FMO DATABASE

FMODB ID: QK7LY

Calculation Name: 4PH1-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4PH1

Chain ID: A

ChEMBL ID:

UniProt ID: A7KWZ1

Base Structure: X-ray

Registration Date: 2025-07-11

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

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. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	145
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-468841.064134
FMO2-HF: Nuclear repulsion	439373.176968
FMO2-HF: Total energy	-29467.887166
FMO2-MP2: Total energy	-29553.94591

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:129:SER)

Summations of interaction energy for fragment #1(A:129:SER)

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.
2.281	3.487	-0.015	-0.55	-0.641	0.001

Interaction energy analysis for fragmet #1(A:129:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.147 / q_NPA : 0.069

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].
4	A	130	VAL	0	-0.046	0.070	3.710	-0.077	0.110	-0.002	-0.009	-0.176	0.000
5	A	131	GLN	0	0.120	-0.104	3.863	2.078	3.097	-0.013	-0.541	-0.465	0.001
6	A	131	GLN	0	-0.061	0.120	6.325	0.084	0.084	0.000	0.000	0.000	0.000
7	A	132	PRO	0	0.017	-0.093	6.268	-0.175	-0.175	0.000	0.000	0.000	0.000
8	A	133	TRP	0	0.098	0.003	8.595	-0.093	-0.093	0.000	0.000	0.000	0.000
9	A	133	TRP	0	-0.022	0.128	10.565	0.022	0.022	0.000	0.000	0.000	0.000
10	A	134	SER	0	0.016	-0.093	9.005	0.002	0.002	0.000	0.000	0.000	0.000
11	A	134	SER	0	-0.045	0.072	8.171	-0.060	-0.060	0.000	0.000	0.000	0.000
12	A	135	THR	0	0.016	-0.057	10.076	-0.154	-0.154	0.000	0.000	0.000	0.000
13	A	135	THR	0	-0.054	0.056	8.109	0.002	0.002	0.000	0.000	0.000	0.000
14	A	136	ILE	0	0.033	-0.109	10.847	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	136	ILE	0	-0.075	0.105	13.476	0.005	0.005	0.000	0.000	0.000	0.000
16	A	137	VAL	0	0.133	-0.082	14.564	-0.020	-0.020	0.000	0.000	0.000	0.000
17	A	137	VAL	0	-0.064	0.113	13.891	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	138	GLN	0	0.104	-0.114	16.534	0.030	0.030	0.000	0.000	0.000	0.000
19	A	138	GLN	0	-0.105	0.068	21.118	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	139	GLY	0	-0.019	-0.099	20.317	-0.019	-0.019	0.000	0.000	0.000	0.000
21	A	140	PRO	0	-0.014	-0.035	21.581	0.001	0.001	0.000	0.000	0.000	0.000
22	A	141	ALA	0	0.126	0.012	24.382	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	141	ALA	0	-0.073	0.111	26.977	0.001	0.001	0.000	0.000	0.000	0.000
24	A	142	GLU	0	0.069	-0.100	23.884	0.008	0.008	0.000	0.000	0.000	0.000
25	A	142	GLU	-1	-0.885	-0.790	21.297	0.006	0.006	0.000	0.000	0.000	0.000
26	A	143	SER	0	0.064	-0.075	25.353	-0.013	-0.013	0.000	0.000	0.000	0.000
27	A	143	SER	0	-0.046	0.077	27.990	0.001	0.001	0.000	0.000	0.000	0.000
28	A	144	TYR	0	0.143	-0.079	25.284	0.004	0.004	0.000	0.000	0.000	0.000
29	A	144	TYR	0	-0.098	0.066	23.817	0.004	0.004	0.000	0.000	0.000	0.000
30	A	145	VAL	0	0.017	-0.136	25.024	0.000	0.000	0.000	0.000	0.000	0.000
31	A	145	VAL	0	-0.036	0.115	28.026	0.000	0.000	0.000	0.000	0.000	0.000
32	A	146	GLU	0	0.086	-0.116	25.294	0.009	0.009	0.000	0.000	0.000	0.000
33	A	146	GLU	-1	-0.925	-0.795	25.001	0.023	0.023	0.000	0.000	0.000	0.000
34	A	147	PHE	0	0.093	-0.070	21.429	0.021	0.021	0.000	0.000	0.000	0.000
35	A	147	PHE	0	-0.127	0.087	17.962	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	148	VAL	0	0.066	-0.105	20.594	0.011	0.011	0.000	0.000	0.000	0.000
37	A	148	VAL	0	-0.079	0.103	22.889	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	149	ASN	0	0.146	-0.086	21.443	0.011	0.011	0.000	0.000	0.000	0.000
39	A	149	ASN	0	-0.108	0.073	24.024	0.003	0.003	0.000	0.000	0.000	0.000
40	A	150	ARG	0	0.089	-0.112	19.738	0.021	0.021	0.000	0.000	0.000	0.000
41	A	150	ARG	1	0.774	1.036	16.482	-0.047	-0.047	0.000	0.000	0.000	0.000
42	A	151	LEU	0	0.138	-0.095	16.844	0.046	0.046	0.000	0.000	0.000	0.000
43	A	151	LEU	0	-0.125	0.117	15.505	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	152	GLN	0	0.065	-0.078	17.172	0.025	0.025	0.000	0.000	0.000	0.000
45	A	152	GLN	0	-0.127	0.084	21.367	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	153	ILE	0	0.031	-0.103	19.106	0.007	0.007	0.000	0.000	0.000	0.000
47	A	153	ILE	0	-0.035	0.095	18.080	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	154	SER	0	0.123	-0.018	14.587	0.029	0.029	0.000	0.000	0.000	0.000
49	A	154	SER	0	-0.040	0.047	13.185	0.026	0.026	0.000	0.000	0.000	0.000
50	A	155	LEU	0	0.071	-0.089	14.304	0.077	0.077	0.000	0.000	0.000	0.000
51	A	155	LEU	0	-0.139	0.053	13.949	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	156	ALA	0	0.085	-0.105	15.611	0.012	0.012	0.000	0.000	0.000	0.000
53	A	156	ALA	0	-0.094	0.077	19.442	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	157	ASP	0	0.068	-0.101	16.167	-0.021	-0.021	0.000	0.000	0.000	0.000
55	A	157	ASP	-1	-1.035	-0.854	15.582	0.297	0.297	0.000	0.000	0.000	0.000
56	A	158	ASN	0	-0.014	-0.078	11.853	0.033	0.033	0.000	0.000	0.000	0.000
57	A	158	ASN	0	-0.174	0.001	10.936	0.115	0.115	0.000	0.000	0.000	0.000
58	A	159	LEU	0	0.093	-0.114	12.203	-0.062	-0.062	0.000	0.000	0.000	0.000
59	A	159	LEU	0	-0.047	0.121	14.239	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	160	PRO	0	0.004	-0.107	10.704	0.044	0.044	0.000	0.000	0.000	0.000
61	A	161	ASP	0	0.044	-0.037	12.324	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	161	ASP	-1	-0.947	-0.832	13.331	0.209	0.209	0.000	0.000	0.000	0.000
63	A	162	GLY	0	-0.016	-0.107	15.232	-0.020	-0.020	0.000	0.000	0.000	0.000
64	A	163	VAL	0	0.023	-0.030	15.691	-0.023	-0.023	0.000	0.000	0.000	0.000
65	A	163	VAL	0	-0.066	0.138	14.743	0.000	0.000	0.000	0.000	0.000	0.000
66	A	164	PRO	0	0.005	-0.120	16.703	0.002	0.002	0.000	0.000	0.000	0.000
67	A	165	LYS	0	0.129	0.016	18.265	-0.010	-0.010	0.000	0.000	0.000	0.000
68	A	165	LYS	1	0.779	1.035	18.452	-0.121	-0.121	0.000	0.000	0.000	0.000
69	A	166	GLU	0	0.022	-0.101	19.363	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	166	GLU	-1	-0.923	-0.851	23.201	0.041	0.041	0.000	0.000	0.000	0.000
71	A	167	PRO	0	0.032	-0.089	19.294	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	168	ILE	0	0.065	0.015	16.124	-0.030	-0.030	0.000	0.000	0.000	0.000
73	A	168	ILE	0	-0.054	0.110	14.158	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	169	ILE	0	0.019	-0.107	17.332	-0.023	-0.023	0.000	0.000	0.000	0.000
75	A	169	ILE	0	-0.067	0.098	19.226	0.004	0.004	0.000	0.000	0.000	0.000
76	A	170	ASP	0	0.096	-0.071	19.646	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	170	ASP	-1	-0.892	-0.815	22.440	-0.021	-0.021	0.000	0.000	0.000	0.000
78	A	171	SER	0	0.066	-0.063	18.709	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	171	SER	0	-0.059	0.056	17.490	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	172	LEU	0	0.011	-0.119	16.492	-0.020	-0.020	0.000	0.000	0.000	0.000
81	A	172	LEU	0	-0.033	0.118	13.022	0.001	0.001	0.000	0.000	0.000	0.000
82	A	173	SER	0	0.091	-0.077	17.573	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	173	SER	0	-0.032	0.057	21.597	0.001	0.001	0.000	0.000	0.000	0.000
84	A	174	TYR	0	0.080	-0.052	20.768	0.011	0.011	0.000	0.000	0.000	0.000
85	A	174	TYR	0	-0.108	0.042	21.283	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	175	ALA	0	0.100	-0.108	17.633	0.010	0.010	0.000	0.000	0.000	0.000
87	A	175	ALA	0	-0.076	0.128	16.948	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	176	ASN	0	0.033	-0.105	16.627	-0.028	-0.028	0.000	0.000	0.000	0.000
89	A	176	ASN	0	-0.163	0.053	13.366	-0.039	-0.039	0.000	0.000	0.000	0.000
90	A	177	ALA	0	0.188	-0.084	17.536	0.010	0.010	0.000	0.000	0.000	0.000
91	A	177	ALA	0	-0.097	0.092	22.230	0.003	0.003	0.000	0.000	0.000	0.000
92	A	178	ASN	0	0.076	-0.047	20.836	-0.022	-0.022	0.000	0.000	0.000	0.000
93	A	178	ASN	0	-0.101	0.065	22.507	0.000	0.000	0.000	0.000	0.000	0.000
94	A	179	LYS	0	0.190	-0.059	22.532	0.002	0.002	0.000	0.000	0.000	0.000
95	A	179	LYS	1	0.822	1.039	24.265	0.110	0.110	0.000	0.000	0.000	0.000
96	A	180	GLU	0	0.019	-0.135	24.767	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	180	GLU	-1	-0.965	-0.838	27.670	-0.067	-0.067	0.000	0.000	0.000	0.000
98	A	181	CYS	0	0.053	-0.118	26.301	0.004	0.004	0.000	0.000	0.000	0.000
99	A	181	CYS	0	-0.070	0.131	25.333	0.005	0.005	0.000	0.000	0.000	0.000
100	A	182	GLN	0	0.111	-0.110	24.487	0.011	0.011	0.000	0.000	0.000	0.000
101	A	182	GLN	0	-0.135	0.093	20.140	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	183	GLN	0	0.096	-0.106	25.622	0.000	0.000	0.000	0.000	0.000	0.000
103	A	183	GLN	0	-0.098	0.094	27.854	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	184	ILE	0	0.067	-0.087	28.921	0.001	0.001	0.000	0.000	0.000	0.000
105	A	184	ILE	0	-0.072	0.093	29.909	0.001	0.001	0.000	0.000	0.000	0.000
106	A	185	LEU	0	0.014	-0.124	27.717	0.006	0.006	0.000	0.000	0.000	0.000
107	A	185	LEU	0	-0.069	0.116	25.305	0.000	0.000	0.000	0.000	0.000	0.000
108	A	186	GLN	0	0.068	-0.099	28.824	0.003	0.003	0.000	0.000	0.000	0.000
109	A	186	GLN	0	-0.029	0.108	26.224	-0.010	-0.010	0.000	0.000	0.000	0.000
110	A	187	GLY	0	-0.034	-0.096	29.703	0.002	0.002	0.000	0.000	0.000	0.000
111	A	188	ARG	0	0.020	0.004	32.655	0.003	0.003	0.000	0.000	0.000	0.000
112	A	188	ARG	1	0.863	1.047	33.036	0.041	0.041	0.000	0.000	0.000	0.000
113	A	189	GLY	0	0.018	-0.079	31.587	0.004	0.004	0.000	0.000	0.000	0.000
114	A	190	LEU	0	-0.020	-0.027	30.080	0.002	0.002	0.000	0.000	0.000	0.000
115	A	190	LEU	0	-0.065	0.091	30.009	0.001	0.001	0.000	0.000	0.000	0.000
116	A	191	VAL	0	0.120	-0.098	26.120	0.005	0.005	0.000	0.000	0.000	0.000
117	A	191	VAL	0	-0.053	0.106	24.573	0.000	0.000	0.000	0.000	0.000	0.000
118	A	192	ALA	0	0.098	-0.091	24.984	-0.006	-0.006	0.000	0.000	0.000	0.000
119	A	192	ALA	0	-0.051	0.110	26.870	0.000	0.000	0.000	0.000	0.000	0.000
120	A	193	ALA	0	0.034	-0.108	26.673	0.004	0.004	0.000	0.000	0.000	0.000
121	A	193	ALA	0	-0.051	0.124	29.170	0.001	0.001	0.000	0.000	0.000	0.000
122	A	194	PRO	0	0.035	-0.063	26.712	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	195	VAL	0	0.048	-0.010	24.905	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	195	VAL	0	-0.010	0.149	23.567	0.001	0.001	0.000	0.000	0.000	0.000
125	A	196	GLY	0	0.026	-0.114	26.146	0.000	0.000	0.000	0.000	0.000	0.000
126	A	197	GLN	0	0.108	0.011	29.586	0.003	0.003	0.000	0.000	0.000	0.000
127	A	197	GLN	0	-0.046	0.102	30.760	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	198	LYS	0	0.048	-0.119	27.294	0.000	0.000	0.000	0.000	0.000	0.000
129	A	198	LYS	1	0.741	0.996	24.097	0.064	0.064	0.000	0.000	0.000	0.000
130	A	199	LEU	0	0.034	-0.126	28.739	-0.005	-0.005	0.000	0.000	0.000	0.000
131	A	199	LEU	0	-0.079	0.108	26.559	0.001	0.001	0.000	0.000	0.000	0.000
132	A	200	GLN	0	0.072	-0.095	29.472	0.001	0.001	0.000	0.000	0.000	0.000
133	A	200	GLN	0	-0.090	0.084	33.271	0.000	0.000	0.000	0.000	0.000	0.000
134	A	201	ALA	0	0.087	-0.114	32.128	0.002	0.002	0.000	0.000	0.000	0.000
135	A	201	ALA	0	-0.095	0.111	31.171	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	202	CYS	0	0.023	-0.137	29.376	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	202	CYS	0	-0.105	0.110	28.756	-0.003	-0.003	0.000	0.000	0.000	0.000
138	A	203	ALA	0	0.139	-0.081	30.890	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	203	ALA	0	-0.077	0.112	33.244	0.001	0.001	0.000	0.000	0.000	0.000
140	A	204	HIS	0	0.001	-0.104	32.956	0.003	0.003	0.000	0.000	0.000	0.000
141	A	204	HIS	0	-0.115	0.075	36.230	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	205	TRP	0	0.068	-0.094	31.163	0.000	0.000	0.000	0.000	0.000	0.000
143	A	205	TRP	0	-0.069	0.075	27.375	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	206	ALA	0	-0.092	-0.125	31.587	0.001	0.001	0.000	0.000	0.000	0.000
145	A	206	ALA	0	0.050	0.029	34.332	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:129:SER)