FMO DATABASE

FMODB ID: JL2Q9

Calculation Name: 3L1X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L1X

Chain ID: A

ChEMBL ID:

UniProt ID: O95155

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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-481458.913531
FMO2-HF: Nuclear repulsion	450105.153677
FMO2-HF: Total energy	-31353.759855
FMO2-MP2: Total energy	-31442.300377

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:1226:SER)

Summations of interaction energy for fragment #1(A:1226: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.
0.919	4.018	0.849	-1.46	-2.487	-0.002

Interaction energy analysis for fragmet #1(A:1226:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.012

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

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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	1228	ALA	0	0.004	0.001	3.204	-0.387	1.835	0.028	-1.011	-1.238	-0.001
4	A	1229	PRO	0	0.056	0.030	4.582	0.195	0.259	-0.001	-0.015	-0.049	0.000
5	A	1230	ASP	-1	-0.832	-0.924	8.272	0.023	0.023	0.000	0.000	0.000	0.000
6	A	1231	GLU	-1	-0.979	-0.980	10.150	-0.097	-0.097	0.000	0.000	0.000	0.000
7	A	1232	PHE	0	-0.021	-0.030	6.707	-0.016	-0.016	0.000	0.000	0.000	0.000
8	A	1233	ARG	1	0.784	0.895	3.709	0.092	0.378	0.000	-0.087	-0.199	0.000
9	A	1234	ASP	-1	-0.743	-0.894	9.253	0.247	0.247	0.000	0.000	0.000	0.000
10	A	1235	PRO	0	-0.010	-0.003	11.581	0.038	0.038	0.000	0.000	0.000	0.000
11	A	1236	LEU	0	-0.068	-0.034	14.029	-0.058	-0.058	0.000	0.000	0.000	0.000
12	A	1237	MET	0	-0.074	-0.039	11.388	-0.071	-0.071	0.000	0.000	0.000	0.000
13	A	1238	ASP	-1	-0.864	-0.905	6.482	0.946	0.946	0.000	0.000	0.000	0.000
14	A	1239	THR	0	-0.037	-0.025	6.670	0.484	0.484	0.000	0.000	0.000	0.000
15	A	1240	LEU	0	-0.003	-0.003	4.452	-0.526	-0.405	-0.001	-0.007	-0.113	0.000
16	A	1241	MET	0	-0.063	-0.009	7.039	-0.282	-0.282	0.000	0.000	0.000	0.000
17	A	1242	THR	0	-0.060	-0.042	9.833	-0.099	-0.099	0.000	0.000	0.000	0.000
18	A	1243	ASP	-1	-0.805	-0.890	11.992	0.059	0.059	0.000	0.000	0.000	0.000
19	A	1244	PRO	0	0.012	0.020	13.704	0.017	0.017	0.000	0.000	0.000	0.000
20	A	1245	VAL	0	-0.007	-0.012	15.855	-0.045	-0.045	0.000	0.000	0.000	0.000
21	A	1246	ARG	1	0.891	0.941	19.173	-0.036	-0.036	0.000	0.000	0.000	0.000
22	A	1247	LEU	0	0.024	0.014	20.472	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	1248	PRO	0	0.013	-0.013	23.655	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	1249	SER	0	-0.047	-0.044	24.164	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	1250	GLY	0	-0.028	-0.012	23.788	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	1251	THR	0	-0.032	-0.005	18.877	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	1252	ILE	0	-0.012	-0.002	15.914	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	1253	MET	0	0.019	0.016	15.393	0.005	0.005	0.000	0.000	0.000	0.000
29	A	1254	ASP	-1	-0.725	-0.831	13.134	0.434	0.434	0.000	0.000	0.000	0.000
30	A	1255	ARG	1	0.878	0.916	15.196	-0.167	-0.167	0.000	0.000	0.000	0.000
31	A	1256	SER	0	-0.041	-0.045	15.318	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	1257	ILE	0	-0.034	-0.006	12.370	-0.031	-0.031	0.000	0.000	0.000	0.000
33	A	1258	ILE	0	0.028	0.007	17.044	-0.035	-0.035	0.000	0.000	0.000	0.000
34	A	1259	LEU	0	0.000	0.003	20.089	-0.025	-0.025	0.000	0.000	0.000	0.000
35	A	1260	ARG	1	0.937	0.973	18.092	-0.348	-0.348	0.000	0.000	0.000	0.000
36	A	1261	HIS	0	-0.043	-0.018	20.893	0.003	0.003	0.000	0.000	0.000	0.000
37	A	1262	LEU	0	-0.001	-0.008	22.575	-0.020	-0.020	0.000	0.000	0.000	0.000
38	A	1263	LEU	0	-0.069	-0.026	24.334	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	1264	ASN	0	-0.114	-0.051	23.735	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	1265	SER	0	0.034	0.019	26.206	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	1266	PRO	0	0.037	0.036	26.814	0.008	0.008	0.000	0.000	0.000	0.000
42	A	1267	THR	0	-0.021	-0.028	26.932	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	1268	ASP	-1	-0.728	-0.841	23.785	0.142	0.142	0.000	0.000	0.000	0.000
44	A	1269	PRO	0	-0.032	-0.023	20.050	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	1270	PHE	0	-0.011	-0.005	17.103	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	1271	ASN	0	-0.047	-0.051	23.045	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	1272	ARG	1	0.922	0.964	26.163	-0.098	-0.098	0.000	0.000	0.000	0.000
48	A	1273	GLN	0	0.006	0.021	28.039	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	1274	THR	0	-0.005	-0.003	28.920	0.007	0.007	0.000	0.000	0.000	0.000
50	A	1275	LEU	0	-0.052	-0.026	24.716	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	1276	THR	0	0.020	-0.008	28.832	0.005	0.005	0.000	0.000	0.000	0.000
52	A	1277	GLU	-1	-0.818	-0.923	25.230	0.140	0.140	0.000	0.000	0.000	0.000
53	A	1278	SER	0	-0.038	-0.024	27.025	0.000	0.000	0.000	0.000	0.000	0.000
54	A	1279	MET	0	-0.061	-0.028	28.208	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	1280	LEU	0	-0.036	-0.004	22.577	0.000	0.000	0.000	0.000	0.000	0.000
56	A	1281	GLU	-1	-0.878	-0.931	24.247	0.057	0.057	0.000	0.000	0.000	0.000
57	A	1282	PRO	0	-0.048	-0.024	20.776	0.014	0.014	0.000	0.000	0.000	0.000
58	A	1283	VAL	0	0.023	0.023	17.624	-0.016	-0.016	0.000	0.000	0.000	0.000
59	A	1284	PRO	0	-0.005	-0.010	17.683	0.001	0.001	0.000	0.000	0.000	0.000
60	A	1285	GLU	-1	-0.869	-0.940	18.023	-0.019	-0.019	0.000	0.000	0.000	0.000
61	A	1286	LEU	0	0.046	0.021	12.824	-0.034	-0.034	0.000	0.000	0.000	0.000
62	A	1287	LYS	1	0.846	0.912	13.373	-0.131	-0.131	0.000	0.000	0.000	0.000
63	A	1288	GLU	-1	-0.834	-0.920	13.661	-0.137	-0.137	0.000	0.000	0.000	0.000
64	A	1289	GLN	0	-0.045	-0.005	12.620	-0.020	-0.020	0.000	0.000	0.000	0.000
65	A	1290	ILE	0	0.024	0.012	7.851	-0.125	-0.125	0.000	0.000	0.000	0.000
66	A	1291	GLN	0	-0.026	-0.021	9.128	-0.163	-0.163	0.000	0.000	0.000	0.000
67	A	1292	ALA	0	-0.022	-0.002	11.247	-0.087	-0.087	0.000	0.000	0.000	0.000
68	A	1293	TRP	0	0.049	0.041	2.328	-0.580	-0.247	0.824	-0.337	-0.821	-0.001
69	A	1294	MET	0	-0.036	-0.017	6.058	-0.165	-0.165	0.000	0.000	0.000	0.000
70	A	1295	ARG	1	0.813	0.893	7.790	0.141	0.141	0.000	0.000	0.000	0.000
71	A	1296	GLU	-1	-0.926	-0.961	9.385	-1.045	-1.045	0.000	0.000	0.000	0.000
72	A	1297	LYS	1	0.850	0.914	4.484	2.392	2.465	-0.001	-0.003	-0.067	0.000
73	A	1298	GLN	0	-0.061	-0.023	7.915	0.228	0.228	0.000	0.000	0.000	0.000
74	A	1299	ASN	0	-0.120	-0.052	9.737	0.197	0.197	0.000	0.000	0.000	0.000
75	A	1300	SER	0	-0.036	-0.018	9.440	0.077	0.077	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1226:SER)