FMO DATABASE

FMODB ID: YVJV2

Calculation Name: 3BAT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BAT

Chain ID: A

ChEMBL ID:

UniProt ID: P03069

Base Structure: X-ray

Registration Date: 2023-09-23

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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-370712.932978
FMO2-HF: Nuclear repulsion	337752.538031
FMO2-HF: Total energy	-32960.394947
FMO2-MP2: Total energy	-33054.46943

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:843:GLU)

Summations of interaction energy for fragment #1(A:843:GLU)

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.
-44.299	-40.58	0.123	-1.439	-2.403	0.004

Interaction energy analysis for fragmet #1(A:843:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.927 / q_NPA : -0.973

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	845	GLU	-1	-0.962	-0.967	2.920	19.642	22.502	0.116	-1.294	-1.681	0.004
4	A	846	MET	0	0.014	-0.004	3.572	-3.315	-2.707	0.007	-0.106	-0.510	0.000
5	A	847	LYS	1	0.886	0.924	3.866	-49.741	-49.490	0.000	-0.039	-0.212	0.000
6	A	848	GLU	-1	-0.850	-0.883	7.410	19.551	19.551	0.000	0.000	0.000	0.000
7	A	849	GLN	0	0.043	0.012	8.653	-1.907	-1.907	0.000	0.000	0.000	0.000
8	A	850	LEU	0	-0.001	-0.007	8.286	-1.598	-1.598	0.000	0.000	0.000	0.000
9	A	851	LYS	1	0.885	0.934	9.663	-26.875	-26.875	0.000	0.000	0.000	0.000
10	A	852	GLN	0	-0.045	-0.031	13.248	-2.111	-2.111	0.000	0.000	0.000	0.000
11	A	853	MET	0	0.002	0.009	14.193	-0.823	-0.823	0.000	0.000	0.000	0.000
12	A	854	ASP	-1	-0.824	-0.908	15.075	16.693	16.693	0.000	0.000	0.000	0.000
13	A	855	LYS	1	0.887	0.933	17.285	-13.804	-13.804	0.000	0.000	0.000	0.000
14	A	856	MET	0	-0.004	-0.010	18.985	-0.702	-0.702	0.000	0.000	0.000	0.000
15	A	857	LYS	1	0.802	0.896	15.806	-17.329	-17.329	0.000	0.000	0.000	0.000
16	A	858	GLU	-1	-0.849	-0.917	21.181	12.669	12.669	0.000	0.000	0.000	0.000
17	A	859	ASP	-1	-0.794	-0.879	23.340	11.618	11.618	0.000	0.000	0.000	0.000
18	A	860	LEU	0	0.009	0.029	24.709	-0.528	-0.528	0.000	0.000	0.000	0.000
19	A	861	ALA	0	0.043	0.020	25.854	-0.463	-0.463	0.000	0.000	0.000	0.000
20	A	862	LYS	1	0.717	0.854	24.125	-12.383	-12.383	0.000	0.000	0.000	0.000
21	A	863	THR	0	0.010	-0.010	28.755	-0.404	-0.404	0.000	0.000	0.000	0.000
22	A	864	GLU	-1	-0.831	-0.903	30.158	8.858	8.858	0.000	0.000	0.000	0.000
23	A	865	ARG	1	0.865	0.920	28.311	-10.369	-10.369	0.000	0.000	0.000	0.000
24	A	866	ILE	0	0.044	0.029	32.861	-0.227	-0.227	0.000	0.000	0.000	0.000
25	A	867	LYS	1	0.797	0.891	33.897	-8.918	-8.918	0.000	0.000	0.000	0.000
26	A	868	LYS	1	0.889	0.931	36.494	-7.929	-7.929	0.000	0.000	0.000	0.000
27	A	869	GLU	-1	-0.906	-0.949	38.177	7.650	7.650	0.000	0.000	0.000	0.000
28	A	870	LEU	0	0.011	0.003	38.667	-0.238	-0.238	0.000	0.000	0.000	0.000
29	A	871	GLU	-1	-0.907	-0.963	38.909	7.620	7.620	0.000	0.000	0.000	0.000
30	A	872	GLU	-1	-0.866	-0.921	41.960	7.256	7.256	0.000	0.000	0.000	0.000
31	A	873	GLN	0	-0.059	-0.021	42.402	-0.313	-0.313	0.000	0.000	0.000	0.000
32	A	874	ASN	0	-0.053	-0.026	45.439	-0.223	-0.223	0.000	0.000	0.000	0.000
33	A	875	VAL	0	0.021	0.006	46.657	-0.154	-0.154	0.000	0.000	0.000	0.000
34	A	876	THR	0	0.014	0.000	48.257	-0.163	-0.163	0.000	0.000	0.000	0.000
35	A	877	LEU	0	-0.022	-0.017	48.863	-0.157	-0.157	0.000	0.000	0.000	0.000
36	A	878	LEU	0	-0.070	-0.033	50.009	-0.162	-0.162	0.000	0.000	0.000	0.000
37	A	879	GLU	-1	-0.933	-0.966	52.420	5.847	5.847	0.000	0.000	0.000	0.000
38	A	880	GLN	0	0.045	0.013	53.544	-0.123	-0.123	0.000	0.000	0.000	0.000
39	A	881	LYS	1	0.923	0.963	54.708	-5.729	-5.729	0.000	0.000	0.000	0.000
40	A	882	ASN	0	-0.016	0.001	56.458	-0.148	-0.148	0.000	0.000	0.000	0.000
41	A	883	ASP	-1	-0.867	-0.918	59.080	5.202	5.202	0.000	0.000	0.000	0.000
42	A	884	LEU	0	-0.048	-0.012	59.077	-0.121	-0.121	0.000	0.000	0.000	0.000
43	A	885	PHE	0	-0.002	-0.015	58.942	-0.075	-0.075	0.000	0.000	0.000	0.000
44	A	886	GLY	0	0.009	0.011	63.602	-0.091	-0.091	0.000	0.000	0.000	0.000
45	A	887	SER	0	-0.032	-0.035	64.747	-0.101	-0.101	0.000	0.000	0.000	0.000
46	A	888	MET	0	-0.058	-0.029	65.149	-0.047	-0.047	0.000	0.000	0.000	0.000
47	A	889	LYS	1	0.896	0.945	67.818	-4.457	-4.457	0.000	0.000	0.000	0.000
48	A	890	GLN	0	-0.015	-0.016	69.541	-0.075	-0.075	0.000	0.000	0.000	0.000
49	A	891	LEU	0	-0.037	-0.015	69.816	-0.084	-0.084	0.000	0.000	0.000	0.000
50	A	892	GLU	-1	-0.917	-0.968	69.415	4.456	4.456	0.000	0.000	0.000	0.000
51	A	893	ASP	-1	-0.828	-0.896	73.729	4.218	4.218	0.000	0.000	0.000	0.000
52	A	894	LYS	1	0.820	0.893	75.665	-4.104	-4.104	0.000	0.000	0.000	0.000
53	A	895	VAL	0	0.011	-0.002	75.985	-0.067	-0.067	0.000	0.000	0.000	0.000
54	A	896	GLU	-1	-0.845	-0.900	78.185	3.822	3.822	0.000	0.000	0.000	0.000
55	A	897	GLU	-1	-0.825	-0.873	79.977	3.870	3.870	0.000	0.000	0.000	0.000
56	A	898	LEU	0	-0.035	-0.033	80.176	-0.066	-0.066	0.000	0.000	0.000	0.000
57	A	899	LEU	0	0.002	0.012	80.469	-0.059	-0.059	0.000	0.000	0.000	0.000
58	A	900	SER	0	0.010	-0.018	84.116	-0.076	-0.076	0.000	0.000	0.000	0.000
59	A	901	LYS	1	0.787	0.884	84.009	-3.838	-3.838	0.000	0.000	0.000	0.000
60	A	902	ASN	0	-0.004	-0.003	85.669	-0.067	-0.067	0.000	0.000	0.000	0.000
61	A	903	TYR	0	0.074	0.048	88.294	-0.057	-0.057	0.000	0.000	0.000	0.000
62	A	904	HIS	0	-0.006	0.010	90.189	-0.042	-0.042	0.000	0.000	0.000	0.000
63	A	905	LEU	0	0.003	-0.012	90.255	-0.054	-0.054	0.000	0.000	0.000	0.000
64	A	906	GLU	-1	-0.913	-0.957	90.489	3.487	3.487	0.000	0.000	0.000	0.000
65	A	907	ASN	0	-0.062	-0.041	93.571	-0.080	-0.080	0.000	0.000	0.000	0.000
66	A	908	GLU	-1	-0.816	-0.874	96.140	3.201	3.201	0.000	0.000	0.000	0.000
67	A	909	VAL	0	-0.004	-0.003	96.544	-0.049	-0.049	0.000	0.000	0.000	0.000
68	A	910	ALA	0	-0.004	0.000	98.431	-0.046	-0.046	0.000	0.000	0.000	0.000
69	A	911	ARG	1	0.791	0.872	100.242	-3.218	-3.218	0.000	0.000	0.000	0.000
70	A	912	LEU	0	-0.001	-0.018	100.129	-0.044	-0.044	0.000	0.000	0.000	0.000
71	A	913	LYS	1	0.847	0.910	100.618	-3.193	-3.193	0.000	0.000	0.000	0.000
72	A	914	LYS	1	0.884	0.939	102.519	-3.146	-3.146	0.000	0.000	0.000	0.000
73	A	915	LEU	0	-0.038	-0.013	105.471	-0.033	-0.033	0.000	0.000	0.000	0.000
74	A	916	VAL	0	-0.029	-0.004	106.865	-0.025	-0.025	0.000	0.000	0.000	0.000
75	A	917	GLY	0	-0.014	0.005	109.589	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	918	GLU	-1	-0.825	-0.884	103.939	3.101	3.101	0.000	0.000	0.000	0.000
77	A	919	ARG	1	0.928	0.952	103.138	-2.893	-2.893	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:843:GLU)