FMO DATABASE

FMODB ID: R8K48

Calculation Name: 1WMI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WMI

Chain ID: A

ChEMBL ID:

UniProt ID: O73966

Base Structure: X-ray

Registration Date: 2023-09-23

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	88
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-682286.744882
FMO2-HF: Nuclear repulsion	646206.427972
FMO2-HF: Total energy	-36080.31691
FMO2-MP2: Total energy	-36188.816395

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:1:MET)

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

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.
-9.911	-6.013	0.707	-1.513	-3.092	-0.006

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.006

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	A	3	TYR	0	-0.025	0.002	3.486	0.750	1.958	0.001	-0.271	-0.938	0.002
4	A	4	ARG	1	1.003	1.004	4.116	-1.591	-1.368	0.000	-0.042	-0.181	0.000
5	A	5	VAL	0	0.051	0.030	6.142	0.384	0.384	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.882	0.934	8.237	0.222	0.222	0.000	0.000	0.000	0.000
7	A	7	ILE	0	0.047	0.020	11.659	-0.021	-0.021	0.000	0.000	0.000	0.000
8	A	8	HIS	0	0.034	0.034	14.724	0.042	0.042	0.000	0.000	0.000	0.000
9	A	9	LYS	1	1.040	0.998	18.275	0.067	0.067	0.000	0.000	0.000	0.000
10	A	10	GLN	0	0.031	-0.003	20.549	-0.011	-0.011	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.030	0.011	17.742	0.001	0.001	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.024	0.006	16.996	-0.011	-0.011	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.962	0.986	19.516	0.125	0.125	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.023	-0.017	22.851	0.003	0.003	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.005	-0.010	16.711	0.003	0.003	0.000	0.000	0.000	0.000
16	A	16	GLN	0	-0.028	-0.003	21.434	0.000	0.000	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.035	-0.005	23.803	0.015	0.015	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.064	-0.026	21.287	0.005	0.005	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.043	0.033	24.755	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	20	LYN	0	0.119	0.057	23.143	-0.032	-0.032	0.000	0.000	0.000	0.000
21	A	21	ALA	0	-0.014	-0.016	21.661	-0.031	-0.031	0.000	0.000	0.000	0.000
22	A	22	HIS	0	-0.047	-0.051	21.114	-0.038	-0.038	0.000	0.000	0.000	0.000
23	A	23	TYR	0	0.029	0.019	16.801	-0.042	-0.042	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.968	0.969	17.206	0.289	0.289	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.986	0.996	16.070	0.272	0.272	0.000	0.000	0.000	0.000
26	A	26	PHE	0	-0.020	-0.006	13.831	-0.055	-0.055	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.012	-0.009	12.538	-0.075	-0.075	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.882	-0.926	11.187	-0.768	-0.768	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.017	-0.022	10.900	-0.125	-0.125	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.827	0.893	7.892	1.162	1.162	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.798	-0.892	7.009	-1.794	-1.794	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.028	-0.017	6.069	-0.512	-0.512	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.043	-0.019	7.375	-0.074	-0.074	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.969	-0.978	2.900	-4.351	-3.399	0.131	-0.351	-0.733	-0.002
35	A	35	TYR	0	-0.027	-0.015	3.069	-4.012	-2.521	0.576	-0.848	-1.219	-0.006
36	A	36	GLU	-1	-0.922	-0.961	4.955	0.155	0.179	-0.001	-0.001	-0.021	0.000
37	A	37	PRO	0	0.027	0.015	8.688	-0.061	-0.061	0.000	0.000	0.000	0.000
38	A	38	VAL	0	0.015	0.007	10.603	0.066	0.066	0.000	0.000	0.000	0.000
39	A	39	PRO	0	0.047	0.058	11.874	0.078	0.078	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.949	0.921	13.896	0.211	0.211	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.926	-0.982	17.644	-0.204	-0.204	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.936	0.981	14.261	0.491	0.491	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.008	-0.004	13.212	0.000	0.000	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.873	-0.928	18.098	-0.197	-0.197	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.019	0.050	16.233	0.025	0.025	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.036	-0.024	19.498	0.025	0.025	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.990	0.979	20.566	0.080	0.080	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.132	-0.062	21.734	0.014	0.014	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.859	-0.936	22.923	-0.053	-0.053	0.000	0.000	0.000	0.000
50	A	50	GLY	0	-0.027	-0.009	22.111	-0.015	-0.015	0.000	0.000	0.000	0.000
51	A	51	THR	0	0.014	-0.006	22.136	0.009	0.009	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.025	0.043	21.235	0.014	0.014	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.923	-0.961	19.227	0.086	0.086	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.077	-0.051	17.764	-0.021	-0.021	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.786	-0.880	17.664	-0.102	-0.102	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.047	-0.035	18.015	-0.042	-0.042	0.000	0.000	0.000	0.000
57	A	57	TYR	0	0.015	-0.003	16.345	0.005	0.005	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.821	0.887	19.480	0.217	0.217	0.000	0.000	0.000	0.000
59	A	59	ALA	0	0.054	0.037	16.958	0.007	0.007	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.873	0.926	19.065	0.222	0.222	0.000	0.000	0.000	0.000
61	A	61	LEU	0	0.039	0.024	16.758	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.040	0.018	20.426	0.002	0.002	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.852	-0.960	24.006	-0.191	-0.191	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.018	-0.012	19.524	0.012	0.012	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.858	0.927	22.089	0.165	0.165	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.009	0.013	16.866	0.022	0.022	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.013	-0.008	19.345	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	68	TYR	0	-0.046	-0.076	13.745	0.019	0.019	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.017	0.006	15.653	0.042	0.042	0.000	0.000	0.000	0.000
70	A	70	VAL	0	0.013	0.011	12.225	-0.090	-0.090	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.004	0.006	13.244	0.064	0.064	0.000	0.000	0.000	0.000
72	A	72	TRP	0	0.046	0.001	12.408	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.957	1.007	12.252	-0.365	-0.365	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.916	-0.972	11.872	0.399	0.399	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.944	0.983	5.170	-1.376	-1.376	0.000	0.000	0.000	0.000
76	A	76	VAL	0	-0.058	-0.028	8.470	-0.206	-0.206	0.000	0.000	0.000	0.000
77	A	77	ILE	0	0.057	0.043	8.681	0.101	0.101	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.889	0.947	11.067	0.065	0.065	0.000	0.000	0.000	0.000
79	A	79	ILE	0	0.055	0.029	12.523	0.034	0.034	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.033	-0.005	15.423	0.041	0.041	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.908	0.945	18.991	0.173	0.173	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.070	0.047	19.261	-0.021	-0.021	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.878	0.930	22.555	0.176	0.176	0.000	0.000	0.000	0.000
84	A	84	PRO	0	0.077	0.035	25.440	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.987	1.047	27.299	0.172	0.172	0.000	0.000	0.000	0.000
86	A	86	GLY	0	-0.042	-0.018	28.351	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.925	0.961	30.373	0.109	0.109	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.099	0.074	32.866	0.001	0.001	0.000	0.000	0.000	0.000

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Overview

Highlights

Manual

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