FMO DATABASE

FMODB ID: 7J8GK

Calculation Name: 3GKU-C-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GKU

Chain ID: C

ChEMBL ID:

UniProt ID: D0VX24

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	138
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1105386.762532
FMO2-HF: Nuclear repulsion	1050428.702702
FMO2-HF: Total energy	-54958.05983
FMO2-MP2: Total energy	-55116.370779

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:0:ACE )

Summations of interaction energy for fragment #1(C:0: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.
2.617	3.544	-0.007	-0.321	-0.599	0

Interaction energy analysis for fragmet #1(C:0:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.058 / 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].
3	C	2	ASP	-1	-0.907	-0.936	3.805	0.308	1.065	-0.007	-0.304	-0.446
4	C	3	MET	0	-0.105	-0.065	6.843	-0.093	-0.093	0.000	0.000	0.000
5	C	4	VAL	0	0.049	0.040	10.571	0.112	0.112	0.000	0.000	0.000
6	C	5	THR	0	0.000	-0.023	13.578	0.029	0.029	0.000	0.000	0.000
7	C	6	VAL	0	0.014	0.025	17.126	0.020	0.020	0.000	0.000	0.000
8	C	7	THR	0	-0.043	-0.049	19.812	0.008	0.008	0.000	0.000	0.000
9	C	8	ALA	0	-0.008	-0.018	23.417	0.001	0.001	0.000	0.000	0.000
10	C	9	LYS	1	0.953	0.996	26.801	0.071	0.071	0.000	0.000	0.000
11	C	10	THR	0	0.008	-0.003	29.571	0.003	0.003	0.000	0.000	0.000
12	C	11	VAL	0	0.081	0.028	25.096	-0.007	-0.007	0.000	0.000	0.000
13	C	12	GLU	-1	-0.879	-0.969	25.570	-0.139	-0.139	0.000	0.000	0.000
14	C	13	GLU	-1	-0.864	-0.940	26.702	-0.098	-0.098	0.000	0.000	0.000
15	C	14	ALA	0	-0.022	-0.011	22.954	-0.006	-0.006	0.000	0.000	0.000
16	C	15	VAL	0	0.013	0.023	22.053	-0.022	-0.022	0.000	0.000	0.000
17	C	16	THR	0	0.018	0.002	22.107	-0.018	-0.018	0.000	0.000	0.000
18	C	17	LYS	1	0.877	0.955	22.406	0.137	0.137	0.000	0.000	0.000
19	C	18	ALA	0	0.027	0.011	18.507	-0.010	-0.010	0.000	0.000	0.000
20	C	19	LEU	0	-0.080	-0.034	18.956	-0.020	-0.020	0.000	0.000	0.000
21	C	20	ILE	0	-0.062	-0.018	19.607	-0.016	-0.016	0.000	0.000	0.000
22	C	21	GLU	-1	-0.910	-0.951	17.319	-0.196	-0.196	0.000	0.000	0.000
23	C	22	LEU	0	-0.057	-0.050	13.054	-0.056	-0.056	0.000	0.000	0.000
24	C	23	GLN	0	0.059	0.062	16.620	0.015	0.015	0.000	0.000	0.000
25	C	24	THR	0	-0.109	-0.073	15.908	-0.031	-0.031	0.000	0.000	0.000
26	C	25	THR	0	0.012	-0.022	18.199	0.018	0.018	0.000	0.000	0.000
27	C	26	SER	0	0.014	0.013	19.743	-0.018	-0.018	0.000	0.000	0.000
28	C	27	ASP	-1	-0.775	-0.863	20.428	-0.221	-0.221	0.000	0.000	0.000
29	C	28	LYS	1	0.872	0.924	15.996	0.242	0.242	0.000	0.000	0.000
30	C	29	LEU	0	0.003	0.022	15.663	-0.066	-0.066	0.000	0.000	0.000
31	C	30	THR	0	-0.026	-0.022	14.401	0.019	0.019	0.000	0.000	0.000
32	C	31	TYR	0	-0.026	-0.024	15.772	-0.030	-0.030	0.000	0.000	0.000
33	C	32	GLU	-1	-0.885	-0.931	16.192	-0.225	-0.225	0.000	0.000	0.000
34	C	33	ILE	0	0.012	-0.005	19.181	0.003	0.003	0.000	0.000	0.000
35	C	34	VAL	0	-0.008	-0.011	21.334	0.008	0.008	0.000	0.000	0.000
36	C	35	GLU	-1	-0.909	-0.960	24.120	-0.094	-0.094	0.000	0.000	0.000
37	C	36	NME	0	-0.020	0.008	27.176	0.007	0.007	0.000	0.000	0.000
38	C	46	ACE	0	0.027	0.005	35.041	0.000	0.000	0.000	0.000	0.000
39	C	47	LYS	1	0.905	0.937	32.491	0.055	0.055	0.000	0.000	0.000
40	C	48	PRO	0	-0.077	-0.032	28.883	-0.001	-0.001	0.000	0.000	0.000
41	C	49	ALA	0	0.169	0.090	27.380	0.000	0.000	0.000	0.000	0.000
42	C	50	ILE	0	-0.074	-0.018	21.380	-0.002	-0.002	0.000	0.000	0.000
43	C	51	ILE	0	0.012	0.024	19.391	0.000	0.000	0.000	0.000	0.000
44	C	52	ARG	1	0.867	0.942	13.105	0.269	0.269	0.000	0.000	0.000
45	C	53	ALA	0	0.029	0.012	15.658	-0.006	-0.006	0.000	0.000	0.000
46	C	54	LYS	1	0.949	0.970	9.057	0.814	0.814	0.000	0.000	0.000
47	C	55	ARG	1	0.921	0.954	11.341	0.642	0.642	0.000	0.000	0.000
48	C	56	LYS	1	0.881	0.945	11.322	0.210	0.210	0.000	0.000	0.000
49	C	57	GLU	-1	-0.899	-0.954	7.985	-0.755	-0.755	0.000	0.000	0.000
50	C	58	THR	0	-0.094	-0.026	10.271	0.182	0.182	0.000	0.000	0.000
51	C	59	LEU	0	0.036	-0.004	11.577	-0.014	-0.014	0.000	0.000	0.000
52	C	60	GLN	0	-0.008	-0.023	10.052	0.046	0.046	0.000	0.000	0.000
53	C	61	ASP	-1	-0.735	-0.884	7.297	-0.811	-0.811	0.000	0.000	0.000
54	C	62	LYS	1	0.880	0.982	8.175	0.437	0.437	0.000	0.000	0.000
55	C	63	ALA	0	0.005	-0.012	10.235	0.068	0.068	0.000	0.000	0.000
56	C	64	ILE	0	-0.007	0.003	6.843	0.030	0.030	0.000	0.000	0.000
57	C	65	GLU	-1	-0.886	-0.925	4.425	0.312	0.482	0.000	-0.017	-0.153
58	C	66	PHE	0	-0.025	-0.037	7.319	0.111	0.111	0.000	0.000	0.000
59	C	67	LEU	0	-0.028	-0.026	10.891	0.030	0.030	0.000	0.000	0.000
60	C	68	GLU	-1	-0.903	-0.957	5.967	1.122	1.122	0.000	0.000	0.000
61	C	69	GLN	0	-0.007	0.000	8.963	0.026	0.026	0.000	0.000	0.000
62	C	70	VAL	0	-0.066	-0.030	10.534	-0.043	-0.043	0.000	0.000	0.000
63	C	71	PHE	0	-0.009	-0.041	13.132	-0.030	-0.030	0.000	0.000	0.000
64	C	72	ASP	-1	-0.897	-0.929	11.335	0.430	0.430	0.000	0.000	0.000
65	C	73	ALA	0	-0.009	0.006	13.398	-0.037	-0.037	0.000	0.000	0.000
66	C	74	MET	0	-0.131	-0.060	15.966	-0.041	-0.041	0.000	0.000	0.000
67	C	75	ASN	0	-0.074	-0.031	16.978	-0.020	-0.020	0.000	0.000	0.000
68	C	76	MET	0	-0.039	-0.026	16.482	-0.030	-0.030	0.000	0.000	0.000
69	C	77	ALA	0	0.039	0.030	14.272	0.036	0.036	0.000	0.000	0.000
70	C	78	VAL	0	-0.020	-0.008	13.762	-0.049	-0.049	0.000	0.000	0.000
71	C	79	ASP	-1	-0.891	-0.949	12.167	0.357	0.357	0.000	0.000	0.000
72	C	80	ILE	0	0.011	0.000	10.560	-0.072	-0.072	0.000	0.000	0.000
73	C	81	SER	0	-0.002	0.000	11.332	0.013	0.013	0.000	0.000	0.000
74	C	82	VAL	0	-0.006	0.008	11.730	-0.001	-0.001	0.000	0.000	0.000
75	C	83	GLU	-1	-0.958	-0.965	14.416	-0.043	-0.043	0.000	0.000	0.000
76	C	84	TYR	0	-0.033	-0.043	16.293	0.004	0.004	0.000	0.000	0.000
77	C	85	ASN	0	0.115	0.107	18.023	-0.016	-0.016	0.000	0.000	0.000
78	C	86	GLU	-1	-0.916	-0.965	19.816	-0.164	-0.164	0.000	0.000	0.000
79	C	87	THR	0	-0.099	-0.078	22.302	0.008	0.008	0.000	0.000	0.000
80	C	88	GLU	-1	-0.975	-1.015	25.501	-0.045	-0.045	0.000	0.000	0.000
81	C	89	LYS	1	0.833	0.949	23.135	0.085	0.085	0.000	0.000	0.000
82	C	90	GLU	-1	-0.958	-0.983	22.336	-0.033	-0.033	0.000	0.000	0.000
83	C	91	MET	0	-0.044	-0.013	15.240	-0.007	-0.007	0.000	0.000	0.000
84	C	92	ASN	0	-0.008	-0.010	19.133	0.016	0.016	0.000	0.000	0.000
85	C	93	VAL	0	0.034	0.013	14.742	-0.005	-0.005	0.000	0.000	0.000
86	C	94	ASN	0	-0.043	-0.042	16.387	0.021	0.021	0.000	0.000	0.000
87	C	95	LEU	0	-0.003	-0.008	15.583	0.016	0.016	0.000	0.000	0.000
88	C	96	LYS	1	0.903	0.929	14.847	-0.159	-0.159	0.000	0.000	0.000
89	C	97	GLY	0	0.005	-0.075	17.828	0.014	0.014	0.000	0.000	0.000
90	C	98	ASP	-1	-0.913	-0.920	18.626	0.185	0.185	0.000	0.000	0.000
91	C	99	ASP	-1	-0.839	-0.929	20.706	0.113	0.113	0.000	0.000	0.000
92	C	100	MET	0	-0.052	0.035	19.253	-0.005	-0.005	0.000	0.000	0.000
93	C	101	GLY	0	-0.019	-0.029	23.010	-0.008	-0.008	0.000	0.000	0.000
94	C	102	ILE	0	0.004	0.004	23.135	-0.011	-0.011	0.000	0.000	0.000
95	C	103	LEU	0	0.045	-0.001	18.740	-0.010	-0.010	0.000	0.000	0.000
96	C	104	ILE	0	-0.037	0.024	22.951	-0.010	-0.010	0.000	0.000	0.000
97	C	105	GLY	0	0.012	0.011	26.250	-0.007	-0.007	0.000	0.000	0.000
98	C	106	LYS	1	0.929	0.937	27.715	-0.049	-0.049	0.000	0.000	0.000
99	C	107	ARG	1	0.917	0.946	30.704	-0.032	-0.032	0.000	0.000	0.000
100	C	108	GLY	0	0.109	0.079	27.967	-0.004	-0.004	0.000	0.000	0.000
101	C	109	GLN	0	-0.108	-0.061	26.956	0.000	0.000	0.000	0.000	0.000
102	C	110	THR	0	0.025	0.017	23.810	-0.004	-0.004	0.000	0.000	0.000
103	C	111	LEU	0	0.111	0.074	21.626	0.002	0.002	0.000	0.000	0.000
104	C	112	ASP	-1	-0.858	-0.931	22.698	0.022	0.022	0.000	0.000	0.000
105	C	113	SER	0	-0.066	-0.027	23.786	-0.008	-0.008	0.000	0.000	0.000
106	C	114	LEU	0	0.076	0.025	17.525	-0.006	-0.006	0.000	0.000	0.000
107	C	115	GLN	0	-0.021	-0.017	19.653	-0.010	-0.010	0.000	0.000	0.000
108	C	116	TYR	0	-0.035	-0.023	20.576	-0.013	-0.013	0.000	0.000	0.000
109	C	117	LEU	0	-0.006	-0.001	18.773	-0.012	-0.012	0.000	0.000	0.000
110	C	118	VAL	0	0.068	0.025	14.638	-0.014	-0.014	0.000	0.000	0.000
111	C	119	SER	0	-0.044	-0.035	17.155	-0.027	-0.027	0.000	0.000	0.000
112	C	120	LEU	0	-0.025	-0.009	19.509	-0.016	-0.016	0.000	0.000	0.000
113	C	121	VAL	0	-0.057	-0.018	14.169	-0.017	-0.017	0.000	0.000	0.000
114	C	122	VAL	0	0.044	0.019	14.639	-0.022	-0.022	0.000	0.000	0.000
115	C	123	ASN	0	0.010	-0.028	16.525	-0.025	-0.025	0.000	0.000	0.000
116	C	124	LYS	1	0.891	0.978	16.251	0.083	0.083	0.000	0.000	0.000
117	C	125	SER	0	-0.088	-0.049	16.145	-0.021	-0.021	0.000	0.000	0.000
118	C	126	SER	0	-0.021	-0.003	18.292	-0.026	-0.026	0.000	0.000	0.000
119	C	127	SER	0	-0.048	-0.015	20.718	0.009	0.009	0.000	0.000	0.000
120	C	128	ASP	-1	-0.859	-0.920	23.895	-0.082	-0.082	0.000	0.000	0.000
121	C	129	TYR	0	0.000	-0.010	23.656	-0.002	-0.002	0.000	0.000	0.000
122	C	130	ILE	0	-0.008	-0.002	19.762	0.000	0.000	0.000	0.000	0.000
123	C	131	ARG	1	0.942	0.970	22.946	0.036	0.036	0.000	0.000	0.000
124	C	132	VAL	0	0.030	0.045	18.318	-0.005	-0.005	0.000	0.000	0.000
125	C	133	LYS	1	0.938	0.996	20.962	0.011	0.011	0.000	0.000	0.000
126	C	134	LEU	0	-0.017	-0.008	17.290	-0.003	-0.003	0.000	0.000	0.000
127	C	135	ASP	-1	-0.873	-0.963	19.903	0.031	0.031	0.000	0.000	0.000
128	C	136	THR	0	0.040	0.039	20.171	0.009	0.009	0.000	0.000	0.000
129	C	137	GLU	-1	-0.746	-0.882	22.602	0.034	0.034	0.000	0.000	0.000
130	C	138	ASN	0	-0.104	-0.041	25.780	-0.010	-0.010	0.000	0.000	0.000
131	C	139	TYR	0	0.063	0.028	26.310	-0.006	-0.006	0.000	0.000	0.000
132	C	140	ARG	1	0.813	0.904	26.883	-0.035	-0.035	0.000	0.000	0.000
133	C	141	GLU	-1	-0.774	-0.875	28.661	0.023	0.023	0.000	0.000	0.000
134	C	142	ARG	1	0.779	0.894	27.004	-0.030	-0.030	0.000	0.000	0.000
135	C	143	ARG	1	0.886	0.943	28.463	-0.011	-0.011	0.000	0.000	0.000
136	C	144	LYS	1	0.818	0.897	33.850	-0.024	-0.024	0.000	0.000	0.000
137	C	145	GLU	-1	-0.946	-0.959	35.859	0.021	0.021	0.000	0.000	0.000
138	C	146	NME	0	-0.022	-0.004	35.477	-0.002	-0.002	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:0:ACE )