FMO DATABASE

FMODB ID: J3989

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

Total energy (hartree)

FMO2-HF: Electronic energy	-273988.861307
FMO2-HF: Nuclear repulsion	248451.151641
FMO2-HF: Total energy	-25537.709666
FMO2-MP2: Total energy	-25612.972429

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.
-57.649	-54.629	0.435	-1.23	-2.224	0.008

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 : -0.903 / q_NPA : -0.956

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	0.073	0.019	2.446	-5.356	-2.790	0.437	-1.191	-1.811	0.008
4	A	95	SER	0	0.044	0.027	4.865	-2.673	-2.508	-0.001	-0.010	-0.154	0.000
5	A	96	SER	0	-0.021	-0.008	6.517	-2.310	-2.310	0.000	0.000	0.000	0.000
6	A	97	GLN	0	0.004	-0.006	4.272	-1.851	-1.562	-0.001	-0.029	-0.259	0.000
7	A	98	TYR	0	0.060	0.033	7.242	-2.633	-2.633	0.000	0.000	0.000	0.000
8	A	99	TRP	0	0.034	0.002	9.805	-2.349	-2.349	0.000	0.000	0.000	0.000
9	A	100	LYS	1	0.942	0.989	9.322	-27.478	-27.478	0.000	0.000	0.000	0.000
10	A	101	GLU	-1	-0.905	-0.957	9.485	26.782	26.782	0.000	0.000	0.000	0.000
11	A	102	VAL	0	-0.058	-0.016	12.382	-1.862	-1.862	0.000	0.000	0.000	0.000
12	A	103	ALA	0	-0.009	-0.014	15.086	-1.272	-1.272	0.000	0.000	0.000	0.000
13	A	104	GLU	-1	-0.972	-0.984	14.032	19.635	19.635	0.000	0.000	0.000	0.000
14	A	105	LYS	1	0.969	0.970	14.924	-19.736	-19.736	0.000	0.000	0.000	0.000
15	A	106	ARG	1	0.968	0.984	18.338	-15.449	-15.449	0.000	0.000	0.000	0.000
16	A	107	ARG	1	0.976	0.997	17.487	-16.780	-16.780	0.000	0.000	0.000	0.000
17	A	108	LYS	1	0.909	0.949	17.692	-17.450	-17.450	0.000	0.000	0.000	0.000
18	A	109	ALA	0	0.082	0.050	22.501	-0.477	-0.477	0.000	0.000	0.000	0.000
19	A	110	LEU	0	-0.011	-0.001	24.318	-0.481	-0.481	0.000	0.000	0.000	0.000
20	A	111	TYR	0	-0.022	-0.016	25.402	-0.569	-0.569	0.000	0.000	0.000	0.000
21	A	112	GLU	-1	-0.930	-0.975	26.096	11.341	11.341	0.000	0.000	0.000	0.000
22	A	113	ALA	0	0.035	0.025	28.586	-0.395	-0.395	0.000	0.000	0.000	0.000
23	A	114	LEU	0	-0.049	-0.024	28.963	-0.369	-0.369	0.000	0.000	0.000	0.000
24	A	115	LYS	1	0.890	0.945	30.649	-9.986	-9.986	0.000	0.000	0.000	0.000
25	A	116	GLU	-1	-0.926	-0.951	32.893	8.710	8.710	0.000	0.000	0.000	0.000
26	A	117	ASN	0	0.031	-0.008	34.245	-0.356	-0.356	0.000	0.000	0.000	0.000
27	A	118	GLU	-1	-0.947	-0.967	35.789	8.691	8.691	0.000	0.000	0.000	0.000
28	A	119	LYS	1	0.894	0.941	35.453	-9.065	-9.065	0.000	0.000	0.000	0.000
29	A	120	LEU	0	0.055	0.030	38.046	-0.232	-0.232	0.000	0.000	0.000	0.000
30	A	121	HIS	0	0.011	-0.001	39.081	-0.343	-0.343	0.000	0.000	0.000	0.000
31	A	122	LYS	1	0.952	0.985	40.289	-8.015	-8.015	0.000	0.000	0.000	0.000
32	A	123	GLU	-1	-0.946	-0.966	42.413	7.229	7.229	0.000	0.000	0.000	0.000
33	A	124	ILE	0	-0.038	-0.024	43.640	-0.180	-0.180	0.000	0.000	0.000	0.000
34	A	125	GLU	-1	-0.914	-0.936	46.479	6.566	6.566	0.000	0.000	0.000	0.000
35	A	126	GLN	0	-0.064	-0.046	47.447	-0.104	-0.104	0.000	0.000	0.000	0.000
36	A	127	LYS	1	0.971	0.975	47.461	-6.711	-6.711	0.000	0.000	0.000	0.000
37	A	128	ASP	-1	-0.881	-0.934	49.854	6.212	6.212	0.000	0.000	0.000	0.000
38	A	129	ASN	0	-0.030	-0.020	52.286	-0.196	-0.196	0.000	0.000	0.000	0.000
39	A	130	GLU	-1	-0.980	-0.979	54.107	5.722	5.722	0.000	0.000	0.000	0.000
40	A	131	ILE	0	0.005	-0.004	53.308	-0.158	-0.158	0.000	0.000	0.000	0.000
41	A	132	ALA	0	-0.034	-0.013	56.679	-0.129	-0.129	0.000	0.000	0.000	0.000
42	A	133	ARG	1	0.916	0.958	58.530	-5.402	-5.402	0.000	0.000	0.000	0.000
43	A	134	LEU	0	0.042	0.017	58.135	-0.111	-0.111	0.000	0.000	0.000	0.000
44	A	135	LYS	1	0.923	0.959	57.951	-5.573	-5.573	0.000	0.000	0.000	0.000
45	A	136	LYS	1	0.889	0.961	62.625	-4.941	-4.941	0.000	0.000	0.000	0.000
46	A	137	GLU	-1	-0.860	-0.941	63.753	4.958	4.958	0.000	0.000	0.000	0.000
47	A	138	ASN	0	-0.059	-0.020	64.813	-0.103	-0.103	0.000	0.000	0.000	0.000
48	A	139	LYS	1	0.973	0.983	66.722	-4.747	-4.747	0.000	0.000	0.000	0.000
49	A	140	GLU	-1	-0.897	-0.952	68.661	4.610	4.610	0.000	0.000	0.000	0.000
50	A	141	LEU	0	-0.004	-0.014	68.043	-0.078	-0.078	0.000	0.000	0.000	0.000
51	A	142	ALA	0	-0.023	-0.003	70.341	-0.067	-0.067	0.000	0.000	0.000	0.000
52	A	143	GLU	-1	-0.934	-0.951	72.195	4.252	4.252	0.000	0.000	0.000	0.000
53	A	144	VAL	0	-0.012	-0.014	74.661	-0.074	-0.074	0.000	0.000	0.000	0.000
54	A	145	ALA	0	-0.018	-0.015	74.421	-0.065	-0.065	0.000	0.000	0.000	0.000
55	A	146	GLU	-1	-0.929	-0.960	76.214	4.119	4.119	0.000	0.000	0.000	0.000
56	A	147	HIS	0	0.003	-0.001	77.945	-0.057	-0.057	0.000	0.000	0.000	0.000
57	A	148	VAL	0	-0.004	-0.008	79.301	-0.065	-0.065	0.000	0.000	0.000	0.000
58	A	149	GLN	0	-0.078	-0.048	76.878	-0.041	-0.041	0.000	0.000	0.000	0.000
59	A	150	TYR	0	-0.048	-0.012	80.772	-0.068	-0.068	0.000	0.000	0.000	0.000
60	A	151	MET	0	-0.079	-0.041	84.065	-0.060	-0.060	0.000	0.000	0.000	0.000
61	A	152	ALA	0	-0.057	-0.004	84.044	-0.059	-0.059	0.000	0.000	0.000	0.000

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