FMO DATABASE

FMODB ID: 9GRY2

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	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	164
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1150316.637559
FMO2-HF: Nuclear repulsion	1086736.164387
FMO2-HF: Total energy	-63580.473172
FMO2-MP2: Total energy	-63768.867011

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.
25.889	30.884	12	-8.78	-8.214	-0.073

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 : -0.941 / q_NPA : -0.975

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	-0.080	-0.048	2.926	-14.103	-10.389	0.093	-1.976	-1.831	0.010
4	B	10	LEU	0	0.001	0.018	2.473	-3.351	-2.279	0.505	-0.550	-1.027	0.000
5	B	11	GLU	-1	-0.792	-0.897	1.963	25.189	25.309	11.403	-6.250	-5.272	-0.083
6	B	12	LYS	1	0.837	0.917	5.378	-44.104	-44.015	-0.001	-0.004	-0.084	0.000
7	B	13	ASP	-1	-0.902	-0.958	6.528	25.282	25.282	0.000	0.000	0.000	0.000
8	B	14	LEU	0	-0.012	-0.009	7.819	-2.316	-2.316	0.000	0.000	0.000	0.000
9	B	15	GLU	-1	-0.915	-0.966	8.422	26.748	26.748	0.000	0.000	0.000	0.000
10	B	16	ALA	0	-0.021	-0.001	11.434	-1.353	-1.353	0.000	0.000	0.000	0.000
11	B	17	VAL	0	0.026	0.010	13.720	-1.084	-1.084	0.000	0.000	0.000	0.000
12	B	18	GLY	0	0.005	0.005	14.721	-0.914	-0.914	0.000	0.000	0.000	0.000
13	B	19	GLN	0	-0.015	-0.011	16.423	-1.283	-1.283	0.000	0.000	0.000	0.000
14	B	20	GLU	-1	-0.908	-0.953	18.479	12.564	12.564	0.000	0.000	0.000	0.000
15	B	21	ALA	0	0.002	-0.008	19.786	-0.757	-0.757	0.000	0.000	0.000	0.000
16	B	22	GLN	0	-0.010	-0.001	19.924	0.038	0.038	0.000	0.000	0.000	0.000
17	B	23	ALA	0	0.035	0.016	22.041	-0.485	-0.485	0.000	0.000	0.000	0.000
18	B	24	LEU	0	-0.052	-0.029	24.237	-0.534	-0.534	0.000	0.000	0.000	0.000
19	B	25	GLU	-1	-0.858	-0.931	25.709	9.509	9.509	0.000	0.000	0.000	0.000
20	B	26	GLU	-1	-0.919	-0.941	27.325	10.234	10.234	0.000	0.000	0.000	0.000
21	B	27	ARG	1	0.823	0.910	24.154	-11.525	-11.525	0.000	0.000	0.000	0.000
22	B	28	LEU	0	-0.021	-0.003	30.260	-0.349	-0.349	0.000	0.000	0.000	0.000
23	B	29	LYS	1	0.830	0.906	30.960	-9.762	-9.762	0.000	0.000	0.000	0.000
24	B	30	ALA	0	0.117	0.050	32.558	-0.251	-0.251	0.000	0.000	0.000	0.000
25	B	31	ALA	0	-0.048	-0.017	34.482	-0.294	-0.294	0.000	0.000	0.000	0.000
26	B	32	GLU	-1	-0.899	-0.959	35.270	8.056	8.056	0.000	0.000	0.000	0.000
27	B	33	GLU	-1	-0.920	-0.941	36.809	8.224	8.224	0.000	0.000	0.000	0.000
28	B	34	GLU	-1	-0.794	-0.898	38.663	6.852	6.852	0.000	0.000	0.000	0.000
29	B	35	LEU	0	-0.021	-0.014	40.095	-0.276	-0.276	0.000	0.000	0.000	0.000
30	B	36	LYS	1	0.822	0.905	38.541	-8.010	-8.010	0.000	0.000	0.000	0.000
31	B	37	GLY	0	0.055	0.027	43.201	-0.158	-0.158	0.000	0.000	0.000	0.000
32	B	38	LEU	0	-0.056	-0.031	44.523	-0.178	-0.178	0.000	0.000	0.000	0.000
33	B	39	LYS	1	0.884	0.923	46.417	-6.657	-6.657	0.000	0.000	0.000	0.000
34	B	40	ASP	-1	-0.800	-0.890	48.654	6.209	6.209	0.000	0.000	0.000	0.000
35	B	41	LYS	1	0.771	0.881	45.019	-7.000	-7.000	0.000	0.000	0.000	0.000
36	B	42	TYR	0	0.024	0.027	51.090	-0.115	-0.115	0.000	0.000	0.000	0.000
37	B	43	LEU	0	0.016	0.007	52.794	-0.123	-0.123	0.000	0.000	0.000	0.000
38	B	44	ARG	1	0.915	0.961	53.510	-5.937	-5.937	0.000	0.000	0.000	0.000
39	B	45	LEU	0	0.058	0.041	55.125	-0.093	-0.093	0.000	0.000	0.000	0.000
40	B	46	LEU	0	-0.021	-0.013	56.792	-0.106	-0.106	0.000	0.000	0.000	0.000
41	B	47	ALA	0	0.011	-0.002	58.701	-0.108	-0.108	0.000	0.000	0.000	0.000
42	B	48	ASP	-1	-0.899	-0.952	60.106	5.098	5.098	0.000	0.000	0.000	0.000
43	B	49	PHE	0	-0.035	-0.033	60.656	-0.108	-0.108	0.000	0.000	0.000	0.000
44	B	50	ASP	-1	-0.837	-0.920	62.830	4.741	4.741	0.000	0.000	0.000	0.000
45	B	51	ASN	0	-0.002	0.014	64.594	-0.132	-0.132	0.000	0.000	0.000	0.000
46	B	52	TYR	0	0.042	0.001	66.229	-0.080	-0.080	0.000	0.000	0.000	0.000
47	B	53	ARG	1	0.836	0.929	62.524	-4.947	-4.947	0.000	0.000	0.000	0.000
48	B	54	LYS	1	0.834	0.915	66.423	-4.735	-4.735	0.000	0.000	0.000	0.000
49	B	55	ARG	1	0.848	0.927	68.748	-4.594	-4.594	0.000	0.000	0.000	0.000
50	B	56	MET	0	-0.008	-0.013	71.359	-0.042	-0.042	0.000	0.000	0.000	0.000
51	B	57	GLU	-1	-0.909	-0.936	74.012	3.982	3.982	0.000	0.000	0.000	0.000
52	B	58	GLU	-1	-0.929	-0.963	76.537	3.915	3.915	0.000	0.000	0.000	0.000
53	B	59	GLU	-1	-0.877	-0.938	73.544	4.268	4.268	0.000	0.000	0.000	0.000
54	B	60	LEU	0	-0.021	-0.012	76.743	-0.046	-0.046	0.000	0.000	0.000	0.000
55	B	61	LYS	1	0.856	0.908	79.321	-3.751	-3.751	0.000	0.000	0.000	0.000
56	B	62	ALA	0	0.003	-0.004	80.040	-0.061	-0.061	0.000	0.000	0.000	0.000
57	B	63	ARG	1	0.879	0.917	77.997	-4.089	-4.089	0.000	0.000	0.000	0.000
58	B	64	GLU	-1	-0.815	-0.880	81.738	3.637	3.637	0.000	0.000	0.000	0.000
59	B	65	ARG	1	0.957	0.970	84.935	-3.727	-3.727	0.000	0.000	0.000	0.000
60	B	66	GLU	-1	-0.890	-0.912	81.022	3.926	3.926	0.000	0.000	0.000	0.000
61	B	67	GLY	0	0.019	0.011	85.213	-0.027	-0.027	0.000	0.000	0.000	0.000
62	B	68	VAL	0	-0.001	-0.006	86.873	-0.042	-0.042	0.000	0.000	0.000	0.000
63	B	69	LEU	0	-0.004	-0.011	87.545	-0.042	-0.042	0.000	0.000	0.000	0.000
64	B	70	LYS	1	0.916	0.965	85.829	-3.734	-3.734	0.000	0.000	0.000	0.000
65	B	71	ALA	0	0.018	0.008	89.296	-0.026	-0.026	0.000	0.000	0.000	0.000
66	B	72	LEU	0	0.007	-0.006	92.412	-0.034	-0.034	0.000	0.000	0.000	0.000
67	B	73	ARG	1	0.926	0.959	86.803	-3.681	-3.681	0.000	0.000	0.000	0.000
68	B	74	ALA	0	0.005	0.012	92.855	-0.019	-0.019	0.000	0.000	0.000	0.000
69	B	75	LEU	0	-0.006	-0.010	94.695	-0.032	-0.032	0.000	0.000	0.000	0.000
70	B	76	LEU	0	-0.017	-0.001	96.056	-0.036	-0.036	0.000	0.000	0.000	0.000
71	B	77	PRO	0	0.054	0.026	97.984	-0.035	-0.035	0.000	0.000	0.000	0.000
72	B	78	VAL	0	-0.014	-0.004	100.985	-0.035	-0.035	0.000	0.000	0.000	0.000
73	B	79	LEU	0	-0.017	-0.008	102.862	-0.034	-0.034	0.000	0.000	0.000	0.000
74	B	80	ASP	-1	-0.879	-0.935	101.359	3.163	3.163	0.000	0.000	0.000	0.000
75	B	81	ASP	-1	-0.866	-0.933	104.761	3.068	3.068	0.000	0.000	0.000	0.000
76	B	82	LEU	0	-0.078	-0.043	106.605	-0.038	-0.038	0.000	0.000	0.000	0.000
77	B	83	ASP	-1	-0.869	-0.928	108.078	2.956	2.956	0.000	0.000	0.000	0.000
78	B	84	ARG	1	0.839	0.913	104.543	-3.092	-3.092	0.000	0.000	0.000	0.000
79	B	85	ALA	0	-0.054	-0.032	110.520	-0.030	-0.030	0.000	0.000	0.000	0.000
80	B	86	LEU	0	-0.011	-0.010	112.765	-0.037	-0.037	0.000	0.000	0.000	0.000
81	B	87	GLU	-1	-0.912	-0.952	111.278	2.898	2.898	0.000	0.000	0.000	0.000
82	B	88	PHE	0	-0.087	-0.054	111.263	-0.018	-0.018	0.000	0.000	0.000	0.000
83	B	89	ALA	0	-0.043	-0.024	116.496	-0.028	-0.028	0.000	0.000	0.000	0.000
84	B	90	GLU	-1	-0.921	-0.956	118.278	2.684	2.684	0.000	0.000	0.000	0.000
85	B	91	ALA	0	-0.068	-0.019	119.526	-0.025	-0.025	0.000	0.000	0.000	0.000
86	B	92	SER	0	-0.059	-0.052	120.736	-0.023	-0.023	0.000	0.000	0.000	0.000
87	B	93	PRO	0	0.068	0.056	120.827	0.025	0.025	0.000	0.000	0.000	0.000
88	B	94	GLU	-1	-0.883	-0.932	121.195	2.633	2.633	0.000	0.000	0.000	0.000
89	B	95	SER	0	-0.054	-0.041	117.520	0.023	0.023	0.000	0.000	0.000	0.000
90	B	96	ILE	0	0.069	0.044	115.134	0.031	0.031	0.000	0.000	0.000	0.000
91	B	97	ARG	1	0.868	0.925	115.742	-2.692	-2.692	0.000	0.000	0.000	0.000
92	B	98	GLN	0	-0.009	-0.007	115.190	0.008	0.008	0.000	0.000	0.000	0.000
93	B	99	GLY	0	0.068	0.036	112.340	0.029	0.029	0.000	0.000	0.000	0.000
94	B	100	VAL	0	0.051	0.014	110.999	0.032	0.032	0.000	0.000	0.000	0.000
95	B	101	ARG	1	0.885	0.956	110.517	-2.811	-2.811	0.000	0.000	0.000	0.000
96	B	102	ALA	0	0.027	0.009	108.787	0.028	0.028	0.000	0.000	0.000	0.000
97	B	103	ILE	0	0.049	0.037	106.327	0.035	0.035	0.000	0.000	0.000	0.000
98	B	104	ARG	1	0.812	0.890	105.529	-2.934	-2.934	0.000	0.000	0.000	0.000
99	B	105	ASP	-1	-0.791	-0.887	105.121	3.026	3.026	0.000	0.000	0.000	0.000
100	B	106	GLY	0	-0.012	0.016	102.869	0.034	0.034	0.000	0.000	0.000	0.000
101	B	107	PHE	0	0.033	0.014	100.367	0.042	0.042	0.000	0.000	0.000	0.000
102	B	108	PHE	0	-0.021	-0.015	100.127	0.030	0.030	0.000	0.000	0.000	0.000
103	B	109	ARG	1	0.884	0.924	98.826	-3.116	-3.116	0.000	0.000	0.000	0.000
104	B	110	ILE	0	0.022	0.019	96.343	0.043	0.043	0.000	0.000	0.000	0.000
105	B	111	LEU	0	-0.040	-0.019	95.363	0.043	0.043	0.000	0.000	0.000	0.000
106	B	112	ALA	0	0.044	0.023	94.460	0.038	0.038	0.000	0.000	0.000	0.000
107	B	113	GLY	0	-0.025	-0.006	92.694	0.042	0.042	0.000	0.000	0.000	0.000
108	B	114	LEU	0	-0.090	-0.049	90.894	0.055	0.055	0.000	0.000	0.000	0.000
109	B	115	GLY	0	-0.033	0.003	89.677	0.043	0.043	0.000	0.000	0.000	0.000
110	B	116	VAL	0	-0.077	-0.050	90.736	0.014	0.014	0.000	0.000	0.000	0.000
111	B	117	GLU	-1	-0.807	-0.874	92.719	3.429	3.429	0.000	0.000	0.000	0.000
112	B	118	GLU	-1	-0.850	-0.921	96.151	3.103	3.103	0.000	0.000	0.000	0.000
113	B	119	VAL	0	-0.049	-0.019	97.383	0.023	0.023	0.000	0.000	0.000	0.000
114	B	120	PRO	0	0.024	0.016	98.425	-0.026	-0.026	0.000	0.000	0.000	0.000
115	B	121	GLY	0	0.058	0.027	101.303	-0.009	-0.009	0.000	0.000	0.000	0.000
116	B	122	GLU	-1	-0.844	-0.928	104.990	2.863	2.863	0.000	0.000	0.000	0.000
117	B	123	GLY	0	-0.016	0.004	108.105	0.005	0.005	0.000	0.000	0.000	0.000
118	B	124	GLU	-1	-0.911	-0.956	102.839	3.142	3.142	0.000	0.000	0.000	0.000
119	B	125	ALA	0	-0.003	-0.007	101.841	-0.026	-0.026	0.000	0.000	0.000	0.000
120	B	126	PHE	0	-0.005	-0.012	102.368	0.018	0.018	0.000	0.000	0.000	0.000
121	B	127	ASP	-1	-0.788	-0.888	96.735	3.349	3.349	0.000	0.000	0.000	0.000
122	B	128	PRO	0	-0.005	-0.001	97.511	0.001	0.001	0.000	0.000	0.000	0.000
123	B	129	ARG	1	0.813	0.900	91.444	-3.396	-3.396	0.000	0.000	0.000	0.000
124	B	130	TYR	0	0.015	-0.013	92.844	0.024	0.024	0.000	0.000	0.000	0.000
125	B	131	HIS	0	-0.045	-0.012	98.161	-0.028	-0.028	0.000	0.000	0.000	0.000
126	B	132	GLU	-1	-0.829	-0.915	101.471	3.093	3.093	0.000	0.000	0.000	0.000
127	B	133	ALA	0	0.010	0.001	103.740	-0.028	-0.028	0.000	0.000	0.000	0.000
128	B	134	VAL	0	-0.044	-0.029	106.721	0.001	0.001	0.000	0.000	0.000	0.000
129	B	135	GLY	0	-0.014	-0.007	109.738	-0.029	-0.029	0.000	0.000	0.000	0.000
130	B	136	LEU	0	-0.041	-0.008	111.711	0.025	0.025	0.000	0.000	0.000	0.000
131	B	137	LEU	0	0.010	-0.002	114.243	-0.021	-0.021	0.000	0.000	0.000	0.000
132	B	138	PRO	0	-0.021	-0.005	115.431	0.021	0.021	0.000	0.000	0.000	0.000
133	B	139	GLY	0	0.033	0.008	113.968	0.009	0.009	0.000	0.000	0.000	0.000
134	B	140	GLU	-1	-0.870	-0.926	110.790	2.912	2.912	0.000	0.000	0.000	0.000
135	B	141	PRO	0	0.031	0.023	111.110	0.016	0.016	0.000	0.000	0.000	0.000
136	B	142	GLY	0	-0.008	-0.006	107.366	0.022	0.022	0.000	0.000	0.000	0.000
137	B	143	LYS	1	0.827	0.919	106.081	-2.937	-2.937	0.000	0.000	0.000	0.000
138	B	144	VAL	0	-0.025	-0.002	105.408	-0.030	-0.030	0.000	0.000	0.000	0.000
139	B	145	ALA	0	0.025	0.018	108.398	-0.008	-0.008	0.000	0.000	0.000	0.000
140	B	146	LYS	1	0.807	0.875	111.262	-2.848	-2.848	0.000	0.000	0.000	0.000
141	B	147	VAL	0	0.025	0.020	106.395	0.018	0.018	0.000	0.000	0.000	0.000
142	B	148	PHE	0	-0.026	-0.007	109.089	-0.015	-0.015	0.000	0.000	0.000	0.000
143	B	149	GLN	0	-0.070	-0.040	104.724	0.017	0.017	0.000	0.000	0.000	0.000
144	B	150	ARG	1	0.890	0.938	103.798	-3.022	-3.022	0.000	0.000	0.000	0.000
145	B	151	GLY	0	0.080	0.049	100.999	0.002	0.002	0.000	0.000	0.000	0.000
146	B	152	PHE	0	-0.038	-0.023	97.081	-0.014	-0.014	0.000	0.000	0.000	0.000
147	B	153	ARG	1	0.812	0.885	92.373	-3.421	-3.421	0.000	0.000	0.000	0.000
148	B	154	MET	0	0.018	0.012	87.476	-0.005	-0.005	0.000	0.000	0.000	0.000
149	B	155	GLY	0	0.021	0.010	88.624	0.046	0.046	0.000	0.000	0.000	0.000
150	B	156	GLU	-1	-0.903	-0.947	85.915	3.605	3.605	0.000	0.000	0.000	0.000
151	B	157	ALA	0	-0.046	-0.018	87.836	-0.028	-0.028	0.000	0.000	0.000	0.000
152	B	158	LEU	0	-0.009	-0.005	89.739	-0.024	-0.024	0.000	0.000	0.000	0.000
153	B	159	VAL	0	-0.029	-0.011	93.113	0.009	0.009	0.000	0.000	0.000	0.000
154	B	160	ARG	1	0.854	0.913	94.788	-3.161	-3.161	0.000	0.000	0.000	0.000
155	B	161	PRO	0	0.056	0.038	98.042	0.005	0.005	0.000	0.000	0.000	0.000
156	B	162	ALA	0	-0.005	-0.007	99.969	-0.018	-0.018	0.000	0.000	0.000	0.000
157	B	163	ARG	1	0.843	0.931	103.265	-3.006	-3.006	0.000	0.000	0.000	0.000
158	B	164	VAL	0	-0.029	-0.023	105.565	-0.020	-0.020	0.000	0.000	0.000	0.000
159	B	165	ALA	0	0.017	0.018	108.150	-0.007	-0.007	0.000	0.000	0.000	0.000
160	B	166	VAL	0	-0.008	-0.006	107.351	0.017	0.017	0.000	0.000	0.000	0.000
161	B	167	GLY	0	0.030	0.011	110.244	-0.028	-0.028	0.000	0.000	0.000	0.000
162	B	168	GLU	-1	-0.911	-0.968	112.488	2.734	2.734	0.000	0.000	0.000	0.000
163	B	169	GLU	-1	-0.922	-0.959	112.187	2.863	2.863	0.000	0.000	0.000	0.000
164	B	170	LYS	1	0.914	0.959	115.501	-2.664	-2.664	0.000	0.000	0.000	0.000

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