FMO DATABASE

FMODB ID: 2J43R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-615284.639348
FMO2-HF: Nuclear repulsion	580449.76788
FMO2-HF: Total energy	-34834.871468
FMO2-MP2: Total energy	-34935.630806

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.
-2.411	-0.16899999999999	0.018	-0.791	-1.467	0.002

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 : 0.950 / q_NPA : 0.959

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	-0.026	-0.013	3.794	-1.131	0.333	-0.012	-0.562	-0.890	0.002
4	A	8	ILE	0	0.040	0.018	6.132	1.810	1.810	0.000	0.000	0.000	0.000
5	A	9	LYS	1	0.874	0.948	8.911	30.390	30.390	0.000	0.000	0.000	0.000
6	A	10	ASN	0	-0.022	-0.017	12.198	1.721	1.721	0.000	0.000	0.000	0.000
7	A	11	ALA	0	0.027	0.017	14.124	-0.201	-0.201	0.000	0.000	0.000	0.000
8	A	12	ASP	-1	-0.861	-0.927	16.105	-12.874	-12.874	0.000	0.000	0.000	0.000
9	A	13	MET	0	-0.052	0.005	16.211	0.454	0.454	0.000	0.000	0.000	0.000
10	A	14	SER	0	0.028	0.012	18.076	-0.528	-0.528	0.000	0.000	0.000	0.000
11	A	15	GLU	-1	-0.884	-0.957	15.450	-15.778	-15.778	0.000	0.000	0.000	0.000
12	A	16	GLU	-1	-0.928	-0.962	14.878	-14.116	-14.116	0.000	0.000	0.000	0.000
13	A	17	MET	0	0.004	0.010	15.699	-0.557	-0.557	0.000	0.000	0.000	0.000
14	A	18	GLN	0	-0.027	-0.029	11.896	-1.850	-1.850	0.000	0.000	0.000	0.000
15	A	19	GLN	0	0.014	0.004	11.080	-1.597	-1.597	0.000	0.000	0.000	0.000
16	A	20	ASP	-1	-0.738	-0.846	11.105	-16.865	-16.865	0.000	0.000	0.000	0.000
17	A	21	SER	0	-0.042	-0.025	11.928	0.176	0.176	0.000	0.000	0.000	0.000
18	A	22	VAL	0	-0.024	-0.012	5.801	-1.086	-1.086	0.000	0.000	0.000	0.000
19	A	23	GLU	-1	-0.915	-0.937	8.081	-19.533	-19.533	0.000	0.000	0.000	0.000
20	A	24	CYS	0	0.013	0.020	9.492	0.067	0.067	0.000	0.000	0.000	0.000
21	A	25	ALA	0	-0.001	-0.019	8.711	0.430	0.430	0.000	0.000	0.000	0.000
22	A	26	THR	0	-0.066	-0.040	6.347	-1.987	-1.987	0.000	0.000	0.000	0.000
23	A	27	GLN	0	0.026	0.017	7.926	0.736	0.736	0.000	0.000	0.000	0.000
24	A	28	ALA	0	-0.036	-0.011	11.390	0.813	0.813	0.000	0.000	0.000	0.000
25	A	29	LEU	0	-0.037	-0.026	7.066	0.447	0.447	0.000	0.000	0.000	0.000
26	A	30	GLU	-1	-0.956	-0.967	9.079	-23.065	-23.065	0.000	0.000	0.000	0.000
27	A	31	LYS	1	0.905	0.970	11.445	15.468	15.468	0.000	0.000	0.000	0.000
28	A	32	TYR	0	-0.057	-0.042	14.304	1.492	1.492	0.000	0.000	0.000	0.000
29	A	33	ASN	0	0.023	0.005	14.545	-1.637	-1.637	0.000	0.000	0.000	0.000
30	A	34	ILE	0	-0.015	-0.001	16.690	-0.409	-0.409	0.000	0.000	0.000	0.000
31	A	35	GLU	-1	-0.849	-0.930	15.278	-18.426	-18.426	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.950	0.978	16.995	12.376	12.376	0.000	0.000	0.000	0.000
33	A	37	ASP	-1	-0.892	-0.956	18.789	-13.403	-13.403	0.000	0.000	0.000	0.000
34	A	38	ILE	0	-0.002	0.004	12.590	0.048	0.048	0.000	0.000	0.000	0.000
35	A	39	ALA	0	-0.003	-0.014	15.651	-0.146	-0.146	0.000	0.000	0.000	0.000
36	A	40	ALA	0	-0.057	-0.032	17.265	0.459	0.459	0.000	0.000	0.000	0.000
37	A	41	HIS	0	-0.002	0.005	14.538	0.910	0.910	0.000	0.000	0.000	0.000
38	A	42	ILE	0	0.085	0.025	12.251	0.346	0.346	0.000	0.000	0.000	0.000
39	A	43	LYS	1	0.806	0.914	16.211	12.386	12.386	0.000	0.000	0.000	0.000
40	A	44	LYS	1	0.899	0.926	19.611	12.479	12.479	0.000	0.000	0.000	0.000
41	A	45	GLU	-1	-0.907	-0.948	16.854	-13.338	-13.338	0.000	0.000	0.000	0.000
42	A	46	PHE	0	0.026	0.002	15.203	0.377	0.377	0.000	0.000	0.000	0.000
43	A	47	ASP	-1	-0.772	-0.888	19.978	-11.284	-11.284	0.000	0.000	0.000	0.000
44	A	48	LYS	1	0.842	0.932	22.328	12.523	12.523	0.000	0.000	0.000	0.000
45	A	49	LYS	1	0.884	0.945	17.587	14.737	14.737	0.000	0.000	0.000	0.000
46	A	50	TYR	0	-0.031	-0.046	18.023	0.253	0.253	0.000	0.000	0.000	0.000
47	A	51	ASN	0	0.003	0.004	23.531	0.175	0.175	0.000	0.000	0.000	0.000
48	A	52	PRO	0	0.001	0.018	25.355	-0.333	-0.333	0.000	0.000	0.000	0.000
49	A	53	THR	0	-0.038	-0.020	26.295	0.240	0.240	0.000	0.000	0.000	0.000
50	A	54	TRP	0	-0.017	-0.006	19.165	-0.387	-0.387	0.000	0.000	0.000	0.000
51	A	55	HIS	0	-0.053	-0.027	21.584	0.269	0.269	0.000	0.000	0.000	0.000
52	A	56	CYS	0	-0.053	-0.018	16.053	-0.748	-0.748	0.000	0.000	0.000	0.000
53	A	57	ILE	0	-0.004	0.008	17.482	0.580	0.580	0.000	0.000	0.000	0.000
54	A	58	VAL	0	0.042	0.016	13.022	-1.071	-1.071	0.000	0.000	0.000	0.000
55	A	59	GLY	0	0.035	0.015	14.205	1.152	1.152	0.000	0.000	0.000	0.000
56	A	60	ARG	1	0.906	0.930	9.143	24.930	24.930	0.000	0.000	0.000	0.000
57	A	61	ASN	0	-0.056	-0.031	13.711	0.396	0.396	0.000	0.000	0.000	0.000
58	A	62	PHE	0	0.037	0.023	15.703	0.827	0.827	0.000	0.000	0.000	0.000
59	A	63	GLY	0	0.039	0.036	18.752	-0.670	-0.670	0.000	0.000	0.000	0.000
60	A	64	SER	0	-0.051	-0.037	20.983	0.393	0.393	0.000	0.000	0.000	0.000
61	A	65	TYR	0	0.033	0.016	23.153	-0.078	-0.078	0.000	0.000	0.000	0.000
62	A	66	VAL	0	-0.010	0.004	22.935	0.310	0.310	0.000	0.000	0.000	0.000
63	A	67	THR	0	0.008	0.007	26.072	0.083	0.083	0.000	0.000	0.000	0.000
64	A	68	HIS	1	0.841	0.919	23.573	12.935	12.935	0.000	0.000	0.000	0.000
65	A	69	GLU	-1	-0.854	-0.924	25.556	-10.466	-10.466	0.000	0.000	0.000	0.000
66	A	70	THR	0	-0.002	-0.012	24.540	-0.527	-0.527	0.000	0.000	0.000	0.000
67	A	71	LYS	1	0.968	0.986	22.320	11.377	11.377	0.000	0.000	0.000	0.000
68	A	72	HIS	0	-0.057	-0.032	20.884	-0.269	-0.269	0.000	0.000	0.000	0.000
69	A	73	PHE	0	0.004	-0.019	18.227	0.219	0.219	0.000	0.000	0.000	0.000
70	A	74	ILE	0	0.034	0.014	12.008	-0.370	-0.370	0.000	0.000	0.000	0.000
71	A	75	TYR	0	0.012	0.016	13.555	-0.415	-0.415	0.000	0.000	0.000	0.000
72	A	76	PHE	0	-0.019	-0.019	7.661	-0.611	-0.611	0.000	0.000	0.000	0.000
73	A	77	TYR	0	-0.006	-0.003	6.412	1.226	1.226	0.000	0.000	0.000	0.000
74	A	78	LEU	0	0.068	0.029	3.185	-5.222	-4.789	0.032	-0.163	-0.302	0.000
75	A	79	GLY	0	0.037	0.037	4.131	4.301	4.619	-0.001	-0.056	-0.260	0.000
76	A	80	GLN	0	-0.046	-0.028	4.751	-6.454	-6.427	-0.001	-0.010	-0.015	0.000
77	A	81	VAL	0	0.021	0.024	6.930	4.427	4.427	0.000	0.000	0.000	0.000
78	A	82	ALA	0	-0.016	-0.004	8.748	-3.183	-3.183	0.000	0.000	0.000	0.000
79	A	83	ILE	0	0.026	-0.003	9.313	1.959	1.959	0.000	0.000	0.000	0.000
80	A	84	LEU	0	-0.022	0.001	12.837	-0.397	-0.397	0.000	0.000	0.000	0.000
81	A	85	LEU	0	-0.007	0.000	15.144	0.651	0.651	0.000	0.000	0.000	0.000
82	A	86	PHE	0	0.006	-0.014	17.066	-0.063	-0.063	0.000	0.000	0.000	0.000
83	A	87	LYS	1	0.923	0.971	20.395	11.311	11.311	0.000	0.000	0.000	0.000
84	A	88	SER	0	-0.027	-0.046	23.524	0.057	0.057	0.000	0.000	0.000	0.000
85	A	89	GLY	0	0.052	0.064	27.043	-0.052	-0.052	0.000	0.000	0.000	0.000

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