FMO DATABASE

FMODB ID: R13V8

Calculation Name: 1PM4-A-Xray315

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1PM4

Chain ID: A

ChEMBL ID:

UniProt ID: Q57221

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

Apendix: None

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. 1.20200129
Remarks	Structural optimization was performed under the unconstrained condition of hydrogen and heavy atoms fixed using MOE with Auto-FMO protocol as OptH.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	117
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-944132.141565
FMO2-HF: Nuclear repulsion	898523.98869
FMO2-HF: Total energy	-45608.152875
FMO2-MP2: Total energy	-45741.386803

3D Structure Molmil

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:14:ACE )

Summations of interaction energy for fragment #1(A:14:ACE )

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.
-0.135	1.454	0.342	-0.867	-1.063	-0.003

Interaction energy analysis for fragmet #1(A:14:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.014

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	16	PRO	0	-0.025	0.003	2.983	-0.089	1.500	0.342	-0.867	-1.063	-0.003
4	A	17	ASN	0	0.045	0.043	5.934	-0.024	-0.024	0.000	0.000	0.000	0.000
5	A	18	ILE	0	-0.037	-0.007	8.495	0.140	0.140	0.000	0.000	0.000	0.000
6	A	19	ALA	0	0.031	0.027	11.159	-0.032	-0.032	0.000	0.000	0.000	0.000
7	A	20	THR	0	0.014	-0.022	14.824	0.027	0.027	0.000	0.000	0.000	0.000
8	A	21	TYR	0	-0.104	-0.077	17.562	-0.010	-0.010	0.000	0.000	0.000	0.000
9	A	22	THR	0	-0.005	-0.011	20.955	0.010	0.010	0.000	0.000	0.000	0.000
10	A	23	GLY	0	0.016	0.011	23.809	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	24	THR	0	-0.030	-0.013	27.392	0.005	0.005	0.000	0.000	0.000	0.000
12	A	25	ILE	0	-0.023	0.003	29.055	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	26	GLN	0	0.065	0.006	31.381	0.003	0.003	0.000	0.000	0.000	0.000
14	A	27	GLY	0	0.038	0.036	34.393	0.002	0.002	0.000	0.000	0.000	0.000
15	A	28	LYS	1	0.806	0.885	35.573	-0.022	-0.022	0.000	0.000	0.000	0.000
16	A	29	GLY	0	0.022	0.035	34.041	0.000	0.000	0.000	0.000	0.000	0.000
17	A	30	GLU	-1	-0.904	-0.978	30.773	0.015	0.015	0.000	0.000	0.000	0.000
18	A	31	VAL	0	0.019	0.010	26.640	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	129	CYS	0	-0.050	0.006	26.155	0.006	0.006	0.000	0.000	0.000	0.000
20	A	33	ILE	0	0.011	0.014	21.128	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	34	ILE	0	-0.041	-0.028	22.603	0.009	0.009	0.000	0.000	0.000	0.000
22	A	35	GLY	0	0.040	0.019	18.844	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	36	ASN	0	-0.029	-0.040	17.483	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	37	LYS	1	0.905	0.961	19.322	0.100	0.100	0.000	0.000	0.000	0.000
25	A	38	GLU	-1	-0.923	-0.972	20.825	-0.102	-0.102	0.000	0.000	0.000	0.000
26	A	39	GLY	0	-0.018	-0.001	21.389	0.003	0.003	0.000	0.000	0.000	0.000
27	A	40	LYS	1	0.958	0.993	16.759	0.196	0.196	0.000	0.000	0.000	0.000
28	A	41	THR	0	-0.026	-0.034	17.156	0.008	0.008	0.000	0.000	0.000	0.000
29	A	42	ARG	1	0.853	0.943	9.491	0.056	0.056	0.000	0.000	0.000	0.000
30	A	43	GLY	0	0.030	0.016	12.755	0.024	0.024	0.000	0.000	0.000	0.000
31	A	44	GLY	0	-0.006	-0.013	9.524	-0.043	-0.043	0.000	0.000	0.000	0.000
32	A	45	GLU	-1	-0.910	-0.966	8.690	0.623	0.623	0.000	0.000	0.000	0.000
33	A	46	LEU	0	-0.070	-0.020	10.302	-0.065	-0.065	0.000	0.000	0.000	0.000
34	A	47	TYR	0	0.023	-0.009	10.654	0.075	0.075	0.000	0.000	0.000	0.000
35	A	48	ALA	0	0.010	0.002	12.599	-0.056	-0.056	0.000	0.000	0.000	0.000
36	A	49	VAL	0	-0.015	-0.002	15.168	0.030	0.030	0.000	0.000	0.000	0.000
37	A	50	LEU	0	0.003	0.011	17.243	-0.021	-0.021	0.000	0.000	0.000	0.000
38	A	51	HIS	1	0.880	0.921	17.136	-0.063	-0.063	0.000	0.000	0.000	0.000
39	A	52	SER	0	0.048	-0.017	22.224	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	53	THR	0	-0.039	-0.020	25.594	0.004	0.004	0.000	0.000	0.000	0.000
41	A	54	ASN	0	-0.042	-0.010	27.387	0.001	0.001	0.000	0.000	0.000	0.000
42	A	55	VAL	0	0.035	0.015	28.964	0.003	0.003	0.000	0.000	0.000	0.000
43	A	56	ASN	0	-0.017	-0.013	30.045	0.007	0.007	0.000	0.000	0.000	0.000
44	A	57	ALA	0	-0.037	0.000	28.328	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	58	ASP	-1	-0.839	-0.913	29.665	0.046	0.046	0.000	0.000	0.000	0.000
46	A	59	MET	0	-0.057	-0.042	26.709	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	60	THR	0	-0.030	-0.003	26.301	0.006	0.006	0.000	0.000	0.000	0.000
48	A	61	LEU	0	0.015	0.016	19.232	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	62	ILE	0	-0.006	-0.016	23.610	0.010	0.010	0.000	0.000	0.000	0.000
50	A	63	LEU	0	-0.003	0.023	18.204	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	64	LEU	0	-0.003	-0.005	22.137	0.003	0.003	0.000	0.000	0.000	0.000
52	A	65	ARG	1	0.891	0.928	17.443	-0.023	-0.023	0.000	0.000	0.000	0.000
53	A	66	ASN	0	0.010	0.002	23.741	0.005	0.005	0.000	0.000	0.000	0.000
54	A	67	VAL	0	-0.008	-0.003	25.389	0.000	0.000	0.000	0.000	0.000	0.000
55	A	68	GLY	0	0.017	-0.003	27.047	0.002	0.002	0.000	0.000	0.000	0.000
56	A	69	GLY	0	0.005	0.016	29.112	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	70	ASN	0	-0.049	-0.031	31.051	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	71	GLY	0	0.027	0.026	31.000	0.000	0.000	0.000	0.000	0.000	0.000
59	A	72	TRP	0	-0.006	0.002	24.193	0.002	0.002	0.000	0.000	0.000	0.000
60	A	73	GLY	0	0.029	0.008	27.362	0.001	0.001	0.000	0.000	0.000	0.000
61	A	74	GLU	-1	-0.839	-0.903	25.779	0.056	0.056	0.000	0.000	0.000	0.000
62	A	75	ILE	0	-0.037	-0.001	20.111	0.002	0.002	0.000	0.000	0.000	0.000
63	A	76	LYS	1	0.869	0.928	17.912	-0.163	-0.163	0.000	0.000	0.000	0.000
64	A	77	ARG	1	0.855	0.901	23.255	-0.061	-0.061	0.000	0.000	0.000	0.000
65	A	78	ASN	0	-0.033	-0.016	20.510	0.013	0.013	0.000	0.000	0.000	0.000
66	A	79	ASP	-1	-0.900	-0.945	23.217	0.066	0.066	0.000	0.000	0.000	0.000
67	A	80	ILE	0	0.014	0.000	22.767	0.008	0.008	0.000	0.000	0.000	0.000
68	A	81	ASP	-1	-0.845	-0.918	20.640	0.075	0.075	0.000	0.000	0.000	0.000
69	A	82	LYS	1	0.847	0.932	19.673	-0.096	-0.096	0.000	0.000	0.000	0.000
70	A	83	PRO	0	-0.019	-0.014	14.754	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	84	LEU	0	-0.014	0.023	16.388	0.008	0.008	0.000	0.000	0.000	0.000
72	A	85	LYS	1	0.945	0.960	10.278	-0.560	-0.560	0.000	0.000	0.000	0.000
73	A	86	TYR	0	-0.055	-0.049	13.917	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	87	GLU	-1	-0.852	-0.886	11.811	0.385	0.385	0.000	0.000	0.000	0.000
75	A	88	ASP	-1	-0.797	-0.898	13.876	0.023	0.023	0.000	0.000	0.000	0.000
76	A	89	TYR	0	-0.032	-0.050	11.206	-0.011	-0.011	0.000	0.000	0.000	0.000
77	A	90	TYR	0	-0.040	-0.009	15.930	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	91	THR	0	0.025	0.009	18.343	-0.011	-0.011	0.000	0.000	0.000	0.000
79	A	92	SER	0	0.002	0.013	20.426	-0.017	-0.017	0.000	0.000	0.000	0.000
80	A	93	GLY	0	0.030	0.023	19.665	0.006	0.006	0.000	0.000	0.000	0.000
81	A	94	LEU	0	-0.007	-0.009	19.847	0.007	0.007	0.000	0.000	0.000	0.000
82	A	95	SER	0	0.005	0.035	19.858	0.000	0.000	0.000	0.000	0.000	0.000
83	A	96	TRP	0	-0.052	-0.032	15.106	0.018	0.018	0.000	0.000	0.000	0.000
84	A	97	ILE	0	-0.006	-0.010	21.303	-0.011	-0.011	0.000	0.000	0.000	0.000
85	A	98	TRP	0	0.055	0.032	15.823	0.022	0.022	0.000	0.000	0.000	0.000
86	A	99	LYS	1	0.939	0.958	22.239	-0.027	-0.027	0.000	0.000	0.000	0.000
87	A	100	ILE	0	0.011	0.012	23.134	0.009	0.009	0.000	0.000	0.000	0.000
88	A	101	LYS	1	0.863	0.920	26.338	-0.024	-0.024	0.000	0.000	0.000	0.000
89	A	102	ASN	0	0.010	-0.004	29.364	0.008	0.008	0.000	0.000	0.000	0.000
90	A	103	ASN	0	-0.016	-0.021	30.186	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	104	SER	0	0.087	0.073	33.414	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	105	SER	0	-0.038	-0.048	35.357	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	106	GLU	-1	-0.905	-0.941	35.282	0.014	0.014	0.000	0.000	0.000	0.000
94	A	107	THR	0	-0.015	-0.002	34.548	0.001	0.001	0.000	0.000	0.000	0.000
95	A	108	SER	0	0.000	-0.002	30.496	0.001	0.001	0.000	0.000	0.000	0.000
96	A	109	ASN	0	0.044	0.034	26.010	0.002	0.002	0.000	0.000	0.000	0.000
97	A	110	TYR	0	0.010	0.029	23.659	0.007	0.007	0.000	0.000	0.000	0.000
98	A	111	SER	0	0.030	-0.006	20.528	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	112	LEU	0	-0.008	0.001	18.375	0.014	0.014	0.000	0.000	0.000	0.000
100	A	113	ASP	-1	-0.838	-0.894	14.043	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	114	ALA	0	0.001	-0.023	14.276	0.036	0.036	0.000	0.000	0.000	0.000
102	A	115	THR	0	-0.028	-0.010	10.331	-0.013	-0.013	0.000	0.000	0.000	0.000
103	A	116	VAL	0	-0.016	-0.004	12.312	0.029	0.029	0.000	0.000	0.000	0.000
104	A	117	HIS	0	-0.007	-0.034	12.366	-0.032	-0.032	0.000	0.000	0.000	0.000
105	A	118	ASP	-1	-0.920	-0.940	14.516	-0.233	-0.233	0.000	0.000	0.000	0.000
106	A	119	ASP	-1	-0.913	-0.959	15.254	-0.325	-0.325	0.000	0.000	0.000	0.000
107	A	120	LYS	1	0.827	0.904	17.432	0.117	0.117	0.000	0.000	0.000	0.000
108	A	121	GLU	-1	-0.896	-0.953	19.285	-0.116	-0.116	0.000	0.000	0.000	0.000
109	A	122	ASP	-1	-0.897	-0.954	22.997	-0.062	-0.062	0.000	0.000	0.000	0.000
110	A	123	SER	0	-0.076	-0.038	26.070	0.008	0.008	0.000	0.000	0.000	0.000
111	A	124	ASP	-1	-0.738	-0.838	20.865	-0.091	-0.091	0.000	0.000	0.000	0.000
112	A	125	VAL	0	-0.039	-0.009	24.109	0.010	0.010	0.000	0.000	0.000	0.000
113	A	126	LEU	0	-0.006	0.003	26.399	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	127	THR	0	-0.026	-0.020	28.872	0.003	0.003	0.000	0.000	0.000	0.000
115	A	128	LYS	1	0.916	0.957	31.754	0.009	0.009	0.000	0.000	0.000	0.000
116	A	130	PRO	0	-0.026	-0.033	29.107	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	131	VAL	-1	-0.928	-0.949	32.262	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:14:ACE )