FMO DATABASE

FMODB ID: 6N9JZ

Calculation Name: 2PFB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PFB

Chain ID: A

ChEMBL ID:

UniProt ID: Q93R11

Base Structure: X-ray

Registration Date: 2023-09-20

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	129
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1050811.79031
FMO2-HF: Nuclear repulsion	1000158.781486
FMO2-HF: Total energy	-50653.008824
FMO2-MP2: Total energy	-50801.244748

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:14:LEU)

Summations of interaction energy for fragment #1(A:14: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.
0.172	2.03	-0.019	-0.785	-1.054	0.001

Interaction energy analysis for fragmet #1(A:14:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.012

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	16	GLN	0	-0.041	-0.021	3.827	-0.092	1.610	-0.017	-0.768	-0.917	0.001
4	A	17	LEU	0	0.022	0.005	5.933	0.021	0.021	0.000	0.000	0.000	0.000
5	A	18	ASP	-1	-0.874	-0.937	8.966	0.007	0.007	0.000	0.000	0.000	0.000
6	A	19	ASN	0	0.001	-0.013	9.948	-0.163	-0.163	0.000	0.000	0.000	0.000
7	A	20	GLN	0	0.032	0.033	11.441	-0.062	-0.062	0.000	0.000	0.000	0.000
8	A	21	LEU	0	0.050	0.030	6.177	0.002	0.002	0.000	0.000	0.000	0.000
9	A	22	CYS	0	0.003	-0.003	9.804	-0.049	-0.049	0.000	0.000	0.000	0.000
10	A	23	PHE	0	-0.024	-0.014	11.803	0.032	0.032	0.000	0.000	0.000	0.000
11	A	24	ALA	0	0.028	0.012	12.271	0.019	0.019	0.000	0.000	0.000	0.000
12	A	25	LEU	0	0.008	0.013	11.108	0.028	0.028	0.000	0.000	0.000	0.000
13	A	26	TYR	0	0.001	-0.001	13.733	0.033	0.033	0.000	0.000	0.000	0.000
14	A	27	SER	0	0.022	0.002	17.061	0.030	0.030	0.000	0.000	0.000	0.000
15	A	28	ALA	0	0.034	0.018	15.945	0.020	0.020	0.000	0.000	0.000	0.000
16	A	29	ASN	0	-0.003	0.001	17.605	0.026	0.026	0.000	0.000	0.000	0.000
17	A	30	LEU	0	0.013	0.012	19.173	0.023	0.023	0.000	0.000	0.000	0.000
18	A	31	ALA	0	0.038	0.010	21.215	0.016	0.016	0.000	0.000	0.000	0.000
19	A	32	MET	0	0.023	0.015	20.252	0.017	0.017	0.000	0.000	0.000	0.000
20	A	33	HIS	0	-0.082	-0.050	22.215	0.018	0.018	0.000	0.000	0.000	0.000
21	A	34	LYS	1	0.838	0.907	25.470	0.106	0.106	0.000	0.000	0.000	0.000
22	A	35	LEU	0	0.002	0.027	25.209	0.007	0.007	0.000	0.000	0.000	0.000
23	A	36	TYR	0	0.011	-0.019	25.957	0.007	0.007	0.000	0.000	0.000	0.000
24	A	37	ARG	1	0.912	0.972	27.587	0.098	0.098	0.000	0.000	0.000	0.000
25	A	38	GLY	0	0.001	-0.003	31.214	0.002	0.002	0.000	0.000	0.000	0.000
26	A	39	LEU	0	0.068	0.030	31.667	0.002	0.002	0.000	0.000	0.000	0.000
27	A	40	LEU	0	-0.025	-0.011	28.665	0.001	0.001	0.000	0.000	0.000	0.000
28	A	41	LYS	1	0.933	0.967	33.268	0.064	0.064	0.000	0.000	0.000	0.000
29	A	42	ALA	0	-0.023	-0.007	36.263	0.002	0.002	0.000	0.000	0.000	0.000
30	A	43	LEU	0	-0.056	-0.031	33.620	0.002	0.002	0.000	0.000	0.000	0.000
31	A	44	ASP	-1	-0.926	-0.942	37.083	-0.067	-0.067	0.000	0.000	0.000	0.000
32	A	45	LEU	0	-0.047	-0.021	32.251	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	46	THR	0	-0.016	-0.021	29.637	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	47	TYR	0	0.093	0.023	21.673	0.006	0.006	0.000	0.000	0.000	0.000
35	A	48	PRO	0	0.026	-0.003	24.463	0.001	0.001	0.000	0.000	0.000	0.000
36	A	49	GLN	0	0.006	0.009	25.828	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	50	TYR	0	0.052	0.030	27.505	0.006	0.006	0.000	0.000	0.000	0.000
38	A	51	LEU	0	0.010	0.009	21.840	0.002	0.002	0.000	0.000	0.000	0.000
39	A	52	VAL	0	0.012	0.009	25.744	0.001	0.001	0.000	0.000	0.000	0.000
40	A	53	MET	0	-0.033	-0.013	27.367	0.005	0.005	0.000	0.000	0.000	0.000
41	A	54	LEU	0	-0.024	0.004	25.773	0.006	0.006	0.000	0.000	0.000	0.000
42	A	55	VAL	0	0.024	0.014	24.462	0.004	0.004	0.000	0.000	0.000	0.000
43	A	56	LEU	0	-0.027	-0.023	27.215	0.005	0.005	0.000	0.000	0.000	0.000
44	A	57	TRP	0	-0.066	-0.046	30.803	0.005	0.005	0.000	0.000	0.000	0.000
45	A	58	GLU	-1	-0.946	-0.954	25.525	-0.097	-0.097	0.000	0.000	0.000	0.000
46	A	59	THR	0	-0.074	-0.031	28.556	0.003	0.003	0.000	0.000	0.000	0.000
47	A	60	ASP	-1	-0.740	-0.877	30.638	-0.071	-0.071	0.000	0.000	0.000	0.000
48	A	61	GLU	-1	-1.019	-1.017	32.963	-0.057	-0.057	0.000	0.000	0.000	0.000
49	A	62	ARG	1	0.896	0.970	28.042	0.080	0.080	0.000	0.000	0.000	0.000
50	A	63	SER	0	-0.003	-0.012	27.916	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	64	VAL	0	-0.002	-0.030	26.308	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	65	SER	0	-0.025	-0.011	23.848	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	66	GLU	-1	-0.811	-0.894	23.188	-0.101	-0.101	0.000	0.000	0.000	0.000
54	A	67	ILE	0	-0.019	-0.011	23.454	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	68	GLY	0	-0.001	-0.007	21.945	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	69	GLU	-1	-0.915	-0.963	18.973	-0.166	-0.166	0.000	0.000	0.000	0.000
57	A	70	ARG	1	0.870	0.948	18.502	0.108	0.108	0.000	0.000	0.000	0.000
58	A	71	LEU	0	-0.042	-0.029	19.422	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	72	TYR	0	-0.025	0.005	14.718	-0.025	-0.025	0.000	0.000	0.000	0.000
60	A	73	LEU	0	-0.052	-0.019	16.561	-0.022	-0.022	0.000	0.000	0.000	0.000
61	A	74	ASP	-1	-0.788	-0.887	19.212	-0.223	-0.223	0.000	0.000	0.000	0.000
62	A	75	SER	0	0.025	-0.016	20.653	0.014	0.014	0.000	0.000	0.000	0.000
63	A	76	ALA	0	-0.010	0.007	23.327	0.014	0.014	0.000	0.000	0.000	0.000
64	A	77	THR	0	-0.005	0.002	21.422	0.007	0.007	0.000	0.000	0.000	0.000
65	A	78	LEU	0	0.013	0.001	23.840	0.012	0.012	0.000	0.000	0.000	0.000
66	A	79	THR	0	-0.036	-0.027	25.691	0.014	0.014	0.000	0.000	0.000	0.000
67	A	80	PRO	0	-0.011	-0.015	27.332	0.011	0.011	0.000	0.000	0.000	0.000
68	A	81	LEU	0	0.002	0.000	25.037	0.009	0.009	0.000	0.000	0.000	0.000
69	A	82	LEU	0	0.050	0.026	28.716	0.008	0.008	0.000	0.000	0.000	0.000
70	A	83	LYS	1	0.939	0.979	31.405	0.083	0.083	0.000	0.000	0.000	0.000
71	A	84	ARG	1	0.907	0.943	29.114	0.116	0.116	0.000	0.000	0.000	0.000
72	A	85	LEU	0	0.041	0.027	30.672	0.004	0.004	0.000	0.000	0.000	0.000
73	A	86	GLN	0	-0.042	-0.024	34.736	0.000	0.000	0.000	0.000	0.000	0.000
74	A	87	ALA	0	-0.064	-0.018	37.350	0.004	0.004	0.000	0.000	0.000	0.000
75	A	88	ALA	0	0.016	0.018	37.498	0.003	0.003	0.000	0.000	0.000	0.000
76	A	89	GLY	0	0.013	0.014	39.396	0.003	0.003	0.000	0.000	0.000	0.000
77	A	90	LEU	0	-0.015	0.008	35.969	0.002	0.002	0.000	0.000	0.000	0.000
78	A	91	VAL	0	0.020	0.006	33.444	0.000	0.000	0.000	0.000	0.000	0.000
79	A	92	THR	0	-0.043	-0.018	36.797	0.002	0.002	0.000	0.000	0.000	0.000
80	A	93	ARG	1	0.947	0.974	32.022	0.090	0.090	0.000	0.000	0.000	0.000
81	A	94	THR	0	0.012	0.003	36.484	0.003	0.003	0.000	0.000	0.000	0.000
82	A	95	ARG	1	1.003	1.004	36.241	0.064	0.064	0.000	0.000	0.000	0.000
83	A	103	VAL	0	-0.051	-0.037	31.582	0.001	0.001	0.000	0.000	0.000	0.000
84	A	104	ILE	0	0.034	0.032	31.591	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	105	ILE	0	-0.043	-0.025	30.803	0.002	0.002	0.000	0.000	0.000	0.000
86	A	106	ALA	0	0.069	0.041	33.534	0.000	0.000	0.000	0.000	0.000	0.000
87	A	107	LEU	0	-0.023	-0.012	34.034	0.000	0.000	0.000	0.000	0.000	0.000
88	A	108	THR	0	-0.040	-0.028	36.980	0.003	0.003	0.000	0.000	0.000	0.000
89	A	109	GLU	-1	-0.894	-0.976	40.255	-0.042	-0.042	0.000	0.000	0.000	0.000
90	A	110	THR	0	-0.003	-0.002	41.255	0.001	0.001	0.000	0.000	0.000	0.000
91	A	111	GLY	0	0.041	0.020	37.819	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	112	ARG	1	0.946	0.977	37.408	0.049	0.049	0.000	0.000	0.000	0.000
93	A	113	ALA	0	-0.003	0.002	39.096	0.001	0.001	0.000	0.000	0.000	0.000
94	A	114	LEU	0	-0.015	-0.003	35.632	0.002	0.002	0.000	0.000	0.000	0.000
95	A	115	ARG	1	0.889	0.943	34.074	0.053	0.053	0.000	0.000	0.000	0.000
96	A	116	SER	0	-0.055	-0.031	36.882	0.001	0.001	0.000	0.000	0.000	0.000
97	A	117	LYS	1	0.931	0.961	38.877	0.049	0.049	0.000	0.000	0.000	0.000
98	A	118	ALA	0	-0.014	-0.002	33.700	0.000	0.000	0.000	0.000	0.000	0.000
99	A	119	GLY	0	0.003	0.012	34.536	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	120	ALA	0	-0.011	-0.012	36.764	0.000	0.000	0.000	0.000	0.000	0.000
101	A	121	VAL	0	-0.007	-0.014	32.181	0.000	0.000	0.000	0.000	0.000	0.000
102	A	122	PRO	0	-0.006	0.012	31.619	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	123	GLU	-1	-0.742	-0.890	28.625	-0.067	-0.067	0.000	0.000	0.000	0.000
104	A	124	GLN	0	-0.030	-0.011	27.428	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	125	VAL	0	-0.016	0.000	27.583	0.001	0.001	0.000	0.000	0.000	0.000
106	A	126	PHE	0	0.021	0.024	22.464	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	127	CYS	0	0.016	0.004	19.496	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	128	ALA	0	0.048	0.033	22.518	0.001	0.001	0.000	0.000	0.000	0.000
109	A	129	SER	0	-0.052	-0.011	24.664	0.005	0.005	0.000	0.000	0.000	0.000
110	A	130	ALA	0	0.038	0.003	22.059	0.003	0.003	0.000	0.000	0.000	0.000
111	A	131	SER	0	-0.045	-0.031	20.697	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	132	SER	0	-0.016	-0.018	20.794	0.006	0.006	0.000	0.000	0.000	0.000
113	A	133	LEU	0	-0.033	0.007	20.750	0.006	0.006	0.000	0.000	0.000	0.000
114	A	134	ASP	-1	-0.856	-0.943	20.064	-0.033	-0.033	0.000	0.000	0.000	0.000
115	A	135	GLU	-1	-0.843	-0.945	18.475	-0.085	-0.085	0.000	0.000	0.000	0.000
116	A	136	LEU	0	-0.018	-0.005	14.896	-0.025	-0.025	0.000	0.000	0.000	0.000
117	A	137	ARG	1	0.909	0.977	15.064	0.007	0.007	0.000	0.000	0.000	0.000
118	A	138	GLN	0	-0.003	-0.009	15.070	0.008	0.008	0.000	0.000	0.000	0.000
119	A	139	LEU	0	0.001	0.012	10.520	0.010	0.010	0.000	0.000	0.000	0.000
120	A	140	LYS	1	0.915	0.961	10.167	-0.049	-0.049	0.000	0.000	0.000	0.000
121	A	141	GLN	0	0.003	-0.009	10.752	0.022	0.022	0.000	0.000	0.000	0.000
122	A	142	GLU	-1	-0.866	-0.940	9.598	0.115	0.115	0.000	0.000	0.000	0.000
123	A	143	LEU	0	-0.029	-0.007	4.396	0.010	0.080	-0.001	-0.007	-0.062	0.000
124	A	144	GLU	-1	-0.921	-0.972	6.465	0.468	0.468	0.000	0.000	0.000	0.000
125	A	145	LYS	1	0.883	0.943	9.192	0.081	0.081	0.000	0.000	0.000	0.000
126	A	146	LEU	0	0.010	0.014	4.209	-0.088	-0.002	-0.001	-0.010	-0.075	0.000
127	A	147	ARG	1	0.918	0.966	5.953	-0.277	-0.277	0.000	0.000	0.000	0.000
128	A	148	SER	0	-0.101	-0.046	6.721	0.018	0.018	0.000	0.000	0.000	0.000
129	A	149	SER	0	-0.017	-0.003	7.973	-0.093	-0.093	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:14:LEU)