FMO DATABASE

FMODB ID: Q1Z5Y

Calculation Name: 3GKU-C-Xray372

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: 2023-06-19

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

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1094140.057039
FMO2-HF: Nuclear repulsion	1039521.24376
FMO2-HF: Total energy	-54618.813279
FMO2-MP2: Total energy	-54775.68319

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:1:MET)

Summations of interaction energy for fragment #1(C:1:MET)

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.
-32.815	-39.983	30.259	-12.936	-10.152	0.101

Interaction energy analysis for fragmet #1(C:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.064 / q_NPA : 0.053

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	C	3	MET	0	-0.088	-0.053	2.995	-1.318	1.187	0.192	-1.406	-1.290	-0.005
4	C	4	VAL	0	0.044	0.049	5.689	-0.234	-0.234	0.000	0.000	0.000	0.000
5	C	5	THR	0	0.003	-0.023	8.928	0.178	0.178	0.000	0.000	0.000	0.000
6	C	6	VAL	0	-0.013	0.011	12.259	-0.082	-0.082	0.000	0.000	0.000	0.000
7	C	7	THR	0	-0.038	-0.038	14.987	0.008	0.008	0.000	0.000	0.000	0.000
8	C	8	ALA	0	0.007	-0.002	18.679	-0.008	-0.008	0.000	0.000	0.000	0.000
9	C	9	LYS	1	0.926	0.976	21.817	-0.216	-0.216	0.000	0.000	0.000	0.000
10	C	10	THR	0	-0.017	-0.022	23.315	-0.011	-0.011	0.000	0.000	0.000	0.000
11	C	11	VAL	0	0.076	0.040	18.431	0.023	0.023	0.000	0.000	0.000	0.000
12	C	12	GLU	-1	-0.872	-0.947	19.196	0.533	0.533	0.000	0.000	0.000	0.000
13	C	13	GLU	-1	-0.865	-0.921	20.467	0.294	0.294	0.000	0.000	0.000	0.000
14	C	14	ALA	0	-0.014	-0.010	17.653	0.005	0.005	0.000	0.000	0.000	0.000
15	C	15	VAL	0	0.007	0.011	15.466	0.075	0.075	0.000	0.000	0.000	0.000
16	C	16	THR	0	-0.016	-0.031	16.252	0.048	0.048	0.000	0.000	0.000	0.000
17	C	17	LYS	1	0.855	0.941	16.906	-0.383	-0.383	0.000	0.000	0.000	0.000
18	C	18	ALA	0	0.016	0.000	12.560	0.004	0.004	0.000	0.000	0.000	0.000
19	C	19	LEU	0	-0.090	-0.047	13.027	0.101	0.101	0.000	0.000	0.000	0.000
20	C	20	ILE	0	-0.030	-0.011	15.028	-0.023	-0.023	0.000	0.000	0.000	0.000
21	C	21	GLU	-1	-0.906	-0.950	12.665	0.504	0.504	0.000	0.000	0.000	0.000
22	C	22	LEU	0	-0.028	-0.019	8.349	0.061	0.061	0.000	0.000	0.000	0.000
23	C	23	GLN	0	0.034	0.020	12.087	-0.020	-0.020	0.000	0.000	0.000	0.000
24	C	24	THR	0	-0.051	-0.026	10.675	-0.002	-0.002	0.000	0.000	0.000	0.000
25	C	25	THR	0	0.024	-0.022	13.211	-0.094	-0.094	0.000	0.000	0.000	0.000
26	C	26	SER	0	0.063	0.024	13.323	0.130	0.130	0.000	0.000	0.000	0.000
27	C	27	ASP	-1	-0.788	-0.836	13.614	0.651	0.651	0.000	0.000	0.000	0.000
28	C	28	LYS	1	0.834	0.899	9.839	-0.469	-0.469	0.000	0.000	0.000	0.000
29	C	29	LEU	0	0.040	0.044	9.105	0.432	0.432	0.000	0.000	0.000	0.000
30	C	30	THR	0	-0.051	-0.051	6.791	-0.087	-0.087	0.000	0.000	0.000	0.000
31	C	31	TYR	0	-0.016	-0.008	8.458	0.363	0.363	0.000	0.000	0.000	0.000
32	C	32	GLU	-1	-0.802	-0.858	9.349	1.033	1.033	0.000	0.000	0.000	0.000
33	C	33	ILE	0	0.013	-0.009	12.643	-0.035	-0.035	0.000	0.000	0.000	0.000
34	C	34	VAL	0	-0.023	-0.013	15.451	-0.042	-0.042	0.000	0.000	0.000	0.000
35	C	35	GLU	-1	-0.920	-0.956	18.196	0.321	0.321	0.000	0.000	0.000	0.000
36	C	47	LYS	1	0.966	0.968	27.261	-0.156	-0.156	0.000	0.000	0.000	0.000
37	C	48	PRO	0	-0.043	-0.014	23.348	0.003	0.003	0.000	0.000	0.000	0.000
38	C	49	ALA	0	0.098	0.057	21.768	0.006	0.006	0.000	0.000	0.000	0.000
39	C	50	ILE	0	-0.043	-0.008	16.140	-0.002	-0.002	0.000	0.000	0.000	0.000
40	C	51	ILE	0	0.000	0.008	13.348	0.008	0.008	0.000	0.000	0.000	0.000
41	C	52	ARG	1	0.833	0.890	8.246	-0.843	-0.843	0.000	0.000	0.000	0.000
42	C	53	ALA	0	0.027	0.008	9.262	0.201	0.201	0.000	0.000	0.000	0.000
43	C	54	LYS	1	0.865	0.907	2.083	-23.496	-34.664	26.950	-10.176	-5.606	0.119
44	C	55	ARG	1	0.911	0.951	5.445	-1.832	-1.696	-0.001	-0.012	-0.122	0.000
45	C	56	LYS	1	0.837	0.918	4.725	0.722	1.085	0.005	-0.062	-0.306	0.000
46	C	57	GLU	-1	-0.831	-0.893	2.291	-6.078	-5.344	3.111	-1.262	-2.582	-0.013
47	C	58	THR	0	-0.007	-0.020	3.787	0.463	0.584	0.003	-0.013	-0.111	0.000
48	C	59	LEU	0	0.003	-0.009	6.673	-0.449	-0.449	0.000	0.000	0.000	0.000
49	C	60	GLN	0	0.007	-0.019	7.865	0.100	0.100	0.000	0.000	0.000	0.000
50	C	61	ASP	-1	-0.776	-0.869	4.321	-2.150	-2.009	-0.001	-0.005	-0.135	0.000
51	C	62	LYS	1	0.788	0.878	5.553	0.822	0.822	0.000	0.000	0.000	0.000
52	C	63	ALA	0	-0.006	-0.006	7.644	0.163	0.163	0.000	0.000	0.000	0.000
53	C	64	ILE	0	-0.013	-0.001	8.135	0.159	0.159	0.000	0.000	0.000	0.000
54	C	65	GLU	-1	-0.844	-0.905	6.060	-2.395	-2.395	0.000	0.000	0.000	0.000
55	C	66	PHE	0	-0.024	-0.020	8.211	0.408	0.408	0.000	0.000	0.000	0.000
56	C	67	LEU	0	-0.019	-0.016	11.108	0.183	0.183	0.000	0.000	0.000	0.000
57	C	68	GLU	-1	-0.887	-0.951	8.763	-0.926	-0.926	0.000	0.000	0.000	0.000
58	C	69	GLN	0	-0.048	-0.024	9.539	0.357	0.357	0.000	0.000	0.000	0.000
59	C	70	VAL	0	-0.046	-0.025	12.314	0.144	0.144	0.000	0.000	0.000	0.000
60	C	71	PHE	0	-0.011	-0.035	15.214	0.090	0.090	0.000	0.000	0.000	0.000
61	C	72	ASP	-1	-0.901	-0.934	13.689	-0.408	-0.408	0.000	0.000	0.000	0.000
62	C	73	ALA	0	-0.008	-0.002	15.742	0.069	0.069	0.000	0.000	0.000	0.000
63	C	74	MET	0	-0.124	-0.057	17.942	0.044	0.044	0.000	0.000	0.000	0.000
64	C	75	ASN	0	-0.108	-0.050	19.266	0.058	0.058	0.000	0.000	0.000	0.000
65	C	76	MET	0	-0.038	-0.021	18.942	0.030	0.030	0.000	0.000	0.000	0.000
66	C	77	ALA	0	0.034	0.024	17.097	-0.044	-0.044	0.000	0.000	0.000	0.000
67	C	78	VAL	0	-0.007	-0.010	16.789	0.029	0.029	0.000	0.000	0.000	0.000
68	C	79	ASP	-1	-0.863	-0.931	15.149	-0.371	-0.371	0.000	0.000	0.000	0.000
69	C	80	ILE	0	0.000	0.001	12.814	0.046	0.046	0.000	0.000	0.000	0.000
70	C	81	SER	0	-0.019	-0.009	14.122	0.008	0.008	0.000	0.000	0.000	0.000
71	C	82	VAL	0	-0.042	-0.027	11.746	0.028	0.028	0.000	0.000	0.000	0.000
72	C	83	GLU	-1	-0.926	-0.945	14.854	-0.242	-0.242	0.000	0.000	0.000	0.000
73	C	84	TYR	0	-0.082	-0.081	13.213	-0.046	-0.046	0.000	0.000	0.000	0.000
74	C	85	ASN	0	0.000	0.002	16.457	0.048	0.048	0.000	0.000	0.000	0.000
75	C	86	GLU	-1	-0.842	-0.917	14.596	-0.072	-0.072	0.000	0.000	0.000	0.000
76	C	87	THR	0	-0.053	-0.036	18.344	0.023	0.023	0.000	0.000	0.000	0.000
77	C	88	GLU	-1	-0.929	-0.954	21.822	-0.077	-0.077	0.000	0.000	0.000	0.000
78	C	89	LYS	1	0.763	0.888	19.271	0.055	0.055	0.000	0.000	0.000	0.000
79	C	90	GLU	-1	-0.895	-0.938	19.592	-0.205	-0.205	0.000	0.000	0.000	0.000
80	C	91	MET	0	-0.036	-0.015	12.260	-0.046	-0.046	0.000	0.000	0.000	0.000
81	C	92	ASN	0	-0.022	-0.009	17.542	0.007	0.007	0.000	0.000	0.000	0.000
82	C	93	VAL	0	0.028	0.009	15.035	-0.026	-0.026	0.000	0.000	0.000	0.000
83	C	94	ASN	0	-0.010	-0.017	17.508	0.034	0.034	0.000	0.000	0.000	0.000
84	C	95	LEU	0	0.015	0.018	17.396	-0.038	-0.038	0.000	0.000	0.000	0.000
85	C	96	LYS	1	0.844	0.899	18.173	0.407	0.407	0.000	0.000	0.000	0.000
86	C	97	GLY	0	0.001	-0.023	20.918	-0.007	-0.007	0.000	0.000	0.000	0.000
87	C	98	ASP	-1	-0.935	-0.941	21.827	-0.214	-0.214	0.000	0.000	0.000	0.000
88	C	99	ASP	-1	-0.823	-0.918	23.579	-0.179	-0.179	0.000	0.000	0.000	0.000
89	C	100	MET	0	-0.041	-0.009	22.134	-0.013	-0.013	0.000	0.000	0.000	0.000
90	C	101	GLY	0	-0.009	-0.001	25.218	0.002	0.002	0.000	0.000	0.000	0.000
91	C	102	ILE	0	0.009	0.003	25.903	0.006	0.006	0.000	0.000	0.000	0.000
92	C	103	LEU	0	0.016	0.004	20.869	0.000	0.000	0.000	0.000	0.000	0.000
93	C	104	ILE	0	-0.007	0.016	25.193	-0.003	-0.003	0.000	0.000	0.000	0.000
94	C	105	GLY	0	0.062	0.041	28.275	0.003	0.003	0.000	0.000	0.000	0.000
95	C	106	LYS	1	0.925	0.928	30.073	0.150	0.150	0.000	0.000	0.000	0.000
96	C	107	ARG	1	0.834	0.906	32.432	0.142	0.142	0.000	0.000	0.000	0.000
97	C	108	GLY	0	0.074	0.052	29.346	0.005	0.005	0.000	0.000	0.000	0.000
98	C	109	GLN	0	-0.035	-0.012	27.857	-0.004	-0.004	0.000	0.000	0.000	0.000
99	C	110	THR	0	0.019	0.003	25.426	-0.003	-0.003	0.000	0.000	0.000	0.000
100	C	111	LEU	0	0.080	0.054	23.003	-0.023	-0.023	0.000	0.000	0.000	0.000
101	C	112	ASP	-1	-0.799	-0.884	23.236	-0.225	-0.225	0.000	0.000	0.000	0.000
102	C	113	SER	0	-0.027	-0.015	23.596	0.001	0.001	0.000	0.000	0.000	0.000
103	C	114	LEU	0	0.018	0.011	19.008	-0.014	-0.014	0.000	0.000	0.000	0.000
104	C	115	GLN	0	0.041	0.029	19.145	-0.046	-0.046	0.000	0.000	0.000	0.000
105	C	116	TYR	0	-0.042	-0.021	19.914	-0.011	-0.011	0.000	0.000	0.000	0.000
106	C	117	LEU	0	0.005	0.002	18.125	-0.001	-0.001	0.000	0.000	0.000	0.000
107	C	118	VAL	0	0.054	0.025	13.659	-0.027	-0.027	0.000	0.000	0.000	0.000
108	C	119	SER	0	0.003	0.000	15.420	-0.026	-0.026	0.000	0.000	0.000	0.000
109	C	120	LEU	0	-0.019	-0.001	17.289	0.013	0.013	0.000	0.000	0.000	0.000
110	C	121	VAL	0	0.006	0.004	11.690	0.036	0.036	0.000	0.000	0.000	0.000
111	C	122	VAL	0	0.059	0.029	11.898	-0.027	-0.027	0.000	0.000	0.000	0.000
112	C	123	ASN	0	-0.008	-0.014	13.400	0.085	0.085	0.000	0.000	0.000	0.000
113	C	124	LYS	1	0.808	0.922	11.666	0.570	0.570	0.000	0.000	0.000	0.000
114	C	125	SER	0	-0.082	-0.057	10.495	-0.003	-0.003	0.000	0.000	0.000	0.000
115	C	126	SER	0	0.002	-0.013	12.112	0.048	0.048	0.000	0.000	0.000	0.000
116	C	127	SER	0	-0.047	-0.021	14.788	0.015	0.015	0.000	0.000	0.000	0.000
117	C	128	ASP	-1	-0.839	-0.903	17.596	-0.029	-0.029	0.000	0.000	0.000	0.000
118	C	129	TYR	0	-0.004	0.023	18.164	-0.031	-0.031	0.000	0.000	0.000	0.000
119	C	130	ILE	0	0.047	0.023	15.283	0.008	0.008	0.000	0.000	0.000	0.000
120	C	131	ARG	1	0.919	0.966	18.690	0.152	0.152	0.000	0.000	0.000	0.000
121	C	132	VAL	0	0.010	0.009	16.113	-0.013	-0.013	0.000	0.000	0.000	0.000
122	C	133	LYS	1	0.839	0.929	19.233	0.257	0.257	0.000	0.000	0.000	0.000
123	C	134	LEU	0	0.001	0.002	18.085	-0.027	-0.027	0.000	0.000	0.000	0.000
124	C	135	ASP	-1	-0.830	-0.926	20.993	-0.184	-0.184	0.000	0.000	0.000	0.000
125	C	136	THR	0	0.002	-0.007	22.268	-0.015	-0.015	0.000	0.000	0.000	0.000
126	C	137	GLU	-1	-0.761	-0.846	24.757	-0.148	-0.148	0.000	0.000	0.000	0.000
127	C	138	ASN	0	-0.024	-0.013	27.449	0.011	0.011	0.000	0.000	0.000	0.000
128	C	139	TYR	0	0.042	0.013	27.013	0.014	0.014	0.000	0.000	0.000	0.000
129	C	140	ARG	1	0.757	0.863	28.679	0.151	0.151	0.000	0.000	0.000	0.000
130	C	141	GLU	-1	-0.778	-0.865	30.211	-0.106	-0.106	0.000	0.000	0.000	0.000
131	C	142	ARG	1	0.783	0.872	28.318	0.190	0.190	0.000	0.000	0.000	0.000
132	C	143	ARG	1	0.799	0.873	28.759	0.140	0.140	0.000	0.000	0.000	0.000
133	C	144	LYS	1	0.836	0.911	34.974	0.111	0.111	0.000	0.000	0.000	0.000
134	C	145	GLU	-1	-0.942	-0.959	37.528	-0.099	-0.099	0.000	0.000	0.000	0.000

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