FMO DATABASE

FMODB ID: 66VKZ

Calculation Name: 4XPM-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XPM

Chain ID: B

ChEMBL ID:

UniProt ID: Q02205

Base Structure: X-ray

Registration Date: 2023-06-19

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	67
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-360312.152029
FMO2-HF: Nuclear repulsion	335566.465671
FMO2-HF: Total energy	-24745.686358
FMO2-MP2: Total energy	-24819.54709

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(B:8:ASP)

Summations of interaction energy for fragment #1(B:8:ASP)

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.
-47.192	-50.108	19.871	-9.251	-7.703	0.095

Interaction energy analysis for fragmet #1(B:8:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.815 / q_NPA : -0.917

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	B	10	LYS	1	0.810	0.890	1.685	-116.715	-120.653	19.815	-8.944	-6.933	0.095
4	B	11	GLY	0	0.025	0.013	5.114	-5.950	-5.818	-0.001	-0.006	-0.124	0.000
5	B	12	THR	0	-0.077	-0.029	8.372	1.646	1.646	0.000	0.000	0.000	0.000
6	B	13	ILE	0	0.032	0.022	11.317	-0.746	-0.746	0.000	0.000	0.000	0.000
7	B	14	ALA	0	0.021	0.030	15.131	0.020	0.020	0.000	0.000	0.000	0.000
8	B	15	PHE	0	0.012	-0.008	17.705	-0.416	-0.416	0.000	0.000	0.000	0.000
9	B	16	ASP	-1	-0.726	-0.845	21.310	11.903	11.903	0.000	0.000	0.000	0.000
10	B	17	THR	0	-0.023	-0.028	24.689	0.234	0.234	0.000	0.000	0.000	0.000
11	B	18	HIS	0	-0.125	-0.064	27.076	-0.669	-0.669	0.000	0.000	0.000	0.000
12	B	19	GLY	0	0.018	0.020	24.353	-0.136	-0.136	0.000	0.000	0.000	0.000
13	B	20	ASN	0	-0.097	-0.049	24.398	0.308	0.308	0.000	0.000	0.000	0.000
14	B	21	VAL	0	0.022	0.003	19.179	0.205	0.205	0.000	0.000	0.000	0.000
15	B	22	ILE	0	-0.076	-0.028	20.304	-0.613	-0.613	0.000	0.000	0.000	0.000
16	B	23	GLU	-1	-0.849	-0.924	14.060	22.709	22.709	0.000	0.000	0.000	0.000
17	B	24	SER	0	0.022	0.016	14.550	-0.189	-0.189	0.000	0.000	0.000	0.000
18	B	25	THR	0	-0.010	-0.018	10.147	1.168	1.168	0.000	0.000	0.000	0.000
19	B	26	GLY	0	0.036	0.013	8.763	1.361	1.361	0.000	0.000	0.000	0.000
20	B	27	VAL	0	-0.015	-0.039	8.367	-2.834	-2.834	0.000	0.000	0.000	0.000
21	B	28	GLY	0	0.024	0.023	10.769	-2.011	-2.011	0.000	0.000	0.000	0.000
22	B	29	SER	0	-0.010	-0.024	12.939	-1.310	-1.310	0.000	0.000	0.000	0.000
23	B	30	GLN	0	-0.123	-0.054	13.736	-1.259	-1.259	0.000	0.000	0.000	0.000
24	B	31	ARG	1	0.848	0.908	13.123	-23.233	-23.233	0.000	0.000	0.000	0.000
25	B	32	ILE	0	0.021	0.021	16.750	-0.150	-0.150	0.000	0.000	0.000	0.000
26	B	33	GLU	-1	-0.892	-0.958	19.322	15.156	15.156	0.000	0.000	0.000	0.000
27	B	34	ASP	-1	-0.787	-0.871	15.667	19.151	19.151	0.000	0.000	0.000	0.000
28	B	35	ILE	0	-0.028	-0.001	19.101	-0.309	-0.309	0.000	0.000	0.000	0.000
29	B	36	GLY	0	0.003	0.017	20.699	-0.604	-0.604	0.000	0.000	0.000	0.000
30	B	37	ASP	-1	-0.877	-0.940	20.913	12.439	12.439	0.000	0.000	0.000	0.000
31	B	38	LEU	0	-0.019	-0.021	15.556	-0.133	-0.133	0.000	0.000	0.000	0.000
32	B	39	SER	0	-0.069	-0.046	19.279	-0.298	-0.298	0.000	0.000	0.000	0.000
33	B	40	LYS	1	0.811	0.902	22.497	-12.617	-12.617	0.000	0.000	0.000	0.000
34	B	41	VAL	0	-0.038	-0.009	18.287	-0.365	-0.365	0.000	0.000	0.000	0.000
35	B	42	THR	0	-0.052	-0.025	21.478	-0.262	-0.262	0.000	0.000	0.000	0.000
36	B	43	LEU	0	-0.027	-0.012	18.409	0.162	0.162	0.000	0.000	0.000	0.000
37	B	44	ASP	-1	-0.794	-0.896	19.039	13.470	13.470	0.000	0.000	0.000	0.000
38	B	45	ALA	0	-0.054	-0.042	21.971	-0.124	-0.124	0.000	0.000	0.000	0.000
39	B	46	GLU	-1	-0.982	-0.983	20.590	12.680	12.680	0.000	0.000	0.000	0.000
40	B	47	GLY	0	-0.021	-0.005	20.627	0.146	0.146	0.000	0.000	0.000	0.000
41	B	48	PHE	0	-0.037	-0.029	14.698	0.824	0.824	0.000	0.000	0.000	0.000
42	B	49	ALA	0	0.019	0.009	15.508	-0.933	-0.933	0.000	0.000	0.000	0.000
43	B	50	GLN	0	-0.051	-0.034	9.870	0.358	0.358	0.000	0.000	0.000	0.000
44	B	51	VAL	0	0.010	0.018	13.229	-1.228	-1.228	0.000	0.000	0.000	0.000
45	B	52	GLN	0	-0.022	-0.027	12.413	1.447	1.447	0.000	0.000	0.000	0.000
46	B	53	GLY	0	0.045	0.032	14.239	-1.203	-1.203	0.000	0.000	0.000	0.000
47	B	54	ASP	-1	-0.835	-0.902	13.836	22.308	22.308	0.000	0.000	0.000	0.000
48	B	55	SER	0	-0.020	-0.013	11.842	-0.349	-0.349	0.000	0.000	0.000	0.000
49	B	56	LEU	0	-0.053	-0.016	7.988	2.854	2.854	0.000	0.000	0.000	0.000
50	B	57	LEU	0	-0.026	0.004	7.462	-2.434	-2.434	0.000	0.000	0.000	0.000
51	B	58	VAL	0	0.020	0.007	8.213	2.906	2.906	0.000	0.000	0.000	0.000
52	B	59	HIS	0	-0.003	-0.006	5.914	-4.211	-4.211	0.000	0.000	0.000	0.000
53	B	60	LEU	0	0.006	-0.006	10.731	0.546	0.546	0.000	0.000	0.000	0.000
54	B	61	TYR	0	-0.021	-0.011	14.183	-0.338	-0.338	0.000	0.000	0.000	0.000
55	B	62	LYS	1	0.876	0.952	16.461	-12.206	-12.206	0.000	0.000	0.000	0.000
56	B	63	ARG	1	0.932	0.968	20.091	-13.054	-13.054	0.000	0.000	0.000	0.000
57	B	64	ASN	0	-0.040	-0.035	22.548	0.324	0.324	0.000	0.000	0.000	0.000
58	B	65	ASP	-1	-0.817	-0.920	25.376	11.219	11.219	0.000	0.000	0.000	0.000
59	B	66	ILE	0	-0.016	0.020	19.829	0.026	0.026	0.000	0.000	0.000	0.000
60	B	67	THR	0	-0.005	-0.004	18.068	-0.059	-0.059	0.000	0.000	0.000	0.000
61	B	68	LEU	0	-0.026	-0.016	13.040	0.134	0.134	0.000	0.000	0.000	0.000
62	B	69	ALA	0	0.023	0.017	13.233	-0.320	-0.320	0.000	0.000	0.000	0.000
63	B	70	VAL	0	-0.017	-0.016	7.781	1.152	1.152	0.000	0.000	0.000	0.000
64	B	71	TYR	0	-0.040	-0.042	7.949	-0.808	-0.808	0.000	0.000	0.000	0.000
65	B	72	THR	0	-0.017	-0.015	2.995	5.154	5.754	0.058	-0.249	-0.409	0.000
66	B	73	SER	0	0.020	0.001	4.160	-1.817	-1.527	-0.001	-0.052	-0.237	0.000
67	B	74	ALA	0	-0.003	0.025	5.760	0.701	0.701	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:8:ASP)