FMO DATABASE

FMODB ID: 851KY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1098430.975707
FMO2-HF: Nuclear repulsion	1048574.46914
FMO2-HF: Total energy	-49856.506567
FMO2-MP2: Total energy	-50003.248874

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.
-93.728	-89.327	0.844	-2.256	-2.988	0.015

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 : -0.891 / q_NPA : -0.960

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	32	VAL	0	-0.068	-0.036	3.751	-13.939	-11.427	-0.003	-1.266	-1.242	0.005
4	A	33	GLY	0	0.037	0.032	5.784	-0.728	-0.728	0.000	0.000	0.000	0.000
5	A	34	LYS	1	0.923	0.960	8.628	-18.202	-18.202	0.000	0.000	0.000	0.000
6	A	35	TRP	0	-0.001	-0.018	5.077	-1.477	-1.477	0.000	0.000	0.000	0.000
7	A	36	GLN	0	-0.006	0.018	11.786	-1.328	-1.328	0.000	0.000	0.000	0.000
8	A	37	LEU	0	0.014	0.011	15.143	0.720	0.720	0.000	0.000	0.000	0.000
9	A	38	ARG	1	0.769	0.862	16.247	-16.489	-16.489	0.000	0.000	0.000	0.000
10	A	39	GLU	-1	-0.894	-0.956	18.297	13.568	13.568	0.000	0.000	0.000	0.000
11	A	40	TYR	0	0.021	0.022	19.035	0.895	0.895	0.000	0.000	0.000	0.000
12	A	41	GLN	0	-0.047	-0.042	19.735	-0.252	-0.252	0.000	0.000	0.000	0.000
13	A	42	TYR	0	0.029	-0.001	21.952	0.344	0.344	0.000	0.000	0.000	0.000
14	A	43	PRO	0	0.057	0.031	24.118	-0.069	-0.069	0.000	0.000	0.000	0.000
15	A	44	ASP	-1	-0.922	-0.957	25.289	10.794	10.794	0.000	0.000	0.000	0.000
16	A	45	GLY	0	-0.004	0.009	26.500	-0.355	-0.355	0.000	0.000	0.000	0.000
17	A	46	LYS	1	0.847	0.929	26.770	-10.852	-10.852	0.000	0.000	0.000	0.000
18	A	47	VAL	0	0.042	0.023	23.339	0.469	0.469	0.000	0.000	0.000	0.000
19	A	48	GLN	0	-0.024	-0.004	24.306	-0.817	-0.817	0.000	0.000	0.000	0.000
20	A	49	LYS	1	0.981	0.981	23.439	-10.923	-10.923	0.000	0.000	0.000	0.000
21	A	50	VAL	0	0.019	0.022	20.936	-0.501	-0.501	0.000	0.000	0.000	0.000
22	A	51	ASP	-1	-0.855	-0.923	21.582	12.813	12.813	0.000	0.000	0.000	0.000
23	A	52	SER	0	-0.015	-0.023	21.475	0.526	0.526	0.000	0.000	0.000	0.000
24	A	53	ILE	0	0.061	0.050	18.103	0.127	0.127	0.000	0.000	0.000	0.000
25	A	54	PHE	0	-0.036	-0.028	15.437	0.705	0.705	0.000	0.000	0.000	0.000
26	A	55	TYR	0	0.033	0.014	12.683	-0.568	-0.568	0.000	0.000	0.000	0.000
27	A	56	GLY	0	0.005	-0.003	11.396	0.824	0.824	0.000	0.000	0.000	0.000
28	A	57	PHE	0	0.037	0.019	7.592	-0.608	-0.608	0.000	0.000	0.000	0.000
29	A	58	GLN	0	-0.002	-0.019	8.437	2.710	2.710	0.000	0.000	0.000	0.000
30	A	59	LYS	1	0.960	0.977	7.723	-33.006	-33.006	0.000	0.000	0.000	0.000
31	A	60	GLY	0	0.090	0.058	8.792	-2.581	-2.581	0.000	0.000	0.000	0.000
32	A	61	SER	0	-0.001	0.004	10.743	-2.283	-2.283	0.000	0.000	0.000	0.000
33	A	62	PHE	0	-0.011	-0.024	11.398	2.378	2.378	0.000	0.000	0.000	0.000
34	A	63	LEU	0	-0.015	-0.011	13.479	-1.846	-1.846	0.000	0.000	0.000	0.000
35	A	64	ALA	0	0.035	0.027	14.922	1.282	1.282	0.000	0.000	0.000	0.000
36	A	65	TYR	0	0.014	-0.010	15.908	-0.364	-0.364	0.000	0.000	0.000	0.000
37	A	66	CYS	0	-0.012	0.011	20.128	0.378	0.378	0.000	0.000	0.000	0.000
38	A	67	MET	0	-0.046	-0.014	19.779	-0.600	-0.600	0.000	0.000	0.000	0.000
39	A	68	ASN	0	0.066	0.035	24.378	-0.316	-0.316	0.000	0.000	0.000	0.000
40	A	69	LYS	1	0.868	0.914	25.501	-11.731	-11.731	0.000	0.000	0.000	0.000
41	A	70	SER	0	-0.003	0.005	29.240	-0.049	-0.049	0.000	0.000	0.000	0.000
42	A	71	GLY	0	0.033	0.024	28.457	-0.240	-0.240	0.000	0.000	0.000	0.000
43	A	72	SER	0	-0.053	-0.016	27.867	0.188	0.188	0.000	0.000	0.000	0.000
44	A	73	TYR	0	-0.023	-0.030	21.931	0.244	0.244	0.000	0.000	0.000	0.000
45	A	74	GLU	-1	-0.816	-0.870	25.056	11.620	11.620	0.000	0.000	0.000	0.000
46	A	75	GLY	0	-0.022	-0.024	21.720	0.629	0.629	0.000	0.000	0.000	0.000
47	A	76	PHE	0	0.005	0.009	20.280	-0.419	-0.419	0.000	0.000	0.000	0.000
48	A	77	TYR	0	0.010	-0.005	17.916	0.972	0.972	0.000	0.000	0.000	0.000
49	A	78	GLY	0	0.068	0.035	16.920	-0.879	-0.879	0.000	0.000	0.000	0.000
50	A	79	TYR	0	0.009	0.019	14.151	1.109	1.109	0.000	0.000	0.000	0.000
51	A	80	TYR	0	-0.046	-0.016	6.039	-2.103	-2.103	0.000	0.000	0.000	0.000
52	A	81	LYS	1	0.832	0.914	11.280	-20.311	-20.311	0.000	0.000	0.000	0.000
53	A	82	LEU	0	0.001	0.001	5.032	-0.271	-0.170	-0.001	-0.001	-0.099	0.000
54	A	83	LYS	1	0.879	0.941	9.267	-21.343	-21.343	0.000	0.000	0.000	0.000
55	A	84	ASP	-1	-0.883	-0.946	11.705	21.639	21.639	0.000	0.000	0.000	0.000
56	A	85	ASP	-1	-0.840	-0.899	9.447	30.149	30.149	0.000	0.000	0.000	0.000
57	A	86	GLU	-1	-0.895	-0.939	10.518	18.800	18.800	0.000	0.000	0.000	0.000
58	A	87	ILE	0	-0.019	-0.004	8.047	2.260	2.260	0.000	0.000	0.000	0.000
59	A	88	SER	0	-0.040	-0.036	10.943	-1.745	-1.745	0.000	0.000	0.000	0.000
60	A	89	ILE	0	-0.050	-0.018	12.420	0.818	0.818	0.000	0.000	0.000	0.000
61	A	90	THR	0	0.036	0.024	14.866	-0.935	-0.935	0.000	0.000	0.000	0.000
62	A	91	LEU	0	-0.031	-0.015	17.705	0.791	0.791	0.000	0.000	0.000	0.000
63	A	92	TRP	0	-0.023	0.000	20.120	-0.241	-0.241	0.000	0.000	0.000	0.000
64	A	93	PRO	0	-0.005	0.002	21.991	-0.038	-0.038	0.000	0.000	0.000	0.000
65	A	94	ASP	-1	-0.760	-0.857	22.621	13.175	13.175	0.000	0.000	0.000	0.000
66	A	95	ASN	0	-0.004	-0.013	24.392	-0.016	-0.016	0.000	0.000	0.000	0.000
67	A	96	SER	0	-0.014	-0.013	26.840	-0.459	-0.459	0.000	0.000	0.000	0.000
68	A	97	SER	0	0.017	-0.016	28.555	-0.117	-0.117	0.000	0.000	0.000	0.000
69	A	98	GLY	0	-0.029	-0.015	31.486	-0.214	-0.214	0.000	0.000	0.000	0.000
70	A	99	ASN	0	-0.030	-0.028	26.037	-0.315	-0.315	0.000	0.000	0.000	0.000
71	A	100	GLU	-1	-0.870	-0.937	30.057	10.715	10.715	0.000	0.000	0.000	0.000
72	A	101	ALA	0	0.006	0.010	31.655	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	102	ALA	0	0.076	0.037	29.889	-0.015	-0.015	0.000	0.000	0.000	0.000
74	A	103	HIS	1	0.745	0.863	25.001	-12.025	-12.025	0.000	0.000	0.000	0.000
75	A	104	GLH	0	-0.033	-0.056	28.812	0.058	0.058	0.000	0.000	0.000	0.000
76	A	105	GLU	-1	-0.938	-0.963	31.715	9.504	9.504	0.000	0.000	0.000	0.000
77	A	106	LEU	0	-0.029	0.003	24.139	0.036	0.036	0.000	0.000	0.000	0.000
78	A	107	VAL	0	-0.026	-0.007	25.987	0.101	0.101	0.000	0.000	0.000	0.000
79	A	108	ASN	0	-0.037	-0.042	28.407	-0.194	-0.194	0.000	0.000	0.000	0.000
80	A	109	SER	0	0.007	0.005	28.987	-0.288	-0.288	0.000	0.000	0.000	0.000
81	A	110	ALA	0	0.018	-0.019	30.138	0.262	0.262	0.000	0.000	0.000	0.000
82	A	111	SER	0	-0.028	-0.025	27.624	0.016	0.016	0.000	0.000	0.000	0.000
83	A	112	TYR	0	-0.004	-0.017	23.117	0.756	0.756	0.000	0.000	0.000	0.000
84	A	113	LYS	1	0.822	0.915	25.778	-9.595	-9.595	0.000	0.000	0.000	0.000
85	A	114	ASN	0	-0.036	-0.016	27.567	0.026	0.026	0.000	0.000	0.000	0.000
86	A	115	PHE	0	-0.042	-0.014	19.286	0.386	0.386	0.000	0.000	0.000	0.000
87	A	116	PHE	0	-0.055	-0.031	18.274	0.647	0.647	0.000	0.000	0.000	0.000
88	A	117	GLY	0	0.033	0.016	22.719	0.113	0.113	0.000	0.000	0.000	0.000
89	A	118	TRP	0	-0.079	-0.054	16.487	0.100	0.100	0.000	0.000	0.000	0.000
90	A	119	GLY	0	0.038	0.035	23.629	-0.045	-0.045	0.000	0.000	0.000	0.000
91	A	120	ASP	-1	-0.816	-0.870	26.301	11.137	11.137	0.000	0.000	0.000	0.000
92	A	121	THR	0	0.052	0.043	23.532	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	122	GLY	0	0.017	0.017	23.275	0.183	0.183	0.000	0.000	0.000	0.000
94	A	123	GLU	-1	-0.897	-0.979	17.434	18.787	18.787	0.000	0.000	0.000	0.000
95	A	124	ARG	1	0.950	0.998	17.879	-15.892	-15.892	0.000	0.000	0.000	0.000
96	A	125	THR	0	0.000	0.021	15.284	1.543	1.543	0.000	0.000	0.000	0.000
97	A	126	PHE	0	-0.057	-0.027	12.867	-1.130	-1.130	0.000	0.000	0.000	0.000
98	A	127	LYS	1	0.849	0.915	12.847	-21.034	-21.034	0.000	0.000	0.000	0.000
99	A	128	VAL	0	-0.001	-0.023	6.398	-0.421	-0.421	0.000	0.000	0.000	0.000
100	A	129	GLU	-1	-0.745	-0.820	9.850	18.538	18.538	0.000	0.000	0.000	0.000
101	A	130	GLU	-1	-0.839	-0.901	9.058	22.729	22.729	0.000	0.000	0.000	0.000
102	A	131	LEU	0	0.031	0.016	2.805	-5.343	-3.614	0.850	-0.980	-1.600	0.010
103	A	132	THR	0	-0.007	0.010	5.361	0.740	0.740	0.000	0.000	0.000	0.000
104	A	133	ASP	-1	-0.826	-0.919	5.129	36.456	36.430	-0.001	-0.004	0.031	0.000
105	A	134	LYS	1	0.850	0.916	6.268	-23.611	-23.611	0.000	0.000	0.000	0.000
106	A	135	LYS	1	0.822	0.899	9.110	-22.427	-22.427	0.000	0.000	0.000	0.000
107	A	136	MET	0	0.048	0.030	7.008	2.062	2.062	0.000	0.000	0.000	0.000
108	A	137	ARG	1	0.781	0.874	9.454	-23.971	-23.971	0.000	0.000	0.000	0.000
109	A	138	LEU	0	0.029	0.023	9.427	1.154	1.154	0.000	0.000	0.000	0.000
110	A	139	ASN	0	-0.038	-0.037	12.857	-2.234	-2.234	0.000	0.000	0.000	0.000
111	A	140	TYR	0	-0.004	-0.033	15.966	0.693	0.693	0.000	0.000	0.000	0.000
112	A	141	GLU	-1	-0.841	-0.902	18.761	12.775	12.775	0.000	0.000	0.000	0.000
113	A	142	GLY	0	0.007	0.003	20.460	-0.708	-0.708	0.000	0.000	0.000	0.000
114	A	143	THR	0	-0.034	-0.012	20.665	-0.307	-0.307	0.000	0.000	0.000	0.000
115	A	144	LYS	1	0.830	0.907	16.974	-15.989	-15.989	0.000	0.000	0.000	0.000
116	A	145	TYR	0	0.004	-0.001	15.131	-0.831	-0.831	0.000	0.000	0.000	0.000
117	A	146	VAL	0	0.005	0.010	14.334	1.835	1.835	0.000	0.000	0.000	0.000
118	A	147	PHE	0	0.054	0.015	11.531	-1.184	-1.184	0.000	0.000	0.000	0.000
119	A	148	ARG	1	0.923	0.950	12.103	-16.914	-16.914	0.000	0.000	0.000	0.000
120	A	149	LYS	1	0.905	0.977	4.398	-40.753	-40.668	-0.001	-0.005	-0.078	0.000
121	A	150	TYR	0	-0.038	-0.010	10.620	-1.551	-1.551	0.000	0.000	0.000	0.000

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