FMO DATABASE

FMODB ID: LJ359

Calculation Name: 1UII-A-Xray372

Preferred Name: Geminin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1UII

Chain ID: A

ChEMBL ID: CHEMBL1293278

UniProt ID: O75496

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	61
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-274752.435896
FMO2-HF: Nuclear repulsion	249213.843908
FMO2-HF: Total energy	-25538.591988
FMO2-MP2: Total energy	-25613.841822

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:92:GLU)

Summations of interaction energy for fragment #1(A:92:GLU)

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.
-58.774	-56.111	0.076	-1.164	-1.575	0.006

Interaction energy analysis for fragmet #1(A:92:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.889 / q_NPA : -0.946

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	94	PRO	0	0.079	0.024	2.824	-5.701	-3.225	0.077	-1.158	-1.395	0.006
4	A	95	SER	0	0.013	0.017	5.516	-3.135	-3.135	0.000	0.000	0.000	0.000
5	A	96	SER	0	-0.019	-0.013	6.662	-1.391	-1.391	0.000	0.000	0.000	0.000
6	A	97	GLN	0	-0.012	-0.019	4.745	2.863	3.050	-0.001	-0.006	-0.180	0.000
7	A	98	TYR	0	0.030	0.020	7.363	-2.665	-2.665	0.000	0.000	0.000	0.000
8	A	99	TRP	0	0.041	0.009	10.446	-2.279	-2.279	0.000	0.000	0.000	0.000
9	A	100	LYS	1	0.965	0.995	9.191	-27.634	-27.634	0.000	0.000	0.000	0.000
10	A	101	GLU	-1	-0.839	-0.915	9.413	25.665	25.665	0.000	0.000	0.000	0.000
11	A	102	VAL	0	-0.035	-0.011	12.840	-1.642	-1.642	0.000	0.000	0.000	0.000
12	A	103	ALA	0	0.000	-0.003	15.222	-1.272	-1.272	0.000	0.000	0.000	0.000
13	A	104	GLU	-1	-0.829	-0.886	14.774	16.593	16.593	0.000	0.000	0.000	0.000
14	A	105	LYS	1	0.911	0.940	13.243	-21.749	-21.749	0.000	0.000	0.000	0.000
15	A	106	ARG	1	0.970	0.984	18.824	-15.510	-15.510	0.000	0.000	0.000	0.000
16	A	107	ARG	1	0.861	0.922	18.372	-16.461	-16.461	0.000	0.000	0.000	0.000
17	A	108	LYS	1	0.829	0.906	17.999	-17.399	-17.399	0.000	0.000	0.000	0.000
18	A	109	ALA	0	0.111	0.059	23.060	-0.506	-0.506	0.000	0.000	0.000	0.000
19	A	110	LEU	0	-0.024	-0.005	24.704	-0.516	-0.516	0.000	0.000	0.000	0.000
20	A	111	TYR	0	-0.001	-0.005	25.762	-0.558	-0.558	0.000	0.000	0.000	0.000
21	A	112	GLU	-1	-0.914	-0.964	25.858	11.631	11.631	0.000	0.000	0.000	0.000
22	A	113	ALA	0	0.028	0.016	29.021	-0.436	-0.436	0.000	0.000	0.000	0.000
23	A	114	LEU	0	-0.025	-0.006	28.965	-0.420	-0.420	0.000	0.000	0.000	0.000
24	A	115	LYS	1	0.836	0.897	31.110	-9.715	-9.715	0.000	0.000	0.000	0.000
25	A	116	GLU	-1	-0.817	-0.885	33.226	8.701	8.701	0.000	0.000	0.000	0.000
26	A	117	ASN	0	-0.031	-0.037	34.346	-0.500	-0.500	0.000	0.000	0.000	0.000
27	A	118	GLU	-1	-0.808	-0.874	35.978	8.548	8.548	0.000	0.000	0.000	0.000
28	A	119	LYS	1	0.819	0.904	35.484	-9.077	-9.077	0.000	0.000	0.000	0.000
29	A	120	LEU	0	0.042	0.020	38.519	-0.216	-0.216	0.000	0.000	0.000	0.000
30	A	121	HIS	0	0.036	0.010	38.741	-0.335	-0.335	0.000	0.000	0.000	0.000
31	A	122	LYS	1	0.846	0.914	39.391	-8.204	-8.204	0.000	0.000	0.000	0.000
32	A	123	GLU	-1	-0.849	-0.906	43.700	7.018	7.018	0.000	0.000	0.000	0.000
33	A	124	ILE	0	-0.036	-0.013	43.831	-0.169	-0.169	0.000	0.000	0.000	0.000
34	A	125	GLU	-1	-0.922	-0.952	46.791	6.598	6.598	0.000	0.000	0.000	0.000
35	A	126	GLN	0	-0.030	-0.018	48.044	-0.139	-0.139	0.000	0.000	0.000	0.000
36	A	127	LYS	1	0.880	0.921	47.278	-6.860	-6.860	0.000	0.000	0.000	0.000
37	A	128	ASP	-1	-0.889	-0.946	50.514	6.130	6.130	0.000	0.000	0.000	0.000
38	A	129	ASN	0	-0.086	-0.049	52.145	-0.245	-0.245	0.000	0.000	0.000	0.000
39	A	130	GLU	-1	-0.956	-0.969	54.331	5.772	5.772	0.000	0.000	0.000	0.000
40	A	131	ILE	0	0.015	-0.007	53.524	-0.156	-0.156	0.000	0.000	0.000	0.000
41	A	132	ALA	0	-0.038	-0.016	56.938	-0.122	-0.122	0.000	0.000	0.000	0.000
42	A	133	ARG	1	0.838	0.886	58.819	-5.359	-5.359	0.000	0.000	0.000	0.000
43	A	134	LEU	0	0.020	0.004	58.552	-0.117	-0.117	0.000	0.000	0.000	0.000
44	A	135	LYS	1	0.918	0.963	57.258	-5.653	-5.653	0.000	0.000	0.000	0.000
45	A	136	LYS	1	0.795	0.888	62.791	-4.905	-4.905	0.000	0.000	0.000	0.000
46	A	137	GLU	-1	-0.793	-0.871	64.663	4.984	4.984	0.000	0.000	0.000	0.000
47	A	138	ASN	0	-0.044	-0.020	65.211	-0.081	-0.081	0.000	0.000	0.000	0.000
48	A	139	LYS	1	0.838	0.908	66.942	-4.587	-4.587	0.000	0.000	0.000	0.000
49	A	140	GLU	-1	-0.793	-0.886	68.818	4.643	4.643	0.000	0.000	0.000	0.000
50	A	141	LEU	0	-0.010	-0.010	68.399	-0.080	-0.080	0.000	0.000	0.000	0.000
51	A	142	ALA	0	-0.013	0.001	70.661	-0.065	-0.065	0.000	0.000	0.000	0.000
52	A	143	GLU	-1	-0.817	-0.885	72.528	4.333	4.333	0.000	0.000	0.000	0.000
53	A	144	VAL	0	-0.011	-0.011	74.826	-0.074	-0.074	0.000	0.000	0.000	0.000
54	A	145	ALA	0	-0.019	-0.009	74.899	-0.066	-0.066	0.000	0.000	0.000	0.000
55	A	146	GLU	-1	-0.896	-0.951	76.578	4.127	4.127	0.000	0.000	0.000	0.000
56	A	147	HIS	0	-0.005	-0.002	78.342	-0.048	-0.048	0.000	0.000	0.000	0.000
57	A	148	VAL	0	0.008	-0.012	79.822	-0.063	-0.063	0.000	0.000	0.000	0.000
58	A	149	GLN	0	-0.053	-0.029	76.966	-0.059	-0.059	0.000	0.000	0.000	0.000
59	A	150	TYR	0	-0.069	-0.018	81.068	-0.069	-0.069	0.000	0.000	0.000	0.000
60	A	151	MET	0	-0.067	-0.029	84.455	-0.062	-0.062	0.000	0.000	0.000	0.000
61	A	152	ALA	0	-0.084	-0.026	84.532	-0.080	-0.080	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:92:GLU)