FMO DATABASE

FMODB ID: YZLN2

Calculation Name: 1PDK-B-Xray372

Preferred Name: Chaperone protein PapD

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1PDK

Chain ID: B

ChEMBL ID: CHEMBL3309037

UniProt ID: P15319

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	OptHSide
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	148
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1262189.735856
FMO2-HF: Nuclear repulsion	1206802.898633
FMO2-HF: Total energy	-55386.837222
FMO2-MP2: Total energy	-55551.106961

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:9:LEU)

Summations of interaction energy for fragment #1(B:9:LEU)

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.
-3.103	0.309	0.731	-1.438	-2.704	-0.003

Interaction energy analysis for fragmet #1(B:9:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : 0.008

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	B	11	ASP	-1	-0.841	-0.932	2.560	-3.866	-0.480	0.732	-1.450	-2.667	-0.003
4	B	12	ARG	1	0.868	0.952	3.978	0.713	0.739	-0.001	0.012	-0.037	0.000
5	B	13	PRO	0	0.038	0.015	7.191	-0.210	-0.210	0.000	0.000	0.000	0.000
6	B	14	CYS	0	-0.098	-0.041	7.388	0.478	0.478	0.000	0.000	0.000	0.000
7	B	15	HIS	0	-0.029	0.005	5.146	0.548	0.548	0.000	0.000	0.000	0.000
8	B	16	VAL	0	0.004	-0.012	10.263	-0.034	-0.034	0.000	0.000	0.000	0.000
9	B	17	SER	0	-0.012	-0.032	9.396	-0.013	-0.013	0.000	0.000	0.000	0.000
10	B	18	GLY	0	0.038	0.006	9.591	0.086	0.086	0.000	0.000	0.000	0.000
11	B	19	ASP	-1	-0.833	-0.893	11.391	0.023	0.023	0.000	0.000	0.000	0.000
12	B	20	SER	0	-0.116	-0.054	13.657	0.010	0.010	0.000	0.000	0.000	0.000
13	B	21	LEU	0	-0.010	-0.008	12.735	-0.019	-0.019	0.000	0.000	0.000	0.000
14	B	22	ASN	0	-0.001	0.006	15.700	-0.001	-0.001	0.000	0.000	0.000	0.000
15	B	23	LYS	1	0.854	0.944	18.213	0.187	0.187	0.000	0.000	0.000	0.000
16	B	24	HIS	0	0.009	-0.001	21.396	0.006	0.006	0.000	0.000	0.000	0.000
17	B	25	VAL	0	-0.011	0.010	25.192	0.006	0.006	0.000	0.000	0.000	0.000
18	B	26	VAL	0	0.052	0.026	27.936	0.001	0.001	0.000	0.000	0.000	0.000
19	B	27	PHE	0	0.024	0.012	31.199	0.003	0.003	0.000	0.000	0.000	0.000
20	B	28	LYS	1	0.836	0.919	31.724	0.053	0.053	0.000	0.000	0.000	0.000
21	B	29	THR	0	-0.030	0.000	37.074	-0.002	-0.002	0.000	0.000	0.000	0.000
22	B	30	ARG	1	0.830	0.889	40.136	0.034	0.034	0.000	0.000	0.000	0.000
23	B	31	ALA	0	0.043	0.021	43.902	-0.001	-0.001	0.000	0.000	0.000	0.000
24	B	32	SER	0	0.046	0.019	45.993	-0.002	-0.002	0.000	0.000	0.000	0.000
25	B	33	ARG	1	0.897	0.932	46.268	0.032	0.032	0.000	0.000	0.000	0.000
26	B	34	ASP	-1	-0.770	-0.854	42.104	-0.039	-0.039	0.000	0.000	0.000	0.000
27	B	35	PHE	0	-0.009	-0.011	39.686	-0.002	-0.002	0.000	0.000	0.000	0.000
28	B	36	TRP	0	-0.014	0.004	45.555	0.001	0.001	0.000	0.000	0.000	0.000
29	B	37	TYR	0	-0.007	-0.020	48.294	0.001	0.001	0.000	0.000	0.000	0.000
30	B	38	PRO	0	0.029	0.029	46.997	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	39	PRO	0	-0.010	-0.021	42.783	0.002	0.002	0.000	0.000	0.000	0.000
32	B	40	GLY	0	0.013	0.024	44.363	-0.002	-0.002	0.000	0.000	0.000	0.000
33	B	41	ARG	1	0.870	0.908	35.281	0.069	0.069	0.000	0.000	0.000	0.000
34	B	42	SER	0	0.020	0.045	35.837	0.003	0.003	0.000	0.000	0.000	0.000
35	B	43	PRO	0	0.042	0.006	35.558	-0.004	-0.004	0.000	0.000	0.000	0.000
36	B	44	THR	0	-0.009	-0.011	30.558	0.000	0.000	0.000	0.000	0.000	0.000
37	B	45	GLU	-1	-0.796	-0.873	29.625	-0.054	-0.054	0.000	0.000	0.000	0.000
38	B	46	SER	0	-0.041	-0.028	25.799	-0.010	-0.010	0.000	0.000	0.000	0.000
39	B	47	PHE	0	-0.006	-0.004	22.185	0.007	0.007	0.000	0.000	0.000	0.000
40	B	48	VAL	0	0.001	-0.001	18.037	-0.012	-0.012	0.000	0.000	0.000	0.000
41	B	49	ILE	0	0.008	-0.001	16.059	0.006	0.006	0.000	0.000	0.000	0.000
42	B	50	ARG	1	0.849	0.908	11.430	0.260	0.260	0.000	0.000	0.000	0.000
43	B	51	LEU	0	-0.023	-0.009	11.844	-0.033	-0.033	0.000	0.000	0.000	0.000
44	B	52	GLU	-1	-0.721	-0.859	6.298	-0.839	-0.839	0.000	0.000	0.000	0.000
45	B	53	ASN	0	-0.003	-0.001	5.390	-0.737	-0.737	0.000	0.000	0.000	0.000
46	B	55	HIS	0	0.085	0.031	9.022	0.158	0.158	0.000	0.000	0.000	0.000
47	B	56	ALA	0	0.085	0.025	13.624	0.030	0.030	0.000	0.000	0.000	0.000
48	B	57	THR	0	-0.016	-0.018	17.370	-0.002	-0.002	0.000	0.000	0.000	0.000
49	B	58	ALA	0	-0.007	-0.011	15.214	0.028	0.028	0.000	0.000	0.000	0.000
50	B	59	VAL	0	0.161	0.077	16.162	-0.003	-0.003	0.000	0.000	0.000	0.000
51	B	60	GLY	0	0.008	0.013	17.694	-0.010	-0.010	0.000	0.000	0.000	0.000
52	B	61	LYS	1	0.866	0.940	18.497	0.371	0.371	0.000	0.000	0.000	0.000
53	B	62	ILE	0	-0.022	-0.005	12.816	0.004	0.004	0.000	0.000	0.000	0.000
54	B	63	VAL	0	-0.015	-0.011	15.492	-0.003	-0.003	0.000	0.000	0.000	0.000
55	B	64	THR	0	-0.050	-0.011	17.683	0.036	0.036	0.000	0.000	0.000	0.000
56	B	65	LEU	0	-0.007	0.002	17.188	-0.019	-0.019	0.000	0.000	0.000	0.000
57	B	66	THR	0	0.049	0.021	21.243	0.026	0.026	0.000	0.000	0.000	0.000
58	B	67	PHE	0	0.048	0.049	22.999	-0.013	-0.013	0.000	0.000	0.000	0.000
59	B	68	LYS	1	0.826	0.891	25.789	0.233	0.233	0.000	0.000	0.000	0.000
60	B	69	GLY	0	0.044	0.006	28.245	0.000	0.000	0.000	0.000	0.000	0.000
61	B	70	THR	0	-0.018	-0.004	31.008	-0.002	-0.002	0.000	0.000	0.000	0.000
62	B	71	GLU	-1	-0.797	-0.877	34.768	-0.107	-0.107	0.000	0.000	0.000	0.000
63	B	72	GLU	-1	-0.788	-0.885	36.552	-0.068	-0.068	0.000	0.000	0.000	0.000
64	B	73	ALA	0	0.030	0.011	39.563	0.001	0.001	0.000	0.000	0.000	0.000
65	B	74	ALA	0	-0.010	-0.001	42.436	0.001	0.001	0.000	0.000	0.000	0.000
66	B	75	LEU	0	-0.076	-0.036	39.957	0.003	0.003	0.000	0.000	0.000	0.000
67	B	76	PRO	0	0.060	0.020	39.114	-0.005	-0.005	0.000	0.000	0.000	0.000
68	B	77	GLY	0	-0.074	-0.047	35.378	0.000	0.000	0.000	0.000	0.000	0.000
69	B	78	HIS	0	-0.049	-0.032	34.414	-0.004	-0.004	0.000	0.000	0.000	0.000
70	B	79	LEU	0	0.001	-0.006	29.927	-0.001	-0.001	0.000	0.000	0.000	0.000
71	B	80	LYS	1	0.799	0.885	34.538	0.081	0.081	0.000	0.000	0.000	0.000
72	B	81	VAL	0	-0.025	0.003	35.548	-0.004	-0.004	0.000	0.000	0.000	0.000
73	B	82	THR	0	-0.052	-0.040	36.528	0.004	0.004	0.000	0.000	0.000	0.000
74	B	83	GLY	0	0.082	0.032	38.897	0.002	0.002	0.000	0.000	0.000	0.000
75	B	84	VAL	0	0.035	-0.005	41.704	-0.001	-0.001	0.000	0.000	0.000	0.000
76	B	85	ASN	0	-0.006	-0.004	42.530	0.002	0.002	0.000	0.000	0.000	0.000
77	B	86	ALA	0	0.040	0.033	41.710	-0.003	-0.003	0.000	0.000	0.000	0.000
78	B	87	GLY	0	0.009	0.007	42.167	0.002	0.002	0.000	0.000	0.000	0.000
79	B	88	ARG	1	0.825	0.915	43.726	0.045	0.045	0.000	0.000	0.000	0.000
80	B	89	LEU	0	-0.003	0.001	39.904	0.001	0.001	0.000	0.000	0.000	0.000
81	B	90	GLY	0	0.026	0.027	38.163	-0.002	-0.002	0.000	0.000	0.000	0.000
82	B	91	ILE	0	-0.046	-0.026	31.907	0.003	0.003	0.000	0.000	0.000	0.000
83	B	92	ALA	0	0.034	0.021	33.916	-0.006	-0.006	0.000	0.000	0.000	0.000
84	B	93	LEU	0	0.013	0.004	27.421	0.001	0.001	0.000	0.000	0.000	0.000
85	B	94	LEU	0	-0.031	-0.014	29.378	0.002	0.002	0.000	0.000	0.000	0.000
86	B	95	ASP	-1	-0.674	-0.829	25.523	-0.224	-0.224	0.000	0.000	0.000	0.000
87	B	96	THR	0	0.005	-0.015	21.877	0.004	0.004	0.000	0.000	0.000	0.000
88	B	97	ASP	-1	-0.884	-0.895	25.242	-0.134	-0.134	0.000	0.000	0.000	0.000
89	B	98	GLY	0	-0.009	-0.004	28.207	0.012	0.012	0.000	0.000	0.000	0.000
90	B	99	SER	0	-0.075	-0.040	29.840	0.014	0.014	0.000	0.000	0.000	0.000
91	B	100	SER	0	-0.048	-0.054	30.806	0.008	0.008	0.000	0.000	0.000	0.000
92	B	101	LEU	0	-0.034	-0.010	31.122	-0.006	-0.006	0.000	0.000	0.000	0.000
93	B	102	LEU	0	-0.054	-0.029	25.342	-0.005	-0.005	0.000	0.000	0.000	0.000
94	B	103	LYS	1	0.953	0.971	30.042	0.114	0.114	0.000	0.000	0.000	0.000
95	B	104	PRO	0	0.035	0.023	30.094	-0.013	-0.013	0.000	0.000	0.000	0.000
96	B	105	GLY	0	-0.036	-0.008	29.211	0.007	0.007	0.000	0.000	0.000	0.000
97	B	106	THR	0	-0.081	-0.038	29.704	-0.004	-0.004	0.000	0.000	0.000	0.000
98	B	107	SER	0	-0.010	-0.010	25.237	-0.006	-0.006	0.000	0.000	0.000	0.000
99	B	108	HIS	1	0.773	0.846	21.824	0.282	0.282	0.000	0.000	0.000	0.000
100	B	109	ASN	0	-0.080	-0.046	24.979	-0.011	-0.011	0.000	0.000	0.000	0.000
101	B	110	LYS	1	0.873	0.947	20.729	0.331	0.331	0.000	0.000	0.000	0.000
102	B	111	GLY	0	-0.020	-0.012	23.180	0.021	0.021	0.000	0.000	0.000	0.000
103	B	112	GLN	0	0.029	0.000	23.855	-0.001	-0.001	0.000	0.000	0.000	0.000
104	B	113	GLY	0	0.063	0.037	24.838	-0.006	-0.006	0.000	0.000	0.000	0.000
105	B	114	GLU	-1	-0.861	-0.903	19.611	-0.334	-0.334	0.000	0.000	0.000	0.000
106	B	115	LYS	1	0.913	0.961	18.106	0.178	0.178	0.000	0.000	0.000	0.000
107	B	116	VAL	0	0.005	-0.016	14.971	-0.043	-0.043	0.000	0.000	0.000	0.000
108	B	117	THR	0	-0.037	-0.020	14.386	0.054	0.054	0.000	0.000	0.000	0.000
109	B	118	GLY	0	0.035	0.028	11.313	-0.036	-0.036	0.000	0.000	0.000	0.000
110	B	119	ASN	0	-0.002	-0.010	6.223	-0.520	-0.520	0.000	0.000	0.000	0.000
111	B	120	SER	0	-0.061	-0.025	9.061	-0.173	-0.173	0.000	0.000	0.000	0.000
112	B	121	LEU	0	-0.037	-0.020	10.672	0.107	0.107	0.000	0.000	0.000	0.000
113	B	122	GLU	-1	-0.814	-0.888	14.208	-0.231	-0.231	0.000	0.000	0.000	0.000
114	B	123	LEU	0	-0.008	-0.010	16.431	0.020	0.020	0.000	0.000	0.000	0.000
115	B	124	PRO	0	-0.001	-0.004	19.415	0.009	0.009	0.000	0.000	0.000	0.000
116	B	125	PHE	0	0.053	0.028	20.322	0.000	0.000	0.000	0.000	0.000	0.000
117	B	126	GLY	0	0.022	0.008	24.666	0.014	0.014	0.000	0.000	0.000	0.000
118	B	127	ALA	0	0.013	0.011	28.047	-0.007	-0.007	0.000	0.000	0.000	0.000
119	B	128	TYR	0	-0.029	-0.011	30.420	0.008	0.008	0.000	0.000	0.000	0.000
120	B	129	VAL	0	0.039	0.035	34.060	-0.004	-0.004	0.000	0.000	0.000	0.000
121	B	130	VAL	0	0.000	-0.017	36.907	0.004	0.004	0.000	0.000	0.000	0.000
122	B	131	ALA	0	0.036	0.025	40.013	-0.001	-0.001	0.000	0.000	0.000	0.000
123	B	132	THR	0	-0.019	-0.012	43.367	-0.002	-0.002	0.000	0.000	0.000	0.000
124	B	133	PRO	0	0.072	0.024	44.904	0.003	0.003	0.000	0.000	0.000	0.000
125	B	134	GLU	-1	-0.750	-0.843	47.734	-0.043	-0.043	0.000	0.000	0.000	0.000
126	B	135	ALA	0	-0.005	0.016	46.529	0.003	0.003	0.000	0.000	0.000	0.000
127	B	136	LEU	0	-0.035	0.001	46.650	0.002	0.002	0.000	0.000	0.000	0.000
128	B	137	ARG	1	0.785	0.851	49.083	0.044	0.044	0.000	0.000	0.000	0.000
129	B	138	THR	0	-0.048	-0.051	51.912	0.002	0.002	0.000	0.000	0.000	0.000
130	B	139	LYS	1	0.868	0.954	50.806	0.037	0.037	0.000	0.000	0.000	0.000
131	B	140	SER	0	0.014	0.007	50.358	0.001	0.001	0.000	0.000	0.000	0.000
132	B	141	VAL	0	-0.046	-0.012	44.577	0.000	0.000	0.000	0.000	0.000	0.000
133	B	142	VAL	0	0.011	0.001	47.084	0.002	0.002	0.000	0.000	0.000	0.000
134	B	143	PRO	0	-0.030	-0.017	45.883	-0.002	-0.002	0.000	0.000	0.000	0.000
135	B	144	GLY	0	0.035	0.006	44.198	0.001	0.001	0.000	0.000	0.000	0.000
136	B	145	ASP	-1	-0.924	-0.949	38.926	-0.037	-0.037	0.000	0.000	0.000	0.000
137	B	146	TYR	0	-0.082	-0.066	36.054	-0.002	-0.002	0.000	0.000	0.000	0.000
138	B	147	GLU	-1	-0.853	-0.916	33.158	-0.064	-0.064	0.000	0.000	0.000	0.000
139	B	148	ALA	0	-0.007	-0.015	32.731	-0.001	-0.001	0.000	0.000	0.000	0.000
140	B	149	THR	0	0.004	0.017	28.989	0.000	0.000	0.000	0.000	0.000	0.000
141	B	150	ALA	0	-0.016	-0.015	26.795	0.001	0.001	0.000	0.000	0.000	0.000
142	B	151	THR	0	-0.026	-0.007	23.371	-0.003	-0.003	0.000	0.000	0.000	0.000
143	B	152	PHE	0	0.022	0.015	17.448	-0.003	-0.003	0.000	0.000	0.000	0.000
144	B	153	GLU	-1	-0.807	-0.906	20.509	-0.270	-0.270	0.000	0.000	0.000	0.000
145	B	154	LEU	0	0.004	0.010	15.003	0.000	0.000	0.000	0.000	0.000	0.000
146	B	155	THR	0	-0.005	-0.007	18.374	0.004	0.004	0.000	0.000	0.000	0.000
147	B	156	TYR	0	-0.030	-0.023	12.187	0.010	0.010	0.000	0.000	0.000	0.000
148	B	157	ARG	1	0.914	0.971	17.291	0.357	0.357	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:9:LEU)