FMO DATABASE

FMODB ID: G6M71

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1098335.04761
FMO2-HF: Nuclear repulsion	1048479.071888
FMO2-HF: Total energy	-49855.975722
FMO2-MP2: Total energy	-50002.687208

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.
-92.089	-87.667	1.052	-2.392	-3.08	0.018

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 : -0.881 / q_NPA : -0.951

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	-0.070	-0.035	3.753	-14.689	-12.111	0.005	-1.321	-1.262	0.006
4	A	33	GLY	0	0.026	0.021	5.774	-0.622	-0.622	0.000	0.000	0.000	0.000
5	A	34	LYS	1	0.939	0.969	8.618	-17.973	-17.973	0.000	0.000	0.000	0.000
6	A	35	TRP	0	0.004	-0.016	5.210	-1.647	-1.647	0.000	0.000	0.000	0.000
7	A	36	GLN	0	0.014	0.004	11.766	-1.852	-1.852	0.000	0.000	0.000	0.000
8	A	37	LEU	0	0.018	0.016	15.025	0.705	0.705	0.000	0.000	0.000	0.000
9	A	38	ARG	1	0.746	0.864	16.068	-16.460	-16.460	0.000	0.000	0.000	0.000
10	A	39	GLU	-1	-0.871	-0.948	18.172	13.637	13.637	0.000	0.000	0.000	0.000
11	A	40	TYR	0	0.018	0.018	18.906	1.079	1.079	0.000	0.000	0.000	0.000
12	A	41	GLN	0	-0.045	-0.035	19.684	-0.406	-0.406	0.000	0.000	0.000	0.000
13	A	42	TYR	0	0.033	-0.004	22.220	0.274	0.274	0.000	0.000	0.000	0.000
14	A	43	PRO	0	0.058	0.030	24.142	-0.096	-0.096	0.000	0.000	0.000	0.000
15	A	44	ASP	-1	-0.925	-0.958	25.532	10.649	10.649	0.000	0.000	0.000	0.000
16	A	45	GLY	0	-0.007	0.009	26.741	-0.348	-0.348	0.000	0.000	0.000	0.000
17	A	46	LYS	1	0.884	0.959	26.913	-10.790	-10.790	0.000	0.000	0.000	0.000
18	A	47	VAL	0	0.031	0.013	23.142	0.474	0.474	0.000	0.000	0.000	0.000
19	A	48	GLN	0	-0.045	-0.016	24.177	-0.724	-0.724	0.000	0.000	0.000	0.000
20	A	49	LYS	1	0.986	0.979	23.312	-10.859	-10.859	0.000	0.000	0.000	0.000
21	A	50	VAL	0	0.002	0.017	20.763	-0.469	-0.469	0.000	0.000	0.000	0.000
22	A	51	ASP	-1	-0.851	-0.913	21.463	12.690	12.690	0.000	0.000	0.000	0.000
23	A	52	SER	0	-0.007	-0.021	21.455	0.496	0.496	0.000	0.000	0.000	0.000
24	A	53	ILE	0	0.055	0.048	18.069	0.114	0.114	0.000	0.000	0.000	0.000
25	A	54	PHE	0	-0.040	-0.026	15.496	0.762	0.762	0.000	0.000	0.000	0.000
26	A	55	TYR	0	0.034	0.013	12.655	-0.553	-0.553	0.000	0.000	0.000	0.000
27	A	56	GLY	0	0.005	-0.003	11.395	0.811	0.811	0.000	0.000	0.000	0.000
28	A	57	PHE	0	0.040	0.021	7.568	-0.653	-0.653	0.000	0.000	0.000	0.000
29	A	58	GLN	0	-0.006	-0.024	8.437	2.331	2.331	0.000	0.000	0.000	0.000
30	A	59	LYS	1	0.955	0.976	7.733	-33.754	-33.754	0.000	0.000	0.000	0.000
31	A	60	GLY	0	0.084	0.053	8.817	-2.550	-2.550	0.000	0.000	0.000	0.000
32	A	61	SER	0	0.005	0.007	10.752	-2.278	-2.278	0.000	0.000	0.000	0.000
33	A	62	PHE	0	-0.003	-0.022	11.405	2.431	2.431	0.000	0.000	0.000	0.000
34	A	63	LEU	0	-0.019	-0.009	13.483	-1.809	-1.809	0.000	0.000	0.000	0.000
35	A	64	ALA	0	0.038	0.027	14.922	1.281	1.281	0.000	0.000	0.000	0.000
36	A	65	TYR	0	0.015	-0.008	15.582	-0.345	-0.345	0.000	0.000	0.000	0.000
37	A	66	CYS	0	-0.027	-0.002	20.128	0.286	0.286	0.000	0.000	0.000	0.000
38	A	67	MET	0	-0.043	-0.015	19.945	-0.580	-0.580	0.000	0.000	0.000	0.000
39	A	68	ASN	0	0.048	0.033	24.363	-0.310	-0.310	0.000	0.000	0.000	0.000
40	A	69	LYS	1	0.873	0.911	25.580	-11.674	-11.674	0.000	0.000	0.000	0.000
41	A	70	SER	0	0.005	0.012	29.223	-0.057	-0.057	0.000	0.000	0.000	0.000
42	A	71	GLY	0	0.033	0.022	28.443	-0.243	-0.243	0.000	0.000	0.000	0.000
43	A	72	SER	0	-0.058	-0.018	27.872	0.182	0.182	0.000	0.000	0.000	0.000
44	A	73	TYR	0	-0.022	-0.031	21.871	0.137	0.137	0.000	0.000	0.000	0.000
45	A	74	GLU	-1	-0.861	-0.919	25.037	11.895	11.895	0.000	0.000	0.000	0.000
46	A	75	GLY	0	-0.023	-0.023	21.720	0.634	0.634	0.000	0.000	0.000	0.000
47	A	76	PHE	0	0.030	0.018	20.328	-0.339	-0.339	0.000	0.000	0.000	0.000
48	A	77	TYR	0	0.007	-0.009	17.920	0.963	0.963	0.000	0.000	0.000	0.000
49	A	78	GLY	0	0.069	0.033	16.926	-0.876	-0.876	0.000	0.000	0.000	0.000
50	A	79	TYR	0	0.008	0.021	14.154	1.069	1.069	0.000	0.000	0.000	0.000
51	A	80	TYR	0	-0.042	-0.011	6.398	-1.348	-1.348	0.000	0.000	0.000	0.000
52	A	81	LYS	1	0.849	0.927	11.265	-20.182	-20.182	0.000	0.000	0.000	0.000
53	A	82	LEU	0	-0.002	-0.001	5.066	-0.403	-0.310	-0.001	-0.001	-0.091	0.000
54	A	83	LYS	1	0.918	0.974	9.282	-20.861	-20.861	0.000	0.000	0.000	0.000
55	A	84	ASP	-1	-0.880	-0.943	11.746	21.512	21.512	0.000	0.000	0.000	0.000
56	A	85	ASP	-1	-0.931	-0.961	9.509	31.517	31.517	0.000	0.000	0.000	0.000
57	A	86	GLU	-1	-0.935	-0.973	10.589	18.783	18.783	0.000	0.000	0.000	0.000
58	A	87	ILE	0	-0.025	-0.007	7.789	2.279	2.279	0.000	0.000	0.000	0.000
59	A	88	SER	0	-0.023	-0.024	10.899	-1.786	-1.786	0.000	0.000	0.000	0.000
60	A	89	ILE	0	-0.060	-0.024	12.441	0.808	0.808	0.000	0.000	0.000	0.000
61	A	90	THR	0	0.018	0.012	14.816	-0.897	-0.897	0.000	0.000	0.000	0.000
62	A	91	LEU	0	-0.030	-0.016	17.668	0.793	0.793	0.000	0.000	0.000	0.000
63	A	92	TRP	0	-0.021	0.002	20.073	-0.205	-0.205	0.000	0.000	0.000	0.000
64	A	93	PRO	0	0.008	0.012	21.996	-0.036	-0.036	0.000	0.000	0.000	0.000
65	A	94	ASP	-1	-0.763	-0.874	22.506	13.325	13.325	0.000	0.000	0.000	0.000
66	A	95	ASN	0	-0.019	-0.015	24.370	-0.153	-0.153	0.000	0.000	0.000	0.000
67	A	96	SER	0	0.015	0.015	26.831	-0.436	-0.436	0.000	0.000	0.000	0.000
68	A	97	SER	0	0.020	-0.014	28.551	-0.118	-0.118	0.000	0.000	0.000	0.000
69	A	98	GLY	0	-0.026	-0.013	31.512	-0.208	-0.208	0.000	0.000	0.000	0.000
70	A	99	ASN	0	-0.042	-0.023	26.263	-0.309	-0.309	0.000	0.000	0.000	0.000
71	A	100	GLU	-1	-0.890	-0.941	30.042	10.604	10.604	0.000	0.000	0.000	0.000
72	A	101	ALA	0	0.015	0.009	31.630	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	102	ALA	0	0.073	0.034	29.856	-0.024	-0.024	0.000	0.000	0.000	0.000
74	A	103	HIS	1	0.752	0.853	24.657	-12.130	-12.130	0.000	0.000	0.000	0.000
75	A	104	GLH	0	0.001	-0.018	28.772	0.060	0.060	0.000	0.000	0.000	0.000
76	A	105	GLU	-1	-0.962	-0.962	31.666	9.406	9.406	0.000	0.000	0.000	0.000
77	A	106	LEU	0	-0.020	0.004	24.066	0.040	0.040	0.000	0.000	0.000	0.000
78	A	107	VAL	0	-0.040	-0.013	25.927	0.110	0.110	0.000	0.000	0.000	0.000
79	A	108	ASN	0	-0.073	-0.051	28.342	-0.154	-0.154	0.000	0.000	0.000	0.000
80	A	109	SER	0	-0.014	-0.011	28.889	-0.280	-0.280	0.000	0.000	0.000	0.000
81	A	110	ALA	0	0.014	-0.021	30.054	0.255	0.255	0.000	0.000	0.000	0.000
82	A	111	SER	0	-0.002	0.012	27.828	0.012	0.012	0.000	0.000	0.000	0.000
83	A	112	TYR	0	0.009	-0.024	23.188	0.752	0.752	0.000	0.000	0.000	0.000
84	A	113	LYS	1	0.888	0.944	25.686	-9.516	-9.516	0.000	0.000	0.000	0.000
85	A	114	ASN	0	-0.041	-0.022	27.467	0.028	0.028	0.000	0.000	0.000	0.000
86	A	115	PHE	0	-0.050	-0.016	19.488	0.340	0.340	0.000	0.000	0.000	0.000
87	A	116	PHE	0	-0.048	-0.026	18.240	0.641	0.641	0.000	0.000	0.000	0.000
88	A	117	GLY	0	0.036	0.018	22.623	0.101	0.101	0.000	0.000	0.000	0.000
89	A	118	TRP	0	-0.080	-0.057	16.706	0.042	0.042	0.000	0.000	0.000	0.000
90	A	119	GLY	0	0.038	0.036	23.550	-0.038	-0.038	0.000	0.000	0.000	0.000
91	A	120	ASP	-1	-0.823	-0.876	26.235	11.063	11.063	0.000	0.000	0.000	0.000
92	A	121	THR	0	0.054	0.036	23.082	-0.048	-0.048	0.000	0.000	0.000	0.000
93	A	122	GLY	0	0.019	0.013	23.187	0.186	0.186	0.000	0.000	0.000	0.000
94	A	123	GLU	-1	-0.940	-0.997	17.842	18.237	18.237	0.000	0.000	0.000	0.000
95	A	124	ARG	1	0.966	1.004	17.606	-15.930	-15.930	0.000	0.000	0.000	0.000
96	A	125	THR	0	-0.019	0.005	15.058	1.435	1.435	0.000	0.000	0.000	0.000
97	A	126	PHE	0	-0.045	-0.023	13.013	-1.166	-1.166	0.000	0.000	0.000	0.000
98	A	127	LYS	1	0.979	0.993	13.057	-19.449	-19.449	0.000	0.000	0.000	0.000
99	A	128	VAL	0	-0.011	-0.027	6.616	-0.408	-0.408	0.000	0.000	0.000	0.000
100	A	129	GLU	-1	-0.720	-0.822	10.059	18.579	18.579	0.000	0.000	0.000	0.000
101	A	130	GLU	-1	-0.901	-0.975	9.203	23.350	23.350	0.000	0.000	0.000	0.000
102	A	131	LEU	0	0.020	0.006	2.670	-5.291	-3.590	1.050	-1.063	-1.688	0.012
103	A	132	THR	0	0.017	0.017	5.257	1.734	1.734	0.000	0.000	0.000	0.000
104	A	133	ASP	-1	-0.893	-0.943	5.028	34.713	34.693	-0.001	-0.004	0.026	0.000
105	A	134	LYS	1	0.860	0.925	6.211	-23.650	-23.650	0.000	0.000	0.000	0.000
106	A	135	LYS	1	0.848	0.942	8.932	-21.707	-21.707	0.000	0.000	0.000	0.000
107	A	136	MET	0	0.049	0.034	7.262	2.039	2.039	0.000	0.000	0.000	0.000
108	A	137	ARG	1	0.794	0.895	9.334	-24.045	-24.045	0.000	0.000	0.000	0.000
109	A	138	LEU	0	0.034	0.034	10.079	1.119	1.119	0.000	0.000	0.000	0.000
110	A	139	ASN	0	-0.076	-0.043	13.133	-2.215	-2.215	0.000	0.000	0.000	0.000
111	A	140	TYR	0	0.012	-0.012	16.215	0.688	0.688	0.000	0.000	0.000	0.000
112	A	141	GLU	-1	-0.860	-0.922	19.012	12.577	12.577	0.000	0.000	0.000	0.000
113	A	142	GLY	0	0.010	0.002	20.712	-0.689	-0.689	0.000	0.000	0.000	0.000
114	A	143	THR	0	-0.043	-0.018	20.968	-0.313	-0.313	0.000	0.000	0.000	0.000
115	A	144	LYS	1	0.826	0.903	17.377	-15.855	-15.855	0.000	0.000	0.000	0.000
116	A	145	TYR	0	-0.002	0.001	15.404	-0.902	-0.902	0.000	0.000	0.000	0.000
117	A	146	VAL	0	0.007	0.003	14.482	1.810	1.810	0.000	0.000	0.000	0.000
118	A	147	PHE	0	0.047	0.015	11.406	-1.191	-1.191	0.000	0.000	0.000	0.000
119	A	148	ARG	1	0.917	0.946	11.978	-17.165	-17.165	0.000	0.000	0.000	0.000
120	A	149	LYS	1	0.955	1.009	4.551	-40.334	-40.264	-0.001	-0.003	-0.065	0.000
121	A	150	TYR	0	-0.044	-0.017	10.599	-1.516	-1.516	0.000	0.000	0.000	0.000

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