FMO DATABASE

FMODB ID: 59LVZ

Calculation Name: 1UII-A-Xray315

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	62
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-275868.266208
FMO2-HF: Nuclear repulsion	250179.032371
FMO2-HF: Total energy	-25689.233837
FMO2-MP2: Total energy	-25764.932701

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:91:ACE )

Summations of interaction energy for fragment #1(A:91:ACE )

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.
2.019	2.804	-0.004	-0.336	-0.445	0

Interaction energy analysis for fragmet #1(A:91:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.013

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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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	A	93	ASN	0	0.026	0.028	3.871	1.092	1.877	-0.004	-0.336	-0.445
4	A	94	PRO	0	0.076	0.021	6.789	0.140	0.140	0.000	0.000	0.000
5	A	95	SER	0	0.058	0.036	9.786	0.071	0.071	0.000	0.000	0.000
6	A	96	SER	0	-0.016	-0.006	9.556	0.045	0.045	0.000	0.000	0.000
7	A	97	GLN	0	-0.006	-0.013	9.331	0.002	0.002	0.000	0.000	0.000
8	A	98	TYR	0	0.063	0.036	11.438	0.082	0.082	0.000	0.000	0.000
9	A	99	TRP	0	0.043	0.006	14.611	0.052	0.052	0.000	0.000	0.000
10	A	100	LYS	1	0.940	0.988	12.785	0.405	0.405	0.000	0.000	0.000
11	A	101	GLU	-1	-0.906	-0.959	14.434	-0.420	-0.420	0.000	0.000	0.000
12	A	102	VAL	0	-0.055	-0.014	17.012	0.044	0.044	0.000	0.000	0.000
13	A	103	ALA	0	-0.009	-0.013	19.081	0.027	0.027	0.000	0.000	0.000
14	A	104	GLU	-1	-0.972	-0.984	18.327	-0.244	-0.244	0.000	0.000	0.000
15	A	105	LYS	1	0.969	0.969	20.190	0.252	0.252	0.000	0.000	0.000
16	A	106	ARG	1	0.971	0.985	23.031	0.155	0.155	0.000	0.000	0.000
17	A	107	ARG	1	0.976	0.998	20.736	0.174	0.174	0.000	0.000	0.000
18	A	108	LYS	1	0.911	0.950	21.744	0.197	0.197	0.000	0.000	0.000
19	A	109	ALA	0	0.082	0.050	26.730	0.008	0.008	0.000	0.000	0.000
20	A	110	LEU	0	-0.009	-0.001	28.603	0.008	0.008	0.000	0.000	0.000
21	A	111	TYR	0	-0.022	-0.016	29.258	0.009	0.009	0.000	0.000	0.000
22	A	112	GLU	-1	-0.931	-0.975	30.578	-0.094	-0.094	0.000	0.000	0.000
23	A	113	ALA	0	0.037	0.025	32.963	0.006	0.006	0.000	0.000	0.000
24	A	114	LEU	0	-0.049	-0.024	32.507	0.005	0.005	0.000	0.000	0.000
25	A	115	LYS	1	0.888	0.944	34.493	0.067	0.067	0.000	0.000	0.000
26	A	116	GLU	-1	-0.924	-0.950	37.102	-0.057	-0.057	0.000	0.000	0.000
27	A	117	ASN	0	0.032	-0.008	38.482	0.004	0.004	0.000	0.000	0.000
28	A	118	GLU	-1	-0.947	-0.966	39.271	-0.050	-0.050	0.000	0.000	0.000
29	A	119	LYS	1	0.894	0.941	39.700	0.060	0.060	0.000	0.000	0.000
30	A	120	LEU	0	0.056	0.030	42.502	0.003	0.003	0.000	0.000	0.000
31	A	121	HIS	0	0.010	-0.001	42.887	0.004	0.004	0.000	0.000	0.000
32	A	122	LYS	1	0.953	0.985	43.820	0.044	0.044	0.000	0.000	0.000
33	A	123	GLU	-1	-0.946	-0.966	46.871	-0.040	-0.040	0.000	0.000	0.000
34	A	124	ILE	0	-0.036	-0.023	47.821	0.002	0.002	0.000	0.000	0.000
35	A	125	GLU	-1	-0.915	-0.937	50.450	-0.029	-0.029	0.000	0.000	0.000
36	A	126	GLN	0	-0.064	-0.046	51.571	0.001	0.001	0.000	0.000	0.000
37	A	127	LYS	1	0.969	0.975	51.947	0.034	0.034	0.000	0.000	0.000
38	A	128	ASP	-1	-0.880	-0.934	53.801	-0.028	-0.028	0.000	0.000	0.000
39	A	129	ASN	0	-0.032	-0.021	55.950	0.002	0.002	0.000	0.000	0.000
40	A	130	GLU	-1	-0.980	-0.979	58.234	-0.025	-0.025	0.000	0.000	0.000
41	A	131	ILE	0	0.007	-0.003	57.707	0.001	0.001	0.000	0.000	0.000
42	A	132	ALA	0	-0.037	-0.014	60.737	0.001	0.001	0.000	0.000	0.000
43	A	133	ARG	1	0.917	0.958	62.558	0.022	0.022	0.000	0.000	0.000
44	A	134	LEU	0	0.040	0.016	62.556	0.001	0.001	0.000	0.000	0.000
45	A	135	LYS	1	0.925	0.960	62.056	0.023	0.023	0.000	0.000	0.000
46	A	136	LYS	1	0.885	0.959	66.816	0.018	0.018	0.000	0.000	0.000
47	A	137	GLU	-1	-0.858	-0.940	67.928	-0.019	-0.019	0.000	0.000	0.000
48	A	138	ASN	0	-0.060	-0.020	69.187	0.001	0.001	0.000	0.000	0.000
49	A	139	LYS	1	0.971	0.982	70.953	0.016	0.016	0.000	0.000	0.000
50	A	140	GLU	-1	-0.898	-0.952	72.792	-0.016	-0.016	0.000	0.000	0.000
51	A	141	LEU	0	-0.004	-0.015	72.441	0.000	0.000	0.000	0.000	0.000
52	A	142	ALA	0	-0.023	-0.003	74.727	0.000	0.000	0.000	0.000	0.000
53	A	143	GLU	-1	-0.940	-0.954	76.561	-0.013	-0.013	0.000	0.000	0.000
54	A	144	VAL	0	-0.014	-0.015	78.907	0.000	0.000	0.000	0.000	0.000
55	A	145	ALA	0	-0.020	-0.016	78.919	0.000	0.000	0.000	0.000	0.000
56	A	146	GLU	-1	-0.933	-0.963	80.613	-0.013	-0.013	0.000	0.000	0.000
57	A	147	HIS	0	-0.009	-0.008	82.370	0.000	0.000	0.000	0.000	0.000
58	A	148	VAL	0	-0.003	-0.008	83.756	0.000	0.000	0.000	0.000	0.000
59	A	149	GLN	0	-0.081	-0.047	81.589	0.000	0.000	0.000	0.000	0.000
60	A	150	TYR	0	-0.073	-0.030	85.211	0.000	0.000	0.000	0.000	0.000
61	A	151	MET	0	-0.122	-0.068	88.488	0.000	0.000	0.000	0.000	0.000
62	A	152	ALA	-1	-0.956	-0.944	88.577	-0.011	-0.011	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:91:ACE )