FMO DATABASE

FMODB ID: 1769Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1478880.668795
FMO2-HF: Nuclear repulsion	1418580.325605
FMO2-HF: Total energy	-60300.34319
FMO2-MP2: Total energy	-60474.70369

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.
0.038	4.174	1.045	-1.709	-3.472	-0.005

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 : 0.027 / q_NPA : -0.001

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	-0.866	-0.934	3.890	2.203	3.607	0.000	-0.517	-0.887	0.002
4	A	157	MET	0	-0.074	-0.014	2.339	-0.535	0.528	0.666	-0.523	-1.206	0.000
5	A	158	GLU	-1	-0.893	-0.942	4.402	-0.778	-0.584	-0.001	-0.025	-0.168	0.000
6	A	159	THR	0	-0.036	-0.040	6.197	0.483	0.483	0.000	0.000	0.000	0.000
7	A	160	LEU	0	-0.024	-0.006	7.945	0.106	0.106	0.000	0.000	0.000	0.000
8	A	161	MET	0	0.006	0.012	8.568	0.047	0.047	0.000	0.000	0.000	0.000
9	A	162	GLU	-1	-0.771	-0.893	10.171	-0.100	-0.100	0.000	0.000	0.000	0.000
10	A	163	SER	0	-0.091	-0.018	12.095	0.092	0.092	0.000	0.000	0.000	0.000
11	A	164	ILE	0	0.001	-0.015	12.028	0.035	0.035	0.000	0.000	0.000	0.000
12	A	165	LYS	1	0.906	0.954	13.602	0.464	0.464	0.000	0.000	0.000	0.000
13	A	166	LYS	1	0.868	0.912	14.962	0.142	0.142	0.000	0.000	0.000	0.000
14	A	167	ALA	0	-0.021	-0.005	17.825	0.020	0.020	0.000	0.000	0.000	0.000
15	A	168	LEU	0	-0.041	-0.015	17.894	0.013	0.013	0.000	0.000	0.000	0.000
16	A	169	GLU	-1	-0.903	-0.939	20.621	-0.115	-0.115	0.000	0.000	0.000	0.000
17	A	170	ARG	1	0.869	0.919	21.861	0.091	0.091	0.000	0.000	0.000	0.000
18	A	171	GLU	-1	-0.803	-0.909	22.670	-0.134	-0.134	0.000	0.000	0.000	0.000
19	A	172	ILE	0	-0.050	-0.017	17.956	-0.020	-0.020	0.000	0.000	0.000	0.000
20	A	173	GLU	-1	-0.874	-0.929	22.264	-0.121	-0.121	0.000	0.000	0.000	0.000
21	A	174	GLN	0	-0.096	-0.041	25.165	0.005	0.005	0.000	0.000	0.000	0.000
22	A	175	GLY	0	0.024	0.018	24.509	0.006	0.006	0.000	0.000	0.000	0.000
23	A	176	ALA	0	-0.086	-0.050	25.525	0.000	0.000	0.000	0.000	0.000	0.000
24	A	177	ILE	0	-0.003	-0.016	19.425	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	178	GLH	0	-0.038	-0.031	16.924	0.013	0.013	0.000	0.000	0.000	0.000
26	A	179	VAL	0	-0.002	-0.010	13.031	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	180	GLU	-1	-0.789	-0.842	12.548	-0.591	-0.591	0.000	0.000	0.000	0.000
28	A	181	ASN	0	0.060	0.009	5.805	0.052	0.052	0.000	0.000	0.000	0.000
29	A	182	LEU	0	-0.007	0.003	9.416	0.036	0.036	0.000	0.000	0.000	0.000
30	A	183	GLY	0	0.016	0.004	8.332	0.115	0.115	0.000	0.000	0.000	0.000
31	A	184	GLN	0	-0.011	-0.022	2.849	-3.407	-1.927	0.381	-0.636	-1.225	-0.007
32	A	185	GLN	0	0.036	0.021	6.456	0.483	0.483	0.000	0.000	0.000	0.000
33	A	186	ILE	0	0.042	0.037	7.966	-0.047	-0.047	0.000	0.000	0.000	0.000
34	A	187	VAL	0	-0.045	-0.011	10.038	0.154	0.154	0.000	0.000	0.000	0.000
35	A	188	ILE	0	0.030	0.014	13.609	0.010	0.010	0.000	0.000	0.000	0.000
36	A	189	ARG	1	0.795	0.872	16.410	0.535	0.535	0.000	0.000	0.000	0.000
37	A	190	MET	0	0.011	0.001	19.850	0.020	0.020	0.000	0.000	0.000	0.000
38	A	191	ARG	1	0.835	0.926	23.191	0.171	0.171	0.000	0.000	0.000	0.000
39	A	192	GLU	-1	-0.674	-0.806	26.478	-0.133	-0.133	0.000	0.000	0.000	0.000
40	A	193	LYS	1	0.986	0.992	29.743	0.140	0.140	0.000	0.000	0.000	0.000
41	A	194	GLY	0	0.009	-0.010	30.389	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	195	ALA	0	0.024	0.027	27.557	0.011	0.011	0.000	0.000	0.000	0.000
43	A	196	PHE	0	0.010	-0.011	27.422	0.006	0.006	0.000	0.000	0.000	0.000
44	A	197	PRO	0	0.000	0.013	32.471	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	198	GLU	-1	-0.854	-0.922	35.096	-0.118	-0.118	0.000	0.000	0.000	0.000
46	A	199	GLY	0	0.008	0.006	35.891	0.006	0.006	0.000	0.000	0.000	0.000
47	A	200	SER	0	-0.012	0.006	35.862	0.004	0.004	0.000	0.000	0.000	0.000
48	A	201	ALA	0	0.075	0.028	32.551	-0.010	-0.010	0.000	0.000	0.000	0.000
49	A	202	PHE	0	-0.037	-0.012	32.646	0.000	0.000	0.000	0.000	0.000	0.000
50	A	203	LEU	0	0.025	0.018	27.870	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	204	GLN	0	-0.022	-0.020	31.698	0.016	0.016	0.000	0.000	0.000	0.000
52	A	205	PRO	0	0.014	-0.008	32.004	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	206	LYS	1	0.957	0.970	31.557	0.080	0.080	0.000	0.000	0.000	0.000
54	A	207	PHE	0	0.056	0.029	24.697	0.002	0.002	0.000	0.000	0.000	0.000
55	A	208	ARG	1	0.848	0.934	27.350	0.077	0.077	0.000	0.000	0.000	0.000
56	A	209	PRO	0	-0.027	-0.025	27.151	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	210	LEU	0	0.035	0.041	22.911	0.003	0.003	0.000	0.000	0.000	0.000
58	A	211	VAL	0	0.038	0.011	22.911	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	212	ARG	1	0.895	0.941	22.164	0.052	0.052	0.000	0.000	0.000	0.000
60	A	213	GLN	0	0.006	0.002	20.898	0.019	0.019	0.000	0.000	0.000	0.000
61	A	214	ILE	0	0.007	-0.003	17.328	0.001	0.001	0.000	0.000	0.000	0.000
62	A	215	ALA	0	0.003	0.003	17.490	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	216	GLU	-1	-0.894	-0.979	18.186	0.022	0.022	0.000	0.000	0.000	0.000
64	A	217	LEU	0	-0.051	-0.017	15.536	0.033	0.033	0.000	0.000	0.000	0.000
65	A	218	VAL	0	0.012	0.007	13.152	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	219	LYS	1	0.786	0.913	13.936	-0.057	-0.057	0.000	0.000	0.000	0.000
67	A	220	ASP	-1	-0.873	-0.932	14.294	0.127	0.127	0.000	0.000	0.000	0.000
68	A	221	VAL	0	-0.030	0.007	8.642	0.095	0.095	0.000	0.000	0.000	0.000
69	A	222	PRO	0	0.019	0.000	8.514	-0.057	-0.057	0.000	0.000	0.000	0.000
70	A	223	GLY	0	0.057	0.039	10.299	-0.122	-0.122	0.000	0.000	0.000	0.000
71	A	224	ILE	0	-0.081	-0.033	11.090	0.070	0.070	0.000	0.000	0.000	0.000
72	A	225	VAL	0	0.018	0.009	13.432	-0.086	-0.086	0.000	0.000	0.000	0.000
73	A	226	ARG	1	0.912	0.955	15.224	0.572	0.572	0.000	0.000	0.000	0.000
74	A	227	VAL	0	0.034	0.018	17.786	-0.036	-0.036	0.000	0.000	0.000	0.000
75	A	228	SER	0	-0.061	-0.033	20.102	0.002	0.002	0.000	0.000	0.000	0.000
76	A	229	GLY	0	0.050	0.042	22.381	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	230	HIS	0	-0.034	-0.029	21.804	0.009	0.009	0.000	0.000	0.000	0.000
78	A	231	THR	0	-0.024	-0.029	27.314	0.013	0.013	0.000	0.000	0.000	0.000
79	A	232	ASP	-1	-0.802	-0.896	29.879	-0.157	-0.157	0.000	0.000	0.000	0.000
80	A	233	ASN	0	0.028	-0.010	32.388	0.003	0.003	0.000	0.000	0.000	0.000
81	A	234	ARG	1	0.828	0.918	34.653	0.126	0.126	0.000	0.000	0.000	0.000
82	A	235	PRO	0	-0.012	-0.013	37.183	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	236	LEU	0	-0.042	-0.011	36.601	0.003	0.003	0.000	0.000	0.000	0.000
84	A	237	ASP	-1	-0.922	-0.944	39.375	-0.078	-0.078	0.000	0.000	0.000	0.000
85	A	238	SER	0	-0.039	-0.042	40.688	0.000	0.000	0.000	0.000	0.000	0.000
86	A	239	GLU	-1	-0.908	-0.952	42.869	-0.063	-0.063	0.000	0.000	0.000	0.000
87	A	240	LEU	0	-0.051	-0.021	40.771	0.001	0.001	0.000	0.000	0.000	0.000
88	A	241	TYR	0	-0.012	-0.007	36.071	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	242	ARG	1	0.881	0.897	36.733	0.092	0.092	0.000	0.000	0.000	0.000
90	A	243	SER	0	0.022	0.007	36.487	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	244	ASN	0	0.051	0.020	33.132	0.007	0.007	0.000	0.000	0.000	0.000
92	A	245	TRP	0	0.028	0.034	28.578	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	246	ASP	-1	-0.794	-0.852	31.832	-0.105	-0.105	0.000	0.000	0.000	0.000
94	A	247	LEU	0	0.019	0.022	32.859	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	248	SER	0	-0.040	-0.035	28.360	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	249	SER	0	-0.003	-0.005	28.411	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	250	GLN	0	0.023	0.000	29.053	0.000	0.000	0.000	0.000	0.000	0.000
98	A	251	ARG	1	0.736	0.861	28.335	0.151	0.151	0.000	0.000	0.000	0.000
99	A	252	ALA	0	0.010	0.010	24.757	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	253	VAL	0	0.003	0.000	25.670	0.000	0.000	0.000	0.000	0.000	0.000
101	A	254	SER	0	-0.022	-0.025	27.821	0.010	0.010	0.000	0.000	0.000	0.000
102	A	255	VAL	0	-0.033	-0.010	22.884	0.007	0.007	0.000	0.000	0.000	0.000
103	A	256	ALA	0	0.021	0.005	23.363	0.006	0.006	0.000	0.000	0.000	0.000
104	A	257	GLN	0	0.031	0.010	24.404	0.011	0.011	0.000	0.000	0.000	0.000
105	A	258	GLU	-1	-0.837	-0.886	26.256	-0.057	-0.057	0.000	0.000	0.000	0.000
106	A	259	MET	0	-0.037	-0.016	18.169	0.003	0.003	0.000	0.000	0.000	0.000
107	A	260	GLU	-1	-0.850	-0.923	23.151	-0.059	-0.059	0.000	0.000	0.000	0.000
108	A	261	LYS	1	0.804	0.904	24.390	0.076	0.076	0.000	0.000	0.000	0.000
109	A	262	VAL	0	-0.046	-0.001	21.109	0.010	0.010	0.000	0.000	0.000	0.000
110	A	263	ARG	1	0.986	0.984	20.899	-0.087	-0.087	0.000	0.000	0.000	0.000
111	A	264	GLY	0	-0.004	-0.006	21.210	0.011	0.011	0.000	0.000	0.000	0.000
112	A	265	PHE	0	0.026	0.007	17.408	0.008	0.008	0.000	0.000	0.000	0.000
113	A	266	SER	0	-0.014	-0.009	18.718	-0.014	-0.014	0.000	0.000	0.000	0.000
114	A	267	HIS	0	0.038	0.003	19.767	-0.017	-0.017	0.000	0.000	0.000	0.000
115	A	268	GLN	0	0.039	0.026	19.846	-0.025	-0.025	0.000	0.000	0.000	0.000
116	A	269	ARG	1	0.781	0.880	12.273	0.077	0.077	0.000	0.000	0.000	0.000
117	A	270	LEU	0	0.008	0.028	17.542	-0.048	-0.048	0.000	0.000	0.000	0.000
118	A	271	ARG	1	0.796	0.886	18.941	0.153	0.153	0.000	0.000	0.000	0.000
119	A	272	VAL	0	0.030	0.015	20.868	-0.019	-0.019	0.000	0.000	0.000	0.000
120	A	273	ARG	1	0.773	0.846	20.626	0.333	0.333	0.000	0.000	0.000	0.000
121	A	274	GLY	0	0.059	0.032	24.820	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	275	MET	0	-0.060	-0.020	23.584	0.004	0.004	0.000	0.000	0.000	0.000
123	A	276	ALA	0	0.014	0.017	27.039	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	277	ASP	-1	-0.867	-0.932	28.576	-0.181	-0.181	0.000	0.000	0.000	0.000
125	A	278	THR	0	-0.062	-0.051	27.422	-0.011	-0.011	0.000	0.000	0.000	0.000
126	A	279	GLU	-1	-0.762	-0.837	21.805	-0.370	-0.370	0.000	0.000	0.000	0.000
127	A	280	PRO	0	-0.015	0.009	24.756	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	281	LEU	0	-0.005	-0.004	21.030	-0.024	-0.024	0.000	0.000	0.000	0.000
129	A	282	LEU	0	-0.021	-0.006	24.162	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	283	PRO	0	0.023	0.028	27.497	0.003	0.003	0.000	0.000	0.000	0.000
131	A	284	ASN	0	0.062	0.035	30.868	0.004	0.004	0.000	0.000	0.000	0.000
132	A	285	ASP	-1	-0.810	-0.895	33.193	-0.157	-0.157	0.000	0.000	0.000	0.000
133	A	286	SER	0	-0.006	-0.015	34.495	0.010	0.010	0.000	0.000	0.000	0.000
134	A	287	ASP	-1	-0.755	-0.866	34.917	-0.127	-0.127	0.000	0.000	0.000	0.000
135	A	288	ASP	-1	-0.888	-0.928	33.264	-0.138	-0.138	0.000	0.000	0.000	0.000
136	A	289	ASN	0	0.007	-0.015	30.454	-0.015	-0.015	0.000	0.000	0.000	0.000
137	A	290	ARG	1	0.736	0.853	30.238	0.124	0.124	0.000	0.000	0.000	0.000
138	A	291	ALA	0	0.009	-0.003	31.274	-0.007	-0.007	0.000	0.000	0.000	0.000
139	A	292	LEU	0	-0.070	-0.034	26.803	-0.007	-0.007	0.000	0.000	0.000	0.000
140	A	293	ASN	0	0.009	-0.015	26.674	-0.036	-0.036	0.000	0.000	0.000	0.000
141	A	294	ARG	1	0.751	0.852	27.421	0.131	0.131	0.000	0.000	0.000	0.000
142	A	295	ARG	1	0.677	0.832	22.041	0.310	0.310	0.000	0.000	0.000	0.000
143	A	296	VAL	0	0.012	-0.002	23.222	0.006	0.006	0.000	0.000	0.000	0.000
144	A	297	GLU	-1	-0.793	-0.892	18.707	-0.425	-0.425	0.000	0.000	0.000	0.000
145	A	298	ILE	0	-0.006	-0.017	16.296	0.033	0.033	0.000	0.000	0.000	0.000
146	A	299	SER	0	-0.034	-0.015	13.461	-0.077	-0.077	0.000	0.000	0.000	0.000
147	A	300	ILE	0	0.016	0.006	9.936	0.083	0.083	0.000	0.000	0.000	0.000
148	A	301	MET	0	-0.031	-0.023	9.806	-0.221	-0.221	0.000	0.000	0.000	0.000
149	A	302	GLN	0	0.057	0.032	4.416	0.687	0.682	-0.001	-0.008	0.014	0.000

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