FMO DATABASE

FMODB ID: 6Y3QZ

Calculation Name: 4PNH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PNH

Chain ID: A

ChEMBL ID:

UniProt ID: Q2T109

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	OptH
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	155
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1420512.650818
FMO2-HF: Nuclear repulsion	1362162.009086
FMO2-HF: Total energy	-58350.641732
FMO2-MP2: Total energy	-58520.213809

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:7:LYS)

Summations of interaction energy for fragment #1(A:7:LYS)

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.
-43.508	-41.033	0.05	-0.865	-1.661	0.004

Interaction energy analysis for fragmet #1(A:7:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.936 / q_NPA : 0.945

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	9	LEU	0	0.007	0.010	3.806	-3.609	-2.101	-0.022	-0.675	-0.811	0.003
4	A	10	VAL	0	0.040	0.016	6.468	2.173	2.173	0.000	0.000	0.000	0.000
5	A	11	VAL	0	-0.018	0.002	10.095	-0.325	-0.325	0.000	0.000	0.000	0.000
6	A	12	LEU	0	0.009	-0.001	12.755	1.061	1.061	0.000	0.000	0.000	0.000
7	A	13	ASP	-1	-0.811	-0.898	15.690	-13.662	-13.662	0.000	0.000	0.000	0.000
8	A	14	ARG	1	0.865	0.914	19.019	12.362	12.362	0.000	0.000	0.000	0.000
9	A	15	ASP	-1	-0.852	-0.929	20.378	-11.303	-11.303	0.000	0.000	0.000	0.000
10	A	16	GLY	0	-0.011	0.009	24.069	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	17	VAL	0	-0.027	0.045	19.237	0.133	0.133	0.000	0.000	0.000	0.000
12	A	18	ILE	0	0.007	-0.008	16.984	-0.097	-0.097	0.000	0.000	0.000	0.000
13	A	19	ASN	0	-0.025	-0.010	21.394	-0.032	-0.032	0.000	0.000	0.000	0.000
14	A	20	VAL	0	-0.026	0.001	24.649	0.197	0.197	0.000	0.000	0.000	0.000
15	A	28	SER	0	0.021	-0.002	33.700	0.025	0.025	0.000	0.000	0.000	0.000
16	A	29	PRO	0	-0.002	-0.006	28.979	-0.160	-0.160	0.000	0.000	0.000	0.000
17	A	30	ASP	-1	-0.771	-0.899	28.181	-10.792	-10.792	0.000	0.000	0.000	0.000
18	A	31	GLU	-1	-1.012	-0.985	29.471	-8.785	-8.785	0.000	0.000	0.000	0.000
19	A	32	TRP	0	-0.033	-0.026	21.365	-0.025	-0.025	0.000	0.000	0.000	0.000
20	A	33	VAL	0	0.012	-0.023	27.001	-0.130	-0.130	0.000	0.000	0.000	0.000
21	A	34	ALA	0	0.007	0.001	22.537	0.009	0.009	0.000	0.000	0.000	0.000
22	A	35	LEU	0	0.015	0.003	24.123	0.455	0.455	0.000	0.000	0.000	0.000
23	A	36	PRO	0	0.047	0.008	23.313	-0.537	-0.537	0.000	0.000	0.000	0.000
24	A	37	GLY	0	0.048	0.020	23.063	-0.346	-0.346	0.000	0.000	0.000	0.000
25	A	38	SER	0	0.001	-0.013	20.064	-0.348	-0.348	0.000	0.000	0.000	0.000
26	A	39	LEU	0	-0.024	-0.004	18.398	-0.809	-0.809	0.000	0.000	0.000	0.000
27	A	40	GLU	-1	-0.874	-0.927	17.918	-13.458	-13.458	0.000	0.000	0.000	0.000
28	A	41	ALA	0	-0.013	-0.011	17.283	-0.731	-0.731	0.000	0.000	0.000	0.000
29	A	42	ILE	0	0.019	0.010	12.969	-0.932	-0.932	0.000	0.000	0.000	0.000
30	A	43	ALA	0	0.063	0.042	12.877	-1.489	-1.489	0.000	0.000	0.000	0.000
31	A	44	ARG	1	0.924	0.964	13.633	14.310	14.310	0.000	0.000	0.000	0.000
32	A	45	LEU	0	-0.005	0.001	10.780	-0.740	-0.740	0.000	0.000	0.000	0.000
33	A	46	ASN	0	0.003	0.001	8.862	-0.357	-0.357	0.000	0.000	0.000	0.000
34	A	47	HIS	0	-0.005	0.007	9.004	-2.703	-2.703	0.000	0.000	0.000	0.000
35	A	48	ALA	0	-0.026	-0.004	9.880	-0.243	-0.243	0.000	0.000	0.000	0.000
36	A	49	GLY	0	-0.050	-0.027	6.075	-0.835	-0.835	0.000	0.000	0.000	0.000
37	A	50	TYR	0	-0.060	-0.028	4.487	-4.986	-4.811	-0.001	-0.011	-0.163	0.000
38	A	51	ARG	1	0.859	0.915	2.652	45.681	46.473	0.073	-0.179	-0.687	0.001
39	A	52	VAL	0	0.025	0.012	6.019	1.214	1.214	0.000	0.000	0.000	0.000
40	A	53	VAL	0	0.016	0.018	8.915	0.282	0.282	0.000	0.000	0.000	0.000
41	A	54	VAL	0	-0.019	-0.004	11.396	1.106	1.106	0.000	0.000	0.000	0.000
42	A	55	ALA	0	0.007	-0.010	15.137	0.145	0.145	0.000	0.000	0.000	0.000
43	A	56	THR	0	0.024	0.007	17.335	0.853	0.853	0.000	0.000	0.000	0.000
44	A	57	ASN	0	0.019	-0.001	20.814	-0.146	-0.146	0.000	0.000	0.000	0.000
45	A	58	GLN	0	0.094	0.031	23.581	0.507	0.507	0.000	0.000	0.000	0.000
46	A	59	SER	0	-0.006	-0.002	25.668	0.311	0.311	0.000	0.000	0.000	0.000
47	A	60	GLY	0	-0.070	-0.050	27.137	0.455	0.455	0.000	0.000	0.000	0.000
48	A	61	ILE	0	0.000	0.025	25.074	-0.196	-0.196	0.000	0.000	0.000	0.000
49	A	62	GLY	0	0.009	-0.011	28.561	0.236	0.236	0.000	0.000	0.000	0.000
50	A	63	ARG	1	0.879	0.927	31.166	8.574	8.574	0.000	0.000	0.000	0.000
51	A	64	GLY	0	0.005	0.005	30.450	0.214	0.214	0.000	0.000	0.000	0.000
52	A	65	LEU	0	0.006	0.028	31.479	0.102	0.102	0.000	0.000	0.000	0.000
53	A	66	PHE	0	-0.018	-0.021	27.344	-0.118	-0.118	0.000	0.000	0.000	0.000
54	A	67	ASP	-1	-0.794	-0.870	31.564	-9.483	-9.483	0.000	0.000	0.000	0.000
55	A	68	MET	0	0.049	-0.011	24.928	-0.312	-0.312	0.000	0.000	0.000	0.000
56	A	69	ALA	0	-0.035	-0.005	27.882	-0.389	-0.389	0.000	0.000	0.000	0.000
57	A	70	THR	0	0.016	-0.003	28.954	-0.184	-0.184	0.000	0.000	0.000	0.000
58	A	71	LEU	0	-0.003	-0.004	23.953	-0.304	-0.304	0.000	0.000	0.000	0.000
59	A	72	ASN	0	-0.032	-0.015	24.090	-0.947	-0.947	0.000	0.000	0.000	0.000
60	A	73	ALA	0	0.015	0.022	24.041	-0.496	-0.496	0.000	0.000	0.000	0.000
61	A	74	MET	0	0.030	0.037	23.829	-0.335	-0.335	0.000	0.000	0.000	0.000
62	A	75	HIS	0	0.030	0.008	16.366	-0.114	-0.114	0.000	0.000	0.000	0.000
63	A	76	LEU	0	-0.012	-0.007	20.323	-0.591	-0.591	0.000	0.000	0.000	0.000
64	A	77	LYS	1	0.868	0.936	22.274	10.569	10.569	0.000	0.000	0.000	0.000
65	A	78	MET	0	-0.019	-0.003	18.148	0.014	0.014	0.000	0.000	0.000	0.000
66	A	79	HIS	0	-0.022	-0.007	15.274	-0.590	-0.590	0.000	0.000	0.000	0.000
67	A	80	ARG	1	0.921	0.945	18.761	11.528	11.528	0.000	0.000	0.000	0.000
68	A	81	ALA	0	-0.021	0.005	21.095	0.198	0.198	0.000	0.000	0.000	0.000
69	A	82	ALA	0	0.025	0.012	16.050	0.071	0.071	0.000	0.000	0.000	0.000
70	A	83	ALA	0	0.011	0.003	17.691	-0.234	-0.234	0.000	0.000	0.000	0.000
71	A	84	ALA	0	-0.043	-0.008	18.620	0.089	0.089	0.000	0.000	0.000	0.000
72	A	85	VAL	0	-0.028	-0.011	18.211	0.446	0.446	0.000	0.000	0.000	0.000
73	A	86	GLY	0	-0.023	0.001	17.060	-0.303	-0.303	0.000	0.000	0.000	0.000
74	A	87	GLY	0	-0.011	0.005	13.986	-0.990	-0.990	0.000	0.000	0.000	0.000
75	A	88	ARG	1	0.867	0.909	9.206	24.933	24.933	0.000	0.000	0.000	0.000
76	A	89	ILE	0	0.006	0.002	10.939	-0.640	-0.640	0.000	0.000	0.000	0.000
77	A	90	ASP	-1	-0.858	-0.931	8.473	-30.082	-30.082	0.000	0.000	0.000	0.000
78	A	91	ALA	0	-0.020	-0.006	11.603	0.386	0.386	0.000	0.000	0.000	0.000
79	A	92	VAL	0	-0.007	0.005	13.753	-0.050	-0.050	0.000	0.000	0.000	0.000
80	A	93	PHE	0	0.003	-0.014	16.508	0.623	0.623	0.000	0.000	0.000	0.000
81	A	94	PHE	0	0.014	0.005	20.166	-0.131	-0.131	0.000	0.000	0.000	0.000
82	A	95	CYS	0	0.045	0.035	21.948	0.690	0.690	0.000	0.000	0.000	0.000
83	A	112	MET	0	-0.006	-0.003	18.977	0.322	0.322	0.000	0.000	0.000	0.000
84	A	113	MET	0	0.046	0.029	15.946	-0.600	-0.600	0.000	0.000	0.000	0.000
85	A	114	LYS	1	0.953	0.946	16.711	11.629	11.629	0.000	0.000	0.000	0.000
86	A	115	LEU	0	0.034	0.030	17.455	-0.047	-0.047	0.000	0.000	0.000	0.000
87	A	116	ILE	0	-0.041	-0.010	12.548	-0.886	-0.886	0.000	0.000	0.000	0.000
88	A	117	ALA	0	0.006	-0.016	12.082	-1.655	-1.655	0.000	0.000	0.000	0.000
89	A	118	GLU	-1	-0.939	-0.943	12.217	-18.250	-18.250	0.000	0.000	0.000	0.000
90	A	119	ARG	1	0.877	0.950	11.737	21.441	21.441	0.000	0.000	0.000	0.000
91	A	120	PHE	0	-0.092	-0.056	7.667	-1.778	-1.778	0.000	0.000	0.000	0.000
92	A	121	GLU	-1	-0.898	-0.938	6.960	-32.940	-32.940	0.000	0.000	0.000	0.000
93	A	122	ILE	0	-0.068	-0.057	5.540	-4.837	-4.837	0.000	0.000	0.000	0.000
94	A	123	ASP	-1	-0.812	-0.910	7.640	-17.965	-17.965	0.000	0.000	0.000	0.000
95	A	124	PRO	0	-0.036	-0.019	10.108	-0.328	-0.328	0.000	0.000	0.000	0.000
96	A	125	ALA	0	0.003	0.020	12.833	0.568	0.568	0.000	0.000	0.000	0.000
97	A	126	ASP	-1	-0.936	-0.956	9.027	-21.206	-21.206	0.000	0.000	0.000	0.000
98	A	127	THR	0	-0.111	-0.061	9.776	-2.126	-2.126	0.000	0.000	0.000	0.000
99	A	128	PRO	0	-0.043	-0.005	11.092	1.367	1.367	0.000	0.000	0.000	0.000
100	A	129	VAL	0	0.004	0.004	13.591	-0.992	-0.992	0.000	0.000	0.000	0.000
101	A	130	VAL	0	-0.018	-0.010	15.795	0.856	0.856	0.000	0.000	0.000	0.000
102	A	131	GLY	0	0.073	0.028	18.184	-0.200	-0.200	0.000	0.000	0.000	0.000
103	A	132	ASP	-1	-0.751	-0.861	21.435	-10.929	-10.929	0.000	0.000	0.000	0.000
104	A	133	SER	0	-0.110	-0.032	24.517	0.598	0.598	0.000	0.000	0.000	0.000
105	A	134	LEU	0	0.114	0.053	25.154	-0.359	-0.359	0.000	0.000	0.000	0.000
106	A	135	ARG	1	0.868	0.929	22.886	11.806	11.806	0.000	0.000	0.000	0.000
107	A	136	ASP	-1	-0.899	-0.957	19.918	-14.267	-14.267	0.000	0.000	0.000	0.000
108	A	137	LEU	0	0.054	0.052	20.637	-0.365	-0.365	0.000	0.000	0.000	0.000
109	A	138	GLN	0	0.030	0.015	22.401	-0.078	-0.078	0.000	0.000	0.000	0.000
110	A	139	ALA	0	-0.060	-0.036	22.316	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	140	GLY	0	0.014	-0.008	18.949	-0.307	-0.307	0.000	0.000	0.000	0.000
112	A	141	ALA	0	0.034	0.008	18.921	-0.385	-0.385	0.000	0.000	0.000	0.000
113	A	142	ALA	0	-0.062	-0.024	21.015	0.069	0.069	0.000	0.000	0.000	0.000
114	A	143	LEU	0	-0.048	-0.033	16.467	0.125	0.125	0.000	0.000	0.000	0.000
115	A	144	GLY	0	0.014	0.023	17.191	-0.528	-0.528	0.000	0.000	0.000	0.000
116	A	145	PHE	0	-0.053	-0.014	12.638	-0.292	-0.292	0.000	0.000	0.000	0.000
117	A	146	ARG	1	0.969	0.984	15.502	16.517	16.517	0.000	0.000	0.000	0.000
118	A	147	PRO	0	-0.010	0.001	17.299	-0.478	-0.478	0.000	0.000	0.000	0.000
119	A	148	HIS	0	-0.011	-0.021	17.245	-0.061	-0.061	0.000	0.000	0.000	0.000
120	A	149	LEU	0	-0.021	-0.020	20.479	-0.046	-0.046	0.000	0.000	0.000	0.000
121	A	150	VAL	0	-0.021	-0.003	21.220	0.063	0.063	0.000	0.000	0.000	0.000
122	A	151	LEU	0	-0.042	-0.023	24.039	0.313	0.313	0.000	0.000	0.000	0.000
123	A	152	THR	0	-0.011	-0.038	25.072	0.305	0.305	0.000	0.000	0.000	0.000
124	A	153	GLY	0	0.046	0.020	27.292	-0.130	-0.130	0.000	0.000	0.000	0.000
125	A	154	LYS	1	0.851	0.913	27.648	10.736	10.736	0.000	0.000	0.000	0.000
126	A	155	GLY	0	0.125	0.062	27.891	0.184	0.184	0.000	0.000	0.000	0.000
127	A	156	LYS	1	0.979	0.990	28.524	8.712	8.712	0.000	0.000	0.000	0.000
128	A	157	LYS	1	0.931	0.970	31.885	8.857	8.857	0.000	0.000	0.000	0.000
129	A	158	THR	0	-0.075	-0.096	27.785	0.240	0.240	0.000	0.000	0.000	0.000
130	A	159	LEU	0	-0.008	-0.006	29.289	0.061	0.061	0.000	0.000	0.000	0.000
131	A	160	ALA	0	-0.049	-0.023	31.260	0.117	0.117	0.000	0.000	0.000	0.000
132	A	161	ALA	0	-0.051	-0.018	33.416	0.190	0.190	0.000	0.000	0.000	0.000
133	A	162	GLY	0	0.022	0.028	32.674	0.138	0.138	0.000	0.000	0.000	0.000
134	A	163	GLY	0	-0.008	-0.007	32.496	-0.033	-0.033	0.000	0.000	0.000	0.000
135	A	164	LEU	0	-0.058	-0.036	27.023	-0.250	-0.250	0.000	0.000	0.000	0.000
136	A	165	PRO	0	0.015	-0.002	24.379	0.197	0.197	0.000	0.000	0.000	0.000
137	A	166	GLU	-1	-0.877	-0.915	26.245	-9.909	-9.909	0.000	0.000	0.000	0.000
138	A	167	GLY	0	-0.006	0.014	23.212	0.106	0.106	0.000	0.000	0.000	0.000
139	A	168	THR	0	-0.080	-0.065	22.381	-0.662	-0.662	0.000	0.000	0.000	0.000
140	A	169	ARG	1	0.906	0.955	19.792	13.527	13.527	0.000	0.000	0.000	0.000
141	A	170	VAL	0	0.021	0.012	23.104	-0.166	-0.166	0.000	0.000	0.000	0.000
142	A	171	HIS	0	-0.004	-0.002	20.566	-0.335	-0.335	0.000	0.000	0.000	0.000
143	A	172	ASP	-1	-0.849	-0.936	24.319	-9.758	-9.758	0.000	0.000	0.000	0.000
144	A	173	ASP	-1	-0.888	-0.959	24.198	-11.340	-11.340	0.000	0.000	0.000	0.000
145	A	174	LEU	0	0.030	0.006	16.983	-0.278	-0.278	0.000	0.000	0.000	0.000
146	A	175	ARG	1	0.913	0.958	19.311	11.213	11.213	0.000	0.000	0.000	0.000
147	A	176	ALA	0	-0.008	-0.003	20.435	-0.285	-0.285	0.000	0.000	0.000	0.000
148	A	177	PHE	0	0.024	0.018	14.053	-0.196	-0.196	0.000	0.000	0.000	0.000
149	A	178	ALA	0	0.019	0.017	15.707	-0.413	-0.413	0.000	0.000	0.000	0.000
150	A	179	LEU	0	-0.069	-0.035	16.220	-0.434	-0.434	0.000	0.000	0.000	0.000
151	A	180	ASP	-1	-0.878	-0.940	18.522	-13.300	-13.300	0.000	0.000	0.000	0.000
152	A	181	PHE	0	-0.009	-0.013	10.470	-0.323	-0.323	0.000	0.000	0.000	0.000
153	A	182	LEU	0	-0.095	-0.046	11.550	-0.788	-0.788	0.000	0.000	0.000	0.000
154	A	183	SER	0	-0.021	-0.014	14.744	0.735	0.735	0.000	0.000	0.000	0.000
155	A	184	LYN	0	-0.048	-0.003	12.445	0.137	0.137	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:LYS)