FMO DATABASE

FMODB ID: 9GV72

Calculation Name: 4E1P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4E1P

Chain ID: A

ChEMBL ID:

UniProt ID: P9WIP7

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	55
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-236132.217973
FMO2-HF: Nuclear repulsion	215665.810316
FMO2-HF: Total energy	-20466.407657
FMO2-MP2: Total energy	-20527.321142

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:LYS)

Summations of interaction energy for fragment #1(A:4:LYS)

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.
-109.549	-106.311	11.56	-7.202	-7.596	-0.073

Interaction energy analysis for fragmet #1(A:4:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.954 / q_NPA : 0.969

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

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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	THR	0	-0.035	-0.018	1.816	-43.896	-41.209	11.553	-6.938	-7.302	-0.072
4	A	7	VAL	0	0.021	0.011	3.906	6.858	7.409	0.007	-0.264	-0.294	-0.001
5	A	8	THR	0	-0.019	-0.011	6.306	-3.574	-3.574	0.000	0.000	0.000	0.000
6	A	9	LEU	0	0.041	0.039	8.952	0.702	0.702	0.000	0.000	0.000	0.000
7	A	10	VAL	0	-0.044	-0.021	11.537	-0.796	-0.796	0.000	0.000	0.000	0.000
8	A	11	ASP	-1	-0.733	-0.845	14.002	-14.587	-14.587	0.000	0.000	0.000	0.000
9	A	12	ASP	-1	-0.788	-0.908	17.543	-16.419	-16.419	0.000	0.000	0.000	0.000
10	A	13	PHE	0	-0.131	-0.051	19.820	0.803	0.803	0.000	0.000	0.000	0.000
11	A	14	ASP	-1	-0.833	-0.921	18.476	-16.222	-16.222	0.000	0.000	0.000	0.000
12	A	15	GLY	0	-0.009	0.015	16.750	-0.121	-0.121	0.000	0.000	0.000	0.000
13	A	16	SER	0	-0.110	-0.065	14.883	-1.388	-1.388	0.000	0.000	0.000	0.000
14	A	17	GLY	0	-0.052	-0.020	14.391	-0.964	-0.964	0.000	0.000	0.000	0.000
15	A	18	ALA	0	-0.020	-0.016	12.549	-0.804	-0.804	0.000	0.000	0.000	0.000
16	A	19	ALA	0	-0.018	-0.009	13.981	1.413	1.413	0.000	0.000	0.000	0.000
17	A	20	ASP	-1	-0.829	-0.900	15.806	-17.857	-17.857	0.000	0.000	0.000	0.000
18	A	21	GLU	-1	-0.845	-0.892	18.331	-12.398	-12.398	0.000	0.000	0.000	0.000
19	A	22	THR	0	0.026	0.000	20.595	-0.332	-0.332	0.000	0.000	0.000	0.000
20	A	23	VAL	0	-0.112	-0.058	22.593	0.635	0.635	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.877	-0.939	26.010	-10.353	-10.353	0.000	0.000	0.000	0.000
22	A	25	PHE	0	-0.080	-0.050	27.256	0.352	0.352	0.000	0.000	0.000	0.000
23	A	26	GLY	0	0.033	0.008	31.459	-0.051	-0.051	0.000	0.000	0.000	0.000
24	A	27	LEU	0	-0.055	-0.023	34.290	0.081	0.081	0.000	0.000	0.000	0.000
25	A	28	ASP	-1	-0.919	-0.960	36.632	-8.252	-8.252	0.000	0.000	0.000	0.000
26	A	29	GLY	0	-0.038	-0.015	39.279	0.108	0.108	0.000	0.000	0.000	0.000
27	A	30	VAL	0	-0.059	-0.021	33.155	0.017	0.017	0.000	0.000	0.000	0.000
28	A	31	THR	0	0.012	0.004	31.257	0.130	0.130	0.000	0.000	0.000	0.000
29	A	32	TYR	0	-0.058	-0.030	28.623	-0.122	-0.122	0.000	0.000	0.000	0.000
30	A	33	GLU	-1	-0.917	-0.958	24.737	-12.656	-12.656	0.000	0.000	0.000	0.000
31	A	34	ILE	0	-0.046	-0.027	22.788	0.022	0.022	0.000	0.000	0.000	0.000
32	A	35	ASP	-1	-0.781	-0.864	17.855	-17.073	-17.073	0.000	0.000	0.000	0.000
33	A	36	LEU	0	-0.075	-0.042	19.817	-0.062	-0.062	0.000	0.000	0.000	0.000
34	A	37	SER	0	0.016	0.004	18.611	0.082	0.082	0.000	0.000	0.000	0.000
35	A	38	THR	0	-0.032	-0.056	19.811	0.965	0.965	0.000	0.000	0.000	0.000
36	A	39	LYS	1	0.893	0.963	22.297	13.931	13.931	0.000	0.000	0.000	0.000
37	A	40	ASN	0	-0.030	-0.038	21.272	1.298	1.298	0.000	0.000	0.000	0.000
38	A	41	ALA	0	0.059	0.046	23.761	0.556	0.556	0.000	0.000	0.000	0.000
39	A	42	THR	0	-0.078	-0.058	25.489	0.759	0.759	0.000	0.000	0.000	0.000
40	A	43	LYS	1	0.823	0.891	27.308	11.035	11.035	0.000	0.000	0.000	0.000
41	A	44	LEU	0	0.057	0.042	27.375	0.487	0.487	0.000	0.000	0.000	0.000
42	A	45	ARG	1	0.806	0.854	26.348	12.212	12.212	0.000	0.000	0.000	0.000
43	A	46	GLY	0	-0.047	-0.025	31.483	0.431	0.431	0.000	0.000	0.000	0.000
44	A	47	ASP	-1	-0.846	-0.905	31.462	-9.771	-9.771	0.000	0.000	0.000	0.000
45	A	48	LEU	0	0.020	0.002	32.283	0.391	0.391	0.000	0.000	0.000	0.000
46	A	49	LYS	1	0.912	0.967	35.570	9.081	9.081	0.000	0.000	0.000	0.000
47	A	50	GLN	0	-0.031	-0.018	37.499	0.194	0.194	0.000	0.000	0.000	0.000
48	A	51	TRP	0	0.031	0.013	37.759	0.358	0.358	0.000	0.000	0.000	0.000
49	A	52	VAL	0	-0.014	-0.005	37.113	0.151	0.151	0.000	0.000	0.000	0.000
50	A	53	ALA	0	-0.059	-0.027	40.425	0.169	0.169	0.000	0.000	0.000	0.000
51	A	54	ALA	0	-0.028	-0.004	43.094	0.192	0.192	0.000	0.000	0.000	0.000
52	A	55	GLY	0	0.016	0.024	43.672	0.133	0.133	0.000	0.000	0.000	0.000
53	A	56	ARG	1	0.916	0.942	44.533	6.844	6.844	0.000	0.000	0.000	0.000
54	A	57	ARG	1	0.961	0.983	40.902	7.558	7.558	0.000	0.000	0.000	0.000
55	A	58	VAL	0	0.043	0.031	42.956	0.201	0.201	0.000	0.000	0.000	0.000

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