FMO DATABASE

FMODB ID: 2J9ZR

Calculation Name: 5MJ0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5MJ0

Chain ID: A

ChEMBL ID:

UniProt ID: Q01151

Base Structure: X-ray

Registration Date: 2023-09-19

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. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-479026.119932
FMO2-HF: Nuclear repulsion	448092.096321
FMO2-HF: Total energy	-30934.023611
FMO2-MP2: Total energy	-31024.281773

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:18:PRO)

Summations of interaction energy for fragment #1(A:18:PRO)

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.
-1.573	2.186	0.035	-1.743	-2.05	-0.003

Interaction energy analysis for fragmet #1(A:18:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / q_NPA : -0.001

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	20	THR	0	-0.049	-0.007	2.827	-1.312	2.131	0.037	-1.699	-1.780	-0.003
4	A	21	PRO	0	0.017	0.020	4.204	-0.171	0.055	-0.001	-0.039	-0.186	0.000
5	A	22	GLU	-1	-0.815	-0.908	6.464	-0.295	-0.295	0.000	0.000	0.000	0.000
6	A	23	VAL	0	0.005	0.011	8.249	0.014	0.014	0.000	0.000	0.000	0.000
7	A	24	LYS	1	0.915	0.956	10.310	0.326	0.326	0.000	0.000	0.000	0.000
8	A	25	VAL	0	0.033	0.021	14.033	-0.003	-0.003	0.000	0.000	0.000	0.000
9	A	26	ALA	0	0.049	0.032	17.753	0.006	0.006	0.000	0.000	0.000	0.000
10	A	27	SER	0	0.006	-0.006	20.583	0.003	0.003	0.000	0.000	0.000	0.000
11	A	28	SER	0	-0.056	-0.041	22.258	0.000	0.000	0.000	0.000	0.000	0.000
12	A	29	GLU	-1	-0.876	-0.921	22.290	-0.077	-0.077	0.000	0.000	0.000	0.000
13	A	30	ASP	-1	-0.807	-0.895	22.919	-0.055	-0.055	0.000	0.000	0.000	0.000
14	A	31	VAL	0	-0.028	-0.015	17.110	-0.011	-0.011	0.000	0.000	0.000	0.000
15	A	32	ASP	-1	-0.801	-0.875	19.869	-0.081	-0.081	0.000	0.000	0.000	0.000
16	A	33	LEU	0	-0.003	0.003	13.317	-0.023	-0.023	0.000	0.000	0.000	0.000
17	A	34	PRO	0	0.035	0.020	13.784	0.014	0.014	0.000	0.000	0.000	0.000
18	A	35	CYS	0	0.019	0.058	13.842	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	36	THR	0	-0.018	-0.048	11.198	0.016	0.016	0.000	0.000	0.000	0.000
20	A	37	ALA	0	0.013	0.006	14.054	-0.028	-0.028	0.000	0.000	0.000	0.000
21	A	38	PRO	0	-0.022	-0.009	15.229	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	39	TRP	0	-0.046	-0.028	17.666	0.011	0.011	0.000	0.000	0.000	0.000
23	A	40	ASP	-1	-0.803	-0.866	21.103	-0.075	-0.075	0.000	0.000	0.000	0.000
24	A	41	PRO	0	-0.019	-0.024	24.528	0.002	0.002	0.000	0.000	0.000	0.000
25	A	42	GLN	0	-0.007	-0.021	26.764	0.005	0.005	0.000	0.000	0.000	0.000
26	A	43	VAL	0	0.023	0.037	27.034	0.006	0.006	0.000	0.000	0.000	0.000
27	A	44	PRO	0	-0.012	0.005	28.011	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	45	TYR	0	-0.058	-0.065	23.637	0.001	0.001	0.000	0.000	0.000	0.000
29	A	46	THR	0	-0.003	0.002	27.193	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	47	VAL	0	0.001	-0.015	21.609	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	48	SER	0	-0.029	-0.003	21.970	0.011	0.011	0.000	0.000	0.000	0.000
32	A	49	TRP	0	-0.013	-0.029	14.940	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	50	VAL	0	-0.011	0.004	15.639	0.014	0.014	0.000	0.000	0.000	0.000
34	A	51	LYS	1	0.895	0.959	14.876	-0.051	-0.051	0.000	0.000	0.000	0.000
35	A	52	LEU	0	-0.047	-0.030	10.213	0.017	0.017	0.000	0.000	0.000	0.000
36	A	53	LEU	0	0.011	0.012	13.483	0.005	0.005	0.000	0.000	0.000	0.000
37	A	86	ASN	0	-0.050	-0.029	21.566	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	87	GLU	-1	-0.884	-0.954	25.478	-0.077	-0.077	0.000	0.000	0.000	0.000
39	A	88	ARG	1	0.843	0.935	16.903	0.191	0.191	0.000	0.000	0.000	0.000
40	A	89	PRO	0	0.038	0.014	22.638	0.002	0.002	0.000	0.000	0.000	0.000
41	A	90	TYR	0	-0.006	-0.024	21.025	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	91	SER	0	-0.025	-0.016	19.261	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	92	LEU	0	-0.024	0.001	18.777	0.014	0.014	0.000	0.000	0.000	0.000
44	A	93	LYS	1	0.859	0.916	20.116	0.072	0.072	0.000	0.000	0.000	0.000
45	A	94	ILE	0	-0.044	-0.023	18.014	0.011	0.011	0.000	0.000	0.000	0.000
46	A	95	ARG	1	0.899	0.919	22.116	0.043	0.043	0.000	0.000	0.000	0.000
47	A	96	ASN	0	-0.037	-0.013	24.358	0.002	0.002	0.000	0.000	0.000	0.000
48	A	97	THR	0	-0.025	0.006	19.690	0.006	0.006	0.000	0.000	0.000	0.000
49	A	98	THR	0	0.058	0.014	21.072	0.005	0.005	0.000	0.000	0.000	0.000
50	A	99	SER	0	0.053	0.024	18.328	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	100	SER	0	0.011	0.007	17.320	0.003	0.003	0.000	0.000	0.000	0.000
52	A	101	ASN	0	0.040	0.018	18.006	0.011	0.011	0.000	0.000	0.000	0.000
53	A	102	SER	0	0.017	0.027	13.154	-0.022	-0.022	0.000	0.000	0.000	0.000
54	A	103	GLY	0	-0.015	-0.005	11.411	0.037	0.037	0.000	0.000	0.000	0.000
55	A	104	THR	0	-0.003	-0.004	7.634	-0.078	-0.078	0.000	0.000	0.000	0.000
56	A	105	TYR	0	-0.014	-0.028	10.278	0.057	0.057	0.000	0.000	0.000	0.000
57	A	106	ARG	1	0.898	0.945	11.510	-0.059	-0.059	0.000	0.000	0.000	0.000
58	A	108	THR	0	-0.032	-0.059	16.489	0.005	0.005	0.000	0.000	0.000	0.000
59	A	109	LEU	0	0.013	0.017	19.189	0.003	0.003	0.000	0.000	0.000	0.000
60	A	110	GLN	0	-0.002	-0.007	22.184	0.007	0.007	0.000	0.000	0.000	0.000
61	A	111	ASP	-1	-0.781	-0.870	25.234	-0.034	-0.034	0.000	0.000	0.000	0.000
62	A	112	PRO	0	-0.002	0.005	28.106	0.006	0.006	0.000	0.000	0.000	0.000
63	A	113	ASP	-1	-0.860	-0.909	31.621	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	114	GLY	0	-0.010	-0.006	31.772	0.000	0.000	0.000	0.000	0.000	0.000
65	A	115	GLN	0	-0.035	-0.025	28.645	0.002	0.002	0.000	0.000	0.000	0.000
66	A	116	ARG	1	0.800	0.876	25.672	0.027	0.027	0.000	0.000	0.000	0.000
67	A	117	ASN	0	-0.043	-0.024	21.479	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	118	LEU	0	0.062	0.050	18.975	0.002	0.002	0.000	0.000	0.000	0.000
69	A	119	SER	0	-0.062	-0.035	15.575	0.014	0.014	0.000	0.000	0.000	0.000
70	A	120	GLY	0	0.043	0.025	12.730	-0.017	-0.017	0.000	0.000	0.000	0.000
71	A	121	LYS	1	0.944	0.970	7.855	-0.148	-0.148	0.000	0.000	0.000	0.000
72	A	122	VAL	0	0.033	0.030	8.923	-0.108	-0.108	0.000	0.000	0.000	0.000
73	A	123	ILE	0	-0.025	-0.009	4.609	0.026	0.116	-0.001	-0.005	-0.084	0.000
74	A	124	LEU	0	0.028	0.022	8.980	-0.034	-0.034	0.000	0.000	0.000	0.000
75	A	125	ARG	1	0.814	0.869	5.729	0.255	0.255	0.000	0.000	0.000	0.000
76	A	126	VAL	0	0.041	0.025	12.854	-0.016	-0.016	0.000	0.000	0.000	0.000
77	A	127	THR	0	-0.037	-0.016	14.947	0.009	0.009	0.000	0.000	0.000	0.000
78	A	128	GLY	0	0.052	0.021	17.501	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	129	SER	0	-0.057	-0.018	21.114	0.016	0.016	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:18:PRO)