FMO DATABASE

FMODB ID: 72JLK

Calculation Name: 1YKE-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YKE

Chain ID: B

ChEMBL ID:

UniProt ID: P47822

Base Structure: X-ray

Registration Date: 2023-06-21

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	119
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-734298.917318
FMO2-HF: Nuclear repulsion	685794.824775
FMO2-HF: Total energy	-48504.092542
FMO2-MP2: Total energy	-48644.949182

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(B:3:ASP)

Summations of interaction energy for fragment #1(B:3: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.
20.722	14.292	26.779	-12.844	-7.503	0.071

Interaction energy analysis for fragmet #1(B:3:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.880 / q_NPA : -0.920

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	B	5	LEU	0	0.044	0.023	3.883	-4.865	-2.666	-0.024	-1.110	-1.065	0.001
4	B	6	THR	0	0.043	-0.005	1.563	-27.942	-39.389	26.739	-10.390	-4.901	0.060
5	B	7	GLN	0	-0.018	-0.003	3.301	-20.567	-17.895	0.066	-1.330	-1.407	0.010
6	B	8	LEU	0	-0.007	0.004	4.855	-7.946	-7.893	-0.001	-0.013	-0.040	0.000
7	B	9	GLN	0	-0.004	-0.014	7.523	-0.522	-0.522	0.000	0.000	0.000	0.000
8	B	10	ILE	0	0.060	0.033	4.908	-2.898	-2.805	-0.001	-0.001	-0.090	0.000
9	B	11	CYS	0	-0.039	-0.023	8.651	-4.014	-4.014	0.000	0.000	0.000	0.000
10	B	12	LEU	0	0.000	0.002	10.720	-2.760	-2.760	0.000	0.000	0.000	0.000
11	B	13	ASP	-1	-0.898	-0.944	11.442	23.503	23.503	0.000	0.000	0.000	0.000
12	B	14	GLN	0	-0.002	0.000	12.134	-3.076	-3.076	0.000	0.000	0.000	0.000
13	B	15	MET	0	-0.062	-0.025	14.519	-1.739	-1.739	0.000	0.000	0.000	0.000
14	B	16	THR	0	0.000	0.000	16.255	-1.638	-1.638	0.000	0.000	0.000	0.000
15	B	17	GLU	-1	-0.909	-0.956	15.599	19.031	19.031	0.000	0.000	0.000	0.000
16	B	18	GLN	0	0.013	-0.005	18.735	-1.357	-1.357	0.000	0.000	0.000	0.000
17	B	19	PHE	0	-0.020	-0.012	20.557	-0.975	-0.975	0.000	0.000	0.000	0.000
18	B	20	CYS	0	-0.034	-0.016	21.518	-0.915	-0.915	0.000	0.000	0.000	0.000
19	B	21	ALA	0	-0.017	-0.002	22.979	-0.739	-0.739	0.000	0.000	0.000	0.000
20	B	22	THR	0	0.015	-0.012	24.467	-0.683	-0.683	0.000	0.000	0.000	0.000
21	B	23	LEU	0	-0.010	0.001	26.395	-0.473	-0.473	0.000	0.000	0.000	0.000
22	B	24	ASN	0	-0.010	-0.008	26.786	-0.792	-0.792	0.000	0.000	0.000	0.000
23	B	25	TYR	0	0.007	0.017	29.013	-0.494	-0.494	0.000	0.000	0.000	0.000
24	B	26	ILE	0	0.028	0.006	30.052	-0.435	-0.435	0.000	0.000	0.000	0.000
25	B	27	ASP	-1	-0.905	-0.953	31.611	9.774	9.774	0.000	0.000	0.000	0.000
26	B	28	LYS	1	0.821	0.894	30.104	-10.880	-10.880	0.000	0.000	0.000	0.000
27	B	29	ASN	0	-0.043	-0.016	33.614	-0.371	-0.371	0.000	0.000	0.000	0.000
28	B	30	HIS	0	0.019	0.009	36.826	-0.100	-0.100	0.000	0.000	0.000	0.000
29	B	31	GLY	0	0.036	0.003	35.610	-0.150	-0.150	0.000	0.000	0.000	0.000
30	B	32	PHE	0	-0.034	-0.020	36.696	-0.042	-0.042	0.000	0.000	0.000	0.000
31	B	33	GLU	-1	-0.920	-0.955	38.183	7.293	7.293	0.000	0.000	0.000	0.000
32	B	34	ARG	1	0.719	0.875	38.201	-8.474	-8.474	0.000	0.000	0.000	0.000
33	B	35	LEU	0	-0.043	-0.008	37.514	-0.109	-0.109	0.000	0.000	0.000	0.000
34	B	48	THR	0	-0.032	-0.031	41.536	-0.103	-0.103	0.000	0.000	0.000	0.000
35	B	49	VAL	0	-0.017	-0.009	40.870	0.137	0.137	0.000	0.000	0.000	0.000
36	B	50	VAL	0	0.052	0.053	36.318	-0.173	-0.173	0.000	0.000	0.000	0.000
37	B	51	PRO	0	0.049	0.018	39.629	-0.092	-0.092	0.000	0.000	0.000	0.000
38	B	52	PRO	0	-0.012	-0.024	39.748	0.209	0.209	0.000	0.000	0.000	0.000
39	B	53	GLU	-1	-0.932	-0.955	39.205	8.048	8.048	0.000	0.000	0.000	0.000
40	B	54	GLU	-1	-0.844	-0.935	36.048	9.003	9.003	0.000	0.000	0.000	0.000
41	B	55	PHE	0	-0.021	0.003	34.712	0.343	0.343	0.000	0.000	0.000	0.000
42	B	56	SER	0	-0.027	-0.026	34.248	0.224	0.224	0.000	0.000	0.000	0.000
43	B	57	ASN	0	-0.007	-0.009	33.473	0.233	0.233	0.000	0.000	0.000	0.000
44	B	58	THR	0	0.020	0.009	29.930	0.370	0.370	0.000	0.000	0.000	0.000
45	B	59	ILE	0	-0.029	-0.011	29.402	0.510	0.510	0.000	0.000	0.000	0.000
46	B	60	ASP	-1	-0.865	-0.931	29.213	10.182	10.182	0.000	0.000	0.000	0.000
47	B	61	GLU	-1	-0.982	-0.986	26.603	12.021	12.021	0.000	0.000	0.000	0.000
48	B	62	LEU	0	0.000	-0.005	24.479	0.617	0.617	0.000	0.000	0.000	0.000
49	B	63	SER	0	-0.017	0.002	24.343	0.760	0.760	0.000	0.000	0.000	0.000
50	B	64	THR	0	0.005	-0.014	25.101	0.318	0.318	0.000	0.000	0.000	0.000
51	B	65	ASP	-1	-0.807	-0.871	20.224	17.053	17.053	0.000	0.000	0.000	0.000
52	B	66	ILE	0	0.017	0.013	20.562	1.048	1.048	0.000	0.000	0.000	0.000
53	B	67	ILE	0	-0.011	0.008	20.854	0.647	0.647	0.000	0.000	0.000	0.000
54	B	68	LEU	0	-0.051	-0.016	18.600	0.387	0.387	0.000	0.000	0.000	0.000
55	B	69	LYS	1	0.881	0.923	16.130	-17.646	-17.646	0.000	0.000	0.000	0.000
56	B	70	THR	0	0.008	-0.007	16.580	1.068	1.068	0.000	0.000	0.000	0.000
57	B	71	ARG	1	0.907	0.959	18.607	-14.060	-14.060	0.000	0.000	0.000	0.000
58	B	72	GLN	0	-0.039	-0.029	13.998	-0.189	-0.189	0.000	0.000	0.000	0.000
59	B	73	ILE	0	0.058	0.020	12.572	1.273	1.273	0.000	0.000	0.000	0.000
60	B	74	ASN	0	-0.034	-0.022	13.860	0.705	0.705	0.000	0.000	0.000	0.000
61	B	75	LYS	1	0.995	1.002	15.287	-16.697	-16.697	0.000	0.000	0.000	0.000
62	B	76	LEU	0	-0.034	-0.002	9.007	0.720	0.720	0.000	0.000	0.000	0.000
63	B	77	ILE	0	-0.019	-0.013	10.645	1.719	1.719	0.000	0.000	0.000	0.000
64	B	78	ASP	-1	-0.901	-0.955	12.949	18.211	18.211	0.000	0.000	0.000	0.000
65	B	79	SER	0	-0.083	-0.044	10.409	-0.468	-0.468	0.000	0.000	0.000	0.000
66	B	80	LEU	0	-0.018	-0.003	8.769	3.106	3.106	0.000	0.000	0.000	0.000
67	B	81	PRO	0	-0.057	-0.027	6.332	-1.941	-1.941	0.000	0.000	0.000	0.000
68	B	82	GLY	0	0.031	-0.007	9.599	0.763	0.763	0.000	0.000	0.000	0.000
69	B	83	VAL	0	-0.004	0.011	12.314	-0.930	-0.930	0.000	0.000	0.000	0.000
70	B	84	ASP	-1	-0.902	-0.943	14.547	16.168	16.168	0.000	0.000	0.000	0.000
71	B	85	VAL	0	-0.083	-0.024	14.714	-0.882	-0.882	0.000	0.000	0.000	0.000
72	B	86	SER	0	0.059	0.029	16.245	0.619	0.619	0.000	0.000	0.000	0.000
73	B	87	ALA	0	0.076	0.021	16.405	0.271	0.271	0.000	0.000	0.000	0.000
74	B	88	GLU	-1	-0.838	-0.897	17.448	11.913	11.913	0.000	0.000	0.000	0.000
75	B	89	GLU	-1	-0.868	-0.947	18.497	14.608	14.608	0.000	0.000	0.000	0.000
76	B	90	GLN	0	-0.044	-0.034	12.643	0.881	0.881	0.000	0.000	0.000	0.000
77	B	91	LEU	0	0.001	0.001	16.071	0.096	0.096	0.000	0.000	0.000	0.000
78	B	92	ARG	1	0.858	0.911	18.083	-12.674	-12.674	0.000	0.000	0.000	0.000
79	B	93	LYS	1	0.856	0.933	15.420	-16.115	-16.115	0.000	0.000	0.000	0.000
80	B	94	ILE	0	0.020	0.012	13.536	-0.024	-0.024	0.000	0.000	0.000	0.000
81	B	95	ASP	-1	-0.811	-0.879	16.533	11.655	11.655	0.000	0.000	0.000	0.000
82	B	96	MET	0	-0.005	0.000	18.949	-0.528	-0.528	0.000	0.000	0.000	0.000
83	B	97	LEU	0	-0.038	-0.027	14.329	-0.291	-0.291	0.000	0.000	0.000	0.000
84	B	98	GLN	0	-0.011	-0.013	17.520	0.346	0.346	0.000	0.000	0.000	0.000
85	B	99	LYS	1	0.822	0.906	19.638	-11.722	-11.722	0.000	0.000	0.000	0.000
86	B	100	LYS	1	1.008	0.996	21.166	-12.628	-12.628	0.000	0.000	0.000	0.000
87	B	101	LEU	0	-0.031	-0.005	17.371	-0.078	-0.078	0.000	0.000	0.000	0.000
88	B	102	VAL	0	-0.010	-0.004	21.110	-0.176	-0.176	0.000	0.000	0.000	0.000
89	B	103	GLU	-1	-0.919	-0.962	24.301	10.644	10.644	0.000	0.000	0.000	0.000
90	B	104	VAL	0	0.026	0.011	22.689	-0.252	-0.252	0.000	0.000	0.000	0.000
91	B	105	GLU	-1	-0.817	-0.882	23.468	11.715	11.715	0.000	0.000	0.000	0.000
92	B	106	ASP	-1	-0.882	-0.948	25.276	9.607	9.607	0.000	0.000	0.000	0.000
93	B	107	GLU	-1	-0.980	-0.989	27.901	9.740	9.740	0.000	0.000	0.000	0.000
94	B	108	LYS	1	0.785	0.871	23.702	-12.173	-12.173	0.000	0.000	0.000	0.000
95	B	109	ILE	0	0.002	-0.002	27.794	-0.327	-0.327	0.000	0.000	0.000	0.000
96	B	110	GLU	-1	-0.837	-0.902	30.316	7.866	7.866	0.000	0.000	0.000	0.000
97	B	111	ALA	0	-0.004	-0.009	30.743	-0.302	-0.302	0.000	0.000	0.000	0.000
98	B	112	ILE	0	0.004	0.007	28.385	-0.225	-0.225	0.000	0.000	0.000	0.000
99	B	113	LYS	1	0.860	0.927	32.828	-8.747	-8.747	0.000	0.000	0.000	0.000
100	B	114	LYS	1	0.849	0.911	36.018	-8.272	-8.272	0.000	0.000	0.000	0.000
101	B	115	LYS	1	0.861	0.930	34.114	-8.925	-8.925	0.000	0.000	0.000	0.000
102	B	116	GLU	-1	-0.724	-0.866	34.760	8.443	8.443	0.000	0.000	0.000	0.000
103	B	117	LYS	1	0.855	0.948	38.136	-7.115	-7.115	0.000	0.000	0.000	0.000
104	B	118	LEU	0	-0.002	0.000	39.436	-0.186	-0.186	0.000	0.000	0.000	0.000
105	B	119	LEU	0	-0.020	-0.005	38.010	-0.099	-0.099	0.000	0.000	0.000	0.000
106	B	120	ARG	1	0.945	0.949	40.178	-7.565	-7.565	0.000	0.000	0.000	0.000
107	B	121	HIS	0	-0.069	-0.020	43.802	-0.194	-0.194	0.000	0.000	0.000	0.000
108	B	122	VAL	0	-0.007	-0.007	43.334	-0.148	-0.148	0.000	0.000	0.000	0.000
109	B	123	ASP	-1	-0.865	-0.946	42.996	7.164	7.164	0.000	0.000	0.000	0.000
110	B	124	SER	0	-0.018	-0.005	46.133	-0.115	-0.115	0.000	0.000	0.000	0.000
111	B	125	LEU	0	-0.032	-0.014	48.602	-0.108	-0.108	0.000	0.000	0.000	0.000
112	B	126	ILE	0	-0.036	-0.017	45.992	-0.080	-0.080	0.000	0.000	0.000	0.000
113	B	127	GLU	-1	-0.966	-0.981	50.091	6.134	6.134	0.000	0.000	0.000	0.000
114	B	128	ASP	-1	-0.917	-0.966	51.795	5.691	5.691	0.000	0.000	0.000	0.000
115	B	129	PHE	0	-0.110	-0.050	52.440	-0.126	-0.126	0.000	0.000	0.000	0.000
116	B	130	VAL	0	-0.034	-0.010	52.755	-0.016	-0.016	0.000	0.000	0.000	0.000
117	B	131	ASP	-1	-0.913	-0.948	55.659	5.205	5.205	0.000	0.000	0.000	0.000
118	B	132	GLY	0	-0.038	-0.028	58.186	-0.007	-0.007	0.000	0.000	0.000	0.000
119	B	133	ILE	0	-0.092	-0.033	58.343	0.035	0.035	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:3:ASP)