FMO DATABASE

FMODB ID: 3QRNL

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	OptH
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	-278802.311408
FMO2-HF: Nuclear repulsion	253136.753342
FMO2-HF: Total energy	-25665.558066
FMO2-MP2: Total energy	-25739.527616

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.
-0.68	-1.774	7.251	-2.417	-3.741	0.003

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 : 0.005 / q_NPA : 0.000

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	0.028	0.006	3.101	-0.427	1.430	0.040	-0.821	-1.076	0.002
4	B	10	LEU	0	0.012	-0.006	2.301	-0.086	-3.436	7.210	-1.419	-2.442	0.001
5	B	11	LYS	1	0.996	1.006	3.945	-0.242	0.157	0.001	-0.177	-0.223	0.000
6	B	12	GLU	-1	-0.888	-0.954	5.626	0.104	0.104	0.000	0.000	0.000	0.000
7	B	13	LEU	0	-0.014	-0.010	7.655	-0.001	-0.001	0.000	0.000	0.000	0.000
8	B	14	GLU	-1	-0.928	-0.959	7.866	0.190	0.190	0.000	0.000	0.000	0.000
9	B	15	ARG	1	0.902	0.966	9.552	0.104	0.104	0.000	0.000	0.000	0.000
10	B	16	LEU	0	0.005	-0.014	11.540	-0.003	-0.003	0.000	0.000	0.000	0.000
11	B	17	LYS	1	0.952	0.991	12.804	-0.217	-0.217	0.000	0.000	0.000	0.000
12	B	18	VAL	0	0.028	0.017	13.422	-0.018	-0.018	0.000	0.000	0.000	0.000
13	B	19	GLU	-1	-0.952	-0.985	15.738	-0.024	-0.024	0.000	0.000	0.000	0.000
14	B	20	ILE	0	-0.040	-0.024	17.330	-0.002	-0.002	0.000	0.000	0.000	0.000
15	B	21	GLN	0	0.019	0.007	17.111	-0.010	-0.010	0.000	0.000	0.000	0.000
16	B	22	ARG	1	0.971	0.982	19.878	-0.007	-0.007	0.000	0.000	0.000	0.000
17	B	23	LEU	0	-0.027	-0.017	21.728	-0.007	-0.007	0.000	0.000	0.000	0.000
18	B	24	GLU	-1	-0.922	-0.964	22.656	0.080	0.080	0.000	0.000	0.000	0.000
19	B	25	ALA	0	-0.001	-0.008	24.432	-0.004	-0.004	0.000	0.000	0.000	0.000
20	B	26	MET	0	-0.058	-0.031	25.500	-0.005	-0.005	0.000	0.000	0.000	0.000
21	B	27	LEU	0	-0.112	-0.043	27.820	-0.002	-0.002	0.000	0.000	0.000	0.000
22	B	28	MET	0	-0.065	-0.001	27.237	0.003	0.003	0.000	0.000	0.000	0.000
23	B	29	PRO	0	-0.047	-0.026	31.285	-0.003	-0.003	0.000	0.000	0.000	0.000
24	B	30	GLU	-1	-0.931	-0.964	33.741	0.003	0.003	0.000	0.000	0.000	0.000
25	B	31	GLU	-1	-1.011	-1.020	35.265	0.018	0.018	0.000	0.000	0.000	0.000
26	B	32	ARG	1	0.827	0.930	36.624	-0.005	-0.005	0.000	0.000	0.000	0.000
27	B	33	ASP	-1	-0.817	-0.894	38.625	0.014	0.014	0.000	0.000	0.000	0.000
28	B	34	GLU	-1	-1.050	-1.039	41.327	0.006	0.006	0.000	0.000	0.000	0.000
29	B	35	ASP	-1	-0.953	-1.002	41.804	0.005	0.005	0.000	0.000	0.000	0.000
30	B	36	ILE	0	-0.036	0.023	37.037	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	37	THR	0	-0.013	0.001	41.072	0.000	0.000	0.000	0.000	0.000	0.000
32	B	38	GLU	-1	-0.963	-1.004	40.296	-0.005	-0.005	0.000	0.000	0.000	0.000
33	B	39	GLU	-1	-0.897	-0.971	40.028	-0.005	-0.005	0.000	0.000	0.000	0.000
34	B	40	GLU	-1	-0.836	-0.916	38.322	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	41	ILE	0	0.023	0.014	35.297	-0.001	-0.001	0.000	0.000	0.000	0.000
36	B	42	ALA	0	-0.068	-0.037	35.588	-0.002	-0.002	0.000	0.000	0.000	0.000
37	B	43	GLU	-1	-0.955	-0.976	36.165	-0.012	-0.012	0.000	0.000	0.000	0.000
38	B	44	LEU	0	0.054	0.035	33.202	-0.002	-0.002	0.000	0.000	0.000	0.000
39	B	45	LEU	0	-0.106	-0.050	30.679	-0.003	-0.003	0.000	0.000	0.000	0.000
40	B	46	GLU	-1	-1.038	-1.021	31.388	-0.022	-0.022	0.000	0.000	0.000	0.000
41	B	47	LEU	0	0.058	0.018	31.912	-0.003	-0.003	0.000	0.000	0.000	0.000
42	B	48	ALA	0	-0.049	-0.015	27.860	-0.003	-0.003	0.000	0.000	0.000	0.000
43	B	49	ARG	1	0.851	0.919	27.217	0.023	0.023	0.000	0.000	0.000	0.000
44	B	50	ASP	-1	-0.876	-0.912	28.795	-0.037	-0.037	0.000	0.000	0.000	0.000
45	B	51	GLU	-1	-0.920	-0.979	23.959	-0.058	-0.058	0.000	0.000	0.000	0.000
46	B	52	ASH	0	-0.178	-0.143	27.220	-0.006	-0.006	0.000	0.000	0.000	0.000
47	B	53	PRO	0	0.006	-0.019	26.442	0.003	0.003	0.000	0.000	0.000	0.000
48	B	54	GLU	-1	-0.941	-0.904	28.208	-0.027	-0.027	0.000	0.000	0.000	0.000
49	B	55	ASN	0	-0.005	-0.002	30.892	0.004	0.004	0.000	0.000	0.000	0.000
50	B	56	TRP	0	-0.117	-0.043	26.207	0.005	0.005	0.000	0.000	0.000	0.000
51	B	57	ILE	0	-0.010	-0.009	26.010	-0.002	-0.002	0.000	0.000	0.000	0.000
52	B	58	ASP	-1	-0.955	-0.955	20.871	-0.042	-0.042	0.000	0.000	0.000	0.000
53	B	59	ALA	0	-0.009	-0.028	22.451	0.004	0.004	0.000	0.000	0.000	0.000
54	B	60	GLU	-1	-0.976	-1.005	18.467	0.026	0.026	0.000	0.000	0.000	0.000
55	B	61	GLU	-1	-0.974	-0.964	21.882	-0.025	-0.025	0.000	0.000	0.000	0.000
56	B	62	LEU	0	-0.051	-0.021	24.653	-0.001	-0.001	0.000	0.000	0.000	0.000
57	B	63	PRO	0	-0.051	-0.037	26.953	0.002	0.002	0.000	0.000	0.000	0.000
58	B	64	GLU	-1	-0.921	-0.966	27.324	0.015	0.015	0.000	0.000	0.000	0.000
59	B	65	PRO	0	-0.115	-0.058	29.584	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	66	GLU	-1	-0.886	-0.915	32.815	0.010	0.010	0.000	0.000	0.000	0.000
61	B	67	ASP	-1	-1.060	-1.035	35.032	0.024	0.024	0.000	0.000	0.000	0.000

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