FMO DATABASE

FMODB ID: G5841

Calculation Name: 3L20-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L20

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

Base Structure: X-ray

Registration Date: 2023-09-22

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	154
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1394256.814953
FMO2-HF: Nuclear repulsion	1331980.815672
FMO2-HF: Total energy	-62275.999281
FMO2-MP2: Total energy	-62455.246836

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:-2:GLY)

Summations of interaction energy for fragment #1(A:-2:GLY)

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.
-1.499	0.481	-0.014	-1.147	-0.818	0.004

Interaction energy analysis for fragmet #1(A:-2:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.028

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	0	HIS	0	-0.002	-0.011	3.869	-0.237	1.743	-0.014	-1.147	-0.818	0.004
4	A	1	MET	0	0.009	0.018	7.228	-0.187	-0.187	0.000	0.000	0.000	0.000
5	A	2	PHE	0	-0.012	0.002	10.518	0.190	0.190	0.000	0.000	0.000	0.000
6	A	3	TYR	0	0.034	0.014	13.467	-0.022	-0.022	0.000	0.000	0.000	0.000
7	A	4	MET	0	-0.019	-0.006	17.050	0.003	0.003	0.000	0.000	0.000	0.000
8	A	5	THR	0	-0.014	-0.020	19.789	0.013	0.013	0.000	0.000	0.000	0.000
9	A	6	ALA	0	0.014	0.016	22.776	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	7	LEU	0	-0.019	-0.009	25.615	0.011	0.011	0.000	0.000	0.000	0.000
11	A	8	PHE	0	0.020	0.007	25.382	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	9	PRO	0	0.004	0.019	31.078	0.007	0.007	0.000	0.000	0.000	0.000
13	A	10	TYR	0	-0.018	-0.036	32.795	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	11	ILE	0	-0.026	-0.010	35.653	0.005	0.005	0.000	0.000	0.000	0.000
15	A	12	ALA	0	0.012	0.008	38.968	0.001	0.001	0.000	0.000	0.000	0.000
16	A	13	PHE	0	0.045	0.013	39.515	0.003	0.003	0.000	0.000	0.000	0.000
17	A	14	GLU	-1	-0.890	-0.957	43.643	-0.051	-0.051	0.000	0.000	0.000	0.000
18	A	15	ASN	0	-0.037	-0.025	44.415	0.001	0.001	0.000	0.000	0.000	0.000
19	A	16	SER	0	0.009	-0.033	39.512	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	17	LYS	1	0.783	0.886	41.006	0.045	0.045	0.000	0.000	0.000	0.000
21	A	18	GLU	-1	-0.842	-0.897	42.085	-0.056	-0.056	0.000	0.000	0.000	0.000
22	A	19	ALA	0	0.025	0.017	41.948	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	20	LEU	0	-0.018	-0.015	36.486	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	21	ALA	0	0.045	0.028	40.167	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	22	TYR	0	-0.010	-0.013	42.644	0.000	0.000	0.000	0.000	0.000	0.000
26	A	23	TYR	0	-0.037	-0.058	39.771	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	24	GLU	-1	-0.951	-0.975	39.156	-0.085	-0.085	0.000	0.000	0.000	0.000
28	A	25	GLU	-1	-0.961	-0.989	40.777	-0.064	-0.064	0.000	0.000	0.000	0.000
29	A	26	VAL	0	-0.062	-0.021	44.301	0.000	0.000	0.000	0.000	0.000	0.000
30	A	27	PHE	0	-0.023	-0.027	40.533	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	28	GLY	0	0.006	0.017	40.339	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	29	ALA	0	-0.055	-0.018	36.910	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	30	THR	0	-0.026	-0.039	32.406	0.007	0.007	0.000	0.000	0.000	0.000
34	A	31	ASP	-1	-0.863	-0.934	28.127	-0.171	-0.171	0.000	0.000	0.000	0.000
35	A	32	VAL	0	0.028	0.022	31.258	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	33	LYS	1	0.725	0.846	26.932	0.165	0.165	0.000	0.000	0.000	0.000
37	A	34	ARG	1	0.781	0.859	32.552	0.059	0.059	0.000	0.000	0.000	0.000
38	A	35	LEU	0	-0.040	-0.005	31.451	0.002	0.002	0.000	0.000	0.000	0.000
39	A	36	GLU	-1	-0.798	-0.893	34.443	-0.052	-0.052	0.000	0.000	0.000	0.000
40	A	37	VAL	0	-0.053	-0.016	37.189	0.000	0.000	0.000	0.000	0.000	0.000
41	A	38	GLY	0	0.059	0.029	38.174	0.002	0.002	0.000	0.000	0.000	0.000
42	A	39	GLU	-1	-0.831	-0.914	39.016	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	40	GLU	-1	-0.821	-0.913	40.860	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	41	GLN	0	-0.054	-0.025	35.477	0.000	0.000	0.000	0.000	0.000	0.000
45	A	42	ALA	0	0.040	0.021	40.912	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	43	SER	0	-0.025	-0.013	43.844	0.000	0.000	0.000	0.000	0.000	0.000
47	A	44	HIS	0	-0.071	-0.037	40.609	0.000	0.000	0.000	0.000	0.000	0.000
48	A	45	PHE	0	-0.017	-0.015	39.005	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	46	GLY	0	-0.042	-0.001	44.712	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	47	MET	0	-0.041	-0.001	45.396	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	48	THR	0	-0.040	-0.062	48.203	0.002	0.002	0.000	0.000	0.000	0.000
52	A	49	LYS	1	0.758	0.843	45.738	0.013	0.013	0.000	0.000	0.000	0.000
53	A	50	GLU	-1	-0.890	-0.950	45.958	-0.024	-0.024	0.000	0.000	0.000	0.000
54	A	51	GLU	-1	-0.835	-0.887	47.366	-0.031	-0.031	0.000	0.000	0.000	0.000
55	A	52	ALA	0	-0.019	-0.020	43.039	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	53	GLN	0	-0.050	-0.022	40.900	0.000	0.000	0.000	0.000	0.000	0.000
57	A	54	GLU	-1	-0.780	-0.866	42.796	-0.048	-0.048	0.000	0.000	0.000	0.000
58	A	55	ALA	0	-0.005	0.015	42.928	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	56	THR	0	-0.034	-0.023	37.338	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	57	MET	0	-0.060	-0.019	35.298	0.001	0.001	0.000	0.000	0.000	0.000
61	A	58	HIS	0	-0.024	-0.020	29.788	0.003	0.003	0.000	0.000	0.000	0.000
62	A	59	ALA	0	0.037	0.008	33.438	0.006	0.006	0.000	0.000	0.000	0.000
63	A	60	GLU	-1	-0.838	-0.890	27.805	-0.175	-0.175	0.000	0.000	0.000	0.000
64	A	61	PHE	0	0.040	0.023	32.471	0.006	0.006	0.000	0.000	0.000	0.000
65	A	62	GLU	-1	-0.897	-0.929	29.301	-0.188	-0.188	0.000	0.000	0.000	0.000
66	A	63	VAL	0	0.057	0.025	33.136	0.010	0.010	0.000	0.000	0.000	0.000
67	A	64	LEU	0	-0.019	-0.012	34.664	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	65	GLY	0	0.025	0.033	30.829	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	66	VAL	0	-0.028	-0.011	29.875	-0.017	-0.017	0.000	0.000	0.000	0.000
70	A	67	LYS	1	0.839	0.903	25.841	0.202	0.202	0.000	0.000	0.000	0.000
71	A	68	VAL	0	-0.013	-0.009	30.934	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	69	LEU	0	-0.022	-0.011	29.226	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	70	CYS	0	-0.016	-0.007	33.365	0.004	0.004	0.000	0.000	0.000	0.000
74	A	71	SER	0	-0.027	0.019	35.719	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	72	ASP	-1	-0.690	-0.830	38.105	-0.060	-0.060	0.000	0.000	0.000	0.000
76	A	73	SER	0	-0.024	-0.017	41.390	0.000	0.000	0.000	0.000	0.000	0.000
77	A	74	PHE	0	-0.042	-0.036	40.330	0.002	0.002	0.000	0.000	0.000	0.000
78	A	75	GLY	0	0.031	0.026	45.612	0.003	0.003	0.000	0.000	0.000	0.000
79	A	76	ARG	1	0.829	0.911	39.711	0.059	0.059	0.000	0.000	0.000	0.000
80	A	77	ALA	0	-0.006	-0.002	43.297	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	78	ASP	-1	-0.919	-0.949	45.335	-0.056	-0.056	0.000	0.000	0.000	0.000
82	A	79	LYS	1	0.832	0.914	46.485	0.057	0.057	0.000	0.000	0.000	0.000
83	A	80	ILE	0	0.030	0.017	44.024	0.000	0.000	0.000	0.000	0.000	0.000
84	A	81	ASN	0	-0.041	-0.018	46.475	0.002	0.002	0.000	0.000	0.000	0.000
85	A	82	ASN	0	0.076	0.033	46.198	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	83	GLY	0	-0.019	0.000	46.826	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	84	ILE	0	-0.040	-0.022	39.963	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	85	SER	0	-0.010	0.004	42.280	0.004	0.004	0.000	0.000	0.000	0.000
89	A	86	LEU	0	-0.030	-0.013	37.596	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	87	LEU	0	-0.014	-0.001	37.827	0.003	0.003	0.000	0.000	0.000	0.000
91	A	88	ILE	0	-0.007	0.001	35.521	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	89	ASP	-1	-0.849	-0.908	34.971	-0.143	-0.143	0.000	0.000	0.000	0.000
93	A	90	TYR	0	0.027	0.028	34.688	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	91	ASP	-1	-0.804	-0.906	34.738	-0.152	-0.152	0.000	0.000	0.000	0.000
95	A	92	VAL	0	-0.026	-0.017	36.448	0.000	0.000	0.000	0.000	0.000	0.000
96	A	93	ASN	0	-0.122	-0.067	37.354	0.009	0.009	0.000	0.000	0.000	0.000
97	A	94	ASN	0	-0.072	-0.037	31.773	0.000	0.000	0.000	0.000	0.000	0.000
98	A	95	LYS	1	0.830	0.899	35.450	0.122	0.122	0.000	0.000	0.000	0.000
99	A	96	GLU	-1	-0.913	-0.972	33.183	-0.141	-0.141	0.000	0.000	0.000	0.000
100	A	97	ASP	-1	-0.848	-0.898	32.620	-0.185	-0.185	0.000	0.000	0.000	0.000
101	A	98	ALA	0	0.012	-0.003	35.365	0.008	0.008	0.000	0.000	0.000	0.000
102	A	99	ASP	-1	-0.862	-0.923	38.404	-0.109	-0.109	0.000	0.000	0.000	0.000
103	A	100	LYS	1	0.897	0.948	34.747	0.141	0.141	0.000	0.000	0.000	0.000
104	A	101	VAL	0	0.026	0.015	37.892	0.005	0.005	0.000	0.000	0.000	0.000
105	A	102	GLU	-1	-0.822	-0.899	40.336	-0.091	-0.091	0.000	0.000	0.000	0.000
106	A	103	ALA	0	-0.032	-0.015	41.722	0.005	0.005	0.000	0.000	0.000	0.000
107	A	104	PHE	0	-0.004	-0.003	40.325	0.004	0.004	0.000	0.000	0.000	0.000
108	A	105	TYR	0	0.044	0.005	42.655	0.005	0.005	0.000	0.000	0.000	0.000
109	A	106	GLU	-1	-0.863	-0.921	45.617	-0.068	-0.068	0.000	0.000	0.000	0.000
110	A	107	GLN	0	-0.065	-0.036	43.623	0.003	0.003	0.000	0.000	0.000	0.000
111	A	108	ILE	0	-0.033	-0.001	44.075	0.004	0.004	0.000	0.000	0.000	0.000
112	A	109	LYS	1	0.746	0.865	47.524	0.072	0.072	0.000	0.000	0.000	0.000
113	A	110	ASP	-1	-0.894	-0.943	50.525	-0.060	-0.060	0.000	0.000	0.000	0.000
114	A	111	HIS	0	0.009	0.035	49.448	0.004	0.004	0.000	0.000	0.000	0.000
115	A	112	SER	0	-0.004	-0.010	52.093	0.000	0.000	0.000	0.000	0.000	0.000
116	A	113	SER	0	-0.136	-0.091	50.150	0.001	0.001	0.000	0.000	0.000	0.000
117	A	114	ILE	0	0.001	0.013	47.173	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	115	GLU	-1	-0.909	-0.929	50.829	-0.060	-0.060	0.000	0.000	0.000	0.000
119	A	116	ILE	0	0.013	-0.005	50.107	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	117	GLU	-1	-0.806	-0.856	50.631	-0.072	-0.072	0.000	0.000	0.000	0.000
121	A	118	LEU	0	-0.049	-0.032	49.032	0.002	0.002	0.000	0.000	0.000	0.000
122	A	119	PRO	0	0.005	-0.009	50.017	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	120	PHE	0	-0.012	0.001	42.993	0.000	0.000	0.000	0.000	0.000	0.000
124	A	121	ALA	0	-0.009	0.003	48.451	0.002	0.002	0.000	0.000	0.000	0.000
125	A	122	ASP	-1	-0.837	-0.929	47.571	-0.093	-0.093	0.000	0.000	0.000	0.000
126	A	123	GLN	0	-0.022	-0.008	47.399	0.007	0.007	0.000	0.000	0.000	0.000
127	A	124	PHE	0	-0.062	-0.039	49.588	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	125	TRP	0	-0.052	-0.036	48.503	0.002	0.002	0.000	0.000	0.000	0.000
129	A	126	GLY	0	0.021	0.019	46.099	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	127	GLY	0	0.031	0.020	43.728	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	128	LYS	1	0.770	0.873	43.777	0.099	0.099	0.000	0.000	0.000	0.000
132	A	129	MET	0	-0.030	-0.010	43.381	-0.005	-0.005	0.000	0.000	0.000	0.000
133	A	130	GLY	0	0.032	0.023	45.527	0.004	0.004	0.000	0.000	0.000	0.000
134	A	131	VAL	0	-0.055	-0.030	45.611	-0.005	-0.005	0.000	0.000	0.000	0.000
135	A	132	PHE	0	-0.017	0.005	43.453	0.003	0.003	0.000	0.000	0.000	0.000
136	A	133	THR	0	-0.013	-0.015	46.870	-0.005	-0.005	0.000	0.000	0.000	0.000
137	A	134	ASP	-1	-0.703	-0.823	44.435	-0.078	-0.078	0.000	0.000	0.000	0.000
138	A	135	LYS	1	0.858	0.917	47.775	0.061	0.061	0.000	0.000	0.000	0.000
139	A	136	TYR	0	-0.070	-0.045	45.261	0.003	0.003	0.000	0.000	0.000	0.000
140	A	137	GLY	0	-0.039	-0.016	47.961	0.003	0.003	0.000	0.000	0.000	0.000
141	A	138	VAL	0	-0.030	-0.010	41.598	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	139	ARG	1	0.787	0.851	44.992	0.082	0.082	0.000	0.000	0.000	0.000
143	A	140	TRP	0	-0.011	-0.023	38.020	-0.008	-0.008	0.000	0.000	0.000	0.000
144	A	141	MET	0	-0.045	-0.032	41.876	0.005	0.005	0.000	0.000	0.000	0.000
145	A	142	LEU	0	0.003	0.016	40.744	-0.006	-0.006	0.000	0.000	0.000	0.000
146	A	143	HIS	0	-0.048	-0.057	39.269	0.011	0.011	0.000	0.000	0.000	0.000
147	A	144	GLY	0	0.053	0.014	39.403	-0.008	-0.008	0.000	0.000	0.000	0.000
148	A	145	GLN	0	-0.058	-0.027	36.819	0.010	0.010	0.000	0.000	0.000	0.000
149	A	146	ASP	-1	-0.779	-0.891	39.364	-0.123	-0.123	0.000	0.000	0.000	0.000
150	A	147	TYR	0	-0.028	-0.012	34.921	-0.002	-0.002	0.000	0.000	0.000	0.000
151	A	148	THR	0	-0.065	-0.037	38.832	-0.002	-0.002	0.000	0.000	0.000	0.000
152	A	149	ALA	0	-0.034	-0.021	41.393	0.004	0.004	0.000	0.000	0.000	0.000
153	A	150	ILE	0	0.060	0.033	42.915	0.004	0.004	0.000	0.000	0.000	0.000
154	A	151	GLN	0	-0.123	-0.052	45.957	0.008	0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:GLY)