FMO DATABASE

FMODB ID: JLVJ9

Calculation Name: 1B88-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B88

Chain ID: A

ChEMBL ID:

UniProt ID: Q5R1B3

Base Structure: X-ray

Registration Date: 2023-06-26

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	OptH
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	113
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-915782.111303
FMO2-HF: Nuclear repulsion	871396.017737
FMO2-HF: Total energy	-44386.093566
FMO2-MP2: Total energy	-44516.467475

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.
-1.26	-4.974	14.277	-3.86	-6.703	-0.017

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 : -0.012 / q_NPA : -0.018

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	3	GLN	0	0.034	0.013	3.814	-0.476	0.870	-0.012	-0.441	-0.893	0.003
4	A	4	VAL	0	0.071	0.021	5.411	0.385	0.385	0.000	0.000	0.000	0.000
5	A	5	ARG	1	0.907	0.951	8.027	0.441	0.441	0.000	0.000	0.000	0.000
6	A	6	GLN	0	0.041	0.021	9.877	0.010	0.010	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.038	0.018	13.598	0.042	0.042	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.061	0.024	15.511	-0.012	-0.012	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.020	-0.015	14.840	-0.025	-0.025	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.011	-0.009	18.642	0.005	0.005	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.007	0.003	22.359	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	12	THR	0	-0.094	-0.062	24.871	0.009	0.009	0.000	0.000	0.000	0.000
13	A	13	VAL	0	-0.076	-0.016	28.538	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	14	TRP	0	0.010	0.015	30.410	0.005	0.005	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.868	-0.961	33.512	-0.066	-0.066	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.000	0.012	35.230	0.002	0.002	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.877	-0.930	31.112	-0.083	-0.083	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.062	-0.019	27.677	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.010	0.018	25.847	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	20	ILE	0	-0.013	-0.013	20.758	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.006	0.027	19.764	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.032	-0.023	15.716	-0.016	-0.016	0.000	0.000	0.000	0.000
23	A	23	CYS	0	-0.044	-0.007	12.776	-0.027	-0.027	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.075	-0.033	9.296	0.033	0.033	0.000	0.000	0.000	0.000
25	A	25	TYR	0	0.026	0.036	7.260	-0.141	-0.141	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.826	-0.909	1.887	-2.858	-8.463	14.280	-3.330	-5.344	-0.020
27	A	27	ASN	0	0.035	0.024	4.067	0.335	0.771	0.010	-0.079	-0.367	0.000
28	A	28	SER	0	-0.002	-0.028	5.762	-0.346	-0.346	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.026	-0.018	7.590	-0.075	-0.075	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.056	-0.008	7.294	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.786	-0.876	11.487	-0.131	-0.131	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.026	-0.019	14.748	0.001	0.001	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.022	-0.012	11.179	-0.036	-0.036	0.000	0.000	0.000	0.000
34	A	34	PRO	0	-0.021	-0.008	15.974	0.018	0.018	0.000	0.000	0.000	0.000
35	A	35	TRP	0	0.038	-0.004	16.578	-0.040	-0.040	0.000	0.000	0.000	0.000
36	A	36	TYR	0	-0.004	-0.006	19.104	0.025	0.025	0.000	0.000	0.000	0.000
37	A	37	GLN	0	0.031	0.013	22.022	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	38	GLN	0	0.019	0.003	23.758	0.010	0.010	0.000	0.000	0.000	0.000
39	A	39	PHE	0	0.077	0.041	25.551	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	40	PRO	0	-0.028	-0.041	28.890	0.000	0.000	0.000	0.000	0.000	0.000
41	A	41	GLY	0	-0.005	0.014	30.244	0.003	0.003	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.980	-0.974	29.783	-0.075	-0.075	0.000	0.000	0.000	0.000
43	A	43	GLY	0	-0.008	0.005	26.592	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	44	PRO	0	-0.078	-0.036	22.250	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	ALA	0	0.076	0.034	24.618	0.001	0.001	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.070	-0.048	21.871	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.001	0.014	23.800	0.008	0.008	0.000	0.000	0.000	0.000
48	A	48	ILE	0	0.044	0.020	22.963	0.006	0.006	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.018	-0.006	20.656	-0.014	-0.014	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.044	-0.020	18.242	0.017	0.017	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.002	0.009	18.636	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.020	-0.062	14.970	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.004	0.005	16.830	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.060	-0.019	19.870	0.007	0.007	0.000	0.000	0.000	0.000
55	A	55	ASN	0	0.071	0.009	19.592	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.962	0.979	20.611	0.123	0.123	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.867	0.924	23.175	0.141	0.141	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.947	-0.960	25.526	-0.098	-0.098	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.917	-0.940	28.194	-0.099	-0.099	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.098	0.032	29.805	0.008	0.008	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.689	0.824	31.236	0.091	0.091	0.000	0.000	0.000	0.000
62	A	62	PHE	0	0.092	0.038	25.645	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	63	THR	0	-0.051	-0.028	24.619	0.006	0.006	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.018	0.027	19.166	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	65	PHE	0	-0.023	-0.019	20.356	0.017	0.017	0.000	0.000	0.000	0.000
66	A	66	PHE	0	-0.056	0.005	13.510	-0.026	-0.026	0.000	0.000	0.000	0.000
67	A	67	ASN	0	0.004	0.016	14.575	0.010	0.010	0.000	0.000	0.000	0.000
68	A	68	LYS	1	1.025	0.998	11.498	0.174	0.174	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.838	0.924	11.216	0.255	0.255	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.849	-0.948	10.390	-0.458	-0.458	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.824	0.922	3.920	1.118	1.227	-0.001	-0.010	-0.099	0.000
72	A	72	LYS	1	0.917	0.955	9.029	0.651	0.651	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.014	-0.006	12.536	0.056	0.056	0.000	0.000	0.000	0.000
74	A	74	SER	0	0.014	-0.004	15.377	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	75	LEU	0	0.008	0.030	18.344	0.015	0.015	0.000	0.000	0.000	0.000
76	A	76	HIS	0	-0.019	-0.033	21.310	0.014	0.014	0.000	0.000	0.000	0.000
77	A	77	ILE	0	0.011	0.005	24.661	0.003	0.003	0.000	0.000	0.000	0.000
78	A	78	ALA	0	-0.009	-0.007	27.401	0.005	0.005	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.904	-0.956	30.526	-0.073	-0.073	0.000	0.000	0.000	0.000
80	A	80	SER	0	-0.027	-0.030	30.099	0.004	0.004	0.000	0.000	0.000	0.000
81	A	81	GLN	0	0.082	0.054	31.899	0.007	0.007	0.000	0.000	0.000	0.000
82	A	82	PRO	0	0.026	-0.001	33.073	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	83	GLY	0	0.002	0.013	33.971	0.000	0.000	0.000	0.000	0.000	0.000
84	A	84	ASP	-1	-0.773	-0.873	29.233	-0.099	-0.099	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.023	-0.009	28.689	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.068	0.027	26.642	0.005	0.005	0.000	0.000	0.000	0.000
87	A	87	THR	0	-0.051	-0.012	21.441	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	88	TYR	0	-0.030	-0.036	21.377	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	89	PHE	0	0.010	-0.001	17.210	-0.021	-0.021	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.036	0.017	13.804	-0.041	-0.041	0.000	0.000	0.000	0.000
91	A	92	ALA	0	0.012	0.002	10.737	0.007	0.007	0.000	0.000	0.000	0.000
92	A	93	SER	0	0.006	-0.001	12.213	-0.018	-0.018	0.000	0.000	0.000	0.000
93	A	94	ALA	0	-0.024	-0.019	12.463	0.000	0.000	0.000	0.000	0.000	0.000
94	A	95	SER	0	-0.016	-0.012	13.650	0.012	0.012	0.000	0.000	0.000	0.000
95	A	96	PHE	0	0.027	0.022	17.397	-0.011	-0.011	0.000	0.000	0.000	0.000
96	A	97	GLY	0	0.012	0.006	20.425	0.009	0.009	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.903	-0.946	20.761	-0.019	-0.019	0.000	0.000	0.000	0.000
98	A	99	ASN	0	-0.019	-0.003	21.060	-0.022	-0.022	0.000	0.000	0.000	0.000
99	A	100	SER	0	0.003	0.012	15.747	0.014	0.014	0.000	0.000	0.000	0.000
100	A	101	LYS	1	0.949	0.963	13.216	0.213	0.213	0.000	0.000	0.000	0.000
101	A	102	LEU	0	0.000	0.004	13.905	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	103	ILE	0	-0.085	-0.052	8.868	-0.025	-0.025	0.000	0.000	0.000	0.000
103	A	104	TRP	0	-0.015	-0.016	11.882	-0.019	-0.019	0.000	0.000	0.000	0.000
104	A	105	GLY	0	-0.001	0.007	11.885	-0.079	-0.079	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.049	-0.058	12.814	0.042	0.042	0.000	0.000	0.000	0.000
106	A	107	GLY	0	-0.021	-0.003	15.320	0.041	0.041	0.000	0.000	0.000	0.000
107	A	108	THR	0	-0.064	-0.019	18.005	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	109	SER	0	-0.014	-0.016	19.969	0.011	0.011	0.000	0.000	0.000	0.000
109	A	110	LEU	0	-0.017	-0.005	23.544	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	111	VAL	0	-0.003	0.004	26.165	0.006	0.006	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.003	0.025	29.561	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	113	ASN	0	-0.011	-0.013	32.050	0.002	0.002	0.000	0.000	0.000	0.000
113	A	114	PRO	0	0.044	0.038	35.470	-0.001	-0.001	0.000	0.000	0.000	0.000

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