FMO DATABASE

FMODB ID: 8J1GY

Calculation Name: 3U28-C-Xray313

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U28

Chain ID: C

ChEMBL ID:

UniProt ID: P33322

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	93
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-651764.900166
FMO2-HF: Nuclear repulsion	615544.267996
FMO2-HF: Total energy	-36220.63217
FMO2-MP2: Total energy	-36325.569265

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(C:32:ACE )

Summations of interaction energy for fragment #1(C:32: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.
46.635	-17.608	96.377	-17.137	-14.994	-0.017

Interaction energy analysis for fragmet #1(C:32:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.169 / q_NPA : -0.167

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	C	34	PRO	0	-0.011	0.070	1.907	10.755	-2.720	15.655	1.102	-3.281	0.005
4	C	35	ASP	-1	-0.804	-0.897	4.489	-1.545	-1.566	0.000	-0.030	0.051	0.000
5	C	36	THR	0	-0.114	-0.059	6.805	0.131	0.131	0.000	0.000	0.000	0.000
6	C	37	VAL	0	-0.022	0.001	4.012	-0.181	-0.048	0.002	-0.032	-0.103	0.000
7	C	38	LEU	0	0.004	-0.011	5.983	0.013	0.013	0.000	0.000	0.000	0.000
8	C	39	GLU	-1	-0.850	-0.931	9.043	0.305	0.305	0.000	0.000	0.000	0.000
9	C	40	MET	0	-0.022	0.003	10.279	-0.052	-0.052	0.000	0.000	0.000	0.000
10	C	41	GLY	0	0.024	0.007	12.067	-0.051	-0.051	0.000	0.000	0.000	0.000
11	C	42	ALA	0	-0.005	0.002	13.461	0.027	0.027	0.000	0.000	0.000	0.000
12	C	43	PHE	0	0.019	-0.001	15.911	-0.013	-0.013	0.000	0.000	0.000	0.000
13	C	44	LEU	0	-0.014	0.002	17.164	-0.032	-0.032	0.000	0.000	0.000	0.000
14	C	45	HIS	1	0.934	0.957	20.468	-0.193	-0.193	0.000	0.000	0.000	0.000
15	C	46	PRO	0	0.010	-0.001	20.444	0.016	0.016	0.000	0.000	0.000	0.000
16	C	47	CYS	0	-0.049	-0.030	21.445	-0.027	-0.027	0.000	0.000	0.000	0.000
17	C	48	GLU	-1	-0.935	-0.962	22.606	0.148	0.148	0.000	0.000	0.000	0.000
18	C	49	GLY	0	-0.014	0.003	21.150	0.000	0.000	0.000	0.000	0.000	0.000
19	C	50	ASP	-1	-0.870	-0.917	18.039	0.298	0.298	0.000	0.000	0.000	0.000
20	C	51	ILE	0	-0.058	-0.035	13.635	-0.028	-0.028	0.000	0.000	0.000	0.000
21	C	52	VAL	0	-0.012	-0.004	17.370	0.007	0.007	0.000	0.000	0.000	0.000
22	C	53	CYS	0	-0.013	0.007	14.877	0.017	0.017	0.000	0.000	0.000	0.000
23	C	54	ARG	1	0.901	0.948	17.533	-0.162	-0.162	0.000	0.000	0.000	0.000
24	C	55	SER	0	-0.009	-0.011	16.492	0.035	0.035	0.000	0.000	0.000	0.000
25	C	56	ILE	0	-0.054	-0.029	13.681	-0.028	-0.028	0.000	0.000	0.000	0.000
26	C	57	ASN	0	0.007	-0.006	12.799	-0.046	-0.046	0.000	0.000	0.000	0.000
27	C	58	THR	0	-0.029	-0.016	16.104	-0.011	-0.011	0.000	0.000	0.000	0.000
28	C	59	LYS	1	0.879	0.947	15.692	-0.045	-0.045	0.000	0.000	0.000	0.000
29	C	60	ILE	0	0.043	0.018	16.661	0.025	0.025	0.000	0.000	0.000	0.000
30	C	61	PRO	0	0.033	0.020	12.751	-0.015	-0.015	0.000	0.000	0.000	0.000
31	C	62	TYR	0	-0.033	-0.025	12.819	-0.027	-0.027	0.000	0.000	0.000	0.000
32	C	63	PHE	0	0.083	0.035	13.754	0.052	0.052	0.000	0.000	0.000	0.000
33	C	64	ASN	0	-0.048	-0.036	13.523	0.002	0.002	0.000	0.000	0.000	0.000
34	C	65	ALA	0	-0.016	0.001	9.586	0.039	0.039	0.000	0.000	0.000	0.000
35	C	66	PRO	0	-0.024	-0.016	5.662	0.018	0.018	0.000	0.000	0.000	0.000
36	C	67	ILE	0	0.011	0.016	6.860	-0.017	-0.017	0.000	0.000	0.000	0.000
37	C	68	TYR	0	-0.074	0.091	2.127	15.332	-11.310	51.105	-17.233	-7.230	-0.006
38	C	69	LEU	0	0.070	0.034	5.008	-0.760	-0.809	0.000	-0.009	0.059	0.000
39	C	70	GLU	-1	-0.891	-0.941	4.964	0.329	0.402	0.000	-0.005	-0.067	0.000
40	C	71	ASN	0	-0.059	-0.031	6.072	0.079	0.079	0.000	0.000	0.000	0.000
41	C	72	LYS	1	0.786	0.919	2.026	10.648	-2.176	16.392	-1.288	-2.280	0.009
42	C	73	THR	0	0.038	0.037	2.243	11.756	0.193	13.221	0.431	-2.088	-0.025
43	C	74	GLN	0	-0.052	-0.026	3.916	0.312	0.482	0.002	-0.065	-0.108	0.000
44	C	75	VAL	0	0.006	0.001	4.934	-0.606	-0.651	0.000	-0.008	0.053	0.000
45	C	76	GLY	0	0.073	0.031	8.172	-0.286	-0.286	0.000	0.000	0.000	0.000
46	C	77	LYS	1	0.854	0.947	8.747	-0.104	-0.104	0.000	0.000	0.000	0.000
47	C	78	VAL	0	-0.012	0.004	11.181	-0.072	-0.072	0.000	0.000	0.000	0.000
48	C	79	ASP	-1	-0.968	-0.983	13.394	0.224	0.224	0.000	0.000	0.000	0.000
49	C	80	GLU	-1	-0.919	-0.952	16.990	0.139	0.139	0.000	0.000	0.000	0.000
50	C	81	ILE	0	-0.033	-0.022	16.944	0.023	0.023	0.000	0.000	0.000	0.000
51	C	82	LEU	0	-0.008	-0.001	20.060	-0.020	-0.020	0.000	0.000	0.000	0.000
52	C	83	GLY	0	0.029	0.022	22.683	0.006	0.006	0.000	0.000	0.000	0.000
53	C	84	PRO	0	-0.006	0.004	25.347	-0.005	-0.005	0.000	0.000	0.000	0.000
54	C	85	LEU	0	0.045	-0.004	25.362	0.006	0.006	0.000	0.000	0.000	0.000
55	C	86	ASN	0	-0.078	-0.029	24.587	0.007	0.007	0.000	0.000	0.000	0.000
56	C	87	GLU	-1	-0.851	-0.925	23.729	0.112	0.112	0.000	0.000	0.000	0.000
57	C	88	VAL	0	0.003	0.020	19.272	0.006	0.006	0.000	0.000	0.000	0.000
58	C	89	PHE	0	0.003	-0.011	19.770	0.010	0.010	0.000	0.000	0.000	0.000
59	C	90	PHE	0	-0.016	-0.013	12.704	-0.004	-0.004	0.000	0.000	0.000	0.000
60	C	91	THR	0	0.063	0.035	17.435	0.015	0.015	0.000	0.000	0.000	0.000
61	C	92	ILE	0	-0.026	-0.008	11.697	0.040	0.040	0.000	0.000	0.000	0.000
62	C	93	LYS	1	1.025	1.010	14.513	-0.305	-0.305	0.000	0.000	0.000	0.000
63	C	94	CYS	0	-0.053	-0.028	13.070	0.093	0.093	0.000	0.000	0.000	0.000
64	C	95	GLY	0	-0.008	-0.014	11.389	-0.042	-0.042	0.000	0.000	0.000	0.000
65	C	96	ASP	-1	-0.919	-0.973	12.411	0.192	0.192	0.000	0.000	0.000	0.000
66	C	97	GLY	0	-0.013	-0.001	13.286	0.033	0.033	0.000	0.000	0.000	0.000
67	C	98	VAL	0	-0.044	-0.001	10.892	0.003	0.003	0.000	0.000	0.000	0.000
68	C	99	GLN	0	0.019	0.005	14.252	-0.021	-0.021	0.000	0.000	0.000	0.000
69	C	100	ALA	0	0.065	0.023	16.900	0.013	0.013	0.000	0.000	0.000	0.000
70	C	101	THR	0	-0.059	-0.047	17.868	0.003	0.003	0.000	0.000	0.000	0.000
71	C	102	SER	0	-0.071	-0.027	16.464	-0.013	-0.013	0.000	0.000	0.000	0.000
72	C	103	PHE	0	0.002	0.014	12.141	0.015	0.015	0.000	0.000	0.000	0.000
73	C	104	LYS	1	0.910	0.955	17.239	-0.223	-0.223	0.000	0.000	0.000	0.000
74	C	105	GLU	-1	-0.920	-0.978	18.172	0.173	0.173	0.000	0.000	0.000	0.000
75	C	106	GLY	0	-0.052	-0.021	18.442	-0.012	-0.012	0.000	0.000	0.000	0.000
76	C	107	ASP	-1	-0.846	-0.913	13.993	0.277	0.277	0.000	0.000	0.000	0.000
77	C	108	LYS	1	0.898	0.951	11.779	-0.177	-0.177	0.000	0.000	0.000	0.000
78	C	109	PHE	0	-0.004	0.000	9.127	0.082	0.082	0.000	0.000	0.000	0.000
79	C	110	TYR	0	0.010	-0.001	5.777	-0.155	-0.155	0.000	0.000	0.000	0.000
80	C	111	ILE	0	0.016	0.003	6.302	0.402	0.402	0.000	0.000	0.000	0.000
81	C	112	ALA	0	0.050	0.028	5.424	-0.218	-0.218	0.000	0.000	0.000	0.000
82	C	113	ALA	0	0.037	0.003	6.649	0.072	0.072	0.000	0.000	0.000	0.000
83	C	114	ASP	-1	-0.929	-0.965	9.182	-0.104	-0.104	0.000	0.000	0.000	0.000
84	C	115	LYS	1	0.894	0.950	8.431	-0.095	-0.095	0.000	0.000	0.000	0.000
85	C	116	LEU	0	0.003	0.008	11.267	0.048	0.048	0.000	0.000	0.000	0.000
86	C	117	LEU	0	-0.020	-0.017	13.859	-0.039	-0.039	0.000	0.000	0.000	0.000
87	C	118	PRO	0	-0.007	0.002	17.665	0.011	0.011	0.000	0.000	0.000	0.000
88	C	119	ILE	0	0.090	0.026	20.401	0.002	0.002	0.000	0.000	0.000	0.000
89	C	120	GLU	-1	-0.919	-0.961	22.614	0.022	0.022	0.000	0.000	0.000	0.000
90	C	121	ARG	1	0.889	0.952	20.505	-0.036	-0.036	0.000	0.000	0.000	0.000
91	C	122	PHE	0	-0.041	-0.026	20.371	0.002	0.002	0.000	0.000	0.000	0.000
92	C	123	LEU	0	-0.067	-0.027	25.974	0.002	0.002	0.000	0.000	0.000	0.000
93	C	124	PRO	-1	-0.924	-0.945	29.053	0.028	0.028	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:32:ACE )