FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: R5M58

Calculation Name: 1VRR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VRR

Chain ID: A

ChEMBL ID:

UniProt ID: Q84AF2

Base Structure: X-ray

Registration Date: 2023-03-13

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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2301085.592015
FMO2-HF: Nuclear repulsion 2220490.00611
FMO2-HF: Total energy -80595.585904
FMO2-MP2: Total energy -80833.329844


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


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


Summations of interaction energy for fragment #1(A:1:MET)
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.
-23.421-34.19861.828-20.472-30.576-0.098
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.063 / q_NPA : -0.065
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   
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].
3A3ILE00.0420.0053.815-0.5991.619-0.024-1.100-1.0940.002
4A4VAL0-0.073-0.0285.9280.0360.0360.0000.0000.0000.000
5A5GLU-1-0.888-0.9438.1100.0320.0320.0000.0000.0000.000
6A6VAL0-0.017-0.00810.0390.0100.0100.0000.0000.0000.000
7A7TYR0-0.025-0.00712.503-0.010-0.0100.0000.0000.0000.000
8A8SER0-0.052-0.06715.9230.0020.0020.0000.0000.0000.000
9A9HIS0-0.027-0.01718.5000.0080.0080.0000.0000.0000.000
10A10LEU0-0.020-0.02221.171-0.010-0.0100.0000.0000.0000.000
11A11ASN0-0.017-0.01822.735-0.006-0.0060.0000.0000.0000.000
12A12GLY00.0730.04420.126-0.010-0.0100.0000.0000.0000.000
13A13LEU00.014-0.00315.196-0.017-0.0170.0000.0000.0000.000
14A14GLU-1-0.824-0.86818.586-0.129-0.1290.0000.0000.0000.000
15A15TYR0-0.068-0.05121.514-0.011-0.0110.0000.0000.0000.000
16A16ILE00.0450.01416.384-0.008-0.0080.0000.0000.0000.000
17A17GLN0-0.028-0.01917.5520.0120.0120.0000.0000.0000.000
18A18VAL0-0.020-0.00120.327-0.005-0.0050.0000.0000.0000.000
19A19HIS0-0.067-0.02923.0780.0150.0150.0000.0000.0000.000
20A20LEU0-0.047-0.02419.6640.0000.0000.0000.0000.0000.000
21A21PRO00.0240.02818.787-0.040-0.0400.0000.0000.0000.000
22A22HIS00.0740.02517.305-0.045-0.0450.0000.0000.0000.000
23A23ILE0-0.0120.00015.225-0.083-0.0830.0000.0000.0000.000
24A24TRP00.0320.01111.555-0.097-0.0970.0000.0000.0000.000
25A25GLU-1-0.914-0.94312.337-0.629-0.6290.0000.0000.0000.000
26A26GLU-1-0.806-0.89910.950-0.733-0.7330.0000.0000.0000.000
27A27ILE0-0.012-0.0139.232-0.262-0.2620.0000.0000.0000.000
28A28GLN0-0.052-0.0357.821-0.352-0.3520.0000.0000.0000.000
29A29GLU-1-0.939-0.9816.279-2.040-2.0400.0000.0000.0000.000
30A30ILE0-0.020-0.0215.804-1.070-1.0700.0000.0000.0000.000
31A31ILE0-0.031-0.0132.650-1.587-0.6240.408-0.337-1.033-0.001
32A32VAL00.012-0.0122.222-11.325-10.2786.376-3.496-3.926-0.042
33A33SER0-0.138-0.0532.4682.4462.7072.153-0.659-1.755-0.012
34A34ILE0-0.0150.0072.410-0.1762.1801.211-0.940-2.628-0.001
35A35ASP-1-0.795-0.8801.660-8.591-18.88123.356-8.553-4.513-0.059
36A36ALA00.039-0.0152.0481.221-0.6496.839-1.749-3.220-0.001
37A37GLU-1-0.928-0.9573.8180.3190.5130.028-0.001-0.2210.000
38A38ALA0-0.023-0.0046.9870.0040.0040.0000.0000.0000.000
39A39CYS0-0.071-0.0345.5850.2030.2030.0000.0000.0000.000
40A40ARG10.8220.9357.731-0.425-0.4250.0000.0000.0000.000
41A41THR00.0220.0029.083-0.060-0.0600.0000.0000.0000.000
42A42LYS10.9180.97411.235-0.309-0.3090.0000.0000.0000.000
43A43GLU-1-0.875-0.93913.0880.1850.1850.0000.0000.0000.000
44A44SER0-0.053-0.03015.239-0.017-0.0170.0000.0000.0000.000
45A45LYS10.9670.97116.609-0.173-0.1730.0000.0000.0000.000
46A46GLU-1-0.895-0.94316.4990.2230.2230.0000.0000.0000.000
47A47LYS11.0080.99220.777-0.119-0.1190.0000.0000.0000.000
48A48THR0-0.063-0.04220.3500.0000.0000.0000.0000.0000.000
49A49LYS10.9520.99014.467-0.250-0.2500.0000.0000.0000.000
50A50GLN00.0010.00118.7750.0080.0080.0000.0000.0000.000
51A51GLY00.0230.01820.406-0.001-0.0010.0000.0000.0000.000
52A52GLN00.0230.02514.180-0.015-0.0150.0000.0000.0000.000
53A53ILE00.0230.00412.1480.0000.0000.0000.0000.0000.000
54A54LEU0-0.080-0.03610.4420.0070.0070.0000.0000.0000.000
55A55TYR00.0510.0234.894-0.064-0.0640.0000.0000.0000.000
56A56SER0-0.037-0.0217.462-0.041-0.0410.0000.0000.0000.000
57A57PRO00.0260.0157.3820.1650.1650.0000.0000.0000.000
58A58VAL0-0.005-0.0158.4120.0670.0670.0000.0000.0000.000
59A59ALA00.0460.0338.296-0.034-0.0340.0000.0000.0000.000
60A60LEU00.017-0.0172.630-0.904-0.2230.995-0.266-1.410-0.001
61A61ASN0-0.015-0.0116.1740.1270.1270.0000.0000.0000.000
62A62GLU-1-0.949-0.9669.1740.0480.0480.0000.0000.0000.000
63A63ALA0-0.0070.0046.331-0.181-0.1810.0000.0000.0000.000
64A64PHE00.004-0.0233.862-1.130-0.4280.103-0.196-0.6090.000
65A65LYS10.9070.9648.349-0.284-0.2840.0000.0000.0000.000
66A66GLU-1-0.928-0.94411.527-0.497-0.4970.0000.0000.0000.000
67A67LYS10.9260.9617.3371.6221.6220.0000.0000.0000.000
68A68LEU00.0080.00110.283-0.036-0.0360.0000.0000.0000.000
69A69GLU-1-0.864-0.94412.592-0.063-0.0630.0000.0000.0000.000
70A70ALA0-0.046-0.00414.2120.0110.0110.0000.0000.0000.000
71A71LYS10.8800.94512.5880.6860.6860.0000.0000.0000.000
72A72GLY0-0.020-0.00515.9300.0170.0170.0000.0000.0000.000
73A73TRP0-0.101-0.04914.3170.0780.0780.0000.0000.0000.000
74A74LYS10.9911.00217.4320.0870.0870.0000.0000.0000.000
75A75GLU-1-0.879-0.93719.7370.0170.0170.0000.0000.0000.000
76A76SER0-0.073-0.03620.644-0.013-0.0130.0000.0000.0000.000
77A77ARG10.9130.96122.922-0.024-0.0240.0000.0000.0000.000
78A78THR00.007-0.00125.552-0.012-0.0120.0000.0000.0000.000
79A79ASN00.006-0.00428.4110.0150.0150.0000.0000.0000.000
80A80TYR00.0130.00328.039-0.004-0.0040.0000.0000.0000.000
81A81TYR00.0050.00333.7340.0050.0050.0000.0000.0000.000
82A82VAL0-0.0190.00333.207-0.001-0.0010.0000.0000.0000.000
83A83THR00.022-0.00536.424-0.001-0.0010.0000.0000.0000.000
84A84ALA00.0190.00039.0390.0010.0010.0000.0000.0000.000
85A85ASP-1-0.914-0.94340.7960.0210.0210.0000.0000.0000.000
86A86PRO00.0520.01540.287-0.001-0.0010.0000.0000.0000.000
87A87LYS10.9300.93041.256-0.016-0.0160.0000.0000.0000.000
88A88LEU00.0750.05742.788-0.001-0.0010.0000.0000.0000.000
89A89ILE0-0.0040.00336.779-0.001-0.0010.0000.0000.0000.000
90A90ARG10.8950.93838.613-0.019-0.0190.0000.0000.0000.000
91A91GLU-1-0.951-0.96540.7270.0090.0090.0000.0000.0000.000
92A92THR0-0.042-0.01839.824-0.001-0.0010.0000.0000.0000.000
93A93LEU0-0.041-0.01835.1890.0000.0000.0000.0000.0000.000
94A94SER0-0.020-0.00536.7160.0000.0000.0000.0000.0000.000
95A95LEU0-0.0150.01338.966-0.002-0.0020.0000.0000.0000.000
96A96GLU-1-0.855-0.92937.047-0.007-0.0070.0000.0000.0000.000
97A97PRO0-0.005-0.01534.7480.0020.0020.0000.0000.0000.000
98A98GLU-1-0.930-0.96437.3890.0100.0100.0000.0000.0000.000
99A99GLU-1-0.899-0.96440.5420.0000.0000.0000.0000.0000.000
100A100GLN0-0.021-0.02836.0120.0030.0030.0000.0000.0000.000
101A101LYS10.9500.97640.261-0.014-0.0140.0000.0000.0000.000
102A102LYS10.9400.98441.7570.0000.0000.0000.0000.0000.000
103A103VAL0-0.006-0.01344.4510.0000.0000.0000.0000.0000.000
104A104ILE0-0.052-0.02340.0530.0010.0010.0000.0000.0000.000
105A105GLU-1-0.826-0.93044.4260.0160.0160.0000.0000.0000.000
106A106ALA0-0.0590.00146.5790.0000.0000.0000.0000.0000.000
107A107ALA0-0.059-0.04747.944-0.001-0.0010.0000.0000.0000.000
108A108GLY0-0.064-0.03149.6430.0010.0010.0000.0000.0000.000
109A109LYS10.8530.94244.323-0.018-0.0180.0000.0000.0000.000
110A110GLU-1-0.887-0.94041.1910.0310.0310.0000.0000.0000.000
111A111ALA00.0160.00540.2930.0010.0010.0000.0000.0000.000
112A112LEU0-0.0150.00035.6960.0010.0010.0000.0000.0000.000
113A113LYS10.8540.93031.111-0.032-0.0320.0000.0000.0000.000
114A114SER00.0150.01529.6710.0070.0070.0000.0000.0000.000
115A115TYR0-0.042-0.05124.380-0.010-0.0100.0000.0000.0000.000
116A116ASN00.0160.03724.1260.0010.0010.0000.0000.0000.000
117A117GLN00.0300.00320.414-0.015-0.0150.0000.0000.0000.000
118A118THR00.0250.00517.7100.0120.0120.0000.0000.0000.000
119A119ASP-1-0.916-0.96415.2590.1170.1170.0000.0000.0000.000
120A120PHE0-0.0040.01312.093-0.036-0.0360.0000.0000.0000.000
121A121VAL0-0.013-0.01516.6190.0100.0100.0000.0000.0000.000
122A122LYS10.8150.89016.7740.3310.3310.0000.0000.0000.000
123A123ASP-1-0.893-0.94120.236-0.188-0.1880.0000.0000.0000.000
124A124ARG10.7770.88722.5310.0680.0680.0000.0000.0000.000
125A125VAL00.0250.03116.7770.0070.0070.0000.0000.0000.000
126A126ALA00.023-0.01018.131-0.002-0.0020.0000.0000.0000.000
127A127ILE0-0.0010.00411.4010.0070.0070.0000.0000.0000.000
128A128GLU-1-0.859-0.93713.5210.1770.1770.0000.0000.0000.000
129A129VAL0-0.0090.0097.3920.0710.0710.0000.0000.0000.000
130A130GLN0-0.016-0.00910.0310.0070.0070.0000.0000.0000.000
131A131PHE0-0.005-0.0173.938-0.273-0.0570.001-0.028-0.1880.000
132A132GLY00.0200.0059.622-0.041-0.0410.0000.0000.0000.000
133A133LYS10.8170.90413.294-0.213-0.2130.0000.0000.0000.000
134A134TYR00.0960.01215.093-0.014-0.0140.0000.0000.0000.000
135A135SER0-0.044-0.00816.014-0.001-0.0010.0000.0000.0000.000
136A136PHE0-0.007-0.01916.044-0.023-0.0230.0000.0000.0000.000
137A137VAL00.0770.07313.664-0.006-0.0060.0000.0000.0000.000
138A138ALA00.0080.01116.467-0.023-0.0230.0000.0000.0000.000
139A139TYR0-0.027-0.01319.911-0.022-0.0220.0000.0000.0000.000
140A140ASP-1-0.731-0.87315.6490.2070.2070.0000.0000.0000.000
141A141LEU0-0.051-0.03517.007-0.028-0.0280.0000.0000.0000.000
142A142PHE0-0.056-0.04620.037-0.019-0.0190.0000.0000.0000.000
143A143VAL0-0.052-0.01522.850-0.011-0.0110.0000.0000.0000.000
144A144LYS10.8480.93618.382-0.149-0.1490.0000.0000.0000.000
145A145HIS00.0330.03016.297-0.046-0.0460.0000.0000.0000.000
146A146MET0-0.0240.00621.777-0.019-0.0190.0000.0000.0000.000
147A147ALA00.0140.01725.102-0.010-0.0100.0000.0000.0000.000
148A148PHE0-0.007-0.01821.271-0.010-0.0100.0000.0000.0000.000
149A149TYR00.032-0.00425.055-0.007-0.0070.0000.0000.0000.000
150A150VAL0-0.026-0.02026.657-0.006-0.0060.0000.0000.0000.000
151A151SER0-0.114-0.05528.987-0.002-0.0020.0000.0000.0000.000
152A152ASP-1-0.879-0.91329.547-0.044-0.0440.0000.0000.0000.000
153A153LYS10.8960.95126.5000.0040.0040.0000.0000.0000.000
154A154ILE0-0.119-0.01019.980-0.009-0.0090.0000.0000.0000.000
155A155ASP-1-0.749-0.86023.029-0.068-0.0680.0000.0000.0000.000
156A156VAL0-0.055-0.03818.5600.0020.0020.0000.0000.0000.000
157A157GLY00.015-0.00118.808-0.008-0.0080.0000.0000.0000.000
158A158VAL0-0.053-0.03212.367-0.009-0.0090.0000.0000.0000.000
159A159GLU-1-0.809-0.92712.5010.2680.2680.0000.0000.0000.000
160A160ILE0-0.017-0.0056.640-0.006-0.0060.0000.0000.0000.000
161A161LEU0-0.014-0.0218.3220.0550.0550.0000.0000.0000.000
162A162PRO0-0.0010.0175.2110.0930.0930.0000.0000.0000.000
163A163MET00.0550.0316.106-0.177-0.1770.0000.0000.0000.000
164A164LYS10.9080.9508.186-0.243-0.2430.0000.0000.0000.000
165A165GLU-1-0.950-0.9947.7230.5210.5210.0000.0000.0000.000
166A166LEU00.0540.0532.730-0.495-0.0700.460-0.126-0.7600.000
167A167SER00.0200.0066.886-0.048-0.0480.0000.0000.0000.000
168A168LYS10.8480.9419.104-0.325-0.3250.0000.0000.0000.000
169A169GLU-1-0.927-0.9778.4460.4060.4060.0000.0000.0000.000
170A170MET00.0140.0265.6020.0140.0140.0000.0000.0000.000
171A171SER0-0.020-0.0239.787-0.035-0.0350.0000.0000.0000.000
172A172SER0-0.034-0.01912.9060.0150.0150.0000.0000.0000.000
173A173GLY0-0.076-0.03915.3690.0030.0030.0000.0000.0000.000
174A174ILE00.0700.0319.485-0.022-0.0220.0000.0000.0000.000
175A175SER0-0.0150.01212.303-0.005-0.0050.0000.0000.0000.000
176A176TYR0-0.016-0.01310.2780.0370.0370.0000.0000.0000.000
177A177TYR00.0700.0329.605-0.050-0.0500.0000.0000.0000.000
178A178GLU-1-0.781-0.90311.4250.2770.2770.0000.0000.0000.000
179A179GLY0-0.029-0.01914.279-0.030-0.0300.0000.0000.0000.000
180A180GLU-1-0.852-0.94514.2190.1800.1800.0000.0000.0000.000
181A181LEU00.0280.02115.200-0.026-0.0260.0000.0000.0000.000
182A182TYR0-0.023-0.00616.855-0.027-0.0270.0000.0000.0000.000
183A183ASN0-0.038-0.01718.845-0.033-0.0330.0000.0000.0000.000
184A184VAL00.0150.03518.955-0.011-0.0110.0000.0000.0000.000
185A185ILE0-0.002-0.00320.487-0.013-0.0130.0000.0000.0000.000
186A186ARG10.8330.91322.860-0.104-0.1040.0000.0000.0000.000
187A187GLN0-0.114-0.05723.748-0.011-0.0110.0000.0000.0000.000
188A188GLY00.0210.01027.228-0.005-0.0050.0000.0000.0000.000
189A189ARG10.9860.97425.7100.0080.0080.0000.0000.0000.000
190A190GLY00.0160.00126.701-0.008-0.0080.0000.0000.0000.000
191A191VAL0-0.0640.01126.450-0.002-0.0020.0000.0000.0000.000
192A192PRO00.0540.01022.4940.0040.0040.0000.0000.0000.000
193A193ALA00.021-0.00225.358-0.005-0.0050.0000.0000.0000.000
194A194VAL00.005-0.00922.374-0.003-0.0030.0000.0000.0000.000
195A195PRO00.0260.02622.8550.0080.0080.0000.0000.0000.000
196A196LEU0-0.033-0.01818.1430.0080.0080.0000.0000.0000.000
197A197VAL00.0240.01913.597-0.017-0.0170.0000.0000.0000.000
198A198LEU0-0.0240.00513.3900.0280.0280.0000.0000.0000.000
199A199ILE00.0230.0047.624-0.060-0.0600.0000.0000.0000.000
200A200GLY00.026-0.0068.0560.1520.1520.0000.0000.0000.000
201A201ILE00.0190.0092.625-1.549-1.1162.723-0.562-2.5930.004
202A202ALA0-0.014-0.0453.492-0.821-0.1620.024-0.206-0.476-0.001
203A203PRO0-0.0570.0601.8043.750-5.02217.175-2.253-6.1500.014