FMO DATABASE

FMODB ID: 53R8Z

Calculation Name: 1BM8-A-Xray372

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: 2023-03-13

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	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-797776.86992
FMO2-HF: Nuclear repulsion	758464.867441
FMO2-HF: Total energy	-39312.002479
FMO2-MP2: Total energy	-39429.854266

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.
-7.998	-1.404	1.023	-2.855	-4.764	0.011

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 : 0.058 / q_NPA : 0.025

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	-0.001	0.018	2.592	-6.338	-1.796	0.842	-2.137	-3.247	0.013
4	A	7	SER	0	0.047	0.033	5.469	-1.087	-1.087	0.000	0.000	0.000	0.000
5	A	8	ALA	0	-0.010	-0.007	9.044	0.254	0.254	0.000	0.000	0.000	0.000
6	A	9	ARG	1	0.859	0.884	11.534	-0.434	-0.434	0.000	0.000	0.000	0.000
7	A	10	TYR	0	-0.059	-0.059	11.395	0.031	0.031	0.000	0.000	0.000	0.000
8	A	11	SER	0	0.007	0.005	17.509	-0.026	-0.026	0.000	0.000	0.000	0.000
9	A	12	GLY	0	0.002	0.006	20.525	-0.022	-0.022	0.000	0.000	0.000	0.000
10	A	13	VAL	0	-0.019	-0.007	17.735	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	14	ASP	-1	-0.816	-0.865	15.193	0.366	0.366	0.000	0.000	0.000	0.000
12	A	15	VAL	0	-0.020	-0.035	11.690	-0.081	-0.081	0.000	0.000	0.000	0.000
13	A	16	TYR	0	0.039	0.016	8.794	0.245	0.245	0.000	0.000	0.000	0.000
14	A	17	GLU	-1	-0.763	-0.831	7.687	0.048	0.048	0.000	0.000	0.000	0.000
15	A	18	PHE	0	0.057	0.034	2.855	-0.820	-0.133	0.081	-0.265	-0.505	-0.001
16	A	19	ILE	0	-0.014	-0.010	2.747	0.838	1.895	0.098	-0.343	-0.812	0.000
17	A	20	HIS	0	0.046	0.034	3.873	-0.865	-0.557	0.002	-0.110	-0.200	-0.001
18	A	21	SER	0	0.027	0.007	6.676	0.212	0.212	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.062	-0.036	9.275	0.116	0.116	0.000	0.000	0.000	0.000
20	A	23	GLY	0	-0.005	-0.006	9.669	0.160	0.160	0.000	0.000	0.000	0.000
21	A	24	SER	0	-0.102	-0.075	7.797	-0.208	-0.208	0.000	0.000	0.000	0.000
22	A	25	ILE	0	-0.040	-0.019	8.068	0.279	0.279	0.000	0.000	0.000	0.000
23	A	26	MET	0	-0.039	0.000	8.917	-0.142	-0.142	0.000	0.000	0.000	0.000
24	A	27	LYS	1	0.790	0.893	11.538	0.363	0.363	0.000	0.000	0.000	0.000
25	A	28	ARG	1	0.744	0.835	13.164	0.115	0.115	0.000	0.000	0.000	0.000
26	A	29	LYS	1	0.898	0.942	12.006	-0.526	-0.526	0.000	0.000	0.000	0.000
27	A	30	LYS	1	0.856	0.927	16.091	-0.017	-0.017	0.000	0.000	0.000	0.000
28	A	31	ASP	-1	-0.718	-0.851	19.231	-0.047	-0.047	0.000	0.000	0.000	0.000
29	A	32	ASP	-1	-0.782	-0.877	15.168	-0.229	-0.229	0.000	0.000	0.000	0.000
30	A	33	TRP	0	-0.044	-0.020	16.960	-0.044	-0.044	0.000	0.000	0.000	0.000
31	A	34	VAL	0	0.023	0.000	12.990	-0.017	-0.017	0.000	0.000	0.000	0.000
32	A	35	ASN	0	-0.009	-0.003	14.732	0.030	0.030	0.000	0.000	0.000	0.000
33	A	36	ALA	0	0.085	0.024	15.386	-0.058	-0.058	0.000	0.000	0.000	0.000
34	A	37	THR	0	-0.025	-0.021	17.709	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	38	HIS	0	-0.007	-0.009	12.449	-0.072	-0.072	0.000	0.000	0.000	0.000
36	A	39	ILE	0	0.047	0.038	13.498	-0.054	-0.054	0.000	0.000	0.000	0.000
37	A	40	LEU	0	-0.016	-0.010	14.616	0.008	0.008	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.872	0.917	14.708	0.219	0.219	0.000	0.000	0.000	0.000
39	A	42	ALA	0	0.068	0.053	11.661	0.020	0.020	0.000	0.000	0.000	0.000
40	A	43	ALA	0	-0.011	0.005	13.315	0.009	0.009	0.000	0.000	0.000	0.000
41	A	44	ASN	0	-0.019	-0.009	15.100	0.041	0.041	0.000	0.000	0.000	0.000
42	A	45	PHE	0	0.052	0.035	17.717	0.041	0.041	0.000	0.000	0.000	0.000
43	A	46	ALA	0	0.094	0.042	20.314	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	47	LYS	1	0.992	0.989	22.815	0.054	0.054	0.000	0.000	0.000	0.000
45	A	48	ALA	0	0.055	0.025	23.823	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	49	LYS	1	0.857	0.951	23.172	0.158	0.158	0.000	0.000	0.000	0.000
47	A	50	ARG	1	0.910	0.946	19.076	0.162	0.162	0.000	0.000	0.000	0.000
48	A	51	THR	0	0.014	0.006	23.157	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	52	ARG	1	0.975	0.992	26.027	0.088	0.088	0.000	0.000	0.000	0.000
50	A	53	ILE	0	0.055	0.025	22.982	0.003	0.003	0.000	0.000	0.000	0.000
51	A	54	LEU	0	-0.013	-0.002	21.333	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	55	GLU	-1	-0.892	-0.958	25.184	-0.057	-0.057	0.000	0.000	0.000	0.000
53	A	56	LYS	1	0.814	0.922	28.337	0.075	0.075	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.826	-0.929	25.246	-0.121	-0.121	0.000	0.000	0.000	0.000
55	A	58	VAL	0	-0.020	-0.006	22.374	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	59	LEU	0	-0.023	-0.014	25.595	0.005	0.005	0.000	0.000	0.000	0.000
57	A	60	LYS	1	0.807	0.907	28.111	0.114	0.114	0.000	0.000	0.000	0.000
58	A	61	GLU	-1	-0.844	-0.908	25.461	-0.107	-0.107	0.000	0.000	0.000	0.000
59	A	62	THR	0	-0.002	0.013	25.906	0.010	0.010	0.000	0.000	0.000	0.000
60	A	63	HIS	0	-0.009	-0.018	24.313	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	64	GLU	-1	-0.819	-0.872	23.552	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	65	LYS	1	0.861	0.919	23.688	0.034	0.034	0.000	0.000	0.000	0.000
63	A	66	VAL	0	0.028	0.028	22.238	0.016	0.016	0.000	0.000	0.000	0.000
64	A	67	GLN	0	-0.018	-0.029	23.380	-0.017	-0.017	0.000	0.000	0.000	0.000
65	A	68	GLY	0	0.032	0.029	25.834	0.005	0.005	0.000	0.000	0.000	0.000
66	A	69	GLY	0	0.004	-0.001	23.481	0.013	0.013	0.000	0.000	0.000	0.000
67	A	70	PHE	0	0.004	-0.007	22.159	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	71	GLY	0	0.058	0.037	19.433	0.027	0.027	0.000	0.000	0.000	0.000
69	A	72	LYS	1	0.814	0.882	11.196	-0.170	-0.170	0.000	0.000	0.000	0.000
70	A	73	TYR	0	0.068	0.031	15.902	-0.060	-0.060	0.000	0.000	0.000	0.000
71	A	74	GLN	0	0.025	0.021	17.547	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	75	GLY	0	-0.002	0.006	18.872	-0.032	-0.032	0.000	0.000	0.000	0.000
73	A	76	THR	0	-0.053	-0.022	20.574	0.024	0.024	0.000	0.000	0.000	0.000
74	A	77	TRP	0	-0.030	-0.012	15.220	-0.046	-0.046	0.000	0.000	0.000	0.000
75	A	78	VAL	0	0.026	0.004	19.070	0.022	0.022	0.000	0.000	0.000	0.000
76	A	79	PRO	0	0.053	0.035	19.439	-0.019	-0.019	0.000	0.000	0.000	0.000
77	A	80	LEU	0	0.049	0.027	15.019	-0.026	-0.026	0.000	0.000	0.000	0.000
78	A	81	ASN	0	0.018	-0.004	18.287	-0.024	-0.024	0.000	0.000	0.000	0.000
79	A	82	ILE	0	0.041	0.023	20.799	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	83	ALA	0	-0.015	-0.009	16.073	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	84	LYS	1	0.948	0.987	15.544	0.284	0.284	0.000	0.000	0.000	0.000
82	A	85	GLN	0	0.079	0.038	17.630	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	86	LEU	0	-0.046	-0.015	18.411	0.003	0.003	0.000	0.000	0.000	0.000
84	A	87	ALA	0	0.001	-0.015	14.674	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	88	GLU	-1	-0.915	-0.952	16.679	-0.252	-0.252	0.000	0.000	0.000	0.000
86	A	89	LYS	1	0.876	0.954	18.932	0.156	0.156	0.000	0.000	0.000	0.000
87	A	90	PHE	0	-0.087	-0.066	18.821	0.022	0.022	0.000	0.000	0.000	0.000
88	A	91	SER	0	-0.003	0.003	18.119	-0.011	-0.011	0.000	0.000	0.000	0.000
89	A	92	VAL	0	-0.007	-0.009	12.977	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	93	TYR	0	0.017	0.000	12.495	-0.106	-0.106	0.000	0.000	0.000	0.000
91	A	94	ASP	-1	-0.873	-0.949	12.468	-0.428	-0.428	0.000	0.000	0.000	0.000
92	A	95	GLN	0	-0.029	-0.004	9.485	-0.078	-0.078	0.000	0.000	0.000	0.000
93	A	96	LEU	0	-0.023	-0.018	7.773	-0.246	-0.246	0.000	0.000	0.000	0.000
94	A	97	LYS	1	0.961	1.001	9.303	0.326	0.326	0.000	0.000	0.000	0.000
95	A	98	PRO	0	0.028	0.015	5.728	0.025	0.025	0.000	0.000	0.000	0.000
96	A	99	LEU	0	-0.011	0.004	7.134	0.051	0.051	0.000	0.000	0.000	0.000
97	A	100	PHE	0	-0.058	-0.048	8.329	0.218	0.218	0.000	0.000	0.000	0.000
98	A	101	ASP	-1	-0.894	-0.960	10.644	-0.435	-0.435	0.000	0.000	0.000	0.000
99	A	102	PHE	0	-0.012	0.016	6.583	0.129	0.129	0.000	0.000	0.000	0.000

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