FMO DATABASE

FMODB ID: 53RJZ

Calculation Name: 7TI9-A-Xray89

Preferred Name:

Target Type:

Ligand Name: glycerol

ligand 3-letter code: GOL

PDB ID: 7TI9

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2022-12-13

Reference: T. Ohyama, K. Kamisaka, C. Watanabe, T. Honma et. al., FMO-based interaction energy analysis of SARS-Cov-2 related protein and ligand complexes, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHLSideSolv
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	Waters within average of the temperature factors of receptor.
Procedure	Auto-FMO protocol ver. 1.20200406

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	145
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613

Total energy (hartree)

FMO2-HF: Electronic energy	-878683.151225
FMO2-HF: Nuclear repulsion	831689.78001
FMO2-HF: Total energy	-46993.371215
FMO2-MP2: Total energy	-47127.573221

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:0:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

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.
-12.627	-7.272	2.67	-4.184	-3.842	-0.04

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.017

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	A	2	PRO	0	-0.006	0.001	3.801	0.342	1.399	-0.017	-0.535	-0.505	0.002
4	A	3	THR	0	-0.012	0.002	6.724	0.606	0.606	0.000	0.000	0.000	0.000
5	A	4	LYS	1	0.899	0.957	8.977	-0.428	-0.428	0.000	0.000	0.000	0.000
6	A	5	VAL	0	-0.025	-0.014	12.420	0.035	0.035	0.000	0.000	0.000	0.000
7	A	6	THR	0	-0.019	-0.010	15.568	-0.028	-0.028	0.000	0.000	0.000	0.000
8	A	7	PHE	0	-0.016	-0.010	18.979	0.002	0.002	0.000	0.000	0.000	0.000
9	A	8	GLY	0	0.011	0.008	22.235	0.009	0.009	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.892	-0.922	25.879	0.037	0.037	0.000	0.000	0.000	0.000
11	A	10	ASP	-1	-0.936	-0.976	23.861	0.064	0.064	0.000	0.000	0.000	0.000
12	A	11	THR	0	-0.047	-0.014	22.236	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	12	VAL	0	-0.026	-0.027	16.092	0.017	0.017	0.000	0.000	0.000	0.000
14	A	13	ILE	0	-0.036	-0.008	15.523	-0.030	-0.030	0.000	0.000	0.000	0.000
15	A	14	GLU	-1	-0.790	-0.881	10.985	0.234	0.234	0.000	0.000	0.000	0.000
16	A	15	VAL	0	-0.025	-0.013	11.054	-0.085	-0.085	0.000	0.000	0.000	0.000
17	A	16	GLN	0	0.023	0.000	3.518	0.974	1.107	0.004	-0.048	-0.089	0.000
18	A	17	GLY	0	-0.036	0.002	7.497	0.135	0.135	0.000	0.000	0.000	0.000
19	A	18	TYR	0	0.019	-0.017	6.370	-0.233	-0.233	0.000	0.000	0.000	0.000
20	A	19	LYS	1	0.931	0.966	10.259	0.469	0.469	0.000	0.000	0.000	0.000
21	A	20	SER	0	-0.026	-0.022	13.220	-0.050	-0.050	0.000	0.000	0.000	0.000
22	A	21	VAL	0	0.006	0.015	14.317	0.032	0.032	0.000	0.000	0.000	0.000
23	A	22	ASN	0	-0.038	-0.008	16.813	0.005	0.005	0.000	0.000	0.000	0.000
24	A	23	ILE	0	-0.011	-0.006	17.631	0.007	0.007	0.000	0.000	0.000	0.000
25	A	24	THR	0	-0.001	-0.010	21.260	0.008	0.008	0.000	0.000	0.000	0.000
26	A	25	PHE	0	-0.076	-0.066	20.895	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	26	GLU	-1	-0.912	-0.958	25.827	-0.100	-0.100	0.000	0.000	0.000	0.000
28	A	27	LEU	0	-0.072	-0.019	23.955	0.003	0.003	0.000	0.000	0.000	0.000
29	A	28	ASP	-1	-0.736	-0.850	28.334	-0.069	-0.069	0.000	0.000	0.000	0.000
30	A	29	GLU	-1	-0.889	-0.932	31.660	-0.081	-0.081	0.000	0.000	0.000	0.000
31	A	30	ARG	1	0.679	0.801	33.832	0.069	0.069	0.000	0.000	0.000	0.000
32	A	31	ILE	0	-0.064	-0.042	29.574	0.001	0.001	0.000	0.000	0.000	0.000
33	A	32	ASP	-1	-0.673	-0.836	28.738	-0.118	-0.118	0.000	0.000	0.000	0.000
34	A	33	LYS	1	0.833	0.907	28.795	0.089	0.089	0.000	0.000	0.000	0.000
35	A	34	VAL	0	-0.019	-0.024	29.371	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	35	LEU	0	0.024	0.016	24.824	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	36	ASN	0	0.088	0.046	24.553	-0.023	-0.023	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.925	-0.927	25.506	-0.119	-0.119	0.000	0.000	0.000	0.000
39	A	38	LYS	1	0.836	0.908	24.938	0.119	0.119	0.000	0.000	0.000	0.000
40	A	39	CYS	0	-0.044	0.005	20.655	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	40	SER	0	0.047	0.032	20.808	-0.011	-0.011	0.000	0.000	0.000	0.000
42	A	41	ALA	0	-0.033	-0.004	18.947	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	42	TYR	0	0.022	0.005	13.803	-0.020	-0.020	0.000	0.000	0.000	0.000
44	A	43	THR	0	-0.058	-0.028	11.260	0.037	0.037	0.000	0.000	0.000	0.000
45	A	44	VAL	0	0.046	0.036	8.799	-0.095	-0.095	0.000	0.000	0.000	0.000
46	A	45	GLU	-1	-0.796	-0.879	2.302	-14.073	-10.491	2.624	-3.246	-2.961	-0.041
47	A	46	LEU	0	-0.036	-0.013	6.874	0.219	0.219	0.000	0.000	0.000	0.000
48	A	47	GLY	0	-0.016	0.002	5.725	0.252	0.252	0.000	0.000	0.000	0.000
49	A	48	THR	0	-0.072	-0.039	6.612	-0.043	-0.043	0.000	0.000	0.000	0.000
50	A	49	GLU	-1	-0.836	-0.919	7.711	-0.091	-0.091	0.000	0.000	0.000	0.000
51	A	50	VAL	0	0.015	0.009	10.539	-0.040	-0.040	0.000	0.000	0.000	0.000
52	A	51	ASN	0	0.012	0.000	12.533	0.008	0.008	0.000	0.000	0.000	0.000
53	A	52	GLU	-1	-0.978	-0.985	7.376	-0.469	-0.469	0.000	0.000	0.000	0.000
54	A	53	PHE	0	0.011	-0.014	11.449	-0.019	-0.019	0.000	0.000	0.000	0.000
55	A	54	ALA	0	0.043	0.021	12.354	0.017	0.017	0.000	0.000	0.000	0.000
56	A	55	CYS	0	-0.009	-0.007	13.694	0.032	0.032	0.000	0.000	0.000	0.000
57	A	56	VAL	0	-0.027	0.002	10.514	0.008	0.008	0.000	0.000	0.000	0.000
58	A	57	VAL	0	0.006	-0.002	13.867	0.021	0.021	0.000	0.000	0.000	0.000
59	A	58	ALA	0	0.021	0.024	17.000	0.022	0.022	0.000	0.000	0.000	0.000
60	A	59	ASP	-1	-0.811	-0.881	16.423	-0.176	-0.176	0.000	0.000	0.000	0.000
61	A	60	ALA	0	-0.063	-0.030	17.221	0.015	0.015	0.000	0.000	0.000	0.000
62	A	61	VAL	0	0.041	0.034	19.040	0.017	0.017	0.000	0.000	0.000	0.000
63	A	62	ILE	0	0.038	0.025	21.942	0.014	0.014	0.000	0.000	0.000	0.000
64	A	63	LYS	1	0.907	0.952	19.518	0.207	0.207	0.000	0.000	0.000	0.000
65	A	64	THR	0	-0.084	-0.058	22.359	0.007	0.007	0.000	0.000	0.000	0.000
66	A	65	LEU	0	-0.004	-0.008	24.639	0.010	0.010	0.000	0.000	0.000	0.000
67	A	66	GLN	0	0.008	0.006	25.966	0.014	0.014	0.000	0.000	0.000	0.000
68	A	67	PRO	0	-0.084	-0.048	26.898	0.009	0.009	0.000	0.000	0.000	0.000
69	A	68	VAL	0	-0.039	-0.016	30.137	0.006	0.006	0.000	0.000	0.000	0.000
70	A	69	SER	0	0.095	0.060	31.003	0.005	0.005	0.000	0.000	0.000	0.000
71	A	70	GLU	-1	-0.876	-0.932	32.640	-0.060	-0.060	0.000	0.000	0.000	0.000
72	A	71	LEU	0	-0.084	-0.048	35.300	0.004	0.004	0.000	0.000	0.000	0.000
73	A	72	LEU	0	0.009	0.009	30.731	0.001	0.001	0.000	0.000	0.000	0.000
74	A	73	THR	0	0.070	0.049	35.102	0.001	0.001	0.000	0.000	0.000	0.000
75	A	74	PRO	0	-0.047	-0.013	37.576	0.003	0.003	0.000	0.000	0.000	0.000
76	A	75	LEU	0	0.002	0.015	35.781	0.003	0.003	0.000	0.000	0.000	0.000
77	A	76	GLY	0	-0.001	0.014	37.861	0.000	0.000	0.000	0.000	0.000	0.000
78	A	77	ILE	0	-0.021	0.010	31.412	0.000	0.000	0.000	0.000	0.000	0.000
79	A	78	ASP	-1	-0.817	-0.893	32.908	-0.062	-0.062	0.000	0.000	0.000	0.000
80	A	79	LEU	0	0.042	0.004	27.663	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	80	ASP	-1	-0.843	-0.898	27.979	-0.076	-0.076	0.000	0.000	0.000	0.000
82	A	81	GLU	-1	-0.955	-0.974	28.582	-0.059	-0.059	0.000	0.000	0.000	0.000
83	A	82	TRP	0	-0.003	-0.013	26.421	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	83	SER	0	-0.099	-0.036	24.299	-0.009	-0.009	0.000	0.000	0.000	0.000
85	A	84	MET	0	-0.080	-0.039	23.124	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	85	ALA	0	0.032	0.039	24.486	0.008	0.008	0.000	0.000	0.000	0.000
87	A	86	THR	0	-0.067	-0.037	22.402	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	87	TYR	0	-0.023	-0.032	20.083	0.000	0.000	0.000	0.000	0.000	0.000
89	A	88	TYR	0	-0.016	-0.004	20.489	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	89	LEU	0	-0.001	-0.003	16.581	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	90	PHE	0	0.025	0.012	20.080	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	91	ASP	-1	-0.827	-0.919	20.382	-0.149	-0.149	0.000	0.000	0.000	0.000
93	A	92	GLU	-1	-0.820	-0.907	21.980	-0.129	-0.129	0.000	0.000	0.000	0.000
94	A	93	SER	0	-0.108	-0.048	24.791	0.014	0.014	0.000	0.000	0.000	0.000
95	A	94	GLY	0	0.035	0.029	25.283	0.009	0.009	0.000	0.000	0.000	0.000
96	A	95	GLU	-1	-0.781	-0.884	21.659	-0.090	-0.090	0.000	0.000	0.000	0.000
97	A	96	PHE	0	-0.024	0.006	18.414	-0.020	-0.020	0.000	0.000	0.000	0.000
98	A	97	LYS	1	0.770	0.863	16.474	0.095	0.095	0.000	0.000	0.000	0.000
99	A	98	LEU	0	0.026	0.006	11.223	0.005	0.005	0.000	0.000	0.000	0.000
100	A	99	ALA	0	-0.034	-0.028	15.659	0.019	0.019	0.000	0.000	0.000	0.000
101	A	100	SER	0	-0.042	-0.026	17.981	-0.025	-0.025	0.000	0.000	0.000	0.000
102	A	101	HIS	0	-0.057	-0.007	19.890	-0.016	-0.016	0.000	0.000	0.000	0.000
103	A	102	MET	0	-0.034	0.003	17.368	-0.019	-0.019	0.000	0.000	0.000	0.000
104	A	103	TYR	0	0.049	0.041	21.361	0.001	0.001	0.000	0.000	0.000	0.000
105	A	104	CYS	0	-0.010	-0.001	21.381	-0.013	-0.013	0.000	0.000	0.000	0.000
106	A	105	SER	0	0.031	0.011	23.004	0.011	0.011	0.000	0.000	0.000	0.000
107	A	106	PHE	0	0.030	0.005	24.720	-0.007	-0.007	0.000	0.000	0.000	0.000
108	A	107	TYR	0	-0.060	-0.031	26.962	0.008	0.008	0.000	0.000	0.000	0.000
109	A	108	PRO	0	-0.017	-0.017	25.932	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	109	PRO	0	-0.037	0.005	24.874	0.002	0.002	0.000	0.000	0.000	0.000
111	A	110	ASP	-1	-0.963	-0.981	27.763	-0.070	-0.070	0.000	0.000	0.000	0.000
112	A	111	GLU	-2	-1.968	-1.979	30.141	-0.119	-0.119	0.000	0.000	0.000	0.000
113	A	301	HOH	0	-0.047	-0.047	2.749	0.440	1.023	0.059	-0.355	-0.287	-0.001
114	A	302	HOH	0	-0.042	-0.034	35.431	0.001	0.001	0.000	0.000	0.000	0.000
115	A	303	HOH	0	-0.019	-0.012	19.806	0.009	0.009	0.000	0.000	0.000	0.000
116	A	304	HOH	0	-0.040	-0.038	20.093	0.002	0.002	0.000	0.000	0.000	0.000
117	A	305	HOH	0	-0.022	-0.022	28.062	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	306	HOH	0	-0.024	-0.016	42.680	0.001	0.001	0.000	0.000	0.000	0.000
119	A	307	HOH	0	-0.027	-0.027	24.508	0.000	0.000	0.000	0.000	0.000	0.000
120	A	308	HOH	0	-0.034	-0.028	17.814	0.012	0.012	0.000	0.000	0.000	0.000
121	A	309	HOH	0	-0.049	-0.041	34.039	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	310	HOH	0	0.009	-0.003	13.398	-0.014	-0.014	0.000	0.000	0.000	0.000
123	A	311	HOH	0	-0.025	-0.024	33.057	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	312	HOH	0	-0.006	-0.016	33.371	0.001	0.001	0.000	0.000	0.000	0.000
125	A	313	HOH	0	-0.021	-0.015	33.645	0.002	0.002	0.000	0.000	0.000	0.000
126	A	314	HOH	0	-0.005	-0.007	8.965	-0.114	-0.114	0.000	0.000	0.000	0.000
127	A	315	HOH	0	-0.032	-0.024	10.339	0.020	0.020	0.000	0.000	0.000	0.000
128	A	316	HOH	0	0.020	0.015	22.006	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	317	HOH	0	-0.065	-0.041	19.548	0.002	0.002	0.000	0.000	0.000	0.000
130	A	318	HOH	0	-0.032	-0.026	31.383	0.002	0.002	0.000	0.000	0.000	0.000
131	A	319	HOH	0	0.039	0.024	29.212	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	320	HOH	0	0.004	-0.004	17.029	0.001	0.001	0.000	0.000	0.000	0.000
133	A	321	HOH	0	-0.039	-0.038	22.685	-0.009	-0.009	0.000	0.000	0.000	0.000
134	A	322	HOH	0	-0.027	-0.017	25.665	0.004	0.004	0.000	0.000	0.000	0.000
135	A	323	HOH	0	-0.048	-0.039	28.740	0.001	0.001	0.000	0.000	0.000	0.000
136	A	326	HOH	0	-0.065	-0.051	13.356	0.018	0.018	0.000	0.000	0.000	0.000
137	A	327	HOH	0	-0.035	-0.031	23.703	-0.003	-0.003	0.000	0.000	0.000	0.000
138	A	329	HOH	0	-0.047	-0.040	36.312	0.000	0.000	0.000	0.000	0.000	0.000
139	A	330	HOH	0	-0.035	-0.026	41.406	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	331	HOH	0	0.005	0.005	13.754	-0.007	-0.007	0.000	0.000	0.000	0.000
141	A	332	HOH	0	-0.037	-0.030	19.736	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	333	HOH	0	-0.038	-0.028	44.622	0.000	0.000	0.000	0.000	0.000	0.000
143	A	334	HOH	0	0.031	0.016	29.129	0.000	0.000	0.000	0.000	0.000	0.000
144	A	335	HOH	0	0.016	0.005	7.866	0.065	0.065	0.000	0.000	0.000	0.000
145	A	336	HOH	0	0.000	0.000	30.630	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)