FMO DATABASE

FMODB ID: 5J5MZ

Calculation Name: 3GL3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GL3

Chain ID: A

ChEMBL ID:

UniProt ID: Q8KDH8

Base Structure: X-ray

Registration Date: 2023-09-23

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	141
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1287733.538382
FMO2-HF: Nuclear repulsion	1233545.436341
FMO2-HF: Total energy	-54188.102041
FMO2-MP2: Total energy	-54345.402635

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:28:SER)

Summations of interaction energy for fragment #1(A:28:SER)

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.
-19.778	-16.497	2.439	-1.914	-3.802	0.016

Interaction energy analysis for fragmet #1(A:28:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.026

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	30	ASP	-1	-0.853	-0.917	3.797	-5.001	-2.943	-0.024	-0.938	-1.095	0.004
4	A	31	LYS	1	0.838	0.895	6.479	1.645	1.645	0.000	0.000	0.000	0.000
5	A	32	GLY	0	0.008	0.006	9.878	-0.015	-0.015	0.000	0.000	0.000	0.000
6	A	33	ASP	-1	-0.813	-0.901	6.258	-5.411	-5.411	0.000	0.000	0.000	0.000
7	A	34	LYS	1	0.803	0.905	9.704	1.525	1.525	0.000	0.000	0.000	0.000
8	A	35	ALA	0	0.039	0.016	8.431	-0.460	-0.460	0.000	0.000	0.000	0.000
9	A	36	PRO	0	0.010	0.005	6.186	0.389	0.389	0.000	0.000	0.000	0.000
10	A	37	ASP	-1	-0.788	-0.858	9.352	-0.267	-0.267	0.000	0.000	0.000	0.000
11	A	38	PHE	0	-0.034	-0.030	11.676	0.079	0.079	0.000	0.000	0.000	0.000
12	A	39	ALA	0	0.028	0.011	14.370	-0.020	-0.020	0.000	0.000	0.000	0.000
13	A	40	LEU	0	-0.050	-0.014	14.579	0.046	0.046	0.000	0.000	0.000	0.000
14	A	41	PRO	0	0.026	0.020	18.730	-0.032	-0.032	0.000	0.000	0.000	0.000
15	A	42	GLY	0	0.053	0.015	21.324	0.013	0.013	0.000	0.000	0.000	0.000
16	A	43	LYS	1	0.905	0.955	23.595	0.006	0.006	0.000	0.000	0.000	0.000
17	A	44	THR	0	-0.017	-0.010	26.874	0.004	0.004	0.000	0.000	0.000	0.000
18	A	45	GLY	0	0.082	0.031	26.386	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	46	VAL	0	-0.042	-0.005	21.597	0.017	0.017	0.000	0.000	0.000	0.000
20	A	47	VAL	0	-0.025	-0.013	18.655	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	48	LYS	1	0.901	0.930	17.867	0.226	0.226	0.000	0.000	0.000	0.000
22	A	49	LEU	0	-0.029	0.014	12.463	0.001	0.001	0.000	0.000	0.000	0.000
23	A	50	SER	0	-0.010	-0.042	16.291	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	51	ASP	-1	-0.855	-0.910	18.142	-0.214	-0.214	0.000	0.000	0.000	0.000
25	A	52	LYS	1	0.786	0.878	18.325	0.219	0.219	0.000	0.000	0.000	0.000
26	A	53	THR	0	0.030	0.026	18.278	-0.032	-0.032	0.000	0.000	0.000	0.000
27	A	54	GLY	0	0.001	0.007	20.032	0.049	0.049	0.000	0.000	0.000	0.000
28	A	55	SER	0	-0.057	-0.036	21.112	0.039	0.039	0.000	0.000	0.000	0.000
29	A	56	VAL	0	-0.012	0.006	18.631	-0.047	-0.047	0.000	0.000	0.000	0.000
30	A	57	VAL	0	-0.023	-0.028	15.621	0.070	0.070	0.000	0.000	0.000	0.000
31	A	58	TYR	0	-0.001	-0.010	15.827	-0.080	-0.080	0.000	0.000	0.000	0.000
32	A	59	LEU	0	-0.018	-0.011	10.367	0.053	0.053	0.000	0.000	0.000	0.000
33	A	60	ASP	-1	-0.820	-0.940	13.160	0.240	0.240	0.000	0.000	0.000	0.000
34	A	61	PHE	0	-0.017	0.003	9.245	0.072	0.072	0.000	0.000	0.000	0.000
35	A	62	TRP	0	-0.022	-0.023	13.749	0.065	0.065	0.000	0.000	0.000	0.000
36	A	63	ALA	0	0.016	-0.010	17.046	0.018	0.018	0.000	0.000	0.000	0.000
37	A	64	SER	0	-0.043	-0.056	19.629	-0.020	-0.020	0.000	0.000	0.000	0.000
38	A	65	TRP	0	0.009	0.004	17.688	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	66	CYS	0	-0.041	-0.005	17.929	0.004	0.004	0.000	0.000	0.000	0.000
40	A	67	GLY	0	0.085	0.039	21.379	-0.033	-0.033	0.000	0.000	0.000	0.000
41	A	68	PRO	0	0.030	0.001	19.579	-0.035	-0.035	0.000	0.000	0.000	0.000
42	A	69	CYS	0	0.041	0.039	18.819	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	70	ARG	1	0.912	0.970	21.511	-0.155	-0.155	0.000	0.000	0.000	0.000
44	A	71	GLN	0	-0.026	-0.026	23.593	-0.023	-0.023	0.000	0.000	0.000	0.000
45	A	72	SER	0	0.031	0.006	19.658	-0.025	-0.025	0.000	0.000	0.000	0.000
46	A	73	PHE	0	0.052	0.020	20.471	-0.037	-0.037	0.000	0.000	0.000	0.000
47	A	74	PRO	0	-0.018	-0.005	24.173	-0.022	-0.022	0.000	0.000	0.000	0.000
48	A	75	TRP	0	0.039	0.012	19.310	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	76	MET	0	0.002	0.008	19.616	-0.035	-0.035	0.000	0.000	0.000	0.000
50	A	77	ASN	0	-0.001	-0.001	23.250	-0.029	-0.029	0.000	0.000	0.000	0.000
51	A	78	GLN	0	-0.005	0.005	26.722	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	79	MET	0	-0.031	-0.013	22.440	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	80	GLN	0	-0.037	-0.028	23.977	-0.025	-0.025	0.000	0.000	0.000	0.000
54	A	81	ALA	0	-0.003	-0.010	25.838	-0.014	-0.014	0.000	0.000	0.000	0.000
55	A	82	LYS	1	0.821	0.905	27.971	0.102	0.102	0.000	0.000	0.000	0.000
56	A	83	TYR	0	-0.002	-0.044	25.099	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	84	LYS	1	0.958	0.998	26.556	0.079	0.079	0.000	0.000	0.000	0.000
58	A	85	ALA	0	-0.022	-0.011	27.596	-0.014	-0.014	0.000	0.000	0.000	0.000
59	A	86	LYS	1	0.961	0.991	27.240	0.201	0.201	0.000	0.000	0.000	0.000
60	A	87	GLY	0	0.014	0.021	25.790	-0.028	-0.028	0.000	0.000	0.000	0.000
61	A	88	PHE	0	0.026	0.014	19.762	-0.035	-0.035	0.000	0.000	0.000	0.000
62	A	89	GLN	0	0.014	0.008	20.990	0.059	0.059	0.000	0.000	0.000	0.000
63	A	90	VAL	0	0.029	0.030	19.285	-0.037	-0.037	0.000	0.000	0.000	0.000
64	A	91	VAL	0	-0.033	-0.026	16.530	0.015	0.015	0.000	0.000	0.000	0.000
65	A	92	ALA	0	0.028	0.014	16.471	0.005	0.005	0.000	0.000	0.000	0.000
66	A	93	VAL	0	0.007	0.003	13.603	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	94	ASN	0	-0.055	-0.049	15.894	0.088	0.088	0.000	0.000	0.000	0.000
68	A	95	LEU	0	0.005	-0.016	12.633	0.032	0.032	0.000	0.000	0.000	0.000
69	A	96	ASP	-1	-0.759	-0.831	17.068	0.385	0.385	0.000	0.000	0.000	0.000
70	A	97	ALA	0	0.013	0.002	20.632	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	98	LYS	1	0.887	0.934	21.786	-0.266	-0.266	0.000	0.000	0.000	0.000
72	A	99	THR	0	0.073	0.023	22.323	0.000	0.000	0.000	0.000	0.000	0.000
73	A	100	GLY	0	0.034	0.024	24.433	-0.015	-0.015	0.000	0.000	0.000	0.000
74	A	101	ASP	-1	-0.798	-0.896	25.760	0.219	0.219	0.000	0.000	0.000	0.000
75	A	102	ALA	0	0.031	0.036	22.974	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	103	MET	0	-0.020	-0.032	24.867	-0.020	-0.020	0.000	0.000	0.000	0.000
77	A	104	LYS	1	0.869	0.936	27.901	-0.205	-0.205	0.000	0.000	0.000	0.000
78	A	105	PHE	0	0.025	0.012	24.543	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	106	LEU	0	-0.007	-0.027	24.181	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	107	ALA	0	-0.038	0.006	28.017	-0.015	-0.015	0.000	0.000	0.000	0.000
81	A	108	GLN	0	-0.060	-0.028	30.829	0.000	0.000	0.000	0.000	0.000	0.000
82	A	109	VAL	0	-0.095	-0.040	26.753	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	110	PRO	0	0.033	0.026	28.334	0.002	0.002	0.000	0.000	0.000	0.000
84	A	111	ALA	0	0.048	0.027	24.789	0.007	0.007	0.000	0.000	0.000	0.000
85	A	112	GLU	-1	-0.965	-0.982	26.700	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	113	PHE	0	0.015	-0.011	21.902	-0.024	-0.024	0.000	0.000	0.000	0.000
87	A	114	THR	0	-0.054	-0.017	20.732	0.013	0.013	0.000	0.000	0.000	0.000
88	A	115	VAL	0	0.005	0.008	20.674	0.001	0.001	0.000	0.000	0.000	0.000
89	A	116	ALA	0	-0.005	0.002	17.590	-0.019	-0.019	0.000	0.000	0.000	0.000
90	A	117	PHE	0	-0.010	-0.005	19.108	0.037	0.037	0.000	0.000	0.000	0.000
91	A	118	ASP	-1	-0.729	-0.850	13.699	0.419	0.419	0.000	0.000	0.000	0.000
92	A	119	PRO	0	0.023	0.018	16.575	0.079	0.079	0.000	0.000	0.000	0.000
93	A	120	LYS	1	0.887	0.949	16.930	-0.235	-0.235	0.000	0.000	0.000	0.000
94	A	121	GLY	0	0.040	0.022	13.990	0.096	0.096	0.000	0.000	0.000	0.000
95	A	122	GLN	0	-0.023	-0.025	12.021	0.168	0.168	0.000	0.000	0.000	0.000
96	A	123	THR	0	0.017	-0.030	9.834	0.139	0.139	0.000	0.000	0.000	0.000
97	A	124	PRO	0	0.026	0.019	7.921	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	125	ARG	1	0.875	0.936	6.428	-0.459	-0.459	0.000	0.000	0.000	0.000
99	A	126	LEU	0	-0.006	0.005	4.881	1.154	1.235	-0.001	-0.002	-0.077	0.000
100	A	127	TYR	0	-0.005	-0.035	4.119	-1.736	-1.619	0.000	-0.064	-0.053	0.000
101	A	128	GLY	0	0.024	0.033	2.494	0.433	1.039	2.227	-1.512	-1.321	0.006
102	A	129	VAL	0	-0.033	-0.015	3.299	-0.973	-1.930	0.064	1.299	-0.405	0.002
103	A	130	LYS	1	0.879	0.923	2.723	-11.493	-10.222	0.174	-0.692	-0.752	0.004
104	A	131	GLY	0	0.020	0.015	8.303	-0.345	-0.345	0.000	0.000	0.000	0.000
105	A	132	MET	0	-0.040	0.041	11.582	0.018	0.018	0.000	0.000	0.000	0.000
106	A	133	PRO	0	0.011	-0.010	14.524	-0.054	-0.054	0.000	0.000	0.000	0.000
107	A	134	THR	0	-0.009	-0.031	8.195	0.161	0.161	0.000	0.000	0.000	0.000
108	A	135	SER	0	0.004	0.019	11.684	-0.062	-0.062	0.000	0.000	0.000	0.000
109	A	136	PHE	0	-0.009	-0.012	5.763	-0.027	-0.027	0.000	0.000	0.000	0.000
110	A	137	LEU	0	-0.015	0.020	11.346	0.089	0.089	0.000	0.000	0.000	0.000
111	A	138	ILE	0	-0.015	-0.015	11.330	-0.198	-0.198	0.000	0.000	0.000	0.000
112	A	139	ASP	-1	-0.749	-0.878	14.191	-0.725	-0.725	0.000	0.000	0.000	0.000
113	A	140	ARG	1	0.884	0.946	16.981	0.347	0.347	0.000	0.000	0.000	0.000
114	A	141	ASN	0	-0.043	-0.023	17.630	0.080	0.080	0.000	0.000	0.000	0.000
115	A	142	GLY	0	-0.022	-0.009	14.974	-0.051	-0.051	0.000	0.000	0.000	0.000
116	A	143	LYS	1	0.888	0.938	12.101	1.322	1.322	0.000	0.000	0.000	0.000
117	A	144	VAL	0	-0.004	0.002	7.520	0.375	0.375	0.000	0.000	0.000	0.000
118	A	145	LEU	0	0.042	0.023	10.837	-0.065	-0.065	0.000	0.000	0.000	0.000
119	A	146	LEU	0	-0.052	-0.028	10.537	0.020	0.020	0.000	0.000	0.000	0.000
120	A	147	GLN	0	0.031	0.023	4.713	-0.775	-0.670	-0.001	-0.005	-0.099	0.000
121	A	148	HIS	0	-0.055	-0.024	8.968	0.015	0.015	0.000	0.000	0.000	0.000
122	A	149	VAL	0	0.017	0.003	9.365	0.122	0.122	0.000	0.000	0.000	0.000
123	A	150	GLY	0	-0.005	0.002	11.929	-0.076	-0.076	0.000	0.000	0.000	0.000
124	A	151	PHE	0	-0.026	-0.024	15.402	-0.071	-0.071	0.000	0.000	0.000	0.000
125	A	152	ARG	1	0.978	0.993	17.293	-0.141	-0.141	0.000	0.000	0.000	0.000
126	A	153	PRO	0	-0.008	-0.012	21.749	-0.027	-0.027	0.000	0.000	0.000	0.000
127	A	154	ALA	0	0.016	0.008	22.825	-0.019	-0.019	0.000	0.000	0.000	0.000
128	A	155	ASP	-1	-0.805	-0.911	18.401	0.115	0.115	0.000	0.000	0.000	0.000
129	A	156	LYS	1	0.904	0.953	20.594	-0.074	-0.074	0.000	0.000	0.000	0.000
130	A	157	GLU	-1	-0.900	-0.935	22.730	-0.095	-0.095	0.000	0.000	0.000	0.000
131	A	158	ALA	0	0.050	0.020	19.691	-0.026	-0.026	0.000	0.000	0.000	0.000
132	A	159	LEU	0	-0.016	-0.012	15.831	-0.052	-0.052	0.000	0.000	0.000	0.000
133	A	160	GLU	-1	-0.753	-0.849	19.350	-0.152	-0.152	0.000	0.000	0.000	0.000
134	A	161	GLN	0	0.011	0.014	22.221	-0.034	-0.034	0.000	0.000	0.000	0.000
135	A	162	GLN	0	-0.013	-0.002	16.428	-0.074	-0.074	0.000	0.000	0.000	0.000
136	A	163	ILE	0	-0.037	-0.014	19.144	-0.045	-0.045	0.000	0.000	0.000	0.000
137	A	164	LEU	0	-0.006	-0.006	20.671	-0.019	-0.019	0.000	0.000	0.000	0.000
138	A	165	ALA	0	0.018	0.010	21.107	-0.005	-0.005	0.000	0.000	0.000	0.000
139	A	166	ALA	0	-0.007	0.002	18.892	-0.016	-0.016	0.000	0.000	0.000	0.000
140	A	167	LEU	0	-0.109	-0.049	20.907	-0.008	-0.008	0.000	0.000	0.000	0.000
141	A	168	GLY	0	-0.078	-0.029	24.158	0.050	0.050	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:28:SER)