FMO DATABASE

FMODB ID: Z63MN

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	OptHSide
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	-1050801.049458
FMO2-HF: Nuclear repulsion	1000147.270464
FMO2-HF: Total energy	-50653.778995
FMO2-MP2: Total energy	-50801.952841

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.
0.162	2.014	-0.018	-0.785	-1.05	0.002

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 : -0.007 / 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	-0.028	-0.022	3.827	-0.070	1.638	-0.016	-0.772	-0.921	0.002
4	A	17	LEU	0	0.025	0.007	5.958	-0.012	-0.012	0.000	0.000	0.000	0.000
5	A	18	ASP	-1	-0.818	-0.904	8.995	0.009	0.009	0.000	0.000	0.000	0.000
6	A	19	ASN	0	-0.031	-0.015	9.968	-0.154	-0.154	0.000	0.000	0.000	0.000
7	A	20	GLN	0	0.025	0.005	11.403	-0.071	-0.071	0.000	0.000	0.000	0.000
8	A	21	LEU	0	0.019	0.016	5.789	0.001	0.001	0.000	0.000	0.000	0.000
9	A	22	CYS	0	-0.004	-0.008	9.808	-0.079	-0.079	0.000	0.000	0.000	0.000
10	A	23	PHE	0	-0.008	-0.004	11.807	0.022	0.022	0.000	0.000	0.000	0.000
11	A	24	ALA	0	0.026	0.011	12.280	0.015	0.015	0.000	0.000	0.000	0.000
12	A	25	LEU	0	0.004	0.010	10.903	0.023	0.023	0.000	0.000	0.000	0.000
13	A	26	TYR	0	-0.001	0.001	13.726	0.032	0.032	0.000	0.000	0.000	0.000
14	A	27	SER	0	0.030	0.006	17.056	0.026	0.026	0.000	0.000	0.000	0.000
15	A	28	ALA	0	0.027	0.015	15.893	0.019	0.019	0.000	0.000	0.000	0.000
16	A	29	ASN	0	0.003	0.000	17.537	0.028	0.028	0.000	0.000	0.000	0.000
17	A	30	LEU	0	0.011	0.007	19.160	0.021	0.021	0.000	0.000	0.000	0.000
18	A	31	ALA	0	0.019	0.007	21.189	0.014	0.014	0.000	0.000	0.000	0.000
19	A	32	MET	0	0.016	0.012	20.070	0.015	0.015	0.000	0.000	0.000	0.000
20	A	33	HIS	0	-0.069	-0.043	22.401	0.018	0.018	0.000	0.000	0.000	0.000
21	A	34	LYS	1	0.863	0.926	25.456	0.097	0.097	0.000	0.000	0.000	0.000
22	A	35	LEU	0	-0.008	0.018	25.270	0.007	0.007	0.000	0.000	0.000	0.000
23	A	36	TYR	0	0.020	-0.013	26.233	0.006	0.006	0.000	0.000	0.000	0.000
24	A	37	ARG	1	0.913	0.969	27.813	0.093	0.093	0.000	0.000	0.000	0.000
25	A	38	GLY	0	0.006	0.001	31.199	0.002	0.002	0.000	0.000	0.000	0.000
26	A	39	LEU	0	0.056	0.024	31.823	0.002	0.002	0.000	0.000	0.000	0.000
27	A	40	LEU	0	-0.018	-0.006	28.600	0.000	0.000	0.000	0.000	0.000	0.000
28	A	41	LYS	1	0.939	0.969	33.258	0.062	0.062	0.000	0.000	0.000	0.000
29	A	42	ALA	0	-0.023	-0.005	36.247	0.002	0.002	0.000	0.000	0.000	0.000
30	A	43	LEU	0	-0.055	-0.031	33.598	0.002	0.002	0.000	0.000	0.000	0.000
31	A	44	ASP	-1	-0.936	-0.947	37.081	-0.065	-0.065	0.000	0.000	0.000	0.000
32	A	45	LEU	0	-0.039	-0.010	32.293	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	46	THR	0	-0.029	-0.048	29.680	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	47	TYR	0	0.078	0.015	21.987	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	48	PRO	0	0.034	0.003	24.555	0.000	0.000	0.000	0.000	0.000	0.000
36	A	49	GLN	0	0.018	0.028	25.898	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	50	TYR	0	0.057	0.027	27.677	0.005	0.005	0.000	0.000	0.000	0.000
38	A	51	LEU	0	0.017	0.016	21.862	0.002	0.002	0.000	0.000	0.000	0.000
39	A	52	VAL	0	0.006	0.002	25.840	0.001	0.001	0.000	0.000	0.000	0.000
40	A	53	MET	0	-0.032	-0.008	27.452	0.004	0.004	0.000	0.000	0.000	0.000
41	A	54	LEU	0	-0.020	0.004	26.078	0.005	0.005	0.000	0.000	0.000	0.000
42	A	55	VAL	0	0.018	0.009	24.391	0.004	0.004	0.000	0.000	0.000	0.000
43	A	56	LEU	0	-0.025	-0.021	27.341	0.005	0.005	0.000	0.000	0.000	0.000
44	A	57	TRP	0	-0.062	-0.051	30.917	0.005	0.005	0.000	0.000	0.000	0.000
45	A	58	GLU	-1	-0.847	-0.866	25.318	-0.102	-0.102	0.000	0.000	0.000	0.000
46	A	59	THR	0	-0.054	-0.021	28.584	0.003	0.003	0.000	0.000	0.000	0.000
47	A	60	ASP	-1	-0.691	-0.841	30.761	-0.072	-0.072	0.000	0.000	0.000	0.000
48	A	61	GLU	-1	-0.992	-0.999	33.053	-0.059	-0.059	0.000	0.000	0.000	0.000
49	A	62	ARG	1	0.828	0.919	28.278	0.086	0.086	0.000	0.000	0.000	0.000
50	A	63	SER	0	-0.015	-0.047	28.338	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	64	VAL	0	-0.021	-0.040	26.549	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	65	SER	0	-0.050	-0.024	23.804	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	66	GLU	-1	-0.738	-0.819	23.425	-0.105	-0.105	0.000	0.000	0.000	0.000
54	A	67	ILE	0	-0.027	-0.016	23.508	-0.008	-0.008	0.000	0.000	0.000	0.000
55	A	68	GLY	0	0.004	-0.004	22.002	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	69	GLU	-1	-0.883	-0.945	19.138	-0.171	-0.171	0.000	0.000	0.000	0.000
57	A	70	ARG	1	0.769	0.864	18.559	0.111	0.111	0.000	0.000	0.000	0.000
58	A	71	LEU	0	-0.041	-0.029	19.535	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	72	TYR	0	-0.029	0.000	14.774	-0.025	-0.025	0.000	0.000	0.000	0.000
60	A	73	LEU	0	-0.056	-0.017	16.609	-0.021	-0.021	0.000	0.000	0.000	0.000
61	A	74	ASP	-1	-0.768	-0.869	19.110	-0.207	-0.207	0.000	0.000	0.000	0.000
62	A	75	SER	0	0.050	-0.004	20.665	0.015	0.015	0.000	0.000	0.000	0.000
63	A	76	ALA	0	-0.044	-0.014	23.514	0.015	0.015	0.000	0.000	0.000	0.000
64	A	77	THR	0	-0.021	-0.013	21.157	0.011	0.011	0.000	0.000	0.000	0.000
65	A	78	LEU	0	0.010	0.004	23.865	0.012	0.012	0.000	0.000	0.000	0.000
66	A	79	THR	0	-0.036	-0.029	25.723	0.015	0.015	0.000	0.000	0.000	0.000
67	A	80	PRO	0	0.011	-0.003	27.347	0.011	0.011	0.000	0.000	0.000	0.000
68	A	81	LEU	0	-0.006	-0.004	25.076	0.010	0.010	0.000	0.000	0.000	0.000
69	A	82	LEU	0	0.047	0.023	28.982	0.008	0.008	0.000	0.000	0.000	0.000
70	A	83	LYS	1	0.945	0.981	31.450	0.083	0.083	0.000	0.000	0.000	0.000
71	A	84	ARG	1	0.893	0.940	29.400	0.113	0.113	0.000	0.000	0.000	0.000
72	A	85	LEU	0	0.035	0.022	30.828	0.005	0.005	0.000	0.000	0.000	0.000
73	A	86	GLN	0	-0.046	-0.023	34.795	0.001	0.001	0.000	0.000	0.000	0.000
74	A	87	ALA	0	-0.069	-0.022	37.396	0.004	0.004	0.000	0.000	0.000	0.000
75	A	88	ALA	0	0.017	0.018	37.530	0.003	0.003	0.000	0.000	0.000	0.000
76	A	89	GLY	0	0.010	0.014	39.457	0.003	0.003	0.000	0.000	0.000	0.000
77	A	90	LEU	0	-0.019	0.005	36.113	0.002	0.002	0.000	0.000	0.000	0.000
78	A	91	VAL	0	0.019	0.004	33.473	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	92	THR	0	-0.037	-0.016	36.867	0.002	0.002	0.000	0.000	0.000	0.000
80	A	93	ARG	1	0.947	0.974	31.639	0.093	0.093	0.000	0.000	0.000	0.000
81	A	94	THR	0	0.020	0.005	36.572	0.002	0.002	0.000	0.000	0.000	0.000
82	A	95	ARG	1	1.031	1.022	36.441	0.065	0.065	0.000	0.000	0.000	0.000
83	A	103	VAL	0	-0.038	-0.021	31.654	0.000	0.000	0.000	0.000	0.000	0.000
84	A	104	ILE	0	-0.007	0.001	31.795	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	105	ILE	0	-0.039	-0.022	30.816	0.003	0.003	0.000	0.000	0.000	0.000
86	A	106	ALA	0	0.066	0.040	33.606	0.000	0.000	0.000	0.000	0.000	0.000
87	A	107	LEU	0	-0.020	-0.011	34.083	0.000	0.000	0.000	0.000	0.000	0.000
88	A	108	THR	0	-0.035	-0.030	37.066	0.003	0.003	0.000	0.000	0.000	0.000
89	A	109	GLU	-1	-0.886	-0.964	40.347	-0.043	-0.043	0.000	0.000	0.000	0.000
90	A	110	THR	0	0.004	-0.005	41.680	0.001	0.001	0.000	0.000	0.000	0.000
91	A	111	GLY	0	0.031	0.017	37.912	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	112	ARG	1	0.852	0.920	37.510	0.055	0.055	0.000	0.000	0.000	0.000
93	A	113	ALA	0	0.003	0.006	39.202	0.001	0.001	0.000	0.000	0.000	0.000
94	A	114	LEU	0	-0.023	-0.007	36.062	0.002	0.002	0.000	0.000	0.000	0.000
95	A	115	ARG	1	0.857	0.921	34.194	0.056	0.056	0.000	0.000	0.000	0.000
96	A	116	SER	0	-0.049	-0.030	36.875	0.001	0.001	0.000	0.000	0.000	0.000
97	A	117	LYS	1	0.936	0.965	38.939	0.049	0.049	0.000	0.000	0.000	0.000
98	A	118	ALA	0	-0.021	-0.004	33.712	0.000	0.000	0.000	0.000	0.000	0.000
99	A	119	GLY	0	0.005	0.013	34.527	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	120	ALA	0	-0.003	-0.006	36.754	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	121	VAL	0	0.003	-0.018	32.339	0.000	0.000	0.000	0.000	0.000	0.000
102	A	122	PRO	0	0.011	0.024	31.548	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	123	GLU	-1	-0.746	-0.879	28.618	-0.068	-0.068	0.000	0.000	0.000	0.000
104	A	124	GLN	0	-0.031	-0.013	27.493	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	125	VAL	0	-0.013	-0.001	27.605	0.000	0.000	0.000	0.000	0.000	0.000
106	A	126	PHE	0	0.017	0.024	22.605	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	127	CYS	0	0.026	0.008	20.199	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	128	ALA	0	0.032	0.025	22.494	0.001	0.001	0.000	0.000	0.000	0.000
109	A	129	SER	0	-0.046	-0.013	24.638	0.005	0.005	0.000	0.000	0.000	0.000
110	A	130	ALA	0	0.035	0.002	22.109	0.004	0.004	0.000	0.000	0.000	0.000
111	A	131	SER	0	-0.046	-0.030	20.678	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	132	SER	0	-0.014	-0.015	20.774	0.007	0.007	0.000	0.000	0.000	0.000
113	A	133	LEU	0	-0.032	0.007	20.589	0.006	0.006	0.000	0.000	0.000	0.000
114	A	134	ASP	-1	-0.778	-0.892	20.049	-0.020	-0.020	0.000	0.000	0.000	0.000
115	A	135	GLU	-1	-0.847	-0.943	18.530	-0.079	-0.079	0.000	0.000	0.000	0.000
116	A	136	LEU	0	-0.026	-0.006	14.955	-0.023	-0.023	0.000	0.000	0.000	0.000
117	A	137	ARG	1	0.851	0.921	15.049	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	138	GLN	0	0.015	0.003	15.059	0.010	0.010	0.000	0.000	0.000	0.000
119	A	139	LEU	0	-0.010	0.007	10.402	0.011	0.011	0.000	0.000	0.000	0.000
120	A	140	LYS	1	0.848	0.909	10.502	-0.079	-0.079	0.000	0.000	0.000	0.000
121	A	141	GLN	0	0.001	-0.018	10.739	0.028	0.028	0.000	0.000	0.000	0.000
122	A	142	GLU	-1	-0.833	-0.898	9.576	0.159	0.159	0.000	0.000	0.000	0.000
123	A	143	LEU	0	-0.018	-0.004	4.424	0.023	0.093	-0.001	-0.006	-0.063	0.000
124	A	144	GLU	-1	-0.844	-0.902	6.460	0.467	0.467	0.000	0.000	0.000	0.000
125	A	145	LYS	1	0.839	0.898	9.185	0.059	0.059	0.000	0.000	0.000	0.000
126	A	146	LEU	0	0.013	0.020	4.415	-0.047	0.027	-0.001	-0.007	-0.066	0.000
127	A	147	ARG	1	0.924	0.989	5.869	-0.277	-0.277	0.000	0.000	0.000	0.000
128	A	148	SER	0	-0.057	-0.031	6.713	-0.030	-0.030	0.000	0.000	0.000	0.000
129	A	149	SER	0	-0.091	-0.059	7.662	-0.048	-0.048	0.000	0.000	0.000	0.000

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