FMO DATABASE

FMODB ID: 89RJY

Calculation Name: 4M78-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4M78

Chain ID: E

ChEMBL ID:

UniProt ID: P38203

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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-499519.121024
FMO2-HF: Nuclear repulsion	468354.740725
FMO2-HF: Total energy	-31164.380299
FMO2-MP2: Total energy	-31255.831293

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(E:6:ILE)

Summations of interaction energy for fragment #1(E:6:ILE)

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.
-7.44	-2.091	0.965	-2.642	-3.67	-0.01

Interaction energy analysis for fragmet #1(E:6:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : 0.004

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	E	8	PRO	0	0.018	-0.009	3.870	-0.810	1.334	-0.010	-1.019	-1.114	0.005
4	E	9	LEU	0	0.047	0.018	5.724	0.489	0.489	0.000	0.000	0.000	0.000
5	E	10	GLU	-1	-0.833	-0.906	2.801	-5.784	-3.284	0.490	-1.433	-1.556	-0.014
6	E	11	VAL	0	-0.067	-0.034	2.559	-0.130	0.522	0.486	-0.188	-0.950	-0.001
7	E	12	ILE	0	-0.008	-0.001	5.290	0.329	0.382	-0.001	-0.002	-0.050	0.000
8	E	13	ASP	-1	-0.901	-0.957	8.543	-0.203	-0.203	0.000	0.000	0.000	0.000
9	E	14	LYS	1	0.928	0.970	5.948	-0.328	-0.328	0.000	0.000	0.000	0.000
10	E	15	THR	0	-0.026	-0.017	9.053	0.150	0.150	0.000	0.000	0.000	0.000
11	E	16	ILE	0	0.019	0.011	10.989	0.019	0.019	0.000	0.000	0.000	0.000
12	E	17	ASN	0	-0.092	-0.048	14.112	0.044	0.044	0.000	0.000	0.000	0.000
13	E	18	GLN	0	-0.072	-0.026	11.179	0.064	0.064	0.000	0.000	0.000	0.000
14	E	19	LYS	1	0.815	0.925	15.640	0.043	0.043	0.000	0.000	0.000	0.000
15	E	20	VAL	0	-0.005	0.003	12.807	0.001	0.001	0.000	0.000	0.000	0.000
16	E	21	LEU	0	0.030	0.025	15.044	0.009	0.009	0.000	0.000	0.000	0.000
17	E	22	ILE	0	-0.030	-0.024	15.027	-0.047	-0.047	0.000	0.000	0.000	0.000
18	E	23	VAL	0	0.043	0.023	16.837	0.031	0.031	0.000	0.000	0.000	0.000
19	E	24	LEU	0	0.018	0.005	18.219	-0.043	-0.043	0.000	0.000	0.000	0.000
20	E	25	GLN	0	-0.028	-0.011	20.630	0.030	0.030	0.000	0.000	0.000	0.000
21	E	26	SER	0	-0.043	-0.019	22.391	0.020	0.020	0.000	0.000	0.000	0.000
22	E	27	ASN	0	0.009	0.011	23.598	-0.017	-0.017	0.000	0.000	0.000	0.000
23	E	28	ARG	1	0.875	0.917	24.306	0.155	0.155	0.000	0.000	0.000	0.000
24	E	29	GLU	-1	-0.872	-0.944	20.469	-0.170	-0.170	0.000	0.000	0.000	0.000
25	E	30	PHE	0	-0.019	-0.024	20.575	0.021	0.021	0.000	0.000	0.000	0.000
26	E	31	GLU	-1	-0.771	-0.862	19.328	-0.095	-0.095	0.000	0.000	0.000	0.000
27	E	32	GLY	0	0.003	-0.007	19.169	0.017	0.017	0.000	0.000	0.000	0.000
28	E	33	THR	0	-0.008	-0.008	18.372	-0.001	-0.001	0.000	0.000	0.000	0.000
29	E	34	LEU	0	-0.006	0.017	13.013	-0.008	-0.008	0.000	0.000	0.000	0.000
30	E	35	VAL	0	-0.006	-0.016	16.976	0.019	0.019	0.000	0.000	0.000	0.000
31	E	36	GLY	0	-0.002	-0.005	16.592	0.011	0.011	0.000	0.000	0.000	0.000
32	E	37	PHE	0	-0.022	-0.013	10.692	0.005	0.005	0.000	0.000	0.000	0.000
33	E	38	ASP	-1	-0.745	-0.855	16.446	-0.380	-0.380	0.000	0.000	0.000	0.000
34	E	39	ASP	-1	-0.894	-0.954	15.031	-0.629	-0.629	0.000	0.000	0.000	0.000
35	E	40	PHE	0	-0.114	-0.050	15.972	-0.049	-0.049	0.000	0.000	0.000	0.000
36	E	41	VAL	0	-0.022	-0.013	13.421	0.006	0.006	0.000	0.000	0.000	0.000
37	E	42	ASN	0	-0.048	-0.033	16.188	0.057	0.057	0.000	0.000	0.000	0.000
38	E	43	VAL	0	-0.002	-0.005	15.956	-0.022	-0.022	0.000	0.000	0.000	0.000
39	E	44	ILE	0	-0.050	-0.014	18.709	0.037	0.037	0.000	0.000	0.000	0.000
40	E	45	LEU	0	0.019	0.012	18.233	-0.004	-0.004	0.000	0.000	0.000	0.000
41	E	46	GLU	-1	-0.919	-0.980	20.892	-0.079	-0.079	0.000	0.000	0.000	0.000
42	E	47	ASP	-1	-0.862	-0.929	22.663	-0.064	-0.064	0.000	0.000	0.000	0.000
43	E	48	ALA	0	-0.020	0.000	23.234	0.003	0.003	0.000	0.000	0.000	0.000
44	E	49	VAL	0	0.018	0.002	24.030	0.006	0.006	0.000	0.000	0.000	0.000
45	E	50	GLU	-1	-0.824	-0.890	24.107	-0.144	-0.144	0.000	0.000	0.000	0.000
46	E	51	TRP	0	0.007	-0.016	23.969	0.019	0.019	0.000	0.000	0.000	0.000
47	E	52	LEU	0	-0.010	0.001	26.131	-0.016	-0.016	0.000	0.000	0.000	0.000
48	E	53	ILE	0	-0.035	-0.020	23.798	0.011	0.011	0.000	0.000	0.000	0.000
49	E	54	ASP	-1	-0.834	-0.942	27.001	-0.107	-0.107	0.000	0.000	0.000	0.000
50	E	55	PRO	0	-0.027	0.025	28.593	0.008	0.008	0.000	0.000	0.000	0.000
51	E	56	GLU	-1	-0.889	-0.949	31.659	-0.060	-0.060	0.000	0.000	0.000	0.000
52	E	57	ASP	-1	-0.920	-0.963	32.829	-0.043	-0.043	0.000	0.000	0.000	0.000
53	E	58	GLU	-1	-0.975	-0.977	30.319	-0.049	-0.049	0.000	0.000	0.000	0.000
54	E	59	SER	0	-0.087	-0.056	28.958	0.000	0.000	0.000	0.000	0.000	0.000
55	E	60	ARG	1	0.797	0.904	30.039	0.070	0.070	0.000	0.000	0.000	0.000
56	E	61	ASN	0	0.026	0.002	25.700	-0.007	-0.007	0.000	0.000	0.000	0.000
57	E	62	GLU	-1	-0.903	-0.936	29.652	-0.073	-0.073	0.000	0.000	0.000	0.000
58	E	63	LYS	1	0.921	0.968	28.491	0.048	0.048	0.000	0.000	0.000	0.000
59	E	64	VAL	0	-0.017	-0.001	29.587	0.005	0.005	0.000	0.000	0.000	0.000
60	E	65	MET	0	-0.044	-0.033	29.652	0.002	0.002	0.000	0.000	0.000	0.000
61	E	66	GLN	0	-0.033	-0.010	27.858	-0.002	-0.002	0.000	0.000	0.000	0.000
62	E	67	HIS	1	0.810	0.893	26.996	0.118	0.118	0.000	0.000	0.000	0.000
63	E	68	HIS	0	0.034	0.017	28.130	0.002	0.002	0.000	0.000	0.000	0.000
64	E	69	GLY	0	0.011	0.011	28.102	-0.002	-0.002	0.000	0.000	0.000	0.000
65	E	70	ARG	1	0.902	0.946	23.835	0.111	0.111	0.000	0.000	0.000	0.000
66	E	71	MET	0	-0.038	-0.008	23.549	0.011	0.011	0.000	0.000	0.000	0.000
67	E	72	LEU	0	-0.022	-0.006	22.547	-0.011	-0.011	0.000	0.000	0.000	0.000
68	E	73	LEU	0	-0.001	0.005	19.679	0.012	0.012	0.000	0.000	0.000	0.000
69	E	74	SER	0	-0.006	-0.010	21.012	-0.026	-0.026	0.000	0.000	0.000	0.000
70	E	75	GLY	0	0.111	0.039	19.146	0.005	0.005	0.000	0.000	0.000	0.000
71	E	76	ASN	0	-0.090	-0.047	19.732	-0.023	-0.023	0.000	0.000	0.000	0.000
72	E	77	ASN	0	-0.039	-0.028	22.186	0.013	0.013	0.000	0.000	0.000	0.000
73	E	78	ILE	0	-0.017	0.010	16.030	0.020	0.020	0.000	0.000	0.000	0.000
74	E	79	ALA	0	-0.050	-0.022	17.004	-0.022	-0.022	0.000	0.000	0.000	0.000
75	E	80	ILE	0	-0.034	-0.017	12.785	-0.061	-0.061	0.000	0.000	0.000	0.000
76	E	81	LEU	0	0.012	0.009	11.128	0.042	0.042	0.000	0.000	0.000	0.000
77	E	82	VAL	0	0.002	-0.004	10.799	-0.062	-0.062	0.000	0.000	0.000	0.000
78	E	83	PRO	0	-0.008	-0.001	8.204	0.033	0.033	0.000	0.000	0.000	0.000
79	E	84	GLY	0	-0.062	-0.045	11.547	0.035	0.035	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:6:ILE)