FMO DATABASE

FMODB ID: JMZ69

Calculation Name: 1BM8-A-Xray308

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BM8

Chain ID: A

ChEMBL ID:

UniProt ID: P39678

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	99
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-797184.975737
FMO2-HF: Nuclear repulsion	757874.081095
FMO2-HF: Total energy	-39310.894643
FMO2-MP2: Total energy	-39428.751405

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:4:GLN )

Summations of interaction energy for fragment #1(A:4:GLN )

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.
-5.056	0.621	0.269	-2.314	-3.63	0.005

Interaction energy analysis for fragmet #1(A:4:GLN )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.059 / 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	6	TYR	0	0.005	0.019	2.967	-2.941	1.024	0.192	-1.693	-2.463	0.007
4	A	7	SER	0	0.051	0.039	5.365	-1.291	-1.291	0.000	-0.001	0.002	0.000
5	A	8	ALA	0	-0.020	-0.008	8.988	0.226	0.226	0.000	0.000	0.000	0.000
6	A	9	ARG	1	0.892	0.933	11.375	-0.479	-0.479	0.000	0.000	0.000	0.000
7	A	10	TYR	0	-0.063	-0.053	11.166	0.006	0.006	0.000	0.000	0.000	0.000
8	A	11	SER	0	0.008	0.003	17.280	-0.025	-0.025	0.000	0.000	0.000	0.000
9	A	12	GLY	0	-0.005	-0.001	20.336	-0.019	-0.019	0.000	0.000	0.000	0.000
10	A	13	VAL	0	-0.015	-0.010	17.531	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	14	ASP	-1	-0.842	-0.901	15.117	0.420	0.420	0.000	0.000	0.000	0.000
12	A	15	VAL	0	-0.021	-0.035	11.408	-0.085	-0.085	0.000	0.000	0.000	0.000
13	A	16	TYR	0	0.041	0.023	8.748	0.268	0.268	0.000	0.000	0.000	0.000
14	A	17	GLU	-1	-0.815	-0.911	7.502	0.015	0.015	0.000	0.000	0.000	0.000
15	A	18	PHE	0	0.058	0.037	3.621	-1.009	-0.553	0.012	-0.217	-0.251	-0.001
16	A	19	ILE	0	-0.017	-0.009	2.890	0.990	1.957	0.063	-0.304	-0.726	0.000
17	A	20	HIS	0	0.028	0.010	3.970	-0.784	-0.495	0.002	-0.099	-0.192	-0.001
18	A	21	SER	0	0.020	0.002	6.625	0.193	0.193	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.039	-0.018	9.335	0.068	0.068	0.000	0.000	0.000	0.000
20	A	23	GLY	0	-0.019	-0.010	9.782	0.143	0.143	0.000	0.000	0.000	0.000
21	A	24	SER	0	-0.061	-0.023	7.904	-0.208	-0.208	0.000	0.000	0.000	0.000
22	A	25	ILE	0	-0.055	-0.023	7.894	0.284	0.284	0.000	0.000	0.000	0.000
23	A	26	MET	0	-0.044	-0.006	8.760	-0.126	-0.126	0.000	0.000	0.000	0.000
24	A	27	LYS	1	0.832	0.909	11.385	0.245	0.245	0.000	0.000	0.000	0.000
25	A	28	ARG	1	0.753	0.868	13.050	0.079	0.079	0.000	0.000	0.000	0.000
26	A	29	LYS	1	0.904	0.936	12.049	-0.654	-0.654	0.000	0.000	0.000	0.000
27	A	30	LYS	1	0.874	0.941	16.079	-0.065	-0.065	0.000	0.000	0.000	0.000
28	A	31	ASP	-1	-0.740	-0.865	19.177	0.000	0.000	0.000	0.000	0.000	0.000
29	A	32	ASP	-1	-0.853	-0.907	16.210	-0.061	-0.061	0.000	0.000	0.000	0.000
30	A	33	TRP	0	-0.070	-0.046	16.893	-0.044	-0.044	0.000	0.000	0.000	0.000
31	A	34	VAL	0	0.023	-0.001	13.017	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	35	ASN	0	-0.011	-0.005	14.597	0.030	0.030	0.000	0.000	0.000	0.000
33	A	36	ALA	0	0.090	0.026	15.256	-0.054	-0.054	0.000	0.000	0.000	0.000
34	A	37	THR	0	-0.026	-0.021	17.591	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	38	HIS	0	0.007	-0.004	12.302	-0.059	-0.059	0.000	0.000	0.000	0.000
36	A	39	ILE	0	0.053	0.044	13.372	-0.049	-0.049	0.000	0.000	0.000	0.000
37	A	40	LEU	0	-0.035	-0.020	14.515	0.010	0.010	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.857	0.903	14.595	0.178	0.178	0.000	0.000	0.000	0.000
39	A	42	ALA	0	0.077	0.064	11.586	0.016	0.016	0.000	0.000	0.000	0.000
40	A	43	ALA	0	-0.025	-0.001	13.221	0.017	0.017	0.000	0.000	0.000	0.000
41	A	44	ASN	0	-0.008	-0.003	15.242	0.029	0.029	0.000	0.000	0.000	0.000
42	A	45	PHE	0	0.005	0.014	17.631	0.035	0.035	0.000	0.000	0.000	0.000
43	A	46	ALA	0	0.075	0.023	20.193	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	47	LYS	1	0.990	0.984	22.707	0.047	0.047	0.000	0.000	0.000	0.000
45	A	48	ALA	0	0.058	0.025	23.757	0.000	0.000	0.000	0.000	0.000	0.000
46	A	49	LYS	1	0.920	0.973	24.111	0.111	0.111	0.000	0.000	0.000	0.000
47	A	50	ARG	1	0.926	0.968	18.925	0.133	0.133	0.000	0.000	0.000	0.000
48	A	51	THR	0	0.009	0.003	23.034	0.001	0.001	0.000	0.000	0.000	0.000
49	A	52	ARG	1	0.963	0.988	25.891	0.069	0.069	0.000	0.000	0.000	0.000
50	A	53	ILE	0	0.037	0.021	23.021	0.003	0.003	0.000	0.000	0.000	0.000
51	A	54	LEU	0	-0.018	-0.005	21.210	0.000	0.000	0.000	0.000	0.000	0.000
52	A	55	GLU	-1	-0.927	-0.988	25.067	-0.036	-0.036	0.000	0.000	0.000	0.000
53	A	56	LYS	1	0.869	0.969	28.252	0.053	0.053	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.906	-1.004	25.369	-0.080	-0.080	0.000	0.000	0.000	0.000
55	A	58	VAL	0	0.006	0.009	22.333	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	59	LEU	0	-0.020	-0.006	25.498	0.006	0.006	0.000	0.000	0.000	0.000
57	A	60	LYS	1	0.856	0.954	28.173	0.074	0.074	0.000	0.000	0.000	0.000
58	A	61	GLU	-1	-0.906	-0.943	25.062	-0.072	-0.072	0.000	0.000	0.000	0.000
59	A	62	THR	0	0.007	0.012	25.920	0.007	0.007	0.000	0.000	0.000	0.000
60	A	63	HIS	0	-0.051	-0.055	24.202	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	64	GLU	-1	-0.856	-0.917	23.392	0.023	0.023	0.000	0.000	0.000	0.000
62	A	65	LYS	1	0.898	0.953	23.543	0.014	0.014	0.000	0.000	0.000	0.000
63	A	66	VAL	0	0.024	0.026	22.069	0.013	0.013	0.000	0.000	0.000	0.000
64	A	67	GLN	0	-0.002	-0.019	23.285	-0.013	-0.013	0.000	0.000	0.000	0.000
65	A	68	GLY	0	0.028	0.025	25.808	0.003	0.003	0.000	0.000	0.000	0.000
66	A	69	GLY	0	0.001	-0.002	23.458	0.012	0.012	0.000	0.000	0.000	0.000
67	A	70	PHE	0	0.009	-0.005	22.313	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	71	GLY	0	0.053	0.038	19.534	0.026	0.026	0.000	0.000	0.000	0.000
69	A	72	LYS	1	0.830	0.902	11.483	-0.160	-0.160	0.000	0.000	0.000	0.000
70	A	73	TYR	0	0.075	0.035	16.025	-0.052	-0.052	0.000	0.000	0.000	0.000
71	A	74	GLN	0	0.018	0.013	17.640	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	75	GLY	0	-0.013	0.005	18.810	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	76	THR	0	-0.046	-0.019	20.389	0.022	0.022	0.000	0.000	0.000	0.000
74	A	77	TRP	0	-0.034	-0.011	15.174	-0.037	-0.037	0.000	0.000	0.000	0.000
75	A	78	VAL	0	0.025	0.004	18.977	0.017	0.017	0.000	0.000	0.000	0.000
76	A	79	PRO	0	0.055	0.035	19.347	-0.013	-0.013	0.000	0.000	0.000	0.000
77	A	80	LEU	0	0.090	0.044	15.034	-0.021	-0.021	0.000	0.000	0.000	0.000
78	A	81	ASN	0	0.008	-0.008	18.256	-0.021	-0.021	0.000	0.000	0.000	0.000
79	A	82	ILE	0	0.056	0.026	20.779	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	83	ALA	0	-0.001	-0.003	15.955	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	84	LYS	1	0.956	0.987	15.825	0.158	0.158	0.000	0.000	0.000	0.000
82	A	85	GLN	0	0.047	0.026	17.619	0.002	0.002	0.000	0.000	0.000	0.000
83	A	86	LEU	0	-0.040	-0.016	18.506	0.001	0.001	0.000	0.000	0.000	0.000
84	A	87	ALA	0	0.008	-0.010	14.664	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	88	GLU	-1	-0.918	-0.954	16.655	-0.164	-0.164	0.000	0.000	0.000	0.000
86	A	89	LYS	1	0.935	0.989	18.944	0.112	0.112	0.000	0.000	0.000	0.000
87	A	90	PHE	0	-0.095	-0.066	18.671	0.016	0.016	0.000	0.000	0.000	0.000
88	A	91	SER	0	-0.010	0.000	18.125	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	92	VAL	0	-0.003	-0.005	12.945	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	93	TYR	0	0.013	-0.001	12.505	-0.076	-0.076	0.000	0.000	0.000	0.000
91	A	94	ASP	-1	-0.880	-0.955	12.517	-0.263	-0.263	0.000	0.000	0.000	0.000
92	A	95	GLN	0	-0.028	0.002	9.453	-0.044	-0.044	0.000	0.000	0.000	0.000
93	A	96	LEU	0	-0.025	-0.021	7.815	-0.173	-0.173	0.000	0.000	0.000	0.000
94	A	97	LYS	1	0.973	1.000	9.316	0.169	0.169	0.000	0.000	0.000	0.000
95	A	98	PRO	0	0.019	0.014	5.796	0.006	0.006	0.000	0.000	0.000	0.000
96	A	99	LEU	0	0.013	0.017	7.147	-0.014	-0.014	0.000	0.000	0.000	0.000
97	A	100	PHE	0	-0.085	-0.059	8.323	0.198	0.198	0.000	0.000	0.000	0.000
98	A	101	ASP	-1	-0.949	-0.994	10.391	-0.266	-0.266	0.000	0.000	0.000	0.000
99	A	102	PHE	-1	-0.840	-0.888	6.351	-0.032	-0.032	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:GLN )