FMO DATABASE

FMODB ID: 4JZ3N

Calculation Name: 3F40-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F40

Chain ID: A

ChEMBL ID:

UniProt ID:

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	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	112
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-957966.648599
FMO2-HF: Nuclear repulsion	910848.276941
FMO2-HF: Total energy	-47118.371658
FMO2-MP2: Total energy	-47251.714112

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:MET)

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

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.
-6.175	-1.267	0.274	-2.617	-2.566	0.008

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.056 / 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	THR	0	0.000	0.017	2.816	-4.753	-0.397	0.264	-2.348	-2.273	0.010
4	A	4	GLN	0	-0.004	-0.008	3.511	-1.690	-1.138	0.010	-0.269	-0.293	-0.002
5	A	5	ILE	0	-0.033	-0.003	5.580	0.014	0.014	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.026	-0.041	7.500	-0.051	-0.051	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.049	-0.019	10.086	0.076	0.076	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.902	0.953	12.756	-0.266	-0.266	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.800	-0.874	10.967	0.585	0.585	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.003	0.009	9.340	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.008	0.005	13.040	-0.039	-0.039	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.000	-0.012	16.300	-0.034	-0.034	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.843	-0.904	11.670	0.988	0.988	0.000	0.000	0.000	0.000
14	A	14	PHE	0	-0.021	-0.006	15.849	-0.033	-0.033	0.000	0.000	0.000	0.000
15	A	15	ILE	0	0.005	0.002	17.667	-0.035	-0.035	0.000	0.000	0.000	0.000
16	A	16	HIS	0	0.005	0.003	18.393	-0.040	-0.040	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.008	0.010	17.852	-0.022	-0.022	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.014	-0.006	19.933	-0.030	-0.030	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.012	-0.019	23.110	-0.034	-0.034	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.096	-0.054	21.829	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.810	-0.896	24.439	0.162	0.162	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.008	0.003	18.879	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	23	PHE	0	0.084	0.020	20.142	0.034	0.034	0.000	0.000	0.000	0.000
24	A	24	PRO	0	0.037	0.010	18.662	0.016	0.016	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.027	-0.002	15.651	0.037	0.037	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.052	0.019	15.552	0.060	0.060	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.873	0.926	17.066	-0.212	-0.212	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.921	0.974	8.475	-0.945	-0.945	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.779	0.879	11.778	-0.715	-0.715	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.051	-0.008	13.934	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.012	-0.019	15.257	-0.032	-0.032	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.907	-0.961	16.405	0.135	0.135	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.059	-0.044	18.558	-0.028	-0.028	0.000	0.000	0.000	0.000
34	A	34	PHE	0	-0.021	0.004	19.541	-0.011	-0.011	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.010	0.010	21.269	-0.017	-0.017	0.000	0.000	0.000	0.000
36	A	36	PHE	0	0.008	-0.003	24.348	0.011	0.011	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.003	-0.003	26.768	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.093	0.043	29.705	0.008	0.008	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.037	-0.012	32.093	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	40	MET	0	-0.042	-0.012	35.026	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	41	GLY	0	-0.029	-0.006	34.662	0.000	0.000	0.000	0.000	0.000	0.000
42	A	42	HIS	0	0.006	-0.008	28.446	0.000	0.000	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.753	0.872	27.697	-0.123	-0.123	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.828	-0.909	26.756	0.128	0.128	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.034	0.020	23.135	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.016	-0.018	19.519	0.000	0.000	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.855	-0.926	21.550	0.185	0.185	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.910	0.956	23.499	-0.118	-0.118	0.000	0.000	0.000	0.000
49	A	49	TYR	0	0.021	0.006	23.232	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	50	MET	0	-0.003	-0.007	20.608	0.003	0.003	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.011	-0.012	24.047	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.807	-0.895	27.181	0.114	0.114	0.000	0.000	0.000	0.000
53	A	53	MET	0	-0.010	0.014	24.126	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.913	-0.949	25.721	0.176	0.176	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.841	0.917	27.638	-0.128	-0.128	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.052	-0.023	30.348	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.822	0.923	28.887	-0.153	-0.153	0.000	0.000	0.000	0.000
58	A	58	PHE	0	0.012	0.013	28.662	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.781	0.894	27.985	-0.165	-0.165	0.000	0.000	0.000	0.000
60	A	60	TYR	0	0.023	-0.002	25.691	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	61	VAL	0	0.020	0.022	27.099	0.011	0.011	0.000	0.000	0.000	0.000
62	A	62	VAL	0	-0.002	-0.006	23.237	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	63	HIS	0	-0.049	-0.032	26.468	0.002	0.002	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.912	0.945	26.681	-0.127	-0.127	0.000	0.000	0.000	0.000
65	A	65	MET	0	-0.005	0.017	17.600	0.002	0.002	0.000	0.000	0.000	0.000
66	A	66	PHE	0	-0.036	-0.009	23.166	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.855	-0.938	16.244	0.319	0.319	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.893	-0.939	21.032	0.104	0.104	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.026	0.026	19.889	0.004	0.004	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.067	-0.031	17.553	0.025	0.025	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.851	-0.905	18.724	0.201	0.201	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.050	0.021	17.642	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	73	CYS	0	-0.038	-0.011	20.937	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.033	-0.005	21.246	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.018	-0.006	25.160	-0.012	-0.012	0.000	0.000	0.000	0.000
76	A	76	TYR	0	-0.002	-0.030	25.067	0.004	0.004	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.794	-0.863	29.166	0.115	0.115	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.017	-0.028	29.435	0.012	0.012	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.038	-0.017	31.554	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	80	MET	0	-0.002	-0.013	32.691	0.007	0.007	0.000	0.000	0.000	0.000
81	A	81	ASN	0	0.015	-0.010	34.729	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	82	GLY	0	0.041	0.031	36.670	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.828	0.926	38.142	-0.083	-0.083	0.000	0.000	0.000	0.000
84	A	84	THR	0	0.010	-0.003	34.990	0.008	0.008	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.030	-0.007	34.893	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.041	0.040	33.942	0.008	0.008	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.025	-0.022	30.943	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	88	SER	0	-0.012	-0.007	29.421	0.005	0.005	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.018	0.009	26.186	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	90	LEU	0	0.026	0.009	24.296	0.008	0.008	0.000	0.000	0.000	0.000
91	A	91	TYR	0	0.001	-0.007	19.664	0.000	0.000	0.000	0.000	0.000	0.000
92	A	92	HIS	1	0.839	0.905	20.112	-0.192	-0.192	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.016	-0.016	14.013	0.026	0.026	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.862	-0.941	15.101	0.160	0.160	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.893	0.940	11.186	-0.204	-0.204	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.019	0.020	9.201	0.088	0.088	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.848	-0.896	10.163	0.484	0.484	0.000	0.000	0.000	0.000
98	A	98	ILE	0	0.006	-0.009	13.138	-0.054	-0.054	0.000	0.000	0.000	0.000
99	A	99	THR	0	-0.006	-0.019	16.576	-0.013	-0.013	0.000	0.000	0.000	0.000
100	A	100	SER	0	-0.013	-0.005	19.071	-0.029	-0.029	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.023	0.003	21.755	0.016	0.016	0.000	0.000	0.000	0.000
102	A	102	HIS	0	0.019	0.018	24.192	-0.020	-0.020	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.034	-0.016	27.619	0.004	0.004	0.000	0.000	0.000	0.000
104	A	104	TYR	0	-0.002	-0.004	29.095	-0.013	-0.013	0.000	0.000	0.000	0.000
105	A	105	PHE	0	0.064	-0.004	31.912	0.003	0.003	0.000	0.000	0.000	0.000
106	A	106	ASP	-1	-0.773	-0.852	35.464	0.073	0.073	0.000	0.000	0.000	0.000
107	A	107	PRO	0	0.009	-0.006	37.659	0.002	0.002	0.000	0.000	0.000	0.000
108	A	108	ARG	1	0.885	0.912	39.203	-0.069	-0.069	0.000	0.000	0.000	0.000
109	A	109	PRO	0	0.035	0.014	40.876	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.038	-0.024	36.796	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	111	PHE	0	-0.063	-0.027	40.798	0.000	0.000	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.925	-0.942	44.353	0.067	0.067	0.000	0.000	0.000	0.000

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