FMO DATABASE

FMODB ID: 529ZZ

Calculation Name: 5GL6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GL6

Chain ID: A

ChEMBL ID:

UniProt ID: A0QVM3

Base Structure: X-ray

Registration Date: 2023-06-21

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	169
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1472354.225521
FMO2-HF: Nuclear repulsion	1409712.309836
FMO2-HF: Total energy	-62641.915686
FMO2-MP2: Total energy	-62828.053939

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:12:ASP)

Summations of interaction energy for fragment #1(A:12:ASP)

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.
66.254	60.49	22.934	-10.933	-6.235	0.068

Interaction energy analysis for fragmet #1(A:12:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.846 / q_NPA : -0.894

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	14	PRO	0	-0.006	0.014	3.851	-5.661	-3.128	-0.002	-1.466	-1.065	0.009
4	A	15	SER	0	-0.010	-0.049	6.715	-0.206	-0.206	0.000	0.000	0.000	0.000
5	A	16	GLN	0	-0.014	-0.026	8.295	-1.788	-1.788	0.000	0.000	0.000	0.000
6	A	17	LYS	1	0.784	0.873	11.438	-20.430	-20.430	0.000	0.000	0.000	0.000
7	A	18	GLN	0	0.065	0.060	7.125	0.575	0.575	0.000	0.000	0.000	0.000
8	A	19	VAL	0	0.016	0.011	10.074	-1.028	-1.028	0.000	0.000	0.000	0.000
9	A	20	ILE	0	0.042	0.017	12.857	-1.157	-1.157	0.000	0.000	0.000	0.000
10	A	21	GLU	-1	-0.833	-0.906	14.311	17.624	17.624	0.000	0.000	0.000	0.000
11	A	22	LEU	0	-0.059	-0.010	12.213	-0.801	-0.801	0.000	0.000	0.000	0.000
12	A	23	LEU	0	-0.015	-0.004	15.380	-0.622	-0.622	0.000	0.000	0.000	0.000
13	A	24	ASP	-1	-0.912	-0.952	18.474	12.773	12.773	0.000	0.000	0.000	0.000
14	A	25	GLY	0	0.030	0.012	21.274	-0.626	-0.626	0.000	0.000	0.000	0.000
15	A	26	GLU	-1	-0.848	-0.897	20.421	12.181	12.181	0.000	0.000	0.000	0.000
16	A	27	PHE	0	0.022	-0.012	19.723	-0.328	-0.328	0.000	0.000	0.000	0.000
17	A	28	ALA	0	0.057	0.043	24.079	-0.530	-0.530	0.000	0.000	0.000	0.000
18	A	29	ARG	1	0.723	0.830	24.209	-12.335	-12.335	0.000	0.000	0.000	0.000
19	A	30	ALA	0	-0.044	-0.023	26.243	-0.399	-0.399	0.000	0.000	0.000	0.000
20	A	31	GLY	0	-0.048	-0.014	28.099	-0.233	-0.233	0.000	0.000	0.000	0.000
21	A	32	TYR	0	-0.066	-0.045	25.936	-0.253	-0.253	0.000	0.000	0.000	0.000
22	A	33	GLU	-1	-0.920	-0.957	25.233	11.477	11.477	0.000	0.000	0.000	0.000
23	A	34	ILE	0	-0.022	-0.029	18.634	0.359	0.359	0.000	0.000	0.000	0.000
24	A	35	ASP	-1	-0.875	-0.916	22.005	13.120	13.120	0.000	0.000	0.000	0.000
25	A	36	ASP	-1	-0.768	-0.863	17.452	17.513	17.513	0.000	0.000	0.000	0.000
26	A	37	VAL	0	0.011	0.001	12.661	0.249	0.249	0.000	0.000	0.000	0.000
27	A	38	VAL	0	-0.035	-0.003	11.933	0.640	0.640	0.000	0.000	0.000	0.000
28	A	39	VAL	0	0.026	0.017	6.144	-0.350	-0.350	0.000	0.000	0.000	0.000
29	A	40	ASN	0	-0.001	-0.004	7.850	4.077	4.077	0.000	0.000	0.000	0.000
30	A	41	ALA	0	0.061	0.024	4.519	-0.249	-0.115	-0.001	-0.010	-0.123	0.000
31	A	42	ALA	0	-0.052	-0.012	6.234	0.744	0.744	0.000	0.000	0.000	0.000
32	A	43	THR	0	-0.077	-0.061	9.154	-3.777	-3.777	0.000	0.000	0.000	0.000
33	A	44	ARG	1	0.940	0.990	9.457	-18.910	-18.910	0.000	0.000	0.000	0.000
34	A	45	PRO	0	-0.008	-0.016	9.850	-2.824	-2.824	0.000	0.000	0.000	0.000
35	A	46	ALA	0	0.076	0.064	6.482	-2.147	-2.147	0.000	0.000	0.000	0.000
36	A	47	ARG	1	0.752	0.832	8.507	-23.777	-23.777	0.000	0.000	0.000	0.000
37	A	48	ILE	0	0.033	0.026	8.256	0.982	0.982	0.000	0.000	0.000	0.000
38	A	49	THR	0	-0.037	-0.046	11.168	-1.169	-1.169	0.000	0.000	0.000	0.000
39	A	50	ILE	0	-0.011	-0.011	14.280	0.300	0.300	0.000	0.000	0.000	0.000
40	A	51	VAL	0	-0.016	-0.003	16.966	-0.688	-0.688	0.000	0.000	0.000	0.000
41	A	52	ALA	0	0.017	-0.003	20.133	-0.023	-0.023	0.000	0.000	0.000	0.000
42	A	53	ASP	-1	-0.821	-0.935	22.812	10.918	10.918	0.000	0.000	0.000	0.000
43	A	54	GLY	0	0.054	0.020	26.639	0.155	0.155	0.000	0.000	0.000	0.000
44	A	55	ASP	-1	-0.934	-0.957	29.978	9.272	9.272	0.000	0.000	0.000	0.000
45	A	56	LYS	1	0.840	0.912	32.780	-9.008	-9.008	0.000	0.000	0.000	0.000
46	A	57	GLY	0	0.018	0.034	30.320	-0.111	-0.111	0.000	0.000	0.000	0.000
47	A	58	LEU	0	-0.026	-0.014	24.315	0.069	0.069	0.000	0.000	0.000	0.000
48	A	59	ASP	-1	-0.873	-0.927	28.740	10.163	10.163	0.000	0.000	0.000	0.000
49	A	60	LEU	0	0.021	-0.015	28.514	0.361	0.361	0.000	0.000	0.000	0.000
50	A	61	ASP	-1	-0.923	-0.949	28.096	10.407	10.407	0.000	0.000	0.000	0.000
51	A	62	ALA	0	0.009	0.006	28.279	0.351	0.351	0.000	0.000	0.000	0.000
52	A	63	VAL	0	0.026	0.018	23.224	0.476	0.476	0.000	0.000	0.000	0.000
53	A	64	ALA	0	0.031	0.023	23.588	0.710	0.710	0.000	0.000	0.000	0.000
54	A	65	MET	0	-0.101	-0.020	24.421	0.517	0.517	0.000	0.000	0.000	0.000
55	A	66	LEU	0	0.069	0.025	22.153	0.387	0.387	0.000	0.000	0.000	0.000
56	A	67	SER	0	-0.016	-0.019	19.749	0.984	0.984	0.000	0.000	0.000	0.000
57	A	68	ARG	1	0.835	0.912	19.487	-11.310	-11.310	0.000	0.000	0.000	0.000
58	A	69	LEU	0	-0.022	0.007	20.329	0.347	0.347	0.000	0.000	0.000	0.000
59	A	70	ALA	0	0.048	0.009	16.615	0.419	0.419	0.000	0.000	0.000	0.000
60	A	71	SER	0	-0.026	-0.031	15.326	0.793	0.793	0.000	0.000	0.000	0.000
61	A	72	GLY	0	-0.008	0.000	15.454	0.665	0.665	0.000	0.000	0.000	0.000
62	A	73	LEU	0	0.000	0.000	16.130	-0.032	-0.032	0.000	0.000	0.000	0.000
63	A	74	LEU	0	-0.009	-0.001	10.747	0.637	0.637	0.000	0.000	0.000	0.000
64	A	75	ASP	-1	-0.850	-0.901	10.991	23.532	23.532	0.000	0.000	0.000	0.000
65	A	76	THR	0	-0.157	-0.084	12.578	-0.556	-0.556	0.000	0.000	0.000	0.000
66	A	77	VAL	0	-0.079	-0.037	7.214	-0.529	-0.529	0.000	0.000	0.000	0.000
67	A	78	ASP	-1	-0.882	-0.946	6.109	31.943	31.943	0.000	0.000	0.000	0.000
68	A	79	THR	0	-0.035	-0.017	4.075	0.784	0.950	0.000	-0.047	-0.118	0.000
69	A	80	GLY	0	-0.024	-0.010	3.224	9.038	10.043	0.084	-0.519	-0.570	-0.004
70	A	81	ASP	-1	-0.961	-0.985	4.954	31.438	31.426	-0.001	-0.004	0.018	0.000
71	A	82	THR	0	-0.073	-0.054	1.580	-27.199	-36.763	22.855	-8.866	-4.426	0.063
72	A	83	PRO	0	-0.052	-0.009	4.751	-4.950	-4.976	-0.001	-0.021	0.049	0.000
73	A	84	TYR	0	-0.037	-0.059	7.623	2.724	2.724	0.000	0.000	0.000	0.000
74	A	85	VAL	0	-0.035	-0.017	9.178	-3.242	-3.242	0.000	0.000	0.000	0.000
75	A	86	LEU	0	-0.001	0.012	12.034	1.420	1.420	0.000	0.000	0.000	0.000
76	A	87	GLU	-1	-0.815	-0.852	14.387	17.196	17.196	0.000	0.000	0.000	0.000
77	A	88	VAL	0	0.011	0.008	16.770	0.576	0.576	0.000	0.000	0.000	0.000
78	A	89	THR	0	-0.050	-0.028	19.570	-0.720	-0.720	0.000	0.000	0.000	0.000
79	A	90	SER	0	0.042	0.029	22.142	0.099	0.099	0.000	0.000	0.000	0.000
80	A	91	PRO	0	0.047	0.028	23.696	0.530	0.530	0.000	0.000	0.000	0.000
81	A	92	GLY	0	-0.013	0.009	24.980	-0.281	-0.281	0.000	0.000	0.000	0.000
82	A	93	VAL	0	-0.008	-0.013	26.468	-0.263	-0.263	0.000	0.000	0.000	0.000
83	A	94	ASP	-1	-0.756	-0.849	28.991	10.859	10.859	0.000	0.000	0.000	0.000
84	A	95	ARG	1	0.785	0.873	30.290	-10.314	-10.314	0.000	0.000	0.000	0.000
85	A	96	PRO	0	0.060	0.032	34.553	0.082	0.082	0.000	0.000	0.000	0.000
86	A	97	LEU	0	-0.070	-0.034	35.393	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	98	THR	0	0.019	0.002	39.227	-0.094	-0.094	0.000	0.000	0.000	0.000
88	A	99	THR	0	-0.001	-0.020	42.483	-0.195	-0.195	0.000	0.000	0.000	0.000
89	A	100	GLU	-1	-0.652	-0.796	42.247	7.479	7.479	0.000	0.000	0.000	0.000
90	A	101	LYS	1	0.961	0.973	41.878	-7.172	-7.172	0.000	0.000	0.000	0.000
91	A	102	HIS	0	-0.004	0.014	39.081	0.123	0.123	0.000	0.000	0.000	0.000
92	A	103	PHE	0	0.105	0.045	37.648	0.232	0.232	0.000	0.000	0.000	0.000
93	A	104	ARG	1	0.835	0.914	36.969	-7.218	-7.218	0.000	0.000	0.000	0.000
94	A	105	ARG	1	0.888	0.947	34.985	-8.864	-8.864	0.000	0.000	0.000	0.000
95	A	106	ALA	0	-0.006	-0.015	33.059	0.246	0.246	0.000	0.000	0.000	0.000
96	A	107	ARG	1	0.882	0.968	32.500	-8.780	-8.780	0.000	0.000	0.000	0.000
97	A	108	GLY	0	0.028	0.022	29.573	0.130	0.130	0.000	0.000	0.000	0.000
98	A	109	ARG	1	0.737	0.862	26.577	-11.154	-11.154	0.000	0.000	0.000	0.000
99	A	110	LYS	1	0.886	0.955	23.882	-13.131	-13.131	0.000	0.000	0.000	0.000
100	A	111	ALA	0	-0.014	-0.017	28.458	-0.075	-0.075	0.000	0.000	0.000	0.000
101	A	112	GLU	-1	-0.810	-0.874	31.732	9.060	9.060	0.000	0.000	0.000	0.000
102	A	113	LEU	0	-0.016	-0.013	33.785	-0.192	-0.192	0.000	0.000	0.000	0.000
103	A	114	SER	0	0.014	-0.004	37.451	0.057	0.057	0.000	0.000	0.000	0.000
104	A	115	LEU	0	0.005	0.008	40.562	-0.039	-0.039	0.000	0.000	0.000	0.000
105	A	116	ALA	0	-0.015	-0.020	43.542	-0.072	-0.072	0.000	0.000	0.000	0.000
106	A	117	ASP	-1	-0.860	-0.899	45.172	6.999	6.999	0.000	0.000	0.000	0.000
107	A	118	GLY	0	-0.019	-0.002	45.463	-0.076	-0.076	0.000	0.000	0.000	0.000
108	A	119	SER	0	-0.083	-0.050	41.790	0.201	0.201	0.000	0.000	0.000	0.000
109	A	120	SER	0	0.008	-0.016	37.681	0.003	0.003	0.000	0.000	0.000	0.000
110	A	121	LEU	0	-0.032	-0.013	35.177	0.004	0.004	0.000	0.000	0.000	0.000
111	A	122	THR	0	0.021	0.019	29.180	0.088	0.088	0.000	0.000	0.000	0.000
112	A	123	ALA	0	-0.037	-0.020	31.473	-0.038	-0.038	0.000	0.000	0.000	0.000
113	A	124	ARG	1	0.720	0.828	24.826	-11.936	-11.936	0.000	0.000	0.000	0.000
114	A	125	LEU	0	-0.011	-0.003	30.706	-0.383	-0.383	0.000	0.000	0.000	0.000
115	A	126	GLY	0	0.080	0.023	32.752	0.285	0.285	0.000	0.000	0.000	0.000
116	A	127	GLY	0	-0.010	-0.005	35.124	-0.050	-0.050	0.000	0.000	0.000	0.000
117	A	128	THR	0	-0.053	-0.050	37.991	-0.065	-0.065	0.000	0.000	0.000	0.000
118	A	129	ASP	-1	-0.912	-0.958	41.498	7.209	7.209	0.000	0.000	0.000	0.000
119	A	130	GLY	0	0.046	0.033	44.310	-0.060	-0.060	0.000	0.000	0.000	0.000
120	A	131	ASP	-1	-0.856	-0.905	47.413	6.539	6.539	0.000	0.000	0.000	0.000
121	A	132	GLN	0	-0.017	-0.019	43.940	0.122	0.122	0.000	0.000	0.000	0.000
122	A	133	VAL	0	-0.046	-0.028	38.304	0.044	0.044	0.000	0.000	0.000	0.000
123	A	134	ASN	0	-0.007	-0.003	37.740	-0.057	-0.057	0.000	0.000	0.000	0.000
124	A	135	VAL	0	-0.024	-0.003	35.246	0.164	0.164	0.000	0.000	0.000	0.000
125	A	136	VAL	0	0.009	0.007	31.062	-0.167	-0.167	0.000	0.000	0.000	0.000
126	A	137	VAL	0	0.031	0.016	31.294	0.196	0.196	0.000	0.000	0.000	0.000
127	A	138	ALA	0	0.061	0.026	28.004	-0.107	-0.107	0.000	0.000	0.000	0.000
128	A	139	GLN	0	-0.021	-0.019	30.024	-0.466	-0.466	0.000	0.000	0.000	0.000
129	A	140	GLY	0	0.026	0.018	29.794	-0.114	-0.114	0.000	0.000	0.000	0.000
130	A	141	LYS	1	0.928	0.958	25.212	-11.357	-11.357	0.000	0.000	0.000	0.000
131	A	142	ASP	-1	-0.854	-0.906	27.688	10.548	10.548	0.000	0.000	0.000	0.000
132	A	143	PHE	0	0.007	-0.003	26.017	0.172	0.172	0.000	0.000	0.000	0.000
133	A	144	ALA	0	-0.018	0.003	32.019	-0.267	-0.267	0.000	0.000	0.000	0.000
134	A	145	VAL	0	0.004	0.004	34.667	0.155	0.155	0.000	0.000	0.000	0.000
135	A	146	ARG	1	0.928	0.967	36.615	-8.423	-8.423	0.000	0.000	0.000	0.000
136	A	147	GLN	0	-0.048	-0.041	39.176	-0.007	-0.007	0.000	0.000	0.000	0.000
137	A	148	ILE	0	0.030	0.014	39.312	-0.066	-0.066	0.000	0.000	0.000	0.000
138	A	149	PRO	0	0.019	0.022	42.967	0.070	0.070	0.000	0.000	0.000	0.000
139	A	150	LEU	0	0.009	-0.013	42.622	0.050	0.050	0.000	0.000	0.000	0.000
140	A	151	ARG	1	0.773	0.872	45.460	-6.363	-6.363	0.000	0.000	0.000	0.000
141	A	152	GLU	-1	-0.855	-0.930	46.358	6.507	6.507	0.000	0.000	0.000	0.000
142	A	153	ILE	0	-0.023	0.000	40.465	0.133	0.133	0.000	0.000	0.000	0.000
143	A	154	THR	0	-0.028	-0.015	43.633	-0.028	-0.028	0.000	0.000	0.000	0.000
144	A	155	LYS	1	0.815	0.888	36.003	-8.720	-8.720	0.000	0.000	0.000	0.000
145	A	156	ALA	0	0.006	0.002	37.741	0.085	0.085	0.000	0.000	0.000	0.000
146	A	157	VAL	0	-0.011	-0.006	32.982	-0.151	-0.151	0.000	0.000	0.000	0.000
147	A	158	VAL	0	-0.028	-0.009	29.749	0.136	0.136	0.000	0.000	0.000	0.000
148	A	159	GLN	0	0.033	0.008	27.798	0.222	0.222	0.000	0.000	0.000	0.000
149	A	160	VAL	0	-0.017	0.004	23.177	0.113	0.113	0.000	0.000	0.000	0.000
150	A	161	GLU	-1	-0.758	-0.865	22.071	12.419	12.419	0.000	0.000	0.000	0.000
151	A	162	PHE	0	0.003	0.007	17.683	-0.116	-0.116	0.000	0.000	0.000	0.000
152	A	163	SER	0	0.000	-0.037	16.092	1.576	1.576	0.000	0.000	0.000	0.000
153	A	164	PRO	0	-0.073	-0.031	15.751	-0.986	-0.986	0.000	0.000	0.000	0.000
154	A	165	PRO	0	0.021	0.003	18.718	-0.124	-0.124	0.000	0.000	0.000	0.000
155	A	166	ASN	0	0.035	0.021	21.240	0.196	0.196	0.000	0.000	0.000	0.000
156	A	167	ARG	1	0.855	0.885	21.585	-13.000	-13.000	0.000	0.000	0.000	0.000
157	A	168	ARG	1	0.858	0.912	23.395	-11.389	-11.389	0.000	0.000	0.000	0.000
158	A	169	GLU	-1	-0.833	-0.894	26.071	11.372	11.372	0.000	0.000	0.000	0.000
159	A	170	LEU	0	0.011	0.003	24.187	-0.406	-0.406	0.000	0.000	0.000	0.000
160	A	171	GLU	-1	-0.809	-0.867	27.283	10.876	10.876	0.000	0.000	0.000	0.000
161	A	172	LEU	0	-0.035	-0.021	29.102	-0.426	-0.426	0.000	0.000	0.000	0.000
162	A	173	ALA	0	-0.012	0.002	30.251	-0.372	-0.372	0.000	0.000	0.000	0.000
163	A	174	GLU	-1	-0.901	-0.986	28.550	10.847	10.847	0.000	0.000	0.000	0.000
164	A	175	GLN	0	-0.088	-0.033	31.508	-0.021	-0.021	0.000	0.000	0.000	0.000
165	A	176	THR	0	0.009	0.019	34.533	-0.379	-0.379	0.000	0.000	0.000	0.000
166	A	177	GLY	0	0.040	0.025	37.217	0.106	0.106	0.000	0.000	0.000	0.000
167	A	178	LYS	1	0.813	0.897	39.468	-7.210	-7.210	0.000	0.000	0.000	0.000
168	A	179	GLY	0	0.039	0.008	36.946	0.047	0.047	0.000	0.000	0.000	0.000
169	A	180	ALA	0	-0.040	-0.003	36.968	0.130	0.130	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:12:ASP)