FMO DATABASE

FMODB ID: M3LMZ

Calculation Name: 3A6M-A-Xray372

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: 2023-03-14

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

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. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	168
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1193322.98515
FMO2-HF: Nuclear repulsion	1127806.906407
FMO2-HF: Total energy	-65516.078743
FMO2-MP2: Total energy	-65710.639367

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:4:ARG)

Summations of interaction energy for fragment #1(A:4:ARG)

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.
-94.5	-91.571	12.975	-7.98	-7.922	-0.038

Interaction energy analysis for fragmet #1(A:4:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.972 / q_NPA : 0.976

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	6	HIS	0	-0.029	-0.007	2.386	1.213	6.198	0.196	-2.525	-2.655	0.013
4	A	7	GLU	-1	-0.790	-0.909	1.874	-51.595	-54.849	12.734	-4.994	-4.486	-0.048
5	A	8	ASN	0	-0.041	-0.018	3.357	-1.407	-0.209	0.045	-0.461	-0.781	-0.003
6	A	9	THR	0	-0.058	-0.041	5.747	4.123	4.123	0.000	0.000	0.000	0.000
7	A	10	LEU	0	-0.011	-0.011	6.961	3.575	3.575	0.000	0.000	0.000	0.000
8	A	11	GLU	-1	-0.786	-0.869	7.469	-25.008	-25.008	0.000	0.000	0.000	0.000
9	A	12	LYS	1	0.900	0.930	9.157	24.647	24.647	0.000	0.000	0.000	0.000
10	A	13	ASP	-1	-0.932	-0.959	11.170	-19.552	-19.552	0.000	0.000	0.000	0.000
11	A	14	LEU	0	-0.069	-0.045	12.165	1.235	1.235	0.000	0.000	0.000	0.000
12	A	15	GLU	-1	-0.966	-0.956	13.326	-18.254	-18.254	0.000	0.000	0.000	0.000
13	A	16	ALA	0	-0.020	-0.014	16.230	0.892	0.892	0.000	0.000	0.000	0.000
14	A	17	VAL	0	0.053	0.032	17.698	0.700	0.700	0.000	0.000	0.000	0.000
15	A	18	GLY	0	0.019	0.008	19.594	0.659	0.659	0.000	0.000	0.000	0.000
16	A	19	GLN	0	-0.083	-0.062	20.131	0.325	0.325	0.000	0.000	0.000	0.000
17	A	20	GLU	-1	-0.989	-0.986	22.932	-11.487	-11.487	0.000	0.000	0.000	0.000
18	A	21	ALA	0	0.000	0.002	23.603	0.309	0.309	0.000	0.000	0.000	0.000
19	A	22	GLN	0	0.050	0.020	25.238	0.289	0.289	0.000	0.000	0.000	0.000
20	A	23	ALA	0	0.034	0.011	27.168	0.404	0.404	0.000	0.000	0.000	0.000
21	A	24	LEU	0	-0.054	-0.034	27.687	0.504	0.504	0.000	0.000	0.000	0.000
22	A	25	GLU	-1	-0.905	-0.941	27.685	-9.636	-9.636	0.000	0.000	0.000	0.000
23	A	26	GLU	-1	-0.896	-0.924	31.163	-8.588	-8.588	0.000	0.000	0.000	0.000
24	A	27	ARG	1	0.875	0.941	32.154	8.972	8.972	0.000	0.000	0.000	0.000
25	A	28	LEU	0	-0.012	-0.008	34.309	0.236	0.236	0.000	0.000	0.000	0.000
26	A	29	LYS	1	0.854	0.915	33.121	8.782	8.782	0.000	0.000	0.000	0.000
27	A	30	ALA	0	0.027	0.006	37.283	0.179	0.179	0.000	0.000	0.000	0.000
28	A	31	ALA	0	-0.023	-0.024	39.309	0.189	0.189	0.000	0.000	0.000	0.000
29	A	32	GLU	-1	-0.786	-0.865	41.239	-6.568	-6.568	0.000	0.000	0.000	0.000
30	A	33	GLU	-1	-0.868	-0.952	42.806	-6.229	-6.229	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-1.000	-0.979	43.358	-6.535	-6.535	0.000	0.000	0.000	0.000
32	A	35	LEU	0	-0.001	-0.001	44.166	0.118	0.118	0.000	0.000	0.000	0.000
33	A	36	LYS	1	0.720	0.838	46.026	6.571	6.571	0.000	0.000	0.000	0.000
34	A	37	GLY	0	0.059	0.028	47.889	0.124	0.124	0.000	0.000	0.000	0.000
35	A	38	LEU	0	0.010	0.012	49.177	0.153	0.153	0.000	0.000	0.000	0.000
36	A	39	LYS	1	0.915	0.960	51.004	5.709	5.709	0.000	0.000	0.000	0.000
37	A	40	ASP	-1	-0.851	-0.899	52.946	-5.328	-5.328	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.987	0.966	53.926	5.641	5.641	0.000	0.000	0.000	0.000
39	A	42	TYR	0	0.031	0.036	55.068	0.087	0.087	0.000	0.000	0.000	0.000
40	A	43	LEU	0	-0.028	-0.010	56.589	0.092	0.092	0.000	0.000	0.000	0.000
41	A	44	ARG	1	0.860	0.906	57.016	5.317	5.317	0.000	0.000	0.000	0.000
42	A	45	LEU	0	0.024	0.021	59.585	0.072	0.072	0.000	0.000	0.000	0.000
43	A	46	LEU	0	-0.050	-0.040	60.369	0.083	0.083	0.000	0.000	0.000	0.000
44	A	47	ALA	0	-0.010	0.006	62.539	0.060	0.060	0.000	0.000	0.000	0.000
45	A	48	ASP	-1	-0.864	-0.943	64.193	-4.688	-4.688	0.000	0.000	0.000	0.000
46	A	49	PHE	0	-0.017	-0.008	65.401	0.096	0.096	0.000	0.000	0.000	0.000
47	A	50	ASP	-1	-0.847	-0.910	66.663	-4.428	-4.428	0.000	0.000	0.000	0.000
48	A	51	ASN	0	-0.039	-0.013	68.427	0.083	0.083	0.000	0.000	0.000	0.000
49	A	52	TYR	0	0.069	0.015	69.841	0.074	0.074	0.000	0.000	0.000	0.000
50	A	53	ARG	1	0.950	0.973	71.014	4.221	4.221	0.000	0.000	0.000	0.000
51	A	54	LYS	1	0.826	0.903	70.549	4.402	4.402	0.000	0.000	0.000	0.000
52	A	55	ARG	1	0.965	0.992	71.967	4.283	4.283	0.000	0.000	0.000	0.000
53	A	56	MET	0	-0.044	-0.027	75.060	0.054	0.054	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.973	-0.977	76.721	-3.857	-3.857	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.888	-0.933	78.542	-3.815	-3.815	0.000	0.000	0.000	0.000
56	A	59	GLU	-1	-0.952	-1.003	79.153	-3.908	-3.908	0.000	0.000	0.000	0.000
57	A	60	LEU	0	-0.022	0.001	79.209	0.038	0.038	0.000	0.000	0.000	0.000
58	A	61	LYS	1	0.944	0.961	82.060	3.818	3.818	0.000	0.000	0.000	0.000
59	A	62	ALA	0	-0.023	0.000	84.733	0.058	0.058	0.000	0.000	0.000	0.000
60	A	63	ARG	1	0.981	0.983	84.835	3.728	3.728	0.000	0.000	0.000	0.000
61	A	64	GLU	-1	-0.926	-0.941	87.201	-3.519	-3.519	0.000	0.000	0.000	0.000
62	A	65	ARG	1	0.960	0.987	89.031	3.478	3.478	0.000	0.000	0.000	0.000
63	A	66	GLU	-1	-0.978	-0.998	89.402	-3.475	-3.475	0.000	0.000	0.000	0.000
64	A	67	GLY	0	0.029	0.010	91.394	0.038	0.038	0.000	0.000	0.000	0.000
65	A	68	VAL	0	0.010	-0.002	93.015	0.044	0.044	0.000	0.000	0.000	0.000
66	A	69	LEU	0	-0.050	-0.022	93.970	0.048	0.048	0.000	0.000	0.000	0.000
67	A	70	LYS	1	0.941	0.978	94.552	3.370	3.370	0.000	0.000	0.000	0.000
68	A	71	ALA	0	0.020	0.011	97.324	0.031	0.031	0.000	0.000	0.000	0.000
69	A	72	LEU	0	0.028	-0.007	98.913	0.036	0.036	0.000	0.000	0.000	0.000
70	A	73	ARG	1	0.914	0.949	96.351	3.265	3.265	0.000	0.000	0.000	0.000
71	A	74	ALA	0	0.008	0.010	101.861	0.029	0.029	0.000	0.000	0.000	0.000
72	A	75	LEU	0	0.019	-0.007	102.727	0.027	0.027	0.000	0.000	0.000	0.000
73	A	76	LEU	0	-0.012	0.018	104.143	0.023	0.023	0.000	0.000	0.000	0.000
74	A	77	PRO	0	0.025	0.011	106.861	0.026	0.026	0.000	0.000	0.000	0.000
75	A	78	VAL	0	-0.010	0.004	109.098	0.028	0.028	0.000	0.000	0.000	0.000
76	A	79	LEU	0	-0.033	-0.015	109.160	0.022	0.022	0.000	0.000	0.000	0.000
77	A	80	ASP	-1	-0.851	-0.924	110.859	-2.846	-2.846	0.000	0.000	0.000	0.000
78	A	81	ASP	-1	-0.909	-0.953	113.352	-2.752	-2.752	0.000	0.000	0.000	0.000
79	A	82	LEU	0	-0.090	-0.054	112.834	0.029	0.029	0.000	0.000	0.000	0.000
80	A	83	ASP	-1	-0.870	-0.925	114.552	-2.742	-2.742	0.000	0.000	0.000	0.000
81	A	84	ARG	1	0.842	0.906	115.435	2.755	2.755	0.000	0.000	0.000	0.000
82	A	85	ALA	0	-0.076	-0.053	119.195	0.029	0.029	0.000	0.000	0.000	0.000
83	A	86	LEU	0	0.002	-0.012	118.710	0.024	0.024	0.000	0.000	0.000	0.000
84	A	87	GLU	-1	-0.945	-0.956	120.466	-2.620	-2.620	0.000	0.000	0.000	0.000
85	A	88	PHE	0	-0.055	-0.020	122.557	0.025	0.025	0.000	0.000	0.000	0.000
86	A	89	ALA	0	-0.019	-0.021	123.644	0.020	0.020	0.000	0.000	0.000	0.000
87	A	90	GLU	-1	-0.933	-0.966	125.387	-2.528	-2.528	0.000	0.000	0.000	0.000
88	A	91	ALA	0	-0.056	-0.009	127.550	0.022	0.022	0.000	0.000	0.000	0.000
89	A	92	SER	0	0.041	-0.001	129.634	0.020	0.020	0.000	0.000	0.000	0.000
90	A	93	PRO	0	0.081	0.051	128.826	-0.023	-0.023	0.000	0.000	0.000	0.000
91	A	94	GLU	-1	-0.839	-0.926	127.759	-2.521	-2.521	0.000	0.000	0.000	0.000
92	A	95	SER	0	-0.046	-0.023	127.367	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	96	ILE	0	0.046	0.040	123.210	-0.022	-0.022	0.000	0.000	0.000	0.000
94	A	97	ARG	1	0.846	0.940	123.186	2.496	2.496	0.000	0.000	0.000	0.000
95	A	98	GLN	0	-0.006	-0.022	122.764	-0.021	-0.021	0.000	0.000	0.000	0.000
96	A	99	GLY	0	0.082	0.051	121.837	-0.019	-0.019	0.000	0.000	0.000	0.000
97	A	100	VAL	0	0.025	0.003	117.968	-0.028	-0.028	0.000	0.000	0.000	0.000
98	A	101	ARG	1	0.810	0.911	117.851	2.588	2.588	0.000	0.000	0.000	0.000
99	A	102	ALA	0	0.049	0.021	117.598	-0.025	-0.025	0.000	0.000	0.000	0.000
100	A	103	ILE	0	0.051	0.034	113.900	-0.026	-0.026	0.000	0.000	0.000	0.000
101	A	104	ARG	1	0.882	0.953	113.363	2.711	2.711	0.000	0.000	0.000	0.000
102	A	105	ASP	-1	-0.932	-0.979	112.644	-2.764	-2.764	0.000	0.000	0.000	0.000
103	A	106	GLY	0	-0.034	-0.023	112.514	-0.024	-0.024	0.000	0.000	0.000	0.000
104	A	107	PHE	0	0.040	0.011	105.915	-0.032	-0.032	0.000	0.000	0.000	0.000
105	A	108	PHE	0	-0.013	-0.013	107.924	-0.026	-0.026	0.000	0.000	0.000	0.000
106	A	109	ARG	1	0.968	0.997	107.444	2.798	2.798	0.000	0.000	0.000	0.000
107	A	110	ILE	0	0.000	0.004	104.912	-0.030	-0.030	0.000	0.000	0.000	0.000
108	A	111	LEU	0	-0.030	-0.021	102.952	-0.036	-0.036	0.000	0.000	0.000	0.000
109	A	112	ALA	0	0.066	0.031	102.704	-0.034	-0.034	0.000	0.000	0.000	0.000
110	A	113	GLY	0	-0.012	0.015	102.738	-0.028	-0.028	0.000	0.000	0.000	0.000
111	A	114	LEU	0	-0.146	-0.067	98.888	-0.037	-0.037	0.000	0.000	0.000	0.000
112	A	115	GLY	0	-0.001	-0.006	98.561	-0.038	-0.038	0.000	0.000	0.000	0.000
113	A	116	VAL	0	-0.080	-0.049	98.980	-0.033	-0.033	0.000	0.000	0.000	0.000
114	A	117	GLU	-1	-0.899	-0.949	101.060	-3.029	-3.029	0.000	0.000	0.000	0.000
115	A	118	GLU	-1	-0.939	-0.987	102.708	-2.936	-2.936	0.000	0.000	0.000	0.000
116	A	119	VAL	0	-0.095	-0.042	101.614	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	120	PRO	0	0.037	0.004	103.713	0.027	0.027	0.000	0.000	0.000	0.000
118	A	121	GLY	0	0.065	0.020	106.895	-0.013	-0.013	0.000	0.000	0.000	0.000
119	A	122	GLU	-1	-0.924	-0.972	109.818	-2.756	-2.756	0.000	0.000	0.000	0.000
120	A	123	GLY	0	-0.015	0.005	113.083	0.010	0.010	0.000	0.000	0.000	0.000
121	A	124	GLU	-1	-0.898	-0.941	107.834	-2.934	-2.934	0.000	0.000	0.000	0.000
122	A	125	ALA	0	-0.066	-0.041	105.696	0.010	0.010	0.000	0.000	0.000	0.000
123	A	126	PHE	0	-0.029	-0.026	103.471	-0.017	-0.017	0.000	0.000	0.000	0.000
124	A	127	ASP	-1	-0.771	-0.846	99.715	-3.225	-3.225	0.000	0.000	0.000	0.000
125	A	128	PRO	0	0.014	-0.015	98.332	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	129	ARG	1	0.824	0.890	95.522	3.247	3.247	0.000	0.000	0.000	0.000
127	A	130	TYR	0	-0.010	-0.014	97.835	-0.009	-0.009	0.000	0.000	0.000	0.000
128	A	131	HIS	0	-0.082	-0.039	100.661	0.024	0.024	0.000	0.000	0.000	0.000
129	A	132	GLU	-1	-0.839	-0.904	100.752	-3.174	-3.174	0.000	0.000	0.000	0.000
130	A	133	ALA	0	-0.013	-0.016	103.521	0.035	0.035	0.000	0.000	0.000	0.000
131	A	134	VAL	0	-0.066	-0.052	105.972	-0.010	-0.010	0.000	0.000	0.000	0.000
132	A	135	GLY	0	0.002	0.003	108.318	0.012	0.012	0.000	0.000	0.000	0.000
133	A	136	LEU	0	-0.047	-0.009	110.518	-0.014	-0.014	0.000	0.000	0.000	0.000
134	A	137	LEU	0	-0.017	-0.006	112.888	0.026	0.026	0.000	0.000	0.000	0.000
135	A	138	PRO	0	-0.008	0.000	115.931	-0.013	-0.013	0.000	0.000	0.000	0.000
136	A	139	GLY	0	0.010	-0.004	116.755	0.006	0.006	0.000	0.000	0.000	0.000
137	A	140	GLU	-1	-0.930	-0.967	113.644	-2.802	-2.802	0.000	0.000	0.000	0.000
138	A	141	PRO	0	0.028	0.001	112.189	-0.023	-0.023	0.000	0.000	0.000	0.000
139	A	142	GLY	0	-0.025	0.003	108.233	-0.009	-0.009	0.000	0.000	0.000	0.000
140	A	143	LYS	1	0.921	0.972	108.253	2.868	2.868	0.000	0.000	0.000	0.000
141	A	144	VAL	0	-0.027	0.004	108.282	0.015	0.015	0.000	0.000	0.000	0.000
142	A	145	ALA	0	0.030	0.016	110.793	0.020	0.020	0.000	0.000	0.000	0.000
143	A	146	LYS	1	0.933	0.961	112.989	2.757	2.757	0.000	0.000	0.000	0.000
144	A	147	VAL	0	0.026	0.021	109.585	-0.026	-0.026	0.000	0.000	0.000	0.000
145	A	148	PHE	0	-0.074	-0.036	110.880	0.026	0.026	0.000	0.000	0.000	0.000
146	A	149	GLN	0	-0.051	-0.045	105.214	-0.020	-0.020	0.000	0.000	0.000	0.000
147	A	150	ARG	1	0.949	1.000	107.605	2.837	2.837	0.000	0.000	0.000	0.000
148	A	151	GLY	0	0.063	0.039	103.972	-0.012	-0.012	0.000	0.000	0.000	0.000
149	A	152	PHE	0	-0.023	-0.009	101.964	0.026	0.026	0.000	0.000	0.000	0.000
150	A	153	ARG	1	0.966	0.991	97.839	3.174	3.174	0.000	0.000	0.000	0.000
151	A	154	MET	0	0.005	0.021	94.955	0.017	0.017	0.000	0.000	0.000	0.000
152	A	155	GLY	0	-0.051	-0.022	94.811	-0.039	-0.039	0.000	0.000	0.000	0.000
153	A	156	GLU	-1	-0.904	-0.968	90.972	-3.399	-3.399	0.000	0.000	0.000	0.000
154	A	157	ALA	0	-0.028	0.004	92.052	-0.001	-0.001	0.000	0.000	0.000	0.000
155	A	158	LEU	0	0.024	0.005	93.556	0.040	0.040	0.000	0.000	0.000	0.000
156	A	159	VAL	0	-0.061	-0.023	95.802	-0.017	-0.017	0.000	0.000	0.000	0.000
157	A	160	ARG	1	0.901	0.933	97.863	3.030	3.030	0.000	0.000	0.000	0.000
158	A	161	PRO	0	0.057	0.046	98.798	0.021	0.021	0.000	0.000	0.000	0.000
159	A	162	ALA	0	0.025	0.003	101.405	0.019	0.019	0.000	0.000	0.000	0.000
160	A	163	ARG	1	0.931	0.979	105.144	2.962	2.962	0.000	0.000	0.000	0.000
161	A	164	VAL	0	-0.040	-0.038	106.598	0.029	0.029	0.000	0.000	0.000	0.000
162	A	165	ALA	0	0.021	0.037	109.037	-0.010	-0.010	0.000	0.000	0.000	0.000
163	A	166	VAL	0	-0.003	-0.010	107.493	0.003	0.003	0.000	0.000	0.000	0.000
164	A	167	GLY	0	0.024	0.013	110.833	0.020	0.020	0.000	0.000	0.000	0.000
165	A	168	GLU	-1	-0.934	-0.978	112.690	-2.779	-2.779	0.000	0.000	0.000	0.000
166	A	169	GLU	-1	-0.907	-0.959	115.079	-2.672	-2.672	0.000	0.000	0.000	0.000
167	A	170	LYS	1	0.974	0.991	117.905	2.574	2.574	0.000	0.000	0.000	0.000
168	A	171	ARG	1	0.944	0.969	119.350	2.649	2.649	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ARG)