FMO DATABASE

FMODB ID: 7GKJK

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	OptHSide
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	-1192404.665033
FMO2-HF: Nuclear repulsion	1126887.391263
FMO2-HF: Total energy	-65517.27377
FMO2-MP2: Total energy	-65711.702234

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.
-94.08	-89.552	10.735	-7.411	-7.851	-0.03

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 : 0.980 / q_NPA : 0.984

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	-0.030	-0.010	2.502	0.495	5.783	0.142	-2.722	-2.707	0.015
4	A	7	GLU	-1	-0.802	-0.917	1.994	-51.097	-52.990	10.555	-4.267	-4.395	-0.043
5	A	8	ASN	0	-0.041	-0.021	3.376	-1.343	-0.210	0.038	-0.422	-0.749	-0.002
6	A	9	THR	0	-0.055	-0.035	5.575	4.114	4.114	0.000	0.000	0.000	0.000
7	A	10	LEU	0	-0.012	-0.011	7.017	3.591	3.591	0.000	0.000	0.000	0.000
8	A	11	GLU	-1	-0.785	-0.868	7.506	-24.628	-24.628	0.000	0.000	0.000	0.000
9	A	12	LYS	1	0.896	0.937	8.971	24.556	24.556	0.000	0.000	0.000	0.000
10	A	13	ASP	-1	-0.941	-0.963	11.250	-19.427	-19.427	0.000	0.000	0.000	0.000
11	A	14	LEU	0	-0.051	-0.035	11.997	1.208	1.208	0.000	0.000	0.000	0.000
12	A	15	GLU	-1	-0.956	-0.963	13.354	-18.066	-18.066	0.000	0.000	0.000	0.000
13	A	16	ALA	0	-0.032	-0.018	16.057	0.890	0.890	0.000	0.000	0.000	0.000
14	A	17	VAL	0	0.053	0.029	17.351	0.703	0.703	0.000	0.000	0.000	0.000
15	A	18	GLY	0	0.021	0.011	19.419	0.656	0.656	0.000	0.000	0.000	0.000
16	A	19	GLN	0	-0.082	-0.062	19.927	0.329	0.329	0.000	0.000	0.000	0.000
17	A	20	GLU	-1	-0.989	-0.988	22.821	-11.562	-11.562	0.000	0.000	0.000	0.000
18	A	21	ALA	0	0.001	0.002	23.428	0.306	0.306	0.000	0.000	0.000	0.000
19	A	22	GLN	0	0.053	0.023	25.084	0.285	0.285	0.000	0.000	0.000	0.000
20	A	23	ALA	0	0.029	0.009	27.015	0.402	0.402	0.000	0.000	0.000	0.000
21	A	24	LEU	0	-0.069	-0.040	27.421	0.496	0.496	0.000	0.000	0.000	0.000
22	A	25	GLU	-1	-0.900	-0.941	27.604	-9.609	-9.609	0.000	0.000	0.000	0.000
23	A	26	GLU	-1	-0.888	-0.921	31.090	-8.547	-8.547	0.000	0.000	0.000	0.000
24	A	27	ARG	1	0.888	0.952	32.108	8.905	8.905	0.000	0.000	0.000	0.000
25	A	28	LEU	0	-0.013	-0.010	34.222	0.239	0.239	0.000	0.000	0.000	0.000
26	A	29	LYS	1	0.844	0.902	32.874	8.783	8.783	0.000	0.000	0.000	0.000
27	A	30	ALA	0	0.032	0.014	37.142	0.179	0.179	0.000	0.000	0.000	0.000
28	A	31	ALA	0	-0.027	-0.021	39.151	0.191	0.191	0.000	0.000	0.000	0.000
29	A	32	GLU	-1	-0.790	-0.868	41.097	-6.561	-6.561	0.000	0.000	0.000	0.000
30	A	33	GLU	-1	-0.869	-0.950	42.665	-6.208	-6.208	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.975	-0.972	43.316	-6.503	-6.503	0.000	0.000	0.000	0.000
32	A	35	LEU	0	-0.024	-0.010	43.897	0.120	0.120	0.000	0.000	0.000	0.000
33	A	36	LYS	1	0.727	0.834	45.946	6.552	6.552	0.000	0.000	0.000	0.000
34	A	37	GLY	0	0.060	0.035	47.738	0.124	0.124	0.000	0.000	0.000	0.000
35	A	38	LEU	0	0.012	0.013	49.022	0.158	0.158	0.000	0.000	0.000	0.000
36	A	39	LYS	1	0.918	0.960	50.850	5.698	5.698	0.000	0.000	0.000	0.000
37	A	40	ASP	-1	-0.788	-0.873	52.794	-5.314	-5.314	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.897	0.926	53.706	5.646	5.646	0.000	0.000	0.000	0.000
39	A	42	TYR	0	0.041	0.039	54.908	0.089	0.089	0.000	0.000	0.000	0.000
40	A	43	LEU	0	-0.024	-0.008	56.428	0.091	0.091	0.000	0.000	0.000	0.000
41	A	44	ARG	1	0.868	0.912	57.187	5.282	5.282	0.000	0.000	0.000	0.000
42	A	45	LEU	0	0.018	0.016	59.638	0.074	0.074	0.000	0.000	0.000	0.000
43	A	46	LEU	0	-0.036	-0.034	60.018	0.086	0.086	0.000	0.000	0.000	0.000
44	A	47	ALA	0	-0.014	0.003	62.379	0.058	0.058	0.000	0.000	0.000	0.000
45	A	48	ASP	-1	-0.872	-0.939	64.041	-4.637	-4.637	0.000	0.000	0.000	0.000
46	A	49	PHE	0	-0.034	-0.013	65.232	0.095	0.095	0.000	0.000	0.000	0.000
47	A	50	ASP	-1	-0.837	-0.908	66.684	-4.400	-4.400	0.000	0.000	0.000	0.000
48	A	51	ASN	0	-0.040	-0.017	68.272	0.090	0.090	0.000	0.000	0.000	0.000
49	A	52	TYR	0	0.065	0.011	69.677	0.068	0.068	0.000	0.000	0.000	0.000
50	A	53	ARG	1	0.855	0.918	70.885	4.194	4.194	0.000	0.000	0.000	0.000
51	A	54	LYS	1	0.828	0.897	70.156	4.401	4.401	0.000	0.000	0.000	0.000
52	A	55	ARG	1	0.936	0.984	72.270	4.251	4.251	0.000	0.000	0.000	0.000
53	A	56	MET	0	-0.015	-0.009	74.785	0.049	0.049	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.815	-0.871	76.433	-3.896	-3.896	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.937	-0.967	78.379	-3.785	-3.785	0.000	0.000	0.000	0.000
56	A	59	GLU	-1	-0.927	-0.990	78.417	-3.929	-3.929	0.000	0.000	0.000	0.000
57	A	60	LEU	0	-0.016	0.004	78.781	0.036	0.036	0.000	0.000	0.000	0.000
58	A	61	LYS	1	0.900	0.932	80.848	3.872	3.872	0.000	0.000	0.000	0.000
59	A	62	ALA	0	-0.032	-0.004	84.569	0.057	0.057	0.000	0.000	0.000	0.000
60	A	63	ARG	1	0.915	0.933	84.816	3.683	3.683	0.000	0.000	0.000	0.000
61	A	64	GLU	-1	-0.924	-0.941	87.025	-3.517	-3.517	0.000	0.000	0.000	0.000
62	A	65	ARG	1	0.973	0.991	88.856	3.464	3.464	0.000	0.000	0.000	0.000
63	A	66	GLU	-1	-0.915	-0.945	88.779	-3.492	-3.492	0.000	0.000	0.000	0.000
64	A	67	GLY	0	0.025	0.006	91.215	0.038	0.038	0.000	0.000	0.000	0.000
65	A	68	VAL	0	0.009	-0.004	92.836	0.045	0.045	0.000	0.000	0.000	0.000
66	A	69	LEU	0	-0.041	-0.020	93.859	0.047	0.047	0.000	0.000	0.000	0.000
67	A	70	LYS	1	0.932	0.975	94.163	3.376	3.376	0.000	0.000	0.000	0.000
68	A	71	ALA	0	0.023	0.017	97.143	0.030	0.030	0.000	0.000	0.000	0.000
69	A	72	LEU	0	0.031	0.000	99.083	0.036	0.036	0.000	0.000	0.000	0.000
70	A	73	ARG	1	0.916	0.945	96.001	3.263	3.263	0.000	0.000	0.000	0.000
71	A	74	ALA	0	0.006	0.009	101.677	0.029	0.029	0.000	0.000	0.000	0.000
72	A	75	LEU	0	0.012	-0.007	102.162	0.027	0.027	0.000	0.000	0.000	0.000
73	A	76	LEU	0	-0.001	0.018	103.966	0.024	0.024	0.000	0.000	0.000	0.000
74	A	77	PRO	0	0.022	0.011	106.816	0.026	0.026	0.000	0.000	0.000	0.000
75	A	78	VAL	0	-0.014	-0.001	108.973	0.029	0.029	0.000	0.000	0.000	0.000
76	A	79	LEU	0	-0.022	-0.010	108.856	0.022	0.022	0.000	0.000	0.000	0.000
77	A	80	ASP	-1	-0.867	-0.930	110.932	-2.843	-2.843	0.000	0.000	0.000	0.000
78	A	81	ASP	-1	-0.878	-0.932	113.181	-2.735	-2.735	0.000	0.000	0.000	0.000
79	A	82	LEU	0	-0.091	-0.050	112.505	0.028	0.028	0.000	0.000	0.000	0.000
80	A	83	ASP	-1	-0.874	-0.931	114.478	-2.738	-2.738	0.000	0.000	0.000	0.000
81	A	84	ARG	1	0.817	0.884	114.602	2.764	2.764	0.000	0.000	0.000	0.000
82	A	85	ALA	0	-0.082	-0.049	119.023	0.029	0.029	0.000	0.000	0.000	0.000
83	A	86	LEU	0	-0.004	-0.012	118.192	0.025	0.025	0.000	0.000	0.000	0.000
84	A	87	GLU	-1	-0.927	-0.952	120.620	-2.623	-2.623	0.000	0.000	0.000	0.000
85	A	88	PHE	0	-0.062	-0.027	122.389	0.028	0.028	0.000	0.000	0.000	0.000
86	A	89	ALA	0	-0.010	-0.016	123.535	0.020	0.020	0.000	0.000	0.000	0.000
87	A	90	GLU	-1	-0.932	-0.953	125.230	-2.524	-2.524	0.000	0.000	0.000	0.000
88	A	91	ALA	0	-0.054	-0.013	127.379	0.022	0.022	0.000	0.000	0.000	0.000
89	A	92	SER	0	0.030	-0.004	129.467	0.019	0.019	0.000	0.000	0.000	0.000
90	A	93	PRO	0	0.090	0.056	128.639	-0.022	-0.022	0.000	0.000	0.000	0.000
91	A	94	GLU	-1	-0.845	-0.921	127.579	-2.524	-2.524	0.000	0.000	0.000	0.000
92	A	95	SER	0	-0.023	-0.015	127.086	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	96	ILE	0	0.043	0.034	123.013	-0.022	-0.022	0.000	0.000	0.000	0.000
94	A	97	ARG	1	0.829	0.923	123.005	2.490	2.490	0.000	0.000	0.000	0.000
95	A	98	GLN	0	-0.039	-0.038	122.578	-0.026	-0.026	0.000	0.000	0.000	0.000
96	A	99	GLY	0	0.081	0.053	121.651	-0.018	-0.018	0.000	0.000	0.000	0.000
97	A	100	VAL	0	0.030	0.005	117.677	-0.028	-0.028	0.000	0.000	0.000	0.000
98	A	101	ARG	1	0.853	0.932	117.665	2.578	2.578	0.000	0.000	0.000	0.000
99	A	102	ALA	0	0.034	0.017	117.407	-0.025	-0.025	0.000	0.000	0.000	0.000
100	A	103	ILE	0	0.045	0.026	113.777	-0.027	-0.027	0.000	0.000	0.000	0.000
101	A	104	ARG	1	0.793	0.892	113.278	2.710	2.710	0.000	0.000	0.000	0.000
102	A	105	ASP	-1	-0.840	-0.925	112.453	-2.763	-2.763	0.000	0.000	0.000	0.000
103	A	106	GLY	0	-0.026	-0.017	112.319	-0.022	-0.022	0.000	0.000	0.000	0.000
104	A	107	PHE	0	0.032	0.010	105.771	-0.033	-0.033	0.000	0.000	0.000	0.000
105	A	108	PHE	0	-0.013	-0.007	107.732	-0.028	-0.028	0.000	0.000	0.000	0.000
106	A	109	ARG	1	0.956	0.996	107.247	2.788	2.788	0.000	0.000	0.000	0.000
107	A	110	ILE	0	0.012	0.007	104.914	-0.029	-0.029	0.000	0.000	0.000	0.000
108	A	111	LEU	0	-0.030	-0.013	102.779	-0.035	-0.035	0.000	0.000	0.000	0.000
109	A	112	ALA	0	0.065	0.025	102.507	-0.034	-0.034	0.000	0.000	0.000	0.000
110	A	113	GLY	0	-0.004	0.018	102.536	-0.028	-0.028	0.000	0.000	0.000	0.000
111	A	114	LEU	0	-0.148	-0.071	98.590	-0.038	-0.038	0.000	0.000	0.000	0.000
112	A	115	GLY	0	-0.002	-0.007	98.363	-0.037	-0.037	0.000	0.000	0.000	0.000
113	A	116	VAL	0	-0.078	-0.052	98.777	-0.033	-0.033	0.000	0.000	0.000	0.000
114	A	117	GLU	-1	-0.903	-0.947	100.860	-3.028	-3.028	0.000	0.000	0.000	0.000
115	A	118	GLU	-1	-0.853	-0.924	102.520	-2.929	-2.929	0.000	0.000	0.000	0.000
116	A	119	VAL	0	-0.082	-0.037	101.346	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	120	PRO	0	0.040	0.010	103.751	0.026	0.026	0.000	0.000	0.000	0.000
118	A	121	GLY	0	0.059	0.021	106.793	-0.012	-0.012	0.000	0.000	0.000	0.000
119	A	122	GLU	-1	-0.865	-0.932	109.707	-2.766	-2.766	0.000	0.000	0.000	0.000
120	A	123	GLY	0	-0.020	0.000	113.007	0.010	0.010	0.000	0.000	0.000	0.000
121	A	124	GLU	-1	-0.905	-0.954	107.825	-2.950	-2.950	0.000	0.000	0.000	0.000
122	A	125	ALA	0	-0.026	-0.015	105.723	0.010	0.010	0.000	0.000	0.000	0.000
123	A	126	PHE	0	-0.026	-0.031	103.313	-0.017	-0.017	0.000	0.000	0.000	0.000
124	A	127	ASP	-1	-0.769	-0.875	99.608	-3.221	-3.221	0.000	0.000	0.000	0.000
125	A	128	PRO	0	0.004	-0.010	98.284	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	129	ARG	1	0.830	0.912	95.498	3.246	3.246	0.000	0.000	0.000	0.000
127	A	130	TYR	0	-0.012	-0.020	97.460	-0.011	-0.011	0.000	0.000	0.000	0.000
128	A	131	HIS	0	-0.077	-0.036	100.539	0.022	0.022	0.000	0.000	0.000	0.000
129	A	132	GLU	-1	-0.872	-0.925	100.974	-3.157	-3.157	0.000	0.000	0.000	0.000
130	A	133	ALA	0	-0.002	-0.005	103.375	0.035	0.035	0.000	0.000	0.000	0.000
131	A	134	VAL	0	-0.062	-0.052	105.842	-0.009	-0.009	0.000	0.000	0.000	0.000
132	A	135	GLY	0	0.010	0.010	108.168	0.012	0.012	0.000	0.000	0.000	0.000
133	A	136	LEU	0	-0.057	-0.019	110.517	-0.013	-0.013	0.000	0.000	0.000	0.000
134	A	137	LEU	0	-0.006	-0.001	112.807	0.025	0.025	0.000	0.000	0.000	0.000
135	A	138	PRO	0	0.016	0.004	115.874	-0.014	-0.014	0.000	0.000	0.000	0.000
136	A	139	GLY	0	0.003	0.000	116.717	0.005	0.005	0.000	0.000	0.000	0.000
137	A	140	GLU	-1	-0.866	-0.915	113.783	-2.810	-2.810	0.000	0.000	0.000	0.000
138	A	141	PRO	0	0.032	0.004	112.182	-0.021	-0.021	0.000	0.000	0.000	0.000
139	A	142	GLY	0	-0.032	0.002	108.240	-0.009	-0.009	0.000	0.000	0.000	0.000
140	A	143	LYS	1	0.844	0.915	108.253	2.837	2.837	0.000	0.000	0.000	0.000
141	A	144	VAL	0	-0.044	-0.004	108.162	0.016	0.016	0.000	0.000	0.000	0.000
142	A	145	ALA	0	0.033	0.017	110.724	0.020	0.020	0.000	0.000	0.000	0.000
143	A	146	LYS	1	0.889	0.943	112.878	2.784	2.784	0.000	0.000	0.000	0.000
144	A	147	VAL	0	0.012	0.006	109.324	-0.027	-0.027	0.000	0.000	0.000	0.000
145	A	148	PHE	0	-0.086	-0.045	110.766	0.026	0.026	0.000	0.000	0.000	0.000
146	A	149	GLN	0	-0.048	-0.036	105.394	-0.017	-0.017	0.000	0.000	0.000	0.000
147	A	150	ARG	1	0.873	0.937	107.413	2.848	2.848	0.000	0.000	0.000	0.000
148	A	151	GLY	0	0.071	0.048	103.778	-0.013	-0.013	0.000	0.000	0.000	0.000
149	A	152	PHE	0	-0.017	-0.008	101.768	0.024	0.024	0.000	0.000	0.000	0.000
150	A	153	ARG	1	0.956	0.990	97.652	3.172	3.172	0.000	0.000	0.000	0.000
151	A	154	MET	0	0.015	0.027	94.803	0.020	0.020	0.000	0.000	0.000	0.000
152	A	155	GLY	0	-0.028	-0.010	94.643	-0.040	-0.040	0.000	0.000	0.000	0.000
153	A	156	GLU	-1	-0.916	-0.968	90.941	-3.386	-3.386	0.000	0.000	0.000	0.000
154	A	157	ALA	0	-0.037	-0.001	91.836	-0.001	-0.001	0.000	0.000	0.000	0.000
155	A	158	LEU	0	0.021	0.003	93.371	0.039	0.039	0.000	0.000	0.000	0.000
156	A	159	VAL	0	-0.046	-0.026	95.609	-0.016	-0.016	0.000	0.000	0.000	0.000
157	A	160	ARG	1	0.878	0.917	97.671	3.026	3.026	0.000	0.000	0.000	0.000
158	A	161	PRO	0	0.059	0.043	98.577	0.021	0.021	0.000	0.000	0.000	0.000
159	A	162	ALA	0	0.001	-0.002	101.218	0.019	0.019	0.000	0.000	0.000	0.000
160	A	163	ARG	1	0.940	0.981	104.870	2.962	2.962	0.000	0.000	0.000	0.000
161	A	164	VAL	0	-0.053	-0.037	106.529	0.029	0.029	0.000	0.000	0.000	0.000
162	A	165	ALA	0	0.032	0.034	108.891	-0.011	-0.011	0.000	0.000	0.000	0.000
163	A	166	VAL	0	-0.003	-0.010	107.368	0.003	0.003	0.000	0.000	0.000	0.000
164	A	167	GLY	0	0.026	0.014	110.766	0.020	0.020	0.000	0.000	0.000	0.000
165	A	168	GLU	-1	-0.939	-0.974	112.675	-2.770	-2.770	0.000	0.000	0.000	0.000
166	A	169	GLU	-1	-0.794	-0.903	115.071	-2.627	-2.627	0.000	0.000	0.000	0.000
167	A	170	LYS	1	0.878	0.946	117.929	2.599	2.599	0.000	0.000	0.000	0.000
168	A	171	ARG	1	0.926	0.956	119.289	2.646	2.646	0.000	0.000	0.000	0.000

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