FMO DATABASE

FMODB ID: V57K1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1263270.865734
FMO2-HF: Nuclear repulsion	1207883.545994
FMO2-HF: Total energy	-55387.31974
FMO2-MP2: Total energy	-55551.581095

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.
-1.834	0.902	1.274	-1.354	-2.655	-0.001

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 : 0.037 / q_NPA : 0.015

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	-0.828	-0.900	2.613	-3.043	-0.312	1.274	-1.404	-2.601	-0.001
4	B	12	ARG	1	0.847	0.911	3.824	0.711	0.716	0.000	0.050	-0.054	0.000
5	B	13	PRO	0	0.050	0.022	6.748	-0.052	-0.052	0.000	0.000	0.000	0.000
6	B	14	CYS	0	-0.122	-0.048	7.909	0.466	0.466	0.000	0.000	0.000	0.000
7	B	15	HIS	0	-0.020	0.002	5.415	0.468	0.468	0.000	0.000	0.000	0.000
8	B	16	VAL	0	0.003	-0.008	10.660	-0.026	-0.026	0.000	0.000	0.000	0.000
9	B	17	SER	0	-0.012	-0.033	9.980	-0.003	-0.003	0.000	0.000	0.000	0.000
10	B	18	GLY	0	0.064	0.027	10.211	0.089	0.089	0.000	0.000	0.000	0.000
11	B	19	ASP	-1	-0.876	-0.937	11.989	-0.085	-0.085	0.000	0.000	0.000	0.000
12	B	20	SER	0	-0.142	-0.080	14.097	0.014	0.014	0.000	0.000	0.000	0.000
13	B	21	LEU	0	-0.006	-0.002	13.289	-0.005	-0.005	0.000	0.000	0.000	0.000
14	B	22	ASN	0	0.001	0.007	16.172	0.012	0.012	0.000	0.000	0.000	0.000
15	B	23	LYS	1	0.840	0.924	18.805	0.207	0.207	0.000	0.000	0.000	0.000
16	B	24	HIS	0	0.000	0.004	21.738	0.010	0.010	0.000	0.000	0.000	0.000
17	B	25	VAL	0	-0.011	-0.003	25.538	0.001	0.001	0.000	0.000	0.000	0.000
18	B	26	VAL	0	0.054	0.026	28.516	0.003	0.003	0.000	0.000	0.000	0.000
19	B	27	PHE	0	0.055	0.028	31.799	0.004	0.004	0.000	0.000	0.000	0.000
20	B	28	LYS	1	0.815	0.911	32.072	0.062	0.062	0.000	0.000	0.000	0.000
21	B	29	THR	0	-0.029	-0.010	37.367	-0.001	-0.001	0.000	0.000	0.000	0.000
22	B	30	ARG	1	0.855	0.902	40.469	0.039	0.039	0.000	0.000	0.000	0.000
23	B	31	ALA	0	0.049	0.031	44.291	0.000	0.000	0.000	0.000	0.000	0.000
24	B	32	SER	0	0.040	0.009	46.119	-0.001	-0.001	0.000	0.000	0.000	0.000
25	B	33	ARG	1	0.877	0.923	46.599	0.037	0.037	0.000	0.000	0.000	0.000
26	B	34	ASP	-1	-0.785	-0.856	42.241	-0.044	-0.044	0.000	0.000	0.000	0.000
27	B	35	PHE	0	-0.027	-0.019	39.866	-0.002	-0.002	0.000	0.000	0.000	0.000
28	B	36	TRP	0	-0.016	-0.001	45.735	0.001	0.001	0.000	0.000	0.000	0.000
29	B	37	TYR	0	-0.002	-0.009	48.533	0.001	0.001	0.000	0.000	0.000	0.000
30	B	38	PRO	0	0.037	0.025	47.509	-0.002	-0.002	0.000	0.000	0.000	0.000
31	B	39	PRO	0	-0.006	-0.012	43.263	0.003	0.003	0.000	0.000	0.000	0.000
32	B	40	GLY	0	0.016	0.003	44.327	-0.003	-0.003	0.000	0.000	0.000	0.000
33	B	41	ARG	1	0.843	0.902	35.822	0.072	0.072	0.000	0.000	0.000	0.000
34	B	42	SER	0	0.012	0.020	36.187	0.002	0.002	0.000	0.000	0.000	0.000
35	B	43	PRO	0	0.050	0.019	35.850	-0.003	-0.003	0.000	0.000	0.000	0.000
36	B	44	THR	0	-0.010	0.011	31.094	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	45	GLU	-1	-0.782	-0.860	29.674	-0.065	-0.065	0.000	0.000	0.000	0.000
38	B	46	SER	0	-0.045	-0.043	25.860	-0.009	-0.009	0.000	0.000	0.000	0.000
39	B	47	PHE	0	-0.002	-0.008	22.789	0.008	0.008	0.000	0.000	0.000	0.000
40	B	48	VAL	0	0.000	0.008	18.621	-0.019	-0.019	0.000	0.000	0.000	0.000
41	B	49	ILE	0	0.027	0.030	16.508	0.003	0.003	0.000	0.000	0.000	0.000
42	B	50	ARG	1	0.834	0.908	11.550	0.334	0.334	0.000	0.000	0.000	0.000
43	B	51	LEU	0	-0.031	-0.002	12.089	-0.021	-0.021	0.000	0.000	0.000	0.000
44	B	52	GLU	-1	-0.698	-0.835	6.668	-0.740	-0.740	0.000	0.000	0.000	0.000
45	B	53	ASN	0	-0.001	-0.011	5.881	-0.473	-0.473	0.000	0.000	0.000	0.000
46	B	55	HIS	0	0.110	0.047	9.627	0.112	0.112	0.000	0.000	0.000	0.000
47	B	56	ALA	0	0.110	0.055	14.354	0.017	0.017	0.000	0.000	0.000	0.000
48	B	57	THR	0	-0.001	-0.010	17.875	0.012	0.012	0.000	0.000	0.000	0.000
49	B	58	ALA	0	-0.010	-0.008	15.373	0.027	0.027	0.000	0.000	0.000	0.000
50	B	59	VAL	0	0.073	0.043	16.476	-0.001	-0.001	0.000	0.000	0.000	0.000
51	B	60	GLY	0	0.042	0.021	17.757	-0.010	-0.010	0.000	0.000	0.000	0.000
52	B	61	LYS	1	0.846	0.931	18.425	0.356	0.356	0.000	0.000	0.000	0.000
53	B	62	ILE	0	0.015	0.013	12.513	0.007	0.007	0.000	0.000	0.000	0.000
54	B	63	VAL	0	-0.014	-0.006	15.594	-0.004	-0.004	0.000	0.000	0.000	0.000
55	B	64	THR	0	-0.021	-0.002	17.629	0.038	0.038	0.000	0.000	0.000	0.000
56	B	65	LEU	0	-0.019	0.008	17.563	-0.014	-0.014	0.000	0.000	0.000	0.000
57	B	66	THR	0	0.031	0.020	21.498	0.024	0.024	0.000	0.000	0.000	0.000
58	B	67	PHE	0	0.045	0.030	23.206	-0.016	-0.016	0.000	0.000	0.000	0.000
59	B	68	LYS	1	0.836	0.904	25.582	0.231	0.231	0.000	0.000	0.000	0.000
60	B	69	GLY	0	0.064	0.014	27.974	-0.002	-0.002	0.000	0.000	0.000	0.000
61	B	70	THR	0	-0.012	0.003	30.757	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	71	GLU	-1	-0.813	-0.890	34.549	-0.107	-0.107	0.000	0.000	0.000	0.000
63	B	72	GLU	-1	-0.780	-0.887	36.488	-0.070	-0.070	0.000	0.000	0.000	0.000
64	B	73	ALA	0	0.024	0.012	39.617	0.000	0.000	0.000	0.000	0.000	0.000
65	B	74	ALA	0	-0.024	-0.008	42.506	0.002	0.002	0.000	0.000	0.000	0.000
66	B	75	LEU	0	-0.052	-0.030	40.284	0.003	0.003	0.000	0.000	0.000	0.000
67	B	76	PRO	0	0.041	0.023	39.402	-0.005	-0.005	0.000	0.000	0.000	0.000
68	B	77	GLY	0	-0.065	-0.048	35.856	0.000	0.000	0.000	0.000	0.000	0.000
69	B	78	HIS	0	-0.018	-0.014	34.933	-0.004	-0.004	0.000	0.000	0.000	0.000
70	B	79	LEU	0	0.023	0.012	30.109	0.000	0.000	0.000	0.000	0.000	0.000
71	B	80	LYS	1	0.801	0.877	34.693	0.081	0.081	0.000	0.000	0.000	0.000
72	B	81	VAL	0	-0.043	0.005	36.184	-0.003	-0.003	0.000	0.000	0.000	0.000
73	B	82	THR	0	-0.059	-0.047	36.736	0.003	0.003	0.000	0.000	0.000	0.000
74	B	83	GLY	0	0.105	0.045	39.163	0.001	0.001	0.000	0.000	0.000	0.000
75	B	84	VAL	0	0.009	-0.008	41.687	-0.001	-0.001	0.000	0.000	0.000	0.000
76	B	85	ASN	0	-0.005	-0.012	42.987	0.003	0.003	0.000	0.000	0.000	0.000
77	B	86	ALA	0	0.051	0.038	41.857	-0.003	-0.003	0.000	0.000	0.000	0.000
78	B	87	GLY	0	-0.013	-0.002	42.377	0.003	0.003	0.000	0.000	0.000	0.000
79	B	88	ARG	1	0.834	0.922	44.279	0.047	0.047	0.000	0.000	0.000	0.000
80	B	89	LEU	0	-0.001	0.002	40.567	0.002	0.002	0.000	0.000	0.000	0.000
81	B	90	GLY	0	0.038	0.027	38.300	-0.001	-0.001	0.000	0.000	0.000	0.000
82	B	91	ILE	0	-0.052	-0.028	32.383	0.004	0.004	0.000	0.000	0.000	0.000
83	B	92	ALA	0	0.035	0.027	34.132	-0.006	-0.006	0.000	0.000	0.000	0.000
84	B	93	LEU	0	-0.002	-0.005	27.850	0.000	0.000	0.000	0.000	0.000	0.000
85	B	94	LEU	0	-0.040	-0.016	29.504	0.004	0.004	0.000	0.000	0.000	0.000
86	B	95	ASP	-1	-0.662	-0.822	25.987	-0.219	-0.219	0.000	0.000	0.000	0.000
87	B	96	THR	0	-0.051	-0.037	22.212	0.002	0.002	0.000	0.000	0.000	0.000
88	B	97	ASP	-1	-0.791	-0.857	25.476	-0.136	-0.136	0.000	0.000	0.000	0.000
89	B	98	GLY	0	-0.014	0.001	28.551	0.012	0.012	0.000	0.000	0.000	0.000
90	B	99	SER	0	-0.079	-0.046	30.210	0.013	0.013	0.000	0.000	0.000	0.000
91	B	100	SER	0	-0.054	-0.060	30.882	0.008	0.008	0.000	0.000	0.000	0.000
92	B	101	LEU	0	-0.022	-0.017	31.439	-0.006	-0.006	0.000	0.000	0.000	0.000
93	B	102	LEU	0	-0.045	-0.012	25.869	-0.002	-0.002	0.000	0.000	0.000	0.000
94	B	103	LYS	1	0.918	0.972	30.547	0.110	0.110	0.000	0.000	0.000	0.000
95	B	104	PRO	0	0.035	0.027	30.706	-0.012	-0.012	0.000	0.000	0.000	0.000
96	B	105	GLY	0	-0.033	-0.014	29.073	0.005	0.005	0.000	0.000	0.000	0.000
97	B	106	THR	0	-0.076	-0.046	29.197	-0.007	-0.007	0.000	0.000	0.000	0.000
98	B	107	SER	0	-0.010	-0.016	25.217	-0.008	-0.008	0.000	0.000	0.000	0.000
99	B	108	HIS	1	0.768	0.844	22.096	0.274	0.274	0.000	0.000	0.000	0.000
100	B	109	ASN	0	-0.055	-0.035	25.309	-0.010	-0.010	0.000	0.000	0.000	0.000
101	B	110	LYS	1	0.855	0.924	20.957	0.319	0.319	0.000	0.000	0.000	0.000
102	B	111	GLY	0	-0.019	-0.012	23.470	0.019	0.019	0.000	0.000	0.000	0.000
103	B	112	GLN	0	-0.006	-0.009	24.433	0.004	0.004	0.000	0.000	0.000	0.000
104	B	113	GLY	0	0.068	0.040	25.212	-0.001	-0.001	0.000	0.000	0.000	0.000
105	B	114	GLU	-1	-0.846	-0.907	20.084	-0.332	-0.332	0.000	0.000	0.000	0.000
106	B	115	LYS	1	0.863	0.924	18.377	0.201	0.201	0.000	0.000	0.000	0.000
107	B	116	VAL	0	-0.017	-0.010	15.124	-0.037	-0.037	0.000	0.000	0.000	0.000
108	B	117	THR	0	-0.026	-0.025	14.268	0.071	0.071	0.000	0.000	0.000	0.000
109	B	118	GLY	0	0.036	0.038	11.621	-0.047	-0.047	0.000	0.000	0.000	0.000
110	B	119	ASN	0	-0.032	-0.029	6.496	-0.484	-0.484	0.000	0.000	0.000	0.000
111	B	120	SER	0	-0.025	-0.008	9.286	-0.192	-0.192	0.000	0.000	0.000	0.000
112	B	121	LEU	0	-0.022	-0.014	11.399	0.114	0.114	0.000	0.000	0.000	0.000
113	B	122	GLU	-1	-0.774	-0.863	14.798	-0.252	-0.252	0.000	0.000	0.000	0.000
114	B	123	LEU	0	0.021	0.000	16.950	0.020	0.020	0.000	0.000	0.000	0.000
115	B	124	PRO	0	-0.012	-0.004	19.936	0.008	0.008	0.000	0.000	0.000	0.000
116	B	125	PHE	0	0.029	0.018	20.615	0.009	0.009	0.000	0.000	0.000	0.000
117	B	126	GLY	0	0.028	0.012	24.860	0.011	0.011	0.000	0.000	0.000	0.000
118	B	127	ALA	0	-0.001	-0.001	28.154	-0.007	-0.007	0.000	0.000	0.000	0.000
119	B	128	TYR	0	-0.032	-0.019	30.856	0.007	0.007	0.000	0.000	0.000	0.000
120	B	129	VAL	0	0.035	0.034	34.538	-0.004	-0.004	0.000	0.000	0.000	0.000
121	B	130	VAL	0	0.007	-0.016	37.277	0.004	0.004	0.000	0.000	0.000	0.000
122	B	131	ALA	0	0.027	0.012	40.387	-0.001	-0.001	0.000	0.000	0.000	0.000
123	B	132	THR	0	-0.001	-0.012	43.779	-0.002	-0.002	0.000	0.000	0.000	0.000
124	B	133	PRO	0	0.036	0.012	45.404	0.004	0.004	0.000	0.000	0.000	0.000
125	B	134	GLU	-1	-0.732	-0.826	48.288	-0.043	-0.043	0.000	0.000	0.000	0.000
126	B	135	ALA	0	-0.008	0.020	47.243	0.003	0.003	0.000	0.000	0.000	0.000
127	B	136	LEU	0	-0.014	0.014	46.737	0.002	0.002	0.000	0.000	0.000	0.000
128	B	137	ARG	1	0.773	0.840	49.298	0.044	0.044	0.000	0.000	0.000	0.000
129	B	138	THR	0	-0.014	-0.041	52.488	0.002	0.002	0.000	0.000	0.000	0.000
130	B	139	LYS	1	0.846	0.938	51.207	0.040	0.040	0.000	0.000	0.000	0.000
131	B	140	SER	0	-0.012	-0.003	51.168	0.000	0.000	0.000	0.000	0.000	0.000
132	B	141	VAL	0	-0.025	-0.013	45.133	-0.001	-0.001	0.000	0.000	0.000	0.000
133	B	142	VAL	0	0.037	0.030	48.076	0.002	0.002	0.000	0.000	0.000	0.000
134	B	143	PRO	0	-0.033	-0.028	46.447	-0.002	-0.002	0.000	0.000	0.000	0.000
135	B	144	GLY	0	0.031	0.016	44.857	0.002	0.002	0.000	0.000	0.000	0.000
136	B	145	ASP	-1	-0.911	-0.942	39.739	-0.042	-0.042	0.000	0.000	0.000	0.000
137	B	146	TYR	0	-0.103	-0.081	36.811	-0.002	-0.002	0.000	0.000	0.000	0.000
138	B	147	GLU	-1	-0.837	-0.913	33.308	-0.074	-0.074	0.000	0.000	0.000	0.000
139	B	148	ALA	0	-0.026	-0.011	33.263	0.000	0.000	0.000	0.000	0.000	0.000
140	B	149	THR	0	-0.003	0.007	29.176	-0.002	-0.002	0.000	0.000	0.000	0.000
141	B	150	ALA	0	0.013	0.003	27.326	0.001	0.001	0.000	0.000	0.000	0.000
142	B	151	THR	0	-0.051	-0.029	22.866	-0.001	-0.001	0.000	0.000	0.000	0.000
143	B	152	PHE	0	0.023	0.018	17.658	-0.005	-0.005	0.000	0.000	0.000	0.000
144	B	153	GLU	-1	-0.810	-0.886	20.619	-0.261	-0.261	0.000	0.000	0.000	0.000
145	B	154	LEU	0	0.007	0.002	14.779	0.002	0.002	0.000	0.000	0.000	0.000
146	B	155	THR	0	0.017	0.002	17.546	-0.007	-0.007	0.000	0.000	0.000	0.000
147	B	156	TYR	0	-0.034	-0.030	11.676	0.019	0.019	0.000	0.000	0.000	0.000
148	B	157	ARG	1	0.863	0.942	16.762	0.355	0.355	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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