FMO DATABASE

FMODB ID: MVKMZ

Calculation Name: 4DYW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DYW

Chain ID: A

ChEMBL ID:

UniProt ID: Q3JWU2

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	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	129
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1088205.40305
FMO2-HF: Nuclear repulsion	1038435.97962
FMO2-HF: Total energy	-49769.42343
FMO2-MP2: Total energy	-49914.988493

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:5:GLU)

Summations of interaction energy for fragment #1(A:5: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.
56.691	59.74	-0.04	-1.793	-1.216	0

Interaction energy analysis for fragmet #1(A:5:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.941 / q_NPA : -0.968

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].
3	A	7	PRO	0	-0.011	0.008	3.842	-3.139	-0.090	-0.040	-1.793	-1.216
4	A	8	ARG	1	0.927	0.975	6.710	-27.340	-27.340	0.000	0.000	0.000
5	A	9	VAL	0	0.022	0.012	8.958	-1.278	-1.278	0.000	0.000	0.000
6	A	10	GLY	0	0.011	-0.003	12.567	-0.016	-0.016	0.000	0.000	0.000
7	A	11	CYS	0	-0.070	-0.034	15.418	-0.470	-0.470	0.000	0.000	0.000
8	A	12	GLY	0	0.081	0.028	19.188	0.119	0.119	0.000	0.000	0.000
9	A	13	ALA	0	-0.004	0.004	22.131	-0.169	-0.169	0.000	0.000	0.000
10	A	14	ALA	0	0.022	0.018	25.912	-0.041	-0.041	0.000	0.000	0.000
11	A	15	ILE	0	0.022	0.006	28.235	-0.220	-0.220	0.000	0.000	0.000
12	A	16	VAL	0	0.000	-0.008	31.411	-0.110	-0.110	0.000	0.000	0.000
13	A	17	ARG	1	0.963	0.979	34.395	-7.817	-7.817	0.000	0.000	0.000
14	A	18	ASP	-1	-0.952	-0.968	38.093	7.112	7.112	0.000	0.000	0.000
15	A	19	GLY	0	-0.007	-0.004	38.224	-0.078	-0.078	0.000	0.000	0.000
16	A	20	ARG	1	0.926	0.957	36.508	-7.236	-7.236	0.000	0.000	0.000
17	A	21	ILE	0	0.006	-0.001	29.037	0.057	0.057	0.000	0.000	0.000
18	A	22	LEU	0	-0.021	-0.004	31.157	-0.091	-0.091	0.000	0.000	0.000
19	A	23	LEU	0	-0.033	-0.006	27.507	0.352	0.352	0.000	0.000	0.000
20	A	24	ILE	0	0.031	0.005	25.539	-0.394	-0.394	0.000	0.000	0.000
21	A	25	LYS	1	0.922	0.976	26.458	-9.275	-9.275	0.000	0.000	0.000
22	A	26	ARG	1	0.926	0.970	18.160	-14.070	-14.070	0.000	0.000	0.000
23	A	27	LYS	1	0.930	0.968	24.307	-10.535	-10.535	0.000	0.000	0.000
24	A	28	ARG	1	0.883	0.943	20.414	-12.446	-12.446	0.000	0.000	0.000
25	A	29	ALA	0	-0.010	0.014	17.085	0.038	0.038	0.000	0.000	0.000
26	A	30	PRO	0	0.076	0.030	13.885	-0.142	-0.142	0.000	0.000	0.000
27	A	31	GLU	-1	-0.801	-0.929	16.470	13.761	13.761	0.000	0.000	0.000
28	A	32	ALA	0	-0.033	-0.011	19.356	-0.454	-0.454	0.000	0.000	0.000
29	A	33	GLY	0	0.006	-0.001	21.903	-0.165	-0.165	0.000	0.000	0.000
30	A	34	CYS	0	-0.073	-0.019	22.692	-0.371	-0.371	0.000	0.000	0.000
31	A	35	TRP	0	0.017	-0.004	24.758	0.060	0.060	0.000	0.000	0.000
32	A	36	GLY	0	-0.002	-0.023	23.766	0.200	0.200	0.000	0.000	0.000
33	A	37	LEU	0	-0.016	-0.009	23.083	-0.339	-0.339	0.000	0.000	0.000
34	A	38	PRO	0	0.030	0.033	23.252	0.366	0.366	0.000	0.000	0.000
35	A	39	GLY	0	-0.013	-0.022	21.232	-0.014	-0.014	0.000	0.000	0.000
36	A	40	GLY	0	0.037	0.029	17.940	-0.032	-0.032	0.000	0.000	0.000
37	A	41	LYS	1	0.871	0.935	13.268	-17.954	-17.954	0.000	0.000	0.000
38	A	42	VAL	0	0.024	0.018	14.905	-0.869	-0.869	0.000	0.000	0.000
39	A	43	ASP	-1	-0.909	-0.945	14.415	17.235	17.235	0.000	0.000	0.000
40	A	44	TRP	0	-0.029	-0.036	12.107	0.308	0.308	0.000	0.000	0.000
41	A	45	LEU	0	-0.029	-0.024	15.356	-0.790	-0.790	0.000	0.000	0.000
42	A	46	GLU	-1	-0.734	-0.817	17.885	12.849	12.849	0.000	0.000	0.000
43	A	47	PRO	0	-0.022	-0.017	19.014	0.406	0.406	0.000	0.000	0.000
44	A	48	VAL	0	0.070	0.029	19.142	-0.139	-0.139	0.000	0.000	0.000
45	A	49	GLU	-1	-0.897	-0.953	20.559	10.790	10.790	0.000	0.000	0.000
46	A	50	ARG	1	0.828	0.897	22.269	-12.740	-12.740	0.000	0.000	0.000
47	A	51	ALA	0	0.016	0.016	19.656	-0.165	-0.165	0.000	0.000	0.000
48	A	52	VAL	0	0.013	0.007	21.681	-0.115	-0.115	0.000	0.000	0.000
49	A	53	CYS	0	-0.057	-0.035	23.699	-0.354	-0.354	0.000	0.000	0.000
50	A	54	ARG	1	0.808	0.892	19.115	-14.002	-14.002	0.000	0.000	0.000
51	A	55	GLU	-1	-0.864	-0.923	19.887	13.787	13.787	0.000	0.000	0.000
52	A	56	ILE	0	-0.012	-0.012	23.664	-0.222	-0.222	0.000	0.000	0.000
53	A	57	GLU	-1	-0.955	-0.970	26.824	9.107	9.107	0.000	0.000	0.000
54	A	58	GLU	-1	-0.934	-0.988	23.059	12.186	12.186	0.000	0.000	0.000
55	A	59	GLU	-1	-0.911	-0.954	22.651	12.176	12.176	0.000	0.000	0.000
56	A	60	LEU	0	-0.053	-0.045	27.227	-0.287	-0.287	0.000	0.000	0.000
57	A	61	GLY	0	-0.020	0.001	30.525	-0.360	-0.360	0.000	0.000	0.000
58	A	62	ILE	0	-0.073	-0.020	31.726	-0.302	-0.302	0.000	0.000	0.000
59	A	63	ALA	0	0.093	0.047	31.438	0.294	0.294	0.000	0.000	0.000
60	A	64	LEU	0	-0.020	-0.026	28.295	-0.278	-0.278	0.000	0.000	0.000
61	A	65	GLU	-1	-0.864	-0.929	32.044	7.953	7.953	0.000	0.000	0.000
62	A	66	ARG	1	0.768	0.866	33.577	-8.060	-8.060	0.000	0.000	0.000
63	A	67	ALA	0	0.032	0.028	28.891	-0.101	-0.101	0.000	0.000	0.000
64	A	68	THR	0	-0.011	0.001	29.912	0.080	0.080	0.000	0.000	0.000
65	A	69	LEU	0	-0.009	-0.006	23.538	0.098	0.098	0.000	0.000	0.000
66	A	70	LEU	0	-0.027	-0.001	26.118	-0.299	-0.299	0.000	0.000	0.000
67	A	71	CYS	0	-0.025	-0.007	23.682	-0.021	-0.021	0.000	0.000	0.000
68	A	72	VAL	0	0.003	-0.016	17.809	0.172	0.172	0.000	0.000	0.000
69	A	73	VAL	0	0.006	0.019	16.958	-0.092	-0.092	0.000	0.000	0.000
70	A	74	ASP	-1	-0.892	-0.933	14.546	17.918	17.918	0.000	0.000	0.000
71	A	75	HIS	0	-0.037	-0.034	11.801	-1.274	-1.274	0.000	0.000	0.000
72	A	76	ILE	0	0.012	0.002	10.135	1.652	1.652	0.000	0.000	0.000
73	A	77	ASP	-1	-0.857	-0.929	10.027	17.027	17.027	0.000	0.000	0.000
74	A	78	ALA	0	0.014	-0.008	8.621	1.304	1.304	0.000	0.000	0.000
75	A	79	ALA	0	-0.043	-0.015	9.243	1.153	1.153	0.000	0.000	0.000
76	A	80	ASN	0	-0.070	-0.039	10.863	-0.069	-0.069	0.000	0.000	0.000
77	A	81	GLY	0	-0.024	0.005	6.672	0.712	0.712	0.000	0.000	0.000
78	A	82	GLU	-1	-0.949	-0.978	5.753	24.743	24.743	0.000	0.000	0.000
79	A	83	HIS	0	0.007	-0.013	6.584	-1.918	-1.918	0.000	0.000	0.000
80	A	84	TRP	0	-0.038	-0.007	8.158	2.034	2.034	0.000	0.000	0.000
81	A	85	VAL	0	0.030	0.018	10.970	-0.836	-0.836	0.000	0.000	0.000
82	A	86	ALA	0	-0.004	-0.009	13.673	0.233	0.233	0.000	0.000	0.000
83	A	87	PRO	0	-0.028	-0.008	16.874	-0.693	-0.693	0.000	0.000	0.000
84	A	88	VAL	0	0.006	0.009	20.236	-0.013	-0.013	0.000	0.000	0.000
85	A	89	TYR	0	0.020	0.001	22.162	-0.296	-0.296	0.000	0.000	0.000
86	A	90	LEU	0	0.000	0.007	26.501	-0.044	-0.044	0.000	0.000	0.000
87	A	91	ALA	0	0.031	0.007	29.876	-0.074	-0.074	0.000	0.000	0.000
88	A	92	HIS	0	0.029	0.015	32.363	-0.009	-0.009	0.000	0.000	0.000
89	A	93	ALA	0	-0.064	-0.042	35.445	-0.256	-0.256	0.000	0.000	0.000
90	A	94	PHE	0	-0.001	0.003	34.180	0.252	0.252	0.000	0.000	0.000
91	A	95	SER	0	-0.001	0.020	35.985	-0.273	-0.273	0.000	0.000	0.000
92	A	96	GLY	0	0.055	0.017	36.244	0.202	0.202	0.000	0.000	0.000
93	A	97	GLU	-1	-0.926	-0.985	38.077	7.547	7.547	0.000	0.000	0.000
94	A	98	PRO	0	-0.048	-0.007	33.593	0.123	0.123	0.000	0.000	0.000
95	A	99	ARG	1	0.944	0.968	33.656	-8.875	-8.875	0.000	0.000	0.000
96	A	100	VAL	0	0.013	0.004	29.537	0.246	0.246	0.000	0.000	0.000
97	A	101	VAL	0	-0.056	-0.012	29.610	-0.293	-0.293	0.000	0.000	0.000
98	A	102	GLU	-1	-0.814	-0.887	25.017	11.827	11.827	0.000	0.000	0.000
99	A	103	PRO	0	-0.008	-0.016	27.898	0.226	0.226	0.000	0.000	0.000
100	A	104	ASP	-1	-0.919	-0.959	25.951	10.465	10.465	0.000	0.000	0.000
101	A	105	ARG	1	0.766	0.866	21.446	-12.263	-12.263	0.000	0.000	0.000
102	A	106	HIS	0	0.041	0.020	23.225	0.112	0.112	0.000	0.000	0.000
103	A	107	GLU	-1	-0.931	-0.980	27.123	9.711	9.711	0.000	0.000	0.000
104	A	108	ALA	0	-0.052	-0.014	29.974	-0.343	-0.343	0.000	0.000	0.000
105	A	109	LEU	0	0.009	0.001	30.362	0.326	0.326	0.000	0.000	0.000
106	A	110	GLY	0	-0.006	0.003	32.435	-0.274	-0.274	0.000	0.000	0.000
107	A	111	TRP	0	0.012	0.015	33.410	0.249	0.249	0.000	0.000	0.000
108	A	112	PHE	0	0.007	-0.006	32.502	-0.171	-0.171	0.000	0.000	0.000
109	A	113	ALA	0	0.038	0.034	35.381	0.106	0.106	0.000	0.000	0.000
110	A	114	LEU	0	-0.001	-0.022	32.788	0.114	0.114	0.000	0.000	0.000
111	A	115	ASP	-1	-0.958	-0.972	34.708	7.582	7.582	0.000	0.000	0.000
112	A	116	ASP	-1	-0.969	-0.978	36.637	7.507	7.507	0.000	0.000	0.000
113	A	117	LEU	0	-0.049	-0.007	30.364	0.124	0.124	0.000	0.000	0.000
114	A	118	PRO	0	0.008	0.020	30.427	-0.081	-0.081	0.000	0.000	0.000
115	A	119	GLN	0	-0.042	-0.021	29.356	0.426	0.426	0.000	0.000	0.000
116	A	120	PRO	0	-0.001	-0.009	25.350	-0.202	-0.202	0.000	0.000	0.000
117	A	121	LEU	0	0.021	0.001	25.542	0.056	0.056	0.000	0.000	0.000
118	A	122	THR	0	-0.001	0.011	20.260	0.040	0.040	0.000	0.000	0.000
119	A	123	HIS	0	-0.023	-0.027	16.973	-0.935	-0.935	0.000	0.000	0.000
120	A	124	ALA	0	0.024	0.002	18.682	-0.266	-0.266	0.000	0.000	0.000
121	A	125	THR	0	0.014	-0.003	20.311	-0.362	-0.362	0.000	0.000	0.000
122	A	126	ARG	1	0.927	0.968	21.328	-12.324	-12.324	0.000	0.000	0.000
123	A	127	ILE	0	0.058	0.036	19.617	-0.235	-0.235	0.000	0.000	0.000
124	A	128	ALA	0	-0.001	-0.005	23.546	-0.277	-0.277	0.000	0.000	0.000
125	A	129	LEU	0	-0.018	-0.030	25.244	-0.379	-0.379	0.000	0.000	0.000
126	A	130	GLU	-1	-0.977	-0.979	25.942	10.569	10.569	0.000	0.000	0.000
127	A	131	GLN	0	-0.074	-0.024	26.565	-0.332	-0.332	0.000	0.000	0.000
128	A	132	VAL	0	-0.053	-0.019	29.158	-0.302	-0.302	0.000	0.000	0.000
129	A	133	THR	0	-0.023	-0.001	31.625	-0.340	-0.340	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:GLU)