FMO DATABASE

FMODB ID: KGZQ3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-682240.200274
FMO2-HF: Nuclear repulsion	646158.420391
FMO2-HF: Total energy	-36081.779883
FMO2-MP2: Total energy	-36190.169188

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.
-13.097	-5.493	2.398	-4.375	-5.63	-0.029

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 : 0.026 / q_NPA : 0.010

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	-0.004	0.013	3.783	0.616	1.892	0.002	-0.475	-0.804	0.002
4	A	4	ARG	1	0.997	1.002	3.498	-1.435	-1.014	0.027	-0.183	-0.266	-0.001
5	A	5	VAL	0	0.034	0.024	5.449	0.755	0.755	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.897	0.948	7.846	0.700	0.700	0.000	0.000	0.000	0.000
7	A	7	ILE	0	0.032	0.010	11.196	0.012	0.012	0.000	0.000	0.000	0.000
8	A	8	HIS	0	0.049	0.036	14.377	0.039	0.039	0.000	0.000	0.000	0.000
9	A	9	LYS	1	1.013	0.995	17.998	0.289	0.289	0.000	0.000	0.000	0.000
10	A	10	GLN	0	0.049	0.005	20.138	0.000	0.000	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.024	0.011	17.474	0.013	0.013	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.007	0.000	16.623	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.962	0.988	19.243	0.232	0.232	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.011	-0.006	22.628	0.014	0.014	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.001	-0.001	16.870	0.013	0.013	0.000	0.000	0.000	0.000
16	A	16	GLN	0	-0.008	0.003	21.206	0.007	0.007	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.031	-0.016	23.428	0.024	0.024	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.075	-0.025	20.795	0.014	0.014	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.052	0.027	24.536	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	20	LYN	0	0.107	0.072	22.485	-0.042	-0.042	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.002	-0.002	21.276	-0.036	-0.036	0.000	0.000	0.000	0.000
22	A	22	HIS	0	-0.012	-0.028	20.625	-0.047	-0.047	0.000	0.000	0.000	0.000
23	A	23	TYR	0	0.037	0.024	16.506	-0.060	-0.060	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.959	0.948	16.996	0.331	0.331	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.940	0.968	15.736	0.316	0.316	0.000	0.000	0.000	0.000
26	A	26	PHE	0	-0.006	-0.002	13.891	-0.051	-0.051	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.042	-0.013	12.483	-0.110	-0.110	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.754	-0.864	10.879	-0.788	-0.788	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.012	-0.004	10.622	-0.111	-0.111	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.811	0.872	7.717	1.563	1.563	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.798	-0.880	6.458	-2.225	-2.225	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.006	0.001	5.842	-0.316	-0.316	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.019	-0.006	6.900	-0.043	-0.043	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.966	-0.978	2.352	-8.939	-5.998	1.618	-2.050	-2.510	-0.018
35	A	35	TYR	0	-0.054	-0.037	2.977	-5.620	-2.684	0.752	-1.665	-2.023	-0.012
36	A	36	GLU	-1	-0.839	-0.911	5.042	-0.031	-0.001	-0.001	-0.002	-0.027	0.000
37	A	37	PRO	0	0.022	0.012	8.506	-0.119	-0.119	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.030	-0.013	10.238	0.060	0.060	0.000	0.000	0.000	0.000
39	A	39	PRO	0	0.018	0.033	11.736	0.094	0.094	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.890	0.914	13.632	0.232	0.232	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.838	-0.932	17.409	-0.231	-0.231	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.787	0.905	14.146	0.532	0.532	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.001	-0.008	13.099	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.760	-0.868	18.152	-0.239	-0.239	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.009	0.020	15.715	0.008	0.008	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.011	-0.007	19.106	0.035	0.035	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.855	0.924	19.172	0.172	0.172	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.110	-0.063	21.508	0.016	0.016	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.807	-0.895	22.719	-0.123	-0.123	0.000	0.000	0.000	0.000
50	A	50	GLY	0	-0.041	-0.040	21.773	-0.034	-0.034	0.000	0.000	0.000	0.000
51	A	51	THR	0	0.008	-0.001	22.500	0.012	0.012	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.010	0.025	21.235	0.019	0.019	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.899	-0.943	19.274	-0.057	-0.057	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.086	-0.065	17.375	-0.046	-0.046	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.712	-0.801	17.230	-0.214	-0.214	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.043	-0.037	17.866	-0.055	-0.055	0.000	0.000	0.000	0.000
57	A	57	TYR	0	0.047	-0.004	16.039	0.031	0.031	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.782	0.877	19.039	0.245	0.245	0.000	0.000	0.000	0.000
59	A	59	ALA	0	0.066	0.054	16.826	0.020	0.020	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.784	0.866	18.881	0.262	0.262	0.000	0.000	0.000	0.000
61	A	61	LEU	0	0.044	0.032	15.893	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.022	0.012	20.005	0.005	0.005	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.820	-0.905	23.679	-0.221	-0.221	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.065	-0.045	19.080	0.010	0.010	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.870	0.928	21.486	0.232	0.232	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.010	-0.005	16.399	0.012	0.012	0.000	0.000	0.000	0.000
67	A	67	ILE	0	0.001	0.005	19.181	0.004	0.004	0.000	0.000	0.000	0.000
68	A	68	TYR	0	-0.077	-0.066	13.208	0.015	0.015	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.004	0.011	15.241	0.063	0.063	0.000	0.000	0.000	0.000
70	A	70	VAL	0	0.030	0.012	11.806	-0.131	-0.131	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.036	-0.022	13.179	0.112	0.112	0.000	0.000	0.000	0.000
72	A	72	TRP	0	0.052	0.000	12.232	-0.117	-0.117	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.902	0.944	13.007	-0.045	-0.045	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.860	-0.902	11.894	0.087	0.087	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.894	0.949	5.785	0.118	0.118	0.000	0.000	0.000	0.000
76	A	76	VAL	0	-0.046	-0.014	7.803	-0.440	-0.440	0.000	0.000	0.000	0.000
77	A	77	ILE	0	0.050	0.030	7.883	0.199	0.199	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.915	0.951	10.633	0.329	0.329	0.000	0.000	0.000	0.000
79	A	79	ILE	0	0.043	0.013	12.497	0.085	0.085	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.026	-0.011	15.262	0.036	0.036	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.916	0.936	18.856	0.271	0.271	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.067	0.054	19.232	-0.013	-0.013	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.897	0.943	22.157	0.263	0.263	0.000	0.000	0.000	0.000
84	A	84	PRO	0	0.088	0.038	25.025	-0.014	-0.014	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.922	0.977	26.863	0.214	0.214	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.004	-0.015	27.735	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.901	0.954	30.247	0.155	0.155	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.089	0.068	32.828	0.003	0.003	0.000	0.000	0.000	0.000

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