FMO DATABASE

FMODB ID: 9GN82

Calculation Name: 3P04-A-Xray318

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P04

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NNN6

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	79
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-463411.21348
FMO2-HF: Nuclear repulsion	433542.774125
FMO2-HF: Total energy	-29868.439355
FMO2-MP2: Total energy	-29954.972809

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:63:ACE )

Summations of interaction energy for fragment #1(A:63:ACE )

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.
-1.367	0.712	0.105	-1.095	-1.092	-0.005

Interaction energy analysis for fragmet #1(A:63:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.006

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	65	TYR	0	-0.021	-0.003	3.865	0.698	1.574	-0.006	-0.410	-0.461	0.000
4	A	66	GLN	0	0.056	0.031	6.804	-0.038	-0.038	0.000	0.000	0.000	0.000
5	A	67	SER	0	-0.063	-0.014	9.438	0.104	0.104	0.000	0.000	0.000	0.000
6	A	68	THR	0	-0.058	-0.031	12.199	0.010	0.010	0.000	0.000	0.000	0.000
7	A	69	ILE	0	-0.019	-0.013	14.390	-0.021	-0.021	0.000	0.000	0.000	0.000
8	A	70	VAL	0	0.067	0.036	16.072	0.019	0.019	0.000	0.000	0.000	0.000
9	A	71	PRO	0	-0.028	-0.013	18.510	0.005	0.005	0.000	0.000	0.000	0.000
10	A	72	VAL	0	-0.004	-0.005	21.966	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	73	GLH	0	-0.079	-0.080	24.617	0.008	0.008	0.000	0.000	0.000	0.000
12	A	74	LEU	0	-0.051	-0.023	26.393	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	75	HIS	0	-0.036	-0.032	29.945	0.009	0.009	0.000	0.000	0.000	0.000
14	A	76	SER	0	0.028	0.017	32.305	0.003	0.003	0.000	0.000	0.000	0.000
15	A	77	PHE	0	-0.033	-0.036	29.582	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	78	GLU	-1	-0.912	-0.951	30.090	-0.076	-0.076	0.000	0.000	0.000	0.000
17	A	79	ASP	-1	-0.768	-0.890	28.074	-0.084	-0.084	0.000	0.000	0.000	0.000
18	A	80	ALA	0	-0.011	-0.002	26.028	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	81	GLN	0	-0.048	-0.026	24.195	-0.018	-0.018	0.000	0.000	0.000	0.000
20	A	82	VAL	0	-0.011	-0.001	22.591	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	83	ILE	0	0.001	0.008	20.645	-0.016	-0.016	0.000	0.000	0.000	0.000
22	A	84	GLY	0	-0.007	-0.024	19.491	-0.020	-0.020	0.000	0.000	0.000	0.000
23	A	85	GLY	0	-0.053	-0.021	18.873	-0.026	-0.026	0.000	0.000	0.000	0.000
24	A	86	ALA	0	0.071	0.035	16.722	-0.030	-0.030	0.000	0.000	0.000	0.000
25	A	87	PHE	0	0.006	-0.002	14.912	-0.045	-0.045	0.000	0.000	0.000	0.000
26	A	88	ARG	1	0.893	0.943	14.158	0.204	0.204	0.000	0.000	0.000	0.000
27	A	89	ASP	-1	-0.968	-0.979	13.504	-0.429	-0.429	0.000	0.000	0.000	0.000
28	A	90	GLY	0	-0.022	-0.004	9.997	-0.112	-0.112	0.000	0.000	0.000	0.000
29	A	91	ASP	-1	-0.826	-0.906	10.103	-0.413	-0.413	0.000	0.000	0.000	0.000
30	A	92	ALA	0	-0.028	-0.024	12.664	0.035	0.035	0.000	0.000	0.000	0.000
31	A	93	VAL	0	-0.015	-0.007	14.443	0.006	0.006	0.000	0.000	0.000	0.000
32	A	94	VAL	0	-0.040	-0.017	18.171	0.014	0.014	0.000	0.000	0.000	0.000
33	A	95	PHE	0	0.019	-0.015	21.224	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	96	ASP	-1	-0.745	-0.817	24.557	-0.034	-0.034	0.000	0.000	0.000	0.000
35	A	97	MET	0	-0.067	-0.043	28.201	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	98	SER	0	-0.042	-0.044	31.017	0.004	0.004	0.000	0.000	0.000	0.000
37	A	99	LEU	0	-0.046	-0.017	33.658	0.003	0.003	0.000	0.000	0.000	0.000
38	A	100	LEU	0	-0.010	0.026	30.925	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	101	SER	0	-0.017	-0.002	35.412	0.004	0.004	0.000	0.000	0.000	0.000
40	A	102	ARG	1	0.978	0.964	36.192	0.026	0.026	0.000	0.000	0.000	0.000
41	A	103	GLU	-1	-0.932	-0.980	36.104	-0.045	-0.045	0.000	0.000	0.000	0.000
42	A	104	GLU	-1	-0.827	-0.918	34.142	-0.051	-0.051	0.000	0.000	0.000	0.000
43	A	105	ALA	0	0.039	0.021	31.878	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	106	ARG	1	0.831	0.895	30.915	0.044	0.044	0.000	0.000	0.000	0.000
45	A	107	ARG	1	0.956	0.985	31.309	0.057	0.057	0.000	0.000	0.000	0.000
46	A	108	ILE	0	0.009	0.015	26.835	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	109	VAL	0	0.007	-0.004	26.704	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	110	ASP	-1	-0.824	-0.897	26.580	-0.058	-0.058	0.000	0.000	0.000	0.000
49	A	111	PHE	0	-0.025	-0.012	23.606	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	112	ALA	0	0.018	-0.001	22.730	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	113	ALA	0	-0.002	-0.012	22.054	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	114	GLY	0	-0.008	0.004	23.055	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	115	LEU	0	-0.052	-0.018	19.539	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	116	CYS	0	-0.036	-0.015	18.232	-0.018	-0.018	0.000	0.000	0.000	0.000
55	A	117	PHE	0	-0.008	0.011	18.493	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	118	ALA	0	-0.035	-0.023	19.924	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	119	LEU	0	-0.041	-0.013	14.501	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	120	HIS	0	0.003	0.018	14.422	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	121	GLY	0	0.018	0.019	14.760	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	122	LYS	1	0.885	0.941	15.813	0.052	0.052	0.000	0.000	0.000	0.000
61	A	123	MET	0	0.010	0.012	17.724	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	124	GLN	0	-0.076	-0.053	18.549	0.014	0.014	0.000	0.000	0.000	0.000
63	A	125	LYS	1	0.950	0.992	22.263	0.017	0.017	0.000	0.000	0.000	0.000
64	A	126	ILE	0	-0.061	-0.023	22.007	0.007	0.007	0.000	0.000	0.000	0.000
65	A	127	ASP	-1	-0.786	-0.891	25.962	-0.016	-0.016	0.000	0.000	0.000	0.000
66	A	128	SER	0	-0.104	-0.071	29.453	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	129	VAL	0	-0.026	0.005	30.961	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	130	THR	0	0.049	0.028	25.093	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	131	PHE	0	-0.024	-0.023	24.166	0.008	0.008	0.000	0.000	0.000	0.000
70	A	132	ALA	0	0.028	0.008	19.178	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	133	VAL	0	-0.031	0.000	17.540	0.011	0.011	0.000	0.000	0.000	0.000
72	A	134	VAL	0	-0.017	-0.022	12.746	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	135	PRO	0	0.056	0.029	10.290	0.036	0.036	0.000	0.000	0.000	0.000
74	A	136	GLU	-1	-0.926	-0.948	10.163	-0.159	-0.159	0.000	0.000	0.000	0.000
75	A	137	LEU	0	-0.053	-0.029	5.313	-0.100	-0.100	0.000	0.000	0.000	0.000
76	A	138	SER	0	0.058	0.026	3.326	0.129	0.288	0.038	-0.074	-0.124	0.000
77	A	139	ASN	0	-0.091	-0.057	3.206	-0.466	0.558	0.073	-0.594	-0.504	-0.005
78	A	140	ILE	0	0.026	0.032	4.387	-0.367	-0.347	0.000	-0.017	-0.003	0.000
79	A	141	NME	0	-0.001	-0.005	5.376	-0.096	-0.096	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:63:ACE )