FMO DATABASE

FMODB ID: 7G32K

Calculation Name: 3MY2-A-Xray317

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MY2

Chain ID: A

ChEMBL ID:

UniProt ID: P0ADV9

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	128
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1095262.266177
FMO2-HF: Nuclear repulsion	1044906.486693
FMO2-HF: Total energy	-50355.779483
FMO2-MP2: Total energy	-50504.810099

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:58:ACE )

Summations of interaction energy for fragment #1(A:58:ACE )

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.
0.38	1.389	-0.003	-0.406	-0.599	0

Interaction energy analysis for fragmet #1(A:58:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.000

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	60	TYR	0	0.011	0.007	3.847	1.147	1.932	-0.005	-0.355	-0.425
4	A	61	ARG	1	0.913	0.961	6.863	0.328	0.328	0.000	0.000	0.000
5	A	62	LEU	0	0.011	0.006	10.521	0.079	0.079	0.000	0.000	0.000
6	A	63	ILE	0	-0.023	-0.005	13.015	-0.009	-0.009	0.000	0.000	0.000
7	A	64	ALA	0	0.018	0.010	16.721	0.018	0.018	0.000	0.000	0.000
8	A	65	GLN	0	0.003	0.010	19.700	-0.003	-0.003	0.000	0.000	0.000
9	A	66	HIS	0	-0.045	-0.051	22.957	-0.011	-0.011	0.000	0.000	0.000
10	A	67	VAL	0	0.001	-0.010	19.878	-0.003	-0.003	0.000	0.000	0.000
11	A	68	GLU	-1	-0.821	-0.840	22.820	-0.047	-0.047	0.000	0.000	0.000
12	A	69	TYR	0	0.011	0.003	19.172	0.000	0.000	0.000	0.000	0.000
13	A	70	TYR	0	-0.078	-0.068	22.773	0.004	0.004	0.000	0.000	0.000
14	A	71	SER	0	0.034	-0.013	23.400	0.002	0.002	0.000	0.000	0.000
15	A	72	ASP	-1	-0.929	-0.945	24.245	-0.023	-0.023	0.000	0.000	0.000
16	A	73	GLN	0	-0.084	-0.052	24.167	0.007	0.007	0.000	0.000	0.000
17	A	74	ALA	0	0.014	0.022	19.610	0.006	0.006	0.000	0.000	0.000
18	A	75	VAL	0	-0.051	-0.018	19.139	0.004	0.004	0.000	0.000	0.000
19	A	76	SER	0	-0.005	-0.003	17.666	-0.005	-0.005	0.000	0.000	0.000
20	A	77	TRP	0	-0.014	-0.007	19.323	0.012	0.012	0.000	0.000	0.000
21	A	78	PHE	0	0.022	-0.003	15.959	-0.013	-0.013	0.000	0.000	0.000
22	A	79	THR	0	-0.005	-0.015	20.632	0.017	0.017	0.000	0.000	0.000
23	A	80	GLN	0	-0.026	-0.008	22.067	-0.014	-0.014	0.000	0.000	0.000
24	A	81	PRO	0	-0.041	0.001	16.486	-0.018	-0.018	0.000	0.000	0.000
25	A	82	VAL	0	0.018	-0.016	15.878	0.019	0.019	0.000	0.000	0.000
26	A	83	LEU	0	0.002	0.007	8.912	-0.052	-0.052	0.000	0.000	0.000
27	A	84	THR	0	-0.065	-0.033	10.705	0.058	0.058	0.000	0.000	0.000
28	A	85	THR	0	0.044	0.023	6.373	-0.215	-0.215	0.000	0.000	0.000
29	A	86	PHE	0	-0.026	-0.026	5.727	0.122	0.122	0.000	0.000	0.000
30	A	87	ASP	-1	-0.822	-0.906	4.802	-0.306	-0.331	0.000	-0.006	0.032
31	A	88	LYS	1	0.908	0.939	5.115	-1.291	-1.291	0.000	0.000	0.000
32	A	89	ASP	-1	-0.867	-0.917	6.897	-0.293	-0.293	0.000	0.000	0.000
33	A	90	LYS	1	0.839	0.917	8.162	1.116	1.116	0.000	0.000	0.000
34	A	91	ILE	0	0.048	0.030	9.402	0.051	0.051	0.000	0.000	0.000
35	A	92	PRO	0	-0.038	-0.028	9.632	-0.027	-0.027	0.000	0.000	0.000
36	A	93	THR	0	-0.033	-0.019	8.309	0.125	0.125	0.000	0.000	0.000
37	A	94	TRP	0	0.023	-0.003	9.296	0.027	0.027	0.000	0.000	0.000
38	A	95	SER	0	-0.061	-0.018	11.642	-0.070	-0.070	0.000	0.000	0.000
39	A	96	VAL	0	0.034	-0.004	12.614	0.040	0.040	0.000	0.000	0.000
40	A	97	LYS	1	0.932	0.981	15.187	0.038	0.038	0.000	0.000	0.000
41	A	98	ALA	0	0.055	0.021	18.370	0.019	0.019	0.000	0.000	0.000
42	A	99	ASP	-1	-0.785	-0.865	20.640	-0.028	-0.028	0.000	0.000	0.000
43	A	100	LYS	1	0.935	0.969	22.067	0.001	0.001	0.000	0.000	0.000
44	A	101	ALA	0	0.001	0.003	17.089	0.010	0.010	0.000	0.000	0.000
45	A	102	LYS	1	0.937	0.985	18.630	-0.024	-0.024	0.000	0.000	0.000
46	A	103	LEU	0	-0.039	-0.005	11.976	0.009	0.009	0.000	0.000	0.000
47	A	104	THR	0	-0.005	-0.017	15.460	-0.013	-0.013	0.000	0.000	0.000
48	A	105	ASN	0	0.077	0.027	14.781	-0.030	-0.030	0.000	0.000	0.000
49	A	106	ASP	-1	-0.886	-0.932	13.393	0.077	0.077	0.000	0.000	0.000
50	A	107	ARG	1	0.886	0.956	8.078	0.105	0.105	0.000	0.000	0.000
51	A	108	MET	0	0.005	0.008	10.707	0.060	0.060	0.000	0.000	0.000
52	A	109	LEU	0	-0.008	-0.008	12.327	-0.049	-0.049	0.000	0.000	0.000
53	A	110	TYR	0	-0.025	-0.031	14.093	0.022	0.022	0.000	0.000	0.000
54	A	111	LEU	0	-0.007	-0.001	14.649	-0.024	-0.024	0.000	0.000	0.000
55	A	112	TYR	0	0.016	-0.010	18.820	0.010	0.010	0.000	0.000	0.000
56	A	113	GLY	0	0.027	0.019	22.551	-0.010	-0.010	0.000	0.000	0.000
57	A	114	HIS	0	-0.041	-0.050	23.348	-0.002	-0.002	0.000	0.000	0.000
58	A	115	VAL	0	-0.010	0.014	18.413	-0.006	-0.006	0.000	0.000	0.000
59	A	116	GLU	-1	-0.837	-0.930	19.645	0.009	0.009	0.000	0.000	0.000
60	A	117	VAL	0	-0.033	-0.014	14.559	-0.012	-0.012	0.000	0.000	0.000
61	A	118	ASN	0	-0.056	-0.044	16.295	0.015	0.015	0.000	0.000	0.000
62	A	119	ALA	0	0.018	0.009	14.842	-0.009	-0.009	0.000	0.000	0.000
63	A	120	LEU	0	-0.071	-0.033	12.831	-0.019	-0.019	0.000	0.000	0.000
64	A	121	VAL	0	0.000	0.003	13.136	-0.014	-0.014	0.000	0.000	0.000
65	A	122	PRO	0	0.017	-0.004	15.815	0.018	0.018	0.000	0.000	0.000
66	A	123	ASP	-1	-0.918	-0.941	15.362	0.133	0.133	0.000	0.000	0.000
67	A	124	SER	0	-0.064	-0.058	15.157	0.042	0.042	0.000	0.000	0.000
68	A	125	GLN	0	0.034	0.020	17.059	-0.024	-0.024	0.000	0.000	0.000
69	A	126	LEU	0	0.040	0.035	15.919	-0.016	-0.016	0.000	0.000	0.000
70	A	127	ARG	1	0.855	0.922	17.714	-0.044	-0.044	0.000	0.000	0.000
71	A	128	ARG	1	0.919	0.963	19.019	-0.030	-0.030	0.000	0.000	0.000
72	A	129	ILE	0	-0.004	0.017	16.679	0.011	0.011	0.000	0.000	0.000
73	A	130	THR	0	0.010	0.013	20.454	-0.011	-0.011	0.000	0.000	0.000
74	A	131	THR	0	-0.050	-0.042	20.863	0.009	0.009	0.000	0.000	0.000
75	A	132	ASP	-1	-0.850	-0.923	23.427	0.022	0.022	0.000	0.000	0.000
76	A	133	ASN	0	-0.046	-0.041	21.988	-0.017	-0.017	0.000	0.000	0.000
77	A	134	ALA	0	-0.012	0.012	17.657	0.011	0.011	0.000	0.000	0.000
78	A	135	GLN	0	-0.074	-0.060	16.315	-0.033	-0.033	0.000	0.000	0.000
79	A	136	ILE	0	-0.018	-0.005	9.826	0.029	0.029	0.000	0.000	0.000
80	A	137	ASN	0	0.051	0.044	8.858	0.033	0.033	0.000	0.000	0.000
81	A	138	LEU	0	-0.001	-0.015	7.082	0.144	0.144	0.000	0.000	0.000
82	A	139	VAL	0	-0.046	-0.018	4.687	-0.035	-0.005	0.000	-0.006	-0.024
83	A	140	THR	0	-0.064	-0.058	4.693	0.699	0.858	0.000	-0.011	-0.148
84	A	141	GLN	0	0.006	-0.011	3.875	-0.049	0.011	0.002	-0.028	-0.034
85	A	142	ASP	-1	-0.807	-0.863	7.825	0.448	0.448	0.000	0.000	0.000
86	A	143	VAL	0	-0.012	-0.010	11.486	-0.040	-0.040	0.000	0.000	0.000
87	A	144	THR	0	-0.019	-0.008	14.095	-0.003	-0.003	0.000	0.000	0.000
88	A	145	SER	0	0.084	0.041	17.794	-0.015	-0.015	0.000	0.000	0.000
89	A	146	GLU	-1	-0.845	-0.924	20.960	0.120	0.120	0.000	0.000	0.000
90	A	147	ASP	-1	-0.807	-0.887	24.279	0.044	0.044	0.000	0.000	0.000
91	A	148	LEU	0	-0.022	-0.028	25.773	0.008	0.008	0.000	0.000	0.000
92	A	149	VAL	0	-0.006	0.015	22.041	0.000	0.000	0.000	0.000	0.000
93	A	150	THR	0	-0.039	-0.014	24.468	-0.003	-0.003	0.000	0.000	0.000
94	A	151	LEU	0	-0.011	-0.005	20.360	0.003	0.003	0.000	0.000	0.000
95	A	152	TYR	0	0.018	-0.015	22.443	-0.008	-0.008	0.000	0.000	0.000
96	A	153	GLY	0	0.025	0.007	22.004	0.009	0.009	0.000	0.000	0.000
97	A	154	THR	0	-0.039	-0.023	22.423	-0.011	-0.011	0.000	0.000	0.000
98	A	155	THR	0	-0.020	-0.013	24.857	-0.005	-0.005	0.000	0.000	0.000
99	A	156	PHE	0	-0.013	0.002	27.118	-0.004	-0.004	0.000	0.000	0.000
100	A	157	ASN	0	0.018	0.009	26.610	0.008	0.008	0.000	0.000	0.000
101	A	158	SER	0	0.021	0.014	25.888	-0.001	-0.001	0.000	0.000	0.000
102	A	159	SER	0	0.030	0.006	26.903	0.002	0.002	0.000	0.000	0.000
103	A	160	GLY	0	0.022	0.021	27.802	0.000	0.000	0.000	0.000	0.000
104	A	161	LEU	0	-0.058	-0.024	27.777	-0.003	-0.003	0.000	0.000	0.000
105	A	162	LYS	1	0.908	0.968	24.275	-0.073	-0.073	0.000	0.000	0.000
106	A	163	MET	0	-0.060	-0.018	17.414	0.009	0.009	0.000	0.000	0.000
107	A	164	ARG	1	0.927	0.966	18.046	-0.170	-0.170	0.000	0.000	0.000
108	A	165	GLY	0	0.042	0.007	15.940	-0.016	-0.016	0.000	0.000	0.000
109	A	166	ASN	0	-0.067	-0.036	9.478	0.102	0.102	0.000	0.000	0.000
110	A	167	LEU	0	0.041	0.031	8.887	-0.031	-0.031	0.000	0.000	0.000
111	A	168	ARG	1	0.870	0.956	5.642	-1.521	-1.521	0.000	0.000	0.000
112	A	169	SER	0	-0.037	-0.034	8.267	-0.094	-0.094	0.000	0.000	0.000
113	A	170	LYS	1	0.921	0.975	11.069	-0.292	-0.292	0.000	0.000	0.000
114	A	171	ASN	0	0.016	0.023	13.463	-0.082	-0.082	0.000	0.000	0.000
115	A	172	ALA	0	0.011	-0.023	15.709	0.024	0.024	0.000	0.000	0.000
116	A	173	GLU	-1	-0.901	-0.937	18.376	0.159	0.159	0.000	0.000	0.000
117	A	174	LEU	0	-0.010	-0.010	21.845	0.002	0.002	0.000	0.000	0.000
118	A	175	ILE	0	-0.013	-0.001	22.774	0.001	0.001	0.000	0.000	0.000
119	A	176	GLU	-1	-0.871	-0.942	26.452	0.065	0.065	0.000	0.000	0.000
120	A	177	LYS	1	0.886	0.932	29.939	-0.054	-0.054	0.000	0.000	0.000
121	A	178	VAL	0	0.022	0.019	28.627	-0.003	-0.003	0.000	0.000	0.000
122	A	179	ARG	1	0.953	0.984	30.914	-0.045	-0.045	0.000	0.000	0.000
123	A	180	THR	0	0.004	0.002	30.040	0.002	0.002	0.000	0.000	0.000
124	A	181	SER	0	-0.009	-0.018	31.104	-0.002	-0.002	0.000	0.000	0.000
125	A	182	TYR	0	-0.015	-0.010	30.790	-0.005	-0.005	0.000	0.000	0.000
126	A	183	GLU	-1	-0.887	-0.945	34.682	0.050	0.050	0.000	0.000	0.000
127	A	184	ILE	0	-0.063	-0.020	37.080	-0.003	-0.003	0.000	0.000	0.000
128	A	185	NME	0	0.012	0.011	39.877	-0.001	-0.001	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:58:ACE )