FMO DATABASE

FMODB ID: 3NY1L

Calculation Name: 1AL0-4-Xray307

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AL0

Chain ID: 4

ChEMBL ID:

UniProt ID: P03641

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	147
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1360617.427257
FMO2-HF: Nuclear repulsion	1303423.224799
FMO2-HF: Total energy	-57194.202458
FMO2-MP2: Total energy	-57361.40998

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(4:6:ACE )

Summations of interaction energy for fragment #1(4:6:ACE )

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.
1.834	2.562	-0.004	-0.291	-0.433	0

Interaction energy analysis for fragmet #1(4:6:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / 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].
3	4	8	SER	0	-0.037	-0.012	3.878	1.002	1.730	-0.004	-0.291	-0.433
4	4	9	VAL	0	0.050	0.045	4.914	0.164	0.164	0.000	0.000	0.000
5	4	10	ARG	0	0.119	0.098	7.564	0.002	0.002	0.000	0.000	0.000
6	4	11	PHE	0	0.110	0.018	10.739	0.070	0.070	0.000	0.000	0.000
7	4	12	GLN	0	-0.015	-0.008	13.166	0.022	0.022	0.000	0.000	0.000
8	4	13	THR	0	-0.060	-0.029	11.558	0.000	0.000	0.000	0.000	0.000
9	4	14	ALA	0	0.004	0.003	10.785	0.043	0.043	0.000	0.000	0.000
10	4	15	LEU	0	0.032	0.015	12.136	0.024	0.024	0.000	0.000	0.000
11	4	16	ALA	0	-0.002	-0.008	15.824	0.008	0.008	0.000	0.000	0.000
12	4	17	SER	0	-0.045	-0.013	12.673	0.013	0.013	0.000	0.000	0.000
13	4	18	ILE	0	0.017	-0.007	12.493	0.006	0.006	0.000	0.000	0.000
14	4	19	LYS	1	0.896	0.969	15.659	-0.078	-0.078	0.000	0.000	0.000
15	4	20	LEU	0	-0.061	-0.022	16.912	-0.006	-0.006	0.000	0.000	0.000
16	4	21	ILE	0	-0.057	-0.016	14.415	-0.008	-0.008	0.000	0.000	0.000
17	4	22	GLN	0	0.028	-0.010	17.880	0.020	0.020	0.000	0.000	0.000
18	4	23	ALA	0	-0.012	0.022	15.913	0.000	0.000	0.000	0.000	0.000
19	4	24	SER	0	-0.019	-0.012	17.125	0.024	0.024	0.000	0.000	0.000
20	4	25	ALA	0	0.008	-0.011	17.303	0.002	0.002	0.000	0.000	0.000
21	4	26	VAL	0	-0.053	-0.007	12.249	0.027	0.027	0.000	0.000	0.000
22	4	27	LEU	0	-0.044	-0.008	14.731	0.000	0.000	0.000	0.000	0.000
23	4	28	ASP	-1	-0.862	-0.933	16.877	0.225	0.225	0.000	0.000	0.000
24	4	29	LEU	0	-0.103	-0.051	19.638	-0.025	-0.025	0.000	0.000	0.000
25	4	30	THR	0	0.007	0.000	22.180	0.011	0.011	0.000	0.000	0.000
26	4	31	GLU	-1	-0.925	-0.977	24.925	0.110	0.110	0.000	0.000	0.000
27	4	32	ASP	-1	-0.907	-0.954	25.961	0.083	0.083	0.000	0.000	0.000
28	4	33	ASP	-1	-0.861	-0.933	25.345	0.091	0.091	0.000	0.000	0.000
29	4	34	PHE	0	-0.013	-0.018	20.761	-0.005	-0.005	0.000	0.000	0.000
30	4	35	ASP	-1	-0.840	-0.923	25.398	0.059	0.059	0.000	0.000	0.000
31	4	36	PHE	0	-0.003	-0.004	28.909	-0.008	-0.008	0.000	0.000	0.000
32	4	37	LEU	0	-0.028	-0.019	23.469	-0.007	-0.007	0.000	0.000	0.000
33	4	38	THR	0	-0.061	-0.031	24.945	-0.006	-0.006	0.000	0.000	0.000
34	4	39	SER	0	-0.004	0.025	27.868	-0.004	-0.004	0.000	0.000	0.000
35	4	40	ASN	0	-0.100	-0.067	31.499	-0.005	-0.005	0.000	0.000	0.000
36	4	41	LYS	1	0.919	0.959	34.293	-0.058	-0.058	0.000	0.000	0.000
37	4	42	VAL	0	0.002	-0.001	35.361	0.000	0.000	0.000	0.000	0.000
38	4	43	TRP	0	-0.028	0.004	28.776	0.000	0.000	0.000	0.000	0.000
39	4	44	ILE	0	0.058	0.025	36.374	-0.004	-0.004	0.000	0.000	0.000
40	4	45	ALA	0	-0.041	-0.026	37.698	0.002	0.002	0.000	0.000	0.000
41	4	46	THR	0	-0.013	-0.016	39.182	-0.001	-0.001	0.000	0.000	0.000
42	4	47	ASP	-1	-0.858	-0.936	34.507	0.045	0.045	0.000	0.000	0.000
43	4	48	ARG	1	0.960	0.984	33.543	-0.024	-0.024	0.000	0.000	0.000
44	4	49	SER	0	0.027	0.008	32.481	0.003	0.003	0.000	0.000	0.000
45	4	50	ARG	1	0.938	0.963	30.155	-0.056	-0.056	0.000	0.000	0.000
46	4	51	ALA	0	0.035	0.046	28.898	0.005	0.005	0.000	0.000	0.000
47	4	52	ARG	1	0.905	0.957	27.513	-0.030	-0.030	0.000	0.000	0.000
48	4	53	ARG	1	0.876	0.945	26.038	-0.082	-0.082	0.000	0.000	0.000
49	4	54	CYS	0	-0.006	-0.012	24.270	0.009	0.009	0.000	0.000	0.000
50	4	55	VAL	0	0.039	0.015	22.906	0.008	0.008	0.000	0.000	0.000
51	4	56	GLU	-1	-0.867	-0.946	21.901	0.061	0.061	0.000	0.000	0.000
52	4	57	ALA	0	0.026	0.012	20.423	0.006	0.006	0.000	0.000	0.000
53	4	58	CYS	0	-0.047	-0.013	18.363	0.022	0.022	0.000	0.000	0.000
54	4	59	VAL	0	-0.052	-0.020	17.074	0.010	0.010	0.000	0.000	0.000
55	4	60	TYR	0	0.009	-0.016	16.378	0.000	0.000	0.000	0.000	0.000
56	4	61	GLY	0	0.083	0.068	15.248	0.015	0.015	0.000	0.000	0.000
57	4	62	THR	0	0.013	-0.045	12.437	0.038	0.038	0.000	0.000	0.000
58	4	63	LEU	0	-0.046	-0.011	11.050	0.021	0.021	0.000	0.000	0.000
59	4	64	ASP	-1	-0.801	-0.882	10.538	0.205	0.205	0.000	0.000	0.000
60	4	65	PHE	0	-0.098	-0.028	9.033	0.116	0.116	0.000	0.000	0.000
61	4	66	VAL	0	-0.086	-0.047	6.620	0.217	0.217	0.000	0.000	0.000
62	4	67	GLY	0	-0.029	-0.001	7.498	-0.178	-0.178	0.000	0.000	0.000
63	4	68	TYR	0	-0.135	-0.141	8.201	-0.095	-0.095	0.000	0.000	0.000
64	4	69	PRO	0	0.007	0.009	11.453	0.049	0.049	0.000	0.000	0.000
65	4	70	ARG	1	0.900	0.928	13.519	-0.178	-0.178	0.000	0.000	0.000
66	4	71	PHE	0	-0.071	-0.038	15.070	-0.035	-0.035	0.000	0.000	0.000
67	4	72	PRO	0	0.012	0.002	19.525	0.010	0.010	0.000	0.000	0.000
68	4	73	ALA	0	0.049	0.038	19.580	-0.006	-0.006	0.000	0.000	0.000
69	4	74	PRO	0	-0.006	0.000	19.254	0.000	0.000	0.000	0.000	0.000
70	4	75	VAL	0	0.068	0.030	22.012	0.006	0.006	0.000	0.000	0.000
71	4	76	GLU	-1	-0.873	-0.969	21.747	-0.033	-0.033	0.000	0.000	0.000
72	4	77	PHE	0	0.001	-0.001	15.957	0.003	0.003	0.000	0.000	0.000
73	4	78	ILE	0	0.028	0.017	20.047	0.012	0.012	0.000	0.000	0.000
74	4	79	ALA	0	-0.001	-0.005	22.675	0.006	0.006	0.000	0.000	0.000
75	4	80	ALA	0	0.058	0.020	19.619	0.005	0.005	0.000	0.000	0.000
76	4	81	VAL	0	0.005	0.017	19.270	0.008	0.008	0.000	0.000	0.000
77	4	82	ILE	0	-0.031	-0.026	21.462	0.004	0.004	0.000	0.000	0.000
78	4	83	ALA	0	-0.033	-0.008	23.714	-0.002	-0.002	0.000	0.000	0.000
79	4	84	TYR	0	-0.089	-0.057	20.248	0.000	0.000	0.000	0.000	0.000
80	4	85	TYR	0	0.000	-0.037	17.898	0.009	0.009	0.000	0.000	0.000
81	4	86	VAL	0	0.035	0.038	23.707	0.002	0.002	0.000	0.000	0.000
82	4	87	HIS	0	0.033	0.031	27.349	-0.006	-0.006	0.000	0.000	0.000
83	4	88	PRO	0	-0.069	-0.049	30.534	-0.003	-0.003	0.000	0.000	0.000
84	4	89	VAL	0	0.025	0.014	32.702	-0.003	-0.003	0.000	0.000	0.000
85	4	90	ASN	0	0.004	-0.014	32.029	-0.004	-0.004	0.000	0.000	0.000
86	4	91	ILE	0	0.041	0.048	29.680	-0.001	-0.001	0.000	0.000	0.000
87	4	92	GLN	0	0.012	0.004	31.708	-0.001	-0.001	0.000	0.000	0.000
88	4	93	THR	0	0.020	-0.007	34.210	0.000	0.000	0.000	0.000	0.000
89	4	94	ALA	0	0.038	0.032	29.049	0.001	0.001	0.000	0.000	0.000
90	4	95	CYS	0	-0.048	-0.022	30.242	-0.001	-0.001	0.000	0.000	0.000
91	4	96	LEU	0	-0.029	-0.026	31.240	-0.001	-0.001	0.000	0.000	0.000
92	4	97	ILE	0	-0.109	-0.043	30.623	0.000	0.000	0.000	0.000	0.000
93	4	98	MET	0	-0.018	0.000	25.708	0.004	0.004	0.000	0.000	0.000
94	4	99	GLU	-1	-0.968	-0.979	29.708	0.008	0.008	0.000	0.000	0.000
95	4	100	GLY	0	-0.045	-0.018	32.197	0.002	0.002	0.000	0.000	0.000
96	4	101	ALA	0	-0.036	-0.033	30.712	0.002	0.002	0.000	0.000	0.000
97	4	102	GLU	-1	-0.940	-0.956	31.098	0.030	0.030	0.000	0.000	0.000
98	4	103	PHE	0	0.001	-0.005	30.027	0.002	0.002	0.000	0.000	0.000
99	4	104	THR	0	-0.002	0.001	25.395	0.004	0.004	0.000	0.000	0.000
100	4	105	GLU	-1	-0.918	-0.973	22.200	0.072	0.072	0.000	0.000	0.000
101	4	106	ASN	0	-0.051	-0.026	24.027	-0.007	-0.007	0.000	0.000	0.000
102	4	107	ILE	0	-0.019	0.006	21.590	-0.003	-0.003	0.000	0.000	0.000
103	4	108	ILE	0	-0.020	-0.007	21.322	-0.005	-0.005	0.000	0.000	0.000
104	4	109	ASN	0	0.074	0.034	25.210	-0.005	-0.005	0.000	0.000	0.000
105	4	110	GLY	0	-0.018	-0.001	28.837	-0.003	-0.003	0.000	0.000	0.000
106	4	111	VAL	0	-0.055	-0.042	24.482	-0.005	-0.005	0.000	0.000	0.000
107	4	112	GLU	-1	-0.868	-0.938	27.624	0.016	0.016	0.000	0.000	0.000
108	4	113	ARG	1	0.914	0.959	28.021	0.024	0.024	0.000	0.000	0.000
109	4	114	PRO	0	-0.037	-0.010	29.660	0.001	0.001	0.000	0.000	0.000
110	4	115	VAL	0	0.051	0.037	27.822	-0.004	-0.004	0.000	0.000	0.000
111	4	116	LYS	1	0.932	0.971	30.544	0.017	0.017	0.000	0.000	0.000
112	4	117	ALA	0	0.108	0.044	31.714	0.000	0.000	0.000	0.000	0.000
113	4	118	ALA	0	-0.013	-0.014	32.462	0.000	0.000	0.000	0.000	0.000
114	4	119	GLU	-1	-0.860	-0.937	29.910	-0.014	-0.014	0.000	0.000	0.000
115	4	120	LEU	0	0.058	0.026	26.369	-0.001	-0.001	0.000	0.000	0.000
116	4	121	PHE	0	0.041	0.011	28.707	0.000	0.000	0.000	0.000	0.000
117	4	122	ALA	0	-0.031	-0.009	30.795	-0.001	-0.001	0.000	0.000	0.000
118	4	123	PHE	0	0.007	0.001	24.897	-0.001	-0.001	0.000	0.000	0.000
119	4	124	THR	0	-0.032	-0.002	26.356	0.000	0.000	0.000	0.000	0.000
120	4	125	LEU	0	-0.027	-0.006	27.532	0.002	0.002	0.000	0.000	0.000
121	4	126	ARG	1	0.949	0.967	27.330	0.025	0.025	0.000	0.000	0.000
122	4	127	VAL	0	-0.006	0.002	22.274	-0.001	-0.001	0.000	0.000	0.000
123	4	128	ARG	1	0.895	0.945	25.210	-0.021	-0.021	0.000	0.000	0.000
124	4	129	ALA	0	-0.071	-0.006	27.341	0.002	0.002	0.000	0.000	0.000
125	4	130	GLY	0	0.038	0.012	26.033	-0.001	-0.001	0.000	0.000	0.000
126	4	131	ASN	0	-0.092	-0.053	25.757	0.000	0.000	0.000	0.000	0.000
127	4	132	THR	0	0.068	-0.003	19.554	0.005	0.005	0.000	0.000	0.000
128	4	133	ASP	-1	-0.879	-0.937	21.059	-0.070	-0.070	0.000	0.000	0.000
129	4	134	VAL	0	-0.029	-0.002	22.500	-0.003	-0.003	0.000	0.000	0.000
130	4	135	LEU	0	-0.043	-0.010	18.028	0.000	0.000	0.000	0.000	0.000
131	4	136	THR	0	0.025	0.000	17.268	-0.005	-0.005	0.000	0.000	0.000
132	4	137	ASP	-1	-0.900	-0.931	18.262	-0.113	-0.113	0.000	0.000	0.000
133	4	138	ALA	0	0.018	-0.008	20.142	-0.010	-0.010	0.000	0.000	0.000
134	4	139	GLU	-1	-0.766	-0.847	12.471	-0.196	-0.196	0.000	0.000	0.000
135	4	140	GLU	-1	-0.963	-0.966	16.262	-0.244	-0.244	0.000	0.000	0.000
136	4	141	ASN	0	-0.019	0.007	17.618	-0.007	-0.007	0.000	0.000	0.000
137	4	142	VAL	0	-0.003	0.000	15.853	0.001	0.001	0.000	0.000	0.000
138	4	143	ARG	1	0.899	0.946	11.188	0.338	0.338	0.000	0.000	0.000
139	4	144	GLN	0	0.004	-0.012	15.881	0.011	0.011	0.000	0.000	0.000
140	4	145	LYS	1	0.806	0.907	18.896	0.082	0.082	0.000	0.000	0.000
141	4	146	LEU	0	0.041	-0.006	14.228	0.007	0.007	0.000	0.000	0.000
142	4	147	ARG	1	0.925	0.976	15.354	0.276	0.276	0.000	0.000	0.000
143	4	148	ALA	0	-0.040	-0.003	17.799	0.007	0.007	0.000	0.000	0.000
144	4	149	GLU	-1	-0.953	-0.964	19.389	-0.048	-0.048	0.000	0.000	0.000
145	4	150	GLY	0	0.008	0.022	18.754	0.013	0.013	0.000	0.000	0.000
146	4	151	VAL	0	-0.081	-0.035	13.105	0.008	0.008	0.000	0.000	0.000
147	4	152	MET	-1	-0.949	-0.980	10.618	-0.307	-0.307	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(4:6:ACE )