FMO DATABASE

FMODB ID: N1MGQ

Calculation Name: 5CLV-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CLV

Chain ID: E

ChEMBL ID:

UniProt ID: P03052

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	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	65
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-357708.121979
FMO2-HF: Nuclear repulsion	333401.003748
FMO2-HF: Total energy	-24307.118231
FMO2-MP2: Total energy	-24380.007562

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(E:2:LYS)

Summations of interaction energy for fragment #1(E:2: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.
-7.13	-5.704	-0.011	-0.601	-0.814	0

Interaction energy analysis for fragmet #1(E:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.961 / q_NPA : 0.954

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].
3	E	4	ARG	1	0.843	0.912	3.666	26.309	27.735	-0.011	-0.601	-0.814
4	E	5	LEU	0	-0.001	0.016	5.991	-0.017	-0.017	0.000	0.000	0.000
5	E	6	THR	0	0.016	-0.015	9.833	0.602	0.602	0.000	0.000	0.000
6	E	7	GLU	-1	-0.787	-0.901	12.878	-13.635	-13.635	0.000	0.000	0.000
7	E	8	SER	0	0.029	0.024	15.327	0.477	0.477	0.000	0.000	0.000
8	E	9	GLN	0	0.058	0.055	11.842	0.191	0.191	0.000	0.000	0.000
9	E	10	PHE	0	-0.011	-0.002	12.103	-0.107	-0.107	0.000	0.000	0.000
10	E	11	GLN	0	-0.042	-0.038	14.475	0.753	0.753	0.000	0.000	0.000
11	E	12	GLU	-1	-0.904	-0.952	17.518	-13.892	-13.892	0.000	0.000	0.000
12	E	13	ALA	0	-0.013	0.001	14.956	0.397	0.397	0.000	0.000	0.000
13	E	14	ILE	0	-0.012	-0.018	16.517	0.350	0.350	0.000	0.000	0.000
14	E	15	GLN	0	-0.008	0.012	18.854	0.685	0.685	0.000	0.000	0.000
15	E	16	GLY	0	0.015	0.006	22.144	-0.144	-0.144	0.000	0.000	0.000
16	E	17	LEU	0	-0.054	-0.008	17.824	0.013	0.013	0.000	0.000	0.000
17	E	18	GLU	-1	-0.884	-0.942	22.127	-10.000	-10.000	0.000	0.000	0.000
18	E	19	VAL	0	-0.080	-0.044	18.786	-0.309	-0.309	0.000	0.000	0.000
19	E	20	GLY	0	0.050	0.028	21.997	0.269	0.269	0.000	0.000	0.000
20	E	21	GLN	0	0.010	-0.022	20.725	-0.221	-0.221	0.000	0.000	0.000
21	E	22	GLN	0	0.014	0.004	19.299	-0.203	-0.203	0.000	0.000	0.000
22	E	23	THR	0	-0.040	-0.022	16.448	-0.435	-0.435	0.000	0.000	0.000
23	E	24	ILE	0	0.054	0.043	15.642	-0.853	-0.853	0.000	0.000	0.000
24	E	25	GLU	-1	-0.755	-0.861	15.288	-13.707	-13.707	0.000	0.000	0.000
25	E	26	ILE	0	-0.057	-0.020	12.802	-0.661	-0.661	0.000	0.000	0.000
26	E	27	ALA	0	0.008	0.007	11.136	-1.129	-1.129	0.000	0.000	0.000
27	E	28	ARG	1	0.836	0.892	10.564	12.291	12.291	0.000	0.000	0.000
28	E	29	GLY	0	0.017	0.001	11.256	-0.675	-0.675	0.000	0.000	0.000
29	E	30	VAL	0	-0.058	-0.033	6.372	-0.998	-0.998	0.000	0.000	0.000
30	E	31	LEU	0	-0.036	-0.014	6.332	-2.304	-2.304	0.000	0.000	0.000
31	E	32	VAL	0	0.024	0.023	7.645	-1.101	-1.101	0.000	0.000	0.000
32	E	33	ASP	-1	-0.830	-0.893	9.968	-16.838	-16.838	0.000	0.000	0.000
33	E	34	GLY	0	-0.047	-0.020	6.218	-0.600	-0.600	0.000	0.000	0.000
34	E	35	LYS	1	0.840	0.912	7.013	14.899	14.899	0.000	0.000	0.000
35	E	36	PRO	0	0.049	0.013	7.696	-0.625	-0.625	0.000	0.000	0.000
36	E	37	GLN	0	0.077	0.037	8.122	2.525	2.525	0.000	0.000	0.000
37	E	38	ALA	0	-0.030	-0.016	10.454	1.247	1.247	0.000	0.000	0.000
38	E	39	THR	0	0.005	0.002	11.935	1.296	1.296	0.000	0.000	0.000
39	E	40	PHE	0	0.076	0.059	11.769	0.893	0.893	0.000	0.000	0.000
40	E	41	ALA	0	-0.036	-0.019	14.809	0.644	0.644	0.000	0.000	0.000
41	E	42	THR	0	-0.052	-0.038	16.754	0.673	0.673	0.000	0.000	0.000
42	E	43	SER	0	-0.046	-0.046	17.372	0.623	0.623	0.000	0.000	0.000
43	E	44	LEU	0	-0.004	0.001	17.754	0.445	0.445	0.000	0.000	0.000
44	E	45	GLY	0	0.022	0.024	20.904	0.367	0.367	0.000	0.000	0.000
45	E	46	LEU	0	-0.030	0.006	17.885	0.108	0.108	0.000	0.000	0.000
46	E	47	THR	0	0.050	0.008	18.838	-0.684	-0.684	0.000	0.000	0.000
47	E	48	ARG	1	1.010	0.977	13.744	17.629	17.629	0.000	0.000	0.000
48	E	49	GLY	0	0.024	0.027	14.270	-0.805	-0.805	0.000	0.000	0.000
49	E	50	ALA	0	0.024	0.016	16.083	-0.180	-0.180	0.000	0.000	0.000
50	E	51	VAL	0	-0.004	0.001	12.067	-0.014	-0.014	0.000	0.000	0.000
51	E	52	SER	0	0.028	0.007	11.233	-0.882	-0.882	0.000	0.000	0.000
52	E	53	GLN	0	0.002	0.004	12.404	-0.007	-0.007	0.000	0.000	0.000
53	E	54	ALA	0	-0.027	0.000	14.785	0.259	0.259	0.000	0.000	0.000
54	E	55	VAL	0	0.015	-0.004	8.058	0.026	0.026	0.000	0.000	0.000
55	E	56	HIS	0	-0.008	-0.003	11.452	-1.059	-1.059	0.000	0.000	0.000
56	E	57	ARG	1	0.919	0.952	12.433	14.178	14.178	0.000	0.000	0.000
57	E	58	VAL	0	0.023	0.014	13.283	0.362	0.362	0.000	0.000	0.000
58	E	59	TRP	0	-0.065	-0.062	7.937	-0.994	-0.994	0.000	0.000	0.000
59	E	60	ALA	0	-0.010	-0.013	11.797	-0.152	-0.152	0.000	0.000	0.000
60	E	61	ALA	0	0.068	0.044	14.234	0.313	0.313	0.000	0.000	0.000
61	E	62	PHE	0	0.002	0.000	11.689	0.315	0.315	0.000	0.000	0.000
62	E	63	GLU	-1	-0.869	-0.920	10.268	-22.968	-22.968	0.000	0.000	0.000
63	E	64	ASP	-1	-0.917	-0.963	14.414	-14.220	-14.220	0.000	0.000	0.000
64	E	65	LYS	1	0.768	0.886	17.581	13.866	13.866	0.000	0.000	0.000
65	E	66	ASN	0	-0.127	-0.068	14.287	0.284	0.284	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:2:LYS)