FMO DATABASE

FMODB ID: YV772

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	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	155
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-952262.840739
FMO2-HF: Nuclear repulsion	888999.86321
FMO2-HF: Total energy	-63262.977529
FMO2-MP2: Total energy	-63448.36681

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.
-5.598	-1.265	5.983	-3.781	-6.537	-0.025

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 : -0.060 / q_NPA : -0.048

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	0.801	0.882	3.859	0.205	1.336	-0.004	-0.391	-0.737	0.002
4	B	5	PRO	0	-0.016	-0.021	5.743	0.354	0.354	0.000	0.000	0.000	0.000
5	B	6	GLU	-1	-0.855	-0.922	8.665	-0.534	-0.534	0.000	0.000	0.000	0.000
6	B	7	GLU	-1	-0.772	-0.875	6.428	-1.102	-1.102	0.000	0.000	0.000	0.000
7	B	8	HIS	0	-0.021	-0.014	7.514	0.152	0.152	0.000	0.000	0.000	0.000
8	B	9	GLU	-1	-0.906	-0.956	9.199	-0.142	-0.142	0.000	0.000	0.000	0.000
9	B	10	ASP	-1	-0.880	-0.939	12.652	-0.063	-0.063	0.000	0.000	0.000	0.000
10	B	11	ILE	0	-0.022	-0.009	8.930	0.080	0.080	0.000	0.000	0.000	0.000
11	B	12	LEU	0	-0.050	-0.029	12.732	0.053	0.053	0.000	0.000	0.000	0.000
12	B	13	ASN	0	-0.056	-0.027	14.895	0.036	0.036	0.000	0.000	0.000	0.000
13	B	14	LYS	1	0.800	0.879	15.288	-0.103	-0.103	0.000	0.000	0.000	0.000
14	B	15	LEU	0	-0.075	-0.053	14.240	0.023	0.023	0.000	0.000	0.000	0.000
15	B	16	LEU	0	-0.046	-0.003	18.070	0.006	0.006	0.000	0.000	0.000	0.000
16	B	17	ASP	-1	-0.828	-0.906	20.835	0.007	0.007	0.000	0.000	0.000	0.000
17	B	18	PRO	0	-0.030	-0.022	22.991	0.012	0.012	0.000	0.000	0.000	0.000
18	B	19	GLU	-1	-1.004	-1.009	25.568	0.015	0.015	0.000	0.000	0.000	0.000
19	B	20	LEU	0	-0.005	0.021	19.283	0.010	0.010	0.000	0.000	0.000	0.000
20	B	21	ALA	0	0.006	0.002	23.390	0.004	0.004	0.000	0.000	0.000	0.000
21	B	22	GLN	0	0.060	0.019	21.577	-0.003	-0.003	0.000	0.000	0.000	0.000
22	B	23	SER	0	-0.016	0.001	21.613	0.007	0.007	0.000	0.000	0.000	0.000
23	B	24	GLU	-1	-0.810	-0.902	18.399	0.124	0.124	0.000	0.000	0.000	0.000
24	B	25	ARG	1	0.871	0.949	17.297	-0.031	-0.031	0.000	0.000	0.000	0.000
25	B	26	THR	0	-0.059	-0.049	17.454	-0.002	-0.002	0.000	0.000	0.000	0.000
26	B	27	GLU	-1	-0.840	-0.908	14.362	0.258	0.258	0.000	0.000	0.000	0.000
27	B	28	ALA	0	0.071	0.042	12.894	0.070	0.070	0.000	0.000	0.000	0.000
28	B	29	LEU	0	0.010	-0.001	12.115	0.005	0.005	0.000	0.000	0.000	0.000
29	B	30	GLN	0	-0.035	-0.011	12.594	-0.009	-0.009	0.000	0.000	0.000	0.000
30	B	31	GLN	0	-0.017	-0.012	8.749	0.045	0.045	0.000	0.000	0.000	0.000
31	B	32	LEU	0	0.036	0.021	7.621	0.144	0.144	0.000	0.000	0.000	0.000
32	B	33	ARG	1	0.872	0.932	8.737	-0.231	-0.231	0.000	0.000	0.000	0.000
33	B	34	VAL	0	-0.004	-0.007	7.068	-0.050	-0.050	0.000	0.000	0.000	0.000
34	B	35	ASN	0	0.048	0.027	2.971	-1.086	-0.045	0.245	-0.576	-0.711	-0.005
35	B	36	TYR	0	-0.022	-0.038	5.322	-0.381	-0.283	-0.001	-0.001	-0.096	0.000
36	B	37	GLY	0	-0.001	-0.008	7.994	-0.067	-0.067	0.000	0.000	0.000	0.000
37	B	38	SER	0	-0.024	-0.009	6.224	-0.019	-0.019	0.000	0.000	0.000	0.000
38	B	39	PHE	0	0.041	0.025	2.232	-3.489	-1.426	5.743	-2.813	-4.993	-0.022
39	B	40	VAL	0	-0.030	-0.001	5.382	-0.109	-0.109	0.000	0.000	0.000	0.000
40	B	41	SER	0	-0.031	-0.026	7.265	-0.016	-0.016	0.000	0.000	0.000	0.000
41	B	42	GLU	-1	-0.910	-0.944	7.516	-0.157	-0.157	0.000	0.000	0.000	0.000
42	B	43	TYR	0	-0.039	-0.032	6.519	-0.013	-0.013	0.000	0.000	0.000	0.000
43	B	44	ASN	0	-0.036	0.001	9.675	0.026	0.026	0.000	0.000	0.000	0.000
44	B	45	ASP	-1	-0.821	-0.900	12.876	-0.060	-0.060	0.000	0.000	0.000	0.000
45	B	46	LEU	0	0.023	0.034	9.642	0.012	0.012	0.000	0.000	0.000	0.000
46	B	47	THR	0	-0.002	-0.005	13.295	-0.019	-0.019	0.000	0.000	0.000	0.000
47	B	48	LYS	1	0.971	0.961	15.970	0.195	0.195	0.000	0.000	0.000	0.000
48	B	49	SER	0	-0.032	-0.011	17.153	0.009	0.009	0.000	0.000	0.000	0.000
49	B	1173	LYS	1	0.805	0.899	14.199	0.068	0.068	0.000	0.000	0.000	0.000
50	B	1174	MET	0	0.087	0.045	10.949	0.009	0.009	0.000	0.000	0.000	0.000
51	B	1175	ARG	1	0.846	0.935	15.205	0.112	0.112	0.000	0.000	0.000	0.000
52	B	1176	ARG	1	0.994	0.996	18.417	0.058	0.058	0.000	0.000	0.000	0.000
53	B	1177	ASP	-1	-0.845	-0.924	15.398	-0.043	-0.043	0.000	0.000	0.000	0.000
54	B	1178	LEU	0	-0.008	0.002	15.403	0.011	0.011	0.000	0.000	0.000	0.000
55	B	1179	GLU	-1	-0.929	-0.972	17.517	-0.051	-0.051	0.000	0.000	0.000	0.000
56	B	1180	GLU	-1	-0.850	-0.915	20.510	0.017	0.017	0.000	0.000	0.000	0.000
57	B	1181	ALA	0	-0.004	-0.001	17.750	0.008	0.008	0.000	0.000	0.000	0.000
58	B	1182	THR	0	-0.070	-0.043	19.824	0.006	0.006	0.000	0.000	0.000	0.000
59	B	1183	LEU	0	0.035	0.016	21.875	0.006	0.006	0.000	0.000	0.000	0.000
60	B	1184	GLN	0	-0.039	-0.028	22.317	0.007	0.007	0.000	0.000	0.000	0.000
61	B	1185	HIS	0	0.008	0.015	17.813	0.012	0.012	0.000	0.000	0.000	0.000
62	B	1186	GLU	-1	-0.950	-0.975	23.391	-0.007	-0.007	0.000	0.000	0.000	0.000
63	B	1187	ALA	0	-0.004	0.000	26.800	0.002	0.002	0.000	0.000	0.000	0.000
64	B	1188	THR	0	-0.027	-0.024	24.770	0.004	0.004	0.000	0.000	0.000	0.000
65	B	1189	ALA	0	-0.008	-0.011	26.677	0.002	0.002	0.000	0.000	0.000	0.000
66	B	1190	ALA	0	-0.059	-0.035	28.325	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	1191	ALA	0	0.009	0.006	30.485	0.000	0.000	0.000	0.000	0.000	0.000
68	B	1192	LEU	0	-0.024	-0.009	28.528	0.001	0.001	0.000	0.000	0.000	0.000
69	B	1193	ARG	1	0.955	0.979	30.533	-0.012	-0.012	0.000	0.000	0.000	0.000
70	B	1194	LYS	1	0.819	0.891	33.875	-0.020	-0.020	0.000	0.000	0.000	0.000
71	B	1195	LYS	1	0.992	0.992	33.590	-0.037	-0.037	0.000	0.000	0.000	0.000
72	B	1196	HIS	0	0.035	0.025	32.130	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	1197	ALA	0	-0.006	-0.001	37.042	-0.001	-0.001	0.000	0.000	0.000	0.000
74	B	1198	ASP	-1	-0.812	-0.881	39.759	0.019	0.019	0.000	0.000	0.000	0.000
75	B	1199	SER	0	0.015	-0.007	39.162	0.000	0.000	0.000	0.000	0.000	0.000
76	B	1200	VAL	0	-0.041	-0.022	40.257	0.000	0.000	0.000	0.000	0.000	0.000
77	B	1201	ALA	0	-0.015	0.000	42.830	-0.001	-0.001	0.000	0.000	0.000	0.000
78	B	1202	GLU	-1	-0.909	-0.952	44.559	0.024	0.024	0.000	0.000	0.000	0.000
79	B	1203	LEU	0	-0.030	-0.006	42.822	0.000	0.000	0.000	0.000	0.000	0.000
80	B	1204	GLY	0	-0.008	-0.004	46.829	-0.001	-0.001	0.000	0.000	0.000	0.000
81	B	1205	GLU	-1	-0.851	-0.940	48.689	0.016	0.016	0.000	0.000	0.000	0.000
82	B	1206	GLN	0	0.006	0.001	48.041	0.000	0.000	0.000	0.000	0.000	0.000
83	B	1207	ILE	0	-0.043	-0.018	48.746	-0.001	-0.001	0.000	0.000	0.000	0.000
84	B	1208	ASP	-1	-0.832	-0.904	52.723	0.011	0.011	0.000	0.000	0.000	0.000
85	B	1209	ASN	0	-0.033	-0.013	54.449	-0.002	-0.002	0.000	0.000	0.000	0.000
86	B	1210	LEU	0	-0.012	-0.009	53.749	0.000	0.000	0.000	0.000	0.000	0.000
87	B	1211	GLN	0	-0.046	-0.013	54.494	-0.001	-0.001	0.000	0.000	0.000	0.000
88	B	1212	ARG	1	0.843	0.902	56.153	-0.012	-0.012	0.000	0.000	0.000	0.000
89	B	1213	VAL	0	-0.015	-0.003	60.446	0.000	0.000	0.000	0.000	0.000	0.000
90	B	1214	LYS	1	0.901	0.942	60.482	-0.012	-0.012	0.000	0.000	0.000	0.000
91	B	1215	GLN	0	-0.031	-0.020	62.609	0.000	0.000	0.000	0.000	0.000	0.000
92	B	1216	LYS	1	0.853	0.918	64.812	-0.011	-0.011	0.000	0.000	0.000	0.000
93	B	1217	LEU	0	0.033	0.016	64.052	0.000	0.000	0.000	0.000	0.000	0.000
94	B	1218	GLU	-1	-0.841	-0.915	65.401	0.011	0.011	0.000	0.000	0.000	0.000
95	B	1219	LYS	1	0.802	0.902	68.047	-0.009	-0.009	0.000	0.000	0.000	0.000
96	B	1220	GLU	-1	-0.746	-0.867	70.521	0.010	0.010	0.000	0.000	0.000	0.000
97	B	1221	LYS	1	0.850	0.937	68.050	-0.011	-0.011	0.000	0.000	0.000	0.000
98	B	1222	SER	0	-0.073	-0.058	71.374	0.000	0.000	0.000	0.000	0.000	0.000
99	B	1223	GLU	-1	-0.860	-0.913	73.968	0.008	0.008	0.000	0.000	0.000	0.000
100	B	1224	PHE	0	0.037	-0.002	74.091	0.000	0.000	0.000	0.000	0.000	0.000
101	B	1225	LYS	1	0.899	0.960	74.991	-0.009	-0.009	0.000	0.000	0.000	0.000
102	B	1226	LEU	0	0.001	-0.015	77.754	0.000	0.000	0.000	0.000	0.000	0.000
103	B	1227	GLU	-1	-0.875	-0.916	80.581	0.007	0.007	0.000	0.000	0.000	0.000
104	B	1228	LEU	0	-0.050	-0.021	79.928	0.000	0.000	0.000	0.000	0.000	0.000
105	B	1229	ASP	-1	-0.930	-0.974	82.859	0.007	0.007	0.000	0.000	0.000	0.000
106	B	1230	ASP	-1	-0.917	-0.913	84.904	0.006	0.006	0.000	0.000	0.000	0.000
107	B	1231	VAL	0	0.044	0.018	86.411	0.000	0.000	0.000	0.000	0.000	0.000
108	B	1232	THR	0	-0.022	-0.021	85.951	0.000	0.000	0.000	0.000	0.000	0.000
109	B	1233	SER	0	-0.030	-0.035	88.242	0.000	0.000	0.000	0.000	0.000	0.000
110	B	1234	ASN	0	-0.015	-0.008	90.151	0.000	0.000	0.000	0.000	0.000	0.000
111	B	1235	MET	0	-0.008	0.001	91.157	0.000	0.000	0.000	0.000	0.000	0.000
112	B	1236	GLU	-1	-0.837	-0.913	91.258	0.006	0.006	0.000	0.000	0.000	0.000
113	B	1237	GLN	0	-0.051	-0.026	93.388	0.000	0.000	0.000	0.000	0.000	0.000
114	B	1238	ILE	0	0.037	0.018	95.280	0.000	0.000	0.000	0.000	0.000	0.000
115	B	211	GLU	-1	-0.882	-0.916	94.340	0.007	0.007	0.000	0.000	0.000	0.000
116	B	212	LYS	1	0.809	0.881	95.011	-0.006	-0.006	0.000	0.000	0.000	0.000
117	B	213	GLU	-1	-0.900	-0.909	100.383	0.005	0.005	0.000	0.000	0.000	0.000
118	B	214	ARG	1	0.792	0.846	97.341	-0.007	-0.007	0.000	0.000	0.000	0.000
119	B	215	ASP	-1	-0.812	-0.878	100.742	0.006	0.006	0.000	0.000	0.000	0.000
120	B	216	PHE	0	-0.016	-0.015	103.887	0.000	0.000	0.000	0.000	0.000	0.000
121	B	217	TYR	0	-0.099	-0.096	105.182	0.000	0.000	0.000	0.000	0.000	0.000
122	B	218	PHE	0	0.062	0.028	106.135	0.000	0.000	0.000	0.000	0.000	0.000
123	B	219	GLY	0	-0.021	-0.011	107.675	0.000	0.000	0.000	0.000	0.000	0.000
124	B	220	LYS	1	0.804	0.919	109.368	-0.005	-0.005	0.000	0.000	0.000	0.000
125	B	221	LEU	0	0.029	0.020	109.683	0.000	0.000	0.000	0.000	0.000	0.000
126	B	222	ARG	1	0.984	0.986	108.665	-0.005	-0.005	0.000	0.000	0.000	0.000
127	B	223	ASN	0	-0.015	-0.007	113.066	0.000	0.000	0.000	0.000	0.000	0.000
128	B	224	ILE	0	-0.010	-0.001	115.443	0.000	0.000	0.000	0.000	0.000	0.000
129	B	225	GLU	-1	-0.833	-0.890	115.493	0.005	0.005	0.000	0.000	0.000	0.000
130	B	226	LEU	0	0.020	0.007	115.069	0.000	0.000	0.000	0.000	0.000	0.000
131	B	227	ILE	0	-0.004	0.005	118.657	0.000	0.000	0.000	0.000	0.000	0.000
132	B	228	CYS	0	-0.060	-0.022	120.632	0.000	0.000	0.000	0.000	0.000	0.000
133	B	229	GLN	0	-0.012	-0.026	119.534	0.000	0.000	0.000	0.000	0.000	0.000
134	B	230	GLU	-1	-1.010	-1.002	122.195	0.004	0.004	0.000	0.000	0.000	0.000
135	B	231	ASN	0	-0.075	-0.050	124.568	0.000	0.000	0.000	0.000	0.000	0.000
136	B	232	GLU	-1	-0.897	-0.925	123.588	0.005	0.005	0.000	0.000	0.000	0.000
137	B	233	GLY	0	-0.026	-0.015	126.820	0.000	0.000	0.000	0.000	0.000	0.000
138	B	234	GLU	-1	-0.987	-0.990	130.279	0.004	0.004	0.000	0.000	0.000	0.000
139	B	235	ASN	0	-0.123	-0.076	129.883	0.000	0.000	0.000	0.000	0.000	0.000
140	B	236	ASP	-1	-0.741	-0.857	128.749	0.004	0.004	0.000	0.000	0.000	0.000
141	B	237	PRO	0	-0.002	-0.007	128.421	0.000	0.000	0.000	0.000	0.000	0.000
142	B	238	VAL	0	-0.106	-0.053	125.689	0.000	0.000	0.000	0.000	0.000	0.000
143	B	239	LEU	0	0.050	0.006	124.373	0.000	0.000	0.000	0.000	0.000	0.000
144	B	240	GLN	0	-0.007	0.006	123.503	0.000	0.000	0.000	0.000	0.000	0.000
145	B	241	ARG	1	0.957	0.975	122.877	-0.004	-0.004	0.000	0.000	0.000	0.000
146	B	242	ILE	0	-0.030	-0.009	119.358	0.000	0.000	0.000	0.000	0.000	0.000
147	B	243	VAL	0	0.031	0.018	118.865	0.000	0.000	0.000	0.000	0.000	0.000
148	B	244	ASP	-1	-0.925	-0.968	118.230	0.005	0.005	0.000	0.000	0.000	0.000
149	B	245	ILE	0	-0.106	-0.062	115.681	0.000	0.000	0.000	0.000	0.000	0.000
150	B	246	LEU	0	-0.063	-0.026	114.353	0.000	0.000	0.000	0.000	0.000	0.000
151	B	247	TYR	0	-0.082	-0.056	113.441	0.000	0.000	0.000	0.000	0.000	0.000
152	B	248	ALA	0	-0.029	0.003	113.668	0.000	0.000	0.000	0.000	0.000	0.000
153	B	249	THR	0	-0.069	-0.045	108.649	0.000	0.000	0.000	0.000	0.000	0.000
154	B	250	ASP	-1	-0.975	-0.989	107.760	0.006	0.006	0.000	0.000	0.000	0.000
155	B	251	GLU	-1	-1.016	-0.989	102.446	0.007	0.007	0.000	0.000	0.000	0.000

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