FMO DATABASE

FMODB ID: 66MNZ

Calculation Name: 4GKF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GKF

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U1T0

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	146
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1527723.222576
FMO2-HF: Nuclear repulsion	1468597.045799
FMO2-HF: Total energy	-59126.176777
FMO2-MP2: Total energy	-59301.826734

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:15:ARG)

Summations of interaction energy for fragment #1(A:15:ARG)

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.
-52.497	-45.275	21.618	-12.297	-16.542	-0.072

Interaction energy analysis for fragmet #1(A:15:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.958 / q_NPA : 0.975

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	17	THR	0	0.028	0.020	3.738	0.298	3.908	-0.044	-1.915	-1.652	0.005
4	A	18	LEU	0	0.062	0.012	4.880	-4.051	-3.983	-0.001	-0.002	-0.065	0.000
5	A	19	GLU	-1	-0.781	-0.887	7.158	-31.832	-31.832	0.000	0.000	0.000	0.000
6	A	20	GLN	0	0.030	0.020	1.972	-5.448	-4.281	7.891	-4.867	-4.191	-0.018
7	A	21	ARG	1	0.933	0.964	3.002	19.623	21.696	0.215	-0.932	-1.356	-0.007
8	A	22	ARG	1	0.792	0.890	4.529	26.130	26.247	-0.001	-0.006	-0.110	0.000
9	A	23	GLY	0	0.022	0.018	3.797	2.014	2.143	0.000	-0.024	-0.105	0.000
10	A	24	GLU	-1	-0.902	-0.948	1.901	-95.976	-95.254	13.216	-5.516	-8.421	-0.053
11	A	25	TYR	0	-0.008	-0.007	2.826	7.959	7.009	0.344	0.991	-0.384	0.001
12	A	26	ALA	0	0.004	-0.006	6.478	3.837	3.837	0.000	0.000	0.000	0.000
13	A	27	TYR	0	-0.037	-0.019	4.404	3.390	3.520	-0.001	-0.008	-0.121	0.000
14	A	28	TYR	0	0.041	-0.002	4.054	5.351	5.507	-0.001	-0.018	-0.137	0.000
15	A	29	VAL	0	0.012	0.010	8.242	2.926	2.926	0.000	0.000	0.000	0.000
16	A	30	ILE	0	-0.033	-0.017	10.153	2.285	2.285	0.000	0.000	0.000	0.000
17	A	31	LYS	1	0.859	0.919	9.571	26.066	26.066	0.000	0.000	0.000	0.000
18	A	32	GLU	-1	-0.799	-0.892	11.647	-17.950	-17.950	0.000	0.000	0.000	0.000
19	A	33	VAL	0	-0.018	-0.019	14.215	1.377	1.377	0.000	0.000	0.000	0.000
20	A	34	ALA	0	-0.005	-0.001	14.506	1.056	1.056	0.000	0.000	0.000	0.000
21	A	35	ASP	-1	-0.862	-0.927	14.028	-19.952	-19.952	0.000	0.000	0.000	0.000
22	A	36	LEU	0	-0.068	-0.022	17.130	0.796	0.796	0.000	0.000	0.000	0.000
23	A	37	ASN	0	-0.047	-0.019	19.952	0.636	0.636	0.000	0.000	0.000	0.000
24	A	38	ASP	-1	-0.867	-0.922	21.821	-11.399	-11.399	0.000	0.000	0.000	0.000
25	A	39	LYS	1	0.971	0.955	22.932	10.956	10.956	0.000	0.000	0.000	0.000
26	A	40	GLN	0	0.103	0.062	24.402	-0.263	-0.263	0.000	0.000	0.000	0.000
27	A	41	LEU	0	-0.037	-0.006	20.270	-0.162	-0.162	0.000	0.000	0.000	0.000
28	A	42	GLU	-1	-0.827	-0.936	18.804	-15.770	-15.770	0.000	0.000	0.000	0.000
29	A	43	GLU	-1	-0.894	-0.943	20.486	-11.890	-11.890	0.000	0.000	0.000	0.000
30	A	44	LYS	1	0.908	0.958	22.915	10.940	10.940	0.000	0.000	0.000	0.000
31	A	45	TYR	0	-0.002	-0.016	15.262	-0.434	-0.434	0.000	0.000	0.000	0.000
32	A	46	ALA	0	0.033	0.010	18.162	-0.550	-0.550	0.000	0.000	0.000	0.000
33	A	47	SER	0	-0.005	0.003	19.209	-0.207	-0.207	0.000	0.000	0.000	0.000
34	A	48	LEU	0	-0.024	-0.011	21.396	0.060	0.060	0.000	0.000	0.000	0.000
35	A	49	VAL	0	0.022	0.003	15.023	-0.042	-0.042	0.000	0.000	0.000	0.000
36	A	50	LYS	1	0.838	0.928	17.470	15.368	15.368	0.000	0.000	0.000	0.000
37	A	51	LYS	1	0.901	0.961	19.303	11.991	11.991	0.000	0.000	0.000	0.000
38	A	52	ALA	0	0.026	0.023	18.546	0.277	0.277	0.000	0.000	0.000	0.000
39	A	53	PRO	0	-0.006	-0.005	17.533	0.322	0.322	0.000	0.000	0.000	0.000
40	A	54	VAL	0	0.028	0.008	19.589	0.306	0.306	0.000	0.000	0.000	0.000
41	A	55	MET	0	-0.035	-0.008	23.054	0.424	0.424	0.000	0.000	0.000	0.000
42	A	56	ILE	0	0.003	0.003	19.783	0.354	0.354	0.000	0.000	0.000	0.000
43	A	57	LEU	0	-0.070	-0.025	21.102	0.305	0.305	0.000	0.000	0.000	0.000
44	A	58	SER	0	-0.056	-0.022	24.259	0.455	0.455	0.000	0.000	0.000	0.000
45	A	59	ASN	0	0.011	0.011	27.059	0.632	0.632	0.000	0.000	0.000	0.000
46	A	60	GLY	0	0.029	0.024	26.012	0.255	0.255	0.000	0.000	0.000	0.000
47	A	61	LEU	0	-0.004	-0.015	21.117	-0.100	-0.100	0.000	0.000	0.000	0.000
48	A	62	LEU	0	0.030	0.018	24.438	-0.098	-0.098	0.000	0.000	0.000	0.000
49	A	63	GLN	0	0.038	0.013	27.400	0.081	0.081	0.000	0.000	0.000	0.000
50	A	64	THR	0	0.017	0.011	22.969	0.126	0.126	0.000	0.000	0.000	0.000
51	A	65	LEU	0	-0.004	-0.014	21.179	-0.074	-0.074	0.000	0.000	0.000	0.000
52	A	66	ALA	0	-0.001	-0.003	24.995	0.090	0.090	0.000	0.000	0.000	0.000
53	A	67	PHE	0	0.005	-0.003	26.600	0.250	0.250	0.000	0.000	0.000	0.000
54	A	68	LEU	0	-0.037	-0.014	21.791	0.113	0.113	0.000	0.000	0.000	0.000
55	A	69	LEU	0	-0.025	-0.015	25.852	0.100	0.100	0.000	0.000	0.000	0.000
56	A	70	ALA	0	-0.017	-0.001	28.064	0.262	0.262	0.000	0.000	0.000	0.000
57	A	71	LYS	1	0.892	0.949	28.234	10.260	10.260	0.000	0.000	0.000	0.000
58	A	72	ALA	0	0.033	0.028	27.027	0.099	0.099	0.000	0.000	0.000	0.000
59	A	73	GLU	-1	-0.937	-0.934	29.174	-9.063	-9.063	0.000	0.000	0.000	0.000
60	A	74	THR	0	-0.083	-0.053	28.168	0.027	0.027	0.000	0.000	0.000	0.000
61	A	75	SER	0	0.002	-0.006	30.681	-0.040	-0.040	0.000	0.000	0.000	0.000
62	A	76	PRO	0	0.021	-0.008	27.728	-0.262	-0.262	0.000	0.000	0.000	0.000
63	A	77	GLU	-1	-0.823	-0.926	27.825	-10.294	-10.294	0.000	0.000	0.000	0.000
64	A	78	LYS	1	0.928	0.964	28.715	9.795	9.795	0.000	0.000	0.000	0.000
65	A	79	ALA	0	0.047	0.025	24.352	-0.282	-0.282	0.000	0.000	0.000	0.000
66	A	80	ASN	0	0.000	-0.015	24.263	-1.060	-1.060	0.000	0.000	0.000	0.000
67	A	81	GLN	0	-0.019	0.008	25.155	-0.602	-0.602	0.000	0.000	0.000	0.000
68	A	82	ILE	0	0.020	0.027	21.928	-0.165	-0.165	0.000	0.000	0.000	0.000
69	A	83	LEU	0	0.004	-0.011	19.154	-0.526	-0.526	0.000	0.000	0.000	0.000
70	A	84	SER	0	-0.092	-0.043	20.729	-0.444	-0.444	0.000	0.000	0.000	0.000
71	A	85	ARG	1	0.945	0.976	22.450	12.601	12.601	0.000	0.000	0.000	0.000
72	A	86	VAL	0	-0.105	-0.041	16.011	-0.267	-0.267	0.000	0.000	0.000	0.000
73	A	87	ASN	0	-0.009	-0.008	17.632	-0.612	-0.612	0.000	0.000	0.000	0.000
74	A	88	GLU	-1	-0.902	-0.931	14.765	-17.750	-17.750	0.000	0.000	0.000	0.000
75	A	89	TYR	0	-0.058	-0.045	5.265	1.325	1.325	0.000	0.000	0.000	0.000
76	A	90	PRO	0	0.005	-0.025	7.544	-0.101	-0.101	0.000	0.000	0.000	0.000
77	A	91	PRO	0	-0.038	0.013	9.880	1.726	1.726	0.000	0.000	0.000	0.000
78	A	92	ARG	1	0.882	0.946	12.991	18.023	18.023	0.000	0.000	0.000	0.000
79	A	93	PHE	0	0.019	-0.010	13.358	1.309	1.309	0.000	0.000	0.000	0.000
80	A	94	ILE	0	0.050	0.025	17.127	1.211	1.211	0.000	0.000	0.000	0.000
81	A	95	GLU	-1	-0.827	-0.906	19.547	-14.758	-14.758	0.000	0.000	0.000	0.000
82	A	96	LYS	1	0.714	0.842	18.448	16.804	16.804	0.000	0.000	0.000	0.000
83	A	97	LEU	0	-0.045	-0.017	21.816	0.559	0.559	0.000	0.000	0.000	0.000
84	A	98	GLY	0	0.038	0.023	24.840	0.121	0.121	0.000	0.000	0.000	0.000
85	A	99	ASN	0	0.005	-0.017	27.115	-0.543	-0.543	0.000	0.000	0.000	0.000
86	A	100	ASP	-1	-0.918	-0.954	28.553	-10.756	-10.756	0.000	0.000	0.000	0.000
87	A	101	LYS	1	0.830	0.922	23.076	12.489	12.489	0.000	0.000	0.000	0.000
88	A	102	ASP	-1	-0.708	-0.851	25.282	-11.721	-11.721	0.000	0.000	0.000	0.000
89	A	103	GLU	-1	-0.867	-0.958	21.914	-12.482	-12.482	0.000	0.000	0.000	0.000
90	A	104	HIS	0	-0.046	-0.029	21.634	-0.612	-0.612	0.000	0.000	0.000	0.000
91	A	105	LEU	0	0.002	-0.001	22.903	-0.451	-0.451	0.000	0.000	0.000	0.000
92	A	106	LEU	0	0.022	0.002	17.669	-0.549	-0.549	0.000	0.000	0.000	0.000
93	A	107	LEU	0	0.015	0.018	16.919	-0.942	-0.942	0.000	0.000	0.000	0.000
94	A	108	TYR	0	0.021	0.005	18.323	-0.535	-0.535	0.000	0.000	0.000	0.000
95	A	109	LEU	0	-0.030	-0.023	19.014	-0.331	-0.331	0.000	0.000	0.000	0.000
96	A	110	HIS	0	0.042	0.043	14.339	-0.682	-0.682	0.000	0.000	0.000	0.000
97	A	111	ILE	0	0.021	0.015	14.812	-1.244	-1.244	0.000	0.000	0.000	0.000
98	A	112	VAL	0	0.000	-0.007	16.837	-0.452	-0.452	0.000	0.000	0.000	0.000
99	A	113	TYR	0	0.055	0.030	12.277	-0.744	-0.744	0.000	0.000	0.000	0.000
100	A	114	TRP	0	-0.013	-0.017	7.932	-1.175	-1.175	0.000	0.000	0.000	0.000
101	A	115	LEU	0	-0.008	-0.013	14.347	-0.236	-0.236	0.000	0.000	0.000	0.000
102	A	116	ARG	1	0.868	0.933	17.011	14.214	14.214	0.000	0.000	0.000	0.000
103	A	117	GLU	-1	-0.940	-0.962	12.680	-19.516	-19.516	0.000	0.000	0.000	0.000
104	A	118	ASN	0	-0.135	-0.071	10.927	-1.545	-1.545	0.000	0.000	0.000	0.000
105	A	119	VAL	0	-0.068	-0.027	14.179	0.375	0.375	0.000	0.000	0.000	0.000
106	A	120	ASP	-1	-0.824	-0.917	17.706	-12.334	-12.334	0.000	0.000	0.000	0.000
107	A	121	ARG	1	0.992	1.005	18.935	14.184	14.184	0.000	0.000	0.000	0.000
108	A	122	ASN	0	-0.058	-0.035	20.948	0.212	0.212	0.000	0.000	0.000	0.000
109	A	123	ILE	0	0.001	0.010	20.474	0.464	0.464	0.000	0.000	0.000	0.000
110	A	124	ASP	-1	-0.834	-0.908	23.409	-11.827	-11.827	0.000	0.000	0.000	0.000
111	A	125	VAL	0	0.026	0.008	25.479	0.267	0.267	0.000	0.000	0.000	0.000
112	A	126	LYS	1	0.916	0.952	27.913	9.972	9.972	0.000	0.000	0.000	0.000
113	A	127	THR	0	0.015	0.011	26.820	0.169	0.169	0.000	0.000	0.000	0.000
114	A	128	LEU	0	-0.024	-0.027	24.312	0.155	0.155	0.000	0.000	0.000	0.000
115	A	129	LEU	0	-0.057	-0.017	28.445	0.148	0.148	0.000	0.000	0.000	0.000
116	A	130	SER	0	-0.050	-0.027	31.440	0.378	0.378	0.000	0.000	0.000	0.000
117	A	131	GLN	0	-0.034	-0.011	25.191	0.050	0.050	0.000	0.000	0.000	0.000
118	A	132	ASP	-1	-0.813	-0.893	27.923	-11.046	-11.046	0.000	0.000	0.000	0.000
119	A	133	TYR	0	0.074	0.011	28.480	-0.358	-0.358	0.000	0.000	0.000	0.000
120	A	134	SER	0	0.010	-0.001	25.610	-0.322	-0.322	0.000	0.000	0.000	0.000
121	A	135	LYS	1	0.855	0.927	22.447	12.277	12.277	0.000	0.000	0.000	0.000
122	A	136	VAL	0	0.076	0.045	23.412	-0.693	-0.693	0.000	0.000	0.000	0.000
123	A	137	LEU	0	-0.006	0.026	23.237	-0.600	-0.600	0.000	0.000	0.000	0.000
124	A	138	TRP	0	-0.004	-0.002	16.616	-0.156	-0.156	0.000	0.000	0.000	0.000
125	A	139	ALA	0	0.043	0.017	19.390	-0.924	-0.924	0.000	0.000	0.000	0.000
126	A	140	THR	0	-0.031	-0.044	19.349	-0.548	-0.548	0.000	0.000	0.000	0.000
127	A	141	LYS	1	0.915	0.952	18.536	14.092	14.092	0.000	0.000	0.000	0.000
128	A	142	GLU	-1	-0.759	-0.841	12.599	-23.985	-23.985	0.000	0.000	0.000	0.000
129	A	143	ALA	0	0.032	0.015	14.644	-1.215	-1.215	0.000	0.000	0.000	0.000
130	A	144	ILE	0	0.001	0.004	15.618	-0.759	-0.759	0.000	0.000	0.000	0.000
131	A	145	ALA	0	-0.039	-0.020	12.289	-0.525	-0.525	0.000	0.000	0.000	0.000
132	A	146	LEU	0	-0.018	-0.007	10.303	-1.639	-1.639	0.000	0.000	0.000	0.000
133	A	147	LEU	0	0.087	0.010	11.571	-1.140	-1.140	0.000	0.000	0.000	0.000
134	A	148	ASN	0	-0.027	-0.003	13.038	0.881	0.881	0.000	0.000	0.000	0.000
135	A	149	TRP	0	-0.076	-0.036	6.193	-1.889	-1.889	0.000	0.000	0.000	0.000
136	A	150	MET	0	0.010	0.014	9.997	-0.538	-0.538	0.000	0.000	0.000	0.000
137	A	151	ARG	1	0.944	0.990	11.441	18.178	18.178	0.000	0.000	0.000	0.000
138	A	152	ARG	1	0.886	0.930	10.809	22.349	22.349	0.000	0.000	0.000	0.000
139	A	153	PHE	0	0.054	0.013	4.983	-0.322	-0.322	0.000	0.000	0.000	0.000
140	A	154	ALA	0	0.035	0.023	10.649	0.843	0.843	0.000	0.000	0.000	0.000
141	A	155	VAL	0	-0.071	-0.030	14.077	0.995	0.995	0.000	0.000	0.000	0.000
142	A	156	ALA	0	-0.036	-0.019	11.529	0.604	0.604	0.000	0.000	0.000	0.000
143	A	157	MET	0	-0.077	-0.029	9.973	-0.946	-0.946	0.000	0.000	0.000	0.000
144	A	158	LEU	0	-0.044	0.002	13.911	0.517	0.517	0.000	0.000	0.000	0.000
145	A	159	LYS	1	0.883	0.950	16.816	14.303	14.303	0.000	0.000	0.000	0.000
146	A	160	GLU	-1	-0.958	-0.997	20.486	-13.178	-13.178	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:15:ARG)