FMO DATABASE

FMODB ID: 39NVL

Calculation Name: 1PDO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PDO

Chain ID: A

ChEMBL ID:

UniProt ID: P69797

Base Structure: X-ray

Registration Date: 2023-06-21

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	129
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1072749.667467
FMO2-HF: Nuclear repulsion	1023811.620175
FMO2-HF: Total energy	-48938.047292
FMO2-MP2: Total energy	-49081.976132

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:THR)

Summations of interaction energy for fragment #1(A:2: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.
-29.745	-19.692	14.114	-10.122	-14.044	-0.011

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / q_NPA : 0.025

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	ALA	0	0.012	0.029	3.496	1.213	3.396	0.025	-1.082	-1.125	0.003
4	A	5	ILE	0	0.007	0.007	5.556	-0.843	-0.722	-0.001	-0.008	-0.111	0.000
5	A	6	VAL	0	-0.018	-0.017	7.942	0.088	0.088	0.000	0.000	0.000	0.000
6	A	7	ILE	0	0.010	0.015	11.341	-0.129	-0.129	0.000	0.000	0.000	0.000
7	A	8	GLY	0	0.032	0.005	14.212	-0.017	-0.017	0.000	0.000	0.000	0.000
8	A	9	THR	0	-0.044	-0.023	17.803	-0.009	-0.009	0.000	0.000	0.000	0.000
9	A	10	HIS	0	-0.048	-0.060	21.217	-0.013	-0.013	0.000	0.000	0.000	0.000
10	A	11	GLY	0	-0.028	0.000	24.662	0.005	0.005	0.000	0.000	0.000	0.000
11	A	12	TRP	0	-0.001	-0.031	22.421	0.002	0.002	0.000	0.000	0.000	0.000
12	A	13	ALA	0	0.009	0.009	21.646	0.014	0.014	0.000	0.000	0.000	0.000
13	A	14	ALA	0	0.017	0.008	16.806	0.015	0.015	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.776	-0.868	16.389	0.274	0.274	0.000	0.000	0.000	0.000
15	A	16	GLN	0	-0.020	-0.027	17.167	0.017	0.017	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.023	0.004	16.660	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	18	LEU	0	0.030	0.026	10.607	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.884	0.935	14.406	-0.267	-0.267	0.000	0.000	0.000	0.000
19	A	20	THR	0	-0.082	-0.052	16.832	-0.027	-0.027	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.024	0.009	12.684	-0.029	-0.029	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.833	-0.921	12.364	0.516	0.516	0.000	0.000	0.000	0.000
22	A	23	MET	0	-0.126	-0.060	14.154	-0.042	-0.042	0.000	0.000	0.000	0.000
23	A	24	LEU	0	-0.086	-0.050	15.564	-0.036	-0.036	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.029	-0.002	9.846	-0.030	-0.030	0.000	0.000	0.000	0.000
25	A	26	GLY	0	-0.005	0.015	11.628	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.977	-1.002	11.687	0.381	0.381	0.000	0.000	0.000	0.000
27	A	28	GLN	0	-0.029	-0.026	7.469	0.198	0.198	0.000	0.000	0.000	0.000
28	A	29	GLU	-1	-0.927	-0.954	4.934	0.610	0.610	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.016	-0.016	2.019	-9.837	-9.265	5.924	-2.832	-3.664	0.029
30	A	31	VAL	0	0.024	0.019	4.844	0.963	0.978	-0.001	-0.009	-0.005	0.000
31	A	32	GLY	0	0.009	0.008	7.529	-0.349	-0.349	0.000	0.000	0.000	0.000
32	A	33	TRP	0	-0.045	-0.020	11.016	-0.039	-0.039	0.000	0.000	0.000	0.000
33	A	34	ILE	0	0.002	0.006	14.460	-0.033	-0.033	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.823	-0.904	18.004	0.126	0.126	0.000	0.000	0.000	0.000
35	A	36	PHE	0	-0.021	-0.009	21.544	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	37	VAL	0	0.004	0.004	24.644	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	38	PRO	0	-0.024	-0.032	28.015	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	39	GLY	0	0.006	0.006	31.390	0.000	0.000	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.812	-0.881	25.842	0.068	0.068	0.000	0.000	0.000	0.000
40	A	41	ASN	0	-0.008	-0.020	28.338	0.000	0.000	0.000	0.000	0.000	0.000
41	A	42	ALA	0	0.037	0.013	25.872	0.005	0.005	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.758	-0.859	24.823	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	44	THR	0	-0.012	-0.014	24.849	0.001	0.001	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.005	-0.002	21.916	0.007	0.007	0.000	0.000	0.000	0.000
45	A	46	ILE	0	-0.018	0.003	20.508	0.010	0.010	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.854	-0.919	19.937	-0.023	-0.023	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.722	0.849	19.518	-0.088	-0.088	0.000	0.000	0.000	0.000
48	A	49	TYR	0	-0.008	-0.033	15.604	0.030	0.030	0.000	0.000	0.000	0.000
49	A	50	ASN	0	-0.018	-0.017	15.407	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.009	-0.003	15.766	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	52	GLN	0	-0.037	-0.013	13.135	0.004	0.004	0.000	0.000	0.000	0.000
52	A	53	LEU	0	0.041	0.017	10.942	0.054	0.054	0.000	0.000	0.000	0.000
53	A	54	ALA	0	-0.060	-0.025	10.942	-0.078	-0.078	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.759	0.866	11.265	-0.193	-0.193	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.010	0.009	6.871	0.126	0.126	0.000	0.000	0.000	0.000
56	A	57	ASP	-1	-0.799	-0.875	2.229	-10.769	-9.338	2.722	-1.895	-2.258	-0.025
57	A	58	THR	0	-0.013	-0.019	4.686	-0.387	-0.497	-0.001	-0.022	0.134	0.000
58	A	59	THR	0	-0.125	-0.081	4.875	0.308	0.308	0.000	0.000	0.000	0.000
59	A	60	LYS	1	0.794	0.884	2.163	1.496	1.637	2.587	-0.946	-1.782	0.003
60	A	61	GLY	0	0.043	0.026	5.877	0.332	0.332	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.078	-0.043	7.166	-0.113	-0.113	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.030	0.009	8.243	0.001	0.001	0.000	0.000	0.000	0.000
63	A	64	PHE	0	-0.004	-0.006	10.093	0.192	0.192	0.000	0.000	0.000	0.000
64	A	65	LEU	0	0.002	0.007	10.567	-0.044	-0.044	0.000	0.000	0.000	0.000
65	A	66	VAL	0	0.005	-0.008	14.328	0.024	0.024	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.759	-0.850	18.080	0.072	0.072	0.000	0.000	0.000	0.000
67	A	68	THR	0	-0.076	-0.055	21.261	-0.014	-0.014	0.000	0.000	0.000	0.000
68	A	69	TRP	0	0.062	0.020	21.522	0.000	0.000	0.000	0.000	0.000	0.000
69	A	70	GLY	0	-0.031	-0.006	24.300	0.001	0.001	0.000	0.000	0.000	0.000
70	A	71	GLY	0	0.038	0.037	25.292	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	72	SER	0	-0.024	-0.019	24.621	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	73	PRO	0	0.051	0.025	20.487	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	74	PHE	0	0.093	0.067	20.275	0.001	0.001	0.000	0.000	0.000	0.000
74	A	75	ASN	0	-0.037	-0.027	21.308	-0.019	-0.019	0.000	0.000	0.000	0.000
75	A	76	ALA	0	-0.021	-0.015	21.746	-0.013	-0.013	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.052	0.029	17.103	-0.013	-0.013	0.000	0.000	0.000	0.000
77	A	78	SER	0	-0.013	-0.025	18.687	-0.030	-0.030	0.000	0.000	0.000	0.000
78	A	79	ARG	1	0.773	0.857	20.811	0.011	0.011	0.000	0.000	0.000	0.000
79	A	80	ILE	0	-0.024	0.006	16.282	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	81	VAL	0	0.030	0.004	15.563	-0.026	-0.026	0.000	0.000	0.000	0.000
81	A	82	VAL	0	-0.084	-0.024	17.877	-0.022	-0.022	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.865	-0.918	20.340	-0.152	-0.152	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.758	0.884	14.985	0.168	0.168	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.879	-0.935	14.516	-0.389	-0.389	0.000	0.000	0.000	0.000
85	A	86	HIS	0	-0.035	-0.029	9.964	-0.100	-0.100	0.000	0.000	0.000	0.000
86	A	87	TYR	0	0.022	0.007	10.894	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	88	GLU	-1	-0.847	-0.917	12.772	-0.105	-0.105	0.000	0.000	0.000	0.000
88	A	89	VAL	0	-0.091	-0.057	13.799	0.048	0.048	0.000	0.000	0.000	0.000
89	A	90	ILE	0	0.032	0.026	13.048	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	91	ALA	0	-0.038	-0.024	16.443	0.033	0.033	0.000	0.000	0.000	0.000
91	A	92	GLY	0	-0.025	-0.006	19.488	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.036	-0.023	15.107	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	94	ASN	0	-0.053	-0.037	17.077	0.000	0.000	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.047	0.018	16.518	0.015	0.015	0.000	0.000	0.000	0.000
95	A	96	PRO	0	0.007	0.002	15.964	0.019	0.019	0.000	0.000	0.000	0.000
96	A	97	MET	0	0.030	0.046	13.597	0.008	0.008	0.000	0.000	0.000	0.000
97	A	98	LEU	0	-0.029	0.003	10.926	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	99	VAL	0	0.020	0.000	11.040	0.076	0.076	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.886	-0.952	11.161	0.056	0.056	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.053	-0.040	7.875	-0.079	-0.079	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.030	-0.026	6.670	-0.036	-0.036	0.000	0.000	0.000	0.000
102	A	103	MET	0	-0.043	-0.009	6.160	-0.095	-0.095	0.000	0.000	0.000	0.000
103	A	104	ALA	0	0.036	0.017	7.190	-0.128	-0.128	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.762	0.860	2.184	-5.754	-3.807	2.369	-1.397	-2.919	-0.003
105	A	106	ASP	-1	-0.844	-0.912	2.845	-5.338	-2.444	0.477	-1.586	-1.785	-0.016
106	A	107	ASP	-1	-0.996	-0.985	3.974	0.076	0.119	0.000	0.022	-0.066	0.000
107	A	108	ASP	-1	-0.915	-0.933	3.565	-1.311	-0.534	0.014	-0.358	-0.433	-0.002
108	A	109	PRO	0	-0.011	0.015	4.890	0.156	0.195	-0.001	-0.009	-0.030	0.000
109	A	110	SER	0	-0.054	-0.070	6.981	-0.231	-0.231	0.000	0.000	0.000	0.000
110	A	111	PHE	0	0.059	0.013	8.115	0.021	0.021	0.000	0.000	0.000	0.000
111	A	112	ASP	-1	-0.914	-0.960	9.585	-0.260	-0.260	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.874	-0.903	11.117	-0.323	-0.323	0.000	0.000	0.000	0.000
113	A	114	LEU	0	0.002	0.015	5.540	0.085	0.085	0.000	0.000	0.000	0.000
114	A	115	VAL	0	-0.012	-0.007	9.766	0.122	0.122	0.000	0.000	0.000	0.000
115	A	116	ALA	0	-0.024	-0.013	12.368	0.060	0.060	0.000	0.000	0.000	0.000
116	A	117	LEU	0	0.064	0.030	11.172	0.039	0.039	0.000	0.000	0.000	0.000
117	A	118	ALA	0	0.049	0.055	11.437	0.045	0.045	0.000	0.000	0.000	0.000
118	A	119	VAL	0	-0.046	-0.036	13.414	0.033	0.033	0.000	0.000	0.000	0.000
119	A	120	GLU	-1	-0.998	-0.993	16.777	-0.054	-0.054	0.000	0.000	0.000	0.000
120	A	121	THR	0	0.017	-0.026	14.776	0.026	0.026	0.000	0.000	0.000	0.000
121	A	122	GLY	0	0.001	0.004	16.862	0.017	0.017	0.000	0.000	0.000	0.000
122	A	123	ARG	1	0.892	0.948	18.173	0.030	0.030	0.000	0.000	0.000	0.000
123	A	124	GLU	-1	-0.813	-0.898	20.254	0.008	0.008	0.000	0.000	0.000	0.000
124	A	125	GLY	0	0.007	0.010	20.766	0.002	0.002	0.000	0.000	0.000	0.000
125	A	126	VAL	0	-0.085	-0.035	21.810	0.006	0.006	0.000	0.000	0.000	0.000
126	A	127	LYS	1	0.802	0.892	23.974	-0.024	-0.024	0.000	0.000	0.000	0.000
127	A	128	ALA	0	-0.002	-0.005	27.481	0.005	0.005	0.000	0.000	0.000	0.000
128	A	129	LEU	0	0.002	-0.001	30.938	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	130	LYS	1	0.952	0.982	32.963	-0.027	-0.027	0.000	0.000	0.000	0.000

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