FMO DATABASE

FMODB ID: YVR32

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1291770.131049
FMO2-HF: Nuclear repulsion	1237581.770731
FMO2-HF: Total energy	-54188.360317
FMO2-MP2: Total energy	-54345.681903

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.
-33.627	-36.508	14.887	-5.968	-6.036	0.041

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 : -0.002 / q_NPA : 0.002

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	-0.824	-0.915	3.796	-1.331	0.153	-0.010	-0.597	-0.877	0.002
4	A	31	LYS	1	0.832	0.897	5.992	1.020	1.020	0.000	0.000	0.000	0.000
5	A	32	GLY	0	0.024	0.009	9.545	0.283	0.283	0.000	0.000	0.000	0.000
6	A	33	ASP	-1	-0.838	-0.895	6.437	-5.207	-5.207	0.000	0.000	0.000	0.000
7	A	34	LYS	1	0.808	0.911	9.860	1.665	1.665	0.000	0.000	0.000	0.000
8	A	35	ALA	0	0.053	0.026	9.080	-0.446	-0.446	0.000	0.000	0.000	0.000
9	A	36	PRO	0	0.015	0.005	7.362	0.464	0.464	0.000	0.000	0.000	0.000
10	A	37	ASP	-1	-0.767	-0.848	10.486	-0.461	-0.461	0.000	0.000	0.000	0.000
11	A	38	PHE	0	-0.038	-0.028	12.513	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	39	ALA	0	0.020	0.009	15.361	0.028	0.028	0.000	0.000	0.000	0.000
13	A	40	LEU	0	-0.052	-0.009	15.160	0.031	0.031	0.000	0.000	0.000	0.000
14	A	41	PRO	0	0.023	0.020	19.421	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	42	GLY	0	0.076	0.017	21.473	0.009	0.009	0.000	0.000	0.000	0.000
16	A	43	LYS	1	0.872	0.942	23.668	0.068	0.068	0.000	0.000	0.000	0.000
17	A	44	THR	0	-0.005	0.003	26.894	0.009	0.009	0.000	0.000	0.000	0.000
18	A	45	GLY	0	0.021	0.020	26.951	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	46	VAL	0	-0.031	-0.011	22.329	0.008	0.008	0.000	0.000	0.000	0.000
20	A	47	VAL	0	-0.021	-0.009	19.214	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	48	LYS	1	0.844	0.907	18.250	0.341	0.341	0.000	0.000	0.000	0.000
22	A	49	LEU	0	-0.019	-0.006	13.009	0.042	0.042	0.000	0.000	0.000	0.000
23	A	50	SER	0	0.007	-0.034	16.985	0.023	0.023	0.000	0.000	0.000	0.000
24	A	51	ASP	-1	-0.840	-0.899	19.304	-0.326	-0.326	0.000	0.000	0.000	0.000
25	A	52	LYS	1	0.799	0.892	18.659	0.328	0.328	0.000	0.000	0.000	0.000
26	A	53	THR	0	0.021	0.007	19.073	0.001	0.001	0.000	0.000	0.000	0.000
27	A	54	GLY	0	0.009	0.014	20.898	0.050	0.050	0.000	0.000	0.000	0.000
28	A	55	SER	0	-0.052	-0.024	21.205	0.051	0.051	0.000	0.000	0.000	0.000
29	A	56	VAL	0	-0.007	0.011	18.382	-0.054	-0.054	0.000	0.000	0.000	0.000
30	A	57	VAL	0	-0.016	-0.022	15.554	0.063	0.063	0.000	0.000	0.000	0.000
31	A	58	TYR	0	-0.004	-0.016	15.459	-0.057	-0.057	0.000	0.000	0.000	0.000
32	A	59	LEU	0	0.003	0.016	10.118	0.051	0.051	0.000	0.000	0.000	0.000
33	A	60	ASP	-1	-0.815	-0.913	12.980	0.291	0.291	0.000	0.000	0.000	0.000
34	A	61	PHE	0	-0.001	-0.003	8.765	0.003	0.003	0.000	0.000	0.000	0.000
35	A	62	TRP	0	-0.025	-0.029	13.064	0.137	0.137	0.000	0.000	0.000	0.000
36	A	63	ALA	0	0.007	-0.014	16.374	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	64	SER	0	-0.044	-0.059	19.126	0.005	0.005	0.000	0.000	0.000	0.000
38	A	65	TRP	0	0.020	0.010	16.789	0.001	0.001	0.000	0.000	0.000	0.000
39	A	66	CYS	0	-0.038	0.000	17.213	0.039	0.039	0.000	0.000	0.000	0.000
40	A	67	GLY	0	0.064	0.023	20.417	-0.026	-0.026	0.000	0.000	0.000	0.000
41	A	68	PRO	0	0.020	-0.001	18.902	-0.042	-0.042	0.000	0.000	0.000	0.000
42	A	69	CYS	0	0.043	0.039	17.642	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	70	ARG	1	0.898	0.971	20.426	-0.180	-0.180	0.000	0.000	0.000	0.000
44	A	71	GLN	0	-0.020	-0.021	22.924	-0.025	-0.025	0.000	0.000	0.000	0.000
45	A	72	SER	0	0.020	0.012	18.670	-0.026	-0.026	0.000	0.000	0.000	0.000
46	A	73	PHE	0	0.055	0.019	19.729	-0.040	-0.040	0.000	0.000	0.000	0.000
47	A	74	PRO	0	0.003	-0.004	23.199	-0.026	-0.026	0.000	0.000	0.000	0.000
48	A	75	TRP	0	0.018	0.006	18.777	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	76	MET	0	0.003	0.010	18.827	-0.035	-0.035	0.000	0.000	0.000	0.000
50	A	77	ASN	0	-0.003	-0.005	22.556	-0.040	-0.040	0.000	0.000	0.000	0.000
51	A	78	GLN	0	-0.010	0.004	26.125	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	79	MET	0	-0.014	-0.002	22.020	-0.023	-0.023	0.000	0.000	0.000	0.000
53	A	80	GLN	0	-0.046	-0.033	23.652	-0.032	-0.032	0.000	0.000	0.000	0.000
54	A	81	ALA	0	-0.018	-0.021	25.313	-0.016	-0.016	0.000	0.000	0.000	0.000
55	A	82	LYS	1	0.830	0.912	27.731	0.045	0.045	0.000	0.000	0.000	0.000
56	A	83	TYR	0	0.003	-0.036	24.909	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	84	LYS	1	0.918	0.979	26.437	0.088	0.088	0.000	0.000	0.000	0.000
58	A	85	ALA	0	0.012	0.006	27.432	-0.016	-0.016	0.000	0.000	0.000	0.000
59	A	86	LYS	1	0.908	0.974	26.850	0.175	0.175	0.000	0.000	0.000	0.000
60	A	87	GLY	0	0.031	0.027	25.947	-0.027	-0.027	0.000	0.000	0.000	0.000
61	A	88	PHE	0	0.027	0.006	19.435	-0.031	-0.031	0.000	0.000	0.000	0.000
62	A	89	GLN	0	-0.001	-0.003	20.862	0.046	0.046	0.000	0.000	0.000	0.000
63	A	90	VAL	0	0.036	0.026	18.918	-0.040	-0.040	0.000	0.000	0.000	0.000
64	A	91	VAL	0	-0.038	-0.037	16.307	0.000	0.000	0.000	0.000	0.000	0.000
65	A	92	ALA	0	0.057	0.037	16.030	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	93	VAL	0	0.001	-0.001	13.837	0.000	0.000	0.000	0.000	0.000	0.000
67	A	94	ASN	0	-0.034	-0.032	15.431	0.083	0.083	0.000	0.000	0.000	0.000
68	A	95	LEU	0	0.005	-0.012	12.188	-0.021	-0.021	0.000	0.000	0.000	0.000
69	A	96	ASP	-1	-0.738	-0.824	16.779	0.313	0.313	0.000	0.000	0.000	0.000
70	A	97	ALA	0	0.001	-0.008	20.336	-0.033	-0.033	0.000	0.000	0.000	0.000
71	A	98	LYS	1	0.893	0.929	21.556	-0.197	-0.197	0.000	0.000	0.000	0.000
72	A	99	THR	0	0.066	0.026	22.594	0.010	0.010	0.000	0.000	0.000	0.000
73	A	100	GLY	0	0.048	0.029	24.639	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	101	ASP	-1	-0.829	-0.898	25.451	0.157	0.157	0.000	0.000	0.000	0.000
75	A	102	ALA	0	0.029	0.026	22.676	0.002	0.002	0.000	0.000	0.000	0.000
76	A	103	MET	0	0.000	-0.008	24.465	-0.013	-0.013	0.000	0.000	0.000	0.000
77	A	104	LYS	1	0.871	0.930	27.636	-0.149	-0.149	0.000	0.000	0.000	0.000
78	A	105	PHE	0	0.026	0.009	23.502	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	106	LEU	0	0.004	-0.015	23.954	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	107	ALA	0	-0.037	-0.004	27.578	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	108	GLN	0	-0.059	-0.026	30.045	0.004	0.004	0.000	0.000	0.000	0.000
82	A	109	VAL	0	-0.107	-0.048	25.643	0.008	0.008	0.000	0.000	0.000	0.000
83	A	110	PRO	0	0.027	0.024	27.697	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	111	ALA	0	0.064	0.032	24.592	0.012	0.012	0.000	0.000	0.000	0.000
85	A	112	GLU	-1	-0.915	-0.947	26.292	-0.016	-0.016	0.000	0.000	0.000	0.000
86	A	113	PHE	0	-0.014	-0.024	21.728	-0.023	-0.023	0.000	0.000	0.000	0.000
87	A	114	THR	0	-0.037	-0.010	20.655	0.003	0.003	0.000	0.000	0.000	0.000
88	A	115	VAL	0	-0.017	-0.006	20.512	0.006	0.006	0.000	0.000	0.000	0.000
89	A	116	ALA	0	0.008	0.002	18.184	-0.016	-0.016	0.000	0.000	0.000	0.000
90	A	117	PHE	0	-0.009	-0.011	19.054	0.038	0.038	0.000	0.000	0.000	0.000
91	A	118	ASP	-1	-0.745	-0.856	14.147	-0.053	-0.053	0.000	0.000	0.000	0.000
92	A	119	PRO	0	0.005	0.010	16.560	0.061	0.061	0.000	0.000	0.000	0.000
93	A	120	LYS	1	0.905	0.957	17.117	0.085	0.085	0.000	0.000	0.000	0.000
94	A	121	GLY	0	0.055	0.027	13.689	0.061	0.061	0.000	0.000	0.000	0.000
95	A	122	GLN	0	-0.011	-0.004	12.120	0.123	0.123	0.000	0.000	0.000	0.000
96	A	123	THR	0	0.031	-0.018	10.342	-0.040	-0.040	0.000	0.000	0.000	0.000
97	A	124	PRO	0	0.010	0.011	8.334	-0.252	-0.252	0.000	0.000	0.000	0.000
98	A	125	ARG	1	0.849	0.915	6.550	-0.212	-0.212	0.000	0.000	0.000	0.000
99	A	126	LEU	0	-0.004	-0.001	5.729	-0.065	-0.065	0.000	0.000	0.000	0.000
100	A	127	TYR	0	0.007	-0.025	5.029	-1.278	-1.278	0.000	0.000	0.000	0.000
101	A	128	GLY	0	0.008	0.021	2.086	-2.205	-1.800	2.823	-1.963	-1.264	-0.003
102	A	129	VAL	0	-0.014	-0.009	3.097	5.080	4.697	0.023	0.827	-0.467	-0.001
103	A	130	LYS	1	0.827	0.882	1.953	-32.352	-36.895	12.052	-4.226	-3.283	0.043
104	A	131	GLY	0	0.028	0.020	7.838	-0.356	-0.356	0.000	0.000	0.000	0.000
105	A	132	MET	0	-0.045	0.021	11.159	-0.053	-0.053	0.000	0.000	0.000	0.000
106	A	133	PRO	0	0.029	-0.009	13.964	-0.048	-0.048	0.000	0.000	0.000	0.000
107	A	134	THR	0	-0.041	-0.025	7.429	0.383	0.383	0.000	0.000	0.000	0.000
108	A	135	SER	0	-0.022	-0.027	10.916	-0.126	-0.126	0.000	0.000	0.000	0.000
109	A	136	PHE	0	-0.010	-0.009	5.126	0.118	0.118	0.000	0.000	0.000	0.000
110	A	137	LEU	0	-0.014	0.014	10.860	0.006	0.006	0.000	0.000	0.000	0.000
111	A	138	ILE	0	-0.010	-0.008	11.135	-0.177	-0.177	0.000	0.000	0.000	0.000
112	A	139	ASP	-1	-0.734	-0.869	14.067	-0.687	-0.687	0.000	0.000	0.000	0.000
113	A	140	ARG	1	0.852	0.944	17.001	0.323	0.323	0.000	0.000	0.000	0.000
114	A	141	ASN	0	-0.061	-0.043	18.135	0.056	0.056	0.000	0.000	0.000	0.000
115	A	142	GLY	0	-0.015	-0.002	15.525	-0.061	-0.061	0.000	0.000	0.000	0.000
116	A	143	LYS	1	0.879	0.925	12.648	1.204	1.204	0.000	0.000	0.000	0.000
117	A	144	VAL	0	0.001	0.002	7.278	0.376	0.376	0.000	0.000	0.000	0.000
118	A	145	LEU	0	0.024	0.014	10.488	-0.014	-0.014	0.000	0.000	0.000	0.000
119	A	146	LEU	0	-0.066	-0.031	9.862	0.099	0.099	0.000	0.000	0.000	0.000
120	A	147	GLN	0	0.018	0.010	4.380	0.094	0.250	-0.001	-0.009	-0.145	0.000
121	A	148	HIS	0	-0.049	-0.016	8.563	0.122	0.122	0.000	0.000	0.000	0.000
122	A	149	VAL	0	0.018	-0.001	9.051	0.090	0.090	0.000	0.000	0.000	0.000
123	A	150	GLY	0	0.013	0.019	11.800	-0.085	-0.085	0.000	0.000	0.000	0.000
124	A	151	PHE	0	-0.024	-0.025	15.217	-0.078	-0.078	0.000	0.000	0.000	0.000
125	A	152	ARG	1	0.932	0.970	16.870	-0.430	-0.430	0.000	0.000	0.000	0.000
126	A	153	PRO	0	-0.004	-0.017	21.663	-0.022	-0.022	0.000	0.000	0.000	0.000
127	A	154	ALA	0	0.034	0.014	22.767	-0.023	-0.023	0.000	0.000	0.000	0.000
128	A	155	ASP	-1	-0.776	-0.888	18.334	0.360	0.360	0.000	0.000	0.000	0.000
129	A	156	LYS	1	0.900	0.961	20.238	-0.154	-0.154	0.000	0.000	0.000	0.000
130	A	157	GLU	-1	-0.892	-0.933	22.534	0.010	0.010	0.000	0.000	0.000	0.000
131	A	158	ALA	0	0.036	0.013	19.009	-0.030	-0.030	0.000	0.000	0.000	0.000
132	A	159	LEU	0	-0.008	-0.013	15.435	-0.053	-0.053	0.000	0.000	0.000	0.000
133	A	160	GLU	-1	-0.771	-0.861	18.941	-0.091	-0.091	0.000	0.000	0.000	0.000
134	A	161	GLN	0	0.011	0.006	21.614	-0.051	-0.051	0.000	0.000	0.000	0.000
135	A	162	GLN	0	-0.026	-0.005	16.138	-0.096	-0.096	0.000	0.000	0.000	0.000
136	A	163	ILE	0	-0.016	-0.008	19.013	-0.056	-0.056	0.000	0.000	0.000	0.000
137	A	164	LEU	0	0.011	0.006	20.536	-0.032	-0.032	0.000	0.000	0.000	0.000
138	A	165	ALA	0	0.003	0.016	20.490	-0.012	-0.012	0.000	0.000	0.000	0.000
139	A	166	ALA	0	-0.004	0.000	18.440	-0.023	-0.023	0.000	0.000	0.000	0.000
140	A	167	LEU	0	-0.084	-0.040	20.460	-0.020	-0.020	0.000	0.000	0.000	0.000
141	A	168	GLY	0	-0.050	-0.032	23.787	0.040	0.040	0.000	0.000	0.000	0.000

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