FMO DATABASE

FMODB ID: 4J65N

Calculation Name: 1PYB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PYB

Chain ID: A

ChEMBL ID:

UniProt ID: O66738

Base Structure: X-ray

Registration Date: 2023-09-23

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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-743391.026498
FMO2-HF: Nuclear repulsion	703634.318267
FMO2-HF: Total energy	-39756.708231
FMO2-MP2: Total energy	-39875.067426

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:5:ALA)

Summations of interaction energy for fragment #1(A:5:ALA)

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.
-1.101	1.791	-0.022	-1.639	-1.232	0.007

Interaction energy analysis for fragmet #1(A:5:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.016

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	7	ILE	0	0.021	0.008	3.794	-1.197	1.695	-0.022	-1.639	-1.232	0.007
4	A	8	GLY	0	0.030	0.026	5.407	0.215	0.215	0.000	0.000	0.000	0.000
5	A	9	ILE	0	-0.018	-0.019	7.175	0.239	0.239	0.000	0.000	0.000	0.000
6	A	10	GLU	-1	-0.919	-0.977	10.567	-0.495	-0.495	0.000	0.000	0.000	0.000
7	A	11	ASP	-1	-0.933	-0.972	8.536	-0.854	-0.854	0.000	0.000	0.000	0.000
8	A	12	PHE	0	-0.006	-0.002	10.453	0.128	0.128	0.000	0.000	0.000	0.000
9	A	13	LEU	0	-0.030	-0.014	11.756	0.055	0.055	0.000	0.000	0.000	0.000
10	A	14	LYS	1	0.929	0.979	12.173	0.512	0.512	0.000	0.000	0.000	0.000
11	A	15	VAL	0	-0.031	0.005	11.685	0.043	0.043	0.000	0.000	0.000	0.000
12	A	16	ASP	-1	-0.891	-0.950	14.931	-0.055	-0.055	0.000	0.000	0.000	0.000
13	A	17	LEU	0	-0.037	-0.010	14.942	0.027	0.027	0.000	0.000	0.000	0.000
14	A	18	ARG	1	0.958	0.965	19.099	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	19	VAL	0	-0.004	0.010	22.739	0.015	0.015	0.000	0.000	0.000	0.000
16	A	20	ALA	0	0.019	-0.007	24.808	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	21	LYS	1	0.856	0.949	27.980	-0.030	-0.030	0.000	0.000	0.000	0.000
18	A	22	VAL	0	0.002	0.017	29.800	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	23	LEU	0	0.039	0.025	32.126	0.000	0.000	0.000	0.000	0.000	0.000
20	A	24	SER	0	-0.004	-0.012	34.940	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	25	ALA	0	-0.009	-0.009	34.457	0.004	0.004	0.000	0.000	0.000	0.000
22	A	26	GLU	-1	-0.949	-0.969	35.377	0.052	0.052	0.000	0.000	0.000	0.000
23	A	27	ARG	1	0.935	0.952	35.942	-0.059	-0.059	0.000	0.000	0.000	0.000
24	A	28	VAL	0	-0.011	-0.002	35.831	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	29	GLU	-1	-0.906	-0.962	38.688	0.054	0.054	0.000	0.000	0.000	0.000
26	A	30	GLY	0	0.003	0.010	40.331	0.001	0.001	0.000	0.000	0.000	0.000
27	A	31	SER	0	-0.055	-0.025	35.124	0.003	0.003	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.891	-0.967	33.511	0.118	0.118	0.000	0.000	0.000	0.000
29	A	33	LYS	1	0.907	0.962	26.912	-0.169	-0.169	0.000	0.000	0.000	0.000
30	A	34	LEU	0	-0.026	0.008	31.050	0.000	0.000	0.000	0.000	0.000	0.000
31	A	35	LEU	0	0.022	0.012	30.079	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.930	0.989	30.546	-0.060	-0.060	0.000	0.000	0.000	0.000
33	A	37	LEU	0	0.000	-0.001	27.943	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	38	THR	0	0.063	0.024	30.530	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	39	LEU	0	-0.025	-0.008	25.975	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	40	SER	0	0.074	0.030	30.187	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	41	LEU	0	-0.074	-0.047	25.555	0.001	0.001	0.000	0.000	0.000	0.000
38	A	42	GLY	0	-0.026	-0.029	29.358	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	43	ASP	-1	-0.918	-0.949	32.002	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	44	GLU	-1	-0.996	-0.995	28.378	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	45	GLU	-1	-0.933	-0.965	31.902	0.029	0.029	0.000	0.000	0.000	0.000
42	A	46	ARG	1	0.826	0.919	24.356	-0.021	-0.021	0.000	0.000	0.000	0.000
43	A	47	THR	0	0.034	0.021	30.300	0.005	0.005	0.000	0.000	0.000	0.000
44	A	48	VAL	0	-0.025	-0.016	24.466	0.002	0.002	0.000	0.000	0.000	0.000
45	A	49	VAL	0	-0.034	-0.007	27.698	0.000	0.000	0.000	0.000	0.000	0.000
46	A	50	ALA	0	-0.029	-0.008	26.177	0.013	0.013	0.000	0.000	0.000	0.000
47	A	51	GLY	0	-0.024	-0.037	25.901	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	52	ILE	0	-0.007	-0.006	26.239	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	53	ALA	0	0.044	0.006	27.837	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	54	LYS	1	0.931	0.975	29.996	-0.108	-0.108	0.000	0.000	0.000	0.000
51	A	55	TYR	0	0.022	0.022	27.377	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	56	TYR	0	0.016	-0.004	26.878	0.000	0.000	0.000	0.000	0.000	0.000
53	A	57	THR	0	0.034	0.024	31.839	0.000	0.000	0.000	0.000	0.000	0.000
54	A	58	PRO	0	0.012	-0.018	34.594	0.001	0.001	0.000	0.000	0.000	0.000
55	A	59	GLU	-1	-0.940	-0.982	35.674	0.066	0.066	0.000	0.000	0.000	0.000
56	A	60	GLU	-1	-0.926	-0.947	33.181	0.081	0.081	0.000	0.000	0.000	0.000
57	A	61	LEU	0	-0.056	-0.037	29.999	0.001	0.001	0.000	0.000	0.000	0.000
58	A	62	VAL	0	-0.021	0.011	32.886	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	63	GLY	0	0.030	0.024	34.425	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	64	LYS	1	0.858	0.942	28.184	-0.105	-0.105	0.000	0.000	0.000	0.000
61	A	65	LYS	1	0.848	0.924	28.453	-0.052	-0.052	0.000	0.000	0.000	0.000
62	A	66	ILE	0	0.060	0.028	23.501	0.007	0.007	0.000	0.000	0.000	0.000
63	A	67	VAL	0	0.021	0.016	19.117	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	68	ILE	0	-0.011	-0.014	20.926	0.024	0.024	0.000	0.000	0.000	0.000
65	A	69	VAL	0	-0.001	0.004	16.259	-0.017	-0.017	0.000	0.000	0.000	0.000
66	A	70	ALA	0	0.018	0.005	19.119	0.001	0.001	0.000	0.000	0.000	0.000
67	A	71	ASN	0	-0.059	-0.041	17.234	0.027	0.027	0.000	0.000	0.000	0.000
68	A	72	LEU	0	0.001	0.017	15.577	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	73	LYN	0	0.038	0.013	18.745	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	74	PRO	0	0.012	0.023	21.808	0.005	0.005	0.000	0.000	0.000	0.000
71	A	75	ARG	1	1.022	0.980	25.243	-0.026	-0.026	0.000	0.000	0.000	0.000
72	A	76	LYS	1	0.920	0.979	20.364	-0.159	-0.159	0.000	0.000	0.000	0.000
73	A	77	ILE	0	0.027	-0.003	23.257	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	78	PHE	0	-0.029	-0.014	23.696	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	79	GLY	0	0.024	0.025	28.277	0.002	0.002	0.000	0.000	0.000	0.000
76	A	80	ILE	0	-0.039	-0.027	26.409	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	81	GLU	-1	-0.873	-0.950	28.023	0.058	0.058	0.000	0.000	0.000	0.000
78	A	82	SER	0	-0.009	-0.011	23.979	0.009	0.009	0.000	0.000	0.000	0.000
79	A	83	GLN	0	-0.020	0.017	25.054	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	84	GLY	0	0.075	0.029	21.772	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	85	MET	0	-0.057	-0.031	18.022	0.005	0.005	0.000	0.000	0.000	0.000
82	A	86	ILE	0	0.028	0.012	19.889	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	87	LEU	0	-0.029	-0.012	15.980	0.025	0.025	0.000	0.000	0.000	0.000
84	A	88	ALA	0	-0.018	-0.014	19.143	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	89	ALA	0	0.010	0.007	18.112	0.042	0.042	0.000	0.000	0.000	0.000
86	A	90	SER	0	-0.046	-0.022	17.219	-0.024	-0.024	0.000	0.000	0.000	0.000
87	A	91	ASP	-1	-0.857	-0.921	18.474	0.314	0.314	0.000	0.000	0.000	0.000
88	A	92	GLY	0	-0.048	-0.030	20.679	0.012	0.012	0.000	0.000	0.000	0.000
89	A	93	GLU	-1	-0.958	-0.990	21.884	0.202	0.202	0.000	0.000	0.000	0.000
90	A	94	ASN	0	-0.027	0.007	24.518	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	95	LEU	0	-0.009	-0.003	22.318	0.019	0.019	0.000	0.000	0.000	0.000
92	A	96	SER	0	0.040	0.016	22.103	-0.025	-0.025	0.000	0.000	0.000	0.000
93	A	97	VAL	0	-0.016	-0.021	22.573	0.014	0.014	0.000	0.000	0.000	0.000
94	A	98	ILE	0	0.007	0.012	17.704	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	99	VAL	0	-0.029	-0.033	22.199	-0.015	-0.015	0.000	0.000	0.000	0.000
96	A	100	PRO	0	-0.070	-0.014	24.169	0.004	0.004	0.000	0.000	0.000	0.000
97	A	101	ASP	-1	-0.852	-0.928	24.675	0.097	0.097	0.000	0.000	0.000	0.000
98	A	102	ARG	1	0.916	0.956	27.274	-0.060	-0.060	0.000	0.000	0.000	0.000
99	A	103	ASP	-1	-0.902	-0.963	29.171	0.048	0.048	0.000	0.000	0.000	0.000
100	A	104	VAL	0	0.026	0.022	26.087	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	105	LYS	1	0.914	0.935	29.360	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	106	GLU	-1	-0.842	-0.924	28.741	0.030	0.030	0.000	0.000	0.000	0.000
103	A	107	GLY	0	0.030	0.020	27.336	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	108	ALA	0	-0.046	-0.033	24.686	-0.010	-0.010	0.000	0.000	0.000	0.000
105	A	109	LYS	1	0.945	0.978	22.618	0.050	0.050	0.000	0.000	0.000	0.000
106	A	110	LEU	0	-0.012	0.004	17.578	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	111	SER	0	0.018	0.017	16.497	-0.025	-0.025	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ALA)