FMO DATABASE

FMODB ID: MVLYZ

Calculation Name: 5TU8-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5TU8

Chain ID: B

ChEMBL ID:

UniProt ID: Q5HKE8

Base Structure: X-ray

Registration Date: 2023-06-22

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	139
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-871842.397842
FMO2-HF: Nuclear repulsion	819184.959931
FMO2-HF: Total energy	-52657.437911
FMO2-MP2: Total energy	-52814.190924

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:16:LYS)

Summations of interaction energy for fragment #1(B:16:LYS)

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.
-249.519	-252.838	42.924	-21.344	-18.26	-0.218

Interaction energy analysis for fragmet #1(B:16:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.793 / q_NPA : 0.879

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	18	ARG	1	0.861	0.935	3.235	33.371	36.421	0.035	-1.312	-1.772	0.004
4	B	19	GLU	-1	-0.831	-0.897	5.321	-26.799	-26.780	-0.001	-0.001	-0.016	0.000
5	B	20	PHE	0	0.050	0.025	9.049	-1.160	-1.160	0.000	0.000	0.000	0.000
6	B	21	ASN	0	-0.064	-0.061	11.847	0.855	0.855	0.000	0.000	0.000	0.000
7	B	22	PRO	0	0.037	0.016	13.671	-0.185	-0.185	0.000	0.000	0.000	0.000
8	B	23	ASP	-1	-0.883	-0.929	16.370	-17.228	-17.228	0.000	0.000	0.000	0.000
9	B	24	LEU	0	-0.103	-0.036	10.220	0.238	0.238	0.000	0.000	0.000	0.000
10	B	25	LYS	1	0.825	0.888	14.792	20.273	20.273	0.000	0.000	0.000	0.000
11	B	26	PRO	0	0.027	-0.008	14.452	-1.437	-1.437	0.000	0.000	0.000	0.000
12	B	27	GLY	0	-0.018	0.009	13.130	0.338	0.338	0.000	0.000	0.000	0.000
13	B	28	GLU	-1	-0.844	-0.880	11.357	-22.449	-22.449	0.000	0.000	0.000	0.000
14	B	29	GLU	-1	-0.826	-0.916	4.557	-53.551	-53.428	-0.001	-0.009	-0.112	0.000
15	B	30	ARG	1	0.850	0.934	7.319	24.039	24.039	0.000	0.000	0.000	0.000
16	B	31	VAL	0	0.012	-0.010	3.791	-1.125	-0.992	-0.001	-0.017	-0.115	0.000
17	B	32	LYS	1	0.849	0.924	6.123	31.889	31.889	0.000	0.000	0.000	0.000
18	B	33	GLN	0	-0.017	-0.013	7.130	3.724	3.724	0.000	0.000	0.000	0.000
19	B	34	LYS	1	0.959	0.973	6.438	26.770	26.770	0.000	0.000	0.000	0.000
20	B	72	GLU	-1	-0.818	-0.886	1.745	-153.070	-162.624	36.745	-15.724	-11.468	-0.174
21	B	73	ILE	0	0.035	0.017	2.578	-9.601	-7.682	1.368	-1.801	-1.487	-0.019
22	B	74	THR	0	-0.023	-0.032	2.156	-7.544	-6.696	4.780	-2.424	-3.204	-0.029
23	B	75	GLU	-1	-0.779	-0.855	4.368	-25.733	-25.590	-0.001	-0.056	-0.086	0.000
24	B	76	TYR	0	-0.056	-0.076	7.296	-1.445	-1.445	0.000	0.000	0.000	0.000
25	B	77	GLY	0	0.047	0.040	9.313	1.656	1.656	0.000	0.000	0.000	0.000
26	B	78	GLY	0	-0.019	-0.014	12.721	-0.728	-0.728	0.000	0.000	0.000	0.000
27	B	79	GLU	-1	-0.799	-0.898	15.358	-17.225	-17.225	0.000	0.000	0.000	0.000
28	B	80	GLU	-1	-0.869	-0.931	17.582	-13.662	-13.662	0.000	0.000	0.000	0.000
29	B	81	ILE	0	-0.068	-0.018	21.056	0.260	0.260	0.000	0.000	0.000	0.000
30	B	82	LYS	1	0.869	0.915	23.347	13.156	13.156	0.000	0.000	0.000	0.000
31	B	83	PRO	0	0.004	0.020	27.053	0.010	0.010	0.000	0.000	0.000	0.000
32	B	84	GLY	0	0.028	0.017	30.245	0.034	0.034	0.000	0.000	0.000	0.000
33	B	85	HIS	0	-0.052	-0.041	33.428	-0.096	-0.096	0.000	0.000	0.000	0.000
34	B	86	LYS	1	0.845	0.911	36.059	8.867	8.867	0.000	0.000	0.000	0.000
35	B	87	ASP	-1	-0.826	-0.912	39.761	-7.336	-7.336	0.000	0.000	0.000	0.000
36	B	88	GLU	-1	-0.977	-1.010	40.715	-7.865	-7.865	0.000	0.000	0.000	0.000
37	B	89	PHE	0	0.013	-0.005	45.026	0.128	0.128	0.000	0.000	0.000	0.000
38	B	90	ASP	-1	-0.811	-0.920	47.166	-6.832	-6.832	0.000	0.000	0.000	0.000
39	B	91	PRO	0	-0.026	-0.028	49.114	0.100	0.100	0.000	0.000	0.000	0.000
40	B	92	ASN	0	-0.072	-0.034	50.591	0.243	0.243	0.000	0.000	0.000	0.000
41	B	93	ALA	0	0.022	0.039	48.994	0.000	0.000	0.000	0.000	0.000	0.000
42	B	94	PRO	0	-0.011	-0.022	50.755	0.134	0.134	0.000	0.000	0.000	0.000
43	B	95	LYS	1	0.810	0.886	53.173	5.294	5.294	0.000	0.000	0.000	0.000
44	B	96	GLY	0	-0.052	-0.025	54.360	0.031	0.031	0.000	0.000	0.000	0.000
45	B	97	SER	0	-0.092	-0.045	49.806	-0.101	-0.101	0.000	0.000	0.000	0.000
46	B	98	GLN	0	0.044	0.005	44.692	0.168	0.168	0.000	0.000	0.000	0.000
47	B	99	GLU	-1	-0.935	-0.956	42.349	-7.446	-7.446	0.000	0.000	0.000	0.000
48	B	100	ASP	-1	-0.821	-0.881	39.954	-7.652	-7.652	0.000	0.000	0.000	0.000
49	B	101	VAL	0	-0.029	-0.021	36.279	-0.072	-0.072	0.000	0.000	0.000	0.000
50	B	102	PRO	0	-0.004	0.001	33.335	-0.130	-0.130	0.000	0.000	0.000	0.000
51	B	103	GLY	0	0.053	0.032	32.338	-0.009	-0.009	0.000	0.000	0.000	0.000
52	B	104	LYS	1	0.764	0.864	27.358	9.970	9.970	0.000	0.000	0.000	0.000
53	B	105	PRO	0	0.023	0.020	23.897	0.200	0.200	0.000	0.000	0.000	0.000
54	B	106	GLY	0	0.022	0.008	24.425	-0.038	-0.038	0.000	0.000	0.000	0.000
55	B	107	VAL	0	-0.038	-0.026	18.264	-0.535	-0.535	0.000	0.000	0.000	0.000
56	B	108	LYS	1	0.850	0.911	18.284	16.396	16.396	0.000	0.000	0.000	0.000
57	B	109	ASN	0	0.046	0.027	15.190	-1.554	-1.554	0.000	0.000	0.000	0.000
58	B	110	PRO	0	-0.054	-0.031	12.594	0.902	0.902	0.000	0.000	0.000	0.000
59	B	111	ASP	-1	-0.877	-0.902	11.812	-25.000	-25.000	0.000	0.000	0.000	0.000
60	B	112	THR	0	-0.025	-0.033	14.916	0.854	0.854	0.000	0.000	0.000	0.000
61	B	113	GLY	0	-0.005	0.005	17.899	0.912	0.912	0.000	0.000	0.000	0.000
62	B	114	GLU	-1	-0.977	-0.983	19.797	-14.598	-14.598	0.000	0.000	0.000	0.000
63	B	115	VAL	0	0.001	-0.002	20.538	-0.614	-0.614	0.000	0.000	0.000	0.000
64	B	116	VAL	0	-0.012	0.000	18.602	0.270	0.270	0.000	0.000	0.000	0.000
65	B	117	THR	0	-0.041	-0.015	22.028	0.248	0.248	0.000	0.000	0.000	0.000
66	B	118	PRO	0	0.047	0.014	24.356	-0.198	-0.198	0.000	0.000	0.000	0.000
67	B	119	PRO	0	0.007	0.010	26.918	-0.117	-0.117	0.000	0.000	0.000	0.000
68	B	120	VAL	0	-0.071	-0.028	28.236	0.333	0.333	0.000	0.000	0.000	0.000
69	B	121	ASP	-1	-0.805	-0.896	31.332	-9.620	-9.620	0.000	0.000	0.000	0.000
70	B	122	ASP	-1	-0.846	-0.920	33.394	-9.563	-9.563	0.000	0.000	0.000	0.000
71	B	123	VAL	0	-0.041	-0.020	35.621	0.113	0.113	0.000	0.000	0.000	0.000
72	B	124	THR	0	-0.002	0.018	39.118	-0.065	-0.065	0.000	0.000	0.000	0.000
73	B	125	LYS	1	0.807	0.900	42.444	7.368	7.368	0.000	0.000	0.000	0.000
74	B	126	TYR	0	-0.021	-0.026	44.875	0.087	0.087	0.000	0.000	0.000	0.000
75	B	127	GLY	0	0.042	0.033	48.571	0.002	0.002	0.000	0.000	0.000	0.000
76	B	128	PRO	0	-0.054	-0.021	51.510	0.049	0.049	0.000	0.000	0.000	0.000
77	B	129	VAL	0	0.015	0.010	54.275	0.005	0.005	0.000	0.000	0.000	0.000
78	B	130	ASP	-1	-0.812	-0.895	56.903	-5.256	-5.256	0.000	0.000	0.000	0.000
79	B	131	GLY	0	0.011	-0.013	60.077	-0.079	-0.079	0.000	0.000	0.000	0.000
80	B	132	ASP	-1	-0.905	-0.941	62.125	-5.065	-5.065	0.000	0.000	0.000	0.000
81	B	133	SER	0	-0.017	-0.010	65.436	0.002	0.002	0.000	0.000	0.000	0.000
82	B	134	ILE	0	-0.001	0.003	67.331	0.022	0.022	0.000	0.000	0.000	0.000
83	B	135	THR	0	-0.011	0.001	70.593	0.021	0.021	0.000	0.000	0.000	0.000
84	B	136	SER	0	0.008	0.004	74.198	-0.016	-0.016	0.000	0.000	0.000	0.000
85	B	137	THR	0	-0.019	-0.015	77.249	0.005	0.005	0.000	0.000	0.000	0.000
86	B	138	GLU	-1	-0.920	-0.954	80.790	-4.015	-4.015	0.000	0.000	0.000	0.000
87	B	139	GLU	-1	-0.949	-0.978	83.651	-3.629	-3.629	0.000	0.000	0.000	0.000
88	B	140	ILE	0	-0.061	-0.027	86.919	-0.010	-0.010	0.000	0.000	0.000	0.000
89	B	141	PRO	0	0.024	0.004	89.610	0.034	0.034	0.000	0.000	0.000	0.000
90	B	142	PHE	0	0.010	0.004	93.037	0.013	0.013	0.000	0.000	0.000	0.000
91	B	143	ASP	-1	-0.817	-0.878	96.126	-3.349	-3.349	0.000	0.000	0.000	0.000
92	B	144	LYS	1	0.824	0.887	98.916	3.265	3.265	0.000	0.000	0.000	0.000
93	B	145	LYS	1	0.810	0.879	99.876	3.286	3.286	0.000	0.000	0.000	0.000
94	B	146	ARG	1	0.929	0.943	105.291	2.955	2.955	0.000	0.000	0.000	0.000
95	B	147	GLU	-1	-0.910	-0.940	109.121	-2.911	-2.911	0.000	0.000	0.000	0.000
96	B	159	VAL	0	-0.047	-0.039	106.198	0.012	0.012	0.000	0.000	0.000	0.000
97	B	160	LYS	1	0.904	0.957	107.996	2.929	2.929	0.000	0.000	0.000	0.000
98	B	161	GLN	0	0.046	0.029	100.793	0.014	0.014	0.000	0.000	0.000	0.000
99	B	162	LYS	1	0.829	0.916	99.754	3.282	3.282	0.000	0.000	0.000	0.000
100	B	163	GLY	0	0.018	0.009	99.700	-0.016	-0.016	0.000	0.000	0.000	0.000
101	B	164	GLU	-1	-0.876	-0.922	94.914	-3.440	-3.440	0.000	0.000	0.000	0.000
102	B	165	PRO	0	0.028	0.027	91.297	0.003	0.003	0.000	0.000	0.000	0.000
103	B	166	GLY	0	0.018	-0.002	90.397	-0.007	-0.007	0.000	0.000	0.000	0.000
104	B	167	THR	0	-0.037	-0.032	85.234	-0.005	-0.005	0.000	0.000	0.000	0.000
105	B	168	LYS	1	0.841	0.906	82.011	3.971	3.971	0.000	0.000	0.000	0.000
106	B	169	THR	0	0.011	0.014	77.307	-0.012	-0.012	0.000	0.000	0.000	0.000
107	B	170	ILE	0	-0.009	-0.006	75.475	0.008	0.008	0.000	0.000	0.000	0.000
108	B	171	THR	0	0.017	0.000	71.651	-0.024	-0.024	0.000	0.000	0.000	0.000
109	B	172	THR	0	-0.009	-0.020	68.972	0.028	0.028	0.000	0.000	0.000	0.000
110	B	173	PRO	0	0.015	0.020	66.417	-0.038	-0.038	0.000	0.000	0.000	0.000
111	B	174	THR	0	-0.010	-0.013	63.878	-0.021	-0.021	0.000	0.000	0.000	0.000
112	B	175	THR	0	-0.002	0.011	58.820	-0.002	-0.002	0.000	0.000	0.000	0.000
113	B	176	LYS	1	0.922	0.955	57.634	5.469	5.469	0.000	0.000	0.000	0.000
114	B	177	ASN	0	0.092	0.053	51.083	-0.116	-0.116	0.000	0.000	0.000	0.000
115	B	178	PRO	0	-0.045	-0.033	51.251	0.082	0.082	0.000	0.000	0.000	0.000
116	B	179	LEU	0	0.004	0.010	47.276	0.031	0.031	0.000	0.000	0.000	0.000
117	B	180	THR	0	-0.066	-0.068	51.239	-0.013	-0.013	0.000	0.000	0.000	0.000
118	B	181	GLY	0	-0.022	-0.002	53.641	0.094	0.094	0.000	0.000	0.000	0.000
119	B	182	GLU	-1	-0.891	-0.901	54.569	-5.798	-5.798	0.000	0.000	0.000	0.000
120	B	183	LYS	1	0.825	0.904	57.750	4.890	4.890	0.000	0.000	0.000	0.000
121	B	184	VAL	0	-0.021	-0.008	55.701	-0.036	-0.036	0.000	0.000	0.000	0.000
122	B	185	GLY	0	-0.010	0.003	59.100	-0.001	-0.001	0.000	0.000	0.000	0.000
123	B	186	GLU	-1	-0.861	-0.928	61.987	-4.808	-4.808	0.000	0.000	0.000	0.000
124	B	187	GLY	0	-0.018	-0.007	65.547	-0.023	-0.023	0.000	0.000	0.000	0.000
125	B	188	LYS	1	0.903	0.938	66.824	4.771	4.771	0.000	0.000	0.000	0.000
126	B	189	SER	0	0.063	0.027	70.279	-0.039	-0.039	0.000	0.000	0.000	0.000
127	B	190	THR	0	-0.036	-0.002	73.071	0.039	0.039	0.000	0.000	0.000	0.000
128	B	191	GLU	-1	-0.793	-0.885	75.495	-4.042	-4.042	0.000	0.000	0.000	0.000
129	B	192	LYS	1	0.938	0.973	79.120	3.981	3.981	0.000	0.000	0.000	0.000
130	B	193	VAL	0	0.015	0.004	81.088	0.001	0.001	0.000	0.000	0.000	0.000
131	B	194	THR	0	-0.040	-0.014	82.109	0.015	0.015	0.000	0.000	0.000	0.000
132	B	195	LYS	1	0.825	0.916	85.038	3.575	3.575	0.000	0.000	0.000	0.000
133	B	196	GLN	0	0.061	0.026	88.692	-0.008	-0.008	0.000	0.000	0.000	0.000
134	B	197	PRO	0	-0.010	-0.005	91.148	0.013	0.013	0.000	0.000	0.000	0.000
135	B	198	VAL	0	-0.019	-0.005	93.587	0.019	0.019	0.000	0.000	0.000	0.000
136	B	199	ASP	-1	-0.792	-0.892	97.076	-3.299	-3.299	0.000	0.000	0.000	0.000
137	B	200	GLU	-1	-0.806	-0.885	99.925	-3.212	-3.212	0.000	0.000	0.000	0.000
138	B	201	ILE	0	-0.017	0.000	102.456	0.019	0.019	0.000	0.000	0.000	0.000
139	B	202	THR	0	0.002	-0.002	105.923	0.018	0.018	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:16:LYS)