FMO DATABASE

FMODB ID: K3L93

Calculation Name: 3P5J-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P5J

Chain ID: C

ChEMBL ID:

UniProt ID: Q9CWY8

Base Structure: X-ray

Registration Date: 2023-06-19

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	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	116
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-752587.20068
FMO2-HF: Nuclear repulsion	710176.948319
FMO2-HF: Total energy	-42410.252362
FMO2-MP2: Total energy	-42536.211535

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(C:14:ILE)

Summations of interaction energy for fragment #1(C:14:ILE)

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.
-8.06	-3.629	9.591	-4.292	-9.731	-0.011

Interaction energy analysis for fragmet #1(C:14:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.033

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	C	16	LEU	0	0.014	-0.020	3.815	-0.457	1.543	-0.030	-0.990	-0.980	0.001
4	C	17	ARG	1	1.004	1.034	6.114	-0.117	-0.117	0.000	0.000	0.000	0.000
5	C	18	PRO	0	0.088	0.034	9.967	-0.056	-0.056	0.000	0.000	0.000	0.000
6	C	19	GLY	0	-0.065	-0.037	12.512	0.036	0.036	0.000	0.000	0.000	0.000
7	C	20	SER	0	0.012	-0.001	10.054	0.035	0.035	0.000	0.000	0.000	0.000
8	C	21	LEU	0	0.048	0.022	10.146	0.006	0.006	0.000	0.000	0.000	0.000
9	C	22	ARG	1	0.920	0.952	13.223	0.150	0.150	0.000	0.000	0.000	0.000
10	C	23	GLY	0	-0.014	-0.002	15.771	0.020	0.020	0.000	0.000	0.000	0.000
11	C	24	ALA	0	0.007	0.027	14.304	0.024	0.024	0.000	0.000	0.000	0.000
12	C	25	ALA	0	0.024	0.011	16.251	0.004	0.004	0.000	0.000	0.000	0.000
13	C	26	PRO	0	-0.013	-0.020	18.764	-0.018	-0.018	0.000	0.000	0.000	0.000
14	C	27	ALA	0	0.018	0.020	18.246	0.015	0.015	0.000	0.000	0.000	0.000
15	C	28	LYS	1	0.848	0.918	20.242	0.131	0.131	0.000	0.000	0.000	0.000
16	C	29	LEU	0	0.007	-0.001	16.925	0.004	0.004	0.000	0.000	0.000	0.000
17	C	30	HIS	0	0.045	0.033	21.461	0.002	0.002	0.000	0.000	0.000	0.000
18	C	31	LEU	0	-0.018	-0.004	19.976	-0.006	-0.006	0.000	0.000	0.000	0.000
19	C	32	LEU	0	0.028	0.006	22.879	0.009	0.009	0.000	0.000	0.000	0.000
20	C	33	PRO	0	0.004	0.026	24.358	-0.009	-0.009	0.000	0.000	0.000	0.000
21	C	34	CYS	0	-0.079	-0.064	25.429	0.011	0.011	0.000	0.000	0.000	0.000
22	C	35	ASP	-1	-0.871	-0.928	20.912	-0.148	-0.148	0.000	0.000	0.000	0.000
23	C	36	VAL	0	-0.070	-0.033	22.707	0.016	0.016	0.000	0.000	0.000	0.000
24	C	37	LEU	0	0.035	0.003	21.626	0.001	0.001	0.000	0.000	0.000	0.000
25	C	38	VAL	0	-0.017	0.006	20.386	0.005	0.005	0.000	0.000	0.000	0.000
26	C	39	SER	0	0.008	0.012	16.604	-0.014	-0.014	0.000	0.000	0.000	0.000
27	C	40	ARG	1	0.954	0.966	18.571	0.036	0.036	0.000	0.000	0.000	0.000
28	C	41	PRO	0	0.005	0.018	20.177	-0.015	-0.015	0.000	0.000	0.000	0.000
29	C	42	ALA	0	0.026	-0.008	21.709	0.003	0.003	0.000	0.000	0.000	0.000
30	C	43	PRO	0	0.006	0.011	24.832	-0.003	-0.003	0.000	0.000	0.000	0.000
31	C	44	VAL	0	0.041	0.016	24.184	0.001	0.001	0.000	0.000	0.000	0.000
32	C	45	ASP	-1	-0.808	-0.914	27.392	-0.064	-0.064	0.000	0.000	0.000	0.000
33	C	46	ARG	1	0.891	0.964	29.705	0.023	0.023	0.000	0.000	0.000	0.000
34	C	47	PHE	0	-0.065	-0.053	30.935	0.003	0.003	0.000	0.000	0.000	0.000
35	C	48	PHE	0	-0.002	0.012	28.347	0.000	0.000	0.000	0.000	0.000	0.000
36	C	49	THR	0	0.058	0.012	29.132	-0.002	-0.002	0.000	0.000	0.000	0.000
37	C	50	PRO	0	-0.016	0.001	31.488	-0.001	-0.001	0.000	0.000	0.000	0.000
38	C	51	ALA	0	-0.026	-0.002	34.186	0.003	0.003	0.000	0.000	0.000	0.000
39	C	52	VAL	0	-0.035	-0.025	31.192	-0.001	-0.001	0.000	0.000	0.000	0.000
40	C	53	ARG	1	0.803	0.916	34.620	0.058	0.058	0.000	0.000	0.000	0.000
41	C	54	HIS	0	0.051	0.011	34.458	-0.005	-0.005	0.000	0.000	0.000	0.000
42	C	55	ASP	-1	-0.847	-0.907	38.285	-0.068	-0.068	0.000	0.000	0.000	0.000
43	C	56	ALA	0	-0.009	-0.003	39.291	-0.003	-0.003	0.000	0.000	0.000	0.000
44	C	57	ASP	-1	-0.916	-0.940	38.464	-0.081	-0.081	0.000	0.000	0.000	0.000
45	C	58	GLY	0	0.007	0.016	35.056	-0.001	-0.001	0.000	0.000	0.000	0.000
46	C	59	LEU	0	0.004	0.003	31.422	0.005	0.005	0.000	0.000	0.000	0.000
47	C	60	GLN	0	0.008	0.005	34.869	-0.004	-0.004	0.000	0.000	0.000	0.000
48	C	61	ALA	0	0.018	0.008	32.551	0.002	0.002	0.000	0.000	0.000	0.000
49	C	62	SER	0	-0.016	-0.007	34.128	0.001	0.001	0.000	0.000	0.000	0.000
50	C	63	PHE	0	0.028	0.008	27.580	0.002	0.002	0.000	0.000	0.000	0.000
51	C	64	ARG	1	0.900	0.947	29.247	0.050	0.050	0.000	0.000	0.000	0.000
52	C	65	GLY	0	0.052	0.031	33.877	0.001	0.001	0.000	0.000	0.000	0.000
53	C	66	ARG	1	0.947	0.980	33.214	0.072	0.072	0.000	0.000	0.000	0.000
54	C	67	GLY	0	0.056	0.026	34.936	-0.002	-0.002	0.000	0.000	0.000	0.000
55	C	68	LEU	0	-0.053	-0.011	30.273	-0.004	-0.004	0.000	0.000	0.000	0.000
56	C	69	ARG	1	0.833	0.899	33.076	0.084	0.084	0.000	0.000	0.000	0.000
57	C	70	GLY	0	0.019	-0.010	30.854	-0.007	-0.007	0.000	0.000	0.000	0.000
58	C	71	GLU	-1	-0.878	-0.952	29.978	-0.128	-0.128	0.000	0.000	0.000	0.000
59	C	72	GLU	-1	-0.851	-0.916	27.116	-0.148	-0.148	0.000	0.000	0.000	0.000
60	C	73	VAL	0	0.006	0.004	24.494	0.001	0.001	0.000	0.000	0.000	0.000
61	C	74	ALA	0	0.014	-0.003	24.951	-0.007	-0.007	0.000	0.000	0.000	0.000
62	C	75	VAL	0	-0.039	-0.011	19.636	-0.014	-0.014	0.000	0.000	0.000	0.000
63	C	76	PRO	0	-0.007	-0.004	20.128	0.015	0.015	0.000	0.000	0.000	0.000
64	C	77	PRO	0	0.048	0.023	22.727	-0.007	-0.007	0.000	0.000	0.000	0.000
65	C	78	GLY	0	0.000	-0.004	22.880	-0.012	-0.012	0.000	0.000	0.000	0.000
66	C	79	PHE	0	-0.032	-0.013	16.002	-0.044	-0.044	0.000	0.000	0.000	0.000
67	C	80	ALA	0	-0.005	-0.004	16.862	0.037	0.037	0.000	0.000	0.000	0.000
68	C	81	GLY	0	0.017	0.021	16.263	-0.058	-0.058	0.000	0.000	0.000	0.000
69	C	82	PHE	0	0.006	-0.009	12.275	0.026	0.026	0.000	0.000	0.000	0.000
70	C	83	VAL	0	0.011	0.022	12.346	-0.037	-0.037	0.000	0.000	0.000	0.000
71	C	84	MET	0	-0.007	-0.012	6.971	0.015	0.015	0.000	0.000	0.000	0.000
72	C	85	VAL	0	0.022	0.019	8.107	-0.007	-0.007	0.000	0.000	0.000	0.000
73	C	86	THR	0	-0.023	-0.007	3.788	-0.120	0.090	0.002	-0.034	-0.179	0.000
74	C	120	ARG	1	0.997	1.006	2.140	-4.824	-4.748	5.799	-1.768	-4.107	0.005
75	C	121	LEU	0	-0.029	-0.035	2.984	-1.163	0.537	0.944	-1.017	-1.627	-0.010
76	C	122	ILE	0	0.002	-0.003	2.330	-1.129	-0.693	2.867	-0.513	-2.789	-0.007
77	C	123	GLY	0	0.033	0.029	3.779	-0.389	-0.380	0.009	0.030	-0.049	0.000
78	C	124	ALA	0	-0.023	-0.028	7.449	0.031	0.031	0.000	0.000	0.000	0.000
79	C	125	THR	0	-0.039	-0.028	10.428	0.049	0.049	0.000	0.000	0.000	0.000
80	C	126	GLY	0	0.031	0.032	13.314	0.039	0.039	0.000	0.000	0.000	0.000
81	C	127	SER	0	-0.029	-0.022	14.830	-0.056	-0.056	0.000	0.000	0.000	0.000
82	C	128	PHE	0	-0.008	-0.004	15.595	0.031	0.031	0.000	0.000	0.000	0.000
83	C	129	SER	0	0.051	0.013	19.530	-0.023	-0.023	0.000	0.000	0.000	0.000
84	C	130	HIS	0	-0.023	-0.012	22.184	0.002	0.002	0.000	0.000	0.000	0.000
85	C	131	PHE	0	-0.080	-0.035	21.385	-0.004	-0.004	0.000	0.000	0.000	0.000
86	C	132	THR	0	0.050	0.039	23.692	0.008	0.008	0.000	0.000	0.000	0.000
87	C	133	LEU	0	-0.002	0.010	24.432	-0.010	-0.010	0.000	0.000	0.000	0.000
88	C	134	TRP	0	-0.040	-0.048	26.333	0.012	0.012	0.000	0.000	0.000	0.000
89	C	135	GLY	0	0.033	0.015	27.769	-0.009	-0.009	0.000	0.000	0.000	0.000
90	C	136	LEU	0	-0.012	-0.028	30.535	0.006	0.006	0.000	0.000	0.000	0.000
91	C	137	GLU	-1	-0.922	-0.960	33.007	-0.071	-0.071	0.000	0.000	0.000	0.000
92	C	138	THR	0	-0.104	-0.059	35.183	0.003	0.003	0.000	0.000	0.000	0.000
93	C	139	VAL	0	0.046	0.022	32.549	-0.003	-0.003	0.000	0.000	0.000	0.000
94	C	140	PRO	0	-0.055	-0.021	28.600	0.000	0.000	0.000	0.000	0.000	0.000
95	C	141	GLY	0	0.053	0.033	31.229	0.000	0.000	0.000	0.000	0.000	0.000
96	C	142	PRO	0	0.069	0.019	30.832	-0.010	-0.010	0.000	0.000	0.000	0.000
97	C	143	ASP	-1	-0.906	-0.939	30.415	-0.145	-0.145	0.000	0.000	0.000	0.000
98	C	144	ALA	0	-0.021	-0.005	27.976	0.003	0.003	0.000	0.000	0.000	0.000
99	C	145	LYS	1	0.935	0.931	23.357	0.183	0.183	0.000	0.000	0.000	0.000
100	C	146	VAL	0	0.009	0.012	21.641	-0.017	-0.017	0.000	0.000	0.000	0.000
101	C	147	HIS	0	0.068	0.028	23.191	-0.030	-0.030	0.000	0.000	0.000	0.000
102	C	148	ARG	1	0.900	0.963	25.355	0.177	0.177	0.000	0.000	0.000	0.000
103	C	149	ALA	0	-0.006	0.001	19.512	-0.009	-0.009	0.000	0.000	0.000	0.000
104	C	150	LEU	0	-0.001	0.000	20.582	-0.029	-0.029	0.000	0.000	0.000	0.000
105	C	151	GLY	0	0.053	0.031	22.281	0.001	0.001	0.000	0.000	0.000	0.000
106	C	152	TRP	0	-0.032	-0.017	16.276	0.021	0.021	0.000	0.000	0.000	0.000
107	C	153	PRO	0	-0.009	-0.010	18.310	0.000	0.000	0.000	0.000	0.000	0.000
108	C	154	SER	0	-0.001	0.000	20.315	0.004	0.004	0.000	0.000	0.000	0.000
109	C	155	LEU	0	0.017	0.012	23.350	0.010	0.010	0.000	0.000	0.000	0.000
110	C	156	ALA	0	-0.024	-0.019	18.684	0.005	0.005	0.000	0.000	0.000	0.000
111	C	157	ALA	0	0.014	0.005	20.766	-0.013	-0.013	0.000	0.000	0.000	0.000
112	C	158	ALA	0	-0.002	-0.002	22.454	0.012	0.012	0.000	0.000	0.000	0.000
113	C	159	ILE	0	-0.056	-0.024	21.560	0.010	0.010	0.000	0.000	0.000	0.000
114	C	160	HIS	0	-0.047	-0.028	18.565	0.011	0.011	0.000	0.000	0.000	0.000
115	C	161	ALA	0	-0.014	0.027	21.596	-0.007	-0.007	0.000	0.000	0.000	0.000
116	C	162	GLN	0	-0.017	-0.009	22.921	0.024	0.024	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:14:ILE)