FMO DATABASE

FMODB ID: VKRK1

Calculation Name: 3ASD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ASD

Chain ID: A

ChEMBL ID:

UniProt ID: Q2W8Q0

Base Structure: X-ray

Registration Date: 2023-09-26

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	137
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1165669.290943
FMO2-HF: Nuclear repulsion	1113698.370148
FMO2-HF: Total energy	-51970.920795
FMO2-MP2: Total energy	-52126.663406

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:78:PHE)

Summations of interaction energy for fragment #1(A:78:PHE)

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.
-23.688	-12.489	7.553	-6.304	-12.445	0.02

Interaction energy analysis for fragmet #1(A:78:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.036

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	80	VAL	0	0.074	0.017	3.047	-0.928	1.943	0.149	-0.959	-2.062	0.003
4	A	81	ASP	-1	-0.882	-0.925	4.623	-0.929	-0.611	0.000	-0.026	-0.292	0.000
5	A	82	VAL	0	-0.025	-0.040	5.076	0.074	0.074	0.000	0.000	0.000	0.000
6	A	83	ALA	0	-0.033	-0.005	2.307	-0.716	-0.918	2.942	-0.957	-1.782	0.000
7	A	84	LEU	0	0.034	0.027	4.152	-0.208	-0.026	0.001	-0.037	-0.145	0.000
8	A	85	HIS	0	0.017	0.000	7.185	0.140	0.140	0.000	0.000	0.000	0.000
9	A	86	LEU	0	-0.045	-0.023	5.570	0.065	0.065	0.000	0.000	0.000	0.000
10	A	87	GLY	0	0.016	-0.002	7.035	0.058	0.058	0.000	0.000	0.000	0.000
11	A	88	ILE	0	-0.016	-0.020	7.981	0.085	0.085	0.000	0.000	0.000	0.000
12	A	89	ALA	0	-0.038	-0.010	11.248	0.039	0.039	0.000	0.000	0.000	0.000
13	A	90	TYR	0	0.023	-0.011	8.220	0.069	0.069	0.000	0.000	0.000	0.000
14	A	91	VAL	0	0.018	0.016	11.886	0.020	0.020	0.000	0.000	0.000	0.000
15	A	92	LYS	1	0.920	0.963	14.118	0.056	0.056	0.000	0.000	0.000	0.000
16	A	93	THR	0	-0.064	-0.026	15.299	0.018	0.018	0.000	0.000	0.000	0.000
17	A	94	GLY	0	0.027	0.024	16.849	0.015	0.015	0.000	0.000	0.000	0.000
18	A	95	ALA	0	-0.053	-0.006	13.851	0.002	0.002	0.000	0.000	0.000	0.000
19	A	96	VAL	0	0.026	-0.015	13.119	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	97	ASP	-1	-0.913	-0.931	12.724	0.105	0.105	0.000	0.000	0.000	0.000
21	A	98	ARG	1	1.021	0.996	9.076	-0.350	-0.350	0.000	0.000	0.000	0.000
22	A	99	GLY	0	-0.003	-0.008	8.308	0.016	0.016	0.000	0.000	0.000	0.000
23	A	100	THR	0	-0.013	-0.020	7.739	-0.165	-0.165	0.000	0.000	0.000	0.000
24	A	101	GLU	-1	-0.881	-0.923	7.289	0.308	0.308	0.000	0.000	0.000	0.000
25	A	102	LEU	0	-0.056	-0.026	2.966	-0.885	-0.150	0.096	-0.171	-0.660	-0.001
26	A	103	LEU	0	-0.012	-0.023	4.139	-1.010	-0.786	-0.001	-0.065	-0.158	0.000
27	A	104	GLU	-1	-0.929	-0.959	6.827	-0.454	-0.454	0.000	0.000	0.000	0.000
28	A	105	ARG	1	0.902	0.946	2.587	-15.407	-10.608	3.865	-2.752	-5.911	0.036
29	A	106	SER	0	-0.085	-0.019	2.721	-4.969	-2.778	0.501	-1.319	-1.372	-0.018
30	A	107	LEU	0	-0.017	-0.042	4.157	0.339	0.420	0.000	-0.018	-0.063	0.000
31	A	108	ALA	0	0.029	-0.003	6.400	0.114	0.114	0.000	0.000	0.000	0.000
32	A	109	ASP	-1	-0.860	-0.891	8.089	-0.628	-0.628	0.000	0.000	0.000	0.000
33	A	110	ALA	0	-0.081	-0.029	6.508	-0.024	-0.024	0.000	0.000	0.000	0.000
34	A	111	PRO	0	-0.065	-0.036	7.303	0.110	0.110	0.000	0.000	0.000	0.000
35	A	112	ASP	-1	-0.967	-0.980	10.049	-0.505	-0.505	0.000	0.000	0.000	0.000
36	A	113	ASN	0	0.100	0.019	6.651	0.397	0.397	0.000	0.000	0.000	0.000
37	A	114	VAL	0	0.015	0.029	10.250	0.108	0.108	0.000	0.000	0.000	0.000
38	A	115	LYS	1	0.945	0.962	12.067	0.537	0.537	0.000	0.000	0.000	0.000
39	A	116	VAL	0	0.041	0.040	12.413	0.074	0.074	0.000	0.000	0.000	0.000
40	A	117	ALA	0	0.053	0.017	11.329	0.077	0.077	0.000	0.000	0.000	0.000
41	A	118	THR	0	-0.038	-0.019	13.386	0.077	0.077	0.000	0.000	0.000	0.000
42	A	119	VAL	0	-0.015	-0.010	16.650	0.046	0.046	0.000	0.000	0.000	0.000
43	A	120	LEU	0	0.020	0.014	13.625	0.043	0.043	0.000	0.000	0.000	0.000
44	A	121	GLY	0	0.015	0.015	16.691	0.035	0.035	0.000	0.000	0.000	0.000
45	A	122	LEU	0	-0.011	-0.019	17.841	0.033	0.033	0.000	0.000	0.000	0.000
46	A	123	THR	0	0.001	0.001	20.670	0.029	0.029	0.000	0.000	0.000	0.000
47	A	124	TYR	0	-0.010	-0.021	15.898	0.035	0.035	0.000	0.000	0.000	0.000
48	A	125	VAL	0	-0.006	0.005	21.221	0.018	0.018	0.000	0.000	0.000	0.000
49	A	126	GLN	0	-0.065	-0.016	23.671	0.005	0.005	0.000	0.000	0.000	0.000
50	A	127	VAL	0	-0.073	-0.040	23.446	0.012	0.012	0.000	0.000	0.000	0.000
51	A	128	GLN	0	-0.035	-0.020	25.966	0.010	0.010	0.000	0.000	0.000	0.000
52	A	129	LYS	1	0.945	0.986	21.196	0.083	0.083	0.000	0.000	0.000	0.000
53	A	130	TYR	0	0.069	0.016	21.047	-0.018	-0.018	0.000	0.000	0.000	0.000
54	A	131	ASP	-1	-0.866	-0.940	20.400	-0.091	-0.091	0.000	0.000	0.000	0.000
55	A	132	LEU	0	-0.049	-0.018	15.762	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	133	ALA	0	-0.021	-0.017	16.426	-0.029	-0.029	0.000	0.000	0.000	0.000
57	A	134	VAL	0	0.029	0.024	17.650	-0.028	-0.028	0.000	0.000	0.000	0.000
58	A	135	PRO	0	0.042	0.012	13.387	-0.021	-0.021	0.000	0.000	0.000	0.000
59	A	136	LEU	0	0.013	0.013	11.657	-0.048	-0.048	0.000	0.000	0.000	0.000
60	A	137	LEU	0	-0.016	-0.008	14.036	-0.045	-0.045	0.000	0.000	0.000	0.000
61	A	138	ILE	0	0.001	-0.001	15.241	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	139	LYS	1	0.930	0.975	10.330	0.275	0.275	0.000	0.000	0.000	0.000
63	A	140	VAL	0	-0.039	-0.014	12.814	-0.051	-0.051	0.000	0.000	0.000	0.000
64	A	141	ALA	0	-0.050	-0.034	14.374	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	142	GLU	-1	-0.944	-0.965	13.441	-0.292	-0.292	0.000	0.000	0.000	0.000
66	A	143	ALA	0	0.030	0.032	11.733	0.004	0.004	0.000	0.000	0.000	0.000
67	A	144	ASN	0	-0.041	-0.029	13.760	0.025	0.025	0.000	0.000	0.000	0.000
68	A	145	PRO	0	0.011	0.016	17.176	0.044	0.044	0.000	0.000	0.000	0.000
69	A	146	ILE	0	0.028	0.014	19.635	0.035	0.035	0.000	0.000	0.000	0.000
70	A	147	ASN	0	-0.004	0.004	20.165	0.035	0.035	0.000	0.000	0.000	0.000
71	A	148	PHE	0	0.033	0.012	22.420	0.004	0.004	0.000	0.000	0.000	0.000
72	A	149	ASN	0	-0.007	-0.024	24.306	0.016	0.016	0.000	0.000	0.000	0.000
73	A	150	VAL	0	0.040	0.025	18.523	0.012	0.012	0.000	0.000	0.000	0.000
74	A	151	ARG	1	0.934	0.969	20.497	0.230	0.230	0.000	0.000	0.000	0.000
75	A	152	PHE	0	0.022	0.005	23.596	0.014	0.014	0.000	0.000	0.000	0.000
76	A	153	ARG	1	0.904	0.947	23.425	0.152	0.152	0.000	0.000	0.000	0.000
77	A	154	LEU	0	0.035	0.035	19.731	0.007	0.007	0.000	0.000	0.000	0.000
78	A	155	GLY	0	0.051	0.023	22.805	0.012	0.012	0.000	0.000	0.000	0.000
79	A	156	VAL	0	-0.071	-0.038	26.250	0.009	0.009	0.000	0.000	0.000	0.000
80	A	157	ALA	0	0.029	0.005	22.842	0.008	0.008	0.000	0.000	0.000	0.000
81	A	158	LEU	0	-0.016	-0.011	22.041	0.009	0.009	0.000	0.000	0.000	0.000
82	A	159	ASP	-1	-0.834	-0.897	25.125	-0.062	-0.062	0.000	0.000	0.000	0.000
83	A	160	ASN	0	0.009	-0.002	27.317	0.001	0.001	0.000	0.000	0.000	0.000
84	A	161	LEU	0	-0.095	-0.051	22.255	0.007	0.007	0.000	0.000	0.000	0.000
85	A	162	GLY	0	0.005	0.024	26.732	0.007	0.007	0.000	0.000	0.000	0.000
86	A	163	ARG	1	0.763	0.868	20.339	0.090	0.090	0.000	0.000	0.000	0.000
87	A	164	PHE	0	0.068	0.012	27.511	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	165	ASP	-1	-0.839	-0.923	29.666	-0.062	-0.062	0.000	0.000	0.000	0.000
89	A	166	GLU	-1	-0.810	-0.884	22.580	-0.096	-0.096	0.000	0.000	0.000	0.000
90	A	167	ALA	0	0.008	0.006	26.319	-0.011	-0.011	0.000	0.000	0.000	0.000
91	A	168	ILE	0	-0.003	0.002	27.709	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	169	ASP	-1	-0.896	-0.939	26.957	-0.094	-0.094	0.000	0.000	0.000	0.000
93	A	170	SER	0	-0.051	-0.037	24.354	-0.014	-0.014	0.000	0.000	0.000	0.000
94	A	171	PHE	0	-0.023	-0.022	26.081	-0.010	-0.010	0.000	0.000	0.000	0.000
95	A	172	LYS	1	0.904	0.953	29.244	0.082	0.082	0.000	0.000	0.000	0.000
96	A	173	ILE	0	0.000	0.003	24.125	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	174	ALA	0	-0.031	-0.014	27.362	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	175	LEU	0	-0.013	-0.025	28.310	0.000	0.000	0.000	0.000	0.000	0.000
99	A	176	GLY	0	-0.025	-0.001	30.530	0.004	0.004	0.000	0.000	0.000	0.000
100	A	177	LEU	0	-0.060	-0.015	25.098	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	178	ARG	1	0.906	0.942	28.103	0.156	0.156	0.000	0.000	0.000	0.000
102	A	179	PRO	0	0.031	0.028	32.510	0.004	0.004	0.000	0.000	0.000	0.000
103	A	180	ASN	0	-0.001	-0.032	35.526	0.005	0.005	0.000	0.000	0.000	0.000
104	A	181	GLU	-1	-0.853	-0.913	32.400	-0.115	-0.115	0.000	0.000	0.000	0.000
105	A	182	GLY	0	0.109	0.048	35.588	0.000	0.000	0.000	0.000	0.000	0.000
106	A	183	LYS	1	0.870	0.942	30.527	0.124	0.124	0.000	0.000	0.000	0.000
107	A	184	VAL	0	0.008	-0.005	31.299	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	185	HIS	0	0.065	0.054	33.787	0.004	0.004	0.000	0.000	0.000	0.000
109	A	186	ARG	1	0.977	0.988	36.860	0.073	0.073	0.000	0.000	0.000	0.000
110	A	187	ALA	0	0.010	0.003	32.431	0.003	0.003	0.000	0.000	0.000	0.000
111	A	188	ILE	0	0.001	0.014	32.822	0.003	0.003	0.000	0.000	0.000	0.000
112	A	189	ALA	0	-0.029	-0.012	34.588	0.004	0.004	0.000	0.000	0.000	0.000
113	A	190	PHE	0	0.006	-0.005	35.918	0.004	0.004	0.000	0.000	0.000	0.000
114	A	191	SER	0	0.021	-0.014	32.229	0.001	0.001	0.000	0.000	0.000	0.000
115	A	192	TYR	0	-0.027	-0.027	34.395	0.001	0.001	0.000	0.000	0.000	0.000
116	A	193	GLU	-1	-0.833	-0.911	37.040	-0.040	-0.040	0.000	0.000	0.000	0.000
117	A	194	GLN	0	-0.088	-0.031	33.750	0.006	0.006	0.000	0.000	0.000	0.000
118	A	195	MET	0	-0.053	-0.014	34.340	0.001	0.001	0.000	0.000	0.000	0.000
119	A	196	GLY	0	-0.019	0.007	37.313	0.003	0.003	0.000	0.000	0.000	0.000
120	A	197	ARG	1	0.873	0.939	35.329	0.053	0.053	0.000	0.000	0.000	0.000
121	A	198	HIS	0	0.019	-0.022	41.191	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	199	GLU	-1	-0.982	-0.982	43.756	-0.040	-0.040	0.000	0.000	0.000	0.000
123	A	200	GLU	-1	-0.912	-0.974	39.361	-0.052	-0.052	0.000	0.000	0.000	0.000
124	A	201	ALA	0	0.002	0.003	40.154	-0.004	-0.004	0.000	0.000	0.000	0.000
125	A	202	LEU	0	0.006	0.019	41.170	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	203	PRO	0	0.017	0.000	42.166	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	204	HIS	1	0.859	0.932	36.718	0.071	0.071	0.000	0.000	0.000	0.000
128	A	205	PHE	0	0.045	0.025	40.551	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	206	LYS	1	0.912	0.952	42.807	0.046	0.046	0.000	0.000	0.000	0.000
130	A	207	LYS	1	0.955	0.972	39.679	0.077	0.077	0.000	0.000	0.000	0.000
131	A	208	ALA	0	-0.035	-0.044	40.003	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	209	ASN	0	-0.069	-0.026	41.314	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	210	GLU	-1	-0.958	-0.961	44.457	-0.060	-0.060	0.000	0.000	0.000	0.000
134	A	211	LEU	0	-0.120	-0.056	39.134	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	212	ASP	-1	-0.926	-0.966	41.732	-0.078	-0.078	0.000	0.000	0.000	0.000
136	A	213	GLU	-1	-0.977	-0.986	44.295	-0.061	-0.061	0.000	0.000	0.000	0.000
137	A	214	GLY	0	-0.048	0.001	47.412	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:78:PHE)