FMO DATABASE

FMODB ID: 2KZKR

Calculation Name: 3FDQ-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FDQ

Chain ID: A

ChEMBL ID:

UniProt ID: P0DJO8

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	142
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1337932.406739
FMO2-HF: Nuclear repulsion	1280690.274603
FMO2-HF: Total energy	-57242.132136
FMO2-MP2: Total energy	-57408.914146

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:3:ACE )

Summations of interaction energy for fragment #1(A:3: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.
-2.636	-1.702	-0.006	-0.418	-0.51	-0.001

Interaction energy analysis for fragmet #1(A:3:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.042 / q_NPA : -0.033

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

Sort

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	5	GLU	-1	-0.881	-0.946	3.847	0.506	1.440	-0.006	-0.418	-0.510	-0.001
4	A	6	ILE	0	0.051	0.030	7.039	0.459	0.459	0.000	0.000	0.000	0.000
5	A	7	ARG	1	0.836	0.882	8.556	0.366	0.366	0.000	0.000	0.000	0.000
6	A	8	LYS	1	0.899	0.943	9.931	0.206	0.206	0.000	0.000	0.000	0.000
7	A	9	LEU	0	0.059	0.045	11.285	0.077	0.077	0.000	0.000	0.000	0.000
8	A	10	LEU	0	0.034	-0.002	13.074	0.082	0.082	0.000	0.000	0.000	0.000
9	A	11	GLN	0	-0.056	-0.023	14.450	0.049	0.049	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.865	-0.929	15.757	-0.120	-0.120	0.000	0.000	0.000	0.000
11	A	13	ILE	0	0.011	0.009	16.649	0.026	0.026	0.000	0.000	0.000	0.000
12	A	14	LYS	1	0.852	0.918	19.092	0.131	0.131	0.000	0.000	0.000	0.000
13	A	15	LYS	1	0.899	0.960	20.281	0.118	0.118	0.000	0.000	0.000	0.000
14	A	16	GLN	0	-0.019	-0.006	21.401	0.024	0.024	0.000	0.000	0.000	0.000
15	A	17	VAL	0	-0.004	0.008	23.301	0.011	0.011	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.903	-0.957	24.675	-0.088	-0.088	0.000	0.000	0.000	0.000
17	A	19	ASN	0	-0.138	-0.070	26.526	0.016	0.016	0.000	0.000	0.000	0.000
18	A	20	PRO	0	0.002	0.034	27.361	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	21	GLY	0	0.047	0.007	27.961	0.010	0.010	0.000	0.000	0.000	0.000
20	A	22	ASN	0	-0.065	-0.050	28.849	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	23	SER	0	-0.079	-0.046	25.995	0.000	0.000	0.000	0.000	0.000	0.000
22	A	24	SER	0	0.058	0.017	24.395	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	25	THR	0	0.041	0.014	22.926	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	26	THR	0	-0.049	-0.007	22.650	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	27	GLU	-1	-0.911	-0.952	20.882	-0.137	-0.137	0.000	0.000	0.000	0.000
26	A	28	ILE	0	0.023	0.017	18.083	-0.025	-0.025	0.000	0.000	0.000	0.000
27	A	29	LYS	1	0.972	1.006	17.574	0.142	0.142	0.000	0.000	0.000	0.000
28	A	30	LYS	1	0.908	0.954	17.818	0.127	0.127	0.000	0.000	0.000	0.000
29	A	31	MET	0	0.014	0.014	12.622	-0.012	-0.012	0.000	0.000	0.000	0.000
30	A	32	ALA	0	0.004	0.001	13.282	-0.069	-0.069	0.000	0.000	0.000	0.000
31	A	33	SER	0	-0.014	-0.001	13.186	-0.074	-0.074	0.000	0.000	0.000	0.000
32	A	34	GLU	-1	-1.011	-1.012	13.412	-0.251	-0.251	0.000	0.000	0.000	0.000
33	A	35	ALA	0	-0.051	-0.016	9.040	-0.019	-0.019	0.000	0.000	0.000	0.000
34	A	36	GLY	0	-0.048	-0.016	9.044	-0.256	-0.256	0.000	0.000	0.000	0.000
35	A	37	ILE	0	-0.031	-0.004	9.047	-0.019	-0.019	0.000	0.000	0.000	0.000
36	A	38	ASP	-1	-0.876	-0.947	12.014	-0.235	-0.235	0.000	0.000	0.000	0.000
37	A	39	GLU	-1	-0.883	-0.966	15.470	-0.258	-0.258	0.000	0.000	0.000	0.000
38	A	40	GLN	0	-0.021	0.001	18.020	0.026	0.026	0.000	0.000	0.000	0.000
39	A	41	THR	0	0.008	-0.014	16.665	0.000	0.000	0.000	0.000	0.000	0.000
40	A	42	ALA	0	0.008	0.014	16.017	0.010	0.010	0.000	0.000	0.000	0.000
41	A	43	GLU	-1	-0.856	-0.954	17.701	-0.179	-0.179	0.000	0.000	0.000	0.000
42	A	44	GLU	-1	-0.982	-0.970	21.340	-0.185	-0.185	0.000	0.000	0.000	0.000
43	A	45	ILE	0	-0.001	-0.007	17.013	0.020	0.020	0.000	0.000	0.000	0.000
44	A	46	TYR	0	0.031	0.012	20.965	0.022	0.022	0.000	0.000	0.000	0.000
45	A	47	HIS	0	-0.064	-0.045	22.459	0.030	0.030	0.000	0.000	0.000	0.000
46	A	48	LEU	0	0.045	0.029	22.907	0.012	0.012	0.000	0.000	0.000	0.000
47	A	49	LEU	0	-0.056	-0.027	21.231	0.013	0.013	0.000	0.000	0.000	0.000
48	A	50	THR	0	-0.014	-0.016	24.644	0.016	0.016	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.905	-0.953	27.581	-0.102	-0.102	0.000	0.000	0.000	0.000
50	A	52	PHE	0	-0.050	-0.027	25.564	0.011	0.011	0.000	0.000	0.000	0.000
51	A	53	TYR	0	0.004	-0.020	23.726	0.007	0.007	0.000	0.000	0.000	0.000
52	A	54	GLN	0	0.021	0.016	29.489	0.006	0.006	0.000	0.000	0.000	0.000
53	A	55	ALA	0	0.047	0.024	32.087	0.006	0.006	0.000	0.000	0.000	0.000
54	A	56	VAL	0	-0.066	-0.034	29.792	0.007	0.007	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.931	-0.971	33.097	-0.050	-0.050	0.000	0.000	0.000	0.000
56	A	58	GLU	-1	-0.962	-0.964	35.421	-0.058	-0.058	0.000	0.000	0.000	0.000
57	A	59	HIS	0	-0.130	-0.069	35.727	0.006	0.006	0.000	0.000	0.000	0.000
58	A	60	GLY	0	-0.064	-0.038	37.848	0.003	0.003	0.000	0.000	0.000	0.000
59	A	61	GLY	0	0.060	0.040	35.033	0.003	0.003	0.000	0.000	0.000	0.000
60	A	62	ILE	0	0.060	0.006	28.818	0.001	0.001	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.961	-0.978	32.595	-0.028	-0.028	0.000	0.000	0.000	0.000
62	A	64	LYS	1	0.894	0.942	34.820	0.036	0.036	0.000	0.000	0.000	0.000
63	A	65	TYR	0	0.019	0.002	30.155	0.003	0.003	0.000	0.000	0.000	0.000
64	A	66	MET	0	-0.019	0.010	28.810	0.001	0.001	0.000	0.000	0.000	0.000
65	A	67	HIS	0	-0.007	0.007	33.204	0.001	0.001	0.000	0.000	0.000	0.000
66	A	68	SER	0	-0.035	-0.007	35.989	0.002	0.002	0.000	0.000	0.000	0.000
67	A	69	ASN	0	-0.026	-0.039	37.650	0.002	0.002	0.000	0.000	0.000	0.000
68	A	70	ILE	0	0.055	0.042	33.955	0.001	0.001	0.000	0.000	0.000	0.000
69	A	71	SER	0	-0.080	-0.044	31.317	0.002	0.002	0.000	0.000	0.000	0.000
70	A	72	TRP	0	-0.032	-0.028	24.573	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	73	LEU	0	0.071	0.053	30.404	0.004	0.004	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.932	0.962	30.130	0.083	0.083	0.000	0.000	0.000	0.000
73	A	75	ILE	0	0.078	0.047	27.990	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	76	GLU	-1	-0.743	-0.851	26.309	-0.094	-0.094	0.000	0.000	0.000	0.000
75	A	77	LEU	0	-0.048	-0.034	25.312	-0.011	-0.011	0.000	0.000	0.000	0.000
76	A	78	GLU	-1	-0.897	-0.951	25.041	-0.122	-0.122	0.000	0.000	0.000	0.000
77	A	79	LEU	0	0.041	0.028	21.429	-0.017	-0.017	0.000	0.000	0.000	0.000
78	A	80	LEU	0	-0.060	-0.030	21.105	-0.022	-0.022	0.000	0.000	0.000	0.000
79	A	81	SER	0	-0.028	-0.031	20.100	-0.017	-0.017	0.000	0.000	0.000	0.000
80	A	82	ALA	0	0.071	0.044	19.752	-0.022	-0.022	0.000	0.000	0.000	0.000
81	A	83	CYS	0	-0.026	-0.012	16.892	-0.042	-0.042	0.000	0.000	0.000	0.000
82	A	84	TYR	0	-0.027	-0.051	15.315	-0.040	-0.040	0.000	0.000	0.000	0.000
83	A	85	GLN	0	-0.047	-0.023	14.948	-0.017	-0.017	0.000	0.000	0.000	0.000
84	A	86	ILE	0	0.057	0.032	12.956	-0.036	-0.036	0.000	0.000	0.000	0.000
85	A	87	ALA	0	0.022	0.004	10.896	-0.117	-0.117	0.000	0.000	0.000	0.000
86	A	88	ILE	0	-0.079	-0.044	10.067	-0.093	-0.093	0.000	0.000	0.000	0.000
87	A	89	LEU	0	-0.047	-0.019	11.163	-0.013	-0.013	0.000	0.000	0.000	0.000
88	A	90	GLU	-1	-0.892	-0.930	7.467	-1.792	-1.792	0.000	0.000	0.000	0.000
89	A	91	ASP	-1	-0.926	-0.963	6.314	-1.135	-1.135	0.000	0.000	0.000	0.000
90	A	92	MET	0	-0.059	-0.013	7.320	0.222	0.222	0.000	0.000	0.000	0.000
91	A	93	LYS	1	0.916	0.956	8.524	-0.037	-0.037	0.000	0.000	0.000	0.000
92	A	94	VAL	0	0.042	0.002	11.234	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	95	LEU	0	-0.041	-0.023	14.650	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	96	ASP	-1	-0.849	-0.935	9.909	0.050	0.050	0.000	0.000	0.000	0.000
95	A	97	ILE	0	-0.014	0.009	12.014	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	98	SER	0	-0.023	-0.035	13.578	0.003	0.003	0.000	0.000	0.000	0.000
97	A	99	GLU	-1	-0.881	-0.942	14.735	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	100	MET	0	0.027	0.044	11.764	-0.013	-0.013	0.000	0.000	0.000	0.000
99	A	101	LEU	0	0.014	0.002	14.616	0.006	0.006	0.000	0.000	0.000	0.000
100	A	102	SER	0	-0.031	-0.023	17.433	0.020	0.020	0.000	0.000	0.000	0.000
101	A	103	LEU	0	-0.067	-0.040	20.009	0.000	0.000	0.000	0.000	0.000	0.000
102	A	104	ASN	0	-0.078	-0.033	19.280	0.006	0.006	0.000	0.000	0.000	0.000
103	A	105	ASP	-1	-0.805	-0.882	14.276	-0.085	-0.085	0.000	0.000	0.000	0.000
104	A	106	LEU	0	-0.027	0.001	13.845	0.002	0.002	0.000	0.000	0.000	0.000
105	A	107	ARG	1	0.850	0.928	17.964	0.057	0.057	0.000	0.000	0.000	0.000
106	A	108	ILE	0	0.043	0.036	17.869	0.004	0.004	0.000	0.000	0.000	0.000
107	A	109	PHE	0	0.034	0.024	19.782	0.010	0.010	0.000	0.000	0.000	0.000
108	A	110	PRO	0	-0.008	0.007	23.451	0.007	0.007	0.000	0.000	0.000	0.000
109	A	111	LYS	1	0.815	0.889	23.991	0.082	0.082	0.000	0.000	0.000	0.000
110	A	112	THR	0	0.055	0.011	23.331	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	113	PRO	0	0.105	0.045	19.353	-0.007	-0.007	0.000	0.000	0.000	0.000
112	A	114	SER	0	-0.008	-0.009	21.123	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	115	GLN	0	-0.021	0.013	23.876	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	116	LEU	0	0.066	0.051	19.698	0.000	0.000	0.000	0.000	0.000	0.000
115	A	117	GLN	0	0.083	0.063	18.722	-0.012	-0.012	0.000	0.000	0.000	0.000
116	A	118	ASN	0	-0.048	-0.043	21.780	0.001	0.001	0.000	0.000	0.000	0.000
117	A	119	THR	0	-0.033	-0.029	25.297	0.004	0.004	0.000	0.000	0.000	0.000
118	A	120	TYR	0	0.067	0.047	18.805	0.003	0.003	0.000	0.000	0.000	0.000
119	A	121	TYR	0	0.009	-0.013	19.120	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	122	LYS	1	0.893	0.950	24.695	0.053	0.053	0.000	0.000	0.000	0.000
121	A	123	LEU	0	0.050	0.030	24.647	0.004	0.004	0.000	0.000	0.000	0.000
122	A	124	LYS	1	0.927	0.976	20.386	0.131	0.131	0.000	0.000	0.000	0.000
123	A	125	LYS	1	0.842	0.935	25.942	0.053	0.053	0.000	0.000	0.000	0.000
124	A	126	GLU	-1	-0.895	-0.945	28.997	-0.068	-0.068	0.000	0.000	0.000	0.000
125	A	127	LEU	0	-0.123	-0.060	30.803	0.007	0.007	0.000	0.000	0.000	0.000
126	A	128	ILE	0	-0.055	-0.025	28.572	0.005	0.005	0.000	0.000	0.000	0.000
127	A	129	GLN	0	0.060	0.033	31.555	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	130	VAL	0	0.016	0.010	28.723	0.000	0.000	0.000	0.000	0.000	0.000
129	A	131	GLU	-1	-0.958	-1.002	31.220	-0.058	-0.058	0.000	0.000	0.000	0.000
130	A	132	ASP	-1	-0.813	-0.903	33.075	-0.067	-0.067	0.000	0.000	0.000	0.000
131	A	133	ILE	0	-0.045	-0.005	31.802	0.004	0.004	0.000	0.000	0.000	0.000
132	A	134	PRO	0	0.012	0.003	34.747	0.001	0.001	0.000	0.000	0.000	0.000
133	A	135	LYS	1	0.786	0.881	34.189	0.041	0.041	0.000	0.000	0.000	0.000
134	A	136	ASN	0	-0.046	-0.017	37.027	0.004	0.004	0.000	0.000	0.000	0.000
135	A	137	LYS	1	0.977	0.980	38.861	0.025	0.025	0.000	0.000	0.000	0.000
136	A	138	PRO	0	0.013	0.016	40.079	0.000	0.000	0.000	0.000	0.000	0.000
137	A	139	GLY	0	0.024	0.006	41.739	0.001	0.001	0.000	0.000	0.000	0.000
138	A	140	ARG	1	0.943	0.962	45.110	0.010	0.010	0.000	0.000	0.000	0.000
139	A	141	LYS	1	1.001	1.010	42.992	0.024	0.024	0.000	0.000	0.000	0.000
140	A	142	ARG	1	0.957	0.973	48.809	0.018	0.018	0.000	0.000	0.000	0.000
141	A	143	LYS	1	0.971	0.985	52.329	0.011	0.011	0.000	0.000	0.000	0.000
142	A	144	NME	0	0.072	0.045	55.138	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ACE )