FMO DATABASE

FMODB ID: 3NY5L

Calculation Name: 3A6M-A-Xray307

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A6M

Chain ID: A

ChEMBL ID:

UniProt ID: Q56236

Base Structure: X-ray

Registration Date: 2021-09-06

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	170
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1197159.334586
FMO2-HF: Nuclear repulsion	1131472.394318
FMO2-HF: Total energy	-65686.940268
FMO2-MP2: Total energy	-65882.023792

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:3:ACE )

Summations of interaction energy for fragment #1(A:3: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.
1.797	1.548	6.67	-3.741	-2.677	-0.03

Interaction energy analysis for fragmet #1(A:3:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : 0.011

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	5	ASN	0	-0.004	0.012	3.858	0.834	1.568	-0.005	-0.347	-0.382	-0.001
4	A	6	HIS	0	-0.022	-0.003	4.167	0.147	0.276	0.000	-0.025	-0.103	0.000
5	A	7	GLU	-1	-0.774	-0.888	2.544	0.867	-0.244	6.675	-3.358	-2.205	-0.029
6	A	8	ASN	0	-0.035	-0.014	4.754	-0.302	-0.303	0.000	-0.011	0.013	0.000
7	A	9	THR	0	-0.056	-0.039	7.143	0.226	0.226	0.000	0.000	0.000	0.000
8	A	10	LEU	0	-0.011	-0.011	8.198	0.082	0.082	0.000	0.000	0.000	0.000
9	A	11	GLU	-1	-0.786	-0.870	8.229	-0.348	-0.348	0.000	0.000	0.000	0.000
10	A	12	LYS	1	0.900	0.929	9.602	0.208	0.208	0.000	0.000	0.000	0.000
11	A	13	ASP	-1	-0.933	-0.958	10.930	0.154	0.154	0.000	0.000	0.000	0.000
12	A	14	LEU	0	-0.069	-0.045	11.653	0.027	0.027	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.966	-0.957	14.079	-0.154	-0.154	0.000	0.000	0.000	0.000
14	A	16	ALA	0	-0.020	-0.014	16.552	0.001	0.001	0.000	0.000	0.000	0.000
15	A	17	VAL	0	0.054	0.033	17.520	0.005	0.005	0.000	0.000	0.000	0.000
16	A	18	GLY	0	0.019	0.009	19.728	0.003	0.003	0.000	0.000	0.000	0.000
17	A	19	GLN	0	-0.084	-0.063	20.603	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.989	-0.986	22.797	0.036	0.036	0.000	0.000	0.000	0.000
19	A	21	ALA	0	-0.001	0.001	23.290	0.006	0.006	0.000	0.000	0.000	0.000
20	A	22	GLN	0	0.051	0.019	25.178	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	23	ALA	0	0.034	0.009	27.160	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	24	LEU	0	-0.058	-0.036	27.267	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.918	-0.951	27.253	0.023	0.023	0.000	0.000	0.000	0.000
24	A	26	GLU	-1	-0.865	-0.894	31.064	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	27	ARG	1	0.851	0.924	31.915	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	28	LEU	0	-0.007	-0.006	33.824	0.000	0.000	0.000	0.000	0.000	0.000
27	A	29	LYS	1	0.869	0.921	34.119	0.003	0.003	0.000	0.000	0.000	0.000
28	A	30	ALA	0	0.017	-0.001	37.123	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	31	ALA	0	-0.021	-0.023	39.156	0.000	0.000	0.000	0.000	0.000	0.000
30	A	32	GLU	-1	-0.778	-0.860	41.074	0.009	0.009	0.000	0.000	0.000	0.000
31	A	33	GLU	-1	-0.886	-0.970	42.573	0.004	0.004	0.000	0.000	0.000	0.000
32	A	34	GLU	-1	-0.995	-0.976	43.146	0.006	0.006	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.002	-0.001	43.696	0.001	0.001	0.000	0.000	0.000	0.000
34	A	36	LYS	1	0.728	0.852	45.649	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	37	GLY	0	0.064	0.027	47.717	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	38	LEU	0	0.006	0.011	49.009	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	39	LYS	1	0.915	0.960	50.772	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	40	ASP	-1	-0.850	-0.898	52.673	0.002	0.002	0.000	0.000	0.000	0.000
39	A	41	LYS	1	0.988	0.966	53.919	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	42	TYR	0	0.028	0.034	54.797	0.000	0.000	0.000	0.000	0.000	0.000
41	A	43	LEU	0	-0.027	-0.009	56.326	0.000	0.000	0.000	0.000	0.000	0.000
42	A	44	ARG	1	0.859	0.906	57.050	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	45	LEU	0	0.022	0.020	59.415	0.000	0.000	0.000	0.000	0.000	0.000
44	A	46	LEU	0	-0.051	-0.040	59.922	0.000	0.000	0.000	0.000	0.000	0.000
45	A	47	ALA	0	-0.008	0.008	62.214	0.000	0.000	0.000	0.000	0.000	0.000
46	A	48	ASP	-1	-0.862	-0.943	63.907	0.003	0.003	0.000	0.000	0.000	0.000
47	A	49	PHE	0	-0.022	-0.010	65.067	0.000	0.000	0.000	0.000	0.000	0.000
48	A	50	ASP	-1	-0.878	-0.926	66.253	0.006	0.006	0.000	0.000	0.000	0.000
49	A	51	ASN	0	-0.029	0.000	68.055	0.000	0.000	0.000	0.000	0.000	0.000
50	A	52	TYR	0	0.066	0.012	69.615	0.000	0.000	0.000	0.000	0.000	0.000
51	A	53	ARG	1	0.922	0.961	70.672	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	54	LYS	1	0.866	0.922	70.408	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	55	ARG	1	0.978	0.996	71.921	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	56	MET	0	-0.045	-0.027	74.857	0.000	0.000	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.967	-0.982	76.354	0.004	0.004	0.000	0.000	0.000	0.000
56	A	58	GLU	-1	-0.890	-0.929	78.199	0.003	0.003	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.950	-1.003	79.041	0.002	0.002	0.000	0.000	0.000	0.000
58	A	60	LEU	0	-0.023	0.001	78.892	0.000	0.000	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.941	0.960	81.618	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	62	ALA	0	-0.020	0.001	84.459	0.000	0.000	0.000	0.000	0.000	0.000
61	A	63	ARG	1	0.979	0.982	84.669	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.926	-0.941	86.929	0.003	0.003	0.000	0.000	0.000	0.000
63	A	65	ARG	1	0.961	0.987	88.735	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	66	GLU	-1	-0.978	-0.998	89.285	0.002	0.002	0.000	0.000	0.000	0.000
65	A	67	GLY	0	0.029	0.010	91.152	0.000	0.000	0.000	0.000	0.000	0.000
66	A	68	VAL	0	0.009	-0.002	92.778	0.000	0.000	0.000	0.000	0.000	0.000
67	A	69	LEU	0	-0.049	-0.022	93.757	0.000	0.000	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.941	0.979	94.441	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	71	ALA	0	0.020	0.011	97.141	0.000	0.000	0.000	0.000	0.000	0.000
70	A	72	LEU	0	0.027	-0.007	98.582	0.000	0.000	0.000	0.000	0.000	0.000
71	A	73	ARG	1	0.916	0.950	96.224	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	74	ALA	0	0.009	0.010	101.663	0.000	0.000	0.000	0.000	0.000	0.000
73	A	75	LEU	0	0.019	-0.006	102.420	0.000	0.000	0.000	0.000	0.000	0.000
74	A	76	LEU	0	-0.013	0.017	103.880	0.000	0.000	0.000	0.000	0.000	0.000
75	A	77	PRO	0	0.025	0.010	106.661	0.000	0.000	0.000	0.000	0.000	0.000
76	A	78	VAL	0	-0.012	0.003	108.832	0.000	0.000	0.000	0.000	0.000	0.000
77	A	79	LEU	0	-0.030	-0.014	108.833	0.000	0.000	0.000	0.000	0.000	0.000
78	A	80	ASP	-1	-0.852	-0.923	110.654	0.001	0.001	0.000	0.000	0.000	0.000
79	A	81	ASP	-1	-0.909	-0.953	113.096	0.001	0.001	0.000	0.000	0.000	0.000
80	A	82	LEU	0	-0.089	-0.054	112.463	0.000	0.000	0.000	0.000	0.000	0.000
81	A	83	ASP	-1	-0.870	-0.925	114.242	0.002	0.002	0.000	0.000	0.000	0.000
82	A	84	ARG	1	0.844	0.907	115.263	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	85	ALA	0	-0.081	-0.054	118.900	0.000	0.000	0.000	0.000	0.000	0.000
84	A	86	LEU	0	0.004	-0.011	118.318	0.000	0.000	0.000	0.000	0.000	0.000
85	A	87	GLU	-1	-0.946	-0.956	120.198	0.001	0.001	0.000	0.000	0.000	0.000
86	A	88	PHE	0	-0.054	-0.021	122.362	0.000	0.000	0.000	0.000	0.000	0.000
87	A	89	ALA	0	-0.019	-0.022	123.365	0.000	0.000	0.000	0.000	0.000	0.000
88	A	90	GLU	-1	-0.932	-0.965	125.031	0.002	0.002	0.000	0.000	0.000	0.000
89	A	91	ALA	0	-0.057	-0.008	127.204	0.000	0.000	0.000	0.000	0.000	0.000
90	A	92	SER	0	0.040	-0.003	129.317	0.000	0.000	0.000	0.000	0.000	0.000
91	A	93	PRO	0	0.080	0.051	128.434	0.000	0.000	0.000	0.000	0.000	0.000
92	A	94	GLU	-1	-0.837	-0.924	127.386	0.002	0.002	0.000	0.000	0.000	0.000
93	A	95	SER	0	-0.046	-0.024	127.089	0.000	0.000	0.000	0.000	0.000	0.000
94	A	96	ILE	0	0.047	0.040	122.855	0.000	0.000	0.000	0.000	0.000	0.000
95	A	97	ARG	1	0.844	0.940	122.852	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	98	GLN	0	-0.004	-0.021	122.433	0.000	0.000	0.000	0.000	0.000	0.000
97	A	99	GLY	0	0.081	0.050	121.575	0.000	0.000	0.000	0.000	0.000	0.000
98	A	100	VAL	0	0.026	0.003	117.597	0.000	0.000	0.000	0.000	0.000	0.000
99	A	101	ARG	1	0.806	0.910	117.533	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	102	ALA	0	0.052	0.022	117.315	0.000	0.000	0.000	0.000	0.000	0.000
101	A	103	ILE	0	0.053	0.034	113.587	0.000	0.000	0.000	0.000	0.000	0.000
102	A	104	ARG	1	0.881	0.952	113.020	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	105	ASP	-1	-0.933	-0.979	112.366	0.002	0.002	0.000	0.000	0.000	0.000
104	A	106	GLY	0	-0.033	-0.023	112.297	0.000	0.000	0.000	0.000	0.000	0.000
105	A	107	PHE	0	0.039	0.010	105.583	0.000	0.000	0.000	0.000	0.000	0.000
106	A	108	PHE	0	-0.014	-0.013	107.669	0.000	0.000	0.000	0.000	0.000	0.000
107	A	109	ARG	1	0.970	0.997	107.232	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	110	ILE	0	-0.001	0.004	104.686	0.000	0.000	0.000	0.000	0.000	0.000
109	A	111	LEU	0	-0.031	-0.023	102.660	0.000	0.000	0.000	0.000	0.000	0.000
110	A	112	ALA	0	0.069	0.033	102.501	0.000	0.000	0.000	0.000	0.000	0.000
111	A	113	GLY	0	-0.012	0.016	102.601	0.000	0.000	0.000	0.000	0.000	0.000
112	A	114	LEU	0	-0.146	-0.067	98.694	0.000	0.000	0.000	0.000	0.000	0.000
113	A	115	GLY	0	-0.001	-0.006	98.379	0.000	0.000	0.000	0.000	0.000	0.000
114	A	116	VAL	0	-0.081	-0.049	98.779	0.000	0.000	0.000	0.000	0.000	0.000
115	A	117	GLU	-1	-0.898	-0.950	100.821	0.002	0.002	0.000	0.000	0.000	0.000
116	A	118	GLU	-1	-0.938	-0.986	102.420	0.002	0.002	0.000	0.000	0.000	0.000
117	A	119	VAL	0	-0.097	-0.042	101.264	0.000	0.000	0.000	0.000	0.000	0.000
118	A	120	PRO	0	0.037	0.005	103.475	0.000	0.000	0.000	0.000	0.000	0.000
119	A	121	GLY	0	0.064	0.020	106.640	0.000	0.000	0.000	0.000	0.000	0.000
120	A	122	GLU	-1	-0.925	-0.973	109.502	0.002	0.002	0.000	0.000	0.000	0.000
121	A	123	GLY	0	-0.013	0.007	112.779	0.000	0.000	0.000	0.000	0.000	0.000
122	A	124	GLU	-1	-0.900	-0.942	107.620	0.002	0.002	0.000	0.000	0.000	0.000
123	A	125	ALA	0	-0.065	-0.040	105.500	0.000	0.000	0.000	0.000	0.000	0.000
124	A	126	PHE	0	-0.031	-0.025	102.993	0.000	0.000	0.000	0.000	0.000	0.000
125	A	127	ASP	-1	-0.770	-0.847	99.408	0.003	0.003	0.000	0.000	0.000	0.000
126	A	128	PRO	0	0.012	-0.014	97.932	0.000	0.000	0.000	0.000	0.000	0.000
127	A	129	ARG	1	0.824	0.890	95.324	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	130	TYR	0	-0.009	-0.014	97.468	0.000	0.000	0.000	0.000	0.000	0.000
129	A	131	HIS	0	-0.086	-0.039	100.280	0.000	0.000	0.000	0.000	0.000	0.000
130	A	132	GLU	-1	-0.833	-0.904	100.107	0.004	0.004	0.000	0.000	0.000	0.000
131	A	133	ALA	0	-0.015	-0.016	102.970	0.000	0.000	0.000	0.000	0.000	0.000
132	A	134	VAL	0	-0.070	-0.053	105.354	0.000	0.000	0.000	0.000	0.000	0.000
133	A	135	GLY	0	0.003	0.004	107.674	0.000	0.000	0.000	0.000	0.000	0.000
134	A	136	LEU	0	-0.044	-0.008	110.001	0.000	0.000	0.000	0.000	0.000	0.000
135	A	137	LEU	0	-0.019	-0.009	112.336	0.000	0.000	0.000	0.000	0.000	0.000
136	A	138	PRO	0	-0.013	-0.001	115.463	0.000	0.000	0.000	0.000	0.000	0.000
137	A	139	GLY	0	0.010	-0.004	116.380	0.000	0.000	0.000	0.000	0.000	0.000
138	A	140	GLU	-1	-0.929	-0.966	113.403	0.003	0.003	0.000	0.000	0.000	0.000
139	A	141	PRO	0	0.025	0.001	111.847	0.000	0.000	0.000	0.000	0.000	0.000
140	A	142	GLY	0	-0.021	0.005	107.904	0.000	0.000	0.000	0.000	0.000	0.000
141	A	143	LYS	1	0.921	0.973	107.968	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	144	VAL	0	-0.027	0.004	107.945	0.000	0.000	0.000	0.000	0.000	0.000
143	A	145	ALA	0	0.035	0.019	110.430	0.000	0.000	0.000	0.000	0.000	0.000
144	A	146	LYS	1	0.928	0.959	112.544	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	147	VAL	0	0.021	0.019	109.110	0.000	0.000	0.000	0.000	0.000	0.000
146	A	148	PHE	0	-0.071	-0.035	110.294	0.000	0.000	0.000	0.000	0.000	0.000
147	A	149	GLN	0	-0.051	-0.044	104.665	0.000	0.000	0.000	0.000	0.000	0.000
148	A	150	ARG	1	0.951	1.000	107.109	-0.002	-0.002	0.000	0.000	0.000	0.000
149	A	151	GLY	0	0.065	0.039	103.524	0.000	0.000	0.000	0.000	0.000	0.000
150	A	152	PHE	0	-0.026	-0.010	101.591	0.000	0.000	0.000	0.000	0.000	0.000
151	A	153	ARG	1	0.967	0.991	97.550	-0.002	-0.002	0.000	0.000	0.000	0.000
152	A	154	MET	0	0.002	0.021	94.701	0.000	0.000	0.000	0.000	0.000	0.000
153	A	155	GLY	0	-0.049	-0.022	94.634	0.000	0.000	0.000	0.000	0.000	0.000
154	A	156	GLU	-1	-0.903	-0.968	90.833	0.003	0.003	0.000	0.000	0.000	0.000
155	A	157	ALA	0	-0.029	0.004	91.728	0.000	0.000	0.000	0.000	0.000	0.000
156	A	158	LEU	0	0.026	0.006	93.231	0.000	0.000	0.000	0.000	0.000	0.000
157	A	159	VAL	0	-0.066	-0.025	95.374	0.000	0.000	0.000	0.000	0.000	0.000
158	A	160	ARG	1	0.900	0.933	97.432	-0.003	-0.003	0.000	0.000	0.000	0.000
159	A	161	PRO	0	0.059	0.046	98.280	0.000	0.000	0.000	0.000	0.000	0.000
160	A	162	ALA	0	0.025	0.003	100.913	0.000	0.000	0.000	0.000	0.000	0.000
161	A	163	ARG	1	0.925	0.978	104.550	-0.003	-0.003	0.000	0.000	0.000	0.000
162	A	164	VAL	0	-0.032	-0.034	106.103	0.000	0.000	0.000	0.000	0.000	0.000
163	A	165	ALA	0	0.015	0.034	108.497	0.000	0.000	0.000	0.000	0.000	0.000
164	A	166	VAL	0	0.002	-0.008	107.030	0.000	0.000	0.000	0.000	0.000	0.000
165	A	167	GLY	0	0.020	0.011	110.377	0.000	0.000	0.000	0.000	0.000	0.000
166	A	168	GLU	-1	-0.931	-0.977	112.282	0.003	0.003	0.000	0.000	0.000	0.000
167	A	169	GLU	-1	-0.910	-0.961	114.651	0.003	0.003	0.000	0.000	0.000	0.000
168	A	170	LYS	1	0.951	0.978	117.522	-0.003	-0.003	0.000	0.000	0.000	0.000
169	A	171	ARG	1	0.858	0.911	119.703	-0.003	-0.003	0.000	0.000	0.000	0.000
170	A	172	NME	0	0.114	0.072	118.109	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:3:ACE )