FMO DATABASE

FMODB ID: JMJZ9

Calculation Name: 3A6M-B-Xray307

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A6M

Chain ID: B

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	166
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1156026.874947
FMO2-HF: Nuclear repulsion	1092277.403459
FMO2-HF: Total energy	-63749.471489
FMO2-MP2: Total energy	-63938.65521

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:6:ACE )

Summations of interaction energy for fragment #1(B:6: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.
2.726	0.541	6.663	-2.106	-2.369	-0.002

Interaction energy analysis for fragmet #1(B:6:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.031

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	B	8	ASN	0	-0.006	-0.010	3.785	0.977	1.873	-0.005	-0.349	-0.541	-0.001
4	B	9	THR	0	-0.026	-0.032	4.201	0.153	0.296	0.000	-0.024	-0.118	0.000
5	B	10	LEU	0	-0.048	0.013	2.094	2.705	-0.650	6.664	-1.685	-1.624	-0.001
6	B	11	GLU	-1	-0.871	-0.939	4.077	-1.571	-1.440	0.004	-0.048	-0.086	0.000
7	B	12	LYS	1	0.873	0.937	7.184	0.695	0.695	0.000	0.000	0.000	0.000
8	B	13	ASP	-1	-0.961	-0.980	7.797	0.021	0.021	0.000	0.000	0.000	0.000
9	B	14	LEU	0	0.017	0.010	8.936	0.061	0.061	0.000	0.000	0.000	0.000
10	B	15	GLU	-1	-0.946	-0.966	11.407	-0.367	-0.367	0.000	0.000	0.000	0.000
11	B	16	ALA	0	-0.012	-0.006	13.509	0.032	0.032	0.000	0.000	0.000	0.000
12	B	17	VAL	0	0.026	0.006	15.033	0.020	0.020	0.000	0.000	0.000	0.000
13	B	18	GLY	0	-0.019	-0.010	16.641	0.010	0.010	0.000	0.000	0.000	0.000
14	B	19	GLN	0	0.005	0.001	18.408	0.015	0.015	0.000	0.000	0.000	0.000
15	B	20	GLU	-1	-0.949	-0.970	20.148	-0.027	-0.027	0.000	0.000	0.000	0.000
16	B	21	ALA	0	-0.011	-0.007	21.912	0.006	0.006	0.000	0.000	0.000	0.000
17	B	22	GLN	0	-0.016	-0.005	21.916	-0.008	-0.008	0.000	0.000	0.000	0.000
18	B	23	ALA	0	0.041	0.015	24.281	0.006	0.006	0.000	0.000	0.000	0.000
19	B	24	LEU	0	-0.070	-0.050	26.118	0.008	0.008	0.000	0.000	0.000	0.000
20	B	25	GLU	-1	-0.860	-0.925	27.881	-0.054	-0.054	0.000	0.000	0.000	0.000
21	B	26	GLU	-1	-0.927	-0.959	29.466	-0.045	-0.045	0.000	0.000	0.000	0.000
22	B	27	ARG	1	0.884	0.947	26.019	0.043	0.043	0.000	0.000	0.000	0.000
23	B	28	LEU	0	-0.043	-0.023	32.656	0.004	0.004	0.000	0.000	0.000	0.000
24	B	29	LYS	1	0.845	0.925	33.062	0.053	0.053	0.000	0.000	0.000	0.000
25	B	30	ALA	0	0.110	0.055	34.934	0.001	0.001	0.000	0.000	0.000	0.000
26	B	31	ALA	0	0.002	0.006	36.658	0.003	0.003	0.000	0.000	0.000	0.000
27	B	32	GLU	-1	-0.937	-0.974	38.043	-0.037	-0.037	0.000	0.000	0.000	0.000
28	B	33	GLU	-1	-0.909	-0.947	38.788	-0.034	-0.034	0.000	0.000	0.000	0.000
29	B	34	GLU	-1	-0.791	-0.902	40.965	-0.018	-0.018	0.000	0.000	0.000	0.000
30	B	35	LEU	0	-0.077	-0.038	41.751	0.002	0.002	0.000	0.000	0.000	0.000
31	B	36	LYS	1	0.853	0.929	41.096	0.034	0.034	0.000	0.000	0.000	0.000
32	B	37	GLY	0	0.041	0.010	45.555	0.000	0.000	0.000	0.000	0.000	0.000
33	B	38	LEU	0	-0.072	-0.028	46.252	0.001	0.001	0.000	0.000	0.000	0.000
34	B	39	LYS	1	0.912	0.936	48.479	0.023	0.023	0.000	0.000	0.000	0.000
35	B	40	ASP	-1	-0.824	-0.902	51.090	-0.020	-0.020	0.000	0.000	0.000	0.000
36	B	41	LYS	1	0.754	0.872	47.509	0.019	0.019	0.000	0.000	0.000	0.000
37	B	42	TYR	0	0.032	0.015	53.296	0.001	0.001	0.000	0.000	0.000	0.000
38	B	43	LEU	0	0.015	0.013	54.992	0.001	0.001	0.000	0.000	0.000	0.000
39	B	44	ARG	1	0.953	0.970	55.085	0.014	0.014	0.000	0.000	0.000	0.000
40	B	45	LEU	0	0.036	0.030	56.477	0.001	0.001	0.000	0.000	0.000	0.000
41	B	46	LEU	0	-0.008	-0.006	59.318	0.001	0.001	0.000	0.000	0.000	0.000
42	B	47	ALA	0	-0.004	0.000	60.989	0.000	0.000	0.000	0.000	0.000	0.000
43	B	48	ASP	-1	-0.892	-0.961	62.120	-0.010	-0.010	0.000	0.000	0.000	0.000
44	B	49	PHE	0	0.001	-0.010	63.112	0.001	0.001	0.000	0.000	0.000	0.000
45	B	50	ASP	-1	-0.858	-0.909	64.824	-0.010	-0.010	0.000	0.000	0.000	0.000
46	B	51	ASN	0	-0.051	-0.010	66.448	0.000	0.000	0.000	0.000	0.000	0.000
47	B	52	TYR	0	0.069	0.004	67.951	0.000	0.000	0.000	0.000	0.000	0.000
48	B	53	ARG	1	0.861	0.945	64.535	0.009	0.009	0.000	0.000	0.000	0.000
49	B	54	LYS	1	0.855	0.917	68.281	0.010	0.010	0.000	0.000	0.000	0.000
50	B	55	ARG	1	0.906	0.990	69.766	0.008	0.008	0.000	0.000	0.000	0.000
51	B	56	MET	0	0.010	-0.016	73.248	0.000	0.000	0.000	0.000	0.000	0.000
52	B	57	GLU	-1	-0.915	-0.940	75.969	-0.006	-0.006	0.000	0.000	0.000	0.000
53	B	58	GLU	-1	-0.928	-0.960	78.242	-0.006	-0.006	0.000	0.000	0.000	0.000
54	B	59	GLU	-1	-0.952	-1.000	75.468	-0.006	-0.006	0.000	0.000	0.000	0.000
55	B	60	LEU	0	-0.021	-0.022	78.382	0.000	0.000	0.000	0.000	0.000	0.000
56	B	61	LYS	1	1.021	1.019	80.896	0.005	0.005	0.000	0.000	0.000	0.000
57	B	62	ALA	0	-0.008	-0.012	82.513	0.000	0.000	0.000	0.000	0.000	0.000
58	B	63	ARG	1	0.960	0.990	79.534	0.005	0.005	0.000	0.000	0.000	0.000
59	B	64	GLU	-1	-0.934	-0.957	83.427	-0.004	-0.004	0.000	0.000	0.000	0.000
60	B	65	ARG	1	0.878	0.931	86.729	0.005	0.005	0.000	0.000	0.000	0.000
61	B	66	GLU	-1	-0.908	-0.943	82.833	-0.005	-0.005	0.000	0.000	0.000	0.000
62	B	67	GLY	0	0.022	0.016	87.000	0.000	0.000	0.000	0.000	0.000	0.000
63	B	68	VAL	0	0.036	0.007	88.749	0.000	0.000	0.000	0.000	0.000	0.000
64	B	69	LEU	0	-0.043	-0.020	89.171	0.000	0.000	0.000	0.000	0.000	0.000
65	B	70	LYS	1	0.949	0.975	86.611	0.003	0.003	0.000	0.000	0.000	0.000
66	B	71	ALA	0	0.005	-0.004	90.900	0.000	0.000	0.000	0.000	0.000	0.000
67	B	72	LEU	0	0.022	0.004	94.000	0.000	0.000	0.000	0.000	0.000	0.000
68	B	73	ARG	1	0.878	0.940	89.474	0.004	0.004	0.000	0.000	0.000	0.000
69	B	74	ALA	0	0.023	0.003	94.472	0.000	0.000	0.000	0.000	0.000	0.000
70	B	75	LEU	0	0.010	-0.004	96.336	0.000	0.000	0.000	0.000	0.000	0.000
71	B	76	LEU	0	-0.024	0.004	98.083	0.000	0.000	0.000	0.000	0.000	0.000
72	B	77	PRO	0	0.041	0.028	99.603	0.000	0.000	0.000	0.000	0.000	0.000
73	B	78	VAL	0	0.003	0.015	102.631	0.000	0.000	0.000	0.000	0.000	0.000
74	B	79	LEU	0	-0.031	-0.020	104.420	0.000	0.000	0.000	0.000	0.000	0.000
75	B	80	ASP	-1	-0.846	-0.921	103.205	-0.003	-0.003	0.000	0.000	0.000	0.000
76	B	81	ASP	-1	-0.940	-0.989	106.047	-0.002	-0.002	0.000	0.000	0.000	0.000
77	B	82	LEU	0	-0.081	-0.045	108.540	0.000	0.000	0.000	0.000	0.000	0.000
78	B	83	ASP	-1	-0.871	-0.923	109.235	-0.003	-0.003	0.000	0.000	0.000	0.000
79	B	84	ARG	1	0.895	0.949	106.390	0.003	0.003	0.000	0.000	0.000	0.000
80	B	85	ALA	0	-0.087	-0.055	112.071	0.000	0.000	0.000	0.000	0.000	0.000
81	B	86	LEU	0	-0.006	-0.021	114.390	0.000	0.000	0.000	0.000	0.000	0.000
82	B	87	GLU	-1	-0.918	-0.943	113.531	-0.003	-0.003	0.000	0.000	0.000	0.000
83	B	88	PHE	0	-0.064	-0.038	113.347	0.000	0.000	0.000	0.000	0.000	0.000
84	B	89	ALA	0	-0.067	-0.035	118.283	0.000	0.000	0.000	0.000	0.000	0.000
85	B	90	GLU	-1	-0.889	-0.934	119.976	-0.002	-0.002	0.000	0.000	0.000	0.000
86	B	91	ALA	0	-0.072	-0.012	121.543	0.000	0.000	0.000	0.000	0.000	0.000
87	B	92	SER	0	-0.036	-0.021	122.454	0.000	0.000	0.000	0.000	0.000	0.000
88	B	93	PRO	0	0.082	0.050	122.792	0.000	0.000	0.000	0.000	0.000	0.000
89	B	94	GLU	-1	-0.915	-0.962	123.191	-0.002	-0.002	0.000	0.000	0.000	0.000
90	B	95	SER	0	-0.091	-0.069	119.523	0.000	0.000	0.000	0.000	0.000	0.000
91	B	96	ILE	0	0.091	0.050	117.329	0.000	0.000	0.000	0.000	0.000	0.000
92	B	97	ARG	1	0.931	0.982	117.633	0.001	0.001	0.000	0.000	0.000	0.000
93	B	98	GLN	0	-0.068	-0.051	116.520	0.000	0.000	0.000	0.000	0.000	0.000
94	B	99	GLY	0	0.066	0.045	114.253	0.000	0.000	0.000	0.000	0.000	0.000
95	B	100	VAL	0	0.051	0.026	112.794	0.000	0.000	0.000	0.000	0.000	0.000
96	B	101	ARG	1	0.893	0.934	112.206	0.001	0.001	0.000	0.000	0.000	0.000
97	B	102	ALA	0	0.029	0.018	110.577	0.000	0.000	0.000	0.000	0.000	0.000
98	B	103	ILE	0	0.060	0.036	107.930	0.000	0.000	0.000	0.000	0.000	0.000
99	B	104	ARG	1	0.878	0.946	107.272	0.001	0.001	0.000	0.000	0.000	0.000
100	B	105	ASP	-1	-0.883	-0.953	106.859	-0.001	-0.001	0.000	0.000	0.000	0.000
101	B	106	GLY	0	-0.048	-0.026	104.720	0.000	0.000	0.000	0.000	0.000	0.000
102	B	107	PHE	0	0.044	0.006	101.653	0.000	0.000	0.000	0.000	0.000	0.000
103	B	108	PHE	0	-0.013	-0.005	101.742	0.000	0.000	0.000	0.000	0.000	0.000
104	B	109	ARG	1	0.946	0.978	100.328	0.002	0.002	0.000	0.000	0.000	0.000
105	B	110	ILE	0	0.018	0.018	97.727	0.000	0.000	0.000	0.000	0.000	0.000
106	B	111	LEU	0	-0.004	-0.016	96.886	0.000	0.000	0.000	0.000	0.000	0.000
107	B	112	ALA	0	0.044	0.027	95.974	0.000	0.000	0.000	0.000	0.000	0.000
108	B	113	GLY	0	-0.027	0.010	94.228	0.000	0.000	0.000	0.000	0.000	0.000
109	B	114	LEU	0	-0.130	-0.062	92.056	0.000	0.000	0.000	0.000	0.000	0.000
110	B	115	GLY	0	-0.014	-0.006	91.448	0.000	0.000	0.000	0.000	0.000	0.000
111	B	116	VAL	0	-0.080	-0.042	92.524	0.000	0.000	0.000	0.000	0.000	0.000
112	B	117	GLU	-1	-0.894	-0.962	95.067	-0.001	-0.001	0.000	0.000	0.000	0.000
113	B	118	GLU	-1	-0.894	-0.932	97.519	-0.001	-0.001	0.000	0.000	0.000	0.000
114	B	119	VAL	0	-0.066	-0.034	98.425	0.000	0.000	0.000	0.000	0.000	0.000
115	B	120	PRO	0	0.020	0.022	99.547	0.000	0.000	0.000	0.000	0.000	0.000
116	B	121	GLY	0	0.072	0.026	102.488	0.000	0.000	0.000	0.000	0.000	0.000
117	B	122	GLU	-1	-0.846	-0.924	106.187	-0.001	-0.001	0.000	0.000	0.000	0.000
118	B	123	GLY	0	-0.013	0.002	108.870	0.000	0.000	0.000	0.000	0.000	0.000
119	B	124	GLU	-1	-0.920	-0.961	103.863	0.000	0.000	0.000	0.000	0.000	0.000
120	B	125	ALA	0	-0.039	-0.029	102.826	0.000	0.000	0.000	0.000	0.000	0.000
121	B	126	PHE	0	0.009	0.011	102.755	0.000	0.000	0.000	0.000	0.000	0.000
122	B	127	ASP	-1	-0.794	-0.904	97.884	0.000	0.000	0.000	0.000	0.000	0.000
123	B	128	PRO	0	-0.012	-0.005	98.215	0.000	0.000	0.000	0.000	0.000	0.000
124	B	129	ARG	1	0.842	0.931	92.769	0.000	0.000	0.000	0.000	0.000	0.000
125	B	130	TYR	0	0.012	-0.031	94.163	0.000	0.000	0.000	0.000	0.000	0.000
126	B	131	HIS	0	-0.075	-0.038	99.394	0.000	0.000	0.000	0.000	0.000	0.000
127	B	132	GLU	-1	-0.880	-0.937	102.563	-0.001	-0.001	0.000	0.000	0.000	0.000
128	B	133	ALA	0	-0.024	-0.016	104.864	0.000	0.000	0.000	0.000	0.000	0.000
129	B	134	VAL	0	-0.021	-0.018	107.974	0.000	0.000	0.000	0.000	0.000	0.000
130	B	135	GLY	0	-0.024	-0.015	110.838	0.000	0.000	0.000	0.000	0.000	0.000
131	B	136	LEU	0	-0.039	-0.006	112.912	0.000	0.000	0.000	0.000	0.000	0.000
132	B	137	LEU	0	0.011	-0.013	115.344	0.000	0.000	0.000	0.000	0.000	0.000
133	B	138	PRO	0	-0.010	0.014	116.270	0.000	0.000	0.000	0.000	0.000	0.000
134	B	139	GLY	0	0.042	0.012	115.296	0.000	0.000	0.000	0.000	0.000	0.000
135	B	140	GLU	-1	-0.962	-0.976	111.303	0.000	0.000	0.000	0.000	0.000	0.000
136	B	141	PRO	0	0.041	0.031	111.915	0.000	0.000	0.000	0.000	0.000	0.000
137	B	142	GLY	0	-0.019	-0.013	108.470	0.000	0.000	0.000	0.000	0.000	0.000
138	B	143	LYS	1	0.905	0.958	105.854	0.000	0.000	0.000	0.000	0.000	0.000
139	B	144	VAL	0	-0.001	0.014	106.183	0.000	0.000	0.000	0.000	0.000	0.000
140	B	145	ALA	0	0.021	0.009	109.033	0.000	0.000	0.000	0.000	0.000	0.000
141	B	146	LYS	1	0.820	0.883	111.973	0.001	0.001	0.000	0.000	0.000	0.000
142	B	147	VAL	0	0.027	0.023	107.669	0.000	0.000	0.000	0.000	0.000	0.000
143	B	148	PHE	0	-0.044	-0.021	110.311	0.000	0.000	0.000	0.000	0.000	0.000
144	B	149	GLN	0	-0.066	-0.042	105.662	0.000	0.000	0.000	0.000	0.000	0.000
145	B	150	ARG	1	0.871	0.927	104.899	0.001	0.001	0.000	0.000	0.000	0.000
146	B	151	GLY	0	0.059	0.034	102.284	0.000	0.000	0.000	0.000	0.000	0.000
147	B	152	PHE	0	-0.036	-0.010	98.443	0.000	0.000	0.000	0.000	0.000	0.000
148	B	153	ARG	1	0.924	0.965	92.485	0.001	0.001	0.000	0.000	0.000	0.000
149	B	154	MET	0	-0.003	0.013	89.744	0.000	0.000	0.000	0.000	0.000	0.000
150	B	155	GLY	0	-0.017	-0.018	89.709	0.000	0.000	0.000	0.000	0.000	0.000
151	B	156	GLU	-1	-0.899	-0.936	86.412	-0.001	-0.001	0.000	0.000	0.000	0.000
152	B	157	ALA	0	-0.028	-0.003	89.352	0.000	0.000	0.000	0.000	0.000	0.000
153	B	158	LEU	0	0.017	-0.001	90.970	0.000	0.000	0.000	0.000	0.000	0.000
154	B	159	VAL	0	-0.064	-0.022	94.675	0.000	0.000	0.000	0.000	0.000	0.000
155	B	160	ARG	1	0.904	0.940	96.199	0.002	0.002	0.000	0.000	0.000	0.000
156	B	161	PRO	0	0.047	0.039	99.334	0.000	0.000	0.000	0.000	0.000	0.000
157	B	162	ALA	0	0.013	0.003	101.232	0.000	0.000	0.000	0.000	0.000	0.000
158	B	163	ARG	1	0.943	0.985	104.556	0.002	0.002	0.000	0.000	0.000	0.000
159	B	164	VAL	0	-0.007	-0.016	106.719	0.000	0.000	0.000	0.000	0.000	0.000
160	B	165	ALA	0	0.010	0.024	109.140	0.000	0.000	0.000	0.000	0.000	0.000
161	B	166	VAL	0	0.004	-0.005	108.527	0.000	0.000	0.000	0.000	0.000	0.000
162	B	167	GLY	0	0.034	0.024	111.296	0.000	0.000	0.000	0.000	0.000	0.000
163	B	168	GLU	-1	-0.940	-0.977	113.325	0.000	0.000	0.000	0.000	0.000	0.000
164	B	169	GLU	-1	-0.939	-0.985	113.403	0.000	0.000	0.000	0.000	0.000	0.000
165	B	170	LYS	1	0.898	0.950	115.920	0.000	0.000	0.000	0.000	0.000	0.000
166	B	171	NME	0	0.019	0.015	118.332	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:6:ACE )