FMO DATABASE

FMODB ID: 4JGKN

Calculation Name: 4XA1-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XA1

Chain ID: B

ChEMBL ID:

UniProt ID: Q15691

Base Structure: X-ray

Registration Date: 2023-09-23

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	155
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-951273.336153
FMO2-HF: Nuclear repulsion	888013.334751
FMO2-HF: Total energy	-63260.001402
FMO2-MP2: Total energy	-63445.60226

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(B:2:PRO)

Summations of interaction energy for fragment #1(B:2:PRO)

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.
6.223	-8.538	39.805	-14.824	-10.22	-0.048

Interaction energy analysis for fragmet #1(B:2:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.090

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	B	4	LYS	1	0.924	0.973	3.759	2.227	3.532	-0.009	-0.449	-0.847	0.002
4	B	5	PRO	0	-0.007	-0.022	5.495	0.423	0.423	0.000	0.000	0.000	0.000
5	B	6	GLU	-1	-0.974	-0.979	8.533	-0.645	-0.645	0.000	0.000	0.000	0.000
6	B	7	GLU	-1	-0.767	-0.908	5.467	-2.542	-2.542	0.000	0.000	0.000	0.000
7	B	8	HIS	0	-0.041	-0.021	7.862	0.248	0.248	0.000	0.000	0.000	0.000
8	B	9	GLU	-1	-0.887	-0.950	9.318	-0.148	-0.148	0.000	0.000	0.000	0.000
9	B	10	ASP	-1	-0.885	-0.935	12.498	-0.318	-0.318	0.000	0.000	0.000	0.000
10	B	11	ILE	0	-0.107	-0.056	9.211	0.112	0.112	0.000	0.000	0.000	0.000
11	B	12	LEU	0	-0.060	-0.039	12.803	0.085	0.085	0.000	0.000	0.000	0.000
12	B	13	ASN	0	0.015	0.014	15.172	0.048	0.048	0.000	0.000	0.000	0.000
13	B	14	LYS	1	0.950	0.983	15.523	0.045	0.045	0.000	0.000	0.000	0.000
14	B	15	LEU	0	-0.074	-0.047	14.717	0.032	0.032	0.000	0.000	0.000	0.000
15	B	16	LEU	0	-0.044	0.001	18.580	0.016	0.016	0.000	0.000	0.000	0.000
16	B	17	ASP	-1	-0.812	-0.912	21.096	-0.026	-0.026	0.000	0.000	0.000	0.000
17	B	18	PRO	0	-0.022	-0.006	23.314	0.013	0.013	0.000	0.000	0.000	0.000
18	B	19	GLU	-1	-0.980	-0.975	25.593	-0.010	-0.010	0.000	0.000	0.000	0.000
19	B	20	LEU	0	-0.023	0.007	19.172	0.007	0.007	0.000	0.000	0.000	0.000
20	B	21	ALA	0	0.045	0.012	23.214	0.011	0.011	0.000	0.000	0.000	0.000
21	B	22	GLN	0	0.017	-0.003	22.402	-0.008	-0.008	0.000	0.000	0.000	0.000
22	B	23	SER	0	-0.043	-0.034	21.685	0.011	0.011	0.000	0.000	0.000	0.000
23	B	24	GLU	-1	-0.846	-0.934	18.597	0.044	0.044	0.000	0.000	0.000	0.000
24	B	25	ARG	1	0.847	0.933	17.481	-0.024	-0.024	0.000	0.000	0.000	0.000
25	B	26	THR	0	-0.065	-0.053	17.424	0.012	0.012	0.000	0.000	0.000	0.000
26	B	27	GLU	-1	-0.956	-0.974	14.536	0.210	0.210	0.000	0.000	0.000	0.000
27	B	28	ALA	0	0.024	0.014	13.256	0.068	0.068	0.000	0.000	0.000	0.000
28	B	29	LEU	0	0.019	0.001	12.474	0.006	0.006	0.000	0.000	0.000	0.000
29	B	30	GLN	0	-0.026	-0.020	12.959	0.102	0.102	0.000	0.000	0.000	0.000
30	B	31	GLN	0	0.023	0.031	9.151	0.072	0.072	0.000	0.000	0.000	0.000
31	B	32	LEU	0	0.027	0.018	7.800	0.223	0.223	0.000	0.000	0.000	0.000
32	B	33	ARG	1	0.907	0.960	9.453	-0.327	-0.327	0.000	0.000	0.000	0.000
33	B	34	VAL	0	-0.008	-0.015	7.643	0.036	0.036	0.000	0.000	0.000	0.000
34	B	35	ASN	0	0.040	0.024	3.192	-0.263	0.516	0.096	-0.413	-0.462	-0.004
35	B	36	TYR	0	0.019	-0.016	5.689	0.137	0.137	0.000	0.000	0.000	0.000
36	B	37	GLY	0	0.002	0.000	8.199	-0.088	-0.088	0.000	0.000	0.000	0.000
37	B	38	SER	0	-0.053	-0.030	8.037	-0.154	-0.154	0.000	0.000	0.000	0.000
38	B	39	PHE	0	0.096	0.115	1.851	6.600	-10.245	39.718	-13.962	-8.911	-0.046
39	B	40	VAL	0	-0.073	-0.004	5.594	-0.307	-0.307	0.000	0.000	0.000	0.000
40	B	41	SER	0	-0.038	-0.050	7.227	-0.162	-0.162	0.000	0.000	0.000	0.000
41	B	42	GLU	-1	-0.886	-0.920	7.630	0.379	0.379	0.000	0.000	0.000	0.000
42	B	43	TYR	0	-0.063	-0.044	7.008	-0.141	-0.141	0.000	0.000	0.000	0.000
43	B	44	ASN	0	-0.064	-0.030	10.148	-0.024	-0.024	0.000	0.000	0.000	0.000
44	B	45	ASP	-1	-0.929	-0.966	13.032	0.125	0.125	0.000	0.000	0.000	0.000
45	B	46	LEU	0	0.015	0.017	10.635	-0.039	-0.039	0.000	0.000	0.000	0.000
46	B	47	THR	0	0.014	0.014	14.194	-0.039	-0.039	0.000	0.000	0.000	0.000
47	B	48	LYS	1	0.989	0.965	16.067	0.113	0.113	0.000	0.000	0.000	0.000
48	B	49	SER	0	-0.062	-0.024	17.064	0.004	0.004	0.000	0.000	0.000	0.000
49	B	1173	LYS	1	0.880	0.969	16.168	-0.129	-0.129	0.000	0.000	0.000	0.000
50	B	1174	MET	0	0.118	0.035	10.393	-0.001	-0.001	0.000	0.000	0.000	0.000
51	B	1175	ARG	1	0.930	0.967	15.819	0.041	0.041	0.000	0.000	0.000	0.000
52	B	1176	ARG	1	0.964	0.988	18.409	-0.043	-0.043	0.000	0.000	0.000	0.000
53	B	1177	ASP	-1	-0.817	-0.908	15.906	0.118	0.118	0.000	0.000	0.000	0.000
54	B	1178	LEU	0	-0.023	-0.003	15.671	0.006	0.006	0.000	0.000	0.000	0.000
55	B	1179	GLU	-1	-0.969	-0.997	17.292	0.011	0.011	0.000	0.000	0.000	0.000
56	B	1180	GLU	-1	-0.848	-0.932	20.353	0.086	0.086	0.000	0.000	0.000	0.000
57	B	1181	ALA	0	-0.022	0.000	17.556	0.006	0.006	0.000	0.000	0.000	0.000
58	B	1182	THR	0	-0.022	-0.014	19.690	-0.002	-0.002	0.000	0.000	0.000	0.000
59	B	1183	LEU	0	0.007	0.014	21.921	-0.002	-0.002	0.000	0.000	0.000	0.000
60	B	1184	GLN	0	-0.039	-0.017	22.135	-0.004	-0.004	0.000	0.000	0.000	0.000
61	B	1185	HIS	0	0.013	-0.001	18.160	0.004	0.004	0.000	0.000	0.000	0.000
62	B	1186	GLU	-1	-0.959	-0.974	23.614	0.022	0.022	0.000	0.000	0.000	0.000
63	B	1187	ALA	0	0.000	0.000	26.990	-0.003	-0.003	0.000	0.000	0.000	0.000
64	B	1188	THR	0	-0.020	-0.012	25.056	0.002	0.002	0.000	0.000	0.000	0.000
65	B	1189	ALA	0	-0.028	-0.025	26.879	-0.002	-0.002	0.000	0.000	0.000	0.000
66	B	1190	ALA	0	-0.043	-0.023	28.418	-0.004	-0.004	0.000	0.000	0.000	0.000
67	B	1191	ALA	0	0.019	0.015	30.847	-0.003	-0.003	0.000	0.000	0.000	0.000
68	B	1192	LEU	0	-0.033	-0.007	28.738	-0.001	-0.001	0.000	0.000	0.000	0.000
69	B	1193	ARG	1	0.971	0.970	30.231	-0.036	-0.036	0.000	0.000	0.000	0.000
70	B	1194	LYS	1	0.876	0.955	34.110	-0.037	-0.037	0.000	0.000	0.000	0.000
71	B	1195	LYS	1	0.982	0.980	33.488	-0.062	-0.062	0.000	0.000	0.000	0.000
72	B	1196	HIS	0	0.035	0.014	31.969	-0.002	-0.002	0.000	0.000	0.000	0.000
73	B	1197	ALA	0	-0.026	-0.013	37.037	-0.002	-0.002	0.000	0.000	0.000	0.000
74	B	1198	ASP	-1	-0.854	-0.927	39.746	0.035	0.035	0.000	0.000	0.000	0.000
75	B	1199	SER	0	-0.010	-0.009	39.704	0.000	0.000	0.000	0.000	0.000	0.000
76	B	1200	VAL	0	-0.032	-0.018	40.102	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	1201	ALA	0	-0.011	0.001	42.763	-0.002	-0.002	0.000	0.000	0.000	0.000
78	B	1202	GLU	-1	-0.892	-0.946	44.834	0.034	0.034	0.000	0.000	0.000	0.000
79	B	1203	LEU	0	-0.027	-0.019	43.149	-0.001	-0.001	0.000	0.000	0.000	0.000
80	B	1204	GLY	0	0.000	-0.002	46.928	-0.001	-0.001	0.000	0.000	0.000	0.000
81	B	1205	GLU	-1	-0.914	-0.956	48.793	0.025	0.025	0.000	0.000	0.000	0.000
82	B	1206	GLN	0	-0.043	-0.023	48.834	-0.001	-0.001	0.000	0.000	0.000	0.000
83	B	1207	ILE	0	-0.039	-0.017	49.079	-0.001	-0.001	0.000	0.000	0.000	0.000
84	B	1208	ASP	-1	-0.873	-0.926	52.848	0.016	0.016	0.000	0.000	0.000	0.000
85	B	1209	ASN	0	-0.046	-0.031	54.915	-0.002	-0.002	0.000	0.000	0.000	0.000
86	B	1210	LEU	0	0.017	0.006	53.915	-0.001	-0.001	0.000	0.000	0.000	0.000
87	B	1211	GLN	0	0.008	0.009	54.748	-0.001	-0.001	0.000	0.000	0.000	0.000
88	B	1212	ARG	1	0.933	0.965	56.947	-0.018	-0.018	0.000	0.000	0.000	0.000
89	B	1213	VAL	0	-0.055	-0.023	60.316	-0.001	-0.001	0.000	0.000	0.000	0.000
90	B	1214	LYS	1	0.950	0.967	60.022	-0.013	-0.013	0.000	0.000	0.000	0.000
91	B	1215	GLN	0	-0.024	-0.030	62.540	0.000	0.000	0.000	0.000	0.000	0.000
92	B	1216	LYS	1	0.907	0.980	64.743	-0.015	-0.015	0.000	0.000	0.000	0.000
93	B	1217	LEU	0	0.049	0.025	64.037	0.000	0.000	0.000	0.000	0.000	0.000
94	B	1218	GLU	-1	-0.941	-0.967	65.471	0.011	0.011	0.000	0.000	0.000	0.000
95	B	1219	LYS	1	0.934	1.000	68.365	-0.013	-0.013	0.000	0.000	0.000	0.000
96	B	1220	GLU	-1	-0.828	-0.932	70.402	0.013	0.013	0.000	0.000	0.000	0.000
97	B	1221	LYS	1	0.942	0.988	69.484	-0.011	-0.011	0.000	0.000	0.000	0.000
98	B	1222	SER	0	-0.079	-0.088	71.606	0.000	0.000	0.000	0.000	0.000	0.000
99	B	1223	GLU	-1	-0.950	-0.964	74.215	0.009	0.009	0.000	0.000	0.000	0.000
100	B	1224	PHE	0	-0.032	-0.023	74.778	0.000	0.000	0.000	0.000	0.000	0.000
101	B	1225	LYS	1	0.879	0.955	74.257	-0.009	-0.009	0.000	0.000	0.000	0.000
102	B	1226	LEU	0	0.046	0.003	77.498	0.000	0.000	0.000	0.000	0.000	0.000
103	B	1227	GLU	-1	-0.839	-0.901	80.523	0.008	0.008	0.000	0.000	0.000	0.000
104	B	1228	LEU	0	-0.024	-0.002	79.806	0.000	0.000	0.000	0.000	0.000	0.000
105	B	1229	ASP	-1	-0.922	-0.970	82.886	0.008	0.008	0.000	0.000	0.000	0.000
106	B	1230	ASP	-1	-1.029	-0.969	84.690	0.007	0.007	0.000	0.000	0.000	0.000
107	B	1231	VAL	0	0.022	-0.020	86.205	0.000	0.000	0.000	0.000	0.000	0.000
108	B	1232	THR	0	-0.030	-0.040	85.463	0.000	0.000	0.000	0.000	0.000	0.000
109	B	1233	SER	0	-0.040	-0.038	88.123	0.000	0.000	0.000	0.000	0.000	0.000
110	B	1234	ASN	0	-0.012	0.010	90.048	0.000	0.000	0.000	0.000	0.000	0.000
111	B	1235	MET	0	0.060	0.026	90.902	0.000	0.000	0.000	0.000	0.000	0.000
112	B	1236	GLU	-1	-0.933	-0.960	89.831	0.007	0.007	0.000	0.000	0.000	0.000
113	B	1237	GLN	0	-0.086	-0.056	93.935	0.000	0.000	0.000	0.000	0.000	0.000
114	B	1238	ILE	0	0.009	0.001	95.376	0.000	0.000	0.000	0.000	0.000	0.000
115	B	211	GLU	-1	-0.929	-0.949	94.842	0.007	0.007	0.000	0.000	0.000	0.000
116	B	212	LYS	1	0.913	0.961	95.717	-0.006	-0.006	0.000	0.000	0.000	0.000
117	B	213	GLU	-1	-0.885	-0.923	100.147	0.006	0.006	0.000	0.000	0.000	0.000
118	B	214	ARG	1	0.873	0.915	98.193	-0.007	-0.007	0.000	0.000	0.000	0.000
119	B	215	ASP	-1	-0.862	-0.925	100.419	0.006	0.006	0.000	0.000	0.000	0.000
120	B	216	PHE	0	-0.055	-0.025	103.513	0.000	0.000	0.000	0.000	0.000	0.000
121	B	217	TYR	0	-0.071	-0.056	105.323	0.000	0.000	0.000	0.000	0.000	0.000
122	B	218	PHE	0	0.050	0.029	105.757	0.000	0.000	0.000	0.000	0.000	0.000
123	B	219	GLY	0	0.012	0.005	107.570	0.000	0.000	0.000	0.000	0.000	0.000
124	B	220	LYS	1	0.872	0.931	109.288	-0.005	-0.005	0.000	0.000	0.000	0.000
125	B	221	LEU	0	0.021	0.010	109.613	0.000	0.000	0.000	0.000	0.000	0.000
126	B	222	ARG	1	0.989	1.002	107.905	-0.005	-0.005	0.000	0.000	0.000	0.000
127	B	223	ASN	0	-0.046	-0.026	112.695	0.000	0.000	0.000	0.000	0.000	0.000
128	B	224	ILE	0	-0.008	0.000	115.318	0.000	0.000	0.000	0.000	0.000	0.000
129	B	225	GLU	-1	-0.845	-0.914	115.459	0.005	0.005	0.000	0.000	0.000	0.000
130	B	226	LEU	0	0.022	0.011	115.809	0.000	0.000	0.000	0.000	0.000	0.000
131	B	227	ILE	0	0.005	0.008	118.519	0.000	0.000	0.000	0.000	0.000	0.000
132	B	228	CYS	0	-0.049	-0.012	120.329	0.000	0.000	0.000	0.000	0.000	0.000
133	B	229	GLN	0	-0.031	-0.028	119.614	0.000	0.000	0.000	0.000	0.000	0.000
134	B	230	GLU	-1	-1.036	-1.011	121.736	0.004	0.004	0.000	0.000	0.000	0.000
135	B	231	ASN	0	-0.078	-0.057	124.666	0.000	0.000	0.000	0.000	0.000	0.000
136	B	232	GLU	-1	-0.875	-0.917	123.742	0.005	0.005	0.000	0.000	0.000	0.000
137	B	233	GLY	0	-0.048	-0.024	126.672	0.000	0.000	0.000	0.000	0.000	0.000
138	B	234	GLU	-1	-0.987	-0.996	130.064	0.004	0.004	0.000	0.000	0.000	0.000
139	B	235	ASN	0	-0.109	-0.053	129.922	0.000	0.000	0.000	0.000	0.000	0.000
140	B	236	ASP	-1	-0.816	-0.911	128.659	0.004	0.004	0.000	0.000	0.000	0.000
141	B	237	PRO	0	0.030	0.012	128.254	0.000	0.000	0.000	0.000	0.000	0.000
142	B	238	VAL	0	-0.043	-0.031	125.670	0.000	0.000	0.000	0.000	0.000	0.000
143	B	239	LEU	0	0.067	0.029	124.205	0.000	0.000	0.000	0.000	0.000	0.000
144	B	240	GLN	0	0.007	0.007	123.471	0.000	0.000	0.000	0.000	0.000	0.000
145	B	241	ARG	1	0.902	0.960	122.664	-0.005	-0.005	0.000	0.000	0.000	0.000
146	B	242	ILE	0	-0.040	-0.021	119.599	0.000	0.000	0.000	0.000	0.000	0.000
147	B	243	VAL	0	0.058	0.018	118.873	0.000	0.000	0.000	0.000	0.000	0.000
148	B	244	ASP	-1	-0.937	-0.965	118.239	0.006	0.006	0.000	0.000	0.000	0.000
149	B	245	ILE	0	-0.094	-0.051	115.172	0.000	0.000	0.000	0.000	0.000	0.000
150	B	246	LEU	0	-0.063	-0.018	114.264	0.000	0.000	0.000	0.000	0.000	0.000
151	B	247	TYR	0	-0.077	-0.048	113.062	0.000	0.000	0.000	0.000	0.000	0.000
152	B	248	ALA	0	-0.034	0.003	113.775	0.000	0.000	0.000	0.000	0.000	0.000
153	B	249	THR	0	-0.088	-0.060	108.277	0.000	0.000	0.000	0.000	0.000	0.000
154	B	250	ASP	-1	-0.945	-0.978	107.107	0.007	0.007	0.000	0.000	0.000	0.000
155	B	251	GLU	-1	-1.007	-0.979	102.221	0.008	0.008	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:2:PRO)