FMO DATABASE

FMODB ID: MVMGZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-734081.871658
FMO2-HF: Nuclear repulsion	685578.841827
FMO2-HF: Total energy	-48503.029831
FMO2-MP2: Total energy	-48644.033901

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.
50.335	55.402	2.251	-3.122	-4.195	0.001

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 : -0.906 / q_NPA : -0.963

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	B	5	LEU	0	0.062	0.033	3.799	-5.821	-3.792	-0.022	-0.899	-1.108	0.003
4	B	6	THR	0	0.072	0.032	2.277	-7.024	-5.313	2.268	-1.850	-2.128	-0.003
5	B	7	GLN	0	0.015	0.001	3.576	-12.021	-10.907	0.007	-0.366	-0.755	0.001
6	B	8	LEU	0	-0.052	-0.004	5.230	-5.455	-5.377	-0.001	-0.005	-0.072	0.000
7	B	9	GLN	0	0.033	-0.011	7.502	0.344	0.344	0.000	0.000	0.000	0.000
8	B	10	ILE	0	0.018	0.028	5.014	-1.636	-1.501	-0.001	-0.002	-0.132	0.000
9	B	11	CYS	0	-0.088	-0.044	8.803	-3.992	-3.992	0.000	0.000	0.000	0.000
10	B	12	LEU	0	-0.020	-0.015	10.893	-2.283	-2.283	0.000	0.000	0.000	0.000
11	B	13	ASP	-1	-0.876	-0.934	12.248	21.747	21.747	0.000	0.000	0.000	0.000
12	B	14	GLN	0	0.048	0.031	11.820	-3.048	-3.048	0.000	0.000	0.000	0.000
13	B	15	MET	0	-0.034	-0.001	15.533	-1.510	-1.510	0.000	0.000	0.000	0.000
14	B	16	THR	0	0.041	0.017	16.450	-1.445	-1.445	0.000	0.000	0.000	0.000
15	B	17	GLU	-1	-0.919	-0.971	16.132	18.321	18.321	0.000	0.000	0.000	0.000
16	B	18	GLN	0	-0.024	-0.031	19.539	-1.057	-1.057	0.000	0.000	0.000	0.000
17	B	19	PHE	0	-0.053	-0.027	21.020	-0.834	-0.834	0.000	0.000	0.000	0.000
18	B	20	CYS	0	-0.066	-0.027	22.320	-0.736	-0.736	0.000	0.000	0.000	0.000
19	B	21	ALA	0	-0.056	-0.024	23.090	-0.645	-0.645	0.000	0.000	0.000	0.000
20	B	22	THR	0	0.021	0.000	24.942	-0.528	-0.528	0.000	0.000	0.000	0.000
21	B	23	LEU	0	-0.010	-0.007	27.224	-0.394	-0.394	0.000	0.000	0.000	0.000
22	B	24	ASN	0	0.053	0.037	27.989	-0.586	-0.586	0.000	0.000	0.000	0.000
23	B	25	TYR	0	0.004	0.020	29.833	-0.509	-0.509	0.000	0.000	0.000	0.000
24	B	26	ILE	0	0.026	-0.007	30.747	-0.364	-0.364	0.000	0.000	0.000	0.000
25	B	27	ASP	-1	-0.885	-0.932	32.355	9.517	9.517	0.000	0.000	0.000	0.000
26	B	28	LYS	1	0.775	0.869	30.654	-10.609	-10.609	0.000	0.000	0.000	0.000
27	B	29	ASN	0	-0.033	-0.019	34.274	-0.308	-0.308	0.000	0.000	0.000	0.000
28	B	30	HIS	0	0.038	0.010	37.366	-0.034	-0.034	0.000	0.000	0.000	0.000
29	B	31	GLY	0	0.027	0.017	36.333	-0.150	-0.150	0.000	0.000	0.000	0.000
30	B	32	PHE	0	-0.014	-0.010	37.344	-0.025	-0.025	0.000	0.000	0.000	0.000
31	B	33	GLU	-1	-0.969	-0.981	38.694	7.117	7.117	0.000	0.000	0.000	0.000
32	B	34	ARG	1	0.791	0.918	38.661	-8.302	-8.302	0.000	0.000	0.000	0.000
33	B	35	LEU	0	-0.034	-0.004	38.126	-0.076	-0.076	0.000	0.000	0.000	0.000
34	B	48	THR	0	-0.036	-0.033	42.288	-0.116	-0.116	0.000	0.000	0.000	0.000
35	B	49	VAL	0	-0.020	-0.009	41.615	0.140	0.140	0.000	0.000	0.000	0.000
36	B	50	VAL	0	0.053	0.047	36.978	-0.131	-0.131	0.000	0.000	0.000	0.000
37	B	51	PRO	0	0.014	-0.004	40.295	-0.102	-0.102	0.000	0.000	0.000	0.000
38	B	52	PRO	0	-0.030	-0.035	40.344	0.193	0.193	0.000	0.000	0.000	0.000
39	B	53	GLU	-1	-0.944	-0.953	39.686	7.932	7.932	0.000	0.000	0.000	0.000
40	B	54	GLU	-1	-0.827	-0.930	36.252	8.917	8.917	0.000	0.000	0.000	0.000
41	B	55	PHE	0	0.006	0.019	35.537	0.345	0.345	0.000	0.000	0.000	0.000
42	B	56	SER	0	0.040	0.029	34.593	0.244	0.244	0.000	0.000	0.000	0.000
43	B	57	ASN	0	-0.025	-0.015	34.197	0.145	0.145	0.000	0.000	0.000	0.000
44	B	58	THR	0	0.025	0.003	30.542	0.349	0.349	0.000	0.000	0.000	0.000
45	B	59	ILE	0	-0.042	-0.041	30.203	0.423	0.423	0.000	0.000	0.000	0.000
46	B	60	ASP	-1	-0.905	-0.960	30.065	10.042	10.042	0.000	0.000	0.000	0.000
47	B	61	GLU	-1	-0.975	-0.987	27.372	11.677	11.677	0.000	0.000	0.000	0.000
48	B	62	LEU	0	-0.028	-0.003	25.146	0.573	0.573	0.000	0.000	0.000	0.000
49	B	63	SER	0	-0.007	0.000	25.151	0.673	0.673	0.000	0.000	0.000	0.000
50	B	64	THR	0	0.016	-0.010	25.762	0.305	0.305	0.000	0.000	0.000	0.000
51	B	65	ASP	-1	-0.888	-0.928	21.284	16.089	16.089	0.000	0.000	0.000	0.000
52	B	66	ILE	0	0.016	-0.001	21.340	1.011	1.011	0.000	0.000	0.000	0.000
53	B	67	ILE	0	-0.017	0.005	21.397	0.543	0.543	0.000	0.000	0.000	0.000
54	B	68	LEU	0	-0.045	-0.013	19.500	0.345	0.345	0.000	0.000	0.000	0.000
55	B	69	LYS	1	0.919	0.965	16.293	-17.865	-17.865	0.000	0.000	0.000	0.000
56	B	70	THR	0	0.031	0.006	16.950	0.961	0.961	0.000	0.000	0.000	0.000
57	B	71	ARG	1	0.925	0.972	18.353	-13.706	-13.706	0.000	0.000	0.000	0.000
58	B	72	GLN	0	-0.043	-0.031	14.331	-0.286	-0.286	0.000	0.000	0.000	0.000
59	B	73	ILE	0	0.051	0.017	12.592	1.163	1.163	0.000	0.000	0.000	0.000
60	B	74	ASN	0	-0.013	-0.010	13.844	0.462	0.462	0.000	0.000	0.000	0.000
61	B	75	LYS	1	1.003	1.000	14.823	-15.820	-15.820	0.000	0.000	0.000	0.000
62	B	76	LEU	0	-0.041	-0.004	9.494	0.676	0.676	0.000	0.000	0.000	0.000
63	B	77	ILE	0	0.011	-0.010	11.064	1.540	1.540	0.000	0.000	0.000	0.000
64	B	78	ASP	-1	-0.952	-0.971	12.830	17.421	17.421	0.000	0.000	0.000	0.000
65	B	79	SER	0	-0.073	-0.046	10.975	-0.289	-0.289	0.000	0.000	0.000	0.000
66	B	80	LEU	0	-0.058	-0.013	8.448	2.176	2.176	0.000	0.000	0.000	0.000
67	B	81	PRO	0	-0.052	-0.027	6.237	-1.452	-1.452	0.000	0.000	0.000	0.000
68	B	82	GLY	0	-0.017	-0.028	9.370	0.801	0.801	0.000	0.000	0.000	0.000
69	B	83	VAL	0	-0.030	-0.003	11.719	-0.975	-0.975	0.000	0.000	0.000	0.000
70	B	84	ASP	-1	-0.897	-0.944	14.136	15.636	15.636	0.000	0.000	0.000	0.000
71	B	85	VAL	0	-0.069	-0.017	14.734	-0.668	-0.668	0.000	0.000	0.000	0.000
72	B	86	SER	0	0.048	0.031	16.343	0.309	0.309	0.000	0.000	0.000	0.000
73	B	87	ALA	0	0.065	0.017	16.233	0.619	0.619	0.000	0.000	0.000	0.000
74	B	88	GLU	-1	-0.830	-0.905	17.313	11.764	11.764	0.000	0.000	0.000	0.000
75	B	89	GLU	-1	-0.936	-0.992	18.524	14.188	14.188	0.000	0.000	0.000	0.000
76	B	90	GLN	0	-0.021	-0.006	12.741	0.742	0.742	0.000	0.000	0.000	0.000
77	B	91	LEU	0	0.042	0.000	16.164	-0.007	-0.007	0.000	0.000	0.000	0.000
78	B	92	ARG	1	0.847	0.932	17.892	-12.542	-12.542	0.000	0.000	0.000	0.000
79	B	93	LYS	1	0.956	0.984	15.779	-16.146	-16.146	0.000	0.000	0.000	0.000
80	B	94	ILE	0	-0.014	-0.007	13.825	0.185	0.185	0.000	0.000	0.000	0.000
81	B	95	ASP	-1	-0.756	-0.859	16.654	11.769	11.769	0.000	0.000	0.000	0.000
82	B	96	MET	0	-0.035	-0.023	19.466	-0.411	-0.411	0.000	0.000	0.000	0.000
83	B	97	LEU	0	-0.053	-0.035	15.057	-0.311	-0.311	0.000	0.000	0.000	0.000
84	B	98	GLN	0	0.006	0.003	18.038	0.357	0.357	0.000	0.000	0.000	0.000
85	B	99	LYS	1	0.858	0.911	20.067	-11.707	-11.707	0.000	0.000	0.000	0.000
86	B	100	LYS	1	0.935	0.971	21.833	-12.789	-12.789	0.000	0.000	0.000	0.000
87	B	101	LEU	0	-0.014	0.000	18.048	-0.015	-0.015	0.000	0.000	0.000	0.000
88	B	102	VAL	0	-0.008	0.002	21.963	-0.117	-0.117	0.000	0.000	0.000	0.000
89	B	103	GLU	-1	-0.907	-0.950	24.917	10.567	10.567	0.000	0.000	0.000	0.000
90	B	104	VAL	0	0.035	0.007	23.368	-0.222	-0.222	0.000	0.000	0.000	0.000
91	B	105	GLU	-1	-0.816	-0.880	24.442	12.007	12.007	0.000	0.000	0.000	0.000
92	B	106	ASP	-1	-0.899	-0.947	26.273	9.827	9.827	0.000	0.000	0.000	0.000
93	B	107	GLU	-1	-0.981	-0.997	28.668	9.932	9.932	0.000	0.000	0.000	0.000
94	B	108	LYS	1	0.778	0.873	24.587	-12.364	-12.364	0.000	0.000	0.000	0.000
95	B	109	ILE	0	-0.009	-0.014	29.002	-0.366	-0.366	0.000	0.000	0.000	0.000
96	B	110	GLU	-1	-0.807	-0.879	31.248	8.045	8.045	0.000	0.000	0.000	0.000
97	B	111	ALA	0	-0.002	0.003	31.530	-0.270	-0.270	0.000	0.000	0.000	0.000
98	B	112	ILE	0	0.010	-0.001	28.768	-0.238	-0.238	0.000	0.000	0.000	0.000
99	B	113	LYS	1	0.869	0.935	33.283	-8.840	-8.840	0.000	0.000	0.000	0.000
100	B	114	LYS	1	0.848	0.894	36.582	-8.397	-8.397	0.000	0.000	0.000	0.000
101	B	115	LYS	1	0.903	0.951	33.816	-9.303	-9.303	0.000	0.000	0.000	0.000
102	B	116	GLU	-1	-0.775	-0.884	35.859	8.499	8.499	0.000	0.000	0.000	0.000
103	B	117	LYS	1	0.858	0.945	38.520	-7.246	-7.246	0.000	0.000	0.000	0.000
104	B	118	LEU	0	0.003	-0.001	39.736	-0.180	-0.180	0.000	0.000	0.000	0.000
105	B	119	LEU	0	-0.013	-0.008	38.304	-0.104	-0.104	0.000	0.000	0.000	0.000
106	B	120	ARG	1	0.940	0.967	40.476	-7.712	-7.712	0.000	0.000	0.000	0.000
107	B	121	HIS	0	-0.085	-0.028	44.074	-0.192	-0.192	0.000	0.000	0.000	0.000
108	B	122	VAL	0	0.011	-0.003	43.380	-0.151	-0.151	0.000	0.000	0.000	0.000
109	B	123	ASP	-1	-0.871	-0.943	43.228	7.272	7.272	0.000	0.000	0.000	0.000
110	B	124	SER	0	-0.031	-0.016	46.354	-0.143	-0.143	0.000	0.000	0.000	0.000
111	B	125	LEU	0	-0.034	-0.019	48.882	-0.114	-0.114	0.000	0.000	0.000	0.000
112	B	126	ILE	0	-0.026	-0.024	46.096	-0.100	-0.100	0.000	0.000	0.000	0.000
113	B	127	GLU	-1	-0.966	-0.977	50.205	6.245	6.245	0.000	0.000	0.000	0.000
114	B	128	ASP	-1	-0.929	-0.958	51.702	5.762	5.762	0.000	0.000	0.000	0.000
115	B	129	PHE	0	-0.118	-0.059	52.531	-0.124	-0.124	0.000	0.000	0.000	0.000
116	B	130	VAL	0	-0.053	-0.014	52.748	-0.035	-0.035	0.000	0.000	0.000	0.000
117	B	131	ASP	-1	-0.910	-0.937	55.698	5.294	5.294	0.000	0.000	0.000	0.000
118	B	132	GLY	0	-0.030	-0.033	58.603	0.020	0.020	0.000	0.000	0.000	0.000
119	B	133	ILE	0	-0.079	-0.029	58.339	0.052	0.052	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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