FMO DATABASE

FMODB ID: MM18Z

Calculation Name: 6M3M-B-Xray99

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 6M3M

Chain ID: B

ChEMBL ID:

UniProt ID: P0DTC9

Base Structure: X-ray

Registration Date: 2020-04-16

Reference: K. Kato, Y. Handa, Y. Kawashima, K. Fukuzawa et. Al., FMO Calculation for SARS Cov-2 related proteins. To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSideSolv
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	167
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1133642.82591
FMO2-HF: Nuclear repulsion	1082454.433912
FMO2-HF: Total energy	-51188.391998
FMO2-MP2: Total energy	-51339.722513

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:48:ASN )

Summations of interaction energy for fragment #1(B:48:ASN )

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.
-7.601	-3.223	0.393	-2.058	-2.714	0.017

Interaction energy analysis for fragmet #1(B:48:ASN )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : ******

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].	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	50	THR	0	-0.010	2.615	-3.027	1.154	0.395	-2.045	-2.532	0.017
4	B	51	ALA	0	-0.038	4.929	-1.797	-1.795	-0.001	-0.006	0.005	0.000
5	B	52	SER	0	0.006	8.623	-0.048	-0.048	0.000	0.000	0.000	0.000
6	B	53	TRP	0	0.032	8.896	0.428	0.428	0.000	0.000	0.000	0.000
7	B	54	PHE	0	-0.023	12.678	-0.017	-0.017	0.000	0.000	0.000	0.000
8	B	55	THR	0	-0.026	15.495	0.074	0.074	0.000	0.000	0.000	0.000
9	B	56	ALA	0	-0.004	17.869	-0.037	-0.037	0.000	0.000	0.000	0.000
10	B	57	LEU	0	0.000	19.442	-0.011	-0.011	0.000	0.000	0.000	0.000
11	B	58	THR	0	-0.035	22.851	0.009	0.009	0.000	0.000	0.000	0.000
12	B	59	GLN	0	-0.004	24.617	-0.004	-0.004	0.000	0.000	0.000	0.000
13	B	60	HIS	0	0.017	27.022	-0.003	-0.003	0.000	0.000	0.000	0.000
14	B	61	GLY	0	-0.006	30.345	-0.007	-0.007	0.000	0.000	0.000	0.000
15	B	62	LYS	1	0.956	31.201	-0.038	-0.038	0.000	0.000	0.000	0.000
16	B	63	GLU	-1	-0.897	32.047	0.029	0.029	0.000	0.000	0.000	0.000
17	B	64	ASP	-1	-0.744	27.603	0.036	0.036	0.000	0.000	0.000	0.000
18	B	65	LEU	0	-0.056	23.182	0.000	0.000	0.000	0.000	0.000	0.000
19	B	66	LYS	1	0.976	26.991	-0.012	-0.012	0.000	0.000	0.000	0.000
20	B	67	PHE	0	0.042	24.494	0.013	0.013	0.000	0.000	0.000	0.000
21	B	68	PRO	0	-0.037	29.141	-0.014	-0.014	0.000	0.000	0.000	0.000
22	B	69	ARG	1	0.936	30.125	0.081	0.081	0.000	0.000	0.000	0.000
23	B	70	GLY	0	0.050	29.115	0.004	0.004	0.000	0.000	0.000	0.000
24	B	71	GLN	0	0.000	28.519	0.013	0.013	0.000	0.000	0.000	0.000
25	B	72	GLY	0	0.072	25.675	-0.010	-0.010	0.000	0.000	0.000	0.000
26	B	73	VAL	0	-0.058	20.429	0.022	0.022	0.000	0.000	0.000	0.000
27	B	74	PRO	0	-0.021	19.221	0.000	0.000	0.000	0.000	0.000	0.000
28	B	75	ILE	0	0.025	21.341	-0.022	-0.022	0.000	0.000	0.000	0.000
29	B	76	ASN	0	0.001	16.931	0.011	0.011	0.000	0.000	0.000	0.000
30	B	77	THR	0	0.032	20.265	-0.025	-0.025	0.000	0.000	0.000	0.000
31	B	78	ASN	0	-0.055	16.120	-0.037	-0.037	0.000	0.000	0.000	0.000
32	B	79	SER	0	0.024	17.791	-0.023	-0.023	0.000	0.000	0.000	0.000
33	B	80	SER	0	0.037	19.477	0.026	0.026	0.000	0.000	0.000	0.000
34	B	81	PRO	0	0.054	21.647	-0.004	-0.004	0.000	0.000	0.000	0.000
35	B	82	ASP	-1	-0.912	22.154	-0.219	-0.219	0.000	0.000	0.000	0.000
36	B	83	ASP	-1	-0.786	17.896	-0.252	-0.252	0.000	0.000	0.000	0.000
37	B	84	GLN	0	-0.020	18.954	-0.014	-0.014	0.000	0.000	0.000	0.000
38	B	85	ILE	0	-0.010	19.467	0.008	0.008	0.000	0.000	0.000	0.000
39	B	86	GLY	0	0.010	17.983	-0.028	-0.028	0.000	0.000	0.000	0.000
40	B	87	TYR	0	-0.045	13.032	0.050	0.050	0.000	0.000	0.000	0.000
41	B	88	TYR	0	-0.018	17.810	0.064	0.064	0.000	0.000	0.000	0.000
42	B	89	ARG	1	0.919	14.505	-0.037	-0.037	0.000	0.000	0.000	0.000
43	B	90	ARG	1	0.806	17.984	0.048	0.048	0.000	0.000	0.000	0.000
44	B	91	ALA	0	-0.025	16.841	-0.012	-0.012	0.000	0.000	0.000	0.000
45	B	92	THR	0	0.025	18.869	0.032	0.032	0.000	0.000	0.000	0.000
46	B	93	ARG	1	0.911	18.872	-0.340	-0.340	0.000	0.000	0.000	0.000
47	B	94	ARG	1	0.982	21.502	-0.103	-0.103	0.000	0.000	0.000	0.000
48	B	95	ILE	0	-0.024	23.497	0.023	0.023	0.000	0.000	0.000	0.000
49	B	96	ARG	1	0.994	22.960	-0.185	-0.185	0.000	0.000	0.000	0.000
50	B	97	GLY	0	0.054	28.555	-0.010	-0.010	0.000	0.000	0.000	0.000
51	B	98	GLY	0	0.024	31.327	-0.005	-0.005	0.000	0.000	0.000	0.000
52	B	99	ASP	-1	-0.841	34.230	0.079	0.079	0.000	0.000	0.000	0.000
53	B	100	GLY	0	-0.067	32.944	-0.006	-0.006	0.000	0.000	0.000	0.000
54	B	101	LYS	1	0.867	32.726	-0.075	-0.075	0.000	0.000	0.000	0.000
55	B	102	MET	0	-0.058	24.707	0.008	0.008	0.000	0.000	0.000	0.000
56	B	103	LYS	1	0.966	28.660	-0.127	-0.127	0.000	0.000	0.000	0.000
57	B	104	ASP	-1	-0.861	26.067	0.109	0.109	0.000	0.000	0.000	0.000
58	B	105	LEU	0	-0.050	23.738	0.005	0.005	0.000	0.000	0.000	0.000
59	B	106	SER	0	0.017	26.022	-0.007	-0.007	0.000	0.000	0.000	0.000
60	B	107	PRO	0	-0.003	23.233	0.035	0.035	0.000	0.000	0.000	0.000
61	B	108	ARG	1	0.843	18.187	-0.421	-0.421	0.000	0.000	0.000	0.000
62	B	109	TRP	0	0.008	19.759	-0.015	-0.015	0.000	0.000	0.000	0.000
63	B	110	TYR	0	-0.014	14.803	0.024	0.024	0.000	0.000	0.000	0.000
64	B	111	PHE	0	0.057	16.372	-0.054	-0.054	0.000	0.000	0.000	0.000
65	B	112	TYR	0	-0.047	10.035	0.116	0.116	0.000	0.000	0.000	0.000
66	B	113	TYR	0	0.096	13.415	-0.017	-0.017	0.000	0.000	0.000	0.000
67	B	114	LEU	0	0.009	14.248	-0.046	-0.046	0.000	0.000	0.000	0.000
68	B	115	GLY	0	0.028	14.382	-0.036	-0.036	0.000	0.000	0.000	0.000
69	B	116	THR	0	-0.016	9.856	-0.097	-0.097	0.000	0.000	0.000	0.000
70	B	117	GLY	0	0.045	9.345	0.185	0.185	0.000	0.000	0.000	0.000
71	B	118	PRO	0	-0.053	9.734	-0.269	-0.269	0.000	0.000	0.000	0.000
72	B	119	GLU	-1	-0.812	10.937	-0.469	-0.469	0.000	0.000	0.000	0.000
73	B	120	ALA	0	0.013	10.229	0.062	0.062	0.000	0.000	0.000	0.000
74	B	121	GLY	0	0.041	12.234	-0.005	-0.005	0.000	0.000	0.000	0.000
75	B	122	LEU	0	-0.045	14.557	0.061	0.061	0.000	0.000	0.000	0.000
76	B	123	PRO	0	0.045	17.652	-0.006	-0.006	0.000	0.000	0.000	0.000
77	B	124	TYR	0	0.034	20.302	0.030	0.030	0.000	0.000	0.000	0.000
78	B	125	GLY	0	-0.009	22.233	0.004	0.004	0.000	0.000	0.000	0.000
79	B	126	ALA	0	-0.061	21.213	0.013	0.013	0.000	0.000	0.000	0.000
80	B	127	ASN	0	0.017	23.301	0.032	0.032	0.000	0.000	0.000	0.000
81	B	128	LYS	1	0.864	17.591	0.272	0.272	0.000	0.000	0.000	0.000
82	B	129	ASP	-1	-0.804	22.940	-0.024	-0.024	0.000	0.000	0.000	0.000
83	B	130	GLY	0	-0.014	21.849	-0.004	-0.004	0.000	0.000	0.000	0.000
84	B	131	ILE	0	-0.059	17.663	0.030	0.030	0.000	0.000	0.000	0.000
85	B	132	ILE	0	-0.025	21.357	-0.010	-0.010	0.000	0.000	0.000	0.000
86	B	133	TRP	0	0.012	18.338	0.015	0.015	0.000	0.000	0.000	0.000
87	B	134	VAL	0	-0.070	21.793	0.018	0.018	0.000	0.000	0.000	0.000
88	B	135	ALA	0	0.025	22.770	-0.019	-0.019	0.000	0.000	0.000	0.000
89	B	136	THR	0	0.034	24.588	0.016	0.016	0.000	0.000	0.000	0.000
90	B	137	GLU	-1	-0.871	26.739	-0.085	-0.085	0.000	0.000	0.000	0.000
91	B	138	GLY	0	-0.016	28.512	0.006	0.006	0.000	0.000	0.000	0.000
92	B	139	ALA	0	-0.042	23.192	-0.012	-0.012	0.000	0.000	0.000	0.000
93	B	140	LEU	0	0.053	21.923	-0.005	-0.005	0.000	0.000	0.000	0.000
94	B	141	ASN	0	-0.070	21.760	-0.029	-0.029	0.000	0.000	0.000	0.000
95	B	142	THR	0	0.040	19.036	-0.006	-0.006	0.000	0.000	0.000	0.000
96	B	143	PRO	0	0.009	14.432	0.044	0.044	0.000	0.000	0.000	0.000
97	B	144	LYS	1	0.832	14.381	0.307	0.307	0.000	0.000	0.000	0.000
98	B	145	ASP	-1	-0.878	9.739	-1.224	-1.224	0.000	0.000	0.000	0.000
99	B	146	HIS	0	-0.084	9.956	-0.137	-0.137	0.000	0.000	0.000	0.000
100	B	147	ILE	0	0.000	11.532	0.065	0.065	0.000	0.000	0.000	0.000
101	B	148	GLY	0	0.048	7.670	0.060	0.060	0.000	0.000	0.000	0.000
102	B	149	THR	0	-0.072	5.514	0.203	0.203	0.000	0.000	0.000	0.000
103	B	150	ARG	1	0.831	6.070	-1.364	-1.364	0.000	0.000	0.000	0.000
104	B	151	ASN	0	0.078	4.698	1.180	1.375	-0.001	-0.007	-0.187	0.000
105	B	152	PRO	0	-0.064	6.252	-0.979	-0.979	0.000	0.000	0.000	0.000
106	B	153	ALA	0	-0.001	8.283	-0.469	-0.469	0.000	0.000	0.000	0.000
107	B	154	ASN	0	-0.010	8.628	-0.164	-0.164	0.000	0.000	0.000	0.000
108	B	155	ASN	0	0.050	9.878	-0.262	-0.262	0.000	0.000	0.000	0.000
109	B	156	ALA	0	0.063	11.831	0.216	0.216	0.000	0.000	0.000	0.000
110	B	157	ALA	0	-0.030	14.150	-0.001	-0.001	0.000	0.000	0.000	0.000
111	B	158	ILE	0	0.016	14.983	-0.072	-0.072	0.000	0.000	0.000	0.000
112	B	159	VAL	0	0.009	17.592	0.004	0.004	0.000	0.000	0.000	0.000
113	B	160	LEU	0	-0.017	19.516	-0.037	-0.037	0.000	0.000	0.000	0.000
114	B	161	GLN	0	-0.054	21.360	-0.026	-0.026	0.000	0.000	0.000	0.000
115	B	162	LEU	0	-0.003	24.273	-0.012	-0.012	0.000	0.000	0.000	0.000
116	B	163	PRO	0	0.041	25.949	0.003	0.003	0.000	0.000	0.000	0.000
117	B	164	GLN	0	0.024	28.927	0.006	0.006	0.000	0.000	0.000	0.000
118	B	165	GLY	0	0.017	32.563	-0.008	-0.008	0.000	0.000	0.000	0.000
119	B	166	THR	0	-0.044	28.411	-0.011	-0.011	0.000	0.000	0.000	0.000
120	B	167	THR	0	-0.011	31.756	0.009	0.009	0.000	0.000	0.000	0.000
121	B	168	LEU	0	-0.007	27.571	0.000	0.000	0.000	0.000	0.000	0.000
122	B	169	PRO	0	-0.028	29.781	-0.004	-0.004	0.000	0.000	0.000	0.000
123	B	170	LYS	1	0.978	32.523	-0.026	-0.026	0.000	0.000	0.000	0.000
124	B	171	GLY	0	-0.004	32.319	0.000	0.000	0.000	0.000	0.000	0.000
125	B	172	PHE	0	0.000	25.283	0.014	0.014	0.000	0.000	0.000	0.000
126	B	173	TYR	0	0.016	28.492	-0.008	-0.008	0.000	0.000	0.000	0.000
127	B	174	ALA	0	0.077	27.766	0.022	0.022	0.000	0.000	0.000	0.000
128	B	201	HOH	0	0.001	29.061	0.006	0.006	0.000	0.000	0.000	0.000
129	B	202	HOH	0	-0.010	22.062	0.006	0.006	0.000	0.000	0.000	0.000
130	B	203	HOH	0	-0.023	12.214	0.076	0.076	0.000	0.000	0.000	0.000
131	B	204	HOH	0	-0.040	30.679	-0.003	-0.003	0.000	0.000	0.000	0.000
132	B	205	HOH	0	-0.033	30.699	0.002	0.002	0.000	0.000	0.000	0.000
133	B	206	HOH	0	-0.005	15.815	-0.032	-0.032	0.000	0.000	0.000	0.000
134	B	207	HOH	0	0.015	23.384	0.015	0.015	0.000	0.000	0.000	0.000
135	B	208	HOH	0	-0.021	18.772	-0.015	-0.015	0.000	0.000	0.000	0.000
136	B	209	HOH	0	0.037	23.595	-0.006	-0.006	0.000	0.000	0.000	0.000
137	B	210	HOH	0	-0.002	21.069	0.001	0.001	0.000	0.000	0.000	0.000
138	B	211	HOH	0	0.042	21.143	0.015	0.015	0.000	0.000	0.000	0.000
139	B	212	HOH	0	-0.003	16.412	0.020	0.020	0.000	0.000	0.000	0.000
140	B	213	HOH	0	0.004	10.889	0.070	0.070	0.000	0.000	0.000	0.000
141	B	214	HOH	0	-0.010	7.085	0.295	0.295	0.000	0.000	0.000	0.000
142	B	215	HOH	0	0.010	21.937	0.016	0.016	0.000	0.000	0.000	0.000
143	B	216	HOH	0	0.002	27.377	-0.006	-0.006	0.000	0.000	0.000	0.000
144	B	217	HOH	0	-0.040	16.992	-0.015	-0.015	0.000	0.000	0.000	0.000
145	B	218	HOH	0	-0.031	18.362	0.024	0.024	0.000	0.000	0.000	0.000
146	B	219	HOH	0	0.010	26.294	0.007	0.007	0.000	0.000	0.000	0.000
147	B	220	HOH	0	-0.039	12.769	0.023	0.023	0.000	0.000	0.000	0.000
148	B	221	HOH	0	0.022	5.209	0.386	0.386	0.000	0.000	0.000	0.000
149	B	222	HOH	0	-0.017	21.144	0.014	0.014	0.000	0.000	0.000	0.000
150	B	223	HOH	0	0.014	13.972	0.001	0.001	0.000	0.000	0.000	0.000
151	B	224	HOH	0	-0.023	27.240	-0.002	-0.002	0.000	0.000	0.000	0.000
152	B	225	HOH	0	-0.010	15.448	0.015	0.015	0.000	0.000	0.000	0.000
153	B	226	HOH	0	0.013	31.815	0.002	0.002	0.000	0.000	0.000	0.000
154	B	227	HOH	0	0.009	30.203	0.003	0.003	0.000	0.000	0.000	0.000
155	B	228	HOH	0	0.022	7.051	-0.063	-0.063	0.000	0.000	0.000	0.000
156	B	229	HOH	0	-0.014	23.015	0.010	0.010	0.000	0.000	0.000	0.000
157	B	230	HOH	0	0.003	14.508	0.022	0.022	0.000	0.000	0.000	0.000
158	B	231	HOH	0	0.007	25.498	0.000	0.000	0.000	0.000	0.000	0.000
159	B	232	HOH	0	-0.041	26.914	-0.006	-0.006	0.000	0.000	0.000	0.000
160	B	233	HOH	0	0.034	16.618	0.015	0.015	0.000	0.000	0.000	0.000
161	B	234	HOH	0	-0.017	12.201	0.018	0.018	0.000	0.000	0.000	0.000
162	B	235	HOH	0	-0.018	24.753	-0.006	-0.006	0.000	0.000	0.000	0.000
163	B	236	HOH	0	-0.007	26.059	0.008	0.008	0.000	0.000	0.000	0.000
164	B	237	HOH	0	0.031	23.668	0.009	0.009	0.000	0.000	0.000	0.000
165	B	238	HOH	0	-0.026	15.749	0.011	0.011	0.000	0.000	0.000	0.000
166	B	239	HOH	0	0.027	6.103	0.225	0.225	0.000	0.000	0.000	0.000
167	B	240	HOH	0	0.019	26.926	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:48:ASN )