FMO DATABASE

FMODB ID: N9R6Q

Calculation Name: 5BYP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5BYP

Chain ID: A

ChEMBL ID:

UniProt ID:

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	121
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1100268.673567
FMO2-HF: Nuclear repulsion	1050411.786084
FMO2-HF: Total energy	-49856.887483
FMO2-MP2: Total energy	-50003.604804

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:30:ASP)

Summations of interaction energy for fragment #1(A:30:ASP)

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.
-106.65	-101.068	1.378	-2.978	-3.982	0.023

Interaction energy analysis for fragmet #1(A:30:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.847 / q_NPA : -0.929

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	32	VAL	0	-0.049	-0.011	3.176	-18.076	-14.253	0.132	-1.992	-1.963	0.013
4	A	33	GLY	0	0.043	0.023	5.135	-1.908	-1.889	-0.001	-0.009	-0.010	0.000
5	A	34	LYS	1	0.911	0.960	8.395	-19.212	-19.212	0.000	0.000	0.000	0.000
6	A	35	TRP	0	0.003	-0.013	4.901	-1.734	-1.659	-0.001	-0.038	-0.036	0.000
7	A	36	GLN	0	-0.004	0.024	11.686	-0.840	-0.840	0.000	0.000	0.000	0.000
8	A	37	LEU	0	0.027	0.010	14.847	0.895	0.895	0.000	0.000	0.000	0.000
9	A	38	ARG	1	0.738	0.847	15.839	-16.690	-16.690	0.000	0.000	0.000	0.000
10	A	39	GLU	-1	-0.888	-0.956	18.051	13.626	13.626	0.000	0.000	0.000	0.000
11	A	40	TYR	0	0.032	0.033	18.643	0.938	0.938	0.000	0.000	0.000	0.000
12	A	41	GLN	0	-0.065	-0.059	19.430	-0.259	-0.259	0.000	0.000	0.000	0.000
13	A	42	TYR	0	0.013	-0.003	21.731	0.401	0.401	0.000	0.000	0.000	0.000
14	A	43	PRO	0	0.041	0.019	24.152	-0.041	-0.041	0.000	0.000	0.000	0.000
15	A	44	ASP	-1	-0.921	-0.954	25.393	10.762	10.762	0.000	0.000	0.000	0.000
16	A	45	GLY	0	-0.001	0.008	26.333	-0.348	-0.348	0.000	0.000	0.000	0.000
17	A	46	LYS	1	0.853	0.933	26.981	-10.985	-10.985	0.000	0.000	0.000	0.000
18	A	47	VAL	0	0.038	0.018	22.860	0.487	0.487	0.000	0.000	0.000	0.000
19	A	48	GLN	0	-0.013	0.007	23.965	-0.889	-0.889	0.000	0.000	0.000	0.000
20	A	49	LYS	1	0.990	0.987	22.983	-11.039	-11.039	0.000	0.000	0.000	0.000
21	A	50	VAL	0	0.013	0.020	20.701	-0.481	-0.481	0.000	0.000	0.000	0.000
22	A	51	ASP	-1	-0.851	-0.922	21.124	12.840	12.840	0.000	0.000	0.000	0.000
23	A	52	SER	0	0.010	-0.015	20.961	0.640	0.640	0.000	0.000	0.000	0.000
24	A	53	ILE	0	0.044	0.047	18.233	0.210	0.210	0.000	0.000	0.000	0.000
25	A	54	PHE	0	-0.038	-0.025	15.239	0.722	0.722	0.000	0.000	0.000	0.000
26	A	55	TYR	0	0.056	0.023	12.953	-0.546	-0.546	0.000	0.000	0.000	0.000
27	A	56	GLY	0	-0.008	-0.011	10.768	0.361	0.361	0.000	0.000	0.000	0.000
28	A	57	PHE	0	0.013	0.018	7.279	-1.083	-1.083	0.000	0.000	0.000	0.000
29	A	58	GLN	0	-0.001	-0.016	7.833	4.530	4.530	0.000	0.000	0.000	0.000
30	A	59	LYS	1	0.952	0.967	7.390	-34.365	-34.365	0.000	0.000	0.000	0.000
31	A	60	GLY	0	0.102	0.062	8.636	-2.591	-2.591	0.000	0.000	0.000	0.000
32	A	61	SER	0	0.012	0.014	10.466	-2.490	-2.490	0.000	0.000	0.000	0.000
33	A	62	PHE	0	-0.019	-0.025	11.329	2.692	2.692	0.000	0.000	0.000	0.000
34	A	63	LEU	0	-0.013	-0.014	13.211	-1.960	-1.960	0.000	0.000	0.000	0.000
35	A	64	ALA	0	-0.001	0.004	14.814	1.251	1.251	0.000	0.000	0.000	0.000
36	A	65	TYR	0	0.018	-0.008	15.369	-0.257	-0.257	0.000	0.000	0.000	0.000
37	A	66	CYS	0	-0.001	0.008	19.959	0.398	0.398	0.000	0.000	0.000	0.000
38	A	67	MET	0	-0.038	-0.009	19.301	-0.728	-0.728	0.000	0.000	0.000	0.000
39	A	68	ASN	0	0.034	0.026	23.986	-0.331	-0.331	0.000	0.000	0.000	0.000
40	A	69	LYS	1	0.905	0.925	25.658	-11.709	-11.709	0.000	0.000	0.000	0.000
41	A	70	SER	0	-0.012	0.003	29.385	-0.040	-0.040	0.000	0.000	0.000	0.000
42	A	71	GLY	0	0.015	0.022	28.394	-0.230	-0.230	0.000	0.000	0.000	0.000
43	A	72	SER	0	-0.020	-0.009	27.525	0.157	0.157	0.000	0.000	0.000	0.000
44	A	73	TYR	0	-0.023	-0.029	21.696	0.380	0.380	0.000	0.000	0.000	0.000
45	A	74	GLU	-1	-0.802	-0.849	25.292	11.729	11.729	0.000	0.000	0.000	0.000
46	A	75	GLY	0	-0.017	-0.033	21.839	0.654	0.654	0.000	0.000	0.000	0.000
47	A	76	PHE	0	-0.002	0.013	19.980	-0.501	-0.501	0.000	0.000	0.000	0.000
48	A	77	TYR	0	0.011	-0.002	17.749	1.021	1.021	0.000	0.000	0.000	0.000
49	A	78	GLY	0	0.058	0.030	16.888	-0.878	-0.878	0.000	0.000	0.000	0.000
50	A	79	TYR	0	-0.005	0.008	14.005	1.255	1.255	0.000	0.000	0.000	0.000
51	A	80	TYR	0	-0.059	-0.018	5.808	-2.559	-2.559	0.000	0.000	0.000	0.000
52	A	81	LYS	1	0.835	0.913	11.094	-20.030	-20.030	0.000	0.000	0.000	0.000
53	A	82	LEU	0	-0.009	0.000	4.849	-0.708	-0.591	-0.001	-0.002	-0.114	0.000
54	A	83	LYS	1	0.871	0.933	9.292	-22.406	-22.406	0.000	0.000	0.000	0.000
55	A	84	ASP	-1	-0.900	-0.951	11.279	22.026	22.026	0.000	0.000	0.000	0.000
56	A	85	ASP	-1	-0.845	-0.918	9.579	27.455	27.455	0.000	0.000	0.000	0.000
57	A	86	GLU	-1	-0.878	-0.929	10.264	18.664	18.664	0.000	0.000	0.000	0.000
58	A	87	ILE	0	-0.031	-0.015	7.990	2.729	2.729	0.000	0.000	0.000	0.000
59	A	88	SER	0	0.006	-0.010	10.805	-1.661	-1.661	0.000	0.000	0.000	0.000
60	A	89	ILE	0	-0.062	-0.022	12.129	1.002	1.002	0.000	0.000	0.000	0.000
61	A	90	THR	0	0.026	0.021	14.531	-0.955	-0.955	0.000	0.000	0.000	0.000
62	A	91	LEU	0	-0.031	-0.009	17.483	0.755	0.755	0.000	0.000	0.000	0.000
63	A	92	TRP	0	-0.006	0.011	19.637	-0.124	-0.124	0.000	0.000	0.000	0.000
64	A	93	PRO	0	0.002	0.006	21.791	0.058	0.058	0.000	0.000	0.000	0.000
65	A	94	ASP	-1	-0.758	-0.853	22.216	13.576	13.576	0.000	0.000	0.000	0.000
66	A	95	ASN	0	0.002	-0.007	24.091	0.026	0.026	0.000	0.000	0.000	0.000
67	A	96	SER	0	-0.014	-0.014	26.242	-0.445	-0.445	0.000	0.000	0.000	0.000
68	A	97	SER	0	0.007	-0.021	28.088	-0.089	-0.089	0.000	0.000	0.000	0.000
69	A	98	GLY	0	-0.025	-0.006	30.608	-0.318	-0.318	0.000	0.000	0.000	0.000
70	A	99	ASN	0	-0.034	-0.040	25.389	-0.292	-0.292	0.000	0.000	0.000	0.000
71	A	100	GLU	-1	-0.885	-0.951	29.583	10.825	10.825	0.000	0.000	0.000	0.000
72	A	101	ALA	0	0.004	0.017	31.367	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	102	ALA	0	0.105	0.047	29.710	0.069	0.069	0.000	0.000	0.000	0.000
74	A	103	HIS	1	0.756	0.879	25.092	-11.998	-11.998	0.000	0.000	0.000	0.000
75	A	104	GLH	0	-0.044	-0.066	28.550	0.089	0.089	0.000	0.000	0.000	0.000
76	A	105	GLU	-1	-0.917	-0.962	31.362	9.696	9.696	0.000	0.000	0.000	0.000
77	A	106	LEU	0	-0.013	0.004	23.655	0.033	0.033	0.000	0.000	0.000	0.000
78	A	107	VAL	0	-0.044	-0.013	25.666	0.083	0.083	0.000	0.000	0.000	0.000
79	A	108	ASN	0	-0.015	-0.025	28.106	-0.233	-0.233	0.000	0.000	0.000	0.000
80	A	109	SER	0	0.024	0.010	28.551	-0.230	-0.230	0.000	0.000	0.000	0.000
81	A	110	ALA	0	0.012	-0.012	30.001	0.209	0.209	0.000	0.000	0.000	0.000
82	A	111	SER	0	-0.030	-0.039	27.290	0.042	0.042	0.000	0.000	0.000	0.000
83	A	112	TYR	0	-0.023	-0.024	22.728	0.746	0.746	0.000	0.000	0.000	0.000
84	A	113	LYS	1	0.794	0.897	25.482	-9.717	-9.717	0.000	0.000	0.000	0.000
85	A	114	ASN	0	-0.029	-0.014	27.533	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	115	PHE	0	-0.038	-0.015	19.321	0.333	0.333	0.000	0.000	0.000	0.000
87	A	116	PHE	0	-0.053	-0.025	18.154	0.788	0.788	0.000	0.000	0.000	0.000
88	A	117	GLY	0	0.031	0.020	22.447	0.191	0.191	0.000	0.000	0.000	0.000
89	A	118	TRP	0	-0.053	-0.050	16.332	0.217	0.217	0.000	0.000	0.000	0.000
90	A	119	GLY	0	0.038	0.036	23.290	-0.102	-0.102	0.000	0.000	0.000	0.000
91	A	120	ASP	-1	-0.832	-0.879	26.122	11.267	11.267	0.000	0.000	0.000	0.000
92	A	121	THR	0	0.049	0.033	23.286	0.113	0.113	0.000	0.000	0.000	0.000
93	A	122	GLY	0	0.053	0.032	22.889	0.036	0.036	0.000	0.000	0.000	0.000
94	A	123	GLU	-1	-0.877	-0.949	17.358	19.246	19.246	0.000	0.000	0.000	0.000
95	A	124	ARG	1	0.919	0.976	17.393	-16.109	-16.109	0.000	0.000	0.000	0.000
96	A	125	THR	0	-0.011	0.003	14.982	1.666	1.666	0.000	0.000	0.000	0.000
97	A	126	PHE	0	-0.073	-0.025	12.618	-1.241	-1.241	0.000	0.000	0.000	0.000
98	A	127	LYS	1	0.834	0.908	12.558	-20.241	-20.241	0.000	0.000	0.000	0.000
99	A	128	VAL	0	0.007	-0.012	6.469	0.009	0.009	0.000	0.000	0.000	0.000
100	A	129	GLU	-1	-0.740	-0.825	9.550	19.215	19.215	0.000	0.000	0.000	0.000
101	A	130	GLU	-1	-0.831	-0.892	9.477	21.662	21.662	0.000	0.000	0.000	0.000
102	A	131	LEU	0	0.014	0.014	2.770	-3.513	-2.121	1.247	-0.862	-1.777	0.010
103	A	132	THR	0	0.020	0.014	5.382	-0.890	-0.890	0.000	0.000	0.000	0.000
104	A	133	ASP	-1	-0.839	-0.921	4.881	37.520	37.473	-0.001	-0.008	0.057	0.000
105	A	134	LYS	1	0.854	0.914	5.856	-24.277	-24.277	0.000	0.000	0.000	0.000
106	A	135	LYS	1	0.810	0.889	8.615	-23.067	-23.067	0.000	0.000	0.000	0.000
107	A	136	MET	0	0.042	0.034	6.715	1.500	1.500	0.000	0.000	0.000	0.000
108	A	137	ARG	1	0.790	0.880	9.303	-23.512	-23.512	0.000	0.000	0.000	0.000
109	A	138	LEU	0	0.037	0.031	9.341	0.812	0.812	0.000	0.000	0.000	0.000
110	A	139	ASN	0	-0.039	-0.045	12.703	-2.192	-2.192	0.000	0.000	0.000	0.000
111	A	140	TYR	0	-0.009	-0.020	15.867	1.018	1.018	0.000	0.000	0.000	0.000
112	A	141	GLU	-1	-0.852	-0.910	18.577	12.706	12.706	0.000	0.000	0.000	0.000
113	A	142	GLY	0	0.004	0.009	20.370	-0.706	-0.706	0.000	0.000	0.000	0.000
114	A	143	THR	0	-0.038	-0.017	20.837	-0.273	-0.273	0.000	0.000	0.000	0.000
115	A	144	LYS	1	0.842	0.906	16.925	-15.900	-15.900	0.000	0.000	0.000	0.000
116	A	145	TYR	0	0.020	0.010	15.324	-0.974	-0.974	0.000	0.000	0.000	0.000
117	A	146	VAL	0	-0.004	0.004	14.284	1.759	1.759	0.000	0.000	0.000	0.000
118	A	147	PHE	0	0.040	0.010	11.329	-0.974	-0.974	0.000	0.000	0.000	0.000
119	A	148	ARG	1	0.916	0.944	11.876	-17.283	-17.283	0.000	0.000	0.000	0.000
120	A	149	LYS	1	0.854	0.969	3.603	-45.731	-45.528	0.003	-0.067	-0.139	0.000
121	A	150	TYR	0	-0.015	-0.011	9.993	-1.760	-1.760	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:30:ASP)