FMO DATABASE

FMODB ID: R9R38

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	OptAll
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	-1054284.763631
FMO2-HF: Nuclear repulsion	1003630.768601
FMO2-HF: Total energy	-50653.995029
FMO2-MP2: Total energy	-50802.151829

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.
-0.094	1.689	-0.018	-0.874	-0.892	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 : -0.014

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	16	GLN	0	-0.015	-0.011	3.868	-0.002	1.721	-0.017	-0.870	-0.837	0.001
4	A	17	LEU	0	0.014	0.004	6.433	-0.103	-0.103	0.000	0.000	0.000	0.000
5	A	18	ASP	-1	-0.784	-0.881	9.666	0.090	0.090	0.000	0.000	0.000	0.000
6	A	19	ASN	0	-0.034	-0.015	10.311	-0.149	-0.149	0.000	0.000	0.000	0.000
7	A	20	GLN	0	-0.003	-0.013	12.125	-0.067	-0.067	0.000	0.000	0.000	0.000
8	A	21	LEU	0	0.026	0.014	6.092	-0.010	-0.010	0.000	0.000	0.000	0.000
9	A	22	CYS	0	-0.014	-0.006	10.263	-0.079	-0.079	0.000	0.000	0.000	0.000
10	A	23	PHE	0	0.005	0.000	12.234	0.003	0.003	0.000	0.000	0.000	0.000
11	A	24	ALA	0	0.039	0.022	12.792	0.006	0.006	0.000	0.000	0.000	0.000
12	A	25	LEU	0	-0.001	0.008	10.678	0.011	0.011	0.000	0.000	0.000	0.000
13	A	26	TYR	0	0.002	-0.001	13.774	0.022	0.022	0.000	0.000	0.000	0.000
14	A	27	SER	0	0.021	0.002	17.064	0.019	0.019	0.000	0.000	0.000	0.000
15	A	28	ALA	0	0.037	0.016	16.000	0.014	0.014	0.000	0.000	0.000	0.000
16	A	29	ASN	0	-0.012	-0.008	17.429	0.021	0.021	0.000	0.000	0.000	0.000
17	A	30	LEU	0	0.015	0.005	19.098	0.016	0.016	0.000	0.000	0.000	0.000
18	A	31	ALA	0	0.005	0.005	21.107	0.011	0.011	0.000	0.000	0.000	0.000
19	A	32	MET	0	0.008	0.010	20.423	0.014	0.014	0.000	0.000	0.000	0.000
20	A	33	HIS	0	-0.041	-0.026	22.437	0.013	0.013	0.000	0.000	0.000	0.000
21	A	34	LYS	1	0.889	0.961	25.077	0.072	0.072	0.000	0.000	0.000	0.000
22	A	35	LEU	0	0.016	0.015	25.039	0.004	0.004	0.000	0.000	0.000	0.000
23	A	36	TYR	0	0.045	-0.003	26.127	0.004	0.004	0.000	0.000	0.000	0.000
24	A	37	ARG	1	0.826	0.911	27.787	0.076	0.076	0.000	0.000	0.000	0.000
25	A	38	GLY	0	0.011	0.001	31.272	0.001	0.001	0.000	0.000	0.000	0.000
26	A	39	LEU	0	0.043	0.022	31.909	0.001	0.001	0.000	0.000	0.000	0.000
27	A	40	LEU	0	-0.010	-0.014	28.523	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	41	LYS	1	0.937	0.969	33.178	0.052	0.052	0.000	0.000	0.000	0.000
29	A	42	ALA	0	-0.008	0.002	36.413	0.002	0.002	0.000	0.000	0.000	0.000
30	A	43	LEU	0	-0.059	-0.034	33.506	0.002	0.002	0.000	0.000	0.000	0.000
31	A	44	ASP	-1	-0.945	-0.951	37.202	-0.060	-0.060	0.000	0.000	0.000	0.000
32	A	45	LEU	0	-0.029	-0.007	32.132	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	46	THR	0	-0.037	-0.050	29.560	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	47	TYR	0	0.061	0.016	22.052	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	48	PRO	0	0.042	0.004	24.569	0.000	0.000	0.000	0.000	0.000	0.000
36	A	49	GLN	0	0.048	0.050	26.093	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	50	TYR	0	0.042	0.022	27.883	0.004	0.004	0.000	0.000	0.000	0.000
38	A	51	LEU	0	0.021	0.016	22.075	0.003	0.003	0.000	0.000	0.000	0.000
39	A	52	VAL	0	0.007	0.004	26.007	0.001	0.001	0.000	0.000	0.000	0.000
40	A	53	MET	0	-0.039	-0.012	27.710	0.004	0.004	0.000	0.000	0.000	0.000
41	A	54	LEU	0	-0.005	0.005	26.358	0.005	0.005	0.000	0.000	0.000	0.000
42	A	55	VAL	0	0.011	0.004	24.445	0.004	0.004	0.000	0.000	0.000	0.000
43	A	56	LEU	0	-0.030	-0.026	27.520	0.005	0.005	0.000	0.000	0.000	0.000
44	A	57	TRP	0	-0.063	-0.041	31.069	0.005	0.005	0.000	0.000	0.000	0.000
45	A	58	GLU	-1	-0.825	-0.853	25.554	-0.091	-0.091	0.000	0.000	0.000	0.000
46	A	59	THR	0	-0.054	-0.021	28.975	0.003	0.003	0.000	0.000	0.000	0.000
47	A	60	ASP	-1	-0.681	-0.829	31.076	-0.066	-0.066	0.000	0.000	0.000	0.000
48	A	61	GLU	-1	-0.993	-0.999	32.892	-0.057	-0.057	0.000	0.000	0.000	0.000
49	A	62	ARG	1	0.805	0.902	28.235	0.082	0.082	0.000	0.000	0.000	0.000
50	A	63	SER	0	-0.033	-0.053	28.205	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	64	VAL	0	-0.025	-0.038	26.659	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	65	SER	0	-0.066	-0.042	23.767	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	66	GLU	-1	-0.713	-0.810	23.463	-0.102	-0.102	0.000	0.000	0.000	0.000
54	A	67	ILE	0	-0.016	-0.012	23.854	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	68	GLY	0	0.003	0.001	22.145	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	69	GLU	-1	-0.868	-0.926	19.207	-0.167	-0.167	0.000	0.000	0.000	0.000
57	A	70	ARG	1	0.764	0.853	18.844	0.101	0.101	0.000	0.000	0.000	0.000
58	A	71	LEU	0	-0.037	-0.024	20.205	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	72	TYR	0	-0.040	-0.009	14.880	-0.020	-0.020	0.000	0.000	0.000	0.000
60	A	73	LEU	0	-0.056	-0.017	16.641	-0.023	-0.023	0.000	0.000	0.000	0.000
61	A	74	ASP	-1	-0.737	-0.834	19.343	-0.203	-0.203	0.000	0.000	0.000	0.000
62	A	75	SER	0	0.042	-0.009	20.952	0.016	0.016	0.000	0.000	0.000	0.000
63	A	76	ALA	0	-0.062	-0.017	23.936	0.016	0.016	0.000	0.000	0.000	0.000
64	A	77	THR	0	-0.011	-0.040	21.330	0.013	0.013	0.000	0.000	0.000	0.000
65	A	78	LEU	0	0.015	0.014	24.041	0.012	0.012	0.000	0.000	0.000	0.000
66	A	79	THR	0	-0.033	-0.026	25.718	0.015	0.015	0.000	0.000	0.000	0.000
67	A	80	PRO	0	0.008	-0.007	27.650	0.011	0.011	0.000	0.000	0.000	0.000
68	A	81	LEU	0	-0.029	-0.008	25.119	0.009	0.009	0.000	0.000	0.000	0.000
69	A	82	LEU	0	0.062	0.030	29.027	0.009	0.009	0.000	0.000	0.000	0.000
70	A	83	LYS	1	0.955	0.981	31.659	0.080	0.080	0.000	0.000	0.000	0.000
71	A	84	ARG	1	0.882	0.939	29.573	0.107	0.107	0.000	0.000	0.000	0.000
72	A	85	LEU	0	0.030	0.020	31.119	0.005	0.005	0.000	0.000	0.000	0.000
73	A	86	GLN	0	-0.057	-0.025	35.077	0.001	0.001	0.000	0.000	0.000	0.000
74	A	87	ALA	0	-0.058	-0.023	37.643	0.004	0.004	0.000	0.000	0.000	0.000
75	A	88	ALA	0	0.007	0.010	37.606	0.003	0.003	0.000	0.000	0.000	0.000
76	A	89	GLY	0	0.024	0.025	39.557	0.003	0.003	0.000	0.000	0.000	0.000
77	A	90	LEU	0	-0.013	0.010	36.334	0.002	0.002	0.000	0.000	0.000	0.000
78	A	91	VAL	0	0.002	-0.004	33.553	0.000	0.000	0.000	0.000	0.000	0.000
79	A	92	THR	0	-0.038	-0.014	36.969	0.002	0.002	0.000	0.000	0.000	0.000
80	A	93	ARG	1	0.950	0.968	31.211	0.094	0.094	0.000	0.000	0.000	0.000
81	A	94	THR	0	0.033	0.024	36.501	0.003	0.003	0.000	0.000	0.000	0.000
82	A	95	ARG	1	0.996	1.008	36.484	0.065	0.065	0.000	0.000	0.000	0.000
83	A	103	VAL	0	-0.013	-0.018	31.865	0.000	0.000	0.000	0.000	0.000	0.000
84	A	104	ILE	0	-0.001	0.000	31.590	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	105	ILE	0	-0.038	-0.026	30.841	0.002	0.002	0.000	0.000	0.000	0.000
86	A	106	ALA	0	0.065	0.037	33.652	0.000	0.000	0.000	0.000	0.000	0.000
87	A	107	LEU	0	-0.024	-0.009	34.316	0.000	0.000	0.000	0.000	0.000	0.000
88	A	108	THR	0	-0.034	-0.043	37.300	0.003	0.003	0.000	0.000	0.000	0.000
89	A	109	GLU	-1	-0.896	-0.960	40.454	-0.039	-0.039	0.000	0.000	0.000	0.000
90	A	110	THR	0	0.001	-0.003	41.633	0.001	0.001	0.000	0.000	0.000	0.000
91	A	111	GLY	0	0.039	0.016	38.021	0.000	0.000	0.000	0.000	0.000	0.000
92	A	112	ARG	1	0.843	0.916	37.471	0.051	0.051	0.000	0.000	0.000	0.000
93	A	113	ALA	0	0.016	0.011	39.232	0.001	0.001	0.000	0.000	0.000	0.000
94	A	114	LEU	0	-0.044	-0.016	36.303	0.002	0.002	0.000	0.000	0.000	0.000
95	A	115	ARG	1	0.852	0.918	34.097	0.047	0.047	0.000	0.000	0.000	0.000
96	A	116	SER	0	-0.031	-0.029	36.799	0.001	0.001	0.000	0.000	0.000	0.000
97	A	117	LYS	1	0.937	0.966	38.911	0.043	0.043	0.000	0.000	0.000	0.000
98	A	118	ALA	0	-0.005	0.003	33.489	0.000	0.000	0.000	0.000	0.000	0.000
99	A	119	GLY	0	-0.004	0.010	34.458	0.000	0.000	0.000	0.000	0.000	0.000
100	A	120	ALA	0	0.000	-0.006	36.741	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	121	VAL	0	-0.002	-0.015	32.445	0.000	0.000	0.000	0.000	0.000	0.000
102	A	122	PRO	0	0.014	0.027	31.674	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	123	GLU	-1	-0.731	-0.876	28.601	-0.056	-0.056	0.000	0.000	0.000	0.000
104	A	124	GLN	0	-0.057	-0.023	27.297	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	125	VAL	0	-0.013	-0.005	27.220	0.001	0.001	0.000	0.000	0.000	0.000
106	A	126	PHE	0	0.012	0.026	22.824	0.000	0.000	0.000	0.000	0.000	0.000
107	A	127	CYS	0	0.028	0.009	20.296	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	128	ALA	0	0.035	0.024	22.585	0.004	0.004	0.000	0.000	0.000	0.000
109	A	129	SER	0	-0.046	-0.015	24.789	0.006	0.006	0.000	0.000	0.000	0.000
110	A	130	ALA	0	0.033	0.004	21.701	0.004	0.004	0.000	0.000	0.000	0.000
111	A	131	SER	0	-0.063	-0.041	20.638	0.002	0.002	0.000	0.000	0.000	0.000
112	A	132	SER	0	-0.003	-0.002	20.846	0.011	0.011	0.000	0.000	0.000	0.000
113	A	133	LEU	0	-0.025	0.002	20.662	0.005	0.005	0.000	0.000	0.000	0.000
114	A	134	ASP	-1	-0.784	-0.876	20.179	0.017	0.017	0.000	0.000	0.000	0.000
115	A	135	GLU	-1	-0.848	-0.942	18.685	-0.043	-0.043	0.000	0.000	0.000	0.000
116	A	136	LEU	0	-0.034	-0.008	14.983	-0.016	-0.016	0.000	0.000	0.000	0.000
117	A	137	ARG	1	0.840	0.909	15.187	-0.033	-0.033	0.000	0.000	0.000	0.000
118	A	138	GLN	0	0.012	0.000	15.346	0.010	0.010	0.000	0.000	0.000	0.000
119	A	139	LEU	0	-0.004	0.003	10.478	0.024	0.024	0.000	0.000	0.000	0.000
120	A	140	LYS	1	0.858	0.914	10.708	-0.142	-0.142	0.000	0.000	0.000	0.000
121	A	141	GLN	0	0.021	-0.022	10.926	0.034	0.034	0.000	0.000	0.000	0.000
122	A	142	GLU	-1	-0.858	-0.904	10.106	0.230	0.230	0.000	0.000	0.000	0.000
123	A	143	LEU	0	-0.001	0.005	4.448	0.058	0.118	-0.001	-0.004	-0.055	0.000
124	A	144	GLU	-1	-0.850	-0.895	6.829	0.576	0.576	0.000	0.000	0.000	0.000
125	A	145	LYS	1	0.836	0.892	9.583	-0.038	-0.038	0.000	0.000	0.000	0.000
126	A	146	LEU	0	0.022	0.033	5.017	0.025	0.025	0.000	0.000	0.000	0.000
127	A	147	ARG	1	0.924	0.979	6.000	-0.559	-0.559	0.000	0.000	0.000	0.000
128	A	148	SER	0	-0.062	-0.037	6.849	-0.057	-0.057	0.000	0.000	0.000	0.000
129	A	149	SER	0	-0.087	-0.054	7.876	-0.150	-0.150	0.000	0.000	0.000	0.000

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