FMO DATABASE

FMODB ID: 1NVVZ

Calculation Name: 4XA1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XA1

Chain ID: A

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	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	153
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-924413.435589
FMO2-HF: Nuclear repulsion	862055.142545
FMO2-HF: Total energy	-62358.293044
FMO2-MP2: Total energy	-62541.23773

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:2:PRO)

Summations of interaction energy for fragment #1(A: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.
-4.13	-0.833	1.593	-1.739	-3.152	-0.013

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.056 / q_NPA : -0.039

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	4	LYS	1	0.841	0.911	3.843	-1.072	0.838	-0.015	-0.765	-1.129	0.000
4	A	5	PRO	0	0.002	-0.016	5.242	-0.131	-0.077	-0.001	-0.005	-0.049	0.000
5	A	6	GLU	-1	-0.842	-0.936	7.677	-0.200	-0.200	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.863	-0.900	5.692	-0.038	-0.038	0.000	0.000	0.000	0.000
7	A	8	HIS	0	-0.034	-0.016	6.899	-0.099	-0.099	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.842	-0.950	8.589	-0.173	-0.173	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.908	-0.925	12.043	-0.106	-0.106	0.000	0.000	0.000	0.000
10	A	11	ILE	0	-0.072	-0.053	9.845	0.060	0.060	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.038	-0.025	11.454	0.028	0.028	0.000	0.000	0.000	0.000
12	A	13	ASN	0	-0.047	-0.021	14.562	0.050	0.050	0.000	0.000	0.000	0.000
13	A	14	LYS	1	0.819	0.901	15.104	0.111	0.111	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.057	-0.031	13.965	0.021	0.021	0.000	0.000	0.000	0.000
15	A	16	LEU	0	0.003	0.019	18.015	0.012	0.012	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.813	-0.893	20.580	-0.061	-0.061	0.000	0.000	0.000	0.000
17	A	18	PRO	0	-0.016	-0.009	22.609	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.972	-0.987	24.615	-0.044	-0.044	0.000	0.000	0.000	0.000
19	A	20	LEU	0	-0.040	0.002	18.385	0.006	0.006	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.048	0.020	22.730	0.001	0.001	0.000	0.000	0.000	0.000
21	A	22	GLN	0	-0.014	-0.036	21.664	-0.015	-0.015	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.022	-0.034	20.682	0.001	0.001	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.772	-0.865	16.403	-0.054	-0.054	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.808	0.917	17.003	0.092	0.092	0.000	0.000	0.000	0.000
25	A	26	THR	0	-0.030	-0.033	16.780	-0.024	-0.024	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.929	-0.954	14.046	-0.043	-0.043	0.000	0.000	0.000	0.000
27	A	28	ALA	0	0.018	0.005	12.289	-0.033	-0.033	0.000	0.000	0.000	0.000
28	A	29	LEU	0	0.022	0.011	11.907	-0.060	-0.060	0.000	0.000	0.000	0.000
29	A	30	GLN	0	-0.012	-0.003	11.954	-0.059	-0.059	0.000	0.000	0.000	0.000
30	A	31	GLN	0	0.016	0.007	7.642	-0.086	-0.086	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.058	0.025	7.282	-0.130	-0.130	0.000	0.000	0.000	0.000
32	A	33	ARG	1	0.901	0.956	8.127	0.164	0.164	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.018	-0.015	6.363	0.006	0.006	0.000	0.000	0.000	0.000
34	A	35	ASN	0	0.041	0.036	2.409	-1.847	-1.104	1.595	-0.794	-1.545	-0.012
35	A	36	TYR	0	0.059	0.037	4.732	-0.179	-0.049	-0.001	-0.005	-0.124	0.000
36	A	37	GLY	0	-0.010	0.007	7.243	0.047	0.047	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.025	-0.033	3.551	-0.598	-0.138	0.015	-0.170	-0.305	-0.001
38	A	39	PHE	0	0.033	0.015	5.449	0.022	0.022	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.010	-0.002	6.573	0.093	0.093	0.000	0.000	0.000	0.000
40	A	41	SER	0	-0.042	-0.025	8.563	0.061	0.061	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.846	-0.915	6.032	-0.366	-0.366	0.000	0.000	0.000	0.000
42	A	43	TYR	0	-0.058	-0.019	8.994	0.067	0.067	0.000	0.000	0.000	0.000
43	A	44	ASN	0	-0.010	-0.022	10.962	0.050	0.050	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.778	-0.870	12.176	-0.123	-0.123	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.004	-0.006	13.963	0.008	0.008	0.000	0.000	0.000	0.000
46	A	47	THR	0	-0.001	0.003	16.156	0.014	0.014	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.854	0.906	8.867	0.312	0.312	0.000	0.000	0.000	0.000
48	A	49	SER	0	-0.028	-0.027	15.093	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	1173	LYS	1	0.769	0.877	17.104	0.077	0.077	0.000	0.000	0.000	0.000
50	A	1174	MET	0	0.020	0.002	15.952	0.010	0.010	0.000	0.000	0.000	0.000
51	A	1175	ARG	1	0.871	0.954	14.051	0.212	0.212	0.000	0.000	0.000	0.000
52	A	1176	ARG	1	0.946	0.972	18.543	0.115	0.115	0.000	0.000	0.000	0.000
53	A	1177	ASP	-1	-0.798	-0.887	21.929	-0.069	-0.069	0.000	0.000	0.000	0.000
54	A	1178	LEU	0	-0.021	0.003	19.780	0.007	0.007	0.000	0.000	0.000	0.000
55	A	1179	GLU	-1	-0.917	-0.959	22.422	-0.102	-0.102	0.000	0.000	0.000	0.000
56	A	1180	GLU	-1	-0.923	-0.979	24.061	-0.065	-0.065	0.000	0.000	0.000	0.000
57	A	1181	ALA	0	-0.034	-0.009	26.160	0.007	0.007	0.000	0.000	0.000	0.000
58	A	1182	THR	0	-0.034	-0.017	25.470	0.006	0.006	0.000	0.000	0.000	0.000
59	A	1183	LEU	0	0.065	0.039	27.506	0.005	0.005	0.000	0.000	0.000	0.000
60	A	1184	GLN	0	0.001	0.006	30.315	0.004	0.004	0.000	0.000	0.000	0.000
61	A	1185	HIS	0	-0.005	0.018	30.966	0.006	0.006	0.000	0.000	0.000	0.000
62	A	1186	GLU	-1	-0.921	-0.966	30.281	-0.061	-0.061	0.000	0.000	0.000	0.000
63	A	1187	ALA	0	-0.039	-0.023	33.891	0.003	0.003	0.000	0.000	0.000	0.000
64	A	1188	THR	0	-0.030	-0.031	35.879	0.004	0.004	0.000	0.000	0.000	0.000
65	A	1189	ALA	0	-0.023	-0.022	36.564	0.003	0.003	0.000	0.000	0.000	0.000
66	A	1190	ALA	0	-0.034	-0.001	38.191	0.002	0.002	0.000	0.000	0.000	0.000
67	A	1191	ALA	0	0.030	0.008	40.020	0.002	0.002	0.000	0.000	0.000	0.000
68	A	1192	LEU	0	-0.028	-0.015	40.406	0.002	0.002	0.000	0.000	0.000	0.000
69	A	1193	ARG	1	0.950	0.967	38.410	0.037	0.037	0.000	0.000	0.000	0.000
70	A	1194	LYS	1	0.835	0.913	43.940	0.029	0.029	0.000	0.000	0.000	0.000
71	A	1195	LYS	1	1.003	1.004	45.981	0.024	0.024	0.000	0.000	0.000	0.000
72	A	1196	HIS	0	-0.016	0.000	46.863	0.002	0.002	0.000	0.000	0.000	0.000
73	A	1197	ALA	0	-0.001	-0.009	48.103	0.001	0.001	0.000	0.000	0.000	0.000
74	A	1198	ASP	-1	-0.816	-0.889	49.825	-0.025	-0.025	0.000	0.000	0.000	0.000
75	A	1199	SER	0	-0.021	-0.018	51.338	0.001	0.001	0.000	0.000	0.000	0.000
76	A	1200	VAL	0	-0.018	-0.010	51.571	0.001	0.001	0.000	0.000	0.000	0.000
77	A	1201	ALA	0	-0.005	0.018	54.148	0.001	0.001	0.000	0.000	0.000	0.000
78	A	1202	GLU	-1	-0.867	-0.923	55.998	-0.017	-0.017	0.000	0.000	0.000	0.000
79	A	1203	LEU	0	-0.002	-0.026	55.453	0.001	0.001	0.000	0.000	0.000	0.000
80	A	1204	GLY	0	-0.004	0.007	58.030	0.001	0.001	0.000	0.000	0.000	0.000
81	A	1205	GLU	-1	-0.897	-0.960	59.443	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	1206	GLN	0	-0.097	-0.046	60.233	0.001	0.001	0.000	0.000	0.000	0.000
83	A	1207	ILE	0	0.003	-0.003	60.024	0.001	0.001	0.000	0.000	0.000	0.000
84	A	1208	ASP	-1	-0.894	-0.935	62.928	-0.015	-0.015	0.000	0.000	0.000	0.000
85	A	1209	ASN	0	-0.048	-0.039	65.484	0.001	0.001	0.000	0.000	0.000	0.000
86	A	1210	LEU	0	-0.002	-0.007	66.546	0.001	0.001	0.000	0.000	0.000	0.000
87	A	1211	GLN	0	-0.042	-0.021	64.764	0.001	0.001	0.000	0.000	0.000	0.000
88	A	1212	ARG	1	0.876	0.933	69.601	0.012	0.012	0.000	0.000	0.000	0.000
89	A	1213	VAL	0	-0.003	-0.006	71.720	0.000	0.000	0.000	0.000	0.000	0.000
90	A	1214	LYS	1	0.838	0.916	71.529	0.010	0.010	0.000	0.000	0.000	0.000
91	A	1215	GLN	0	0.037	0.006	71.574	0.000	0.000	0.000	0.000	0.000	0.000
92	A	1216	LYS	1	0.812	0.906	75.512	0.010	0.010	0.000	0.000	0.000	0.000
93	A	1217	LEU	0	0.012	-0.007	76.189	0.000	0.000	0.000	0.000	0.000	0.000
94	A	1218	GLU	-1	-0.862	-0.912	75.556	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	1219	LYS	1	0.800	0.886	79.489	0.009	0.009	0.000	0.000	0.000	0.000
96	A	1220	GLU	-1	-0.772	-0.871	81.589	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	1221	LYS	1	0.948	0.981	80.900	0.008	0.008	0.000	0.000	0.000	0.000
98	A	1222	SER	0	-0.055	-0.036	83.367	0.000	0.000	0.000	0.000	0.000	0.000
99	A	1223	GLU	-1	-0.773	-0.857	85.147	-0.008	-0.008	0.000	0.000	0.000	0.000
100	A	1224	PHE	0	0.047	0.023	86.590	0.000	0.000	0.000	0.000	0.000	0.000
101	A	1225	LYS	1	0.783	0.892	87.753	0.007	0.007	0.000	0.000	0.000	0.000
102	A	1226	LEU	0	-0.027	-0.040	87.975	0.000	0.000	0.000	0.000	0.000	0.000
103	A	1227	GLU	-1	-0.897	-0.938	91.329	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	1228	LEU	0	-0.019	-0.006	91.851	0.000	0.000	0.000	0.000	0.000	0.000
105	A	1229	ASP	-1	-0.837	-0.896	92.333	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	1230	ASP	-1	-0.960	-0.975	95.365	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	1231	VAL	0	0.009	-0.006	97.500	0.000	0.000	0.000	0.000	0.000	0.000
108	A	1232	THR	0	-0.049	-0.037	97.513	0.000	0.000	0.000	0.000	0.000	0.000
109	A	1233	SER	0	-0.019	-0.016	99.231	0.000	0.000	0.000	0.000	0.000	0.000
110	A	1234	ASN	0	-0.036	-0.008	101.549	0.000	0.000	0.000	0.000	0.000	0.000
111	A	1235	MET	0	-0.017	-0.013	102.969	0.000	0.000	0.000	0.000	0.000	0.000
112	A	1236	GLU	-1	-0.876	-0.932	102.380	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	1237	GLN	0	-0.082	-0.041	106.382	0.000	0.000	0.000	0.000	0.000	0.000
114	A	1238	ILE	0	0.029	0.005	106.758	0.000	0.000	0.000	0.000	0.000	0.000
115	A	211	GLU	-1	-0.857	-0.908	107.598	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	212	LYS	1	0.969	0.983	110.548	0.004	0.004	0.000	0.000	0.000	0.000
117	A	213	GLU	-1	-0.901	-0.930	112.169	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	214	ARG	1	0.788	0.863	110.422	0.004	0.004	0.000	0.000	0.000	0.000
119	A	215	ASP	-1	-0.836	-0.902	113.493	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	216	PHE	0	-0.025	-0.014	116.405	0.000	0.000	0.000	0.000	0.000	0.000
121	A	217	TYR	0	-0.088	-0.068	115.987	0.000	0.000	0.000	0.000	0.000	0.000
122	A	218	PHE	0	0.051	0.022	118.914	0.000	0.000	0.000	0.000	0.000	0.000
123	A	219	GLY	0	0.045	0.026	120.439	0.000	0.000	0.000	0.000	0.000	0.000
124	A	220	LYS	1	0.851	0.943	121.532	0.004	0.004	0.000	0.000	0.000	0.000
125	A	221	LEU	0	0.009	0.008	122.429	0.000	0.000	0.000	0.000	0.000	0.000
126	A	222	ARG	1	0.889	0.940	124.293	0.003	0.003	0.000	0.000	0.000	0.000
127	A	223	ASN	0	-0.053	-0.042	125.586	0.000	0.000	0.000	0.000	0.000	0.000
128	A	224	ILE	0	0.003	-0.012	127.735	0.000	0.000	0.000	0.000	0.000	0.000
129	A	225	GLU	-1	-0.778	-0.847	127.904	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	226	LEU	0	-0.034	-0.019	129.023	0.000	0.000	0.000	0.000	0.000	0.000
131	A	227	ILE	0	0.005	0.011	132.166	0.000	0.000	0.000	0.000	0.000	0.000
132	A	228	CYS	0	-0.068	-0.037	133.474	0.000	0.000	0.000	0.000	0.000	0.000
133	A	229	GLN	0	0.005	0.004	131.315	0.000	0.000	0.000	0.000	0.000	0.000
134	A	230	GLU	-1	-0.985	-0.983	136.268	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	231	ASN	0	-0.086	-0.049	138.338	0.000	0.000	0.000	0.000	0.000	0.000
136	A	232	GLU	-1	-0.949	-0.961	137.170	-0.003	-0.003	0.000	0.000	0.000	0.000
137	A	233	GLY	0	-0.010	-0.009	141.102	0.000	0.000	0.000	0.000	0.000	0.000
138	A	234	GLU	-1	-0.987	-0.994	144.075	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	235	ASN	0	-0.066	-0.033	142.538	0.000	0.000	0.000	0.000	0.000	0.000
140	A	236	ASP	-1	-0.802	-0.901	141.672	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	237	PRO	0	0.005	-0.003	141.532	0.000	0.000	0.000	0.000	0.000	0.000
142	A	238	VAL	0	-0.075	-0.048	138.086	0.000	0.000	0.000	0.000	0.000	0.000
143	A	239	LEU	0	0.054	0.014	137.318	0.000	0.000	0.000	0.000	0.000	0.000
144	A	240	GLN	0	-0.033	-0.008	136.311	0.000	0.000	0.000	0.000	0.000	0.000
145	A	241	ARG	1	0.955	0.981	135.163	0.003	0.003	0.000	0.000	0.000	0.000
146	A	242	ILE	0	-0.028	-0.010	131.837	0.000	0.000	0.000	0.000	0.000	0.000
147	A	243	VAL	0	0.037	0.009	131.570	0.000	0.000	0.000	0.000	0.000	0.000
148	A	244	ASP	-1	-0.889	-0.939	131.559	-0.003	-0.003	0.000	0.000	0.000	0.000
149	A	245	ILE	0	-0.107	-0.055	127.744	0.000	0.000	0.000	0.000	0.000	0.000
150	A	246	LEU	0	-0.056	-0.020	127.287	0.000	0.000	0.000	0.000	0.000	0.000
151	A	247	TYR	0	-0.082	-0.069	126.573	0.000	0.000	0.000	0.000	0.000	0.000
152	A	248	ALA	0	-0.003	0.023	126.391	0.000	0.000	0.000	0.000	0.000	0.000
153	A	249	THR	0	-0.062	-0.031	121.504	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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