FMO DATABASE

FMODB ID: 1N53Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1391138.225081
FMO2-HF: Nuclear repulsion	1328862.751462
FMO2-HF: Total energy	-62275.47362
FMO2-MP2: Total energy	-62454.621109

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.
-1.724	0.344	-0.024	-1.19	-0.854	0.003

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 : 0.020 / q_NPA : 0.014

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	0.026	0.001	3.818	-0.791	1.277	-0.024	-1.190	-0.854	0.003
4	A	1	MET	0	-0.008	0.017	7.238	0.024	0.024	0.000	0.000	0.000	0.000
5	A	2	PHE	0	-0.034	-0.009	10.310	0.185	0.185	0.000	0.000	0.000	0.000
6	A	3	TYR	0	0.037	0.009	13.401	0.025	0.025	0.000	0.000	0.000	0.000
7	A	4	MET	0	-0.004	0.004	17.049	-0.020	-0.020	0.000	0.000	0.000	0.000
8	A	5	THR	0	-0.020	-0.024	19.792	0.015	0.015	0.000	0.000	0.000	0.000
9	A	6	ALA	0	0.014	0.012	22.952	0.002	0.002	0.000	0.000	0.000	0.000
10	A	7	LEU	0	-0.032	-0.007	25.834	0.007	0.007	0.000	0.000	0.000	0.000
11	A	8	PHE	0	0.029	0.003	25.616	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	9	PRO	0	0.012	0.025	31.224	0.004	0.004	0.000	0.000	0.000	0.000
13	A	10	TYR	0	-0.019	-0.032	32.810	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	11	ILE	0	-0.017	-0.012	35.638	0.004	0.004	0.000	0.000	0.000	0.000
15	A	12	ALA	0	0.004	0.007	39.033	0.001	0.001	0.000	0.000	0.000	0.000
16	A	13	PHE	0	0.046	0.012	39.392	0.003	0.003	0.000	0.000	0.000	0.000
17	A	14	GLU	-1	-0.904	-0.967	43.476	-0.060	-0.060	0.000	0.000	0.000	0.000
18	A	15	ASN	0	-0.024	-0.016	44.638	0.001	0.001	0.000	0.000	0.000	0.000
19	A	16	SER	0	0.020	-0.036	39.393	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	17	LYS	1	0.807	0.902	41.056	0.044	0.044	0.000	0.000	0.000	0.000
21	A	18	GLU	-1	-0.949	-0.978	42.193	-0.051	-0.051	0.000	0.000	0.000	0.000
22	A	19	ALA	0	-0.017	-0.010	42.290	0.000	0.000	0.000	0.000	0.000	0.000
23	A	20	LEU	0	-0.005	-0.017	36.682	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	21	ALA	0	0.001	0.013	40.292	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	22	TYR	0	0.009	-0.023	42.712	0.000	0.000	0.000	0.000	0.000	0.000
26	A	23	TYR	0	-0.060	-0.064	39.441	0.000	0.000	0.000	0.000	0.000	0.000
27	A	24	GLU	-1	-0.940	-0.966	38.627	-0.071	-0.071	0.000	0.000	0.000	0.000
28	A	25	GLU	-1	-1.010	-1.004	40.220	-0.053	-0.053	0.000	0.000	0.000	0.000
29	A	26	VAL	0	-0.077	-0.028	43.557	0.001	0.001	0.000	0.000	0.000	0.000
30	A	27	PHE	0	-0.022	-0.029	40.008	0.000	0.000	0.000	0.000	0.000	0.000
31	A	28	GLY	0	0.012	0.021	39.519	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	29	ALA	0	-0.043	-0.020	36.313	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	30	THR	0	0.009	-0.001	32.022	0.007	0.007	0.000	0.000	0.000	0.000
34	A	31	ASP	-1	-0.889	-0.949	27.715	-0.149	-0.149	0.000	0.000	0.000	0.000
35	A	32	VAL	0	0.012	0.015	31.017	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	33	LYS	1	0.756	0.872	26.617	0.155	0.155	0.000	0.000	0.000	0.000
37	A	34	ARG	1	0.834	0.891	32.085	0.057	0.057	0.000	0.000	0.000	0.000
38	A	35	LEU	0	-0.045	-0.012	31.323	0.004	0.004	0.000	0.000	0.000	0.000
39	A	36	GLU	-1	-0.822	-0.914	34.294	-0.051	-0.051	0.000	0.000	0.000	0.000
40	A	37	VAL	0	-0.037	-0.013	36.914	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	38	GLY	0	0.030	0.014	38.284	0.003	0.003	0.000	0.000	0.000	0.000
42	A	39	GLU	-1	-0.790	-0.897	39.013	-0.022	-0.022	0.000	0.000	0.000	0.000
43	A	40	GLU	-1	-0.894	-0.957	40.482	-0.023	-0.023	0.000	0.000	0.000	0.000
44	A	41	GLN	0	-0.051	-0.021	35.708	0.000	0.000	0.000	0.000	0.000	0.000
45	A	42	ALA	0	0.032	0.021	40.993	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	43	SER	0	0.005	0.002	44.304	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	44	HIS	0	-0.073	-0.040	40.582	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	45	PHE	0	-0.012	-0.009	39.050	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	46	GLY	0	-0.054	-0.004	45.048	0.000	0.000	0.000	0.000	0.000	0.000
50	A	47	MET	0	-0.013	0.013	44.973	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	48	THR	0	-0.064	-0.065	48.282	0.002	0.002	0.000	0.000	0.000	0.000
52	A	49	LYS	1	0.778	0.838	45.983	0.020	0.020	0.000	0.000	0.000	0.000
53	A	50	GLU	-1	-0.905	-0.943	46.250	-0.027	-0.027	0.000	0.000	0.000	0.000
54	A	51	GLU	-1	-0.839	-0.899	47.428	-0.037	-0.037	0.000	0.000	0.000	0.000
55	A	52	ALA	0	0.005	-0.007	43.016	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	53	GLN	0	-0.033	-0.003	40.658	0.000	0.000	0.000	0.000	0.000	0.000
57	A	54	GLU	-1	-0.813	-0.888	42.818	-0.045	-0.045	0.000	0.000	0.000	0.000
58	A	55	ALA	0	-0.024	0.009	42.654	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	56	THR	0	-0.035	-0.031	37.190	0.000	0.000	0.000	0.000	0.000	0.000
60	A	57	MET	0	-0.065	-0.033	35.132	0.000	0.000	0.000	0.000	0.000	0.000
61	A	58	HIS	0	-0.017	-0.013	29.839	0.000	0.000	0.000	0.000	0.000	0.000
62	A	59	ALA	0	0.015	0.005	33.562	0.006	0.006	0.000	0.000	0.000	0.000
63	A	60	GLU	-1	-0.824	-0.884	27.771	-0.179	-0.179	0.000	0.000	0.000	0.000
64	A	61	PHE	0	0.027	0.006	32.422	0.008	0.008	0.000	0.000	0.000	0.000
65	A	62	GLU	-1	-0.905	-0.952	28.387	-0.173	-0.173	0.000	0.000	0.000	0.000
66	A	63	VAL	0	0.037	0.021	32.599	0.010	0.010	0.000	0.000	0.000	0.000
67	A	64	LEU	0	-0.032	-0.017	34.047	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	65	GLY	0	0.019	0.026	30.184	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	66	VAL	0	-0.030	-0.008	29.175	-0.017	-0.017	0.000	0.000	0.000	0.000
70	A	67	LYS	1	0.839	0.901	25.763	0.204	0.204	0.000	0.000	0.000	0.000
71	A	68	VAL	0	-0.003	0.004	30.675	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	69	LEU	0	-0.028	-0.014	29.254	0.000	0.000	0.000	0.000	0.000	0.000
73	A	70	CYS	0	-0.017	-0.008	33.409	0.004	0.004	0.000	0.000	0.000	0.000
74	A	71	SER	0	-0.034	0.005	35.629	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	72	ASP	-1	-0.709	-0.818	38.154	-0.067	-0.067	0.000	0.000	0.000	0.000
76	A	73	SER	0	0.008	0.014	41.258	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	74	PHE	0	-0.017	-0.028	40.204	0.000	0.000	0.000	0.000	0.000	0.000
78	A	75	GLY	0	-0.012	-0.009	45.440	0.002	0.002	0.000	0.000	0.000	0.000
79	A	76	ARG	1	0.865	0.927	39.669	0.077	0.077	0.000	0.000	0.000	0.000
80	A	77	ALA	0	0.001	0.016	43.268	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	78	ASP	-1	-0.928	-0.952	45.244	-0.068	-0.068	0.000	0.000	0.000	0.000
82	A	79	LYS	1	0.954	0.966	46.427	0.058	0.058	0.000	0.000	0.000	0.000
83	A	80	ILE	0	0.012	0.018	43.967	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	81	ASN	0	-0.040	-0.017	46.615	0.001	0.001	0.000	0.000	0.000	0.000
85	A	82	ASN	0	0.044	0.020	46.418	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	83	GLY	0	-0.017	-0.006	46.649	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	84	ILE	0	-0.047	-0.026	39.764	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	85	SER	0	0.003	0.015	42.704	0.004	0.004	0.000	0.000	0.000	0.000
89	A	86	LEU	0	-0.033	-0.015	37.421	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	87	LEU	0	-0.020	-0.007	37.261	0.005	0.005	0.000	0.000	0.000	0.000
91	A	88	ILE	0	-0.013	-0.002	34.823	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	89	ASP	-1	-0.852	-0.919	34.231	-0.138	-0.138	0.000	0.000	0.000	0.000
93	A	90	TYR	0	0.030	0.034	33.974	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	91	ASP	-1	-0.834	-0.918	33.594	-0.135	-0.135	0.000	0.000	0.000	0.000
95	A	92	VAL	0	-0.022	-0.021	35.435	0.003	0.003	0.000	0.000	0.000	0.000
96	A	93	ASN	0	-0.095	-0.049	36.633	0.011	0.011	0.000	0.000	0.000	0.000
97	A	94	ASN	0	-0.065	-0.023	30.848	0.004	0.004	0.000	0.000	0.000	0.000
98	A	95	LYS	1	0.885	0.932	34.549	0.090	0.090	0.000	0.000	0.000	0.000
99	A	96	GLU	-1	-0.912	-0.971	32.056	-0.103	-0.103	0.000	0.000	0.000	0.000
100	A	97	ASP	-1	-0.863	-0.920	31.810	-0.152	-0.152	0.000	0.000	0.000	0.000
101	A	98	ALA	0	0.011	-0.007	34.582	0.004	0.004	0.000	0.000	0.000	0.000
102	A	99	ASP	-1	-0.866	-0.922	37.921	-0.081	-0.081	0.000	0.000	0.000	0.000
103	A	100	LYS	1	0.904	0.956	33.897	0.105	0.105	0.000	0.000	0.000	0.000
104	A	101	VAL	0	0.011	0.005	36.835	0.004	0.004	0.000	0.000	0.000	0.000
105	A	102	GLU	-1	-0.838	-0.914	39.269	-0.076	-0.076	0.000	0.000	0.000	0.000
106	A	103	ALA	0	-0.049	-0.019	40.687	0.004	0.004	0.000	0.000	0.000	0.000
107	A	104	PHE	0	0.003	-0.006	39.701	0.003	0.003	0.000	0.000	0.000	0.000
108	A	105	TYR	0	0.055	0.013	41.804	0.003	0.003	0.000	0.000	0.000	0.000
109	A	106	GLU	-1	-0.857	-0.915	44.677	-0.056	-0.056	0.000	0.000	0.000	0.000
110	A	107	GLN	0	-0.076	-0.034	42.643	0.002	0.002	0.000	0.000	0.000	0.000
111	A	108	ILE	0	-0.025	-0.004	43.409	0.002	0.002	0.000	0.000	0.000	0.000
112	A	109	LYS	1	0.769	0.879	46.948	0.059	0.059	0.000	0.000	0.000	0.000
113	A	110	ASP	-1	-0.905	-0.955	49.976	-0.051	-0.051	0.000	0.000	0.000	0.000
114	A	111	HIS	0	0.019	0.036	49.164	0.002	0.002	0.000	0.000	0.000	0.000
115	A	112	SER	0	0.009	-0.009	51.530	0.000	0.000	0.000	0.000	0.000	0.000
116	A	113	SER	0	-0.114	-0.066	49.368	0.000	0.000	0.000	0.000	0.000	0.000
117	A	114	ILE	0	-0.029	0.000	46.640	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	115	GLU	-1	-0.904	-0.940	50.366	-0.058	-0.058	0.000	0.000	0.000	0.000
119	A	116	ILE	0	-0.022	-0.018	49.663	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	117	GLU	-1	-0.815	-0.870	50.308	-0.072	-0.072	0.000	0.000	0.000	0.000
121	A	118	LEU	0	-0.040	-0.026	48.485	0.002	0.002	0.000	0.000	0.000	0.000
122	A	119	PRO	0	-0.014	-0.020	49.503	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	120	PHE	0	-0.001	0.000	42.193	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	121	ALA	0	-0.027	-0.010	47.740	0.003	0.003	0.000	0.000	0.000	0.000
125	A	122	ASP	-1	-0.876	-0.952	46.890	-0.080	-0.080	0.000	0.000	0.000	0.000
126	A	123	GLN	0	-0.012	-0.002	46.799	0.005	0.005	0.000	0.000	0.000	0.000
127	A	124	PHE	0	-0.051	-0.034	48.911	0.000	0.000	0.000	0.000	0.000	0.000
128	A	125	TRP	0	-0.062	-0.046	47.848	0.001	0.001	0.000	0.000	0.000	0.000
129	A	126	GLY	0	0.023	0.024	45.300	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	127	GLY	0	0.021	0.022	42.918	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	128	LYS	1	0.807	0.904	42.785	0.084	0.084	0.000	0.000	0.000	0.000
132	A	129	MET	0	0.012	0.010	43.185	-0.006	-0.006	0.000	0.000	0.000	0.000
133	A	130	GLY	0	0.013	0.018	44.583	0.005	0.005	0.000	0.000	0.000	0.000
134	A	131	VAL	0	-0.034	-0.011	44.944	-0.005	-0.005	0.000	0.000	0.000	0.000
135	A	132	PHE	0	0.005	0.015	42.994	0.004	0.004	0.000	0.000	0.000	0.000
136	A	133	THR	0	-0.002	0.001	46.580	-0.006	-0.006	0.000	0.000	0.000	0.000
137	A	134	ASP	-1	-0.755	-0.832	44.083	-0.076	-0.076	0.000	0.000	0.000	0.000
138	A	135	LYS	1	0.975	0.984	47.470	0.058	0.058	0.000	0.000	0.000	0.000
139	A	136	TYR	0	-0.087	-0.047	45.362	0.003	0.003	0.000	0.000	0.000	0.000
140	A	137	GLY	0	-0.018	0.003	47.440	0.000	0.000	0.000	0.000	0.000	0.000
141	A	138	VAL	0	-0.015	0.001	41.525	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	139	ARG	1	0.786	0.850	44.930	0.084	0.084	0.000	0.000	0.000	0.000
143	A	140	TRP	0	-0.032	-0.036	37.649	-0.009	-0.009	0.000	0.000	0.000	0.000
144	A	141	MET	0	-0.029	-0.025	41.423	0.004	0.004	0.000	0.000	0.000	0.000
145	A	142	LEU	0	-0.018	0.005	39.976	-0.006	-0.006	0.000	0.000	0.000	0.000
146	A	143	HIS	0	-0.037	-0.053	38.615	0.010	0.010	0.000	0.000	0.000	0.000
147	A	144	GLY	0	0.024	0.003	38.578	-0.007	-0.007	0.000	0.000	0.000	0.000
148	A	145	GLN	0	-0.034	-0.026	36.209	0.009	0.009	0.000	0.000	0.000	0.000
149	A	146	ASP	-1	-0.791	-0.900	38.557	-0.104	-0.104	0.000	0.000	0.000	0.000
150	A	147	TYR	0	-0.035	-0.019	34.158	-0.003	-0.003	0.000	0.000	0.000	0.000
151	A	148	THR	0	-0.070	-0.035	37.937	-0.002	-0.002	0.000	0.000	0.000	0.000
152	A	149	ALA	0	-0.037	-0.021	40.774	0.001	0.001	0.000	0.000	0.000	0.000
153	A	150	ILE	0	0.043	0.017	42.385	0.004	0.004	0.000	0.000	0.000	0.000
154	A	151	GLN	0	-0.078	-0.028	45.804	0.006	0.006	0.000	0.000	0.000	0.000

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