FMO DATABASE

FMODB ID: 9GRM2

Calculation Name: 3D33-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D33

Chain ID: A

ChEMBL ID:

UniProt ID: A6KX32

Base Structure: X-ray

Registration Date: 2023-03-14

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	94
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-667130.694575
FMO2-HF: Nuclear repulsion	630140.623889
FMO2-HF: Total energy	-36990.070686
FMO2-MP2: Total energy	-37097.521131

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:34:PRO)

Summations of interaction energy for fragment #1(A:34:PRO)

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.
-5.71	-2.796	0.206	-1.647	-1.473	-0.004

Interaction energy analysis for fragmet #1(A:34:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.021

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	36	LYS	1	0.885	0.932	2.927	-2.313	0.601	0.206	-1.647	-1.473	-0.004
4	A	37	ASP	-1	-0.873	-0.943	5.614	-0.533	-0.533	0.000	0.000	0.000	0.000
5	A	38	VAL	0	-0.103	-0.050	7.705	-0.004	-0.004	0.000	0.000	0.000	0.000
6	A	39	GLU	-1	-0.888	-0.932	11.360	-0.517	-0.517	0.000	0.000	0.000	0.000
7	A	40	LEU	0	-0.079	-0.044	13.300	0.049	0.049	0.000	0.000	0.000	0.000
8	A	41	ASP	-1	-0.874	-0.922	16.621	-0.388	-0.388	0.000	0.000	0.000	0.000
9	A	42	GLY	0	-0.008	-0.022	19.946	0.009	0.009	0.000	0.000	0.000	0.000
10	A	43	ARG	1	0.778	0.881	23.256	0.154	0.154	0.000	0.000	0.000	0.000
11	A	44	TRP	0	0.053	0.004	22.939	-0.011	-0.011	0.000	0.000	0.000	0.000
12	A	45	ASP	-1	-0.840	-0.901	24.935	-0.135	-0.135	0.000	0.000	0.000	0.000
13	A	46	ASP	-1	-0.947	-0.961	27.423	-0.101	-0.101	0.000	0.000	0.000	0.000
14	A	54	ASN	0	-0.037	-0.035	16.177	-0.015	-0.015	0.000	0.000	0.000	0.000
15	A	55	CYS	0	0.018	0.029	17.856	0.027	0.027	0.000	0.000	0.000	0.000
16	A	56	PRO	0	0.034	0.024	17.691	-0.019	-0.019	0.000	0.000	0.000	0.000
17	A	57	ILE	0	-0.001	0.006	16.955	0.002	0.002	0.000	0.000	0.000	0.000
18	A	58	THR	0	-0.004	0.000	11.849	-0.033	-0.033	0.000	0.000	0.000	0.000
19	A	59	VAL	0	0.050	0.007	12.218	0.061	0.061	0.000	0.000	0.000	0.000
20	A	60	PHE	0	-0.010	0.007	7.067	-0.047	-0.047	0.000	0.000	0.000	0.000
21	A	61	THR	0	-0.006	-0.009	8.233	0.373	0.373	0.000	0.000	0.000	0.000
22	A	62	ASP	-1	-0.944	-0.970	6.605	-1.622	-1.622	0.000	0.000	0.000	0.000
23	A	63	GLY	0	0.027	0.012	7.459	0.479	0.479	0.000	0.000	0.000	0.000
24	A	64	TYR	0	-0.056	-0.040	9.447	-0.078	-0.078	0.000	0.000	0.000	0.000
25	A	65	LEU	0	-0.013	-0.001	11.793	0.141	0.141	0.000	0.000	0.000	0.000
26	A	66	LEU	0	0.020	0.017	11.357	-0.192	-0.192	0.000	0.000	0.000	0.000
27	A	67	THR	0	-0.022	-0.021	11.384	0.199	0.199	0.000	0.000	0.000	0.000
28	A	68	LEU	0	0.026	0.021	12.667	-0.095	-0.095	0.000	0.000	0.000	0.000
29	A	69	LYS	1	0.900	0.939	12.213	0.208	0.208	0.000	0.000	0.000	0.000
30	A	70	ASN	0	0.085	0.037	15.918	-0.026	-0.026	0.000	0.000	0.000	0.000
31	A	71	ALA	0	-0.053	-0.034	17.645	0.028	0.028	0.000	0.000	0.000	0.000
32	A	72	SER	0	-0.056	-0.044	19.402	0.022	0.022	0.000	0.000	0.000	0.000
33	A	73	PRO	0	-0.042	-0.017	22.387	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	74	ASP	-1	-0.809	-0.875	24.746	-0.117	-0.117	0.000	0.000	0.000	0.000
35	A	75	ARG	1	0.767	0.874	26.652	0.145	0.145	0.000	0.000	0.000	0.000
36	A	76	ASP	-1	-0.859	-0.918	27.364	-0.111	-0.111	0.000	0.000	0.000	0.000
37	A	77	MET	0	-0.048	-0.035	21.180	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	78	THR	0	-0.021	-0.003	25.916	0.012	0.012	0.000	0.000	0.000	0.000
39	A	79	ILE	0	-0.050	-0.008	19.792	-0.020	-0.020	0.000	0.000	0.000	0.000
40	A	80	ARG	1	0.931	0.965	23.142	0.214	0.214	0.000	0.000	0.000	0.000
41	A	81	ILE	0	-0.006	0.001	19.103	-0.032	-0.032	0.000	0.000	0.000	0.000
42	A	82	THR	0	-0.024	-0.016	22.546	0.038	0.038	0.000	0.000	0.000	0.000
43	A	83	ASP	-1	-0.779	-0.892	23.283	-0.282	-0.282	0.000	0.000	0.000	0.000
44	A	84	MET	0	0.009	-0.004	22.055	0.033	0.033	0.000	0.000	0.000	0.000
45	A	85	ALA	0	-0.033	0.016	25.070	0.017	0.017	0.000	0.000	0.000	0.000
46	A	86	LYS	1	0.825	0.881	27.630	0.196	0.196	0.000	0.000	0.000	0.000
47	A	87	GLY	0	0.004	0.020	28.213	0.014	0.014	0.000	0.000	0.000	0.000
48	A	88	GLY	0	-0.038	-0.016	28.716	0.013	0.013	0.000	0.000	0.000	0.000
49	A	89	VAL	0	-0.006	-0.003	26.658	-0.022	-0.022	0.000	0.000	0.000	0.000
50	A	90	VAL	0	-0.044	-0.021	22.853	0.016	0.016	0.000	0.000	0.000	0.000
51	A	91	TYR	0	-0.017	-0.013	22.444	0.005	0.005	0.000	0.000	0.000	0.000
52	A	92	GLU	-1	-0.909	-0.962	25.066	-0.182	-0.182	0.000	0.000	0.000	0.000
53	A	93	ASN	0	-0.058	-0.034	23.778	0.027	0.027	0.000	0.000	0.000	0.000
54	A	94	ASP	-1	-0.826	-0.890	26.208	-0.160	-0.160	0.000	0.000	0.000	0.000
55	A	95	ILE	0	-0.037	-0.028	22.927	0.007	0.007	0.000	0.000	0.000	0.000
56	A	96	PRO	0	0.004	0.002	27.014	0.000	0.000	0.000	0.000	0.000	0.000
57	A	97	GLU	-1	-0.846	-0.922	27.421	-0.090	-0.090	0.000	0.000	0.000	0.000
58	A	98	VAL	0	-0.061	-0.029	26.800	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	99	GLN	0	-0.062	-0.044	25.385	0.000	0.000	0.000	0.000	0.000	0.000
60	A	100	SER	0	-0.030	-0.025	23.291	-0.015	-0.015	0.000	0.000	0.000	0.000
61	A	101	ALA	0	0.034	0.019	20.725	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	102	TYR	0	-0.054	-0.043	14.060	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	103	ILE	0	0.024	0.034	17.540	0.024	0.024	0.000	0.000	0.000	0.000
64	A	104	THR	0	-0.037	-0.016	14.698	-0.043	-0.043	0.000	0.000	0.000	0.000
65	A	105	ILE	0	0.016	0.014	16.160	0.044	0.044	0.000	0.000	0.000	0.000
66	A	106	SER	0	-0.014	-0.001	16.238	-0.079	-0.079	0.000	0.000	0.000	0.000
67	A	107	ILE	0	0.040	0.016	13.336	0.030	0.030	0.000	0.000	0.000	0.000
68	A	108	ALA	0	-0.016	-0.011	16.899	0.000	0.000	0.000	0.000	0.000	0.000
69	A	109	ASN	0	-0.056	-0.040	17.759	0.022	0.022	0.000	0.000	0.000	0.000
70	A	110	PHE	0	0.037	0.032	19.330	0.024	0.024	0.000	0.000	0.000	0.000
71	A	111	PRO	0	0.001	-0.005	20.454	-0.016	-0.016	0.000	0.000	0.000	0.000
72	A	112	ALA	0	-0.026	0.007	19.208	-0.029	-0.029	0.000	0.000	0.000	0.000
73	A	113	GLU	-1	-0.847	-0.914	19.243	-0.289	-0.289	0.000	0.000	0.000	0.000
74	A	114	GLU	-1	-0.934	-0.973	18.389	-0.557	-0.557	0.000	0.000	0.000	0.000
75	A	115	TYR	0	-0.056	-0.062	18.682	0.080	0.080	0.000	0.000	0.000	0.000
76	A	116	LYS	1	0.949	0.978	18.946	0.229	0.229	0.000	0.000	0.000	0.000
77	A	117	LEU	0	-0.039	-0.026	15.961	0.020	0.020	0.000	0.000	0.000	0.000
78	A	118	GLU	-1	-0.909	-0.966	19.734	-0.257	-0.257	0.000	0.000	0.000	0.000
79	A	119	ILE	0	0.000	-0.001	17.967	0.005	0.005	0.000	0.000	0.000	0.000
80	A	120	THR	0	0.006	-0.005	22.338	0.002	0.002	0.000	0.000	0.000	0.000
81	A	121	GLY	0	0.000	-0.004	25.820	0.002	0.002	0.000	0.000	0.000	0.000
82	A	122	THR	0	-0.041	0.013	27.632	0.004	0.004	0.000	0.000	0.000	0.000
83	A	123	PRO	0	-0.009	-0.030	31.304	0.005	0.005	0.000	0.000	0.000	0.000
84	A	124	SER	0	-0.021	-0.022	30.682	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	125	GLY	0	0.040	0.028	26.611	0.001	0.001	0.000	0.000	0.000	0.000
86	A	126	HIS	0	-0.040	-0.030	25.160	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	127	LEU	0	0.018	0.023	19.135	0.001	0.001	0.000	0.000	0.000	0.000
88	A	128	THR	0	-0.004	-0.015	20.631	0.011	0.011	0.000	0.000	0.000	0.000
89	A	129	GLY	0	0.087	0.052	16.600	-0.017	-0.017	0.000	0.000	0.000	0.000
90	A	130	TYR	0	-0.025	-0.010	16.145	0.067	0.067	0.000	0.000	0.000	0.000
91	A	131	PHE	0	-0.034	-0.021	13.478	-0.117	-0.117	0.000	0.000	0.000	0.000
92	A	132	THR	0	0.073	0.038	14.341	0.081	0.081	0.000	0.000	0.000	0.000
93	A	133	LYS	1	0.778	0.924	13.983	0.260	0.260	0.000	0.000	0.000	0.000
94	A	134	GLU	-1	-0.893	-0.958	13.420	-0.495	-0.495	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:34:PRO)