FMO DATABASE

FMODB ID: YV1J2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-744793.992874
FMO2-HF: Nuclear repulsion	705035.856636
FMO2-HF: Total energy	-39758.136238
FMO2-MP2: Total energy	-39876.450314

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.
-0.554	1.85	-0.013	-1.368	-1.023	0.005

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 : 0.032 / q_NPA : 0.017

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	0.024	0.007	3.884	-0.906	1.498	-0.013	-1.368	-1.023	0.005
4	A	8	GLY	0	0.022	0.027	5.802	0.236	0.236	0.000	0.000	0.000	0.000
5	A	9	ILE	0	-0.035	-0.028	7.628	0.222	0.222	0.000	0.000	0.000	0.000
6	A	10	GLU	-1	-0.849	-0.920	10.909	-0.425	-0.425	0.000	0.000	0.000	0.000
7	A	11	ASP	-1	-0.845	-0.926	8.633	-0.674	-0.674	0.000	0.000	0.000	0.000
8	A	12	PHE	0	0.002	-0.003	10.849	0.106	0.106	0.000	0.000	0.000	0.000
9	A	13	LEU	0	0.000	-0.002	12.316	0.044	0.044	0.000	0.000	0.000	0.000
10	A	14	LYS	1	0.752	0.872	11.574	0.518	0.518	0.000	0.000	0.000	0.000
11	A	15	VAL	0	-0.022	0.003	11.996	0.034	0.034	0.000	0.000	0.000	0.000
12	A	16	ASP	-1	-0.793	-0.866	15.201	0.013	0.013	0.000	0.000	0.000	0.000
13	A	17	LEU	0	-0.014	-0.008	14.924	0.022	0.022	0.000	0.000	0.000	0.000
14	A	18	ARG	1	0.744	0.829	18.980	-0.035	-0.035	0.000	0.000	0.000	0.000
15	A	19	VAL	0	-0.009	0.007	22.731	0.016	0.016	0.000	0.000	0.000	0.000
16	A	20	ALA	0	0.012	0.004	25.178	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	21	LYS	1	0.778	0.873	28.008	-0.048	-0.048	0.000	0.000	0.000	0.000
18	A	22	VAL	0	0.002	0.020	30.068	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	23	LEU	0	-0.004	0.012	32.296	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	24	SER	0	-0.046	-0.033	35.009	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	25	ALA	0	0.058	0.025	34.477	0.005	0.005	0.000	0.000	0.000	0.000
22	A	26	GLU	-1	-0.821	-0.904	35.327	0.063	0.063	0.000	0.000	0.000	0.000
23	A	27	ARG	1	0.846	0.904	36.256	-0.065	-0.065	0.000	0.000	0.000	0.000
24	A	28	VAL	0	0.006	0.002	36.129	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	29	GLU	-1	-0.896	-0.955	38.973	0.059	0.059	0.000	0.000	0.000	0.000
26	A	30	GLY	0	-0.002	0.013	40.718	0.001	0.001	0.000	0.000	0.000	0.000
27	A	31	SER	0	-0.051	-0.029	35.633	0.003	0.003	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.768	-0.880	33.883	0.121	0.121	0.000	0.000	0.000	0.000
29	A	33	LYS	1	0.900	0.946	27.065	-0.178	-0.178	0.000	0.000	0.000	0.000
30	A	34	LEU	0	0.005	0.019	31.062	0.003	0.003	0.000	0.000	0.000	0.000
31	A	35	LEU	0	0.025	0.028	30.836	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.766	0.858	30.756	-0.063	-0.063	0.000	0.000	0.000	0.000
33	A	37	LEU	0	-0.016	0.003	28.485	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	38	THR	0	0.076	0.044	30.756	0.002	0.002	0.000	0.000	0.000	0.000
35	A	39	LEU	0	-0.029	-0.019	26.460	0.002	0.002	0.000	0.000	0.000	0.000
36	A	40	SER	0	0.060	0.012	30.579	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	41	LEU	0	-0.037	-0.052	25.484	0.006	0.006	0.000	0.000	0.000	0.000
38	A	42	GLY	0	-0.031	-0.016	29.323	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	43	ASP	-1	-0.900	-0.955	31.968	0.010	0.010	0.000	0.000	0.000	0.000
40	A	44	GLU	-1	-0.856	-0.891	28.052	0.021	0.021	0.000	0.000	0.000	0.000
41	A	45	GLU	-1	-0.895	-0.949	31.987	0.043	0.043	0.000	0.000	0.000	0.000
42	A	46	ARG	1	0.715	0.832	24.263	-0.045	-0.045	0.000	0.000	0.000	0.000
43	A	47	THR	0	0.001	-0.015	30.254	0.003	0.003	0.000	0.000	0.000	0.000
44	A	48	VAL	0	-0.048	-0.033	24.344	0.003	0.003	0.000	0.000	0.000	0.000
45	A	49	VAL	0	-0.019	-0.002	27.644	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	50	ALA	0	0.029	0.023	26.212	0.016	0.016	0.000	0.000	0.000	0.000
47	A	51	GLY	0	-0.023	-0.012	26.372	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	52	ILE	0	-0.021	-0.020	26.212	0.010	0.010	0.000	0.000	0.000	0.000
49	A	53	ALA	0	0.008	0.001	27.838	-0.014	-0.014	0.000	0.000	0.000	0.000
50	A	54	LYS	1	0.793	0.862	29.794	-0.120	-0.120	0.000	0.000	0.000	0.000
51	A	55	TYR	0	0.017	0.016	27.384	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	56	TYR	0	0.013	0.008	27.259	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	57	THR	0	-0.032	-0.022	32.071	0.001	0.001	0.000	0.000	0.000	0.000
54	A	58	PRO	0	0.011	-0.015	34.655	0.002	0.002	0.000	0.000	0.000	0.000
55	A	59	GLU	-1	-0.861	-0.922	35.982	0.078	0.078	0.000	0.000	0.000	0.000
56	A	60	GLU	-1	-0.814	-0.874	33.224	0.095	0.095	0.000	0.000	0.000	0.000
57	A	61	LEU	0	-0.033	-0.030	29.776	0.004	0.004	0.000	0.000	0.000	0.000
58	A	62	VAL	0	-0.004	0.008	32.733	0.000	0.000	0.000	0.000	0.000	0.000
59	A	63	GLY	0	-0.018	-0.005	34.886	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	64	LYS	1	0.757	0.869	29.111	-0.107	-0.107	0.000	0.000	0.000	0.000
61	A	65	LYS	1	0.851	0.911	28.971	-0.063	-0.063	0.000	0.000	0.000	0.000
62	A	66	ILE	0	0.052	0.022	24.162	0.004	0.004	0.000	0.000	0.000	0.000
63	A	67	VAL	0	0.024	0.020	19.837	-0.015	-0.015	0.000	0.000	0.000	0.000
64	A	68	ILE	0	-0.020	-0.016	21.094	0.022	0.022	0.000	0.000	0.000	0.000
65	A	69	VAL	0	-0.001	0.002	16.161	-0.015	-0.015	0.000	0.000	0.000	0.000
66	A	70	ALA	0	0.021	0.015	19.080	0.001	0.001	0.000	0.000	0.000	0.000
67	A	71	ASN	0	-0.025	-0.025	17.107	0.021	0.021	0.000	0.000	0.000	0.000
68	A	72	LEU	0	-0.018	0.011	15.110	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	73	LYN	0	0.064	0.038	18.821	0.006	0.006	0.000	0.000	0.000	0.000
70	A	74	PRO	0	0.033	0.028	21.956	0.002	0.002	0.000	0.000	0.000	0.000
71	A	75	ARG	1	0.976	0.965	25.325	-0.044	-0.044	0.000	0.000	0.000	0.000
72	A	76	LYS	1	0.888	0.933	19.973	-0.185	-0.185	0.000	0.000	0.000	0.000
73	A	77	ILE	0	0.002	-0.005	23.231	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	78	PHE	0	-0.019	-0.010	23.383	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	79	GLY	0	0.027	0.021	28.369	0.000	0.000	0.000	0.000	0.000	0.000
76	A	80	ILE	0	-0.022	-0.011	26.654	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	81	GLU	-1	-0.790	-0.864	28.093	0.070	0.070	0.000	0.000	0.000	0.000
78	A	82	SER	0	0.001	-0.020	23.409	0.015	0.015	0.000	0.000	0.000	0.000
79	A	83	GLN	0	-0.027	0.020	24.647	0.000	0.000	0.000	0.000	0.000	0.000
80	A	84	GLY	0	0.074	0.039	21.851	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	85	MET	0	-0.028	-0.007	18.091	0.004	0.004	0.000	0.000	0.000	0.000
82	A	86	ILE	0	0.052	0.025	20.088	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	87	LEU	0	-0.012	-0.003	16.348	0.028	0.028	0.000	0.000	0.000	0.000
84	A	88	ALA	0	-0.018	-0.010	19.468	-0.017	-0.017	0.000	0.000	0.000	0.000
85	A	89	ALA	0	-0.020	-0.011	18.337	0.042	0.042	0.000	0.000	0.000	0.000
86	A	90	SER	0	-0.044	-0.026	17.328	-0.014	-0.014	0.000	0.000	0.000	0.000
87	A	91	ASP	-1	-0.835	-0.891	18.413	0.309	0.309	0.000	0.000	0.000	0.000
88	A	92	GLY	0	-0.050	-0.037	20.849	0.016	0.016	0.000	0.000	0.000	0.000
89	A	93	GLU	-1	-0.959	-0.981	21.798	0.201	0.201	0.000	0.000	0.000	0.000
90	A	94	ASN	0	-0.029	0.002	24.659	-0.017	-0.017	0.000	0.000	0.000	0.000
91	A	95	LEU	0	-0.010	-0.012	22.633	0.023	0.023	0.000	0.000	0.000	0.000
92	A	96	SER	0	0.015	-0.007	22.515	-0.021	-0.021	0.000	0.000	0.000	0.000
93	A	97	VAL	0	-0.005	-0.013	22.940	0.015	0.015	0.000	0.000	0.000	0.000
94	A	98	ILE	0	0.001	0.011	17.851	-0.013	-0.013	0.000	0.000	0.000	0.000
95	A	99	VAL	0	-0.009	-0.014	22.297	-0.014	-0.014	0.000	0.000	0.000	0.000
96	A	100	PRO	0	-0.033	0.000	24.540	0.005	0.005	0.000	0.000	0.000	0.000
97	A	101	ASP	-1	-0.868	-0.937	25.020	0.102	0.102	0.000	0.000	0.000	0.000
98	A	102	ARG	1	0.886	0.932	27.725	-0.073	-0.073	0.000	0.000	0.000	0.000
99	A	103	ASP	-1	-0.835	-0.906	29.572	0.059	0.059	0.000	0.000	0.000	0.000
100	A	104	VAL	0	-0.026	-0.004	26.437	-0.007	-0.007	0.000	0.000	0.000	0.000
101	A	105	LYS	1	0.948	0.965	29.692	-0.015	-0.015	0.000	0.000	0.000	0.000
102	A	106	GLU	-1	-0.785	-0.866	29.129	0.046	0.046	0.000	0.000	0.000	0.000
103	A	107	GLY	0	0.014	0.018	27.408	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	108	ALA	0	-0.065	-0.040	25.963	-0.008	-0.008	0.000	0.000	0.000	0.000
105	A	109	LYS	1	0.994	0.996	22.439	0.031	0.031	0.000	0.000	0.000	0.000
106	A	110	LEU	0	-0.009	0.000	18.444	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	111	SER	0	-0.017	0.001	17.030	-0.024	-0.024	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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