FMO DATABASE

FMODB ID: N9L9Q

Calculation Name: 4J4F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J4F

Chain ID: A

ChEMBL ID:

UniProt ID: P81180

Base Structure: X-ray

Registration Date: 2023-06-22

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	OptH
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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-567959.744949
FMO2-HF: Nuclear repulsion	528735.63084
FMO2-HF: Total energy	-39224.114109
FMO2-MP2: Total energy	-39336.226397

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:1:LEU)

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

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.
-0.107	2.141	0.004	-0.864	-1.388	0.002

Interaction energy analysis for fragmet #1(A:1:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.011

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	3	LYS	1	0.953	0.970	3.465	-0.405	1.563	-0.001	-0.812	-1.154	0.002
4	A	4	PHE	0	0.075	0.034	6.417	0.293	0.293	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.017	-0.003	9.074	0.090	0.090	0.000	0.000	0.000	0.000
6	A	6	GLN	0	-0.015	-0.014	8.692	-0.040	-0.040	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.012	0.016	10.748	0.023	0.023	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.072	-0.040	12.806	-0.016	-0.016	0.000	0.000	0.000	0.000
9	A	9	TYR	0	0.005	-0.005	14.882	-0.014	-0.014	0.000	0.000	0.000	0.000
10	A	10	ASN	0	0.008	-0.006	18.123	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.012	-0.002	15.494	0.001	0.001	0.000	0.000	0.000	0.000
12	A	12	ALA	0	0.004	0.020	18.127	0.003	0.003	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.021	0.007	15.566	-0.012	-0.012	0.000	0.000	0.000	0.000
14	A	14	GLN	0	0.024	0.020	19.445	0.010	0.010	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.016	-0.004	21.486	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.008	-0.014	18.281	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.009	-0.006	17.193	-0.020	-0.020	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.014	0.010	12.303	0.004	0.004	0.000	0.000	0.000	0.000
19	A	19	THR	0	-0.010	-0.029	16.242	0.008	0.008	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.001	-0.026	15.013	0.004	0.004	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.013	-0.005	17.087	0.006	0.006	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.902	-0.952	14.954	0.262	0.262	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.904	0.951	14.521	-0.107	-0.107	0.000	0.000	0.000	0.000
24	A	25	THR	0	0.043	0.007	13.454	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	26	ASN	0	-0.067	-0.026	15.946	0.021	0.021	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.060	0.044	18.815	-0.020	-0.020	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.010	-0.002	20.534	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	29	TYR	0	0.015	-0.001	17.429	0.017	0.017	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.023	-0.022	17.455	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	31	THR	0	0.021	0.036	17.929	0.004	0.004	0.000	0.000	0.000	0.000
31	A	32	SER	0	-0.072	-0.015	15.642	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	33	SER	0	0.058	0.016	16.951	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.027	-0.004	10.638	0.007	0.007	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.809	-0.894	14.876	-0.148	-0.148	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.025	-0.024	11.692	-0.026	-0.026	0.000	0.000	0.000	0.000
36	A	37	ASN	0	0.005	-0.010	14.303	-0.028	-0.028	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.022	0.001	14.732	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	39	VAL	0	-0.021	-0.009	9.585	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	40	ILE	0	-0.035	-0.012	10.778	-0.054	-0.054	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.875	-0.932	13.165	-0.194	-0.194	0.000	0.000	0.000	0.000
41	A	42	ASN	0	-0.031	-0.022	16.222	-0.019	-0.019	0.000	0.000	0.000	0.000
42	A	43	VAL	0	0.038	0.015	16.406	0.009	0.009	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.905	-0.955	19.237	-0.146	-0.146	0.000	0.000	0.000	0.000
44	A	45	GLY	0	-0.026	-0.010	21.927	0.006	0.006	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.067	-0.035	17.530	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	47	LEU	0	0.000	0.006	15.318	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.910	0.955	12.818	0.254	0.254	0.000	0.000	0.000	0.000
48	A	49	TRP	0	-0.053	-0.028	8.171	-0.022	-0.022	0.000	0.000	0.000	0.000
49	A	50	GLN	0	0.013	0.017	10.187	0.018	0.018	0.000	0.000	0.000	0.000
50	A	51	GLY	0	-0.023	-0.001	10.140	-0.040	-0.040	0.000	0.000	0.000	0.000
51	A	52	SER	0	-0.030	-0.036	11.789	0.000	0.000	0.000	0.000	0.000	0.000
52	A	53	ASN	0	0.069	0.033	13.443	0.010	0.010	0.000	0.000	0.000	0.000
53	A	54	PHE	0	0.047	0.005	16.950	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	55	ILE	0	0.018	0.003	18.469	0.002	0.002	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.940	-0.962	17.166	-0.127	-0.127	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.077	-0.032	13.148	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	58	CYS	0	-0.045	-0.014	15.569	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.884	0.944	18.558	0.103	0.103	0.000	0.000	0.000	0.000
59	A	60	ASN	0	-0.040	-0.045	21.822	0.001	0.001	0.000	0.000	0.000	0.000
60	A	61	THR	0	0.003	0.009	23.073	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	62	GLN	0	-0.042	-0.021	25.499	0.009	0.009	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.020	0.024	28.109	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	64	ALA	0	-0.036	-0.023	29.391	0.003	0.003	0.000	0.000	0.000	0.000
64	A	65	GLY	0	0.002	0.000	31.186	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	66	SER	0	0.008	-0.015	34.348	0.001	0.001	0.000	0.000	0.000	0.000
66	A	67	SER	0	0.010	0.008	32.219	0.001	0.001	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.907	-0.942	27.992	-0.090	-0.090	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.024	0.006	23.767	0.004	0.004	0.000	0.000	0.000	0.000
69	A	70	ALA	0	-0.017	-0.023	24.814	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	71	ALA	0	0.011	-0.005	21.177	0.003	0.003	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.842	-0.901	20.106	-0.094	-0.094	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.923	0.977	11.800	0.163	0.163	0.000	0.000	0.000	0.000
73	A	75	THR	0	0.045	0.029	10.541	-0.036	-0.036	0.000	0.000	0.000	0.000
74	A	76	ARG	1	0.982	0.971	3.763	0.286	0.566	0.005	-0.052	-0.234	0.000
75	A	77	ALA	0	0.001	0.001	6.793	-0.080	-0.080	0.000	0.000	0.000	0.000
76	A	78	GLN	0	-0.037	-0.026	7.935	0.105	0.105	0.000	0.000	0.000	0.000
77	A	79	GLN	0	0.003	0.010	11.440	0.045	0.045	0.000	0.000	0.000	0.000
78	A	80	PHE	0	-0.012	-0.017	14.084	-0.019	-0.019	0.000	0.000	0.000	0.000
79	A	81	VAL	0	0.002	0.004	15.403	0.008	0.008	0.000	0.000	0.000	0.000
80	A	82	SER	0	0.019	0.012	17.832	0.000	0.000	0.000	0.000	0.000	0.000
81	A	83	THR	0	-0.049	-0.020	18.655	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	84	LYS	1	0.967	0.969	20.911	0.093	0.093	0.000	0.000	0.000	0.000
83	A	85	ILE	0	0.035	0.033	21.791	-0.009	-0.009	0.000	0.000	0.000	0.000
84	A	86	ASN	0	0.089	0.051	24.520	0.009	0.009	0.000	0.000	0.000	0.000
85	A	87	LEU	0	-0.010	-0.016	27.018	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.854	-0.944	29.241	-0.067	-0.067	0.000	0.000	0.000	0.000
87	A	89	ASP	-1	-0.988	-0.970	26.470	-0.100	-0.100	0.000	0.000	0.000	0.000
88	A	90	HIS	1	0.833	0.891	26.171	0.102	0.102	0.000	0.000	0.000	0.000
89	A	91	ILE	0	-0.036	0.006	28.501	0.001	0.001	0.000	0.000	0.000	0.000
90	A	92	ALA	0	0.060	0.043	31.703	0.002	0.002	0.000	0.000	0.000	0.000
91	A	93	ASN	0	-0.011	-0.011	35.265	0.001	0.001	0.000	0.000	0.000	0.000
92	A	94	ILE	0	-0.010	-0.017	37.460	0.001	0.001	0.000	0.000	0.000	0.000
93	A	95	ASP	-1	-0.945	-0.975	40.241	-0.038	-0.038	0.000	0.000	0.000	0.000
94	A	96	GLY	0	0.000	0.003	42.538	0.001	0.001	0.000	0.000	0.000	0.000
95	A	97	THR	0	-0.053	-0.021	37.860	0.000	0.000	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.035	-0.013	34.409	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	99	LYS	1	0.936	0.966	33.907	0.059	0.059	0.000	0.000	0.000	0.000
98	A	100	TYR	0	-0.009	0.005	25.835	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.924	-0.965	30.303	-0.065	-0.065	0.000	0.000	0.000	0.000

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