FMO DATABASE

FMODB ID: YY9M2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-800004.913973
FMO2-HF: Nuclear repulsion	760692.637193
FMO2-HF: Total energy	-39312.27678
FMO2-MP2: Total energy	-39430.121518

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.
-17.581	-13.013	7.52	-5.101	-6.989	0.033

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 : 0.072 / q_NPA : 0.038

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	-0.020	-0.001	1.926	-16.106	-13.494	7.292	-4.401	-5.503	0.033
4	A	7	SER	0	0.025	0.016	5.576	-0.853	-0.853	0.000	0.000	0.000	0.000
5	A	8	ALA	0	0.004	0.003	9.243	0.295	0.295	0.000	0.000	0.000	0.000
6	A	9	ARG	1	0.866	0.914	11.453	-0.429	-0.429	0.000	0.000	0.000	0.000
7	A	10	TYR	0	-0.048	-0.053	10.958	0.077	0.077	0.000	0.000	0.000	0.000
8	A	11	SER	0	-0.015	-0.009	17.437	-0.035	-0.035	0.000	0.000	0.000	0.000
9	A	12	GLY	0	0.025	0.025	20.762	-0.031	-0.031	0.000	0.000	0.000	0.000
10	A	13	VAL	0	-0.030	-0.016	18.173	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	14	ASP	-1	-0.770	-0.860	15.590	0.324	0.324	0.000	0.000	0.000	0.000
12	A	15	VAL	0	-0.046	-0.044	11.551	-0.087	-0.087	0.000	0.000	0.000	0.000
13	A	16	TYR	0	0.065	0.033	9.093	0.201	0.201	0.000	0.000	0.000	0.000
14	A	17	GLU	-1	-0.753	-0.833	7.760	0.340	0.340	0.000	0.000	0.000	0.000
15	A	18	PHE	0	0.056	0.030	3.115	-0.374	0.137	0.021	-0.187	-0.346	-0.001
16	A	19	ILE	0	-0.019	-0.012	2.570	0.750	1.954	0.206	-0.434	-0.977	0.001
17	A	20	HIS	0	0.053	0.044	4.009	-1.049	-0.808	0.001	-0.079	-0.163	0.000
18	A	21	SER	0	0.036	0.011	6.845	0.294	0.294	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.053	-0.038	9.485	0.162	0.162	0.000	0.000	0.000	0.000
20	A	23	GLY	0	-0.025	-0.011	9.782	0.150	0.150	0.000	0.000	0.000	0.000
21	A	24	SER	0	-0.094	-0.068	7.847	-0.223	-0.223	0.000	0.000	0.000	0.000
22	A	25	ILE	0	-0.038	-0.021	8.410	0.223	0.223	0.000	0.000	0.000	0.000
23	A	26	MET	0	-0.052	-0.004	9.228	-0.188	-0.188	0.000	0.000	0.000	0.000
24	A	27	LYS	1	0.797	0.889	11.620	0.608	0.608	0.000	0.000	0.000	0.000
25	A	28	ARG	1	0.745	0.841	13.265	0.146	0.146	0.000	0.000	0.000	0.000
26	A	29	LYS	1	0.839	0.901	12.088	-0.344	-0.344	0.000	0.000	0.000	0.000
27	A	30	LYS	1	0.858	0.928	16.155	0.046	0.046	0.000	0.000	0.000	0.000
28	A	31	ASP	-1	-0.739	-0.857	19.196	-0.117	-0.117	0.000	0.000	0.000	0.000
29	A	32	ASP	-1	-0.769	-0.870	15.197	-0.427	-0.427	0.000	0.000	0.000	0.000
30	A	33	TRP	0	-0.027	-0.009	17.104	-0.044	-0.044	0.000	0.000	0.000	0.000
31	A	34	VAL	0	0.019	-0.001	13.277	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	35	ASN	0	0.009	-0.003	15.100	0.036	0.036	0.000	0.000	0.000	0.000
33	A	36	ALA	0	0.075	0.033	15.780	-0.056	-0.056	0.000	0.000	0.000	0.000
34	A	37	THR	0	-0.036	-0.021	18.025	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	38	HIS	0	-0.009	-0.014	12.886	-0.067	-0.067	0.000	0.000	0.000	0.000
36	A	39	ILE	0	0.029	0.032	13.837	-0.045	-0.045	0.000	0.000	0.000	0.000
37	A	40	LEU	0	-0.005	-0.013	14.846	0.005	0.005	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.851	0.930	14.025	0.227	0.227	0.000	0.000	0.000	0.000
39	A	42	ALA	0	0.073	0.047	11.767	0.032	0.032	0.000	0.000	0.000	0.000
40	A	43	ALA	0	-0.005	0.004	13.263	0.009	0.009	0.000	0.000	0.000	0.000
41	A	44	ASN	0	-0.013	-0.008	15.121	0.048	0.048	0.000	0.000	0.000	0.000
42	A	45	PHE	0	0.049	0.036	17.477	0.046	0.046	0.000	0.000	0.000	0.000
43	A	46	ALA	0	0.113	0.050	20.281	0.003	0.003	0.000	0.000	0.000	0.000
44	A	47	LYS	1	0.974	0.984	22.723	0.017	0.017	0.000	0.000	0.000	0.000
45	A	48	ALA	0	0.052	0.023	23.804	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	49	LYS	1	0.830	0.951	23.012	0.159	0.159	0.000	0.000	0.000	0.000
47	A	50	ARG	1	0.918	0.952	19.005	0.123	0.123	0.000	0.000	0.000	0.000
48	A	51	THR	0	0.010	0.001	23.111	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	52	ARG	1	0.973	0.976	25.992	0.072	0.072	0.000	0.000	0.000	0.000
50	A	53	ILE	0	0.047	0.024	23.048	0.001	0.001	0.000	0.000	0.000	0.000
51	A	54	LEU	0	-0.003	-0.004	21.484	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	55	GLU	-1	-0.887	-0.948	25.283	-0.057	-0.057	0.000	0.000	0.000	0.000
53	A	56	LYS	1	0.818	0.925	28.392	0.077	0.077	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.831	-0.926	25.041	-0.141	-0.141	0.000	0.000	0.000	0.000
55	A	58	VAL	0	-0.019	0.000	22.641	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	59	LEU	0	-0.035	-0.030	25.832	0.004	0.004	0.000	0.000	0.000	0.000
57	A	60	LYS	1	0.826	0.908	28.220	0.144	0.144	0.000	0.000	0.000	0.000
58	A	61	GLU	-1	-0.839	-0.892	25.853	-0.142	-0.142	0.000	0.000	0.000	0.000
59	A	62	THR	0	-0.020	0.001	26.195	0.013	0.013	0.000	0.000	0.000	0.000
60	A	63	HIS	0	0.005	-0.009	24.587	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	64	GLU	-1	-0.802	-0.872	23.641	-0.037	-0.037	0.000	0.000	0.000	0.000
62	A	65	LYS	1	0.889	0.930	23.801	0.046	0.046	0.000	0.000	0.000	0.000
63	A	66	VAL	0	0.027	0.036	21.944	0.019	0.019	0.000	0.000	0.000	0.000
64	A	67	GLN	0	-0.019	-0.025	23.219	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	68	GLY	0	0.052	0.027	25.697	0.011	0.011	0.000	0.000	0.000	0.000
66	A	69	GLY	0	0.003	0.008	23.693	0.015	0.015	0.000	0.000	0.000	0.000
67	A	70	PHE	0	-0.008	-0.017	22.050	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	71	GLY	0	0.076	0.045	19.313	0.027	0.027	0.000	0.000	0.000	0.000
69	A	72	LYS	1	0.831	0.889	10.820	-0.505	-0.505	0.000	0.000	0.000	0.000
70	A	73	TYR	0	0.065	0.032	15.857	-0.076	-0.076	0.000	0.000	0.000	0.000
71	A	74	GLN	0	0.008	0.009	17.601	-0.020	-0.020	0.000	0.000	0.000	0.000
72	A	75	GLY	0	-0.025	-0.005	18.750	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	76	THR	0	-0.039	-0.022	20.878	0.018	0.018	0.000	0.000	0.000	0.000
74	A	77	TRP	0	-0.046	-0.025	15.426	-0.052	-0.052	0.000	0.000	0.000	0.000
75	A	78	VAL	0	0.013	-0.005	19.474	0.028	0.028	0.000	0.000	0.000	0.000
76	A	79	PRO	0	0.048	0.032	19.656	-0.031	-0.031	0.000	0.000	0.000	0.000
77	A	80	LEU	0	0.019	0.017	15.522	-0.020	-0.020	0.000	0.000	0.000	0.000
78	A	81	ASN	0	0.015	0.004	18.441	-0.035	-0.035	0.000	0.000	0.000	0.000
79	A	82	ILE	0	0.043	0.021	20.854	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	83	ALA	0	-0.038	-0.020	16.226	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	84	LYS	1	0.896	0.962	15.906	0.450	0.450	0.000	0.000	0.000	0.000
82	A	85	GLN	0	0.123	0.054	17.765	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	86	LEU	0	-0.059	-0.023	18.581	0.017	0.017	0.000	0.000	0.000	0.000
84	A	87	ALA	0	0.004	-0.012	14.992	0.006	0.006	0.000	0.000	0.000	0.000
85	A	88	GLU	-1	-0.923	-0.964	17.015	-0.337	-0.337	0.000	0.000	0.000	0.000
86	A	89	LYS	1	0.867	0.943	19.355	0.185	0.185	0.000	0.000	0.000	0.000
87	A	90	PHE	0	-0.061	-0.052	19.028	0.034	0.034	0.000	0.000	0.000	0.000
88	A	91	SER	0	-0.003	0.006	18.317	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	92	VAL	0	-0.002	-0.006	13.129	-0.013	-0.013	0.000	0.000	0.000	0.000
90	A	93	TYR	0	0.006	0.000	12.791	-0.127	-0.127	0.000	0.000	0.000	0.000
91	A	94	ASP	-1	-0.852	-0.944	12.633	-0.615	-0.615	0.000	0.000	0.000	0.000
92	A	95	GLN	0	-0.022	-0.001	9.509	-0.122	-0.122	0.000	0.000	0.000	0.000
93	A	96	LEU	0	-0.017	-0.017	7.989	-0.319	-0.319	0.000	0.000	0.000	0.000
94	A	97	LYS	1	0.947	0.995	9.744	0.541	0.541	0.000	0.000	0.000	0.000
95	A	98	PRO	0	0.046	0.027	6.238	0.052	0.052	0.000	0.000	0.000	0.000
96	A	99	LEU	0	-0.027	-0.008	7.722	-0.070	-0.070	0.000	0.000	0.000	0.000
97	A	100	PHE	0	-0.044	-0.045	8.999	0.249	0.249	0.000	0.000	0.000	0.000
98	A	101	ASP	-1	-0.867	-0.944	11.134	-0.707	-0.707	0.000	0.000	0.000	0.000
99	A	102	PHE	0	-0.006	0.023	6.444	0.119	0.119	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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