FMO DATABASE

FMODB ID: R8588

Calculation Name: 5NLB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5NLB

Chain ID: A

ChEMBL ID:

UniProt ID: Q13618

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	154
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1360223.324736
FMO2-HF: Nuclear repulsion	1298158.593656
FMO2-HF: Total energy	-62064.73108
FMO2-MP2: Total energy	-62238.350301

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:51:THR)

Summations of interaction energy for fragment #1(A:51:THR)

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.
0.766	2.384	-0.02	-0.823	-0.775	0.002

Interaction energy analysis for fragmet #1(A:51:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.021

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	53	SER	0	0.006	0.005	3.871	0.937	2.555	-0.020	-0.823	-0.775	0.002
4	A	54	TYR	0	0.013	0.007	7.184	-0.484	-0.484	0.000	0.000	0.000	0.000
5	A	55	THR	0	-0.024	-0.025	10.713	0.039	0.039	0.000	0.000	0.000	0.000
6	A	56	LEU	0	0.017	0.017	14.411	-0.059	-0.059	0.000	0.000	0.000	0.000
7	A	57	GLU	-1	-0.862	-0.940	17.814	0.190	0.190	0.000	0.000	0.000	0.000
8	A	58	ASP	-1	-0.841	-0.920	20.740	0.190	0.190	0.000	0.000	0.000	0.000
9	A	59	HIS	0	0.008	0.015	19.885	-0.015	-0.015	0.000	0.000	0.000	0.000
10	A	60	THR	0	-0.005	-0.002	21.386	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	61	LYS	1	0.861	0.922	23.715	-0.202	-0.202	0.000	0.000	0.000	0.000
12	A	62	GLN	0	0.005	0.002	23.760	0.007	0.007	0.000	0.000	0.000	0.000
13	A	63	ALA	0	-0.002	-0.005	24.040	-0.012	-0.012	0.000	0.000	0.000	0.000
14	A	64	PHE	0	-0.001	-0.001	26.164	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	65	GLY	0	0.032	0.025	29.145	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	66	ILE	0	-0.014	-0.008	26.500	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	67	MET	0	-0.011	-0.003	27.649	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	68	ASN	0	0.018	0.007	31.372	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	69	GLU	-1	-0.877	-0.910	33.566	0.130	0.130	0.000	0.000	0.000	0.000
20	A	70	LEU	0	-0.008	-0.006	30.831	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	71	ARG	1	0.900	0.955	35.054	-0.138	-0.138	0.000	0.000	0.000	0.000
22	A	72	LEU	0	-0.035	-0.012	37.400	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	73	SER	0	-0.049	-0.040	38.107	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	74	GLN	0	-0.072	-0.055	40.103	0.001	0.001	0.000	0.000	0.000	0.000
25	A	75	GLN	0	-0.012	-0.002	36.316	0.005	0.005	0.000	0.000	0.000	0.000
26	A	76	LEU	0	0.000	-0.017	31.939	0.007	0.007	0.000	0.000	0.000	0.000
27	A	77	CYS	0	-0.094	-0.021	35.234	0.006	0.006	0.000	0.000	0.000	0.000
28	A	78	ASP	-1	-0.763	-0.870	35.244	0.174	0.174	0.000	0.000	0.000	0.000
29	A	79	VAL	0	-0.027	-0.012	37.898	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	80	THR	0	-0.016	-0.009	40.220	0.000	0.000	0.000	0.000	0.000	0.000
31	A	81	LEU	0	0.010	0.003	41.550	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	82	GLN	0	0.066	0.027	45.207	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	83	VAL	0	-0.018	0.017	46.628	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	84	LYS	1	0.848	0.911	49.390	-0.074	-0.074	0.000	0.000	0.000	0.000
35	A	85	TYR	0	0.034	0.017	53.088	0.000	0.000	0.000	0.000	0.000	0.000
36	A	86	GLN	0	-0.008	-0.006	55.036	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	87	ASP	-1	-0.866	-0.929	58.678	0.052	0.052	0.000	0.000	0.000	0.000
38	A	88	ALA	0	-0.050	-0.024	55.837	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	89	PRO	0	-0.022	-0.003	56.426	0.001	0.001	0.000	0.000	0.000	0.000
40	A	90	ALA	0	-0.026	-0.023	53.593	0.002	0.002	0.000	0.000	0.000	0.000
41	A	91	ALA	0	0.007	0.017	49.902	0.000	0.000	0.000	0.000	0.000	0.000
42	A	92	GLN	0	0.001	-0.029	48.093	0.003	0.003	0.000	0.000	0.000	0.000
43	A	93	PHE	0	-0.019	0.001	43.347	0.000	0.000	0.000	0.000	0.000	0.000
44	A	94	MET	0	0.006	0.021	41.462	0.000	0.000	0.000	0.000	0.000	0.000
45	A	95	ALA	0	0.005	-0.004	37.715	0.000	0.000	0.000	0.000	0.000	0.000
46	A	96	HIS	0	0.056	0.042	33.098	0.003	0.003	0.000	0.000	0.000	0.000
47	A	97	LYS	1	0.824	0.908	34.761	-0.159	-0.159	0.000	0.000	0.000	0.000
48	A	98	VAL	0	0.037	0.005	28.406	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	99	VAL	0	0.002	0.023	30.358	0.007	0.007	0.000	0.000	0.000	0.000
50	A	100	LEU	0	0.023	0.008	32.078	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	101	ALA	0	0.018	0.016	32.509	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	102	SER	0	-0.067	-0.035	29.135	0.009	0.009	0.000	0.000	0.000	0.000
53	A	103	SER	0	-0.023	-0.016	30.708	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	104	SER	0	-0.011	0.000	33.235	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	105	PRO	0	0.016	0.004	34.374	0.008	0.008	0.000	0.000	0.000	0.000
56	A	106	VAL	0	0.025	0.035	35.522	0.001	0.001	0.000	0.000	0.000	0.000
57	A	107	PHE	0	0.037	-0.001	36.995	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	108	LYS	1	0.827	0.900	30.010	-0.184	-0.184	0.000	0.000	0.000	0.000
59	A	109	ALA	0	-0.016	-0.006	34.862	0.004	0.004	0.000	0.000	0.000	0.000
60	A	110	MET	0	-0.067	-0.023	37.526	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	111	PHE	0	0.019	-0.012	36.156	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	112	THR	0	0.017	0.026	34.836	0.012	0.012	0.000	0.000	0.000	0.000
63	A	113	ASN	0	-0.043	-0.015	35.402	0.000	0.000	0.000	0.000	0.000	0.000
64	A	114	GLY	0	-0.030	-0.006	37.244	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	115	LEU	0	0.025	0.001	40.532	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	116	ARG	1	0.865	0.907	42.734	-0.086	-0.086	0.000	0.000	0.000	0.000
67	A	117	GLU	-1	-0.799	-0.903	41.955	0.098	0.098	0.000	0.000	0.000	0.000
68	A	118	GLN	0	-0.068	-0.019	36.865	0.004	0.004	0.000	0.000	0.000	0.000
69	A	119	GLY	0	0.028	0.002	38.747	0.010	0.010	0.000	0.000	0.000	0.000
70	A	120	MET	0	-0.049	-0.005	40.787	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	121	GLU	-1	-0.831	-0.903	39.863	0.137	0.137	0.000	0.000	0.000	0.000
72	A	122	VAL	0	-0.095	-0.047	42.655	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	123	VAL	0	-0.003	0.000	44.094	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	124	SER	0	-0.063	-0.041	46.798	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	125	ILE	0	-0.004	-0.008	44.440	0.002	0.002	0.000	0.000	0.000	0.000
76	A	126	GLU	-1	-0.846	-0.925	48.331	0.069	0.069	0.000	0.000	0.000	0.000
77	A	127	GLY	0	-0.014	0.001	49.473	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	128	ILE	0	-0.010	-0.019	49.360	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	129	HIS	0	0.014	0.003	50.687	0.004	0.004	0.000	0.000	0.000	0.000
80	A	130	PRO	0	0.051	0.017	49.171	0.002	0.002	0.000	0.000	0.000	0.000
81	A	131	LYS	1	0.980	0.995	47.955	-0.062	-0.062	0.000	0.000	0.000	0.000
82	A	132	VAL	0	0.015	-0.002	46.725	0.002	0.002	0.000	0.000	0.000	0.000
83	A	133	MET	0	0.005	0.014	44.320	0.005	0.005	0.000	0.000	0.000	0.000
84	A	134	GLU	-1	-0.883	-0.924	43.150	0.088	0.088	0.000	0.000	0.000	0.000
85	A	135	ARG	1	0.774	0.862	42.639	-0.079	-0.079	0.000	0.000	0.000	0.000
86	A	136	LEU	0	0.007	0.001	40.714	0.004	0.004	0.000	0.000	0.000	0.000
87	A	137	ILE	0	-0.011	-0.004	38.908	0.008	0.008	0.000	0.000	0.000	0.000
88	A	138	GLU	-1	-0.852	-0.926	38.041	0.100	0.100	0.000	0.000	0.000	0.000
89	A	139	PHE	0	0.003	0.023	35.040	0.008	0.008	0.000	0.000	0.000	0.000
90	A	140	ALA	0	-0.029	-0.024	34.619	0.008	0.008	0.000	0.000	0.000	0.000
91	A	141	TYR	0	-0.019	-0.045	33.237	0.010	0.010	0.000	0.000	0.000	0.000
92	A	142	THR	0	-0.065	-0.052	33.264	0.004	0.004	0.000	0.000	0.000	0.000
93	A	143	ALA	0	-0.027	0.002	31.640	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	144	SER	0	-0.016	-0.004	33.796	-0.010	-0.010	0.000	0.000	0.000	0.000
95	A	145	ILE	0	0.030	0.003	37.271	0.002	0.002	0.000	0.000	0.000	0.000
96	A	146	SER	0	0.009	0.020	40.894	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	147	MET	0	-0.029	-0.012	42.327	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	148	GLY	0	0.044	0.005	46.482	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	149	GLU	-1	-0.832	-0.905	50.105	0.049	0.049	0.000	0.000	0.000	0.000
100	A	150	LYS	1	0.888	0.944	52.959	-0.045	-0.045	0.000	0.000	0.000	0.000
101	A	151	CYS	0	0.020	0.006	49.766	0.000	0.000	0.000	0.000	0.000	0.000
102	A	152	VAL	0	0.030	0.028	47.422	0.003	0.003	0.000	0.000	0.000	0.000
103	A	153	LEU	0	0.026	0.033	48.778	0.002	0.002	0.000	0.000	0.000	0.000
104	A	154	HIS	0	0.030	0.002	50.260	0.003	0.003	0.000	0.000	0.000	0.000
105	A	155	VAL	0	0.002	-0.007	44.767	0.003	0.003	0.000	0.000	0.000	0.000
106	A	156	MET	0	0.041	0.027	45.426	0.004	0.004	0.000	0.000	0.000	0.000
107	A	157	ASN	0	0.000	-0.004	45.871	0.002	0.002	0.000	0.000	0.000	0.000
108	A	158	GLY	0	0.007	0.002	46.176	0.001	0.001	0.000	0.000	0.000	0.000
109	A	159	ALA	0	-0.010	-0.012	41.775	0.004	0.004	0.000	0.000	0.000	0.000
110	A	160	VAL	0	-0.002	0.002	42.021	0.004	0.004	0.000	0.000	0.000	0.000
111	A	161	MET	0	-0.031	0.007	43.736	0.002	0.002	0.000	0.000	0.000	0.000
112	A	162	TYR	0	-0.004	-0.017	41.145	0.000	0.000	0.000	0.000	0.000	0.000
113	A	163	GLN	0	-0.031	-0.015	37.708	0.010	0.010	0.000	0.000	0.000	0.000
114	A	164	ILE	0	-0.006	-0.001	36.223	0.008	0.008	0.000	0.000	0.000	0.000
115	A	165	ASP	-1	-0.790	-0.900	36.348	0.095	0.095	0.000	0.000	0.000	0.000
116	A	166	SER	0	-0.022	-0.009	33.911	-0.007	-0.007	0.000	0.000	0.000	0.000
117	A	167	VAL	0	0.034	0.014	36.043	-0.006	-0.006	0.000	0.000	0.000	0.000
118	A	168	VAL	0	0.020	0.013	39.028	-0.006	-0.006	0.000	0.000	0.000	0.000
119	A	169	ARG	1	0.716	0.802	37.810	-0.071	-0.071	0.000	0.000	0.000	0.000
120	A	170	ALA	0	0.016	0.017	38.957	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	171	CYS	0	-0.072	-0.035	40.708	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	172	SER	0	-0.023	-0.043	43.051	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	173	ASP	-1	-0.792	-0.868	40.561	0.055	0.055	0.000	0.000	0.000	0.000
124	A	174	PHE	0	-0.049	-0.014	43.945	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	175	LEU	0	0.001	-0.011	45.671	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	176	VAL	0	-0.038	-0.003	46.672	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	177	GLN	0	-0.092	-0.039	46.602	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	178	GLN	0	-0.042	-0.038	49.799	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	179	LEU	0	-0.012	0.003	53.184	0.000	0.000	0.000	0.000	0.000	0.000
130	A	180	ASP	-1	-0.768	-0.872	54.689	0.030	0.030	0.000	0.000	0.000	0.000
131	A	181	PRO	0	-0.049	-0.040	58.324	0.001	0.001	0.000	0.000	0.000	0.000
132	A	182	SER	0	-0.090	-0.058	60.680	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	183	ASN	0	0.017	-0.003	58.106	0.000	0.000	0.000	0.000	0.000	0.000
134	A	184	ALA	0	-0.007	0.003	57.299	0.002	0.002	0.000	0.000	0.000	0.000
135	A	185	ILE	0	0.015	0.008	57.836	0.001	0.001	0.000	0.000	0.000	0.000
136	A	186	GLY	0	0.036	0.023	58.813	0.001	0.001	0.000	0.000	0.000	0.000
137	A	187	ILE	0	0.005	-0.002	52.766	0.002	0.002	0.000	0.000	0.000	0.000
138	A	188	ALA	0	0.015	0.007	54.065	0.002	0.002	0.000	0.000	0.000	0.000
139	A	189	ASN	0	-0.022	-0.009	55.451	0.000	0.000	0.000	0.000	0.000	0.000
140	A	190	PHE	0	-0.022	-0.022	52.765	0.001	0.001	0.000	0.000	0.000	0.000
141	A	191	ALA	0	-0.007	-0.003	50.867	0.002	0.002	0.000	0.000	0.000	0.000
142	A	192	GLU	-1	-0.885	-0.926	51.138	0.039	0.039	0.000	0.000	0.000	0.000
143	A	193	GLN	0	-0.025	-0.019	52.960	0.001	0.001	0.000	0.000	0.000	0.000
144	A	194	ILE	0	-0.020	-0.013	47.787	0.002	0.002	0.000	0.000	0.000	0.000
145	A	195	GLY	0	0.021	0.029	48.762	0.004	0.004	0.000	0.000	0.000	0.000
146	A	196	CYS	0	-0.041	-0.029	43.603	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	197	VAL	0	0.051	0.044	46.719	0.000	0.000	0.000	0.000	0.000	0.000
148	A	198	GLU	-1	-0.822	-0.869	42.752	0.057	0.057	0.000	0.000	0.000	0.000
149	A	199	LEU	0	0.017	-0.008	46.036	-0.002	-0.002	0.000	0.000	0.000	0.000
150	A	200	HIS	0	-0.011	-0.003	48.541	-0.002	-0.002	0.000	0.000	0.000	0.000
151	A	201	GLN	0	-0.015	-0.019	48.065	-0.003	-0.003	0.000	0.000	0.000	0.000
152	A	202	ARG	1	0.810	0.889	43.402	-0.049	-0.049	0.000	0.000	0.000	0.000
153	A	203	ALA	0	0.004	0.029	50.626	-0.001	-0.001	0.000	0.000	0.000	0.000
154	A	204	ARG	1	0.924	0.961	53.887	-0.024	-0.024	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:51:THR)