FMO DATABASE

FMODB ID: 729GK

Calculation Name: 3WKV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WKV

Chain ID: A

ChEMBL ID:

UniProt ID: Q3U2S8

Base Structure: X-ray

Registration Date: 2023-09-20

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	149
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1303877.095602
FMO2-HF: Nuclear repulsion	1244311.746469
FMO2-HF: Total energy	-59565.349132
FMO2-MP2: Total energy	-59743.320988

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:84:PHE)

Summations of interaction energy for fragment #1(A:84: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.
-7.419	-3.289	0.302	-1.855	-2.576	0.013

Interaction energy analysis for fragmet #1(A:84:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.020

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	86	SER	0	0.067	0.038	2.989	-3.368	0.435	0.301	-1.810	-2.294	0.013
4	A	87	ARG	1	0.990	0.984	3.801	-1.467	-1.140	0.001	-0.045	-0.282	0.000
5	A	88	LEU	0	0.032	0.024	8.002	-0.239	-0.239	0.000	0.000	0.000	0.000
6	A	89	ARG	1	0.905	0.955	7.735	-1.223	-1.223	0.000	0.000	0.000	0.000
7	A	90	LYS	1	0.941	0.994	7.502	-0.510	-0.510	0.000	0.000	0.000	0.000
8	A	91	LEU	0	-0.020	-0.042	9.464	-0.141	-0.141	0.000	0.000	0.000	0.000
9	A	92	PHE	0	0.073	0.050	12.462	-0.060	-0.060	0.000	0.000	0.000	0.000
10	A	93	SER	0	0.346	0.276	12.671	-0.059	-0.059	0.000	0.000	0.000	0.000
11	A	94	SER	0	0.468	0.628	15.290	-0.086	-0.086	0.000	0.000	0.000	0.000
12	A	95	HIS	1	0.183	0.109	17.968	-0.303	-0.303	0.000	0.000	0.000	0.000
13	A	96	ARG	1	0.950	0.955	22.038	-0.168	-0.168	0.000	0.000	0.000	0.000
14	A	97	PHE	0	0.018	-0.005	17.307	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	98	GLN	0	0.030	0.020	20.700	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	99	VAL	0	0.061	0.029	23.495	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	100	ILE	0	-0.041	-0.013	22.679	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	101	ILE	0	0.069	0.012	21.874	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	102	ILE	0	0.006	0.022	25.201	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	103	CYS	0	-0.063	-0.037	28.455	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	104	LEU	0	0.037	0.014	24.414	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	105	VAL	0	-0.016	0.009	27.679	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	106	VAL	0	-0.035	-0.018	29.929	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	107	LEU	0	0.002	-0.005	30.874	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	108	ASP	-1	-0.635	-0.838	29.907	0.148	0.148	0.000	0.000	0.000	0.000
26	A	109	ALA	0	-0.079	-0.046	32.533	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	110	LEU	0	0.029	-0.019	35.083	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	111	LEU	0	-0.013	0.028	32.223	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	112	VAL	0	0.041	0.023	34.711	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	113	LEU	0	-0.044	-0.009	37.227	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	114	ALA	0	0.005	-0.010	39.986	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	115	GLU	-1	-0.785	-0.886	37.579	0.081	0.081	0.000	0.000	0.000	0.000
33	A	116	LEU	0	0.046	0.015	40.272	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	117	LEU	0	-0.032	-0.019	42.974	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	118	LEU	0	-0.109	-0.061	43.344	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	119	ASP	-1	-0.896	-0.932	43.657	0.061	0.061	0.000	0.000	0.000	0.000
37	A	120	LEU	0	-0.091	-0.032	46.034	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	121	LYS	1	0.823	0.923	47.704	-0.059	-0.059	0.000	0.000	0.000	0.000
39	A	132	VAL	0	-0.017	-0.007	47.151	0.001	0.001	0.000	0.000	0.000	0.000
40	A	133	THR	0	0.069	0.025	44.932	0.000	0.000	0.000	0.000	0.000	0.000
41	A	134	ALA	0	0.027	0.002	42.235	0.002	0.002	0.000	0.000	0.000	0.000
42	A	135	PHE	0	0.001	-0.001	40.817	0.002	0.002	0.000	0.000	0.000	0.000
43	A	136	HIS	0	0.076	0.047	38.931	0.004	0.004	0.000	0.000	0.000	0.000
44	A	137	TYR	0	0.009	0.014	35.671	0.003	0.003	0.000	0.000	0.000	0.000
45	A	138	MET	0	-0.012	-0.023	36.212	0.004	0.004	0.000	0.000	0.000	0.000
46	A	139	SER	0	-0.016	0.002	35.156	0.006	0.006	0.000	0.000	0.000	0.000
47	A	140	PHE	0	0.071	0.027	32.746	0.008	0.008	0.000	0.000	0.000	0.000
48	A	141	ALA	0	-0.008	0.001	31.964	0.008	0.008	0.000	0.000	0.000	0.000
49	A	142	ILE	0	-0.024	-0.021	30.368	0.009	0.009	0.000	0.000	0.000	0.000
50	A	143	LEU	0	0.065	0.023	29.889	0.013	0.013	0.000	0.000	0.000	0.000
51	A	144	VAL	0	-0.014	0.007	26.711	0.016	0.016	0.000	0.000	0.000	0.000
52	A	145	PHE	0	-0.080	-0.043	26.042	0.012	0.012	0.000	0.000	0.000	0.000
53	A	146	PHE	0	0.080	0.031	24.963	0.018	0.018	0.000	0.000	0.000	0.000
54	A	147	MET	0	-0.055	-0.017	24.577	0.021	0.021	0.000	0.000	0.000	0.000
55	A	148	LEU	0	0.006	-0.003	21.430	0.031	0.031	0.000	0.000	0.000	0.000
56	A	149	ASP	-1	-0.929	-0.968	20.300	0.254	0.254	0.000	0.000	0.000	0.000
57	A	150	LEU	0	0.018	0.014	19.946	0.049	0.049	0.000	0.000	0.000	0.000
58	A	151	GLY	0	0.039	0.025	19.296	0.046	0.046	0.000	0.000	0.000	0.000
59	A	152	LEU	0	-0.038	-0.031	15.480	0.081	0.081	0.000	0.000	0.000	0.000
60	A	153	ARG	1	0.852	0.921	14.376	-0.315	-0.315	0.000	0.000	0.000	0.000
61	A	154	ILE	0	-0.003	0.006	16.498	0.021	0.021	0.000	0.000	0.000	0.000
62	A	155	PHE	0	-0.010	0.012	10.671	0.107	0.107	0.000	0.000	0.000	0.000
63	A	156	ALA	0	-0.052	-0.023	10.981	0.217	0.217	0.000	0.000	0.000	0.000
64	A	157	TYR	0	0.034	0.014	10.590	-0.064	-0.064	0.000	0.000	0.000	0.000
65	A	158	GLY	0	0.056	0.066	7.322	0.080	0.080	0.000	0.000	0.000	0.000
66	A	158	PRO	0	-0.090	-0.074	4.933	0.135	0.135	0.000	0.000	0.000	0.000
67	A	159	LYS	1	0.986	0.968	6.209	-0.678	-0.678	0.000	0.000	0.000	0.000
68	A	160	ASN	0	-0.058	-0.028	9.643	-0.125	-0.125	0.000	0.000	0.000	0.000
69	A	161	PHE	0	0.081	0.050	13.696	-0.022	-0.022	0.000	0.000	0.000	0.000
70	A	162	PHE	0	-0.065	-0.036	17.640	0.006	0.006	0.000	0.000	0.000	0.000
71	A	163	THR	0	0.027	-0.003	19.184	-0.016	-0.016	0.000	0.000	0.000	0.000
72	A	164	ASN	0	0.010	0.014	14.421	0.047	0.047	0.000	0.000	0.000	0.000
73	A	165	PRO	0	-0.008	0.010	18.198	0.025	0.025	0.000	0.000	0.000	0.000
74	A	166	TRP	0	0.055	0.011	20.732	0.017	0.017	0.000	0.000	0.000	0.000
75	A	167	GLU	-1	-0.774	-0.880	17.148	0.443	0.443	0.000	0.000	0.000	0.000
76	A	168	VAL	0	-0.038	-0.026	16.235	0.015	0.015	0.000	0.000	0.000	0.000
77	A	169	ALA	0	-0.010	-0.007	18.683	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	170	ASP	-1	-0.848	-0.927	21.540	0.289	0.289	0.000	0.000	0.000	0.000
79	A	171	GLY	0	0.012	0.006	19.012	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	172	LEU	0	-0.028	-0.019	19.834	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	173	ILE	0	0.061	0.036	21.024	-0.026	-0.026	0.000	0.000	0.000	0.000
82	A	174	VAL	0	-0.010	0.059	21.951	-0.024	-0.024	0.000	0.000	0.000	0.000
83	A	175	VAL	0	-0.018	-0.011	18.876	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	176	VAL	0	-0.009	-0.025	22.188	-0.021	-0.021	0.000	0.000	0.000	0.000
85	A	177	SER	0	-0.055	-0.081	25.068	-0.022	-0.022	0.000	0.000	0.000	0.000
86	A	178	PHE	0	0.056	0.001	24.769	-0.014	-0.014	0.000	0.000	0.000	0.000
87	A	179	VAL	0	-0.055	-0.010	22.967	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	180	LEU	0	0.001	-0.006	25.985	-0.018	-0.018	0.000	0.000	0.000	0.000
89	A	181	ASP	-1	-0.810	-0.915	28.506	0.146	0.146	0.000	0.000	0.000	0.000
90	A	182	LEU	0	-0.007	-0.003	25.031	-0.011	-0.011	0.000	0.000	0.000	0.000
91	A	183	VAL	0	-0.050	-0.024	29.020	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	184	LEU	0	-0.017	-0.032	31.322	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	185	LEU	0	-0.068	0.004	30.220	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	186	PHE	0	-0.014	-0.015	30.465	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	187	LYS	1	0.827	0.918	35.890	-0.084	-0.084	0.000	0.000	0.000	0.000
96	A	188	SER	0	0.006	0.014	39.553	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	189	HIS	0	-0.026	-0.018	35.381	0.004	0.004	0.000	0.000	0.000	0.000
98	A	190	HIS	0	0.045	0.021	39.142	0.005	0.005	0.000	0.000	0.000	0.000
99	A	191	PHE	0	-0.012	-0.017	41.916	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	192	GLU	-1	-0.837	-0.933	42.686	0.067	0.067	0.000	0.000	0.000	0.000
101	A	193	ALA	0	-0.054	-0.024	38.814	0.003	0.003	0.000	0.000	0.000	0.000
102	A	194	LEU	0	0.063	0.040	38.048	0.007	0.007	0.000	0.000	0.000	0.000
103	A	195	GLY	0	0.055	0.010	38.137	0.006	0.006	0.000	0.000	0.000	0.000
104	A	196	LEU	0	0.009	-0.004	36.615	0.005	0.005	0.000	0.000	0.000	0.000
105	A	197	LEU	0	0.089	0.032	32.502	0.007	0.007	0.000	0.000	0.000	0.000
106	A	198	ILE	0	-0.067	-0.040	34.053	0.009	0.009	0.000	0.000	0.000	0.000
107	A	199	LEU	0	-0.081	-0.048	34.975	0.007	0.007	0.000	0.000	0.000	0.000
108	A	200	LEU	0	-0.004	0.024	31.002	0.006	0.006	0.000	0.000	0.000	0.000
109	A	201	ARG	1	0.830	0.967	30.525	-0.110	-0.110	0.000	0.000	0.000	0.000
110	A	202	LEU	0	-0.077	-0.033	31.080	0.010	0.010	0.000	0.000	0.000	0.000
111	A	203	TRP	0	0.035	0.029	27.044	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	204	ARG	1	0.849	0.925	26.814	-0.171	-0.171	0.000	0.000	0.000	0.000
113	A	205	VAL	0	0.074	0.047	27.964	0.012	0.012	0.000	0.000	0.000	0.000
114	A	206	ALA	0	0.003	0.016	29.574	0.009	0.009	0.000	0.000	0.000	0.000
115	A	207	ARG	1	0.880	0.964	25.120	-0.236	-0.236	0.000	0.000	0.000	0.000
116	A	208	ILE	0	-0.029	-0.029	24.057	0.012	0.012	0.000	0.000	0.000	0.000
117	A	209	ILE	0	0.035	0.016	26.156	0.006	0.006	0.000	0.000	0.000	0.000
118	A	210	ASN	0	-0.013	-0.018	28.022	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	211	GLY	0	0.010	-0.002	23.856	0.001	0.001	0.000	0.000	0.000	0.000
120	A	212	ILE	0	-0.030	-0.001	23.593	0.016	0.016	0.000	0.000	0.000	0.000
121	A	213	ILE	0	-0.034	0.003	26.071	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	214	ILE	0	0.046	0.006	22.630	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	215	SER	0	-0.040	-0.047	23.196	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	216	ARG	1	0.962	0.971	24.451	-0.164	-0.164	0.000	0.000	0.000	0.000
125	A	217	MET	0	-0.016	0.023	27.196	-0.011	-0.011	0.000	0.000	0.000	0.000
126	A	218	LYS	1	1.015	0.998	20.788	-0.212	-0.212	0.000	0.000	0.000	0.000
127	A	219	GLN	0	-0.059	-0.028	23.942	-0.026	-0.026	0.000	0.000	0.000	0.000
128	A	220	LEU	0	-0.140	-0.077	24.979	-0.013	-0.013	0.000	0.000	0.000	0.000
129	A	221	GLU	-1	-0.935	-0.987	27.032	0.149	0.149	0.000	0.000	0.000	0.000
130	A	222	ASP	-1	-0.843	-0.910	22.996	0.177	0.177	0.000	0.000	0.000	0.000
131	A	223	LYS	1	0.929	0.968	26.150	-0.133	-0.133	0.000	0.000	0.000	0.000
132	A	224	ILE	0	0.000	0.005	28.921	-0.009	-0.009	0.000	0.000	0.000	0.000
133	A	225	GLU	-1	-0.849	-0.913	27.131	0.075	0.075	0.000	0.000	0.000	0.000
134	A	226	GLU	-1	-1.033	-1.014	26.859	0.090	0.090	0.000	0.000	0.000	0.000
135	A	227	LEU	0	-0.126	-0.066	30.073	-0.004	-0.004	0.000	0.000	0.000	0.000
136	A	228	LEU	0	0.053	0.024	33.064	-0.006	-0.006	0.000	0.000	0.000	0.000
137	A	229	SER	0	0.043	0.041	30.984	-0.007	-0.007	0.000	0.000	0.000	0.000
138	A	230	LYS	1	0.967	0.990	31.720	-0.059	-0.059	0.000	0.000	0.000	0.000
139	A	231	ILE	0	0.033	0.002	34.970	-0.004	-0.004	0.000	0.000	0.000	0.000
140	A	232	TYR	0	0.020	0.007	35.406	-0.004	-0.004	0.000	0.000	0.000	0.000
141	A	233	HIS	0	-0.080	-0.036	35.361	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	234	LEU	0	-0.029	-0.037	37.416	-0.003	-0.003	0.000	0.000	0.000	0.000
143	A	235	GLU	-1	-0.920	-0.948	40.587	0.038	0.038	0.000	0.000	0.000	0.000
144	A	236	ASN	0	-0.001	0.000	38.146	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	237	GLU	-1	-0.990	-0.992	39.471	0.024	0.024	0.000	0.000	0.000	0.000
146	A	238	ILE	0	-0.037	-0.010	42.953	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	239	ALA	0	0.013	0.006	45.749	-0.002	-0.002	0.000	0.000	0.000	0.000
148	A	240	ARG	1	0.817	0.905	42.742	-0.021	-0.021	0.000	0.000	0.000	0.000
149	A	241	LEU	0	-0.035	0.002	47.135	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:84:PHE)