FMO DATABASE

FMODB ID: Z6Q8N

Calculation Name: 3L1P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L1P

Chain ID: A

ChEMBL ID:

UniProt ID: P20263

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	150
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1334181.900353
FMO2-HF: Nuclear repulsion	1273679.850179
FMO2-HF: Total energy	-60502.050174
FMO2-MP2: Total energy	-60681.082064

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:1:ASP)

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

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.
-364.141	-368.163	35.115	-15.339	-15.755	0.176

Interaction energy analysis for fragmet #1(A:1:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.736 / q_NPA : -0.869

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	3	LYS	1	0.901	0.927	1.792	-77.514	-77.841	14.583	-7.459	-6.797	0.078
4	A	4	ALA	0	0.008	0.011	2.219	-10.313	-9.371	5.065	-1.636	-4.371	0.022
5	A	5	LEU	0	0.045	0.025	3.621	-12.537	-11.862	0.100	-0.245	-0.530	0.004
6	A	6	GLN	0	0.005	-0.004	6.294	-2.638	-2.638	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.906	0.954	1.706	-119.594	-124.906	15.367	-5.999	-4.057	0.072
8	A	8	GLU	-1	-0.815	-0.876	7.357	22.767	22.767	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.027	-0.028	9.508	-3.506	-3.506	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.822	-0.896	10.788	19.461	19.461	0.000	0.000	0.000	0.000
11	A	11	GLN	0	0.004	0.006	11.626	-1.716	-1.716	0.000	0.000	0.000	0.000
12	A	12	PHE	0	0.048	0.022	13.445	-1.622	-1.622	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.014	-0.015	15.235	-1.426	-1.426	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.796	0.892	14.109	-22.587	-22.587	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.026	0.024	17.629	-0.943	-0.943	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.016	-0.004	19.424	-0.853	-0.853	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.900	0.943	20.195	-16.298	-16.298	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.006	-0.007	22.080	-0.284	-0.284	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.802	0.894	23.423	-13.301	-13.301	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.777	0.837	25.287	-12.568	-12.568	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.057	-0.030	25.942	-0.415	-0.415	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.041	-0.028	27.213	-0.374	-0.374	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.010	0.014	28.723	-0.229	-0.229	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.008	0.017	31.529	-0.261	-0.261	0.000	0.000	0.000	0.000
25	A	25	TYR	0	0.028	0.037	30.249	-0.096	-0.096	0.000	0.000	0.000	0.000
26	A	26	THR	0	0.010	-0.038	30.657	0.452	0.452	0.000	0.000	0.000	0.000
27	A	27	GLN	0	-0.015	-0.031	25.437	-0.111	-0.111	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.039	-0.032	29.226	0.213	0.213	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.736	-0.819	32.279	9.444	9.444	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.036	0.055	26.049	0.007	0.007	0.000	0.000	0.000	0.000
31	A	31	GLY	0	-0.011	-0.012	28.936	0.071	0.071	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.007	-0.017	29.828	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	33	THR	0	0.074	0.009	31.396	-0.067	-0.067	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.011	0.003	25.607	0.055	0.055	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.073	-0.049	29.431	-0.056	-0.056	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.029	-0.014	32.510	-0.137	-0.137	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.061	0.052	29.221	-0.124	-0.124	0.000	0.000	0.000	0.000
38	A	38	PHE	0	0.048	0.021	26.576	0.093	0.093	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.004	0.010	29.835	0.028	0.028	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.752	0.850	27.677	-10.950	-10.950	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.056	0.054	29.754	0.242	0.242	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.097	-0.053	25.742	0.182	0.182	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.019	-0.007	28.856	-0.254	-0.254	0.000	0.000	0.000	0.000
44	A	44	GLN	0	0.154	0.070	28.651	0.532	0.532	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.005	-0.003	27.231	0.322	0.322	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.078	-0.038	24.237	0.228	0.228	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.074	0.046	23.507	0.749	0.749	0.000	0.000	0.000	0.000
48	A	48	SER	0	0.003	-0.010	23.276	0.689	0.689	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.908	0.947	21.626	-12.636	-12.636	0.000	0.000	0.000	0.000
50	A	50	PHE	0	0.000	0.001	17.540	0.869	0.869	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.693	-0.813	18.468	14.394	14.394	0.000	0.000	0.000	0.000
52	A	52	ALA	0	-0.014	0.008	19.229	0.097	0.097	0.000	0.000	0.000	0.000
53	A	53	LEU	0	0.015	0.014	12.682	0.441	0.441	0.000	0.000	0.000	0.000
54	A	54	GLN	0	-0.045	-0.013	16.061	0.227	0.227	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.072	-0.051	17.240	-1.342	-1.342	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.032	0.019	15.499	1.204	1.204	0.000	0.000	0.000	0.000
57	A	57	LEU	0	0.112	0.047	8.848	-1.120	-1.120	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.992	1.011	13.199	-19.457	-19.457	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.028	-0.038	15.051	-1.444	-1.444	0.000	0.000	0.000	0.000
60	A	60	MET	0	0.016	0.026	14.608	-1.231	-1.231	0.000	0.000	0.000	0.000
61	A	61	SER	0	0.030	-0.008	12.835	0.004	0.004	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.848	0.940	14.987	-15.603	-15.603	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.031	-0.012	18.577	-0.666	-0.666	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.771	0.839	11.563	-23.011	-23.011	0.000	0.000	0.000	0.000
65	A	65	PRO	0	0.018	0.023	17.139	-0.381	-0.381	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.038	-0.011	19.466	-0.640	-0.640	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.005	-0.008	20.763	-0.541	-0.541	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.788	-0.878	16.530	18.761	18.761	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.825	0.884	21.064	-13.705	-13.705	0.000	0.000	0.000	0.000
70	A	70	TRP	0	-0.013	-0.008	24.175	-0.222	-0.222	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.008	-0.011	22.231	-0.288	-0.288	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.808	-0.879	22.653	13.107	13.107	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.882	-0.923	26.047	9.829	9.829	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.043	-0.021	28.065	-0.389	-0.389	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.774	-0.866	26.191	11.932	11.932	0.000	0.000	0.000	0.000
76	A	76	ASN	0	-0.104	-0.047	29.619	-0.280	-0.280	0.000	0.000	0.000	0.000
77	A	77	ASN	0	-0.010	-0.021	32.749	-0.492	-0.492	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.910	-0.962	33.068	9.416	9.416	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.019	-0.025	35.297	-0.177	-0.177	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.055	0.013	38.190	-0.173	-0.173	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.088	-0.032	31.159	0.130	0.130	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.880	-0.929	36.467	8.164	8.164	0.000	0.000	0.000	0.000
83	A	83	ILE	0	-0.007	0.000	38.695	-0.160	-0.160	0.000	0.000	0.000	0.000
84	A	84	SER	0	-0.079	-0.035	38.640	-0.149	-0.149	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.712	0.847	37.599	-8.526	-8.526	0.000	0.000	0.000	0.000
86	A	86	SER	0	0.040	0.030	40.022	0.127	0.127	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.775	-0.871	41.133	7.173	7.173	0.000	0.000	0.000	0.000
88	A	88	THR	0	-0.148	-0.099	40.298	0.272	0.272	0.000	0.000	0.000	0.000
89	A	89	LEU	0	0.052	0.043	40.553	0.190	0.190	0.000	0.000	0.000	0.000
90	A	90	VAL	0	0.085	0.051	38.858	0.160	0.160	0.000	0.000	0.000	0.000
91	A	91	GLN	0	0.038	0.014	38.349	0.320	0.320	0.000	0.000	0.000	0.000
92	A	92	ALA	0	0.036	-0.001	35.128	-0.169	-0.169	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.929	0.995	34.679	-8.635	-8.635	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.933	0.954	30.790	-9.683	-9.683	0.000	0.000	0.000	0.000
95	A	95	ARG	1	0.970	0.967	29.153	-10.872	-10.872	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.940	0.984	34.745	-8.083	-8.083	0.000	0.000	0.000	0.000
97	A	97	ARG	1	0.974	0.974	33.511	-9.280	-9.280	0.000	0.000	0.000	0.000
98	A	98	THR	0	0.042	0.024	37.659	-0.038	-0.038	0.000	0.000	0.000	0.000
99	A	99	SER	0	-0.021	0.000	40.184	0.105	0.105	0.000	0.000	0.000	0.000
100	A	100	ILE	0	0.017	0.015	41.232	-0.141	-0.141	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.709	-0.812	43.619	6.723	6.723	0.000	0.000	0.000	0.000
102	A	102	ASN	0	0.051	0.013	44.638	0.220	0.220	0.000	0.000	0.000	0.000
103	A	103	ARG	1	0.937	0.929	46.634	-6.268	-6.268	0.000	0.000	0.000	0.000
104	A	104	VAL	0	0.033	0.038	46.397	-0.027	-0.027	0.000	0.000	0.000	0.000
105	A	105	ARG	1	0.836	0.909	40.743	-7.730	-7.730	0.000	0.000	0.000	0.000
106	A	106	TRP	0	0.038	0.021	45.282	0.150	0.150	0.000	0.000	0.000	0.000
107	A	107	SER	0	0.022	0.002	47.682	-0.035	-0.035	0.000	0.000	0.000	0.000
108	A	108	LEU	0	-0.026	-0.015	44.037	-0.032	-0.032	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.778	-0.873	42.980	7.732	7.732	0.000	0.000	0.000	0.000
110	A	110	THR	0	0.024	0.026	45.983	-0.067	-0.067	0.000	0.000	0.000	0.000
111	A	111	MET	0	-0.041	0.001	47.351	-0.177	-0.177	0.000	0.000	0.000	0.000
112	A	112	PHE	0	-0.040	-0.030	41.019	0.138	0.138	0.000	0.000	0.000	0.000
113	A	113	LEU	0	0.007	0.007	43.510	-0.022	-0.022	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.910	0.934	46.251	-6.292	-6.292	0.000	0.000	0.000	0.000
115	A	115	SER	0	0.032	0.010	47.797	-0.122	-0.122	0.000	0.000	0.000	0.000
116	A	116	PRO	0	0.008	0.010	42.454	0.081	0.081	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.930	0.958	41.587	-7.401	-7.401	0.000	0.000	0.000	0.000
118	A	118	PRO	0	0.025	0.024	44.798	-0.091	-0.091	0.000	0.000	0.000	0.000
119	A	119	SER	0	0.046	0.027	46.524	-0.092	-0.092	0.000	0.000	0.000	0.000
120	A	120	LEU	0	0.025	0.008	47.930	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	121	GLN	0	0.098	0.063	49.070	0.098	0.098	0.000	0.000	0.000	0.000
122	A	122	GLN	0	0.049	0.010	50.207	-0.137	-0.137	0.000	0.000	0.000	0.000
123	A	123	ILE	0	-0.082	-0.042	45.104	0.054	0.054	0.000	0.000	0.000	0.000
124	A	124	THR	0	0.000	-0.009	48.758	0.045	0.045	0.000	0.000	0.000	0.000
125	A	125	HIS	0	0.035	0.026	51.587	-0.024	-0.024	0.000	0.000	0.000	0.000
126	A	126	ILE	0	0.009	-0.005	48.249	0.000	0.000	0.000	0.000	0.000	0.000
127	A	127	ALA	0	-0.044	-0.017	48.736	0.028	0.028	0.000	0.000	0.000	0.000
128	A	128	ASN	0	0.009	-0.005	49.977	-0.017	-0.017	0.000	0.000	0.000	0.000
129	A	129	GLN	0	-0.008	0.013	53.460	-0.023	-0.023	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.048	-0.027	48.912	-0.026	-0.026	0.000	0.000	0.000	0.000
131	A	131	GLY	0	0.037	0.037	50.645	0.077	0.077	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.081	-0.045	45.294	0.185	0.185	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.765	-0.876	45.019	6.817	6.817	0.000	0.000	0.000	0.000
134	A	134	LYS	1	0.888	0.910	45.528	-6.827	-6.827	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.827	-0.901	41.556	7.496	7.496	0.000	0.000	0.000	0.000
136	A	136	VAL	0	-0.003	-0.010	40.998	0.221	0.221	0.000	0.000	0.000	0.000
137	A	137	VAL	0	0.047	0.036	41.457	0.191	0.191	0.000	0.000	0.000	0.000
138	A	138	ARG	1	0.885	0.933	41.169	-7.505	-7.505	0.000	0.000	0.000	0.000
139	A	139	VAL	0	0.011	0.019	36.180	0.196	0.196	0.000	0.000	0.000	0.000
140	A	140	TRP	0	0.027	0.025	37.765	0.292	0.292	0.000	0.000	0.000	0.000
141	A	141	PHE	0	0.065	0.015	39.221	0.171	0.171	0.000	0.000	0.000	0.000
142	A	142	SER	0	-0.073	-0.041	36.455	0.045	0.045	0.000	0.000	0.000	0.000
143	A	143	ASN	0	-0.027	-0.025	33.549	0.437	0.437	0.000	0.000	0.000	0.000
144	A	144	ARG	1	0.777	0.878	35.500	-7.759	-7.759	0.000	0.000	0.000	0.000
145	A	145	ARG	1	0.895	0.934	37.713	-8.098	-8.098	0.000	0.000	0.000	0.000
146	A	146	GLN	0	-0.001	-0.006	30.970	-0.067	-0.067	0.000	0.000	0.000	0.000
147	A	147	LYS	1	0.928	0.980	32.880	-8.800	-8.800	0.000	0.000	0.000	0.000
148	A	148	GLY	0	0.030	0.026	34.665	0.080	0.080	0.000	0.000	0.000	0.000
149	A	149	LYS	1	0.931	0.959	32.633	-9.682	-9.682	0.000	0.000	0.000	0.000
150	A	150	ARG	1	0.903	0.958	28.499	-10.433	-10.433	0.000	0.000	0.000	0.000

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