FMO DATABASE

FMODB ID: 39MYL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-914688.973895
FMO2-HF: Nuclear repulsion	870302.047364
FMO2-HF: Total energy	-44386.926531
FMO2-MP2: Total energy	-44517.184929

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.
-2.147	0.661	6.004	-2.895	-5.918	-0.004

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 : 0.027 / q_NPA : 0.021

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	0.035	0.004	3.814	-0.121	2.042	-0.015	-0.967	-1.181	0.006
4	A	4	VAL	0	0.076	0.024	5.451	0.603	0.603	0.000	0.000	0.000	0.000
5	A	5	ARG	1	0.914	0.954	8.046	1.166	1.166	0.000	0.000	0.000	0.000
6	A	6	GLN	0	0.046	0.020	9.896	0.106	0.106	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.039	0.014	13.616	-0.050	-0.050	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.062	0.023	15.528	0.021	0.021	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.026	0.001	14.681	-0.045	-0.045	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.025	-0.018	18.660	0.018	0.018	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.000	0.002	22.377	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	12	THR	0	-0.068	-0.046	24.889	0.007	0.007	0.000	0.000	0.000	0.000
13	A	13	VAL	0	-0.068	-0.020	28.481	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	14	TRP	0	0.023	0.021	30.427	0.004	0.004	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.866	-0.957	33.529	-0.102	-0.102	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.005	0.008	35.218	0.003	0.003	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.919	-0.945	30.974	-0.136	-0.136	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.033	-0.003	27.601	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.006	0.016	25.867	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	20	ILE	0	-0.010	-0.011	20.751	0.002	0.002	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.003	0.025	19.722	-0.025	-0.025	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.035	-0.029	15.852	0.033	0.033	0.000	0.000	0.000	0.000
23	A	23	CYS	0	-0.030	-0.002	12.791	-0.028	-0.028	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.038	-0.007	9.000	0.076	0.076	0.000	0.000	0.000	0.000
25	A	25	TYR	0	0.028	0.033	7.261	-0.292	-0.292	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.801	-0.882	2.172	-3.767	-3.688	6.010	-1.852	-4.237	-0.010
27	A	27	ASN	0	0.034	0.031	4.358	1.288	1.701	0.009	-0.059	-0.363	0.000
28	A	28	SER	0	0.037	0.003	6.084	-0.565	-0.565	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.031	-0.025	8.249	-0.228	-0.228	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.049	-0.014	7.666	-0.053	-0.053	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.735	-0.844	11.581	0.198	0.198	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.013	-0.012	14.832	-0.038	-0.038	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.026	-0.006	11.155	-0.035	-0.035	0.000	0.000	0.000	0.000
34	A	34	PRO	0	-0.010	0.001	16.151	0.004	0.004	0.000	0.000	0.000	0.000
35	A	35	TRP	0	0.033	-0.007	16.746	-0.058	-0.058	0.000	0.000	0.000	0.000
36	A	36	TYR	0	-0.014	-0.013	18.901	0.025	0.025	0.000	0.000	0.000	0.000
37	A	37	GLN	0	0.018	0.000	22.057	-0.013	-0.013	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.021	-0.026	23.786	0.020	0.020	0.000	0.000	0.000	0.000
39	A	39	PHE	0	0.084	0.041	25.570	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	40	PRO	0	-0.009	-0.034	28.903	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	41	GLY	0	-0.010	0.013	30.244	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.972	-0.966	29.842	-0.126	-0.126	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.004	0.016	26.627	-0.015	-0.015	0.000	0.000	0.000	0.000
44	A	44	PRO	0	-0.050	-0.030	22.202	0.006	0.006	0.000	0.000	0.000	0.000
45	A	45	ALA	0	0.060	0.032	24.656	0.009	0.009	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.075	-0.049	22.039	-0.011	-0.011	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.019	0.016	23.844	0.010	0.010	0.000	0.000	0.000	0.000
48	A	48	ILE	0	0.047	0.026	22.821	0.013	0.013	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.044	-0.022	20.697	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.046	-0.020	18.347	0.014	0.014	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.016	0.009	18.700	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.030	-0.050	15.683	-0.022	-0.022	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.006	0.002	17.444	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.071	-0.020	20.512	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	55	ASN	0	0.061	0.018	19.841	0.000	0.000	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.970	0.985	20.805	0.059	0.059	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.884	0.926	23.648	0.062	0.062	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.908	-0.960	25.560	-0.077	-0.077	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.930	-0.945	28.202	-0.090	-0.090	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.069	0.018	29.839	0.007	0.007	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.688	0.817	31.250	0.113	0.113	0.000	0.000	0.000	0.000
62	A	62	PHE	0	0.084	0.043	26.131	-0.014	-0.014	0.000	0.000	0.000	0.000
63	A	63	THR	0	-0.063	-0.034	24.534	0.014	0.014	0.000	0.000	0.000	0.000
64	A	64	ILE	0	0.006	0.038	19.235	-0.018	-0.018	0.000	0.000	0.000	0.000
65	A	65	PHE	0	-0.037	-0.017	20.499	0.027	0.027	0.000	0.000	0.000	0.000
66	A	66	PHE	0	-0.035	-0.027	13.585	-0.027	-0.027	0.000	0.000	0.000	0.000
67	A	67	ASN	0	-0.018	-0.019	14.996	0.053	0.053	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.925	0.953	12.067	-0.268	-0.268	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.827	0.901	11.530	0.130	0.130	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.820	-0.883	10.439	-0.221	-0.221	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.818	0.904	3.894	-0.246	-0.093	0.000	-0.017	-0.137	0.000
72	A	72	LYS	1	0.883	0.934	9.129	0.561	0.561	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.027	-0.008	12.723	0.070	0.070	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.001	-0.003	15.379	-0.041	-0.041	0.000	0.000	0.000	0.000
75	A	75	LEU	0	0.020	0.029	18.337	0.032	0.032	0.000	0.000	0.000	0.000
76	A	76	HIS	0	-0.021	-0.030	21.310	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	77	ILE	0	0.008	0.000	24.653	0.010	0.010	0.000	0.000	0.000	0.000
78	A	78	ALA	0	-0.004	-0.008	27.395	0.000	0.000	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.902	-0.955	30.517	-0.096	-0.096	0.000	0.000	0.000	0.000
80	A	80	SER	0	-0.011	-0.016	29.918	0.001	0.001	0.000	0.000	0.000	0.000
81	A	81	GLN	0	0.056	0.050	31.883	0.003	0.003	0.000	0.000	0.000	0.000
82	A	82	PRO	0	0.032	0.003	33.063	-0.009	-0.009	0.000	0.000	0.000	0.000
83	A	83	GLY	0	0.001	0.011	33.960	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	84	ASP	-1	-0.780	-0.874	29.179	-0.139	-0.139	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.011	-0.009	28.683	-0.019	-0.019	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.038	0.026	26.812	0.006	0.006	0.000	0.000	0.000	0.000
87	A	87	THR	0	-0.034	-0.005	21.365	-0.019	-0.019	0.000	0.000	0.000	0.000
88	A	88	TYR	0	-0.012	-0.010	21.338	0.013	0.013	0.000	0.000	0.000	0.000
89	A	89	PHE	0	-0.005	-0.003	17.137	-0.043	-0.043	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.032	0.016	13.813	-0.076	-0.076	0.000	0.000	0.000	0.000
91	A	92	ALA	0	0.015	0.001	10.793	0.034	0.034	0.000	0.000	0.000	0.000
92	A	93	SER	0	0.022	0.020	12.296	-0.024	-0.024	0.000	0.000	0.000	0.000
93	A	94	ALA	0	-0.018	-0.019	12.590	0.028	0.028	0.000	0.000	0.000	0.000
94	A	95	SER	0	-0.037	-0.022	13.759	0.013	0.013	0.000	0.000	0.000	0.000
95	A	96	PHE	0	0.030	0.017	17.504	-0.027	-0.027	0.000	0.000	0.000	0.000
96	A	97	GLY	0	0.013	0.007	20.527	0.015	0.015	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.882	-0.943	20.541	0.095	0.095	0.000	0.000	0.000	0.000
98	A	99	ASN	0	-0.033	-0.009	21.171	-0.028	-0.028	0.000	0.000	0.000	0.000
99	A	100	SER	0	-0.026	0.007	15.915	0.029	0.029	0.000	0.000	0.000	0.000
100	A	101	LYS	1	0.944	0.959	13.483	0.242	0.242	0.000	0.000	0.000	0.000
101	A	102	LEU	0	0.025	0.018	14.006	0.020	0.020	0.000	0.000	0.000	0.000
102	A	103	ILE	0	-0.081	-0.057	9.019	-0.068	-0.068	0.000	0.000	0.000	0.000
103	A	104	TRP	0	-0.025	-0.021	11.955	0.004	0.004	0.000	0.000	0.000	0.000
104	A	105	GLY	0	-0.007	0.008	11.897	-0.138	-0.138	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.047	-0.057	12.553	0.018	0.018	0.000	0.000	0.000	0.000
106	A	107	GLY	0	-0.010	0.002	15.320	0.049	0.049	0.000	0.000	0.000	0.000
107	A	108	THR	0	-0.081	-0.040	18.040	-0.031	-0.031	0.000	0.000	0.000	0.000
108	A	109	SER	0	0.000	-0.005	19.988	0.033	0.033	0.000	0.000	0.000	0.000
109	A	110	LEU	0	-0.027	-0.017	23.563	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	111	VAL	0	-0.003	0.005	26.183	0.009	0.009	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.004	0.012	29.579	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	113	ASN	0	-0.023	-0.008	32.068	0.008	0.008	0.000	0.000	0.000	0.000
113	A	114	PRO	0	0.058	0.036	35.488	-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)