FMO DATABASE

FMODB ID: MVVYZ

Calculation Name: 5DPR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DPR

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H492

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	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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1104721.803896
FMO2-HF: Nuclear repulsion	1053798.228683
FMO2-HF: Total energy	-50923.575213
FMO2-MP2: Total energy	-51072.570998

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:6:GLU)

Summations of interaction energy for fragment #1(A:6:GLU)

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.
-39.619	-37.949	-0.016	-0.803	-0.852	0.005

Interaction energy analysis for fragmet #1(A:6:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.937 / q_NPA : -0.975

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	8	VAL	0	0.006	-0.001	3.804	-3.742	-2.072	-0.016	-0.803	-0.852	0.005
4	A	9	ASN	0	-0.036	-0.024	6.497	-2.946	-2.946	0.000	0.000	0.000	0.000
5	A	10	VAL	0	0.006	0.007	9.392	-1.409	-1.409	0.000	0.000	0.000	0.000
6	A	11	GLY	0	-0.023	0.010	12.522	-0.608	-0.608	0.000	0.000	0.000	0.000
7	A	12	SER	0	0.105	0.026	15.614	0.433	0.433	0.000	0.000	0.000	0.000
8	A	13	PRO	0	-0.055	-0.043	18.818	-0.346	-0.346	0.000	0.000	0.000	0.000
9	A	14	SER	0	0.032	0.011	22.058	-0.351	-0.351	0.000	0.000	0.000	0.000
10	A	15	ASP	-1	-0.909	-0.939	19.500	13.851	13.851	0.000	0.000	0.000	0.000
11	A	16	ARG	1	0.904	0.956	19.484	-13.369	-13.369	0.000	0.000	0.000	0.000
12	A	17	PRO	0	0.014	0.008	22.876	-0.339	-0.339	0.000	0.000	0.000	0.000
13	A	18	PHE	0	0.044	0.006	26.338	0.129	0.129	0.000	0.000	0.000	0.000
14	A	19	LYS	1	0.853	0.901	29.332	-8.741	-8.741	0.000	0.000	0.000	0.000
15	A	20	GLN	0	-0.028	-0.013	23.764	0.259	0.259	0.000	0.000	0.000	0.000
16	A	21	ARG	1	0.817	0.917	25.600	-10.725	-10.725	0.000	0.000	0.000	0.000
17	A	22	ARG	1	0.942	0.990	27.578	-8.906	-8.906	0.000	0.000	0.000	0.000
18	A	23	SER	0	0.063	0.036	31.196	-0.080	-0.080	0.000	0.000	0.000	0.000
19	A	24	PHE	0	0.088	0.023	32.891	0.001	0.001	0.000	0.000	0.000	0.000
20	A	25	ALA	0	0.049	0.023	35.719	-0.177	-0.177	0.000	0.000	0.000	0.000
21	A	26	ASP	-1	-0.904	-0.965	34.404	8.380	8.380	0.000	0.000	0.000	0.000
22	A	27	ARG	1	0.754	0.892	32.691	-8.857	-8.857	0.000	0.000	0.000	0.000
23	A	28	CYS	0	0.033	0.041	37.148	-0.146	-0.146	0.000	0.000	0.000	0.000
24	A	29	LYS	1	0.937	0.975	39.600	-7.697	-7.697	0.000	0.000	0.000	0.000
25	A	30	GLU	-1	-0.874	-0.935	36.483	8.211	8.211	0.000	0.000	0.000	0.000
26	A	31	VAL	0	-0.024	-0.011	39.928	-0.120	-0.120	0.000	0.000	0.000	0.000
27	A	32	GLN	0	-0.013	0.001	42.215	-0.076	-0.076	0.000	0.000	0.000	0.000
28	A	33	GLN	0	-0.007	-0.015	42.896	-0.052	-0.052	0.000	0.000	0.000	0.000
29	A	34	ILE	0	-0.033	-0.010	41.461	-0.100	-0.100	0.000	0.000	0.000	0.000
30	A	35	ARG	1	0.983	0.984	44.813	-6.485	-6.485	0.000	0.000	0.000	0.000
31	A	36	ASP	-1	-0.887	-0.927	47.528	6.037	6.037	0.000	0.000	0.000	0.000
32	A	37	GLN	0	-0.081	-0.036	46.184	-0.019	-0.019	0.000	0.000	0.000	0.000
33	A	38	HIS	0	-0.089	-0.060	45.379	-0.166	-0.166	0.000	0.000	0.000	0.000
34	A	39	PRO	0	0.048	0.029	48.785	0.080	0.080	0.000	0.000	0.000	0.000
35	A	40	SER	0	-0.044	-0.011	51.217	0.031	0.031	0.000	0.000	0.000	0.000
36	A	41	LYS	1	0.916	0.953	46.234	-6.515	-6.515	0.000	0.000	0.000	0.000
37	A	42	ILE	0	0.090	0.051	43.466	0.037	0.037	0.000	0.000	0.000	0.000
38	A	43	PRO	0	-0.055	-0.013	40.829	0.144	0.144	0.000	0.000	0.000	0.000
39	A	44	VAL	0	0.034	0.001	37.878	0.058	0.058	0.000	0.000	0.000	0.000
40	A	45	ILE	0	-0.032	-0.010	32.879	0.175	0.175	0.000	0.000	0.000	0.000
41	A	46	ILE	0	-0.013	-0.012	33.356	-0.043	-0.043	0.000	0.000	0.000	0.000
42	A	47	GLU	-1	-0.861	-0.934	28.525	10.432	10.432	0.000	0.000	0.000	0.000
43	A	48	ARG	1	0.913	0.961	21.807	-12.643	-12.643	0.000	0.000	0.000	0.000
44	A	49	TYR	0	0.040	0.012	27.444	0.229	0.229	0.000	0.000	0.000	0.000
45	A	50	LYS	1	0.935	0.966	22.317	-12.001	-12.001	0.000	0.000	0.000	0.000
46	A	51	GLY	0	0.047	0.018	23.286	0.551	0.551	0.000	0.000	0.000	0.000
47	A	52	GLU	-1	-0.767	-0.862	24.351	10.875	10.875	0.000	0.000	0.000	0.000
48	A	53	LYS	1	0.796	0.880	20.058	-12.854	-12.854	0.000	0.000	0.000	0.000
49	A	54	GLN	0	-0.004	0.022	23.832	0.226	0.226	0.000	0.000	0.000	0.000
50	A	55	LEU	0	-0.024	-0.004	26.691	-0.083	-0.083	0.000	0.000	0.000	0.000
51	A	56	PRO	0	0.049	0.035	26.058	0.477	0.477	0.000	0.000	0.000	0.000
52	A	57	VAL	0	-0.013	-0.016	23.426	-0.296	-0.296	0.000	0.000	0.000	0.000
53	A	58	LEU	0	0.013	0.003	26.690	-0.130	-0.130	0.000	0.000	0.000	0.000
54	A	59	ASP	-1	-0.822	-0.896	28.392	9.680	9.680	0.000	0.000	0.000	0.000
55	A	60	LYS	1	0.817	0.917	29.782	-8.408	-8.408	0.000	0.000	0.000	0.000
56	A	61	THR	0	0.007	-0.001	29.796	0.155	0.155	0.000	0.000	0.000	0.000
57	A	62	LYS	1	0.914	0.955	32.198	-8.757	-8.757	0.000	0.000	0.000	0.000
58	A	63	PHE	0	-0.030	-0.032	34.274	-0.036	-0.036	0.000	0.000	0.000	0.000
59	A	64	LEU	0	0.032	0.029	38.811	-0.042	-0.042	0.000	0.000	0.000	0.000
60	A	65	VAL	0	-0.023	-0.008	41.943	-0.021	-0.021	0.000	0.000	0.000	0.000
61	A	66	PRO	0	-0.020	-0.004	44.565	-0.063	-0.063	0.000	0.000	0.000	0.000
62	A	67	ASP	-1	-0.791	-0.902	48.379	6.207	6.207	0.000	0.000	0.000	0.000
63	A	68	HIS	0	-0.006	-0.014	50.241	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	69	VAL	0	-0.066	-0.012	46.216	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	70	ASN	0	0.015	0.016	48.399	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	71	MET	0	0.065	0.028	42.897	0.186	0.186	0.000	0.000	0.000	0.000
67	A	72	SER	0	0.020	0.019	44.056	0.180	0.180	0.000	0.000	0.000	0.000
68	A	73	GLU	-1	-0.903	-0.961	45.212	6.372	6.372	0.000	0.000	0.000	0.000
69	A	74	LEU	0	0.022	0.006	40.451	0.133	0.133	0.000	0.000	0.000	0.000
70	A	75	VAL	0	0.000	-0.009	39.997	0.227	0.227	0.000	0.000	0.000	0.000
71	A	76	LYS	1	0.930	0.959	40.200	-6.488	-6.488	0.000	0.000	0.000	0.000
72	A	77	ILE	0	-0.033	-0.015	40.341	0.123	0.123	0.000	0.000	0.000	0.000
73	A	78	ILE	0	-0.001	-0.003	35.356	0.150	0.150	0.000	0.000	0.000	0.000
74	A	79	ARG	1	0.918	0.985	36.088	-7.834	-7.834	0.000	0.000	0.000	0.000
75	A	80	ARG	1	0.945	0.961	37.003	-7.086	-7.086	0.000	0.000	0.000	0.000
76	A	81	ARG	1	0.839	0.929	34.634	-8.574	-8.574	0.000	0.000	0.000	0.000
77	A	82	LEU	0	-0.005	0.003	30.666	0.200	0.200	0.000	0.000	0.000	0.000
78	A	83	GLN	0	-0.058	-0.015	32.826	0.133	0.133	0.000	0.000	0.000	0.000
79	A	84	LEU	0	-0.015	0.010	32.339	0.139	0.139	0.000	0.000	0.000	0.000
80	A	85	ASN	0	0.028	0.013	34.183	-0.413	-0.413	0.000	0.000	0.000	0.000
81	A	86	PRO	0	-0.010	-0.024	37.364	0.038	0.038	0.000	0.000	0.000	0.000
82	A	87	THR	0	0.014	-0.008	36.463	-0.064	-0.064	0.000	0.000	0.000	0.000
83	A	88	GLN	0	-0.060	0.000	32.037	0.166	0.166	0.000	0.000	0.000	0.000
84	A	89	ALA	0	0.034	0.018	34.786	-0.226	-0.226	0.000	0.000	0.000	0.000
85	A	90	PHE	0	-0.012	-0.038	33.895	0.279	0.279	0.000	0.000	0.000	0.000
86	A	91	PHE	0	0.001	0.021	35.218	-0.290	-0.290	0.000	0.000	0.000	0.000
87	A	92	LEU	0	-0.020	-0.020	35.398	0.275	0.275	0.000	0.000	0.000	0.000
88	A	93	LEU	0	0.003	-0.002	34.640	-0.238	-0.238	0.000	0.000	0.000	0.000
89	A	94	VAL	0	0.030	0.004	37.073	0.183	0.183	0.000	0.000	0.000	0.000
90	A	95	ASN	0	0.019	0.013	38.264	0.077	0.077	0.000	0.000	0.000	0.000
91	A	96	GLN	0	-0.016	-0.011	33.843	-0.045	-0.045	0.000	0.000	0.000	0.000
92	A	97	HIS	0	0.040	0.034	38.221	-0.168	-0.168	0.000	0.000	0.000	0.000
93	A	98	SER	0	0.027	-0.005	40.286	0.105	0.105	0.000	0.000	0.000	0.000
94	A	99	MET	0	0.046	0.028	41.142	-0.238	-0.238	0.000	0.000	0.000	0.000
95	A	100	VAL	0	-0.072	-0.022	42.422	-0.128	-0.128	0.000	0.000	0.000	0.000
96	A	101	SER	0	0.001	-0.033	44.216	-0.122	-0.122	0.000	0.000	0.000	0.000
97	A	102	VAL	0	-0.019	0.025	46.139	-0.153	-0.153	0.000	0.000	0.000	0.000
98	A	103	SER	0	-0.035	-0.038	48.159	0.085	0.085	0.000	0.000	0.000	0.000
99	A	104	THR	0	0.032	0.019	49.895	-0.046	-0.046	0.000	0.000	0.000	0.000
100	A	105	PRO	0	0.050	0.028	49.475	0.153	0.153	0.000	0.000	0.000	0.000
101	A	106	ILE	0	0.015	-0.011	43.079	0.043	0.043	0.000	0.000	0.000	0.000
102	A	107	ALA	0	0.013	0.006	47.308	0.084	0.084	0.000	0.000	0.000	0.000
103	A	108	ASP	-1	-0.857	-0.925	49.707	5.819	5.819	0.000	0.000	0.000	0.000
104	A	109	ILE	0	-0.061	-0.026	44.499	0.030	0.030	0.000	0.000	0.000	0.000
105	A	110	TYR	0	-0.082	-0.067	43.413	0.054	0.054	0.000	0.000	0.000	0.000
106	A	111	GLU	-1	-0.935	-0.980	46.087	6.220	6.220	0.000	0.000	0.000	0.000
107	A	112	GLN	0	-0.105	-0.057	47.896	-0.046	-0.046	0.000	0.000	0.000	0.000
108	A	113	GLU	-1	-0.896	-0.958	42.655	7.038	7.038	0.000	0.000	0.000	0.000
109	A	114	LYS	1	0.803	0.937	41.910	-6.280	-6.280	0.000	0.000	0.000	0.000
110	A	115	ASP	-1	-0.814	-0.900	37.342	8.085	8.085	0.000	0.000	0.000	0.000
111	A	116	GLU	-1	-0.912	-0.956	39.840	7.259	7.259	0.000	0.000	0.000	0.000
112	A	117	ASP	-1	-0.783	-0.909	36.680	8.031	8.031	0.000	0.000	0.000	0.000
113	A	118	GLY	0	0.035	0.020	39.982	-0.061	-0.061	0.000	0.000	0.000	0.000
114	A	119	PHE	0	-0.043	-0.011	37.201	-0.065	-0.065	0.000	0.000	0.000	0.000
115	A	120	LEU	0	0.062	0.040	39.918	-0.031	-0.031	0.000	0.000	0.000	0.000
116	A	121	TYR	0	-0.097	-0.076	32.949	0.333	0.333	0.000	0.000	0.000	0.000
117	A	122	MET	0	-0.009	0.000	35.500	-0.113	-0.113	0.000	0.000	0.000	0.000
118	A	123	VAL	0	0.006	0.010	30.617	0.312	0.312	0.000	0.000	0.000	0.000
119	A	124	TYR	0	-0.008	-0.002	28.861	-0.220	-0.220	0.000	0.000	0.000	0.000
120	A	125	ALA	0	-0.022	-0.029	30.631	0.431	0.431	0.000	0.000	0.000	0.000
121	A	126	SER	0	0.013	-0.008	30.100	-0.343	-0.343	0.000	0.000	0.000	0.000
122	A	127	GLN	0	-0.009	0.007	29.526	-0.221	-0.221	0.000	0.000	0.000	0.000
123	A	128	GLU	-1	-0.897	-0.956	34.187	7.622	7.622	0.000	0.000	0.000	0.000
124	A	129	THR	0	-0.030	-0.012	33.271	0.031	0.031	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:GLU)