FMO DATABASE

FMODB ID: P9MY2

Calculation Name: 1T6F-A-Xray27

Preferred Name: Geminin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1T6F

Chain ID: A

ChEMBL ID: CHEMBL1293278

UniProt ID: O75496

Base Structure: X-ray

Registration Date: 2018-07-26

Reference:

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water	Apo structure with with a 3 angstrom solvent shell.
Procedure	Auto-FMO protocol ver. 1.20180227

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	86
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-191330.16047
FMO2-HF: Nuclear repulsion	172471.466102
FMO2-HF: Total energy	-18858.694368
FMO2-MP2: Total energy	-18913.261993

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:1:THR)

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

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.
-54.472	-74.476	67.1	-27.107	-19.989	-0.04

Interaction energy analysis for fragmet #1(A:1:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : 0.041

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	3	TYR	0	-0.002	0.019	2.754	-4.734	-0.794	0.660	-1.954	-2.646	0.013
4	A	4	GLU	-1	-0.814	-0.904	1.961	-33.031	-27.454	11.944	-8.575	-8.946	-0.052
5	A	5	ALA	0	0.037	0.021	3.451	-0.144	0.706	0.008	-0.362	-0.496	0.001
6	A	6	LEU	0	0.008	0.002	4.973	0.680	0.827	-0.001	-0.012	-0.133	0.000
7	A	7	LYS	1	0.951	0.986	7.148	-0.238	-0.238	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.846	-0.916	7.656	-1.079	-1.079	0.000	0.000	0.000	0.000
9	A	9	ASN	0	-0.042	-0.022	9.076	0.310	0.310	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.800	-0.872	11.046	-0.089	-0.089	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.925	0.975	11.789	0.747	0.747	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.029	0.003	11.449	0.069	0.069	0.000	0.000	0.000	0.000
13	A	13	HIS	0	0.035	0.040	14.941	0.073	0.073	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.854	0.928	17.135	0.179	0.179	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.797	-0.865	16.756	-0.385	-0.385	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.003	-0.006	17.835	0.027	0.027	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.759	-0.816	21.035	-0.104	-0.104	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.026	-0.001	22.914	0.002	0.002	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.941	0.968	20.903	0.257	0.257	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.769	-0.857	24.785	-0.153	-0.153	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.014	-0.005	26.953	0.014	0.014	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.837	-0.899	28.442	-0.124	-0.124	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.019	0.010	27.324	0.009	0.009	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.025	-0.004	31.007	0.008	0.008	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.952	0.966	30.391	0.103	0.103	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.061	0.036	32.261	0.006	0.006	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.864	0.921	32.372	0.104	0.104	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.920	0.977	36.916	0.061	0.061	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.782	-0.836	38.824	-0.064	-0.064	0.000	0.000	0.000	0.000
30	A	30	ASN	0	0.016	-0.006	37.936	0.005	0.005	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.871	0.948	41.105	0.057	0.057	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.883	-0.939	42.928	-0.049	-0.049	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.012	-0.001	42.480	0.003	0.003	0.000	0.000	0.000	0.000
34	A	34	ALA	0	-0.036	-0.011	44.782	0.002	0.002	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.920	-0.919	46.634	-0.044	-0.044	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.115	-0.033	49.179	0.002	0.002	0.000	0.000	0.000	0.000
37	A	37	ALA	-1	-0.915	-0.951	51.290	-0.036	-0.036	0.000	0.000	0.000	0.000
38	A	38	HOH	0	-0.041	-0.025	36.052	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	39	HOH	0	-0.069	-0.061	39.004	0.000	0.000	0.000	0.000	0.000	0.000
40	A	40	HOH	0	0.002	0.004	33.062	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	41	HOH	0	-0.033	-0.027	17.128	0.005	0.005	0.000	0.000	0.000	0.000
42	A	44	HOH	0	-0.036	-0.023	48.070	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	45	HOH	0	-0.050	-0.038	11.414	0.022	0.022	0.000	0.000	0.000	0.000
44	A	46	HOH	0	-0.010	0.003	13.941	0.012	0.012	0.000	0.000	0.000	0.000
45	A	47	HOH	0	-0.030	-0.023	48.609	0.000	0.000	0.000	0.000	0.000	0.000
46	A	48	HOH	0	-0.034	-0.026	29.132	0.004	0.004	0.000	0.000	0.000	0.000
47	A	49	HOH	0	-0.040	-0.025	42.228	0.000	0.000	0.000	0.000	0.000	0.000
48	A	50	HOH	0	0.038	0.026	14.646	-0.019	-0.019	0.000	0.000	0.000	0.000
49	A	52	HOH	0	-0.043	-0.035	32.188	0.003	0.003	0.000	0.000	0.000	0.000
50	A	53	HOH	0	0.015	0.004	31.417	0.001	0.001	0.000	0.000	0.000	0.000
51	A	55	HOH	0	-0.016	-0.013	6.739	0.052	0.052	0.000	0.000	0.000	0.000
52	A	56	HOH	0	-0.004	0.000	32.335	0.002	0.002	0.000	0.000	0.000	0.000
53	A	58	HOH	0	-0.022	-0.022	22.204	0.005	0.005	0.000	0.000	0.000	0.000
54	A	60	HOH	0	-0.005	-0.008	21.038	-0.008	-0.008	0.000	0.000	0.000	0.000
55	A	61	HOH	0	-0.053	-0.035	51.776	0.001	0.001	0.000	0.000	0.000	0.000
56	A	62	HOH	0	-0.060	-0.056	19.069	0.004	0.004	0.000	0.000	0.000	0.000
57	A	63	HOH	0	-0.004	0.004	27.074	0.005	0.005	0.000	0.000	0.000	0.000
58	A	64	HOH	0	-0.019	-0.031	1.638	-4.082	-18.155	23.215	-6.248	-2.894	0.023
59	A	66	HOH	0	0.034	0.020	44.652	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	67	HOH	0	-0.053	-0.036	17.124	0.017	0.017	0.000	0.000	0.000	0.000
61	A	68	HOH	0	-0.056	-0.039	25.296	0.002	0.002	0.000	0.000	0.000	0.000
62	A	72	HOH	0	-0.011	-0.002	24.727	0.006	0.006	0.000	0.000	0.000	0.000
63	A	73	HOH	0	-0.039	-0.026	39.485	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	74	HOH	0	-0.017	-0.021	22.137	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	75	HOH	0	-0.049	-0.029	15.471	0.014	0.014	0.000	0.000	0.000	0.000
66	A	76	HOH	0	0.036	0.015	2.018	-5.569	-7.858	8.387	-3.796	-2.303	-0.033
67	A	77	HOH	0	-0.005	0.004	6.322	0.396	0.396	0.000	0.000	0.000	0.000
68	A	78	HOH	0	-0.016	-0.012	20.391	0.000	0.000	0.000	0.000	0.000	0.000
69	A	79	HOH	0	-0.017	-0.016	28.951	0.002	0.002	0.000	0.000	0.000	0.000
70	A	80	HOH	0	-0.038	-0.023	17.043	0.008	0.008	0.000	0.000	0.000	0.000
71	A	81	HOH	0	-0.074	-0.058	18.628	0.004	0.004	0.000	0.000	0.000	0.000
72	A	82	HOH	0	-0.085	-0.075	45.767	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	84	HOH	0	-0.051	-0.036	22.762	0.003	0.003	0.000	0.000	0.000	0.000
74	A	87	HOH	0	-0.016	-0.018	19.127	0.017	0.017	0.000	0.000	0.000	0.000
75	A	88	HOH	0	-0.044	-0.053	41.462	0.000	0.000	0.000	0.000	0.000	0.000
76	A	90	HOH	0	-0.016	-0.014	38.137	0.000	0.000	0.000	0.000	0.000	0.000
77	A	92	HOH	0	-0.031	-0.036	26.400	0.003	0.003	0.000	0.000	0.000	0.000
78	A	95	HOH	0	0.008	0.003	9.963	0.083	0.083	0.000	0.000	0.000	0.000
79	A	96	HOH	0	-0.040	-0.040	8.582	0.158	0.158	0.000	0.000	0.000	0.000
80	A	99	HOH	0	-0.019	-0.018	26.710	0.004	0.004	0.000	0.000	0.000	0.000
81	A	100	HOH	0	-0.052	-0.036	27.294	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	101	HOH	0	-0.048	-0.031	4.803	0.533	0.533	0.000	0.000	0.000	0.000
83	A	102	HOH	0	0.033	0.021	20.437	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	106	HOH	0	-0.005	-0.039	1.750	-8.620	-22.776	22.887	-6.160	-2.571	0.008
85	A	108	HOH	0	-0.037	-0.032	11.775	0.041	0.041	0.000	0.000	0.000	0.000
86	B	91	HOH	0	0.043	0.035	30.456	0.003	0.003	0.000	0.000	0.000	0.000

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