FMO DATABASE

FMODB ID: LJ4L9

Calculation Name: 1WMI-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WMI

Chain ID: B

ChEMBL ID:

UniProt ID: O73966

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	61
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-278318.175286
FMO2-HF: Nuclear repulsion	252651.908434
FMO2-HF: Total energy	-25666.266851
FMO2-MP2: Total energy	-25740.156806

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:7:GLY)

Summations of interaction energy for fragment #1(B:7:GLY)

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.
-2.813	0.381	1.873	-1.926	-3.142	0.011

Interaction energy analysis for fragmet #1(B:7:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.004

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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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	9	VAL	0	0.021	0.004	2.974	-0.023	1.749	0.043	-0.776	-1.039	0.001
4	B	10	LEU	0	0.011	-0.002	2.640	-2.822	-1.785	1.830	-0.981	-1.886	0.010
5	B	11	LYS	1	0.987	0.999	3.947	-0.105	0.280	0.000	-0.169	-0.217	0.000
6	B	12	GLU	-1	-0.880	-0.945	5.626	0.023	0.023	0.000	0.000	0.000	0.000
7	B	13	LEU	0	-0.022	-0.015	7.651	0.022	0.022	0.000	0.000	0.000	0.000
8	B	14	GLU	-1	-0.828	-0.901	8.056	0.244	0.244	0.000	0.000	0.000	0.000
9	B	15	ARG	1	0.844	0.928	9.553	0.106	0.106	0.000	0.000	0.000	0.000
10	B	16	LEU	0	-0.010	-0.019	11.540	0.002	0.002	0.000	0.000	0.000	0.000
11	B	17	LYS	1	0.841	0.914	12.321	-0.271	-0.271	0.000	0.000	0.000	0.000
12	B	18	VAL	0	0.033	0.020	13.519	-0.018	-0.018	0.000	0.000	0.000	0.000
13	B	19	GLU	-1	-0.878	-0.936	15.739	-0.050	-0.050	0.000	0.000	0.000	0.000
14	B	20	ILE	0	-0.037	-0.025	16.832	-0.003	-0.003	0.000	0.000	0.000	0.000
15	B	21	GLN	0	0.023	0.013	17.204	-0.004	-0.004	0.000	0.000	0.000	0.000
16	B	22	ARG	1	0.945	0.972	19.706	0.000	0.000	0.000	0.000	0.000	0.000
17	B	23	LEU	0	-0.045	-0.020	21.732	-0.008	-0.008	0.000	0.000	0.000	0.000
18	B	24	GLU	-1	-0.913	-0.967	22.599	0.083	0.083	0.000	0.000	0.000	0.000
19	B	25	ALA	0	0.015	0.013	24.446	-0.004	-0.004	0.000	0.000	0.000	0.000
20	B	26	MET	0	-0.058	-0.031	25.765	-0.006	-0.006	0.000	0.000	0.000	0.000
21	B	27	LEU	0	-0.112	-0.040	27.745	-0.002	-0.002	0.000	0.000	0.000	0.000
22	B	28	MET	0	-0.038	-0.004	27.846	0.004	0.004	0.000	0.000	0.000	0.000
23	B	29	PRO	0	-0.043	-0.022	31.286	-0.004	-0.004	0.000	0.000	0.000	0.000
24	B	30	GLU	-1	-0.864	-0.916	33.829	0.003	0.003	0.000	0.000	0.000	0.000
25	B	31	GLU	-1	-1.007	-1.016	35.265	0.021	0.021	0.000	0.000	0.000	0.000
26	B	32	ARG	1	0.778	0.883	36.624	-0.005	-0.005	0.000	0.000	0.000	0.000
27	B	33	ASP	-1	-0.841	-0.902	38.450	0.018	0.018	0.000	0.000	0.000	0.000
28	B	34	GLU	-1	-1.030	-1.029	41.326	0.009	0.009	0.000	0.000	0.000	0.000
29	B	35	ASP	-1	-0.957	-0.998	42.055	0.008	0.008	0.000	0.000	0.000	0.000
30	B	36	ILE	0	-0.051	0.013	36.915	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	37	THR	0	-0.039	-0.048	41.072	0.000	0.000	0.000	0.000	0.000	0.000
32	B	38	GLU	-1	-0.969	-1.007	40.275	-0.005	-0.005	0.000	0.000	0.000	0.000
33	B	39	GLU	-1	-0.866	-0.916	40.028	-0.003	-0.003	0.000	0.000	0.000	0.000
34	B	40	GLU	-1	-0.849	-0.927	38.234	0.001	0.001	0.000	0.000	0.000	0.000
35	B	41	ILE	0	0.018	0.009	35.228	-0.001	-0.001	0.000	0.000	0.000	0.000
36	B	42	ALA	0	-0.065	-0.032	35.588	-0.002	-0.002	0.000	0.000	0.000	0.000
37	B	43	GLU	-1	-0.958	-0.978	36.165	-0.009	-0.009	0.000	0.000	0.000	0.000
38	B	44	LEU	0	0.079	0.043	33.136	-0.002	-0.002	0.000	0.000	0.000	0.000
39	B	45	LEU	0	-0.097	-0.047	30.628	-0.003	-0.003	0.000	0.000	0.000	0.000
40	B	46	GLU	-1	-1.042	-1.023	31.388	-0.021	-0.021	0.000	0.000	0.000	0.000
41	B	47	LEU	0	0.047	0.018	31.338	-0.003	-0.003	0.000	0.000	0.000	0.000
42	B	48	ALA	0	-0.038	-0.012	27.852	-0.003	-0.003	0.000	0.000	0.000	0.000
43	B	49	ARG	1	0.826	0.907	27.217	0.022	0.022	0.000	0.000	0.000	0.000
44	B	50	ASP	-1	-0.837	-0.899	28.795	-0.035	-0.035	0.000	0.000	0.000	0.000
45	B	51	GLU	-1	-0.963	-0.981	24.042	-0.058	-0.058	0.000	0.000	0.000	0.000
46	B	52	ASH	0	-0.146	-0.111	27.219	-0.005	-0.005	0.000	0.000	0.000	0.000
47	B	53	PRO	0	0.011	-0.015	26.390	0.003	0.003	0.000	0.000	0.000	0.000
48	B	54	GLU	-1	-0.956	-0.921	28.207	-0.022	-0.022	0.000	0.000	0.000	0.000
49	B	55	ASN	0	-0.054	-0.038	30.838	0.005	0.005	0.000	0.000	0.000	0.000
50	B	56	TRP	0	-0.100	-0.040	26.109	0.006	0.006	0.000	0.000	0.000	0.000
51	B	57	ILE	0	-0.016	-0.011	25.998	-0.002	-0.002	0.000	0.000	0.000	0.000
52	B	58	ASP	-1	-0.928	-0.946	20.599	-0.024	-0.024	0.000	0.000	0.000	0.000
53	B	59	ALA	0	-0.016	-0.029	22.432	0.004	0.004	0.000	0.000	0.000	0.000
54	B	60	GLU	-1	-0.974	-1.001	18.393	0.054	0.054	0.000	0.000	0.000	0.000
55	B	61	GLU	-1	-0.982	-0.979	21.881	-0.009	-0.009	0.000	0.000	0.000	0.000
56	B	62	LEU	0	-0.050	-0.012	24.653	-0.003	-0.003	0.000	0.000	0.000	0.000
57	B	63	PRO	0	-0.041	-0.034	26.952	0.003	0.003	0.000	0.000	0.000	0.000
58	B	64	GLU	-1	-0.915	-0.965	27.157	0.030	0.030	0.000	0.000	0.000	0.000
59	B	65	PRO	0	-0.116	-0.048	29.584	-0.002	-0.002	0.000	0.000	0.000	0.000
60	B	66	GLU	-1	-0.901	-0.928	32.814	0.019	0.019	0.000	0.000	0.000	0.000
61	B	67	ASP	-1	-1.055	-1.035	35.424	0.035	0.035	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:7:GLY)