FMO DATABASE

FMODB ID: 4932N

Calculation Name: 3R8K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R8K

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y5Z4

Base Structure: X-ray

Registration Date: 2023-06-21

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	180
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1856286.763775
FMO2-HF: Nuclear repulsion	1785404.616579
FMO2-HF: Total energy	-70882.147196
FMO2-MP2: Total energy	-71090.348064

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:19:ALA)

Summations of interaction energy for fragment #1(A:19:ALA)

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.
-1.018	1.036	0	-1.072	-0.983	0.003

Interaction energy analysis for fragmet #1(A:19:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.006

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].	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	21	GLU	-1	-0.929	-0.949	3.767	-1.660	0.394	-1.072	-0.983	0.003
4	A	22	THR	0	-0.026	-0.031	5.995	0.249	0.249	0.000	0.000	0.000
5	A	23	PRO	0	-0.012	0.010	8.317	0.072	0.072	0.000	0.000	0.000
6	A	24	GLY	0	0.030	0.012	11.814	0.062	0.062	0.000	0.000	0.000
7	A	25	TRP	0	-0.030	-0.013	12.527	0.012	0.012	0.000	0.000	0.000
8	A	26	LYS	1	0.933	0.949	15.211	0.020	0.020	0.000	0.000	0.000
9	A	27	ALA	0	0.038	0.024	17.841	-0.013	-0.013	0.000	0.000	0.000
10	A	28	PRO	0	-0.013	0.009	20.114	0.003	0.003	0.000	0.000	0.000
11	A	29	GLU	-1	-0.823	-0.900	23.753	0.022	0.022	0.000	0.000	0.000
12	A	30	ASP	-1	-0.901	-0.961	26.697	-0.004	-0.004	0.000	0.000	0.000
13	A	31	ALA	0	-0.055	-0.025	22.764	0.001	0.001	0.000	0.000	0.000
14	A	32	GLY	0	-0.009	0.003	24.876	0.007	0.007	0.000	0.000	0.000
15	A	33	PRO	0	-0.001	0.017	25.549	0.000	0.000	0.000	0.000	0.000
16	A	34	GLN	0	0.034	0.017	20.281	0.021	0.021	0.000	0.000	0.000
17	A	35	PRO	0	-0.004	0.007	21.768	0.000	0.000	0.000	0.000	0.000
18	A	36	GLY	0	0.020	0.008	23.862	0.016	0.016	0.000	0.000	0.000
19	A	37	SER	0	-0.051	-0.029	26.432	-0.004	-0.004	0.000	0.000	0.000
20	A	38	TYR	0	-0.082	-0.084	27.999	-0.007	-0.007	0.000	0.000	0.000
21	A	39	GLU	-1	-0.859	-0.906	29.714	0.064	0.064	0.000	0.000	0.000
22	A	40	ILE	0	0.018	0.001	30.884	-0.003	-0.003	0.000	0.000	0.000
23	A	41	ARG	1	0.724	0.821	34.222	-0.054	-0.054	0.000	0.000	0.000
24	A	42	HIS	0	0.011	0.006	37.563	0.001	0.001	0.000	0.000	0.000
25	A	43	TYR	0	-0.039	-0.004	40.492	0.001	0.001	0.000	0.000	0.000
26	A	44	GLY	0	0.068	0.026	43.755	-0.002	-0.002	0.000	0.000	0.000
27	A	45	PRO	0	-0.037	-0.008	46.491	0.001	0.001	0.000	0.000	0.000
28	A	46	ALA	0	-0.015	-0.015	50.074	0.000	0.000	0.000	0.000	0.000
29	A	47	LYS	1	0.835	0.910	51.787	-0.016	-0.016	0.000	0.000	0.000
30	A	48	TRP	0	-0.004	-0.009	47.221	0.003	0.003	0.000	0.000	0.000
31	A	49	VAL	0	-0.022	-0.001	54.406	-0.002	-0.002	0.000	0.000	0.000
32	A	50	SER	0	0.033	-0.020	54.824	0.002	0.002	0.000	0.000	0.000
33	A	51	THR	0	-0.019	-0.013	56.710	-0.001	-0.001	0.000	0.000	0.000
34	A	52	SER	0	-0.003	-0.006	56.853	0.001	0.001	0.000	0.000	0.000
35	A	53	VAL	0	-0.032	-0.017	57.239	-0.001	-0.001	0.000	0.000	0.000
36	A	54	GLU	-1	-0.811	-0.868	57.136	0.026	0.026	0.000	0.000	0.000
37	A	55	SER	0	-0.018	-0.027	55.877	0.000	0.000	0.000	0.000	0.000
38	A	56	MET	0	0.013	0.010	54.194	0.000	0.000	0.000	0.000	0.000
39	A	57	ASP	-1	-0.891	-0.926	52.944	0.042	0.042	0.000	0.000	0.000
40	A	58	TRP	0	0.054	0.007	47.628	0.000	0.000	0.000	0.000	0.000
41	A	59	ASP	-1	-0.779	-0.895	49.624	0.049	0.049	0.000	0.000	0.000
42	A	60	SER	0	0.001	0.001	52.204	-0.001	-0.001	0.000	0.000	0.000
43	A	61	ALA	0	0.040	0.033	54.225	-0.001	-0.001	0.000	0.000	0.000
44	A	62	ILE	0	-0.005	-0.008	50.277	-0.001	-0.001	0.000	0.000	0.000
45	A	63	GLN	0	-0.018	-0.008	53.621	-0.001	-0.001	0.000	0.000	0.000
46	A	64	THR	0	-0.017	-0.013	55.977	-0.001	-0.001	0.000	0.000	0.000
47	A	65	GLY	0	0.037	0.006	56.978	-0.001	-0.001	0.000	0.000	0.000
48	A	66	PHE	0	0.012	-0.006	54.180	-0.001	-0.001	0.000	0.000	0.000
49	A	67	THR	0	-0.040	-0.019	56.400	-0.001	-0.001	0.000	0.000	0.000
50	A	68	LYS	1	0.827	0.892	59.870	-0.025	-0.025	0.000	0.000	0.000
51	A	69	LEU	0	-0.009	0.014	55.347	-0.001	-0.001	0.000	0.000	0.000
52	A	70	ASN	0	0.020	-0.001	57.968	-0.001	-0.001	0.000	0.000	0.000
53	A	71	SER	0	-0.038	-0.038	59.318	-0.001	-0.001	0.000	0.000	0.000
54	A	72	TYR	0	-0.025	-0.033	59.674	-0.001	-0.001	0.000	0.000	0.000
55	A	73	ILE	0	0.006	0.011	56.827	-0.001	-0.001	0.000	0.000	0.000
56	A	74	GLN	0	-0.027	-0.026	59.772	-0.001	-0.001	0.000	0.000	0.000
57	A	75	GLY	0	0.004	0.016	63.390	0.000	0.000	0.000	0.000	0.000
58	A	76	LYS	1	0.858	0.941	65.651	-0.024	-0.024	0.000	0.000	0.000
59	A	77	ASN	0	-0.019	-0.058	64.547	-0.001	-0.001	0.000	0.000	0.000
60	A	78	GLU	-1	-0.816	-0.913	67.276	0.015	0.015	0.000	0.000	0.000
61	A	79	LYS	1	0.762	0.881	65.067	-0.017	-0.017	0.000	0.000	0.000
62	A	80	GLU	-1	-0.952	-0.960	68.976	0.018	0.018	0.000	0.000	0.000
63	A	81	MET	0	-0.052	-0.006	62.486	0.000	0.000	0.000	0.000	0.000
64	A	82	LYS	1	0.851	0.918	62.564	-0.024	-0.024	0.000	0.000	0.000
65	A	83	ILE	0	-0.018	-0.003	57.936	-0.001	-0.001	0.000	0.000	0.000
66	A	84	LYS	1	0.824	0.894	55.406	-0.025	-0.025	0.000	0.000	0.000
67	A	85	MET	0	0.047	0.027	52.807	0.000	0.000	0.000	0.000	0.000
68	A	86	THR	0	-0.077	-0.065	50.722	0.001	0.001	0.000	0.000	0.000
69	A	87	ALA	0	-0.020	0.004	46.455	0.001	0.001	0.000	0.000	0.000
70	A	88	PRO	0	-0.022	-0.004	44.200	-0.001	-0.001	0.000	0.000	0.000
71	A	89	VAL	0	0.020	0.003	46.525	-0.003	-0.003	0.000	0.000	0.000
72	A	90	THR	0	-0.038	-0.028	46.257	0.002	0.002	0.000	0.000	0.000
73	A	91	SER	0	-0.033	-0.015	47.799	-0.002	-0.002	0.000	0.000	0.000
74	A	92	TYR	0	-0.021	-0.032	47.599	0.002	0.002	0.000	0.000	0.000
75	A	93	VAL	0	-0.009	-0.002	48.098	-0.001	-0.001	0.000	0.000	0.000
76	A	94	GLU	-1	-0.810	-0.895	48.850	0.024	0.024	0.000	0.000	0.000
77	A	95	PRO	0	-0.054	-0.031	48.492	-0.001	-0.001	0.000	0.000	0.000
78	A	96	GLY	0	0.078	0.048	51.750	-0.002	-0.002	0.000	0.000	0.000
79	A	97	SER	0	-0.073	-0.051	53.311	0.000	0.000	0.000	0.000	0.000
80	A	98	GLY	0	0.011	0.007	51.809	-0.001	-0.001	0.000	0.000	0.000
81	A	99	PRO	0	-0.018	-0.020	48.491	0.000	0.000	0.000	0.000	0.000
82	A	100	PHE	0	-0.020	-0.004	50.253	0.001	0.001	0.000	0.000	0.000
83	A	101	SER	0	-0.038	-0.002	54.076	-0.002	-0.002	0.000	0.000	0.000
84	A	102	GLU	-1	-0.950	-0.972	54.873	0.028	0.028	0.000	0.000	0.000
85	A	103	SER	0	-0.067	-0.042	52.830	0.000	0.000	0.000	0.000	0.000
86	A	104	THR	0	0.058	0.012	54.854	0.000	0.000	0.000	0.000	0.000
87	A	105	ILE	0	-0.054	-0.015	51.865	0.001	0.001	0.000	0.000	0.000
88	A	106	THR	0	0.043	0.016	52.859	-0.001	-0.001	0.000	0.000	0.000
89	A	107	ILE	0	-0.051	-0.011	52.264	0.002	0.002	0.000	0.000	0.000
90	A	108	SER	0	0.020	-0.019	51.633	-0.002	-0.002	0.000	0.000	0.000
91	A	109	LEU	0	-0.034	-0.005	51.653	0.002	0.002	0.000	0.000	0.000
92	A	110	TYR	0	0.068	0.040	49.717	-0.001	-0.001	0.000	0.000	0.000
93	A	111	ILE	0	0.013	0.033	51.859	0.001	0.001	0.000	0.000	0.000
94	A	112	PRO	0	-0.005	0.010	53.186	0.000	0.000	0.000	0.000	0.000
95	A	113	SER	0	0.045	0.007	51.961	-0.001	-0.001	0.000	0.000	0.000
96	A	114	GLU	-1	-0.815	-0.881	53.939	0.023	0.023	0.000	0.000	0.000
97	A	115	GLN	0	-0.066	-0.054	57.316	-0.001	-0.001	0.000	0.000	0.000
98	A	116	GLN	0	-0.017	-0.011	53.527	-0.001	-0.001	0.000	0.000	0.000
99	A	117	PHE	0	-0.035	-0.008	56.984	-0.001	-0.001	0.000	0.000	0.000
100	A	118	ASP	-1	-0.836	-0.921	59.939	0.014	0.014	0.000	0.000	0.000
101	A	119	PRO	0	0.044	0.033	59.332	0.000	0.000	0.000	0.000	0.000
102	A	120	PRO	0	-0.044	-0.015	61.930	-0.001	-0.001	0.000	0.000	0.000
103	A	121	ARG	1	0.943	0.986	63.642	-0.014	-0.014	0.000	0.000	0.000
104	A	122	PRO	0	-0.006	-0.003	63.149	0.000	0.000	0.000	0.000	0.000
105	A	123	LEU	0	-0.007	0.003	65.557	-0.001	-0.001	0.000	0.000	0.000
106	A	124	GLU	-1	-0.857	-0.901	65.564	0.023	0.023	0.000	0.000	0.000
107	A	125	SER	0	0.002	-0.014	66.198	0.000	0.000	0.000	0.000	0.000
108	A	126	ASP	-1	-0.822	-0.874	63.748	0.023	0.023	0.000	0.000	0.000
109	A	127	VAL	0	-0.047	-0.017	60.759	0.001	0.001	0.000	0.000	0.000
110	A	128	PHE	0	-0.017	-0.019	57.369	-0.001	-0.001	0.000	0.000	0.000
111	A	129	ILE	0	-0.013	-0.012	58.932	0.001	0.001	0.000	0.000	0.000
112	A	130	GLU	-1	-0.777	-0.838	52.690	0.025	0.025	0.000	0.000	0.000
113	A	131	ASP	-1	-0.833	-0.921	55.129	0.017	0.017	0.000	0.000	0.000
114	A	132	ARG	1	0.795	0.882	48.468	-0.029	-0.029	0.000	0.000	0.000
115	A	133	ALA	0	0.035	0.009	50.655	0.000	0.000	0.000	0.000	0.000
116	A	134	GLU	-1	-0.906	-0.945	45.863	0.015	0.015	0.000	0.000	0.000
117	A	135	MET	0	-0.022	-0.010	43.998	0.000	0.000	0.000	0.000	0.000
118	A	136	THR	0	-0.011	-0.003	37.673	0.001	0.001	0.000	0.000	0.000
119	A	137	VAL	0	-0.050	-0.027	39.276	0.000	0.000	0.000	0.000	0.000
120	A	138	PHE	0	0.027	0.019	33.855	0.002	0.002	0.000	0.000	0.000
121	A	139	VAL	0	-0.016	-0.016	35.089	0.000	0.000	0.000	0.000	0.000
122	A	140	ARG	1	0.893	0.923	29.590	-0.098	-0.098	0.000	0.000	0.000
123	A	141	SER	0	-0.015	-0.015	34.425	-0.001	-0.001	0.000	0.000	0.000
124	A	142	PHE	0	-0.044	-0.020	34.369	0.005	0.005	0.000	0.000	0.000
125	A	143	ASP	-1	-0.829	-0.908	33.723	0.103	0.103	0.000	0.000	0.000
126	A	144	GLY	0	0.009	-0.002	36.743	-0.001	-0.001	0.000	0.000	0.000
127	A	145	PHE	0	0.002	-0.016	40.467	-0.003	-0.003	0.000	0.000	0.000
128	A	146	SER	0	0.014	-0.004	43.150	0.002	0.002	0.000	0.000	0.000
129	A	147	SER	0	0.004	0.003	44.626	0.000	0.000	0.000	0.000	0.000
130	A	148	ALA	0	0.006	0.001	45.002	0.001	0.001	0.000	0.000	0.000
131	A	149	GLN	0	-0.019	-0.011	43.719	0.003	0.003	0.000	0.000	0.000
132	A	150	LYS	1	0.806	0.903	36.473	-0.089	-0.089	0.000	0.000	0.000
133	A	151	ASN	0	0.017	-0.008	40.109	0.005	0.005	0.000	0.000	0.000
134	A	152	GLN	0	0.021	0.007	40.667	0.001	0.001	0.000	0.000	0.000
135	A	153	GLU	-1	-0.807	-0.868	36.563	0.089	0.089	0.000	0.000	0.000
136	A	154	GLN	0	-0.002	-0.010	34.076	0.005	0.005	0.000	0.000	0.000
137	A	155	LEU	0	0.012	0.009	36.102	0.001	0.001	0.000	0.000	0.000
138	A	156	LEU	0	0.004	0.010	37.002	-0.001	-0.001	0.000	0.000	0.000
139	A	157	THR	0	-0.044	-0.015	31.363	0.003	0.003	0.000	0.000	0.000
140	A	158	LEU	0	-0.007	-0.009	32.255	0.003	0.003	0.000	0.000	0.000
141	A	159	ALA	0	0.001	-0.004	33.317	-0.002	-0.002	0.000	0.000	0.000
142	A	160	SER	0	-0.072	-0.048	31.954	-0.001	-0.001	0.000	0.000	0.000
143	A	161	ILE	0	0.048	0.015	27.403	-0.002	-0.002	0.000	0.000	0.000
144	A	162	LEU	0	-0.033	-0.011	29.453	-0.004	-0.004	0.000	0.000	0.000
145	A	163	ARG	1	0.804	0.883	31.781	-0.044	-0.044	0.000	0.000	0.000
146	A	164	GLU	-1	-0.975	-0.978	26.759	0.087	0.087	0.000	0.000	0.000
147	A	165	ASP	-1	-0.857	-0.909	26.003	0.065	0.065	0.000	0.000	0.000
148	A	166	GLY	0	-0.032	-0.015	28.058	-0.006	-0.006	0.000	0.000	0.000
149	A	167	LYS	1	0.795	0.899	28.878	-0.036	-0.036	0.000	0.000	0.000
150	A	168	VAL	0	0.011	0.001	33.301	0.001	0.001	0.000	0.000	0.000
151	A	169	PHE	0	0.024	0.020	35.060	-0.002	-0.002	0.000	0.000	0.000
152	A	170	ASP	-1	-0.833	-0.939	38.958	0.023	0.023	0.000	0.000	0.000
153	A	171	GLU	-1	-0.884	-0.917	39.911	0.035	0.035	0.000	0.000	0.000
154	A	172	LYS	1	0.887	0.958	42.904	-0.021	-0.021	0.000	0.000	0.000
155	A	173	VAL	0	0.011	0.017	46.147	0.002	0.002	0.000	0.000	0.000
156	A	174	TYR	0	-0.018	-0.012	43.191	0.002	0.002	0.000	0.000	0.000
157	A	175	TYR	0	0.051	0.015	43.437	-0.002	-0.002	0.000	0.000	0.000
158	A	176	THR	0	-0.045	-0.012	43.096	0.003	0.003	0.000	0.000	0.000
159	A	177	ALA	0	0.017	-0.004	42.446	-0.003	-0.003	0.000	0.000	0.000
160	A	178	GLY	0	0.045	0.034	42.940	0.004	0.004	0.000	0.000	0.000
161	A	179	TYR	0	-0.056	-0.070	41.361	-0.003	-0.003	0.000	0.000	0.000
162	A	180	ASN	0	-0.090	-0.051	41.789	-0.002	-0.002	0.000	0.000	0.000
163	A	181	SER	0	0.025	0.038	45.572	0.001	0.001	0.000	0.000	0.000
164	A	182	PRO	0	0.029	0.017	47.390	0.000	0.000	0.000	0.000	0.000
165	A	183	VAL	0	0.022	0.003	49.804	-0.001	-0.001	0.000	0.000	0.000
166	A	184	LYS	1	0.870	0.947	44.345	-0.061	-0.061	0.000	0.000	0.000
167	A	185	LEU	0	-0.010	0.002	47.889	-0.001	-0.001	0.000	0.000	0.000
168	A	186	LEU	0	0.022	0.005	43.476	0.000	0.000	0.000	0.000	0.000
169	A	187	ASN	0	-0.041	-0.025	40.330	-0.001	-0.001	0.000	0.000	0.000
170	A	188	ARG	1	0.898	0.970	38.653	-0.056	-0.056	0.000	0.000	0.000
171	A	189	ASN	0	0.021	0.021	34.275	-0.002	-0.002	0.000	0.000	0.000
172	A	190	ASN	0	0.024	0.010	38.616	-0.007	-0.007	0.000	0.000	0.000
173	A	191	GLU	-1	-0.709	-0.817	38.124	0.062	0.062	0.000	0.000	0.000
174	A	192	VAL	0	-0.010	0.009	38.172	-0.004	-0.004	0.000	0.000	0.000
175	A	193	TRP	0	-0.015	-0.035	38.488	0.001	0.001	0.000	0.000	0.000
176	A	194	LEU	0	0.016	0.025	38.009	-0.001	-0.001	0.000	0.000	0.000
177	A	195	ILE	0	0.022	0.015	39.564	0.000	0.000	0.000	0.000	0.000
178	A	196	GLN	0	0.001	-0.002	36.564	0.002	0.002	0.000	0.000	0.000
179	A	197	LYS	1	0.841	0.917	40.032	-0.024	-0.024	0.000	0.000	0.000
180	A	198	ASN	0	0.000	0.005	40.920	-0.001	-0.001	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:19:ALA)