0.000	0.000	0.000
27	A	56	LEU	0	0.016	0.013	11.429	1.244	1.244	0.000	0.000	0.000	0.000
28	A	57	THR	0	-0.031	-0.019	12.471	-1.737	-1.737	0.000	0.000	0.000	0.000
29	A	58	ASN	0	0.014	0.005	12.047	1.877	1.877	0.000	0.000	0.000	0.000
30	A	59	TYR	0	-0.011	-0.019	7.443	-0.395	-0.395	0.000	0.000	0.000	0.000
31	A	60	MET	0	-0.032	-0.025	10.178	-0.374	-0.374	0.000	0.000	0.000	0.000
32	A	61	LYS	1	0.895	0.951	12.076	-13.946	-13.946	0.000	0.000	0.000	0.000
33	A	62	HIS	1	0.863	0.925	10.527	-19.563	-19.563	0.000	0.000	0.000	0.000
34	A	63	ASN	0	-0.037	-0.038	15.280	0.206	0.206	0.000	0.000	0.000	0.000
35	A	64	TYR	0	-0.074	-0.040	13.254	-0.328	-0.328	0.000	0.000	0.000	0.000
36	A	65	LYS	1	0.903	0.966	20.270	-11.595	-11.595	0.000	0.000	0.000	0.000
37	A	66	TYR	0	0.033	-0.005	19.835	0.523	0.523	0.000	0.000	0.000	0.000
38	A	67	ASP	-1	-0.806	-0.890	25.824	9.675	9.675	0.000	0.000	0.000	0.000
39	A	68	ALA	0	0.002	-0.013	29.350	0.063	0.063	0.000	0.000	0.000	0.000
40	A	69	ASN	0	-0.044	-0.031	30.872	-0.175	-0.175	0.000	0.000	0.000	0.000
41	A	70	ASN	0	-0.007	0.009	26.651	0.207	0.207	0.000	0.000	0.000	0.000
42	A	71	GLN	0	-0.020	-0.001	25.087	0.517	0.517	0.000	0.000	0.000	0.000
43	A	72	ARG	1	0.915	0.968	15.695	-15.370	-15.370	0.000	0.000	0.000	0.000
44	A	73	THR	0	-0.004	0.003	23.166	-0.199	-0.199	0.000	0.000	0.000	0.000
45	A	74	GLU	-1	-0.839	-0.919	22.141	11.073	11.073	0.000	0.000	0.000	0.000
46	A	75	ASP	-1	-0.812	-0.906	15.978	16.682	16.682	0.000	0.000	0.000	0.000
47	A	76	GLU	-1	-0.813	-0.877	18.362	12.523	12.523	0.000	0.000	0.000	0.000
48	A	77	ALA	0	0.020	0.016	14.754	0.538	0.538	0.000	0.000	0.000	0.000
49	A	78	GLN	0	-0.023	-0.025	16.090	-0.178	-0.178	0.000	0.000	0.000	0.000
50	A	79	LYS	1	0.912	0.955	14.674	-13.529	-13.529	0.000	0.000	0.000	0.000
51	A	80	TRP	0	0.022	0.020	14.767	-1.251	-1.251	0.000	0.000	0.000	0.000
52	A	81	ASN	0	-0.116	-0.070	16.544	0.578	0.578	0.000	0.000	0.000	0.000
53	A	82	SER	0	0.102	0.035	17.984	-0.359	-0.359	0.000	0.000	0.000	0.000
54	A	83	ASN	0	-0.011	-0.005	19.702	0.026	0.026	0.000	0.000	0.000	0.000
55	A	84	LYS	1	0.919	0.973	22.662	-11.150	-11.150	0.000	0.000	0.000	0.000
56	A	85	ASN	0	-0.023	-0.008	21.575	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	86	ARG	1	0.882	0.936	21.350	-12.084	-12.084	0.000	0.000	0.000	0.000
58	A	87	TRP	0	0.079	0.043	13.944	0.437	0.437	0.000	0.000	0.000	0.000
59	A	88	GLU	-1	-0.874	-0.931	19.297	11.833	11.833	0.000	0.000	0.000	0.000
60	A	89	ASN	0	0.028	0.031	19.377	0.810	0.810	0.000	0.000	0.000	0.000
61	A	90	ASN	0	0.000	-0.007	16.201	-0.719	-0.719	0.000	0.000	0.000	0.000
62	A	91	LEU	0	0.008	0.006	16.186	-0.479	-0.479	0.000	0.000	0.000	0.000
63	A	92	CYS	0	-0.028	0.001	19.197	0.083	0.083	0.000	0.000	0.000	0.000
64	A	93	ILE	0	0.023	0.032	16.590	-0.305	-0.305	0.000	0.000	0.000	0.000
65	A	94	ARG	1	0.835	0.901	20.971	-10.726	-10.726	0.000	0.000	0.000	0.000
66	A	95	TYR	0	-0.017	-0.007	17.928	0.111	0.111	0.000	0.000	0.000	0.000
67	A	96	THR	0	-0.006	0.001	24.860	-0.370	-0.370	0.000	0.000	0.000	0.000
68	A	97	TYR	0	-0.020	-0.027	24.047	0.232	0.232	0.000	0.000	0.000	0.000
69	A	98	GLY	0	0.026	0.016	29.808	-0.304	-0.304	0.000	0.000	0.000	0.000
70	A	99	ASN	0	-0.025	-0.039	32.396	0.221	0.221	0.000	0.000	0.000	0.000
71	A	100	LYS	1	0.931	0.952	33.099	-8.037	-8.037	0.000	0.000	0.000	0.000
72	A	101	SER	0	0.033	0.040	29.907	0.156	0.156	0.000	0.000	0.000	0.000
73	A	102	MET	0	0.044	0.051	21.884	-0.113	-0.113	0.000	0.000	0.000	0.000
74	A	103	THR	0	-0.009	-0.010	27.002	0.011	0.011	0.000	0.000	0.000	0.000
75	A	104	THR	0	-0.021	-0.010	21.622	0.191	0.191	0.000	0.000	0.000	0.000
76	A	105	GLU	-1	-0.824	-0.899	24.266	9.878	9.878	0.000	0.000	0.000	0.000
77	A	106	TYR	0	0.009	-0.001	18.442	0.618	0.618	0.000	0.000	0.000	0.000
78	A	107	TYR	0	-0.041	-0.039	22.590	-0.513	-0.513	0.000	0.000	0.000	0.000
79	A	108	LYS	1	0.912	0.949	20.458	-12.460	-12.460	0.000	0.000	0.000	0.000
80	A	109	TRP	0	-0.019	0.006	22.917	-0.510	-0.510	0.000	0.000	0.000	0.000
81	A	110	ASN	0	-0.013	-0.010	24.737	0.031	0.031	0.000	0.000	0.000	0.000
82	A	111	SER	0	0.032	0.001	26.681	-0.156	-0.156	0.000	0.000	0.000	0.000
83	A	112	LYS	1	0.944	0.960	28.691	-8.918	-8.918	0.000	0.000	0.000	0.000
84	A	113	LYS	1	0.928	0.982	31.423	-8.746	-8.746	0.000	0.000	0.000	0.000
85	A	114	LYS	1	0.905	0.962	29.579	-8.811	-8.811	0.000	0.000	0.000	0.000
86	A	115	GLU	-1	-0.850	-0.927	29.476	8.616	8.616	0.000	0.000	0.000	0.000
87	A	116	TYR	0	-0.062	-0.072	21.747	0.288	0.288	0.000	0.000	0.000	0.000
88	A	117	ILE	0	-0.040	-0.030	26.915	-0.281	-0.281	0.000	0.000	0.000	0.000
89	A	118	LEU	0	0.031	0.023	26.791	0.369	0.369	0.000	0.000	0.000	0.000
90	A	119	VAL	0	-0.023	-0.004	24.521	-0.176	-0.176	0.000	0.000	0.000	0.000
91	A	120	PRO	0	-0.002	0.008	26.322	0.273	0.273	0.000	0.000	0.000	0.000
92	A	121	GLU	-1	-0.897	-0.959	26.955	10.296	10.296	0.000	0.000	0.000	0.000
93	A	122	MET	0	-0.041	-0.031	20.688	0.114	0.114	0.000	0.000	0.000	0.000
94	A	123	THR	0	-0.032	-0.013	23.809	0.492	0.492	0.000	0.000	0.000	0.000
95	A	124	VAL	0	-0.022	0.001	22.609	-0.100	-0.100	0.000	0.000	0.000	0.000
96	A	125	THR	0	-0.001	-0.009	25.622	-0.043	-0.043	0.000	0.000	0.000	0.000
97	A	126	MET	0	-0.026	-0.011	23.114	0.095	0.095	0.000	0.000	0.000	0.000
98	A	127	ASP	-1	-0.966	-0.982	27.194	9.919	9.919	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:30:ASP)