FMO DATABASE

FMODB ID: 2239R

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:

Apendix: None

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	67
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-360701.226128
FMO2-HF: Nuclear repulsion	335955.597936
FMO2-HF: Total energy	-24745.628191
FMO2-MP2: Total energy	-24819.504911

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.
-40.257	-41.505	17.649	-8.621	-7.779	0.092

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 : -0.835 / q_NPA : -0.930

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	0.807	0.890	1.750	-109.724	-111.575	17.646	-8.500	-7.294	0.092
4	B	11	GLY	0	0.019	0.000	5.112	-5.442	-5.312	-0.001	-0.006	-0.123	0.000
5	B	12	THR	0	-0.062	-0.021	8.364	1.505	1.505	0.000	0.000	0.000	0.000
6	B	13	ILE	0	0.026	0.019	11.229	-0.695	-0.695	0.000	0.000	0.000	0.000
7	B	14	ALA	0	0.018	0.028	15.016	-0.052	-0.052	0.000	0.000	0.000	0.000
8	B	15	PHE	0	0.023	-0.004	17.482	-0.458	-0.458	0.000	0.000	0.000	0.000
9	B	16	ASP	-1	-0.753	-0.880	21.071	12.051	12.051	0.000	0.000	0.000	0.000
10	B	17	THR	0	-0.029	-0.022	24.486	0.168	0.168	0.000	0.000	0.000	0.000
11	B	18	HIS	0	-0.116	-0.049	27.141	-0.667	-0.667	0.000	0.000	0.000	0.000
12	B	19	GLY	0	0.004	0.009	24.753	-0.145	-0.145	0.000	0.000	0.000	0.000
13	B	20	ASN	0	-0.051	-0.019	24.660	0.303	0.303	0.000	0.000	0.000	0.000
14	B	21	VAL	0	-0.010	-0.008	19.166	0.274	0.274	0.000	0.000	0.000	0.000
15	B	22	ILE	0	-0.053	-0.027	20.031	-0.595	-0.595	0.000	0.000	0.000	0.000
16	B	23	GLU	-1	-0.866	-0.929	14.175	22.924	22.924	0.000	0.000	0.000	0.000
17	B	24	SER	0	0.005	0.015	14.635	-0.049	-0.049	0.000	0.000	0.000	0.000
18	B	25	THR	0	0.018	0.010	10.398	1.007	1.007	0.000	0.000	0.000	0.000
19	B	26	GLY	0	0.039	0.010	8.608	1.167	1.167	0.000	0.000	0.000	0.000
20	B	27	VAL	0	-0.023	-0.038	8.513	-2.926	-2.926	0.000	0.000	0.000	0.000
21	B	28	GLY	0	0.030	0.021	10.824	-2.157	-2.157	0.000	0.000	0.000	0.000
22	B	29	SER	0	-0.020	-0.029	12.858	-1.315	-1.315	0.000	0.000	0.000	0.000
23	B	30	GLN	0	-0.108	-0.053	13.732	-1.276	-1.276	0.000	0.000	0.000	0.000
24	B	31	ARG	1	0.837	0.891	13.230	-23.469	-23.469	0.000	0.000	0.000	0.000
25	B	32	ILE	0	0.037	0.037	16.607	-0.336	-0.336	0.000	0.000	0.000	0.000
26	B	33	GLU	-1	-0.909	-0.966	19.014	14.942	14.942	0.000	0.000	0.000	0.000
27	B	34	ASP	-1	-0.843	-0.902	16.229	18.729	18.729	0.000	0.000	0.000	0.000
28	B	35	ILE	0	-0.042	-0.011	19.755	-0.296	-0.296	0.000	0.000	0.000	0.000
29	B	36	GLY	0	0.019	0.024	21.246	-0.473	-0.473	0.000	0.000	0.000	0.000
30	B	37	ASP	-1	-0.844	-0.925	21.304	12.679	12.679	0.000	0.000	0.000	0.000
31	B	38	LEU	0	-0.002	-0.004	16.241	-0.207	-0.207	0.000	0.000	0.000	0.000
32	B	39	SER	0	-0.086	-0.046	20.007	-0.356	-0.356	0.000	0.000	0.000	0.000
33	B	40	LYS	1	0.820	0.904	23.017	-12.584	-12.584	0.000	0.000	0.000	0.000
34	B	41	VAL	0	-0.052	-0.016	19.092	-0.370	-0.370	0.000	0.000	0.000	0.000
35	B	42	THR	0	-0.055	-0.023	22.269	-0.293	-0.293	0.000	0.000	0.000	0.000
36	B	43	LEU	0	-0.057	-0.026	19.032	0.181	0.181	0.000	0.000	0.000	0.000
37	B	44	ASP	-1	-0.779	-0.892	19.678	13.335	13.335	0.000	0.000	0.000	0.000
38	B	45	ALA	0	-0.048	-0.039	22.532	-0.057	-0.057	0.000	0.000	0.000	0.000
39	B	46	GLU	-1	-0.991	-0.987	21.048	12.644	12.644	0.000	0.000	0.000	0.000
40	B	47	GLY	0	-0.030	-0.005	21.125	0.344	0.344	0.000	0.000	0.000	0.000
41	B	48	PHE	0	-0.008	-0.021	14.996	0.982	0.982	0.000	0.000	0.000	0.000
42	B	49	ALA	0	0.020	0.011	16.209	-0.896	-0.896	0.000	0.000	0.000	0.000
43	B	50	GLN	0	-0.049	-0.026	10.659	0.427	0.427	0.000	0.000	0.000	0.000
44	B	51	VAL	0	0.010	0.018	14.181	-1.082	-1.082	0.000	0.000	0.000	0.000
45	B	52	GLN	0	-0.013	-0.029	12.709	1.167	1.167	0.000	0.000	0.000	0.000
46	B	53	GLY	0	0.019	0.036	14.704	-1.099	-1.099	0.000	0.000	0.000	0.000
47	B	54	ASP	-1	-0.776	-0.873	13.920	21.817	21.817	0.000	0.000	0.000	0.000
48	B	55	SER	0	-0.034	-0.021	11.948	-0.268	-0.268	0.000	0.000	0.000	0.000
49	B	56	LEU	0	-0.079	-0.029	8.215	2.584	2.584	0.000	0.000	0.000	0.000
50	B	57	LEU	0	-0.025	-0.003	7.945	-2.234	-2.234	0.000	0.000	0.000	0.000
51	B	58	VAL	0	0.021	0.005	8.911	2.605	2.605	0.000	0.000	0.000	0.000
52	B	59	HIS	0	-0.025	-0.018	6.684	-3.711	-3.711	0.000	0.000	0.000	0.000
53	B	60	LEU	0	0.009	-0.005	11.484	0.581	0.581	0.000	0.000	0.000	0.000
54	B	61	TYR	0	-0.005	-0.004	14.951	-0.482	-0.482	0.000	0.000	0.000	0.000
55	B	62	LYS	1	0.887	0.963	16.862	-12.171	-12.171	0.000	0.000	0.000	0.000
56	B	63	ARG	1	0.931	0.967	20.404	-13.182	-13.182	0.000	0.000	0.000	0.000
57	B	64	ASN	0	-0.035	-0.026	22.627	0.390	0.390	0.000	0.000	0.000	0.000
58	B	65	ASP	-1	-0.838	-0.922	25.490	11.299	11.299	0.000	0.000	0.000	0.000
59	B	66	ILE	0	-0.017	-0.001	19.950	-0.007	-0.007	0.000	0.000	0.000	0.000
60	B	67	THR	0	-0.017	-0.008	18.101	0.010	0.010	0.000	0.000	0.000	0.000
61	B	68	LEU	0	-0.020	-0.012	12.818	0.241	0.241	0.000	0.000	0.000	0.000
62	B	69	ALA	0	0.030	0.016	13.684	-0.304	-0.304	0.000	0.000	0.000	0.000
63	B	70	VAL	0	-0.018	-0.012	7.665	1.319	1.319	0.000	0.000	0.000	0.000
64	B	71	TYR	0	-0.029	-0.047	8.512	-0.875	-0.875	0.000	0.000	0.000	0.000
65	B	72	THR	0	0.012	0.012	3.445	5.911	6.178	0.005	-0.097	-0.175	0.000
66	B	73	SER	0	0.008	0.004	4.282	-1.815	-1.609	-0.001	-0.018	-0.187	0.000
67	B	74	ALA	0	0.026	0.030	6.137	0.225	0.225	0.000	0.000	0.000	0.000

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