FMO DATABASE

FMODB ID: 3J7RL

Calculation Name: 1P1L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1P1L

Chain ID: A

ChEMBL ID:

UniProt ID: O28301

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-787868.413584
FMO2-HF: Nuclear repulsion	745735.957072
FMO2-HF: Total energy	-42132.456512
FMO2-MP2: Total energy	-42253.317734

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:1:MET)

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

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.
-5.254	0.426	0.452	-2.77	-3.361	-0.002

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.010

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

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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	3	ASN	0	-0.010	-0.016	3.787	-1.058	1.074	-0.019	-1.089	-1.024	0.003
4	A	4	PHE	0	0.015	-0.002	5.971	0.286	0.286	0.000	0.000	0.000	0.000
5	A	5	ILE	0	-0.002	-0.005	9.677	0.155	0.155	0.000	0.000	0.000	0.000
6	A	6	TYR	0	0.015	0.007	11.687	0.045	0.045	0.000	0.000	0.000	0.000
7	A	7	ILE	0	0.002	-0.008	14.994	0.048	0.048	0.000	0.000	0.000	0.000
8	A	8	THR	0	-0.037	-0.019	18.084	-0.015	-0.015	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.015	0.005	21.807	0.012	0.012	0.000	0.000	0.000	0.000
10	A	10	PRO	0	0.065	0.040	24.571	0.001	0.001	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.015	-0.016	27.886	0.006	0.006	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.049	0.027	26.692	-0.016	-0.016	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.856	-0.917	27.430	-0.206	-0.206	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.785	-0.876	25.689	-0.232	-0.232	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.029	0.002	23.500	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.863	-0.949	23.004	-0.322	-0.322	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.822	0.913	24.384	0.192	0.192	0.000	0.000	0.000	0.000
18	A	18	ILE	0	0.033	-0.001	19.829	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.006	-0.004	19.613	-0.033	-0.033	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.880	0.925	19.880	0.258	0.258	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.932	0.981	21.094	0.242	0.242	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.003	-0.006	15.730	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.049	-0.016	16.407	-0.031	-0.031	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.950	-0.973	18.190	-0.275	-0.275	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.877	0.947	18.128	0.261	0.261	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.896	0.965	14.960	0.502	0.502	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.019	0.005	12.975	-0.050	-0.050	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.004	0.003	11.861	-0.193	-0.193	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.030	0.028	11.842	0.124	0.124	0.000	0.000	0.000	0.000
30	A	30	CYS	0	-0.054	-0.028	13.583	0.137	0.137	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.041	0.019	14.794	-0.091	-0.091	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.052	-0.021	17.231	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	33	ILE	0	0.045	0.017	19.227	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	34	PHE	0	-0.011	-0.002	19.529	0.015	0.015	0.000	0.000	0.000	0.000
35	A	35	PRO	0	0.007	0.021	24.461	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	36	ILE	0	-0.016	-0.005	23.332	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.938	0.971	27.072	0.169	0.169	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.028	-0.041	26.146	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	39	PHE	0	-0.007	-0.021	28.205	0.017	0.017	0.000	0.000	0.000	0.000
40	A	40	PHE	0	0.008	0.012	27.422	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	41	TRP	0	-0.002	0.004	29.286	0.007	0.007	0.000	0.000	0.000	0.000
42	A	42	TRP	0	0.000	0.000	29.664	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.916	-0.964	32.536	-0.076	-0.076	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.025	-0.017	35.400	0.002	0.002	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.822	0.919	35.760	0.091	0.091	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.013	-0.006	32.644	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.835	-0.906	32.786	-0.104	-0.104	0.000	0.000	0.000	0.000
48	A	48	ALA	0	-0.005	-0.025	32.106	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.006	0.005	30.611	0.007	0.007	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.048	-0.021	30.486	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.762	-0.814	25.686	-0.245	-0.245	0.000	0.000	0.000	0.000
52	A	52	PHE	0	0.001	-0.012	24.867	0.002	0.002	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.037	0.034	20.412	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	54	MET	0	-0.020	-0.008	18.554	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.017	-0.003	13.739	-0.033	-0.033	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.008	-0.004	12.541	0.008	0.008	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.867	0.949	10.465	0.920	0.920	0.000	0.000	0.000	0.000
58	A	58	THR	0	0.037	-0.018	8.420	0.251	0.251	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.870	0.931	4.156	-1.060	-0.635	0.002	-0.120	-0.307	0.000
60	A	60	SER	0	0.000	-0.029	2.501	-2.563	0.171	0.472	-1.534	-1.672	-0.005
61	A	61	GLU	-1	-0.889	-0.923	4.404	0.845	1.111	-0.001	-0.015	-0.250	0.000
62	A	62	LYS	1	0.894	0.955	6.216	0.913	0.913	0.000	0.000	0.000	0.000
63	A	63	PHE	0	-0.031	-0.022	8.208	0.129	0.129	0.000	0.000	0.000	0.000
64	A	64	ALA	0	-0.005	-0.007	10.079	0.078	0.078	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.820	-0.920	11.795	-0.259	-0.259	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.013	-0.005	11.993	0.031	0.031	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.802	0.874	14.056	0.213	0.213	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.814	-0.884	15.805	-0.124	-0.124	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.897	-0.935	17.608	-0.230	-0.230	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.006	-0.017	17.218	0.020	0.020	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.889	0.942	19.888	0.175	0.175	0.000	0.000	0.000	0.000
72	A	72	ALA	0	-0.027	0.000	21.840	0.022	0.022	0.000	0.000	0.000	0.000
73	A	73	MET	0	-0.101	-0.037	22.882	0.007	0.007	0.000	0.000	0.000	0.000
74	A	74	HIS	0	-0.073	-0.020	22.044	0.019	0.019	0.000	0.000	0.000	0.000
75	A	75	SER	0	-0.009	-0.035	25.173	0.025	0.025	0.000	0.000	0.000	0.000
76	A	76	TYR	0	-0.117	-0.093	24.701	0.023	0.023	0.000	0.000	0.000	0.000
77	A	77	THR	0	0.040	0.022	26.161	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	78	THR	0	-0.058	-0.057	23.352	0.006	0.006	0.000	0.000	0.000	0.000
79	A	79	PRO	0	0.027	0.036	21.087	0.001	0.001	0.000	0.000	0.000	0.000
80	A	80	CYS	0	0.005	0.012	18.117	0.002	0.002	0.000	0.000	0.000	0.000
81	A	81	ILE	0	-0.006	-0.010	14.471	-0.038	-0.038	0.000	0.000	0.000	0.000
82	A	82	CYS	0	-0.031	-0.013	13.656	0.063	0.063	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.004	0.007	8.088	-0.102	-0.102	0.000	0.000	0.000	0.000
84	A	84	ILE	0	-0.013	-0.010	9.346	0.182	0.182	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.006	0.004	5.470	-0.434	-0.434	0.000	0.000	0.000	0.000
86	A	86	ILE	0	-0.016	0.003	4.949	0.599	0.599	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.953	-0.968	4.541	-1.296	-1.258	-0.001	-0.007	-0.029	0.000
88	A	88	ARG	1	0.937	0.951	6.607	0.720	0.720	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.037	0.007	7.978	-0.030	-0.030	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.044	-0.005	8.714	0.029	0.029	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.865	0.906	7.567	0.513	0.513	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.792	-0.896	8.865	-0.815	-0.815	0.000	0.000	0.000	0.000
93	A	93	PHE	0	-0.046	-0.020	10.647	0.023	0.023	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.008	-0.012	4.678	-0.021	0.064	-0.001	-0.005	-0.079	0.000
95	A	95	ASP	-1	-0.790	-0.883	7.334	-1.164	-1.164	0.000	0.000	0.000	0.000
96	A	96	TRP	0	-0.005	0.008	8.547	0.096	0.096	0.000	0.000	0.000	0.000
97	A	97	ILE	0	-0.046	-0.023	7.878	0.116	0.116	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.779	-0.875	5.269	-2.563	-2.563	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.920	-0.952	8.217	-0.268	-0.268	0.000	0.000	0.000	0.000
100	A	100	THR	0	-0.126	-0.060	11.688	0.168	0.168	0.000	0.000	0.000	0.000
101	A	101	VAL	0	-0.084	-0.051	8.476	0.099	0.099	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.945	-0.957	7.343	-0.069	-0.069	0.000	0.000	0.000	0.000

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