FMO DATABASE

FMODB ID: 6RY3Z

Calculation Name: 3RWN-B-Xray549

Preferred Name:

Target Type:

Ligand Name: phosphate ion

Ligand 3-letter code: PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3RWN

Chain ID: B

ChEMBL ID:

UniProt ID: Q716G6

Base Structure: X-ray

Registration Date: 2025-10-12

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	154
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1323774.28181
FMO2-HF: Nuclear repulsion	1266936.486088
FMO2-HF: Total energy	-56837.795722
FMO2-MP2: Total energy	-57005.820082

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(B:129:GLY)

Summations of interaction energy for fragment #1(B:129:GLY)

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.
27.538	29.377	0.027	-0.685	-1.18	-0.003

Interaction energy analysis for fragmet #1(B:129:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.864 / q_NPA : 0.910

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	131	SER	0	0.084	0.047	3.857	1.869	3.014	-0.007	-0.463	-0.675	-0.002
4	B	132	ARG	1	0.906	0.948	3.222	49.942	50.422	0.035	-0.154	-0.360	-0.001
5	B	133	ILE	0	0.009	0.019	4.003	2.458	2.672	-0.001	-0.068	-0.145	0.000
6	B	134	ASP	-1	-0.788	-0.900	6.627	-34.574	-34.574	0.000	0.000	0.000	0.000
7	B	135	ALA	0	-0.012	-0.011	8.216	3.693	3.693	0.000	0.000	0.000	0.000
8	B	136	LEU	0	-0.021	-0.008	7.553	2.898	2.898	0.000	0.000	0.000	0.000
9	B	137	GLU	-1	-0.906	-0.934	10.518	-25.801	-25.801	0.000	0.000	0.000	0.000
10	B	138	TYR	0	-0.069	-0.041	12.392	2.256	2.256	0.000	0.000	0.000	0.000
11	B	139	ALA	0	-0.027	-0.017	13.366	1.528	1.528	0.000	0.000	0.000	0.000
12	B	140	THR	0	-0.070	-0.063	13.970	1.577	1.577	0.000	0.000	0.000	0.000
13	B	141	THR	0	-0.023	-0.007	16.287	1.267	1.267	0.000	0.000	0.000	0.000
14	B	142	ARG	1	0.799	0.907	18.297	12.614	12.614	0.000	0.000	0.000	0.000
15	B	143	LYS	1	0.809	0.906	19.521	15.483	15.483	0.000	0.000	0.000	0.000
16	B	144	LYS	1	0.847	0.894	23.484	11.155	11.155	0.000	0.000	0.000	0.000
17	B	145	SER	0	0.000	0.038	27.315	-0.105	-0.105	0.000	0.000	0.000	0.000
18	B	146	GLU	-1	-0.893	-0.948	30.848	-9.734	-9.734	0.000	0.000	0.000	0.000
19	B	147	VAL	0	-0.046	-0.012	33.242	0.005	0.005	0.000	0.000	0.000	0.000
20	B	148	VAL	0	-0.007	-0.009	36.736	0.137	0.137	0.000	0.000	0.000	0.000
21	B	149	TYR	0	0.039	0.016	39.965	-0.042	-0.042	0.000	0.000	0.000	0.000
22	B	150	SER	0	0.023	-0.010	43.521	0.082	0.082	0.000	0.000	0.000	0.000
23	B	151	GLY	0	-0.009	0.005	45.913	0.031	0.031	0.000	0.000	0.000	0.000
24	B	152	VAL	0	-0.027	0.000	47.081	0.091	0.091	0.000	0.000	0.000	0.000
25	B	153	SER	0	0.010	-0.012	50.074	0.081	0.081	0.000	0.000	0.000	0.000
26	B	154	VAL	0	0.002	0.006	48.144	0.023	0.023	0.000	0.000	0.000	0.000
27	B	155	THR	0	-0.009	0.001	51.353	0.045	0.045	0.000	0.000	0.000	0.000
28	B	156	ILE	0	0.000	0.000	47.562	-0.090	-0.090	0.000	0.000	0.000	0.000
29	B	157	PRO	0	0.004	-0.004	51.059	0.115	0.115	0.000	0.000	0.000	0.000
30	B	158	THR	0	0.019	-0.001	52.785	-0.094	-0.094	0.000	0.000	0.000	0.000
31	B	159	ALA	0	-0.005	0.017	53.932	0.024	0.024	0.000	0.000	0.000	0.000
32	B	160	PRO	0	0.018	0.011	49.187	-0.093	-0.093	0.000	0.000	0.000	0.000
33	B	161	THR	0	-0.001	-0.006	47.564	0.064	0.064	0.000	0.000	0.000	0.000
34	B	162	ASN	0	-0.029	-0.020	42.122	-0.190	-0.190	0.000	0.000	0.000	0.000
35	B	163	LEU	0	0.055	0.012	40.636	0.068	0.068	0.000	0.000	0.000	0.000
36	B	164	VAL	0	0.000	0.013	38.193	0.001	0.001	0.000	0.000	0.000	0.000
37	B	165	SER	0	-0.008	-0.025	41.242	-0.045	-0.045	0.000	0.000	0.000	0.000
38	B	166	LEU	0	0.007	0.017	44.494	0.097	0.097	0.000	0.000	0.000	0.000
39	B	167	LEU	0	0.005	-0.003	40.452	0.071	0.071	0.000	0.000	0.000	0.000
40	B	168	LYS	1	0.812	0.898	41.596	7.421	7.421	0.000	0.000	0.000	0.000
41	B	169	THR	0	-0.072	-0.036	43.008	0.078	0.078	0.000	0.000	0.000	0.000
42	B	170	LEU	0	-0.025	0.002	44.468	0.134	0.134	0.000	0.000	0.000	0.000
43	B	171	THR	0	0.024	0.006	43.536	-0.163	-0.163	0.000	0.000	0.000	0.000
44	B	172	PRO	0	-0.047	-0.023	39.182	0.105	0.105	0.000	0.000	0.000	0.000
45	B	173	SER	0	0.013	0.007	41.667	0.061	0.061	0.000	0.000	0.000	0.000
46	B	174	SER	0	-0.026	-0.012	37.250	-0.134	-0.134	0.000	0.000	0.000	0.000
47	B	175	GLY	0	0.053	0.031	34.568	0.026	0.026	0.000	0.000	0.000	0.000
48	B	176	THR	0	-0.012	-0.025	32.246	0.216	0.216	0.000	0.000	0.000	0.000
49	B	177	LEU	0	-0.009	-0.001	33.667	-0.211	-0.211	0.000	0.000	0.000	0.000
50	B	178	ALA	0	0.046	0.050	31.902	-0.171	-0.171	0.000	0.000	0.000	0.000
51	B	179	PRO	0	-0.007	-0.017	26.923	0.034	0.034	0.000	0.000	0.000	0.000
52	B	180	PHE	0	0.045	0.012	25.220	0.004	0.004	0.000	0.000	0.000	0.000
53	B	181	PHE	0	-0.022	-0.018	30.787	0.203	0.203	0.000	0.000	0.000	0.000
54	B	182	ASP	-1	-0.760	-0.849	34.395	-8.764	-8.764	0.000	0.000	0.000	0.000
55	B	183	THR	0	0.017	-0.013	35.774	0.211	0.211	0.000	0.000	0.000	0.000
56	B	184	VAL	0	-0.014	0.000	38.294	0.287	0.287	0.000	0.000	0.000	0.000
57	B	185	ASN	0	-0.070	-0.067	36.745	0.407	0.407	0.000	0.000	0.000	0.000
58	B	186	ASN	0	-0.019	0.015	39.654	0.075	0.075	0.000	0.000	0.000	0.000
59	B	187	LYS	1	0.908	0.965	35.693	8.709	8.709	0.000	0.000	0.000	0.000
60	B	188	MET	0	-0.012	0.010	32.223	-0.098	-0.098	0.000	0.000	0.000	0.000
61	B	189	VAL	0	-0.015	-0.014	30.411	0.112	0.112	0.000	0.000	0.000	0.000
62	B	190	VAL	0	0.003	0.001	26.721	-0.061	-0.061	0.000	0.000	0.000	0.000
63	B	191	PHE	0	0.018	0.010	22.157	-0.036	-0.036	0.000	0.000	0.000	0.000
64	B	192	ASN	0	0.016	-0.001	22.998	-0.068	-0.068	0.000	0.000	0.000	0.000
65	B	193	GLU	-1	-0.823	-0.893	18.816	-16.613	-16.613	0.000	0.000	0.000	0.000
66	B	194	ASN	0	0.048	0.035	19.163	0.949	0.949	0.000	0.000	0.000	0.000
67	B	195	LYS	1	0.827	0.920	18.886	15.229	15.229	0.000	0.000	0.000	0.000
68	B	196	THR	0	0.008	0.005	21.573	0.323	0.323	0.000	0.000	0.000	0.000
69	B	197	LEU	0	-0.013	0.028	24.805	-0.262	-0.262	0.000	0.000	0.000	0.000
70	B	198	PHE	0	0.004	-0.011	25.308	0.437	0.437	0.000	0.000	0.000	0.000
71	B	199	PHE	0	0.036	0.006	29.606	0.019	0.019	0.000	0.000	0.000	0.000
72	B	200	LYS	1	0.915	0.950	33.036	9.258	9.258	0.000	0.000	0.000	0.000
73	B	201	LEU	0	0.021	0.025	35.957	-0.048	-0.048	0.000	0.000	0.000	0.000
74	B	202	SER	0	-0.033	-0.028	39.363	0.056	0.056	0.000	0.000	0.000	0.000
75	B	203	ILE	0	-0.029	-0.013	41.656	-0.029	-0.029	0.000	0.000	0.000	0.000
76	B	204	VAL	0	0.009	0.006	45.263	0.072	0.072	0.000	0.000	0.000	0.000
77	B	205	GLY	0	0.045	0.001	48.093	-0.019	-0.019	0.000	0.000	0.000	0.000
78	B	206	THR	0	-0.042	-0.005	51.461	0.057	0.057	0.000	0.000	0.000	0.000
79	B	207	TRP	0	-0.024	-0.013	50.687	-0.058	-0.058	0.000	0.000	0.000	0.000
80	B	208	PRO	0	0.017	0.010	56.564	0.045	0.045	0.000	0.000	0.000	0.000
81	B	209	SER	0	0.042	0.021	60.351	-0.042	-0.042	0.000	0.000	0.000	0.000
82	B	210	GLY	0	0.015	0.015	62.373	0.073	0.073	0.000	0.000	0.000	0.000
83	B	211	THR	0	-0.052	-0.037	58.331	0.037	0.037	0.000	0.000	0.000	0.000
84	B	212	ALA	0	0.034	0.013	59.603	-0.069	-0.069	0.000	0.000	0.000	0.000
85	B	213	ASN	0	-0.048	-0.022	57.705	-0.112	-0.112	0.000	0.000	0.000	0.000
86	B	214	ARG	1	0.773	0.868	54.394	5.828	5.828	0.000	0.000	0.000	0.000
87	B	215	SER	0	0.009	0.012	50.523	-0.072	-0.072	0.000	0.000	0.000	0.000
88	B	216	MET	0	0.011	0.035	46.617	0.046	0.046	0.000	0.000	0.000	0.000
89	B	217	GLN	0	0.015	0.020	46.132	-0.028	-0.028	0.000	0.000	0.000	0.000
90	B	218	LEU	0	-0.014	-0.013	39.633	0.049	0.049	0.000	0.000	0.000	0.000
91	B	219	THR	0	-0.010	0.009	42.259	-0.055	-0.055	0.000	0.000	0.000	0.000
92	B	220	PHE	0	0.022	0.013	35.874	-0.004	-0.004	0.000	0.000	0.000	0.000
93	B	221	SER	0	0.017	0.015	39.223	0.006	0.006	0.000	0.000	0.000	0.000
94	B	222	GLY	0	0.074	0.033	36.261	-0.277	-0.277	0.000	0.000	0.000	0.000
95	B	223	SER	0	-0.027	-0.013	35.083	0.097	0.097	0.000	0.000	0.000	0.000
96	B	224	VAL	0	0.021	0.017	37.227	0.211	0.211	0.000	0.000	0.000	0.000
97	B	225	PRO	0	-0.057	-0.015	38.134	-0.179	-0.179	0.000	0.000	0.000	0.000
98	B	226	ASP	-1	-0.826	-0.903	36.393	-8.448	-8.448	0.000	0.000	0.000	0.000
99	B	227	THR	0	-0.044	-0.052	39.945	0.019	0.019	0.000	0.000	0.000	0.000
100	B	228	LEU	0	0.001	0.008	38.175	0.030	0.030	0.000	0.000	0.000	0.000
101	B	229	VAL	0	0.020	-0.012	42.507	0.149	0.149	0.000	0.000	0.000	0.000
102	B	230	SER	0	-0.019	0.011	45.586	-0.012	-0.012	0.000	0.000	0.000	0.000
103	B	231	SER	0	0.003	-0.024	47.197	0.135	0.135	0.000	0.000	0.000	0.000
104	B	232	ARG	1	0.802	0.892	48.335	6.402	6.402	0.000	0.000	0.000	0.000
105	B	233	ASN	0	0.089	0.031	53.573	0.077	0.077	0.000	0.000	0.000	0.000
106	B	234	SER	0	0.038	0.008	57.364	-0.066	-0.066	0.000	0.000	0.000	0.000
107	B	235	ALA	0	-0.006	0.015	57.796	0.040	0.040	0.000	0.000	0.000	0.000
108	B	236	THR	0	-0.052	-0.012	52.607	-0.107	-0.107	0.000	0.000	0.000	0.000
109	B	237	THR	0	0.053	0.024	55.919	-0.021	-0.021	0.000	0.000	0.000	0.000
110	B	238	THR	0	-0.010	0.008	50.991	-0.001	-0.001	0.000	0.000	0.000	0.000
111	B	239	ASP	-1	-0.669	-0.824	52.550	-5.902	-5.902	0.000	0.000	0.000	0.000
112	B	240	ASN	0	0.011	0.011	47.442	-0.019	-0.019	0.000	0.000	0.000	0.000
113	B	241	ILE	0	-0.008	0.010	44.568	-0.004	-0.004	0.000	0.000	0.000	0.000
114	B	242	LEU	0	-0.024	-0.014	39.020	-0.151	-0.151	0.000	0.000	0.000	0.000
115	B	243	LEU	0	-0.003	0.004	40.822	0.086	0.086	0.000	0.000	0.000	0.000
116	B	244	ALA	0	-0.022	-0.024	35.764	-0.158	-0.158	0.000	0.000	0.000	0.000
117	B	245	THR	0	0.026	0.021	34.426	0.156	0.156	0.000	0.000	0.000	0.000
118	B	246	PHE	0	-0.029	-0.011	29.526	-0.253	-0.253	0.000	0.000	0.000	0.000
119	B	247	PHE	0	0.032	0.013	29.867	0.237	0.237	0.000	0.000	0.000	0.000
120	B	248	SER	0	0.033	0.010	26.786	-0.503	-0.503	0.000	0.000	0.000	0.000
121	B	249	VAL	0	-0.058	-0.024	24.898	0.324	0.324	0.000	0.000	0.000	0.000
122	B	250	ASP	-1	-0.877	-0.928	24.287	-12.016	-12.016	0.000	0.000	0.000	0.000
123	B	251	LYS	1	0.843	0.898	18.838	15.526	15.526	0.000	0.000	0.000	0.000
124	B	252	ASP	-1	-0.882	-0.939	23.514	-12.612	-12.612	0.000	0.000	0.000	0.000
125	B	253	GLY	0	0.050	0.042	26.283	0.451	0.451	0.000	0.000	0.000	0.000
126	B	254	PHE	0	-0.001	-0.004	28.758	0.059	0.059	0.000	0.000	0.000	0.000
127	B	255	LEU	0	0.038	0.005	29.560	0.130	0.130	0.000	0.000	0.000	0.000
128	B	256	ALA	0	0.007	0.002	26.408	0.056	0.056	0.000	0.000	0.000	0.000
129	B	257	THR	0	-0.041	-0.003	28.252	-0.029	-0.029	0.000	0.000	0.000	0.000
130	B	258	ASN	0	-0.056	-0.026	31.033	0.397	0.397	0.000	0.000	0.000	0.000
131	B	259	GLY	0	-0.003	0.009	32.345	0.260	0.260	0.000	0.000	0.000	0.000
132	B	260	SER	0	-0.051	-0.047	33.439	0.172	0.172	0.000	0.000	0.000	0.000
133	B	261	THR	0	-0.006	-0.025	36.156	-0.086	-0.086	0.000	0.000	0.000	0.000
134	B	262	LEU	0	-0.005	0.014	36.466	0.092	0.092	0.000	0.000	0.000	0.000
135	B	263	THR	0	-0.017	-0.012	40.485	0.167	0.167	0.000	0.000	0.000	0.000
136	B	264	ILE	0	-0.023	-0.007	44.233	-0.023	-0.023	0.000	0.000	0.000	0.000
137	B	265	GLN	0	-0.025	-0.025	45.968	0.080	0.080	0.000	0.000	0.000	0.000
138	B	266	SER	0	0.002	-0.009	49.466	-0.104	-0.104	0.000	0.000	0.000	0.000
139	B	267	ASN	0	-0.019	-0.033	51.100	0.146	0.146	0.000	0.000	0.000	0.000
140	B	268	GLY	0	0.023	0.011	54.456	-0.013	-0.013	0.000	0.000	0.000	0.000
141	B	269	ALA	0	0.002	0.003	56.809	0.120	0.120	0.000	0.000	0.000	0.000
142	B	270	SER	0	0.011	0.022	55.244	-0.099	-0.099	0.000	0.000	0.000	0.000
143	B	271	PHE	0	0.028	0.009	49.623	0.024	0.024	0.000	0.000	0.000	0.000
144	B	272	THR	0	0.005	0.002	53.225	-0.021	-0.021	0.000	0.000	0.000	0.000
145	B	273	ALA	0	-0.006	-0.008	48.175	-0.013	-0.013	0.000	0.000	0.000	0.000
146	B	274	THR	0	0.028	-0.001	50.003	-0.004	-0.004	0.000	0.000	0.000	0.000
147	B	275	THR	0	-0.049	-0.029	44.346	-0.068	-0.068	0.000	0.000	0.000	0.000
148	B	276	ILE	0	-0.005	0.016	42.019	0.004	0.004	0.000	0.000	0.000	0.000
149	B	277	LYS	1	0.949	0.980	37.056	8.343	8.343	0.000	0.000	0.000	0.000
150	B	278	ILE	0	-0.001	-0.001	36.382	0.092	0.092	0.000	0.000	0.000	0.000
151	B	279	ILE	0	-0.025	-0.017	31.404	-0.106	-0.106	0.000	0.000	0.000	0.000
152	B	280	ALA	0	0.031	0.015	30.605	0.181	0.181	0.000	0.000	0.000	0.000
153	B	281	GLU	-1	-0.866	-0.945	26.497	-11.677	-11.677	0.000	0.000	0.000	0.000
154	B	282	GLN	-1	-0.703	-0.851	21.936	-14.110	-14.110	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:129:GLY)