FMO DATABASE

FMODB ID: R5648

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	OptHSide
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	-1094141.338115
FMO2-HF: Nuclear repulsion	1039523.635181
FMO2-HF: Total energy	-54617.702934
FMO2-MP2: Total energy	-54774.751129

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.
-34.787	-42.283	28.803	-12.091	-9.216	0.099

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 : 0.065 / q_NPA : 0.048

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	-0.082	-0.046	3.288	0.418	2.343	0.059	-1.042	-0.942	0.000
4	C	4	VAL	0	0.035	0.031	5.949	-0.407	-0.407	0.000	0.000	0.000	0.000
5	C	5	THR	0	-0.006	-0.026	8.994	0.153	0.153	0.000	0.000	0.000	0.000
6	C	6	VAL	0	0.010	0.026	12.225	-0.099	-0.099	0.000	0.000	0.000	0.000
7	C	7	THR	0	-0.041	-0.038	14.822	0.009	0.009	0.000	0.000	0.000	0.000
8	C	8	ALA	0	-0.022	-0.021	18.436	-0.025	-0.025	0.000	0.000	0.000	0.000
9	C	9	LYS	1	0.955	0.996	21.601	-0.245	-0.245	0.000	0.000	0.000	0.000
10	C	10	THR	0	-0.014	-0.013	24.035	-0.006	-0.006	0.000	0.000	0.000	0.000
11	C	11	VAL	0	0.084	0.037	18.884	0.023	0.023	0.000	0.000	0.000	0.000
12	C	12	GLU	-1	-0.883	-0.964	19.565	0.554	0.554	0.000	0.000	0.000	0.000
13	C	13	GLU	-1	-0.878	-0.946	20.724	0.338	0.338	0.000	0.000	0.000	0.000
14	C	14	ALA	0	-0.003	-0.008	17.605	0.008	0.008	0.000	0.000	0.000	0.000
15	C	15	VAL	0	0.023	0.030	15.837	0.095	0.095	0.000	0.000	0.000	0.000
16	C	16	THR	0	0.006	0.004	16.366	0.054	0.054	0.000	0.000	0.000	0.000
17	C	17	LYS	1	0.872	0.940	17.556	-0.469	-0.469	0.000	0.000	0.000	0.000
18	C	18	ALA	0	0.017	0.004	12.766	0.006	0.006	0.000	0.000	0.000	0.000
19	C	19	LEU	0	-0.064	-0.038	13.616	0.028	0.028	0.000	0.000	0.000	0.000
20	C	20	ILE	0	-0.056	-0.020	14.473	0.002	0.002	0.000	0.000	0.000	0.000
21	C	21	GLU	-1	-0.926	-0.955	12.556	0.603	0.603	0.000	0.000	0.000	0.000
22	C	22	LEU	0	-0.052	-0.039	8.490	0.060	0.060	0.000	0.000	0.000	0.000
23	C	23	GLN	0	0.013	0.025	12.315	0.022	0.022	0.000	0.000	0.000	0.000
24	C	24	THR	0	-0.055	-0.052	10.821	-0.092	-0.092	0.000	0.000	0.000	0.000
25	C	25	THR	0	0.022	-0.023	13.037	-0.036	-0.036	0.000	0.000	0.000	0.000
26	C	26	SER	0	0.044	0.023	13.330	0.123	0.123	0.000	0.000	0.000	0.000
27	C	27	ASP	-1	-0.814	-0.855	14.000	0.499	0.499	0.000	0.000	0.000	0.000
28	C	28	LYS	1	0.882	0.919	9.888	-0.329	-0.329	0.000	0.000	0.000	0.000
29	C	29	LEU	0	-0.026	0.008	8.899	0.437	0.437	0.000	0.000	0.000	0.000
30	C	30	THR	0	-0.048	-0.037	7.256	-0.165	-0.165	0.000	0.000	0.000	0.000
31	C	31	TYR	0	-0.004	-0.013	9.055	0.286	0.286	0.000	0.000	0.000	0.000
32	C	32	GLU	-1	-0.806	-0.871	9.948	1.502	1.502	0.000	0.000	0.000	0.000
33	C	33	ILE	0	0.013	0.001	12.770	-0.078	-0.078	0.000	0.000	0.000	0.000
34	C	34	VAL	0	0.001	0.002	15.672	-0.033	-0.033	0.000	0.000	0.000	0.000
35	C	35	GLU	-1	-0.938	-0.967	18.342	0.394	0.394	0.000	0.000	0.000	0.000
36	C	47	LYS	1	0.946	0.959	27.729	-0.216	-0.216	0.000	0.000	0.000	0.000
37	C	48	PRO	0	-0.084	-0.039	23.774	0.000	0.000	0.000	0.000	0.000	0.000
38	C	49	ALA	0	0.151	0.080	21.902	0.003	0.003	0.000	0.000	0.000	0.000
39	C	50	ILE	0	-0.044	-0.006	16.563	-0.012	-0.012	0.000	0.000	0.000	0.000
40	C	51	ILE	0	0.000	0.016	13.730	0.020	0.020	0.000	0.000	0.000	0.000
41	C	52	ARG	1	0.815	0.869	8.445	-1.416	-1.416	0.000	0.000	0.000	0.000
42	C	53	ALA	0	0.026	0.015	9.891	0.219	0.219	0.000	0.000	0.000	0.000
43	C	54	LYS	1	0.893	0.925	2.045	-24.434	-35.092	25.352	-9.691	-5.003	0.113
44	C	55	ARG	1	0.938	0.971	5.851	-1.120	-1.120	0.000	0.000	0.000	0.000
45	C	56	LYS	1	0.871	0.944	4.761	0.779	1.071	0.002	-0.029	-0.265	0.000
46	C	57	GLU	-1	-0.859	-0.909	2.198	-7.913	-7.240	3.382	-1.332	-2.723	-0.014
47	C	58	THR	0	-0.067	-0.047	3.634	0.886	1.010	0.009	0.007	-0.140	0.000
48	C	59	LEU	0	0.026	0.002	6.530	-0.471	-0.471	0.000	0.000	0.000	0.000
49	C	60	GLN	0	-0.019	-0.030	7.736	0.139	0.139	0.000	0.000	0.000	0.000
50	C	61	ASP	-1	-0.735	-0.861	4.461	-3.059	-2.911	-0.001	-0.004	-0.143	0.000
51	C	62	LYS	1	0.814	0.923	5.799	1.182	1.182	0.000	0.000	0.000	0.000
52	C	63	ALA	0	0.024	0.002	7.674	0.064	0.064	0.000	0.000	0.000	0.000
53	C	64	ILE	0	-0.014	-0.002	8.365	0.176	0.176	0.000	0.000	0.000	0.000
54	C	65	GLU	-1	-0.862	-0.913	5.640	-3.176	-3.176	0.000	0.000	0.000	0.000
55	C	66	PHE	0	-0.013	-0.028	7.791	0.484	0.484	0.000	0.000	0.000	0.000
56	C	67	LEU	0	-0.028	-0.023	10.771	0.226	0.226	0.000	0.000	0.000	0.000
57	C	68	GLU	-1	-0.920	-0.962	8.323	-1.176	-1.176	0.000	0.000	0.000	0.000
58	C	69	GLN	0	-0.039	-0.017	9.333	0.420	0.420	0.000	0.000	0.000	0.000
59	C	70	VAL	0	-0.061	-0.035	12.362	0.162	0.162	0.000	0.000	0.000	0.000
60	C	71	PHE	0	0.001	-0.034	15.114	0.095	0.095	0.000	0.000	0.000	0.000
61	C	72	ASP	-1	-0.887	-0.924	13.705	-0.489	-0.489	0.000	0.000	0.000	0.000
62	C	73	ALA	0	-0.024	-0.004	15.756	0.079	0.079	0.000	0.000	0.000	0.000
63	C	74	MET	0	-0.120	-0.057	17.868	0.047	0.047	0.000	0.000	0.000	0.000
64	C	75	ASN	0	-0.097	-0.042	19.285	0.061	0.061	0.000	0.000	0.000	0.000
65	C	76	MET	0	-0.021	-0.015	18.996	0.035	0.035	0.000	0.000	0.000	0.000
66	C	77	ALA	0	0.025	0.026	16.899	-0.053	-0.053	0.000	0.000	0.000	0.000
67	C	78	VAL	0	0.001	-0.008	16.405	0.034	0.034	0.000	0.000	0.000	0.000
68	C	79	ASP	-1	-0.854	-0.927	14.948	-0.465	-0.465	0.000	0.000	0.000	0.000
69	C	80	ILE	0	-0.001	0.002	12.612	0.047	0.047	0.000	0.000	0.000	0.000
70	C	81	SER	0	-0.008	0.000	13.668	-0.014	-0.014	0.000	0.000	0.000	0.000
71	C	82	VAL	0	-0.005	-0.001	11.837	0.067	0.067	0.000	0.000	0.000	0.000
72	C	83	GLU	-1	-0.934	-0.948	15.111	-0.341	-0.341	0.000	0.000	0.000	0.000
73	C	84	TYR	0	-0.042	-0.050	13.606	-0.023	-0.023	0.000	0.000	0.000	0.000
74	C	85	ASN	0	0.024	0.031	16.366	0.046	0.046	0.000	0.000	0.000	0.000
75	C	86	GLU	-1	-0.895	-0.962	14.860	-0.205	-0.205	0.000	0.000	0.000	0.000
76	C	87	THR	0	-0.043	-0.031	18.322	0.027	0.027	0.000	0.000	0.000	0.000
77	C	88	GLU	-1	-0.939	-0.982	21.721	-0.138	-0.138	0.000	0.000	0.000	0.000
78	C	89	LYS	1	0.789	0.916	18.923	0.127	0.127	0.000	0.000	0.000	0.000
79	C	90	GLU	-1	-0.901	-0.947	19.435	-0.270	-0.270	0.000	0.000	0.000	0.000
80	C	91	MET	0	-0.049	-0.016	12.200	-0.054	-0.054	0.000	0.000	0.000	0.000
81	C	92	ASN	0	-0.021	-0.009	17.663	0.021	0.021	0.000	0.000	0.000	0.000
82	C	93	VAL	0	0.042	0.015	15.119	-0.022	-0.022	0.000	0.000	0.000	0.000
83	C	94	ASN	0	-0.044	-0.041	17.549	0.042	0.042	0.000	0.000	0.000	0.000
84	C	95	LEU	0	-0.004	-0.012	17.306	-0.055	-0.055	0.000	0.000	0.000	0.000
85	C	96	LYS	1	0.866	0.906	17.503	0.520	0.520	0.000	0.000	0.000	0.000
86	C	97	GLY	0	-0.013	-0.050	20.459	-0.010	-0.010	0.000	0.000	0.000	0.000
87	C	98	ASP	-1	-0.940	-0.926	21.574	-0.251	-0.251	0.000	0.000	0.000	0.000
88	C	99	ASP	-1	-0.833	-0.925	23.471	-0.215	-0.215	0.000	0.000	0.000	0.000
89	C	100	MET	0	-0.039	0.000	21.682	-0.007	-0.007	0.000	0.000	0.000	0.000
90	C	101	GLY	0	-0.011	-0.005	25.296	0.000	0.000	0.000	0.000	0.000	0.000
91	C	102	ILE	0	-0.002	0.005	25.443	0.005	0.005	0.000	0.000	0.000	0.000
92	C	103	LEU	0	0.035	0.001	20.484	0.003	0.003	0.000	0.000	0.000	0.000
93	C	104	ILE	0	-0.018	0.016	24.938	0.000	0.000	0.000	0.000	0.000	0.000
94	C	105	GLY	0	0.018	0.020	28.141	0.000	0.000	0.000	0.000	0.000	0.000
95	C	106	LYS	1	0.908	0.921	29.544	0.180	0.180	0.000	0.000	0.000	0.000
96	C	107	ARG	1	0.909	0.944	32.024	0.171	0.171	0.000	0.000	0.000	0.000
97	C	108	GLY	0	0.102	0.077	29.146	0.006	0.006	0.000	0.000	0.000	0.000
98	C	109	GLN	0	-0.088	-0.048	27.773	-0.006	-0.006	0.000	0.000	0.000	0.000
99	C	110	THR	0	0.044	0.020	25.385	-0.003	-0.003	0.000	0.000	0.000	0.000
100	C	111	LEU	0	0.096	0.067	22.589	-0.029	-0.029	0.000	0.000	0.000	0.000
101	C	112	ASP	-1	-0.809	-0.895	23.150	-0.284	-0.284	0.000	0.000	0.000	0.000
102	C	113	SER	0	-0.032	-0.005	23.624	-0.005	-0.005	0.000	0.000	0.000	0.000
103	C	114	LEU	0	0.039	0.012	18.910	-0.017	-0.017	0.000	0.000	0.000	0.000
104	C	115	GLN	0	0.014	0.010	19.398	-0.044	-0.044	0.000	0.000	0.000	0.000
105	C	116	TYR	0	-0.040	-0.024	19.576	-0.020	-0.020	0.000	0.000	0.000	0.000
106	C	117	LEU	0	0.001	0.004	18.025	-0.002	-0.002	0.000	0.000	0.000	0.000
107	C	118	VAL	0	0.061	0.026	13.655	-0.038	-0.038	0.000	0.000	0.000	0.000
108	C	119	SER	0	-0.020	-0.017	15.169	-0.052	-0.052	0.000	0.000	0.000	0.000
109	C	120	LEU	0	-0.024	-0.006	16.675	-0.004	-0.004	0.000	0.000	0.000	0.000
110	C	121	VAL	0	-0.038	-0.014	11.403	0.040	0.040	0.000	0.000	0.000	0.000
111	C	122	VAL	0	0.030	0.006	11.808	0.011	0.011	0.000	0.000	0.000	0.000
112	C	123	ASN	0	0.006	-0.025	13.067	0.085	0.085	0.000	0.000	0.000	0.000
113	C	124	LYS	1	0.888	0.972	12.452	0.629	0.629	0.000	0.000	0.000	0.000
114	C	125	SER	0	-0.087	-0.041	10.558	0.033	0.033	0.000	0.000	0.000	0.000
115	C	126	SER	0	-0.023	-0.024	12.511	0.035	0.035	0.000	0.000	0.000	0.000
116	C	127	SER	0	-0.028	-0.009	14.908	0.021	0.021	0.000	0.000	0.000	0.000
117	C	128	ASP	-1	-0.844	-0.897	17.899	-0.089	-0.089	0.000	0.000	0.000	0.000
118	C	129	TYR	0	-0.012	0.001	18.433	-0.035	-0.035	0.000	0.000	0.000	0.000
119	C	130	ILE	0	0.023	0.014	15.583	0.009	0.009	0.000	0.000	0.000	0.000
120	C	131	ARG	1	0.930	0.967	19.017	0.223	0.223	0.000	0.000	0.000	0.000
121	C	132	VAL	0	0.015	0.014	16.289	-0.021	-0.021	0.000	0.000	0.000	0.000
122	C	133	LYS	1	0.841	0.945	19.469	0.331	0.331	0.000	0.000	0.000	0.000
123	C	134	LEU	0	-0.009	-0.015	18.019	-0.037	-0.037	0.000	0.000	0.000	0.000
124	C	135	ASP	-1	-0.825	-0.937	21.035	-0.239	-0.239	0.000	0.000	0.000	0.000
125	C	136	THR	0	-0.004	0.001	22.067	-0.019	-0.019	0.000	0.000	0.000	0.000
126	C	137	GLU	-1	-0.768	-0.862	24.678	-0.200	-0.200	0.000	0.000	0.000	0.000
127	C	138	ASN	0	-0.034	-0.005	27.777	0.015	0.015	0.000	0.000	0.000	0.000
128	C	139	TYR	0	0.064	0.032	27.260	0.018	0.018	0.000	0.000	0.000	0.000
129	C	140	ARG	1	0.761	0.855	28.594	0.201	0.201	0.000	0.000	0.000	0.000
130	C	141	GLU	-1	-0.762	-0.875	30.163	-0.141	-0.141	0.000	0.000	0.000	0.000
131	C	142	ARG	1	0.718	0.844	27.917	0.238	0.238	0.000	0.000	0.000	0.000
132	C	143	ARG	1	0.887	0.944	29.065	0.194	0.194	0.000	0.000	0.000	0.000
133	C	144	LYS	1	0.823	0.901	34.813	0.142	0.142	0.000	0.000	0.000	0.000
134	C	145	GLU	-1	-0.957	-0.959	37.200	-0.125	-0.125	0.000	0.000	0.000	0.000

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