FMO DATABASE

FMODB ID: 3QMNL

Calculation Name: 3A6M-B-Xray372

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: 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	164
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1152150.465066
FMO2-HF: Nuclear repulsion	1088571.851477
FMO2-HF: Total energy	-63578.613589
FMO2-MP2: Total energy	-63767.269712

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:7:GLU)

Summations of interaction energy for fragment #1(B:7:GLU)

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.
21.931	25.244	15.963	-10.341	-8.934	-0.041

Interaction energy analysis for fragmet #1(B:7:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.914 / q_NPA : -0.947

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	9	THR	0	-0.023	-0.035	3.483	-15.900	-12.347	0.094	-1.803	-1.844	0.014
4	B	10	LEU	0	-0.040	0.009	1.551	-4.135	-8.458	12.310	-4.715	-3.271	-0.008
5	B	11	GLU	-1	-0.799	-0.920	2.406	24.555	28.520	3.560	-3.818	-3.707	-0.047
6	B	12	LYS	1	0.865	0.935	5.399	-43.831	-43.713	-0.001	-0.005	-0.112	0.000
7	B	13	ASP	-1	-0.956	-0.978	7.101	24.035	24.035	0.000	0.000	0.000	0.000
8	B	14	LEU	0	0.011	0.008	7.495	-2.676	-2.676	0.000	0.000	0.000	0.000
9	B	15	GLU	-1	-0.955	-0.972	8.969	26.297	26.297	0.000	0.000	0.000	0.000
10	B	16	ALA	0	-0.010	-0.005	11.885	-1.175	-1.175	0.000	0.000	0.000	0.000
11	B	17	VAL	0	0.027	0.006	13.889	-1.211	-1.211	0.000	0.000	0.000	0.000
12	B	18	GLY	0	-0.022	-0.012	15.034	-0.954	-0.954	0.000	0.000	0.000	0.000
13	B	19	GLN	0	0.000	-0.002	16.850	-1.126	-1.126	0.000	0.000	0.000	0.000
14	B	20	GLU	-1	-0.947	-0.969	18.676	12.411	12.411	0.000	0.000	0.000	0.000
15	B	21	ALA	0	-0.015	-0.008	20.360	-0.652	-0.652	0.000	0.000	0.000	0.000
16	B	22	GLN	0	-0.009	-0.001	20.028	0.116	0.116	0.000	0.000	0.000	0.000
17	B	23	ALA	0	0.041	0.016	22.447	-0.407	-0.407	0.000	0.000	0.000	0.000
18	B	24	LEU	0	-0.068	-0.048	24.564	-0.554	-0.554	0.000	0.000	0.000	0.000
19	B	25	GLU	-1	-0.861	-0.927	26.124	9.559	9.559	0.000	0.000	0.000	0.000
20	B	26	GLU	-1	-0.927	-0.959	27.871	10.220	10.220	0.000	0.000	0.000	0.000
21	B	27	ARG	1	0.888	0.948	24.765	-11.279	-11.279	0.000	0.000	0.000	0.000
22	B	28	LEU	0	-0.044	-0.023	31.069	-0.350	-0.350	0.000	0.000	0.000	0.000
23	B	29	LYS	1	0.847	0.926	31.050	-9.749	-9.749	0.000	0.000	0.000	0.000
24	B	30	ALA	0	0.108	0.056	33.037	-0.191	-0.191	0.000	0.000	0.000	0.000
25	B	31	ALA	0	0.001	0.006	35.004	-0.278	-0.278	0.000	0.000	0.000	0.000
26	B	32	GLU	-1	-0.937	-0.975	35.826	8.068	8.068	0.000	0.000	0.000	0.000
27	B	33	GLU	-1	-0.912	-0.948	36.895	8.378	8.378	0.000	0.000	0.000	0.000
28	B	34	GLU	-1	-0.788	-0.900	39.041	6.814	6.814	0.000	0.000	0.000	0.000
29	B	35	LEU	0	-0.078	-0.039	40.175	-0.258	-0.258	0.000	0.000	0.000	0.000
30	B	36	LYS	1	0.855	0.930	38.819	-7.929	-7.929	0.000	0.000	0.000	0.000
31	B	37	GLY	0	0.039	0.011	43.629	-0.141	-0.141	0.000	0.000	0.000	0.000
32	B	38	LEU	0	-0.071	-0.028	44.825	-0.158	-0.158	0.000	0.000	0.000	0.000
33	B	39	LYS	1	0.911	0.936	46.507	-6.603	-6.603	0.000	0.000	0.000	0.000
34	B	40	ASP	-1	-0.822	-0.900	49.152	6.215	6.215	0.000	0.000	0.000	0.000
35	B	41	LYS	1	0.753	0.871	45.942	-6.939	-6.939	0.000	0.000	0.000	0.000
36	B	42	TYR	0	0.033	0.015	51.811	-0.073	-0.073	0.000	0.000	0.000	0.000
37	B	43	LEU	0	0.016	0.013	53.460	-0.107	-0.107	0.000	0.000	0.000	0.000
38	B	44	ARG	1	0.952	0.970	53.605	-5.913	-5.913	0.000	0.000	0.000	0.000
39	B	45	LEU	0	0.035	0.029	55.122	-0.087	-0.087	0.000	0.000	0.000	0.000
40	B	46	LEU	0	-0.002	-0.005	57.763	-0.086	-0.086	0.000	0.000	0.000	0.000
41	B	47	ALA	0	-0.011	-0.002	59.463	-0.093	-0.093	0.000	0.000	0.000	0.000
42	B	48	ASP	-1	-0.895	-0.961	60.578	5.101	5.101	0.000	0.000	0.000	0.000
43	B	49	PHE	0	0.003	-0.010	61.696	-0.088	-0.088	0.000	0.000	0.000	0.000
44	B	50	ASP	-1	-0.859	-0.909	63.275	4.769	4.769	0.000	0.000	0.000	0.000
45	B	51	ASN	0	-0.050	-0.010	64.916	-0.142	-0.142	0.000	0.000	0.000	0.000
46	B	52	TYR	0	0.070	0.005	66.607	-0.080	-0.080	0.000	0.000	0.000	0.000
47	B	53	ARG	1	0.861	0.943	63.096	-4.925	-4.925	0.000	0.000	0.000	0.000
48	B	54	LYS	1	0.855	0.917	66.630	-4.755	-4.755	0.000	0.000	0.000	0.000
49	B	55	ARG	1	0.906	0.991	68.234	-4.616	-4.616	0.000	0.000	0.000	0.000
50	B	56	MET	0	0.011	-0.015	71.850	-0.037	-0.037	0.000	0.000	0.000	0.000
51	B	57	GLU	-1	-0.917	-0.941	74.539	3.981	3.981	0.000	0.000	0.000	0.000
52	B	58	GLU	-1	-0.929	-0.960	76.724	3.928	3.928	0.000	0.000	0.000	0.000
53	B	59	GLU	-1	-0.952	-1.000	74.032	4.215	4.215	0.000	0.000	0.000	0.000
54	B	60	LEU	0	-0.020	-0.022	77.106	-0.041	-0.041	0.000	0.000	0.000	0.000
55	B	61	LYS	1	1.019	1.019	79.525	-3.763	-3.763	0.000	0.000	0.000	0.000
56	B	62	ALA	0	-0.007	-0.011	81.027	-0.059	-0.059	0.000	0.000	0.000	0.000
57	B	63	ARG	1	0.960	0.990	78.314	-4.095	-4.095	0.000	0.000	0.000	0.000
58	B	64	GLU	-1	-0.934	-0.957	82.062	3.645	3.645	0.000	0.000	0.000	0.000
59	B	65	ARG	1	0.877	0.930	85.396	-3.705	-3.705	0.000	0.000	0.000	0.000
60	B	66	GLU	-1	-0.907	-0.943	81.481	3.926	3.926	0.000	0.000	0.000	0.000
61	B	67	GLY	0	0.024	0.017	85.641	-0.026	-0.026	0.000	0.000	0.000	0.000
62	B	68	VAL	0	0.034	0.007	87.478	-0.040	-0.040	0.000	0.000	0.000	0.000
63	B	69	LEU	0	-0.042	-0.019	87.729	-0.043	-0.043	0.000	0.000	0.000	0.000
64	B	70	LYS	1	0.950	0.975	85.466	-3.775	-3.775	0.000	0.000	0.000	0.000
65	B	71	ALA	0	0.004	-0.004	89.618	-0.021	-0.021	0.000	0.000	0.000	0.000
66	B	72	LEU	0	0.023	0.004	92.760	-0.032	-0.032	0.000	0.000	0.000	0.000
67	B	73	ARG	1	0.879	0.939	88.091	-3.648	-3.648	0.000	0.000	0.000	0.000
68	B	74	ALA	0	0.023	0.003	93.273	-0.023	-0.023	0.000	0.000	0.000	0.000
69	B	75	LEU	0	0.008	-0.004	95.110	-0.028	-0.028	0.000	0.000	0.000	0.000
70	B	76	LEU	0	-0.022	0.005	96.708	-0.035	-0.035	0.000	0.000	0.000	0.000
71	B	77	PRO	0	0.039	0.027	98.317	-0.032	-0.032	0.000	0.000	0.000	0.000
72	B	78	VAL	0	0.005	0.015	101.364	-0.035	-0.035	0.000	0.000	0.000	0.000
73	B	79	LEU	0	-0.031	-0.021	103.112	-0.033	-0.033	0.000	0.000	0.000	0.000
74	B	80	ASP	-1	-0.847	-0.922	101.867	3.166	3.166	0.000	0.000	0.000	0.000
75	B	81	ASP	-1	-0.941	-0.989	104.852	3.070	3.070	0.000	0.000	0.000	0.000
76	B	82	LEU	0	-0.080	-0.044	107.255	-0.040	-0.040	0.000	0.000	0.000	0.000
77	B	83	ASP	-1	-0.871	-0.923	107.838	2.969	2.969	0.000	0.000	0.000	0.000
78	B	84	ARG	1	0.894	0.949	105.089	-3.090	-3.090	0.000	0.000	0.000	0.000
79	B	85	ALA	0	-0.086	-0.054	110.771	-0.030	-0.030	0.000	0.000	0.000	0.000
80	B	86	LEU	0	-0.005	-0.020	113.092	-0.035	-0.035	0.000	0.000	0.000	0.000
81	B	87	GLU	-1	-0.918	-0.943	112.170	2.889	2.889	0.000	0.000	0.000	0.000
82	B	88	PHE	0	-0.064	-0.038	112.147	-0.018	-0.018	0.000	0.000	0.000	0.000
83	B	89	ALA	0	-0.066	-0.036	117.018	-0.028	-0.028	0.000	0.000	0.000	0.000
84	B	90	GLU	-1	-0.889	-0.934	118.661	2.678	2.678	0.000	0.000	0.000	0.000
85	B	91	ALA	0	-0.072	-0.012	120.236	-0.025	-0.025	0.000	0.000	0.000	0.000
86	B	92	SER	0	-0.035	-0.020	121.191	-0.026	-0.026	0.000	0.000	0.000	0.000
87	B	93	PRO	0	0.083	0.049	121.579	0.022	0.022	0.000	0.000	0.000	0.000
88	B	94	GLU	-1	-0.916	-0.963	121.998	2.611	2.611	0.000	0.000	0.000	0.000
89	B	95	SER	0	-0.089	-0.068	118.368	0.023	0.023	0.000	0.000	0.000	0.000
90	B	96	ILE	0	0.091	0.049	116.098	0.031	0.031	0.000	0.000	0.000	0.000
91	B	97	ARG	1	0.930	0.981	116.485	-2.699	-2.699	0.000	0.000	0.000	0.000
92	B	98	GLN	0	-0.068	-0.051	115.471	0.037	0.037	0.000	0.000	0.000	0.000
93	B	99	GLY	0	0.066	0.045	113.122	0.027	0.027	0.000	0.000	0.000	0.000
94	B	100	VAL	0	0.050	0.026	111.670	0.034	0.034	0.000	0.000	0.000	0.000
95	B	101	ARG	1	0.893	0.933	111.119	-2.805	-2.805	0.000	0.000	0.000	0.000
96	B	102	ALA	0	0.029	0.018	109.499	0.026	0.026	0.000	0.000	0.000	0.000
97	B	103	ILE	0	0.061	0.036	106.761	0.035	0.035	0.000	0.000	0.000	0.000
98	B	104	ARG	1	0.877	0.946	106.172	-2.942	-2.942	0.000	0.000	0.000	0.000
99	B	105	ASP	-1	-0.883	-0.953	105.828	3.025	3.025	0.000	0.000	0.000	0.000
100	B	106	GLY	0	-0.049	-0.027	103.675	0.036	0.036	0.000	0.000	0.000	0.000
101	B	107	PHE	0	0.043	0.006	100.557	0.042	0.042	0.000	0.000	0.000	0.000
102	B	108	PHE	0	-0.010	-0.004	100.689	0.025	0.025	0.000	0.000	0.000	0.000
103	B	109	ARG	1	0.946	0.978	99.367	-3.115	-3.115	0.000	0.000	0.000	0.000
104	B	110	ILE	0	0.017	0.017	96.602	0.042	0.042	0.000	0.000	0.000	0.000
105	B	111	LEU	0	-0.002	-0.014	95.832	0.044	0.044	0.000	0.000	0.000	0.000
106	B	112	ALA	0	0.043	0.026	94.975	0.038	0.038	0.000	0.000	0.000	0.000
107	B	113	GLY	0	-0.029	0.008	93.235	0.045	0.045	0.000	0.000	0.000	0.000
108	B	114	LEU	0	-0.130	-0.062	91.000	0.052	0.052	0.000	0.000	0.000	0.000
109	B	115	GLY	0	-0.013	-0.006	90.505	0.035	0.035	0.000	0.000	0.000	0.000
110	B	116	VAL	0	-0.077	-0.041	91.580	0.012	0.012	0.000	0.000	0.000	0.000
111	B	117	GLU	-1	-0.896	-0.961	94.275	3.390	3.390	0.000	0.000	0.000	0.000
112	B	118	GLU	-1	-0.893	-0.932	96.661	3.107	3.107	0.000	0.000	0.000	0.000
113	B	119	VAL	0	-0.068	-0.035	97.613	0.015	0.015	0.000	0.000	0.000	0.000
114	B	120	PRO	0	0.022	0.022	98.848	-0.029	-0.029	0.000	0.000	0.000	0.000
115	B	121	GLY	0	0.074	0.026	101.787	-0.007	-0.007	0.000	0.000	0.000	0.000
116	B	122	GLU	-1	-0.844	-0.923	105.466	2.865	2.865	0.000	0.000	0.000	0.000
117	B	123	GLY	0	-0.019	-0.001	108.225	0.008	0.008	0.000	0.000	0.000	0.000
118	B	124	GLU	-1	-0.918	-0.959	103.301	3.125	3.125	0.000	0.000	0.000	0.000
119	B	125	ALA	0	-0.039	-0.029	102.294	-0.024	-0.024	0.000	0.000	0.000	0.000
120	B	126	PHE	0	0.012	0.012	102.104	0.021	0.021	0.000	0.000	0.000	0.000
121	B	127	ASP	-1	-0.796	-0.903	97.255	3.338	3.338	0.000	0.000	0.000	0.000
122	B	128	PRO	0	-0.012	-0.005	97.558	-0.006	-0.006	0.000	0.000	0.000	0.000
123	B	129	ARG	1	0.842	0.931	92.063	-3.400	-3.400	0.000	0.000	0.000	0.000
124	B	130	TYR	0	0.012	-0.032	93.451	0.022	0.022	0.000	0.000	0.000	0.000
125	B	131	HIS	0	-0.070	-0.037	98.614	-0.025	-0.025	0.000	0.000	0.000	0.000
126	B	132	GLU	-1	-0.888	-0.938	101.780	3.097	3.097	0.000	0.000	0.000	0.000
127	B	133	ALA	0	-0.019	-0.015	104.041	-0.026	-0.026	0.000	0.000	0.000	0.000
128	B	134	VAL	0	-0.017	-0.017	107.202	-0.002	-0.002	0.000	0.000	0.000	0.000
129	B	135	GLY	0	-0.026	-0.016	110.013	-0.025	-0.025	0.000	0.000	0.000	0.000
130	B	136	LEU	0	-0.040	-0.006	112.185	0.024	0.024	0.000	0.000	0.000	0.000
131	B	137	LEU	0	0.010	-0.012	114.644	-0.021	-0.021	0.000	0.000	0.000	0.000
132	B	138	PRO	0	-0.011	0.013	115.627	0.021	0.021	0.000	0.000	0.000	0.000
133	B	139	GLY	0	0.042	0.012	114.703	0.012	0.012	0.000	0.000	0.000	0.000
134	B	140	GLU	-1	-0.962	-0.976	110.863	2.919	2.919	0.000	0.000	0.000	0.000
135	B	141	PRO	0	0.045	0.032	111.476	0.014	0.014	0.000	0.000	0.000	0.000
136	B	142	GLY	0	-0.021	-0.014	107.964	0.022	0.022	0.000	0.000	0.000	0.000
137	B	143	LYS	1	0.906	0.958	105.371	-2.993	-2.993	0.000	0.000	0.000	0.000
138	B	144	VAL	0	-0.002	0.013	105.521	-0.029	-0.029	0.000	0.000	0.000	0.000
139	B	145	ALA	0	0.017	0.007	108.376	-0.007	-0.007	0.000	0.000	0.000	0.000
140	B	146	LYS	1	0.824	0.884	111.246	-2.836	-2.836	0.000	0.000	0.000	0.000
141	B	147	VAL	0	0.036	0.026	106.819	0.018	0.018	0.000	0.000	0.000	0.000
142	B	148	PHE	0	-0.050	-0.023	109.491	-0.017	-0.017	0.000	0.000	0.000	0.000
143	B	149	GLN	0	-0.068	-0.043	104.657	0.018	0.018	0.000	0.000	0.000	0.000
144	B	150	ARG	1	0.871	0.927	103.980	-3.024	-3.024	0.000	0.000	0.000	0.000
145	B	151	GLY	0	0.056	0.032	101.365	0.002	0.002	0.000	0.000	0.000	0.000
146	B	152	PHE	0	-0.032	-0.009	97.497	-0.014	-0.014	0.000	0.000	0.000	0.000
147	B	153	ARG	1	0.924	0.966	91.731	-3.442	-3.442	0.000	0.000	0.000	0.000
148	B	154	MET	0	-0.001	0.014	88.721	-0.009	-0.009	0.000	0.000	0.000	0.000
149	B	155	GLY	0	-0.019	-0.019	88.871	0.040	0.040	0.000	0.000	0.000	0.000
150	B	156	GLU	-1	-0.899	-0.936	85.640	3.644	3.644	0.000	0.000	0.000	0.000
151	B	157	ALA	0	-0.028	-0.003	88.413	-0.028	-0.028	0.000	0.000	0.000	0.000
152	B	158	LEU	0	0.014	-0.003	90.069	-0.024	-0.024	0.000	0.000	0.000	0.000
153	B	159	VAL	0	-0.059	-0.020	93.758	0.005	0.005	0.000	0.000	0.000	0.000
154	B	160	ARG	1	0.905	0.941	95.196	-3.150	-3.150	0.000	0.000	0.000	0.000
155	B	161	PRO	0	0.045	0.040	98.353	0.005	0.005	0.000	0.000	0.000	0.000
156	B	162	ALA	0	0.012	0.003	100.332	-0.022	-0.022	0.000	0.000	0.000	0.000
157	B	163	ARG	1	0.947	0.986	103.682	-2.977	-2.977	0.000	0.000	0.000	0.000
158	B	164	VAL	0	-0.011	-0.018	105.935	-0.020	-0.020	0.000	0.000	0.000	0.000
159	B	165	ALA	0	0.011	0.025	108.336	-0.003	-0.003	0.000	0.000	0.000	0.000
160	B	166	VAL	0	0.001	-0.005	107.863	0.012	0.012	0.000	0.000	0.000	0.000
161	B	167	GLY	0	0.037	0.025	110.630	-0.027	-0.027	0.000	0.000	0.000	0.000
162	B	168	GLU	-1	-0.947	-0.980	112.749	2.739	2.739	0.000	0.000	0.000	0.000
163	B	169	GLU	-1	-0.949	-0.981	113.017	2.843	2.843	0.000	0.000	0.000	0.000
164	B	170	LYS	1	0.932	0.965	115.441	-2.670	-2.670	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:7:GLU)