FMO DATABASE

FMODB ID: 3QV2L

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	OptHSide
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	-274447.096483
FMO2-HF: Nuclear repulsion	248908.733282
FMO2-HF: Total energy	-25538.363202
FMO2-MP2: Total energy	-25613.650028

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.
-59.179	-56.027	0.345	-1.275	-2.222	0.009

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 : -0.899 / q_NPA : -0.951

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	0.068	0.018	2.509	-6.159	-3.440	0.347	-1.244	-1.822	0.009
4	A	95	SER	0	0.036	0.022	4.842	-2.867	-2.711	-0.001	-0.010	-0.145	0.000
5	A	96	SER	0	-0.019	-0.005	6.562	-1.610	-1.610	0.000	0.000	0.000	0.000
6	A	97	GLN	0	-0.007	-0.018	4.216	3.169	3.446	-0.001	-0.021	-0.255	0.000
7	A	98	TYR	0	0.016	0.009	7.324	-2.636	-2.636	0.000	0.000	0.000	0.000
8	A	99	TRP	0	0.054	0.011	10.102	-2.275	-2.275	0.000	0.000	0.000	0.000
9	A	100	LYS	1	0.959	1.000	9.170	-27.433	-27.433	0.000	0.000	0.000	0.000
10	A	101	GLU	-1	-0.829	-0.914	9.104	25.303	25.303	0.000	0.000	0.000	0.000
11	A	102	VAL	0	-0.045	-0.011	12.614	-1.692	-1.692	0.000	0.000	0.000	0.000
12	A	103	ALA	0	-0.002	-0.007	15.240	-1.217	-1.217	0.000	0.000	0.000	0.000
13	A	104	GLU	-1	-0.814	-0.886	14.632	16.854	16.854	0.000	0.000	0.000	0.000
14	A	105	LYS	1	0.901	0.940	13.032	-21.406	-21.406	0.000	0.000	0.000	0.000
15	A	106	ARG	1	0.973	0.989	18.546	-15.408	-15.408	0.000	0.000	0.000	0.000
16	A	107	ARG	1	0.874	0.933	18.005	-16.602	-16.602	0.000	0.000	0.000	0.000
17	A	108	LYS	1	0.845	0.901	17.442	-17.489	-17.489	0.000	0.000	0.000	0.000
18	A	109	ALA	0	0.075	0.046	22.685	-0.482	-0.482	0.000	0.000	0.000	0.000
19	A	110	LEU	0	-0.016	-0.005	24.537	-0.505	-0.505	0.000	0.000	0.000	0.000
20	A	111	TYR	0	-0.013	-0.010	25.606	-0.560	-0.560	0.000	0.000	0.000	0.000
21	A	112	GLU	-1	-0.916	-0.964	26.348	11.291	11.291	0.000	0.000	0.000	0.000
22	A	113	ALA	0	0.022	0.018	28.788	-0.427	-0.427	0.000	0.000	0.000	0.000
23	A	114	LEU	0	-0.022	-0.007	28.991	-0.409	-0.409	0.000	0.000	0.000	0.000
24	A	115	LYS	1	0.842	0.902	30.830	-9.742	-9.742	0.000	0.000	0.000	0.000
25	A	116	GLU	-1	-0.834	-0.898	33.073	8.575	8.575	0.000	0.000	0.000	0.000
26	A	117	ASN	0	-0.032	-0.045	33.919	-0.481	-0.481	0.000	0.000	0.000	0.000
27	A	118	GLU	-1	-0.831	-0.880	35.912	8.550	8.550	0.000	0.000	0.000	0.000
28	A	119	LYS	1	0.837	0.903	34.765	-9.124	-9.124	0.000	0.000	0.000	0.000
29	A	120	LEU	0	0.036	0.016	38.170	-0.219	-0.219	0.000	0.000	0.000	0.000
30	A	121	HIS	0	0.019	0.003	39.050	-0.332	-0.332	0.000	0.000	0.000	0.000
31	A	122	LYS	1	0.892	0.950	39.311	-8.186	-8.186	0.000	0.000	0.000	0.000
32	A	123	GLU	-1	-0.858	-0.906	43.107	7.024	7.024	0.000	0.000	0.000	0.000
33	A	124	ILE	0	-0.033	-0.022	43.552	-0.175	-0.175	0.000	0.000	0.000	0.000
34	A	125	GLU	-1	-0.909	-0.940	46.680	6.544	6.544	0.000	0.000	0.000	0.000
35	A	126	GLN	0	-0.033	-0.019	47.976	-0.136	-0.136	0.000	0.000	0.000	0.000
36	A	127	LYS	1	0.888	0.919	46.845	-6.846	-6.846	0.000	0.000	0.000	0.000
37	A	128	ASP	-1	-0.893	-0.941	50.366	6.152	6.152	0.000	0.000	0.000	0.000
38	A	129	ASN	0	-0.098	-0.059	51.962	-0.243	-0.243	0.000	0.000	0.000	0.000
39	A	130	GLU	-1	-0.957	-0.966	54.099	5.735	5.735	0.000	0.000	0.000	0.000
40	A	131	ILE	0	0.010	-0.007	53.338	-0.159	-0.159	0.000	0.000	0.000	0.000
41	A	132	ALA	0	-0.035	-0.012	56.890	-0.128	-0.128	0.000	0.000	0.000	0.000
42	A	133	ARG	1	0.856	0.903	58.728	-5.349	-5.349	0.000	0.000	0.000	0.000
43	A	134	LEU	0	0.023	0.007	58.280	-0.116	-0.116	0.000	0.000	0.000	0.000
44	A	135	LYS	1	0.924	0.963	57.748	-5.597	-5.597	0.000	0.000	0.000	0.000
45	A	136	LYS	1	0.781	0.884	62.838	-4.902	-4.902	0.000	0.000	0.000	0.000
46	A	137	GLU	-1	-0.799	-0.883	64.250	4.963	4.963	0.000	0.000	0.000	0.000
47	A	138	ASN	0	-0.050	-0.017	65.087	-0.086	-0.086	0.000	0.000	0.000	0.000
48	A	139	LYS	1	0.982	0.988	66.930	-4.685	-4.685	0.000	0.000	0.000	0.000
49	A	140	GLU	-1	-0.790	-0.877	68.645	4.638	4.638	0.000	0.000	0.000	0.000
50	A	141	LEU	0	-0.007	-0.016	68.221	-0.078	-0.078	0.000	0.000	0.000	0.000
51	A	142	ALA	0	-0.023	-0.003	70.537	-0.067	-0.067	0.000	0.000	0.000	0.000
52	A	143	GLU	-1	-0.940	-0.958	72.408	4.266	4.266	0.000	0.000	0.000	0.000
53	A	144	VAL	0	-0.004	-0.009	74.865	-0.073	-0.073	0.000	0.000	0.000	0.000
54	A	145	ALA	0	-0.019	-0.013	74.617	-0.065	-0.065	0.000	0.000	0.000	0.000
55	A	146	GLU	-1	-0.906	-0.953	76.433	4.110	4.110	0.000	0.000	0.000	0.000
56	A	147	HIS	0	0.010	0.002	78.162	-0.052	-0.052	0.000	0.000	0.000	0.000
57	A	148	VAL	0	-0.010	-0.013	79.539	-0.065	-0.065	0.000	0.000	0.000	0.000
58	A	149	GLN	0	-0.063	-0.037	76.751	-0.054	-0.054	0.000	0.000	0.000	0.000
59	A	150	TYR	0	-0.068	-0.016	81.003	-0.072	-0.072	0.000	0.000	0.000	0.000
60	A	151	MET	0	-0.071	-0.039	84.276	-0.061	-0.061	0.000	0.000	0.000	0.000
61	A	152	ALA	0	-0.080	-0.016	84.194	-0.083	-0.083	0.000	0.000	0.000	0.000

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