FMO DATABASE

FMODB ID: Z675N

Calculation Name: 1CMI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1CMI

Chain ID: A

ChEMBL ID:

UniProt ID: P63167

Base Structure: X-ray

Registration Date: 2023-06-22

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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-617312.154923
FMO2-HF: Nuclear repulsion	582476.475995
FMO2-HF: Total energy	-34835.678927
FMO2-MP2: Total energy	-34936.402537

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:5:LYS)

Summations of interaction energy for fragment #1(A:5: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.
-8.397	-4.171	0.128	-1.806	-2.547	-0.005

Interaction energy analysis for fragmet #1(A:5:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.962 / q_NPA : 0.963

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	7	VAL	0	-0.044	-0.028	3.517	-1.021	0.440	-0.003	-0.563	-0.895	0.001
4	A	8	ILE	0	0.052	0.020	6.081	1.406	1.406	0.000	0.000	0.000	0.000
5	A	9	LYS	1	0.828	0.936	8.064	32.876	32.876	0.000	0.000	0.000	0.000
6	A	10	ASN	0	-0.022	-0.020	12.255	1.781	1.781	0.000	0.000	0.000	0.000
7	A	11	ALA	0	0.018	0.010	14.376	-0.707	-0.707	0.000	0.000	0.000	0.000
8	A	12	ASP	-1	-0.812	-0.891	16.433	-12.607	-12.607	0.000	0.000	0.000	0.000
9	A	13	MET	0	-0.056	-0.009	16.197	0.397	0.397	0.000	0.000	0.000	0.000
10	A	14	SER	0	-0.004	-0.026	17.846	-0.607	-0.607	0.000	0.000	0.000	0.000
11	A	15	GLU	-1	-0.901	-0.957	15.500	-15.571	-15.571	0.000	0.000	0.000	0.000
12	A	16	GLU	-1	-0.807	-0.887	14.888	-14.621	-14.621	0.000	0.000	0.000	0.000
13	A	17	MET	0	-0.008	0.016	15.477	-0.608	-0.608	0.000	0.000	0.000	0.000
14	A	18	GLN	0	-0.001	-0.019	12.645	-1.874	-1.874	0.000	0.000	0.000	0.000
15	A	19	GLN	0	-0.004	0.010	10.892	-1.560	-1.560	0.000	0.000	0.000	0.000
16	A	20	ASP	-1	-0.747	-0.833	10.949	-16.401	-16.401	0.000	0.000	0.000	0.000
17	A	21	SER	0	-0.059	-0.041	12.128	-0.064	-0.064	0.000	0.000	0.000	0.000
18	A	22	VAL	0	-0.008	-0.011	5.788	-1.311	-1.311	0.000	0.000	0.000	0.000
19	A	23	GLU	-1	-0.919	-0.947	7.818	-19.631	-19.631	0.000	0.000	0.000	0.000
20	A	24	CYS	0	-0.025	0.001	9.595	0.150	0.150	0.000	0.000	0.000	0.000
21	A	25	ALA	0	0.027	-0.007	8.805	0.274	0.274	0.000	0.000	0.000	0.000
22	A	26	THR	0	-0.048	-0.030	6.001	-2.085	-2.085	0.000	0.000	0.000	0.000
23	A	27	GLN	0	0.025	0.014	7.817	0.883	0.883	0.000	0.000	0.000	0.000
24	A	28	ALA	0	-0.058	-0.019	11.398	0.997	0.997	0.000	0.000	0.000	0.000
25	A	29	LEU	0	-0.019	-0.029	7.198	0.398	0.398	0.000	0.000	0.000	0.000
26	A	30	GLU	-1	-0.963	-0.972	9.063	-22.890	-22.890	0.000	0.000	0.000	0.000
27	A	31	LYS	1	0.856	0.937	11.487	15.706	15.706	0.000	0.000	0.000	0.000
28	A	32	TYR	0	-0.051	-0.038	14.344	1.560	1.560	0.000	0.000	0.000	0.000
29	A	33	ASN	0	-0.001	-0.001	14.695	-1.806	-1.806	0.000	0.000	0.000	0.000
30	A	34	ILE	0	0.017	0.008	16.672	0.055	0.055	0.000	0.000	0.000	0.000
31	A	35	GLU	-1	-0.847	-0.930	14.473	-18.980	-18.980	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.828	0.898	16.721	13.358	13.358	0.000	0.000	0.000	0.000
33	A	37	ASP	-1	-0.816	-0.904	18.806	-13.423	-13.423	0.000	0.000	0.000	0.000
34	A	38	ILE	0	0.026	0.022	12.235	0.195	0.195	0.000	0.000	0.000	0.000
35	A	39	ALA	0	0.022	0.003	15.463	0.062	0.062	0.000	0.000	0.000	0.000
36	A	40	ALA	0	-0.038	-0.019	17.207	0.564	0.564	0.000	0.000	0.000	0.000
37	A	41	HIS	0	0.039	0.042	15.153	1.159	1.159	0.000	0.000	0.000	0.000
38	A	42	ILE	0	0.070	0.018	12.401	0.466	0.466	0.000	0.000	0.000	0.000
39	A	43	LYS	1	0.783	0.866	16.300	12.461	12.461	0.000	0.000	0.000	0.000
40	A	44	LYS	1	0.929	0.957	19.763	13.100	13.100	0.000	0.000	0.000	0.000
41	A	45	GLU	-1	-0.816	-0.887	17.351	-12.617	-12.617	0.000	0.000	0.000	0.000
42	A	46	PHE	0	0.013	0.005	14.949	0.322	0.322	0.000	0.000	0.000	0.000
43	A	47	ASP	-1	-0.799	-0.888	19.970	-11.376	-11.376	0.000	0.000	0.000	0.000
44	A	48	LYS	1	0.738	0.848	21.802	12.816	12.816	0.000	0.000	0.000	0.000
45	A	49	LYS	1	0.833	0.909	17.491	14.645	14.645	0.000	0.000	0.000	0.000
46	A	50	TYR	0	-0.005	-0.037	18.241	0.380	0.380	0.000	0.000	0.000	0.000
47	A	51	ASN	0	0.010	0.010	23.484	0.363	0.363	0.000	0.000	0.000	0.000
48	A	52	PRO	0	0.041	0.020	25.467	-0.345	-0.345	0.000	0.000	0.000	0.000
49	A	53	THR	0	-0.081	-0.043	26.424	0.269	0.269	0.000	0.000	0.000	0.000
50	A	54	TRP	0	-0.004	0.004	19.334	-0.355	-0.355	0.000	0.000	0.000	0.000
51	A	55	HIS	0	-0.027	0.000	21.696	0.174	0.174	0.000	0.000	0.000	0.000
52	A	56	CYS	0	-0.061	-0.037	16.175	-0.788	-0.788	0.000	0.000	0.000	0.000
53	A	57	ILE	0	-0.004	0.009	17.536	0.667	0.667	0.000	0.000	0.000	0.000
54	A	58	VAL	0	0.010	0.002	12.973	-1.073	-1.073	0.000	0.000	0.000	0.000
55	A	59	GLY	0	0.054	0.029	13.643	1.314	1.314	0.000	0.000	0.000	0.000
56	A	60	ARG	1	0.906	0.923	8.467	26.985	26.985	0.000	0.000	0.000	0.000
57	A	61	ASN	0	-0.040	-0.018	12.872	-0.187	-0.187	0.000	0.000	0.000	0.000
58	A	62	PHE	0	0.009	0.016	14.668	0.902	0.902	0.000	0.000	0.000	0.000
59	A	63	GLY	0	0.038	0.024	18.152	-0.620	-0.620	0.000	0.000	0.000	0.000
60	A	64	SER	0	-0.057	-0.031	20.616	0.393	0.393	0.000	0.000	0.000	0.000
61	A	65	TYR	0	0.027	0.010	22.885	-0.303	-0.303	0.000	0.000	0.000	0.000
62	A	66	VAL	0	-0.006	0.005	22.601	0.346	0.346	0.000	0.000	0.000	0.000
63	A	67	THR	0	0.013	0.013	25.784	0.003	0.003	0.000	0.000	0.000	0.000
64	A	68	HIS	1	0.837	0.904	23.280	12.863	12.863	0.000	0.000	0.000	0.000
65	A	69	GLU	-1	-0.794	-0.899	25.848	-10.590	-10.590	0.000	0.000	0.000	0.000
66	A	70	THR	0	-0.029	-0.001	24.665	-0.410	-0.410	0.000	0.000	0.000	0.000
67	A	71	LYS	1	0.925	0.945	22.440	11.506	11.506	0.000	0.000	0.000	0.000
68	A	72	HIS	0	-0.013	-0.004	21.037	-0.167	-0.167	0.000	0.000	0.000	0.000
69	A	73	PHE	0	0.004	-0.009	18.199	0.095	0.095	0.000	0.000	0.000	0.000
70	A	74	ILE	0	0.013	0.002	11.932	-0.298	-0.298	0.000	0.000	0.000	0.000
71	A	75	TYR	0	0.025	0.013	13.127	-0.362	-0.362	0.000	0.000	0.000	0.000
72	A	76	PHE	0	0.021	0.004	7.733	-0.510	-0.510	0.000	0.000	0.000	0.000
73	A	77	TYR	0	0.003	-0.004	6.242	0.744	0.744	0.000	0.000	0.000	0.000
74	A	78	LEU	0	0.045	0.019	3.090	-4.174	-3.502	0.079	-0.254	-0.497	0.000
75	A	79	GLY	0	0.034	0.027	3.507	3.362	4.099	0.008	-0.228	-0.517	0.001
76	A	80	GLN	0	-0.050	-0.023	3.101	-19.515	-18.159	0.044	-0.761	-0.638	-0.007
77	A	81	VAL	0	0.007	0.018	5.740	5.181	5.181	0.000	0.000	0.000	0.000
78	A	82	ALA	0	-0.008	0.002	8.279	-3.163	-3.163	0.000	0.000	0.000	0.000
79	A	83	ILE	0	0.031	0.000	9.412	1.926	1.926	0.000	0.000	0.000	0.000
80	A	84	LEU	0	-0.002	0.009	12.819	-0.524	-0.524	0.000	0.000	0.000	0.000
81	A	85	LEU	0	-0.002	0.004	14.982	0.468	0.468	0.000	0.000	0.000	0.000
82	A	86	PHE	0	-0.003	-0.012	17.130	-0.107	-0.107	0.000	0.000	0.000	0.000
83	A	87	LYS	1	0.879	0.970	20.460	11.290	11.290	0.000	0.000	0.000	0.000
84	A	88	SER	0	0.005	-0.016	23.670	-0.074	-0.074	0.000	0.000	0.000	0.000
85	A	89	GLY	0	0.010	0.023	27.138	0.066	0.066	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LYS)