FMO DATABASE

FMODB ID: 9G142

Calculation Name: 3P04-A-Xray372

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: 2023-06-20

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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-459492.720085
FMO2-HF: Nuclear repulsion	429795.210516
FMO2-HF: Total energy	-29697.50957
FMO2-MP2: Total energy	-29783.50308

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:64:SER)

Summations of interaction energy for fragment #1(A:64:SER)

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.
-15.113	-10.356	1.408	-2.633	-3.533	-0.005

Interaction energy analysis for fragmet #1(A:64:SER)

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 : -0.030

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	66	GLN	0	0.048	0.025	3.674	-2.183	-0.286	-0.007	-0.795	-1.096	0.000
4	A	67	SER	0	-0.062	-0.013	6.172	0.552	0.552	0.000	0.000	0.000	0.000
5	A	68	THR	0	-0.057	-0.031	9.600	-0.178	-0.178	0.000	0.000	0.000	0.000
6	A	69	ILE	0	-0.021	-0.015	12.197	-0.027	-0.027	0.000	0.000	0.000	0.000
7	A	70	VAL	0	0.067	0.036	12.520	0.168	0.168	0.000	0.000	0.000	0.000
8	A	71	PRO	0	-0.028	-0.014	15.164	0.018	0.018	0.000	0.000	0.000	0.000
9	A	72	VAL	0	-0.005	-0.005	18.259	0.021	0.021	0.000	0.000	0.000	0.000
10	A	73	GLH	0	-0.081	-0.081	20.978	0.012	0.012	0.000	0.000	0.000	0.000
11	A	74	LEU	0	-0.048	-0.022	22.464	0.005	0.005	0.000	0.000	0.000	0.000
12	A	75	HIS	0	-0.037	-0.032	26.084	0.030	0.030	0.000	0.000	0.000	0.000
13	A	76	SER	0	0.028	0.018	28.041	0.023	0.023	0.000	0.000	0.000	0.000
14	A	77	PHE	0	-0.033	-0.035	25.505	-0.020	-0.020	0.000	0.000	0.000	0.000
15	A	78	GLU	-1	-0.913	-0.951	25.568	-0.277	-0.277	0.000	0.000	0.000	0.000
16	A	79	ASP	-1	-0.769	-0.890	23.652	-0.367	-0.367	0.000	0.000	0.000	0.000
17	A	80	ALA	0	-0.005	-0.001	21.655	-0.052	-0.052	0.000	0.000	0.000	0.000
18	A	81	GLN	0	-0.051	-0.028	19.644	-0.057	-0.057	0.000	0.000	0.000	0.000
19	A	82	VAL	0	-0.012	0.000	18.107	-0.045	-0.045	0.000	0.000	0.000	0.000
20	A	83	ILE	0	0.001	0.008	16.508	-0.084	-0.084	0.000	0.000	0.000	0.000
21	A	84	GLY	0	-0.006	-0.024	15.102	-0.121	-0.121	0.000	0.000	0.000	0.000
22	A	85	GLY	0	-0.055	-0.022	14.021	-0.094	-0.094	0.000	0.000	0.000	0.000
23	A	86	ALA	0	0.074	0.036	11.815	-0.076	-0.076	0.000	0.000	0.000	0.000
24	A	87	PHE	0	0.004	-0.003	10.247	-0.276	-0.276	0.000	0.000	0.000	0.000
25	A	88	ARG	1	0.892	0.941	9.820	0.430	0.430	0.000	0.000	0.000	0.000
26	A	89	ASP	-1	-0.966	-0.978	8.023	-1.143	-1.143	0.000	0.000	0.000	0.000
27	A	90	GLY	0	-0.026	-0.005	5.300	-0.490	-0.490	0.000	0.000	0.000	0.000
28	A	91	ASP	-1	-0.821	-0.903	6.231	-3.002	-3.002	0.000	0.000	0.000	0.000
29	A	92	ALA	0	-0.033	-0.025	8.828	0.263	0.263	0.000	0.000	0.000	0.000
30	A	93	VAL	0	-0.018	-0.008	11.287	0.109	0.109	0.000	0.000	0.000	0.000
31	A	94	VAL	0	-0.032	-0.014	14.793	0.043	0.043	0.000	0.000	0.000	0.000
32	A	95	PHE	0	0.014	-0.017	18.197	0.032	0.032	0.000	0.000	0.000	0.000
33	A	96	ASP	-1	-0.744	-0.816	21.224	-0.334	-0.334	0.000	0.000	0.000	0.000
34	A	97	MET	0	-0.068	-0.043	24.966	0.004	0.004	0.000	0.000	0.000	0.000
35	A	98	SER	0	-0.040	-0.044	27.641	0.029	0.029	0.000	0.000	0.000	0.000
36	A	99	LEU	0	-0.045	-0.018	30.202	0.022	0.022	0.000	0.000	0.000	0.000
37	A	100	LEU	0	-0.012	0.026	27.163	0.007	0.007	0.000	0.000	0.000	0.000
38	A	101	SER	0	-0.017	-0.002	31.751	0.010	0.010	0.000	0.000	0.000	0.000
39	A	102	ARG	1	0.979	0.964	32.620	0.205	0.205	0.000	0.000	0.000	0.000
40	A	103	GLU	-1	-0.932	-0.980	32.646	-0.248	-0.248	0.000	0.000	0.000	0.000
41	A	104	GLU	-1	-0.828	-0.919	30.280	-0.265	-0.265	0.000	0.000	0.000	0.000
42	A	105	ALA	0	0.039	0.020	28.313	-0.023	-0.023	0.000	0.000	0.000	0.000
43	A	106	ARG	1	0.832	0.895	27.523	0.296	0.296	0.000	0.000	0.000	0.000
44	A	107	ARG	1	0.955	0.985	27.819	0.251	0.251	0.000	0.000	0.000	0.000
45	A	108	ILE	0	0.009	0.016	23.065	-0.021	-0.021	0.000	0.000	0.000	0.000
46	A	109	VAL	0	0.000	-0.007	23.173	-0.041	-0.041	0.000	0.000	0.000	0.000
47	A	110	ASP	-1	-0.819	-0.895	23.250	-0.364	-0.364	0.000	0.000	0.000	0.000
48	A	111	PHE	0	-0.027	-0.013	19.188	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	112	ALA	0	0.020	0.000	19.262	-0.041	-0.041	0.000	0.000	0.000	0.000
50	A	113	ALA	0	-0.001	-0.010	18.657	-0.070	-0.070	0.000	0.000	0.000	0.000
51	A	114	GLY	0	-0.010	0.002	19.784	-0.016	-0.016	0.000	0.000	0.000	0.000
52	A	115	LEU	0	-0.049	-0.017	15.745	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	116	CYS	0	-0.035	-0.015	15.055	-0.107	-0.107	0.000	0.000	0.000	0.000
54	A	117	PHE	0	-0.009	0.011	15.368	-0.039	-0.039	0.000	0.000	0.000	0.000
55	A	118	ALA	0	-0.036	-0.024	15.939	0.009	0.009	0.000	0.000	0.000	0.000
56	A	119	LEU	0	-0.040	-0.011	10.412	0.053	0.053	0.000	0.000	0.000	0.000
57	A	120	HIS	0	0.003	0.018	11.137	-0.179	-0.179	0.000	0.000	0.000	0.000
58	A	121	GLY	0	0.016	0.018	12.334	-0.157	-0.157	0.000	0.000	0.000	0.000
59	A	122	LYS	1	0.888	0.943	13.239	0.926	0.926	0.000	0.000	0.000	0.000
60	A	123	MET	0	0.014	0.014	15.552	-0.036	-0.036	0.000	0.000	0.000	0.000
61	A	124	GLN	0	-0.080	-0.055	17.189	-0.027	-0.027	0.000	0.000	0.000	0.000
62	A	125	LYS	1	0.952	0.993	20.213	0.334	0.334	0.000	0.000	0.000	0.000
63	A	126	ILE	0	-0.058	-0.021	20.073	0.005	0.005	0.000	0.000	0.000	0.000
64	A	127	ASP	-1	-0.786	-0.891	23.980	-0.330	-0.330	0.000	0.000	0.000	0.000
65	A	128	SER	0	-0.104	-0.071	27.025	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	129	VAL	0	-0.026	0.005	28.164	0.006	0.006	0.000	0.000	0.000	0.000
67	A	130	THR	0	0.048	0.029	22.518	-0.019	-0.019	0.000	0.000	0.000	0.000
68	A	131	PHE	0	-0.026	-0.024	21.274	0.017	0.017	0.000	0.000	0.000	0.000
69	A	132	ALA	0	0.023	0.007	16.618	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	133	VAL	0	-0.028	0.001	14.044	0.065	0.065	0.000	0.000	0.000	0.000
71	A	134	VAL	0	-0.017	-0.021	10.800	-0.081	-0.081	0.000	0.000	0.000	0.000
72	A	135	PRO	0	0.058	0.030	7.226	0.309	0.309	0.000	0.000	0.000	0.000
73	A	136	GLU	-1	-0.920	-0.945	8.231	-1.352	-1.352	0.000	0.000	0.000	0.000
74	A	137	LEU	0	-0.041	-0.026	6.088	-0.865	-0.865	0.000	0.000	0.000	0.000
75	A	138	SER	0	0.017	0.007	2.515	-7.345	-4.607	1.416	-1.817	-2.337	-0.005
76	A	139	ASN	0	-0.066	-0.041	4.276	1.243	1.365	-0.001	-0.021	-0.100	0.000
77	A	140	ILE	0	0.032	0.028	5.500	-0.116	-0.116	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:64:SER)