FMO DATABASE

FMODB ID: 6NMMZ

Calculation Name: 1L4A-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1L4A

Chain ID: B

ChEMBL ID:

UniProt ID: Q95PA1

Base Structure: X-ray

Registration Date: 2023-09-20

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	82
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-361207.478134
FMO2-HF: Nuclear repulsion	327418.518968
FMO2-HF: Total energy	-33788.959166
FMO2-MP2: Total energy	-33882.303755

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:178:GLY)

Summations of interaction energy for fragment #1(B:178:GLY)

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.
-3.197	-0.491	1.373	-1.832	-2.249	0.001

Interaction energy analysis for fragmet #1(B:178:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.007

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	B	180	SER	0	0.085	0.038	3.059	-1.464	0.584	0.016	-1.022	-1.043	0.000
4	B	181	ALA	0	-0.039	-0.014	2.216	-1.699	-1.219	1.354	-0.749	-1.085	0.001
5	B	182	SER	0	0.059	0.025	3.989	-0.118	0.060	0.003	-0.061	-0.121	0.000
6	B	183	GLY	0	0.024	0.025	6.467	0.080	0.080	0.000	0.000	0.000	0.000
7	B	184	ILE	0	0.054	0.029	6.607	0.141	0.141	0.000	0.000	0.000	0.000
8	B	185	ILE	0	-0.007	0.005	7.971	0.003	0.003	0.000	0.000	0.000	0.000
9	B	186	MET	0	0.003	-0.003	10.366	-0.043	-0.043	0.000	0.000	0.000	0.000
10	B	187	GLU	-1	-0.903	-0.955	10.058	0.011	0.011	0.000	0.000	0.000	0.000
11	B	188	THR	0	-0.041	-0.034	12.373	0.008	0.008	0.000	0.000	0.000	0.000
12	B	189	GLN	0	-0.080	-0.040	13.692	-0.032	-0.032	0.000	0.000	0.000	0.000
13	B	190	GLN	0	0.050	0.030	16.695	0.003	0.003	0.000	0.000	0.000	0.000
14	B	191	ALA	0	0.007	0.005	17.496	-0.002	-0.002	0.000	0.000	0.000	0.000
15	B	192	LYS	1	0.937	0.960	17.440	-0.192	-0.192	0.000	0.000	0.000	0.000
16	B	193	GLN	0	-0.047	-0.018	20.946	-0.001	-0.001	0.000	0.000	0.000	0.000
17	B	194	THR	0	0.027	-0.002	22.292	-0.005	-0.005	0.000	0.000	0.000	0.000
18	B	195	LEU	0	-0.051	-0.018	23.255	-0.002	-0.002	0.000	0.000	0.000	0.000
19	B	196	ALA	0	0.036	0.020	25.031	-0.003	-0.003	0.000	0.000	0.000	0.000
20	B	197	ASP	-1	-0.857	-0.916	26.650	0.013	0.013	0.000	0.000	0.000	0.000
21	B	198	ILE	0	-0.096	-0.051	26.169	-0.004	-0.004	0.000	0.000	0.000	0.000
22	B	199	GLU	-1	-0.939	-0.984	28.261	0.072	0.072	0.000	0.000	0.000	0.000
23	B	200	ALA	0	-0.014	0.001	31.025	-0.002	-0.002	0.000	0.000	0.000	0.000
24	B	201	ARG	1	1.001	0.997	30.843	-0.024	-0.024	0.000	0.000	0.000	0.000
25	B	202	HIS	0	-0.048	-0.022	33.459	-0.003	-0.003	0.000	0.000	0.000	0.000
26	B	203	ALA	0	0.033	0.019	35.191	-0.001	-0.001	0.000	0.000	0.000	0.000
27	B	204	ASP	-1	-0.908	-0.950	37.279	0.018	0.018	0.000	0.000	0.000	0.000
28	B	205	ILE	0	-0.046	-0.028	36.523	-0.002	-0.002	0.000	0.000	0.000	0.000
29	B	206	MET	0	0.027	0.024	38.797	-0.001	-0.001	0.000	0.000	0.000	0.000
30	B	207	LYS	1	0.946	0.984	40.858	-0.021	-0.021	0.000	0.000	0.000	0.000
31	B	208	LEU	0	-0.027	-0.015	43.032	-0.001	-0.001	0.000	0.000	0.000	0.000
32	B	209	GLU	-1	-0.819	-0.907	43.034	0.029	0.029	0.000	0.000	0.000	0.000
33	B	210	THR	0	-0.070	-0.044	44.293	0.000	0.000	0.000	0.000	0.000	0.000
34	B	211	SER	0	0.023	-0.003	46.762	0.000	0.000	0.000	0.000	0.000	0.000
35	B	212	ILE	0	-0.053	-0.016	46.767	-0.001	-0.001	0.000	0.000	0.000	0.000
36	B	213	ARG	1	0.825	0.896	43.887	-0.029	-0.029	0.000	0.000	0.000	0.000
37	B	214	GLU	-1	-0.885	-0.927	50.705	0.018	0.018	0.000	0.000	0.000	0.000
38	B	215	LEU	0	-0.004	-0.005	53.029	-0.001	-0.001	0.000	0.000	0.000	0.000
39	B	216	HIS	0	-0.067	-0.053	53.037	-0.001	-0.001	0.000	0.000	0.000	0.000
40	B	217	ASP	-1	-0.858	-0.920	53.837	0.020	0.020	0.000	0.000	0.000	0.000
41	B	218	MET	0	-0.009	-0.003	56.497	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	219	PHE	0	-0.038	-0.022	57.317	-0.001	-0.001	0.000	0.000	0.000	0.000
43	B	220	MET	0	-0.030	-0.008	56.833	-0.001	-0.001	0.000	0.000	0.000	0.000
44	B	221	ASP	-1	-0.871	-0.939	60.433	0.016	0.016	0.000	0.000	0.000	0.000
45	B	222	MET	0	-0.061	-0.035	62.578	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	223	ALA	0	-0.016	-0.003	63.422	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	224	MET	0	0.002	0.004	61.503	0.000	0.000	0.000	0.000	0.000	0.000
48	B	225	LEU	0	-0.032	0.002	66.028	0.000	0.000	0.000	0.000	0.000	0.000
49	B	226	VAL	0	0.001	-0.010	68.328	0.000	0.000	0.000	0.000	0.000	0.000
50	B	227	GLU	-1	-0.919	-0.948	68.711	0.011	0.011	0.000	0.000	0.000	0.000
51	B	228	SER	0	-0.055	-0.044	69.624	0.000	0.000	0.000	0.000	0.000	0.000
52	B	229	GLN	0	-0.087	-0.068	71.509	0.000	0.000	0.000	0.000	0.000	0.000
53	B	230	GLY	0	0.052	0.036	73.650	0.000	0.000	0.000	0.000	0.000	0.000
54	B	231	GLU	-1	-0.797	-0.872	75.067	0.011	0.011	0.000	0.000	0.000	0.000
55	B	232	MET	0	-0.095	-0.058	75.116	0.000	0.000	0.000	0.000	0.000	0.000
56	B	233	ILE	0	-0.017	0.000	76.854	0.000	0.000	0.000	0.000	0.000	0.000
57	B	234	ASP	-1	-0.837	-0.914	78.435	0.008	0.008	0.000	0.000	0.000	0.000
58	B	235	ARG	1	0.778	0.865	78.339	-0.011	-0.011	0.000	0.000	0.000	0.000
59	B	236	ILE	0	-0.076	-0.036	82.689	0.000	0.000	0.000	0.000	0.000	0.000
60	B	237	GLU	-1	-0.926	-0.959	83.968	0.006	0.006	0.000	0.000	0.000	0.000
61	B	238	TYR	0	-0.005	-0.003	85.479	0.000	0.000	0.000	0.000	0.000	0.000
62	B	239	ASN	0	-0.025	-0.017	86.416	0.000	0.000	0.000	0.000	0.000	0.000
63	B	240	VAL	0	-0.007	-0.002	88.314	0.000	0.000	0.000	0.000	0.000	0.000
64	B	241	GLU	-1	-0.964	-0.978	89.024	0.006	0.006	0.000	0.000	0.000	0.000
65	B	242	ALA	0	-0.017	-0.005	91.575	0.000	0.000	0.000	0.000	0.000	0.000
66	B	243	ALA	0	-0.044	-0.020	92.930	0.000	0.000	0.000	0.000	0.000	0.000
67	B	244	VAL	0	-0.017	-0.020	93.548	0.000	0.000	0.000	0.000	0.000	0.000
68	B	245	ASP	-1	-0.838	-0.920	95.882	0.005	0.005	0.000	0.000	0.000	0.000
69	B	246	TYR	0	-0.002	0.002	96.054	0.000	0.000	0.000	0.000	0.000	0.000
70	B	247	ILE	0	-0.074	-0.021	98.473	0.000	0.000	0.000	0.000	0.000	0.000
71	B	248	GLU	-1	-0.831	-0.899	99.984	0.004	0.004	0.000	0.000	0.000	0.000
72	B	249	THR	0	0.013	-0.004	101.359	0.000	0.000	0.000	0.000	0.000	0.000
73	B	250	ALA	0	0.009	0.005	103.541	0.000	0.000	0.000	0.000	0.000	0.000
74	B	251	LYS	1	0.768	0.869	101.426	-0.005	-0.005	0.000	0.000	0.000	0.000
75	B	252	VAL	0	-0.013	-0.003	105.977	0.000	0.000	0.000	0.000	0.000	0.000
76	B	253	ASP	-1	-0.862	-0.927	108.221	0.005	0.005	0.000	0.000	0.000	0.000
77	B	254	THR	0	-0.080	-0.054	108.203	0.000	0.000	0.000	0.000	0.000	0.000
78	B	255	LYS	1	0.972	0.990	110.957	-0.004	-0.004	0.000	0.000	0.000	0.000
79	B	256	LYS	1	0.891	0.945	113.298	-0.004	-0.004	0.000	0.000	0.000	0.000
80	B	257	ALA	0	0.007	-0.001	114.849	0.000	0.000	0.000	0.000	0.000	0.000
81	B	258	VAL	0	-0.018	0.003	116.719	0.000	0.000	0.000	0.000	0.000	0.000
82	B	259	LYS	1	0.916	0.969	118.341	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:178:GLY)