FMO DATABASE

FMODB ID: 3NRLL

Calculation Name: 7KAG-A-Xray172

Preferred Name:

Target Type:

Ligand Name: 1,2-ethanediol

ligand 3-letter code: EDO

PDB ID: 7KAG

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2020-11-02

Reference: A. Yamamoto, K. Kato, Y. Handa, Y. Kawashima, K. Fukuzawa et. Al., FMO Calculation for SARS Cov-2 related proteins. 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	Selected crystal waters in PDB.
Procedure	Manual calculation

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	122
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-824138.219385
FMO2-HF: Nuclear repulsion	779023.323201
FMO2-HF: Total energy	-45114.896184
FMO2-MP2: Total energy	-45244.162117

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:1:ALA )

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

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.
-278.082	-272.341	5.797	-6.425	-5.113	-0.084

Interaction energy analysis for fragmet #1(A:1:ALA )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.791 / q_NPA : 0.893

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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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	3	THR	0	0.006	0.012	3.850	2.284	3.247	-0.001	-0.389	-0.573	0.000
4	A	4	LYS	1	0.871	0.928	6.332	30.814	30.814	0.000	0.000	0.000	0.000
5	A	5	VAL	0	-0.005	0.006	8.578	0.772	0.772	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.002	0.001	12.226	0.538	0.538	0.000	0.000	0.000	0.000
7	A	7	PHE	0	-0.008	-0.014	14.965	0.165	0.165	0.000	0.000	0.000	0.000
8	A	8	GLY	0	-0.007	0.011	18.274	0.865	0.865	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.868	-0.921	19.948	-13.073	-13.073	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.922	-0.959	19.945	-13.608	-13.608	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.108	-0.039	18.032	-0.736	-0.736	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.001	-0.020	11.654	-0.506	-0.506	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.018	0.002	12.589	0.415	0.415	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.858	-0.916	7.046	-35.644	-35.644	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.013	-0.006	8.518	1.804	1.804	0.000	0.000	0.000	0.000
16	A	16	GLN	0	-0.042	-0.051	2.135	-4.782	-3.520	0.445	-0.922	-0.785	-0.009
17	A	17	GLY	0	-0.002	0.017	6.138	5.787	5.787	0.000	0.000	0.000	0.000
18	A	18	TYR	0	0.001	-0.012	6.282	-3.623	-3.623	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.872	0.926	9.479	21.901	21.901	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.014	-0.006	12.702	-0.332	-0.332	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.025	-0.012	14.701	0.462	0.462	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.079	-0.038	17.277	0.576	0.576	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.019	-0.013	18.411	-0.064	-0.064	0.000	0.000	0.000	0.000
24	A	24	THR	0	-0.030	-0.009	22.401	0.324	0.324	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.059	-0.058	22.513	-0.277	-0.277	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.869	-0.937	27.310	-10.074	-10.074	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.046	-0.020	26.264	-0.044	-0.044	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.766	-0.901	30.334	-8.780	-8.780	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.951	-0.966	33.432	-8.379	-8.379	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.673	0.822	35.272	8.640	8.640	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.033	-0.026	31.558	0.006	0.006	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.692	-0.841	30.110	-10.645	-10.645	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.810	0.898	30.194	8.969	8.969	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.000	-0.017	30.950	-0.159	-0.159	0.000	0.000	0.000	0.000
35	A	35	LEU	0	0.020	0.015	26.648	-0.332	-0.332	0.000	0.000	0.000	0.000
36	A	36	ASN	0	0.088	0.026	25.989	-0.844	-0.844	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.949	-0.937	26.824	-10.006	-10.006	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.867	0.930	25.907	10.475	10.475	0.000	0.000	0.000	0.000
39	A	39	CYS	0	-0.017	0.016	22.300	-0.171	-0.171	0.000	0.000	0.000	0.000
40	A	40	SER	0	0.032	0.032	22.006	-0.552	-0.552	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.024	-0.003	19.871	-0.313	-0.313	0.000	0.000	0.000	0.000
42	A	42	TYR	0	0.035	0.006	14.883	-0.724	-0.724	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.064	-0.052	11.167	0.496	0.496	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.044	0.053	9.758	-1.568	-1.568	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.786	-0.888	1.975	-116.466	-112.950	5.353	-5.114	-3.755	-0.075
46	A	46	LEU	0	-0.053	-0.039	6.869	2.855	2.855	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.033	-0.006	6.983	2.996	2.996	0.000	0.000	0.000	0.000
48	A	48	THR	0	-0.016	0.005	7.565	0.565	0.565	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.884	-0.940	9.236	-25.875	-25.875	0.000	0.000	0.000	0.000
50	A	50	VAL	0	0.004	-0.014	12.785	-0.071	-0.071	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.021	-0.007	15.599	0.079	0.079	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.872	-0.934	9.762	-29.169	-29.169	0.000	0.000	0.000	0.000
53	A	53	PHE	0	-0.020	-0.022	13.262	0.213	0.213	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.033	0.004	14.346	0.623	0.623	0.000	0.000	0.000	0.000
55	A	55	CYS	0	-0.044	-0.007	15.728	1.126	1.126	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.007	0.008	13.374	0.615	0.615	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.031	0.017	16.257	0.697	0.697	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.042	0.032	18.957	0.785	0.785	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.849	-0.916	18.653	-15.343	-15.343	0.000	0.000	0.000	0.000
60	A	60	ALA	0	-0.038	-0.013	19.200	0.640	0.640	0.000	0.000	0.000	0.000
61	A	61	VAL	0	0.032	0.032	21.140	0.690	0.690	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.017	0.013	23.805	0.583	0.583	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.800	0.872	20.499	15.126	15.126	0.000	0.000	0.000	0.000
64	A	64	THR	0	-0.055	-0.035	24.202	0.311	0.311	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.005	-0.003	26.523	0.474	0.474	0.000	0.000	0.000	0.000
66	A	66	GLN	0	0.016	-0.003	28.413	0.618	0.618	0.000	0.000	0.000	0.000
67	A	67	PRO	0	-0.080	-0.034	28.878	0.378	0.378	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.033	-0.015	31.983	0.323	0.323	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.043	0.033	33.075	0.330	0.330	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.922	-0.960	34.729	-7.864	-7.864	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.045	-0.036	37.547	0.241	0.241	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.015	0.013	32.646	0.094	0.094	0.000	0.000	0.000	0.000
73	A	73	THR	0	0.018	0.019	37.228	0.189	0.189	0.000	0.000	0.000	0.000
74	A	74	PRO	0	-0.078	-0.042	39.938	0.150	0.150	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.037	-0.008	37.774	0.163	0.163	0.000	0.000	0.000	0.000
76	A	76	GLY	0	-0.010	0.000	40.056	-0.027	-0.027	0.000	0.000	0.000	0.000
77	A	77	ILE	0	-0.047	-0.012	33.660	-0.079	-0.079	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.798	-0.908	35.233	-9.110	-9.110	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.034	-0.024	29.998	-0.275	-0.275	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.886	-0.924	30.494	-10.199	-10.199	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.976	-0.992	31.141	-9.188	-9.188	0.000	0.000	0.000	0.000
82	A	82	TRP	0	0.035	0.004	28.811	-0.480	-0.480	0.000	0.000	0.000	0.000
83	A	83	SER	0	-0.060	-0.028	26.494	-0.572	-0.572	0.000	0.000	0.000	0.000
84	A	84	MET	0	-0.081	-0.035	26.203	-0.530	-0.530	0.000	0.000	0.000	0.000
85	A	85	ALA	0	-0.002	0.026	27.896	0.054	0.054	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.055	-0.034	24.882	-0.411	-0.411	0.000	0.000	0.000	0.000
87	A	87	TYR	0	-0.013	-0.029	22.385	0.400	0.400	0.000	0.000	0.000	0.000
88	A	88	TYR	0	-0.017	-0.004	22.370	-0.901	-0.901	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.002	-0.008	18.076	0.074	0.074	0.000	0.000	0.000	0.000
90	A	90	PHE	0	-0.006	-0.001	21.262	-0.428	-0.428	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.853	-0.944	21.896	-13.449	-13.449	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.895	-0.937	23.015	-11.459	-11.459	0.000	0.000	0.000	0.000
93	A	93	SER	0	-0.101	-0.048	25.922	0.634	0.634	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.038	0.025	26.508	0.259	0.259	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.794	-0.899	22.781	-13.975	-13.975	0.000	0.000	0.000	0.000
96	A	96	PHE	0	0.024	0.022	20.191	-0.488	-0.488	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.750	0.854	17.633	13.826	13.826	0.000	0.000	0.000	0.000
98	A	98	LEU	0	0.049	0.032	12.232	0.710	0.710	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.018	0.014	16.417	-0.328	-0.328	0.000	0.000	0.000	0.000
100	A	100	SER	0	0.006	-0.011	18.118	-0.532	-0.532	0.000	0.000	0.000	0.000
101	A	101	HIS	0	0.027	0.037	19.519	0.037	0.037	0.000	0.000	0.000	0.000
102	A	102	MET	0	-0.056	-0.005	18.356	-0.861	-0.861	0.000	0.000	0.000	0.000
103	A	103	TYR	0	0.074	0.052	22.184	0.214	0.214	0.000	0.000	0.000	0.000
104	A	104	CYS	0	-0.056	-0.024	23.097	-0.554	-0.554	0.000	0.000	0.000	0.000
105	A	105	SER	0	0.038	0.012	24.684	0.577	0.577	0.000	0.000	0.000	0.000
106	A	106	PHE	0	0.006	0.006	26.640	-0.464	-0.464	0.000	0.000	0.000	0.000
107	A	107	TYR	0	-0.026	-0.016	29.063	0.179	0.179	0.000	0.000	0.000	0.000
108	A	108	PRO	0	-0.006	-0.012	27.518	-0.381	-0.381	0.000	0.000	0.000	0.000
109	A	109	PRO	0	-0.049	-0.017	26.250	0.250	0.250	0.000	0.000	0.000	0.000
110	A	110	ASP	-1	-0.932	-0.961	29.272	-9.653	-9.653	0.000	0.000	0.000	0.000
111	A	111	GLU	-2	-1.994	-1.986	32.560	-18.531	-18.531	0.000	0.000	0.000	0.000
112	A	301	HOH	0	-0.025	-0.029	29.775	-0.058	-0.058	0.000	0.000	0.000	0.000
113	A	302	HOH	0	-0.036	-0.026	17.192	0.261	0.261	0.000	0.000	0.000	0.000
114	A	303	HOH	0	-0.022	-0.025	8.767	0.724	0.724	0.000	0.000	0.000	0.000
115	A	304	HOH	0	-0.011	-0.012	25.077	-0.009	-0.009	0.000	0.000	0.000	0.000
116	A	305	HOH	0	-0.009	-0.013	14.829	-0.641	-0.641	0.000	0.000	0.000	0.000
117	A	306	HOH	0	-0.071	-0.052	28.996	0.176	0.176	0.000	0.000	0.000	0.000
118	A	307	HOH	0	-0.014	-0.022	11.936	0.778	0.778	0.000	0.000	0.000	0.000
119	A	308	HOH	0	-0.025	-0.022	19.894	0.108	0.108	0.000	0.000	0.000	0.000
120	A	309	HOH	0	-0.046	-0.044	25.588	0.061	0.061	0.000	0.000	0.000	0.000
121	A	310	HOH	0	0.025	0.019	37.364	-0.091	-0.091	0.000	0.000	0.000	0.000
122	A	311	HOH	0	0.024	0.017	21.615	0.137	0.137	0.000	0.000	0.000	0.000

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