FMO DATABASE

FMODB ID: 22MKR

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	OptAll
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	-1191804.582243
FMO2-HF: Nuclear repulsion	1126286.013125
FMO2-HF: Total energy	-65518.569118
FMO2-MP2: Total energy	-65712.790839

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.
-100.879	-96.076	11.928	-8.32	-8.41	-0.054

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 : 0.977

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	-0.035	0.016	2.877	1.834	6.165	0.062	-2.150	-2.243	0.007
4	A	7	GLU	-1	-0.763	-0.903	1.871	-58.065	-60.009	11.281	-4.862	-4.475	-0.049
5	A	8	ASN	0	-0.040	-0.039	2.775	-2.947	-0.656	0.586	-1.299	-1.578	-0.012
6	A	9	THR	0	-0.087	-0.049	5.123	4.123	4.248	-0.001	-0.009	-0.114	0.000
7	A	10	LEU	0	-0.018	-0.015	7.226	3.327	3.327	0.000	0.000	0.000	0.000
8	A	11	GLU	-1	-0.812	-0.889	6.561	-25.361	-25.361	0.000	0.000	0.000	0.000
9	A	12	LYS	1	0.910	0.956	9.275	24.742	24.742	0.000	0.000	0.000	0.000
10	A	13	ASP	-1	-0.945	-0.973	11.837	-19.619	-19.619	0.000	0.000	0.000	0.000
11	A	14	LEU	0	-0.056	-0.034	11.847	1.133	1.133	0.000	0.000	0.000	0.000
12	A	15	GLU	-1	-0.932	-0.957	13.158	-17.744	-17.744	0.000	0.000	0.000	0.000
13	A	16	ALA	0	-0.017	-0.006	16.029	0.934	0.934	0.000	0.000	0.000	0.000
14	A	17	VAL	0	0.035	0.012	17.832	0.800	0.800	0.000	0.000	0.000	0.000
15	A	18	GLY	0	0.028	0.026	19.100	0.667	0.667	0.000	0.000	0.000	0.000
16	A	19	GLN	0	-0.075	-0.055	19.681	0.366	0.366	0.000	0.000	0.000	0.000
17	A	20	GLU	-1	-0.972	-0.976	22.650	-11.595	-11.595	0.000	0.000	0.000	0.000
18	A	21	ALA	0	0.024	0.002	23.435	0.505	0.505	0.000	0.000	0.000	0.000
19	A	22	GLN	0	0.009	0.013	24.856	0.361	0.361	0.000	0.000	0.000	0.000
20	A	23	ALA	0	0.026	0.003	26.803	0.447	0.447	0.000	0.000	0.000	0.000
21	A	24	LEU	0	-0.062	-0.042	27.889	0.484	0.484	0.000	0.000	0.000	0.000
22	A	25	GLU	-1	-0.892	-0.949	27.770	-9.525	-9.525	0.000	0.000	0.000	0.000
23	A	26	GLU	-1	-0.882	-0.911	31.083	-8.458	-8.458	0.000	0.000	0.000	0.000
24	A	27	ARG	1	0.909	0.952	32.102	8.991	8.991	0.000	0.000	0.000	0.000
25	A	28	LEU	0	-0.010	0.000	34.213	0.252	0.252	0.000	0.000	0.000	0.000
26	A	29	LYS	1	0.822	0.894	32.577	8.820	8.820	0.000	0.000	0.000	0.000
27	A	30	ALA	0	0.004	0.001	36.776	0.199	0.199	0.000	0.000	0.000	0.000
28	A	31	ALA	0	-0.014	-0.013	38.830	0.211	0.211	0.000	0.000	0.000	0.000
29	A	32	GLU	-1	-0.817	-0.876	40.652	-6.501	-6.501	0.000	0.000	0.000	0.000
30	A	33	GLU	-1	-0.864	-0.942	42.545	-6.225	-6.225	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.951	-0.970	43.306	-6.472	-6.472	0.000	0.000	0.000	0.000
32	A	35	LEU	0	-0.024	-0.014	43.627	0.136	0.136	0.000	0.000	0.000	0.000
33	A	36	LYS	1	0.708	0.828	45.870	6.558	6.558	0.000	0.000	0.000	0.000
34	A	37	GLY	0	0.061	0.029	47.767	0.140	0.140	0.000	0.000	0.000	0.000
35	A	38	LEU	0	-0.002	0.004	48.737	0.162	0.162	0.000	0.000	0.000	0.000
36	A	39	LYS	1	0.958	0.977	50.564	5.730	5.730	0.000	0.000	0.000	0.000
37	A	40	ASP	-1	-0.799	-0.867	52.582	-5.313	-5.313	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.887	0.938	53.333	5.743	5.743	0.000	0.000	0.000	0.000
39	A	42	TYR	0	0.028	0.021	54.673	0.100	0.100	0.000	0.000	0.000	0.000
40	A	43	LEU	0	0.000	-0.010	56.339	0.090	0.090	0.000	0.000	0.000	0.000
41	A	44	ARG	1	0.850	0.912	57.239	5.284	5.284	0.000	0.000	0.000	0.000
42	A	45	LEU	0	0.053	0.035	59.577	0.092	0.092	0.000	0.000	0.000	0.000
43	A	46	LEU	0	-0.005	-0.004	60.028	0.086	0.086	0.000	0.000	0.000	0.000
44	A	47	ALA	0	-0.014	-0.008	62.147	0.086	0.086	0.000	0.000	0.000	0.000
45	A	48	ASP	-1	-0.884	-0.951	63.921	-4.666	-4.666	0.000	0.000	0.000	0.000
46	A	49	PHE	0	-0.068	-0.028	65.038	0.092	0.092	0.000	0.000	0.000	0.000
47	A	50	ASP	-1	-0.818	-0.900	66.358	-4.379	-4.379	0.000	0.000	0.000	0.000
48	A	51	ASN	0	-0.043	-0.010	68.037	0.114	0.114	0.000	0.000	0.000	0.000
49	A	52	TYR	0	0.022	-0.004	69.446	0.072	0.072	0.000	0.000	0.000	0.000
50	A	53	ARG	1	0.860	0.900	70.764	4.197	4.197	0.000	0.000	0.000	0.000
51	A	54	LYS	1	0.805	0.887	70.164	4.416	4.416	0.000	0.000	0.000	0.000
52	A	55	ARG	1	0.900	0.954	72.665	4.219	4.219	0.000	0.000	0.000	0.000
53	A	56	MET	0	-0.020	-0.017	74.525	0.054	0.054	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.824	-0.875	76.610	-3.894	-3.894	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.834	-0.893	78.574	-3.775	-3.775	0.000	0.000	0.000	0.000
56	A	59	GLU	-1	-0.855	-0.925	77.986	-3.949	-3.949	0.000	0.000	0.000	0.000
57	A	60	LEU	0	-0.024	-0.011	78.492	0.047	0.047	0.000	0.000	0.000	0.000
58	A	61	LYS	1	0.836	0.887	80.938	3.884	3.884	0.000	0.000	0.000	0.000
59	A	62	ALA	0	-0.044	-0.016	84.487	0.059	0.059	0.000	0.000	0.000	0.000
60	A	63	ARG	1	0.843	0.875	84.433	3.677	3.677	0.000	0.000	0.000	0.000
61	A	64	GLU	-1	-0.930	-0.949	86.716	-3.523	-3.523	0.000	0.000	0.000	0.000
62	A	65	ARG	1	0.970	0.980	88.603	3.464	3.464	0.000	0.000	0.000	0.000
63	A	66	GLU	-1	-0.852	-0.889	88.698	-3.495	-3.495	0.000	0.000	0.000	0.000
64	A	67	GLY	0	0.016	0.010	91.041	0.041	0.041	0.000	0.000	0.000	0.000
65	A	68	VAL	0	0.012	-0.001	92.747	0.046	0.046	0.000	0.000	0.000	0.000
66	A	69	LEU	0	-0.030	-0.021	93.724	0.048	0.048	0.000	0.000	0.000	0.000
67	A	70	LYS	1	0.929	0.972	94.646	3.361	3.361	0.000	0.000	0.000	0.000
68	A	71	ALA	0	0.032	0.013	97.091	0.034	0.034	0.000	0.000	0.000	0.000
69	A	72	LEU	0	0.007	0.000	98.882	0.035	0.035	0.000	0.000	0.000	0.000
70	A	73	ARG	1	0.925	0.949	95.752	3.268	3.268	0.000	0.000	0.000	0.000
71	A	74	ALA	0	0.004	0.012	101.564	0.028	0.028	0.000	0.000	0.000	0.000
72	A	75	LEU	0	0.007	-0.002	102.022	0.029	0.029	0.000	0.000	0.000	0.000
73	A	76	LEU	0	-0.021	-0.004	103.520	0.026	0.026	0.000	0.000	0.000	0.000
74	A	77	PRO	0	0.034	0.018	106.618	0.024	0.024	0.000	0.000	0.000	0.000
75	A	78	VAL	0	-0.011	-0.003	108.980	0.030	0.030	0.000	0.000	0.000	0.000
76	A	79	LEU	0	-0.025	-0.009	109.299	0.020	0.020	0.000	0.000	0.000	0.000
77	A	80	ASP	-1	-0.873	-0.933	111.061	-2.840	-2.840	0.000	0.000	0.000	0.000
78	A	81	ASP	-1	-0.879	-0.945	113.355	-2.735	-2.735	0.000	0.000	0.000	0.000
79	A	82	LEU	0	-0.075	-0.034	112.655	0.028	0.028	0.000	0.000	0.000	0.000
80	A	83	ASP	-1	-0.875	-0.936	114.382	-2.740	-2.740	0.000	0.000	0.000	0.000
81	A	84	ARG	1	0.859	0.919	114.356	2.768	2.768	0.000	0.000	0.000	0.000
82	A	85	ALA	0	-0.071	-0.047	119.089	0.029	0.029	0.000	0.000	0.000	0.000
83	A	86	LEU	0	-0.016	-0.022	118.125	0.027	0.027	0.000	0.000	0.000	0.000
84	A	87	GLU	-1	-0.933	-0.951	120.274	-2.630	-2.630	0.000	0.000	0.000	0.000
85	A	88	PHE	0	-0.072	-0.031	122.219	0.026	0.026	0.000	0.000	0.000	0.000
86	A	89	ALA	0	-0.038	-0.018	123.532	0.022	0.022	0.000	0.000	0.000	0.000
87	A	90	GLU	-1	-0.893	-0.959	125.124	-2.526	-2.526	0.000	0.000	0.000	0.000
88	A	91	ALA	0	-0.053	-0.012	127.335	0.021	0.021	0.000	0.000	0.000	0.000
89	A	92	SER	0	-0.008	-0.016	129.449	0.022	0.022	0.000	0.000	0.000	0.000
90	A	93	PRO	0	0.059	0.029	128.517	-0.021	-0.021	0.000	0.000	0.000	0.000
91	A	94	GLU	-1	-0.837	-0.906	127.507	-2.525	-2.525	0.000	0.000	0.000	0.000
92	A	95	SER	0	0.012	0.007	126.796	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	96	ILE	0	0.033	0.040	123.147	-0.023	-0.023	0.000	0.000	0.000	0.000
94	A	97	ARG	1	0.846	0.918	122.984	2.489	2.489	0.000	0.000	0.000	0.000
95	A	98	GLN	0	-0.032	-0.040	122.642	-0.027	-0.027	0.000	0.000	0.000	0.000
96	A	99	GLY	0	0.069	0.042	121.502	-0.020	-0.020	0.000	0.000	0.000	0.000
97	A	100	VAL	0	0.021	-0.001	117.885	-0.028	-0.028	0.000	0.000	0.000	0.000
98	A	101	ARG	1	0.846	0.932	117.630	2.573	2.573	0.000	0.000	0.000	0.000
99	A	102	ALA	0	0.034	0.020	117.267	-0.025	-0.025	0.000	0.000	0.000	0.000
100	A	103	ILE	0	0.048	0.032	113.973	-0.027	-0.027	0.000	0.000	0.000	0.000
101	A	104	ARG	1	0.807	0.884	113.311	2.710	2.710	0.000	0.000	0.000	0.000
102	A	105	ASP	-1	-0.833	-0.911	112.400	-2.776	-2.776	0.000	0.000	0.000	0.000
103	A	106	GLY	0	-0.014	-0.011	112.232	-0.019	-0.019	0.000	0.000	0.000	0.000
104	A	107	PHE	0	0.030	0.011	105.826	-0.032	-0.032	0.000	0.000	0.000	0.000
105	A	108	PHE	0	-0.020	-0.016	107.743	-0.027	-0.027	0.000	0.000	0.000	0.000
106	A	109	ARG	1	0.932	0.979	107.482	2.788	2.788	0.000	0.000	0.000	0.000
107	A	110	ILE	0	0.004	0.012	104.730	-0.026	-0.026	0.000	0.000	0.000	0.000
108	A	111	LEU	0	-0.050	-0.022	102.910	-0.035	-0.035	0.000	0.000	0.000	0.000
109	A	112	ALA	0	0.086	0.044	102.529	-0.035	-0.035	0.000	0.000	0.000	0.000
110	A	113	GLY	0	-0.026	-0.004	102.594	-0.027	-0.027	0.000	0.000	0.000	0.000
111	A	114	LEU	0	-0.103	-0.053	98.760	-0.038	-0.038	0.000	0.000	0.000	0.000
112	A	115	GLY	0	-0.026	-0.005	98.251	-0.043	-0.043	0.000	0.000	0.000	0.000
113	A	116	VAL	0	-0.100	-0.059	98.884	-0.026	-0.026	0.000	0.000	0.000	0.000
114	A	117	GLU	-1	-0.880	-0.941	100.832	-3.018	-3.018	0.000	0.000	0.000	0.000
115	A	118	GLU	-1	-0.832	-0.892	102.590	-2.935	-2.935	0.000	0.000	0.000	0.000
116	A	119	VAL	0	-0.066	-0.025	101.628	-0.017	-0.017	0.000	0.000	0.000	0.000
117	A	120	PRO	0	0.038	0.012	103.850	0.028	0.028	0.000	0.000	0.000	0.000
118	A	121	GLY	0	0.058	0.026	106.821	-0.009	-0.009	0.000	0.000	0.000	0.000
119	A	122	GLU	-1	-0.835	-0.917	110.047	-2.779	-2.779	0.000	0.000	0.000	0.000
120	A	123	GLY	0	-0.014	0.007	113.540	0.012	0.012	0.000	0.000	0.000	0.000
121	A	124	GLU	-1	-0.908	-0.942	108.230	-2.960	-2.960	0.000	0.000	0.000	0.000
122	A	125	ALA	0	-0.017	-0.016	106.270	0.011	0.011	0.000	0.000	0.000	0.000
123	A	126	PHE	0	-0.017	-0.019	103.543	-0.013	-0.013	0.000	0.000	0.000	0.000
124	A	127	ASP	-1	-0.772	-0.879	99.725	-3.228	-3.228	0.000	0.000	0.000	0.000
125	A	128	PRO	0	0.002	-0.010	98.594	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	129	ARG	1	0.827	0.912	95.499	3.249	3.249	0.000	0.000	0.000	0.000
127	A	130	TYR	0	-0.017	-0.023	97.715	-0.012	-0.012	0.000	0.000	0.000	0.000
128	A	131	HIS	0	-0.061	-0.023	100.657	0.021	0.021	0.000	0.000	0.000	0.000
129	A	132	GLU	-1	-0.902	-0.951	101.651	-3.149	-3.149	0.000	0.000	0.000	0.000
130	A	133	ALA	0	0.016	0.001	103.556	0.035	0.035	0.000	0.000	0.000	0.000
131	A	134	VAL	0	-0.055	-0.028	106.116	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	135	GLY	0	0.006	0.005	108.306	0.017	0.017	0.000	0.000	0.000	0.000
133	A	136	LEU	0	-0.048	-0.011	110.561	-0.020	-0.020	0.000	0.000	0.000	0.000
134	A	137	LEU	0	0.006	-0.002	113.015	0.024	0.024	0.000	0.000	0.000	0.000
135	A	138	PRO	0	0.000	0.005	116.411	-0.012	-0.012	0.000	0.000	0.000	0.000
136	A	139	GLY	0	0.003	-0.007	117.045	0.007	0.007	0.000	0.000	0.000	0.000
137	A	140	GLU	-1	-0.834	-0.903	113.744	-2.821	-2.821	0.000	0.000	0.000	0.000
138	A	141	PRO	0	-0.011	-0.018	112.665	-0.021	-0.021	0.000	0.000	0.000	0.000
139	A	142	GLY	0	0.002	0.018	108.827	-0.012	-0.012	0.000	0.000	0.000	0.000
140	A	143	LYS	1	0.823	0.910	108.571	2.831	2.831	0.000	0.000	0.000	0.000
141	A	144	VAL	0	-0.035	-0.011	108.758	0.010	0.010	0.000	0.000	0.000	0.000
142	A	145	ALA	0	0.019	0.007	111.305	0.022	0.022	0.000	0.000	0.000	0.000
143	A	146	LYS	1	0.783	0.870	113.271	2.793	2.793	0.000	0.000	0.000	0.000
144	A	147	VAL	0	0.008	0.013	109.467	-0.027	-0.027	0.000	0.000	0.000	0.000
145	A	148	PHE	0	-0.025	-0.020	110.758	0.033	0.033	0.000	0.000	0.000	0.000
146	A	149	GLN	0	-0.068	-0.042	105.613	-0.016	-0.016	0.000	0.000	0.000	0.000
147	A	150	ARG	1	0.861	0.904	107.593	2.849	2.849	0.000	0.000	0.000	0.000
148	A	151	GLY	0	0.063	0.041	104.015	-0.013	-0.013	0.000	0.000	0.000	0.000
149	A	152	PHE	0	-0.015	-0.010	101.889	0.025	0.025	0.000	0.000	0.000	0.000
150	A	153	ARG	1	0.944	0.974	97.664	3.179	3.179	0.000	0.000	0.000	0.000
151	A	154	MET	0	0.028	0.024	94.708	0.026	0.026	0.000	0.000	0.000	0.000
152	A	155	GLY	0	0.003	0.006	94.631	-0.042	-0.042	0.000	0.000	0.000	0.000
153	A	156	GLU	-1	-0.916	-0.965	91.755	-3.345	-3.345	0.000	0.000	0.000	0.000
154	A	157	ALA	0	-0.037	-0.004	92.043	-0.007	-0.007	0.000	0.000	0.000	0.000
155	A	158	LEU	0	-0.002	-0.003	93.587	0.038	0.038	0.000	0.000	0.000	0.000
156	A	159	VAL	0	-0.018	-0.006	95.627	-0.020	-0.020	0.000	0.000	0.000	0.000
157	A	160	ARG	1	0.851	0.910	97.692	3.037	3.037	0.000	0.000	0.000	0.000
158	A	161	PRO	0	0.060	0.042	98.765	0.016	0.016	0.000	0.000	0.000	0.000
159	A	162	ALA	0	-0.004	-0.005	101.400	0.020	0.020	0.000	0.000	0.000	0.000
160	A	163	ARG	1	0.931	0.978	104.965	2.975	2.975	0.000	0.000	0.000	0.000
161	A	164	VAL	0	-0.018	-0.014	106.501	0.034	0.034	0.000	0.000	0.000	0.000
162	A	165	ALA	0	0.025	0.019	108.973	-0.011	-0.011	0.000	0.000	0.000	0.000
163	A	166	VAL	0	0.005	0.002	107.771	0.006	0.006	0.000	0.000	0.000	0.000
164	A	167	GLY	0	0.018	0.006	111.118	0.022	0.022	0.000	0.000	0.000	0.000
165	A	168	GLU	-1	-0.946	-0.974	113.127	-2.775	-2.775	0.000	0.000	0.000	0.000
166	A	169	GLU	-1	-0.759	-0.877	115.604	-2.622	-2.622	0.000	0.000	0.000	0.000
167	A	170	LYS	1	0.848	0.926	118.442	2.609	2.609	0.000	0.000	0.000	0.000
168	A	171	ARG	1	0.924	0.954	119.434	2.662	2.662	0.000	0.000	0.000	0.000

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