FMO DATABASE

FMODB ID: V5KY1

Calculation Name: 3WPX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WPX

Chain ID: A

ChEMBL ID:

UniProt ID: O06874

Base Structure: X-ray

Registration Date: 2023-06-22

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	149
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1474020.273454
FMO2-HF: Nuclear repulsion	1413720.209746
FMO2-HF: Total energy	-60300.063708
FMO2-MP2: Total energy	-60474.391619

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:154:SER)

Summations of interaction energy for fragment #1(A:154:SER)

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.
-4.398	0.892	0.841	-2.275	-3.857	-0.001

Interaction energy analysis for fragmet #1(A:154:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.067 / q_NPA : 0.025

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	156	GLU	-1	-0.868	-0.953	3.398	-5.136	-3.000	0.019	-0.906	-1.249	0.001
4	A	157	MET	0	-0.065	-0.002	2.356	-0.076	1.668	0.760	-0.893	-1.611	0.001
5	A	158	GLU	-1	-0.891	-0.940	4.431	0.445	0.679	-0.001	-0.046	-0.187	0.000
6	A	159	THR	0	-0.020	-0.024	6.151	0.558	0.558	0.000	0.000	0.000	0.000
7	A	160	LEU	0	-0.025	-0.006	7.624	0.303	0.303	0.000	0.000	0.000	0.000
8	A	161	MET	0	0.011	0.008	8.484	0.245	0.245	0.000	0.000	0.000	0.000
9	A	162	GLU	-1	-0.778	-0.896	10.086	-0.101	-0.101	0.000	0.000	0.000	0.000
10	A	163	SER	0	-0.081	-0.016	12.113	0.119	0.119	0.000	0.000	0.000	0.000
11	A	164	ILE	0	-0.002	-0.005	11.849	0.075	0.075	0.000	0.000	0.000	0.000
12	A	165	LYS	1	0.923	0.966	13.963	0.204	0.204	0.000	0.000	0.000	0.000
13	A	166	LYS	1	0.860	0.908	14.534	0.347	0.347	0.000	0.000	0.000	0.000
14	A	167	ALA	0	-0.035	-0.001	17.783	0.030	0.030	0.000	0.000	0.000	0.000
15	A	168	LEU	0	-0.046	-0.031	18.178	0.023	0.023	0.000	0.000	0.000	0.000
16	A	169	GLU	-1	-0.919	-0.949	20.619	-0.100	-0.100	0.000	0.000	0.000	0.000
17	A	170	ARG	1	0.903	0.937	21.641	0.133	0.133	0.000	0.000	0.000	0.000
18	A	171	GLU	-1	-0.804	-0.907	22.892	-0.111	-0.111	0.000	0.000	0.000	0.000
19	A	172	ILE	0	-0.069	-0.034	17.938	0.009	0.009	0.000	0.000	0.000	0.000
20	A	173	GLU	-1	-0.932	-0.953	22.180	-0.059	-0.059	0.000	0.000	0.000	0.000
21	A	174	GLN	0	-0.054	-0.020	24.895	0.010	0.010	0.000	0.000	0.000	0.000
22	A	175	GLY	0	0.015	0.006	24.954	0.008	0.008	0.000	0.000	0.000	0.000
23	A	176	ALA	0	-0.104	-0.066	25.565	0.005	0.005	0.000	0.000	0.000	0.000
24	A	177	ILE	0	0.025	-0.003	19.508	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	178	GLH	0	-0.033	-0.033	17.237	0.003	0.003	0.000	0.000	0.000	0.000
26	A	179	VAL	0	0.009	-0.003	12.898	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	180	GLU	-1	-0.784	-0.840	12.753	-0.016	-0.016	0.000	0.000	0.000	0.000
28	A	181	ASN	0	0.048	-0.012	5.856	-0.186	-0.186	0.000	0.000	0.000	0.000
29	A	182	LEU	0	0.007	0.002	9.411	0.087	0.087	0.000	0.000	0.000	0.000
30	A	183	GLY	0	0.012	0.008	8.758	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	184	GLN	0	-0.022	-0.022	3.304	-1.439	-0.247	0.064	-0.422	-0.834	-0.003
32	A	185	GLN	0	0.010	0.011	6.624	-0.074	-0.074	0.000	0.000	0.000	0.000
33	A	186	ILE	0	0.039	0.032	7.417	0.020	0.020	0.000	0.000	0.000	0.000
34	A	187	VAL	0	-0.037	-0.006	10.206	0.035	0.035	0.000	0.000	0.000	0.000
35	A	188	ILE	0	0.023	0.008	13.847	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	189	ARG	1	0.800	0.894	16.659	0.055	0.055	0.000	0.000	0.000	0.000
37	A	190	MET	0	0.000	0.001	19.963	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	191	ARG	1	0.848	0.951	23.188	0.064	0.064	0.000	0.000	0.000	0.000
39	A	192	GLU	-1	-0.665	-0.800	26.414	-0.033	-0.033	0.000	0.000	0.000	0.000
40	A	193	LYS	1	0.984	0.987	29.598	0.035	0.035	0.000	0.000	0.000	0.000
41	A	194	GLY	0	-0.002	-0.011	30.251	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	195	ALA	0	-0.009	0.001	28.071	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	196	PHE	0	0.014	-0.009	27.202	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	197	PRO	0	-0.019	0.010	32.413	0.002	0.002	0.000	0.000	0.000	0.000
45	A	198	GLU	-1	-0.847	-0.922	35.488	-0.022	-0.022	0.000	0.000	0.000	0.000
46	A	199	GLY	0	0.011	0.008	36.187	0.001	0.001	0.000	0.000	0.000	0.000
47	A	200	SER	0	-0.010	0.002	36.194	0.000	0.000	0.000	0.000	0.000	0.000
48	A	201	ALA	0	0.069	0.027	32.267	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	202	PHE	0	-0.043	-0.017	32.197	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	203	LEU	0	0.043	0.021	27.768	0.000	0.000	0.000	0.000	0.000	0.000
51	A	204	GLN	0	0.001	-0.010	31.627	0.004	0.004	0.000	0.000	0.000	0.000
52	A	205	PRO	0	0.016	-0.001	31.680	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	206	LYS	1	0.949	0.965	31.738	0.054	0.054	0.000	0.000	0.000	0.000
54	A	207	PHE	0	0.058	0.028	24.723	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	208	ARG	1	0.840	0.931	27.003	0.058	0.058	0.000	0.000	0.000	0.000
56	A	209	PRO	0	-0.001	-0.013	26.539	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	210	LEU	0	0.046	0.047	22.688	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	211	VAL	0	0.031	0.010	22.425	-0.017	-0.017	0.000	0.000	0.000	0.000
59	A	212	ARG	1	0.900	0.940	21.743	0.093	0.093	0.000	0.000	0.000	0.000
60	A	213	GLN	0	0.014	0.021	20.639	0.000	0.000	0.000	0.000	0.000	0.000
61	A	214	ILE	0	0.015	0.002	16.828	-0.028	-0.028	0.000	0.000	0.000	0.000
62	A	215	ALA	0	-0.005	-0.012	17.063	-0.033	-0.033	0.000	0.000	0.000	0.000
63	A	216	GLU	-1	-0.911	-0.986	17.918	-0.221	-0.221	0.000	0.000	0.000	0.000
64	A	217	LEU	0	-0.052	-0.022	15.027	-0.024	-0.024	0.000	0.000	0.000	0.000
65	A	218	VAL	0	0.017	0.012	12.623	-0.071	-0.071	0.000	0.000	0.000	0.000
66	A	219	LYS	1	0.766	0.903	13.629	0.283	0.283	0.000	0.000	0.000	0.000
67	A	220	ASP	-1	-0.873	-0.925	14.015	-0.321	-0.321	0.000	0.000	0.000	0.000
68	A	221	VAL	0	-0.036	-0.003	8.203	-0.081	-0.081	0.000	0.000	0.000	0.000
69	A	222	PRO	0	-0.001	-0.002	8.486	0.113	0.113	0.000	0.000	0.000	0.000
70	A	223	GLY	0	0.056	0.025	9.672	-0.039	-0.039	0.000	0.000	0.000	0.000
71	A	224	ILE	0	-0.062	-0.024	11.270	-0.021	-0.021	0.000	0.000	0.000	0.000
72	A	225	VAL	0	0.012	0.012	13.177	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	226	ARG	1	0.905	0.952	15.574	0.046	0.046	0.000	0.000	0.000	0.000
74	A	227	VAL	0	0.017	0.012	17.665	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	228	SER	0	-0.033	-0.022	20.130	0.019	0.019	0.000	0.000	0.000	0.000
76	A	229	GLY	0	0.048	0.041	22.457	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	230	HIS	0	-0.029	-0.027	21.901	0.001	0.001	0.000	0.000	0.000	0.000
78	A	231	THR	0	-0.035	-0.028	27.393	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	232	ASP	-1	-0.820	-0.908	30.113	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	233	ASN	0	0.026	-0.012	32.401	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	234	ARG	1	0.893	0.968	34.689	0.005	0.005	0.000	0.000	0.000	0.000
82	A	235	PRO	0	-0.006	-0.004	37.555	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	236	LEU	0	-0.030	-0.013	36.890	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	237	ASP	-1	-0.918	-0.957	39.986	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	238	SER	0	-0.054	-0.030	40.814	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	239	GLU	-1	-0.889	-0.949	43.038	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	240	LEU	0	-0.057	-0.025	40.566	0.000	0.000	0.000	0.000	0.000	0.000
88	A	241	TYR	0	-0.011	-0.005	35.742	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	242	ARG	1	0.882	0.905	36.665	0.015	0.015	0.000	0.000	0.000	0.000
90	A	243	SER	0	0.013	0.002	36.777	0.002	0.002	0.000	0.000	0.000	0.000
91	A	244	ASN	0	0.108	0.042	33.415	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	245	TRP	0	0.009	0.031	28.885	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	246	ASP	-1	-0.789	-0.862	31.863	-0.020	-0.020	0.000	0.000	0.000	0.000
94	A	247	LEU	0	0.019	0.022	33.046	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	248	SER	0	-0.055	-0.044	28.465	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	249	SER	0	0.010	-0.005	28.333	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	250	GLN	0	0.018	-0.006	28.725	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	251	ARG	1	0.765	0.878	28.287	0.032	0.032	0.000	0.000	0.000	0.000
99	A	252	ALA	0	-0.007	-0.001	24.437	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	253	VAL	0	0.009	0.003	25.386	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	254	SER	0	-0.041	-0.023	27.651	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	255	VAL	0	-0.001	-0.005	22.563	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	256	ALA	0	0.013	0.006	23.111	-0.011	-0.011	0.000	0.000	0.000	0.000
104	A	257	GLN	0	0.029	0.014	24.139	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	258	GLU	-1	-0.853	-0.903	26.066	-0.088	-0.088	0.000	0.000	0.000	0.000
106	A	259	MET	0	-0.030	-0.014	17.858	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	260	GLU	-1	-0.871	-0.924	22.903	-0.093	-0.093	0.000	0.000	0.000	0.000
108	A	261	LYS	1	0.821	0.913	24.182	0.085	0.085	0.000	0.000	0.000	0.000
109	A	262	VAL	0	-0.054	-0.007	21.316	0.004	0.004	0.000	0.000	0.000	0.000
110	A	263	ARG	1	1.014	1.004	21.327	0.184	0.184	0.000	0.000	0.000	0.000
111	A	264	GLY	0	-0.035	-0.030	21.388	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	265	PHE	0	0.017	0.013	17.029	-0.019	-0.019	0.000	0.000	0.000	0.000
113	A	266	SER	0	-0.016	-0.010	18.606	0.026	0.026	0.000	0.000	0.000	0.000
114	A	267	HIS	0	0.041	-0.001	19.918	0.002	0.002	0.000	0.000	0.000	0.000
115	A	268	GLN	0	0.039	0.021	20.049	0.004	0.004	0.000	0.000	0.000	0.000
116	A	269	ARG	1	0.814	0.905	12.584	0.318	0.318	0.000	0.000	0.000	0.000
117	A	270	LEU	0	0.024	0.040	17.453	0.000	0.000	0.000	0.000	0.000	0.000
118	A	271	ARG	1	0.825	0.899	18.893	0.062	0.062	0.000	0.000	0.000	0.000
119	A	272	VAL	0	0.029	0.021	20.918	-0.009	-0.009	0.000	0.000	0.000	0.000
120	A	273	ARG	1	0.796	0.873	20.826	0.019	0.019	0.000	0.000	0.000	0.000
121	A	274	GLY	0	0.047	0.023	24.454	-0.007	-0.007	0.000	0.000	0.000	0.000
122	A	275	MET	0	-0.060	-0.014	23.663	0.004	0.004	0.000	0.000	0.000	0.000
123	A	276	ALA	0	0.012	0.017	27.022	0.005	0.005	0.000	0.000	0.000	0.000
124	A	277	ASP	-1	-0.896	-0.941	28.937	0.002	0.002	0.000	0.000	0.000	0.000
125	A	278	THR	0	-0.041	-0.048	27.301	0.004	0.004	0.000	0.000	0.000	0.000
126	A	279	GLU	-1	-0.791	-0.870	22.065	0.008	0.008	0.000	0.000	0.000	0.000
127	A	280	PRO	0	-0.018	0.005	24.819	-0.008	-0.008	0.000	0.000	0.000	0.000
128	A	281	LEU	0	-0.007	-0.002	21.454	0.004	0.004	0.000	0.000	0.000	0.000
129	A	282	LEU	0	-0.021	-0.014	24.665	0.006	0.006	0.000	0.000	0.000	0.000
130	A	283	PRO	0	0.022	0.028	27.875	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	284	ASN	0	0.041	0.013	31.164	-0.006	-0.006	0.000	0.000	0.000	0.000
132	A	285	ASP	-1	-0.866	-0.942	33.543	0.009	0.009	0.000	0.000	0.000	0.000
133	A	286	SER	0	0.007	-0.001	34.809	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	287	ASP	-1	-0.823	-0.915	35.474	-0.007	-0.007	0.000	0.000	0.000	0.000
135	A	288	ASP	-1	-0.909	-0.946	33.318	-0.012	-0.012	0.000	0.000	0.000	0.000
136	A	289	ASN	0	-0.016	-0.021	30.856	-0.005	-0.005	0.000	0.000	0.000	0.000
137	A	290	ARG	1	0.807	0.903	30.562	0.001	0.001	0.000	0.000	0.000	0.000
138	A	291	ALA	0	0.014	0.003	31.592	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	292	LEU	0	-0.035	-0.014	26.764	-0.006	-0.006	0.000	0.000	0.000	0.000
140	A	293	ASN	0	-0.002	-0.009	26.611	-0.004	-0.004	0.000	0.000	0.000	0.000
141	A	294	ARG	1	0.747	0.860	27.425	0.020	0.020	0.000	0.000	0.000	0.000
142	A	295	ARG	1	0.700	0.845	22.048	0.017	0.017	0.000	0.000	0.000	0.000
143	A	296	VAL	0	0.012	-0.007	22.839	0.004	0.004	0.000	0.000	0.000	0.000
144	A	297	GLU	-1	-0.805	-0.899	18.808	-0.052	-0.052	0.000	0.000	0.000	0.000
145	A	298	ILE	0	-0.012	-0.015	15.954	0.007	0.007	0.000	0.000	0.000	0.000
146	A	299	SER	0	-0.033	-0.026	13.689	-0.030	-0.030	0.000	0.000	0.000	0.000
147	A	300	ILE	0	0.007	-0.002	9.648	0.026	0.026	0.000	0.000	0.000	0.000
148	A	301	MET	0	-0.027	-0.027	9.633	-0.026	-0.026	0.000	0.000	0.000	0.000
149	A	302	GLN	0	0.058	0.033	4.566	0.097	0.081	-0.001	-0.008	0.024	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:154:SER)