FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: ZVLVN

Calculation Name: 4OPH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OPH

Chain ID: A

ChEMBL ID:

UniProt ID: Q20NS3

Base Structure: X-ray

Registration Date: 2023-09-22

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2082182.54485
FMO2-HF: Nuclear repulsion 2001720.62243
FMO2-HF: Total energy -80461.92242
FMO2-MP2: Total energy -80694.515297


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:2:ASP)


Summations of interaction energy for fragment #1(A:2:ASP)
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.
-9.110.419000000000034.281-5.923-7.8880.043
Interaction energy analysis for fragmet #1(A:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.847 / q_NPA : -0.942
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].
3A4ASN00.0630.0422.454-38.757-32.1983.042-4.498-5.1030.049
4A5THR0-0.0060.0012.414-11.675-9.0931.237-1.337-2.482-0.006
5A6VAL00.0230.0344.059-5.679-5.2910.002-0.088-0.3030.000
6A7SER0-0.031-0.0486.217-5.339-5.3390.0000.0000.0000.000
7A8SER00.012-0.0036.679-4.518-4.5180.0000.0000.0000.000
8A9PHE0-0.022-0.0058.108-3.165-3.1650.0000.0000.0000.000
9A10GLN00.0550.0189.775-3.213-3.2130.0000.0000.0000.000
10A11VAL00.0190.02011.783-2.029-2.0290.0000.0000.0000.000
11A12ASP-1-0.861-0.91712.67720.40120.4010.0000.0000.0000.000
12A13CYS0-0.050-0.02513.194-1.719-1.7190.0000.0000.0000.000
13A14PHE00.0070.02215.766-1.473-1.4730.0000.0000.0000.000
14A15LEU00.0240.00016.824-1.158-1.1580.0000.0000.0000.000
15A16TRP0-0.051-0.02918.374-1.140-1.1400.0000.0000.0000.000
16A17HIS00.0080.00019.987-0.790-0.7900.0000.0000.0000.000
17A18VAL0-0.011-0.00221.408-0.774-0.7740.0000.0000.0000.000
18A19ARG10.8570.92619.782-14.825-14.8250.0000.0000.0000.000
19A20LYS10.8570.93324.240-10.791-10.7910.0000.0000.0000.000
20A21ARG10.9530.96126.138-11.316-11.3160.0000.0000.0000.000
21A22PHE00.0080.00927.635-0.394-0.3940.0000.0000.0000.000
22A23ALA0-0.025-0.02828.738-0.350-0.3500.0000.0000.0000.000
23A24ASP-1-0.898-0.92930.3089.8289.8280.0000.0000.0000.000
24A25GLN0-0.061-0.00531.948-0.197-0.1970.0000.0000.0000.000
25A26GLU-1-0.970-0.99833.4637.9437.9430.0000.0000.0000.000
26A27LEU0-0.029-0.01832.668-0.097-0.0970.0000.0000.0000.000
27A28GLY0-0.086-0.02531.056-0.003-0.0030.0000.0000.0000.000
28A29ASP-1-0.780-0.90431.4599.5369.5360.0000.0000.0000.000
29A30ALA00.056-0.00731.5520.2560.2560.0000.0000.0000.000
30A31PRO00.0400.02729.3840.2970.2970.0000.0000.0000.000
31A32PHE0-0.039-0.03025.7280.5680.5680.0000.0000.0000.000
32A33LEU00.0320.03126.6690.4820.4820.0000.0000.0000.000
33A34ASP-1-0.897-0.95627.33310.22010.2200.0000.0000.0000.000
34A35ARG10.9480.96322.435-11.330-11.3300.0000.0000.0000.000
35A36LEU0-0.0220.01122.3510.5910.5910.0000.0000.0000.000
36A37ARG10.9310.98022.641-10.440-10.4400.0000.0000.0000.000
37A38ALA0-0.043-0.02922.0880.2980.2980.0000.0000.0000.000
38A39ASP-1-0.796-0.90118.63115.47115.4710.0000.0000.0000.000
39A40GLN0-0.0190.00617.9020.4960.4960.0000.0000.0000.000
40A41ALA0-0.058-0.03218.8630.3080.3080.0000.0000.0000.000
41A42SER0-0.016-0.00815.5800.7300.7300.0000.0000.0000.000
42A43LEU00.0280.01613.5771.0421.0420.0000.0000.0000.000
43A44ARG10.9500.97814.305-12.532-12.5320.0000.0000.0000.000
44A45GLY0-0.016-0.00715.2260.1950.1950.0000.0000.0000.000
45A46ARG10.9050.9448.304-23.922-23.9220.0000.0000.0000.000
46A47GLY00.0120.01010.1841.4131.4130.0000.0000.0000.000
47A48SER0-0.024-0.01311.9980.1390.1390.0000.0000.0000.000
48A49THR0-0.042-0.0259.5020.0080.0080.0000.0000.0000.000
49A50LEU0-0.060-0.0185.6960.7770.7770.0000.0000.0000.000
50A51GLY0-0.0160.0098.3690.8380.8380.0000.0000.0000.000
51A52LEU0-0.034-0.0178.1590.3640.3640.0000.0000.0000.000
52A53ASP-1-0.874-0.93312.18015.64615.6460.0000.0000.0000.000
53A54ILE0-0.001-0.02614.5260.5540.5540.0000.0000.0000.000
54A55GLU-1-0.887-0.92916.40514.06214.0620.0000.0000.0000.000
55A56THR00.033-0.01515.9010.4900.4900.0000.0000.0000.000
56A57ALA00.0340.03212.7580.5880.5880.0000.0000.0000.000
57A58THR00.025-0.00914.2350.8380.8380.0000.0000.0000.000
58A59ARG10.8870.95917.143-14.695-14.6950.0000.0000.0000.000
59A60ALA0-0.0030.01113.835-0.139-0.1390.0000.0000.0000.000
60A61GLY00.0240.00014.7310.2650.2650.0000.0000.0000.000
61A62LYS10.8730.93515.598-14.100-14.1000.0000.0000.0000.000
62A63GLN00.0300.00717.519-0.424-0.4240.0000.0000.0000.000
63A64ILE0-0.064-0.03011.8430.1180.1180.0000.0000.0000.000
64A65VAL00.007-0.00415.810-0.181-0.1810.0000.0000.0000.000
65A66GLU-1-0.905-0.94717.99713.27813.2780.0000.0000.0000.000
66A67ARG10.9420.96616.681-18.777-18.7770.0000.0000.0000.000
67A68ILE00.004-0.00414.715-0.156-0.1560.0000.0000.0000.000
68A69LEU0-0.016-0.01218.770-0.511-0.5110.0000.0000.0000.000
69A70GLU-1-0.904-0.94521.76512.07212.0720.0000.0000.0000.000
70A71GLU-1-1.022-0.99418.27016.69216.6920.0000.0000.0000.000
71A72GLU-1-0.992-0.93221.74413.64813.6480.0000.0000.0000.000
72A73SER0-0.090-0.07123.5220.4290.4290.0000.0000.0000.000
73A74ASP-1-0.869-0.95226.08011.27311.2730.0000.0000.0000.000
74A75GLU-1-0.903-0.96227.8719.8219.8210.0000.0000.0000.000
75A76ALA0-0.063-0.04230.753-0.023-0.0230.0000.0000.0000.000
76A77LEU00.0140.02725.572-0.114-0.1140.0000.0000.0000.000
77A78LYS10.7460.86324.408-12.529-12.5290.0000.0000.0000.000
78A79MET00.0000.00126.822-0.342-0.3420.0000.0000.0000.000
79A80THR00.002-0.00829.235-0.009-0.0090.0000.0000.0000.000
80A81ILE0-0.022-0.02027.593-0.239-0.2390.0000.0000.0000.000
81A82ALA00.0690.03330.6140.2100.2100.0000.0000.0000.000
82A83SER0-0.067-0.01831.098-0.233-0.2330.0000.0000.0000.000
83A84VAL00.022-0.00332.172-0.175-0.1750.0000.0000.0000.000
84A85PRO0-0.039-0.01334.635-0.230-0.2300.0000.0000.0000.000
85A86ALA00.0050.00035.8910.0220.0220.0000.0000.0000.000
86A87SER00.0250.01934.170-0.323-0.3230.0000.0000.0000.000
87A88ARG10.9360.97937.280-7.663-7.6630.0000.0000.0000.000
88A89TYR00.008-0.00833.3160.1560.1560.0000.0000.0000.000
89A90LEU0-0.071-0.02338.015-0.349-0.3490.0000.0000.0000.000
90A91THR0-0.023-0.01638.3880.2950.2950.0000.0000.0000.000
91A92ASP-1-0.744-0.79639.7927.7997.7990.0000.0000.0000.000
92A93MET0-0.060-0.02836.067-0.125-0.1250.0000.0000.0000.000
93A94THR00.0170.03340.8950.1050.1050.0000.0000.0000.000
94A95LEU00.045-0.01839.2340.1520.1520.0000.0000.0000.000
95A96GLU-1-0.923-0.95640.2527.4557.4550.0000.0000.0000.000
96A97GLU-1-0.811-0.90540.9677.5737.5730.0000.0000.0000.000
97A98MET0-0.072-0.04835.4940.2150.2150.0000.0000.0000.000
98A99SER0-0.118-0.09036.0650.2690.2690.0000.0000.0000.000
99A100ARG10.9951.04937.295-7.814-7.8140.0000.0000.0000.000
100A101ASP-1-0.940-0.96937.4078.1678.1670.0000.0000.0000.000
101A102TRP0-0.034-0.03831.916-0.107-0.1070.0000.0000.0000.000
102A103PHE0-0.033-0.01634.3700.2310.2310.0000.0000.0000.000
103A104MET0-0.0180.01829.7650.0130.0130.0000.0000.0000.000
104A105LEU0-0.020-0.00834.8000.0820.0820.0000.0000.0000.000
105A106MET0-0.061-0.02234.4600.1640.1640.0000.0000.0000.000
106A107PRO00.0220.00629.8880.0550.0550.0000.0000.0000.000
107A108LYS10.9110.96328.734-10.154-10.1540.0000.0000.0000.000
108A109GLN00.0270.00424.635-0.411-0.4110.0000.0000.0000.000
109A110LYS10.9310.97023.331-12.051-12.0510.0000.0000.0000.000
110A111VAL00.019-0.00118.683-0.101-0.1010.0000.0000.0000.000
111A112ALA0-0.037-0.01920.5380.2920.2920.0000.0000.0000.000
112A113GLY00.0710.04820.147-0.259-0.2590.0000.0000.0000.000
113A114SER0-0.032-0.04718.418-0.125-0.1250.0000.0000.0000.000
114A115LEU00.0260.02620.068-0.434-0.4340.0000.0000.0000.000
115A116CYS0-0.074-0.02722.7700.2420.2420.0000.0000.0000.000
116A117ILE00.0310.00824.069-0.484-0.4840.0000.0000.0000.000
117A118ARG10.9050.95925.036-11.662-11.6620.0000.0000.0000.000
118A119MET00.0410.01229.137-0.263-0.2630.0000.0000.0000.000
119A120ASP-1-0.743-0.88032.2548.9138.9130.0000.0000.0000.000
120A121GLN0-0.032-0.02733.910-0.046-0.0460.0000.0000.0000.000
121A122ALA0-0.049-0.01835.571-0.188-0.1880.0000.0000.0000.000
122A123ILE00.005-0.00838.630-0.086-0.0860.0000.0000.0000.000
123A124MET0-0.029-0.00440.7010.0610.0610.0000.0000.0000.000
124A125ASP-1-0.890-0.93643.4696.6706.6700.0000.0000.0000.000
125A126LYS10.8690.93443.685-7.007-7.0070.0000.0000.0000.000
126A127ASN00.0260.00345.0800.0360.0360.0000.0000.0000.000
127A128ILE0-0.033-0.02039.8060.0020.0020.0000.0000.0000.000
128A129ILE0-0.005-0.00642.000-0.014-0.0140.0000.0000.0000.000
129A130LEU0-0.012-0.00635.5960.1320.1320.0000.0000.0000.000
130A131LYS10.8840.93738.439-7.665-7.6650.0000.0000.0000.000
131A132ALA00.015-0.00634.8500.2720.2720.0000.0000.0000.000
132A133ASN00.0730.05135.575-0.321-0.3210.0000.0000.0000.000
133A134PHE0-0.018-0.02133.5910.4080.4080.0000.0000.0000.000
134A135SER00.007-0.00232.934-0.202-0.2020.0000.0000.0000.000
135A136VAL00.017-0.00734.1650.1840.1840.0000.0000.0000.000
136A137ILE00.0130.03733.197-0.149-0.1490.0000.0000.0000.000
137A138PHE0-0.054-0.03835.0030.0050.0050.0000.0000.0000.000
138A139ASP-1-0.901-0.96039.0827.9747.9740.0000.0000.0000.000
139A140ARG10.9510.97234.158-8.678-8.6780.0000.0000.0000.000
140A141LEU00.0200.00232.4430.0380.0380.0000.0000.0000.000
141A142GLU-1-0.921-0.94329.32910.68810.6880.0000.0000.0000.000
142A143THR00.001-0.00527.8350.4940.4940.0000.0000.0000.000
143A144LEU0-0.042-0.01428.604-0.501-0.5010.0000.0000.0000.000
144A145ILE0-0.047-0.02529.0830.3400.3400.0000.0000.0000.000
145A146LEU0-0.048-0.04630.3900.2730.2730.0000.0000.0000.000
146A147LEU0-0.0040.01631.574-0.351-0.3510.0000.0000.0000.000
147A148ARG10.8590.93932.820-9.007-9.0070.0000.0000.0000.000
148A149ALA0-0.0130.00235.463-0.192-0.1920.0000.0000.0000.000
149A150PHE00.011-0.01837.6070.0340.0340.0000.0000.0000.000
150A151THR0-0.086-0.09241.148-0.067-0.0670.0000.0000.0000.000
151A152GLU-1-0.931-0.97443.8766.3546.3540.0000.0000.0000.000
152A153GLU-1-0.961-0.96546.5576.8716.8710.0000.0000.0000.000
153A154GLY00.0350.06444.8100.1510.1510.0000.0000.0000.000
154A155ALA00.0530.02942.2150.0520.0520.0000.0000.0000.000
155A156ILE0-0.030-0.00935.6600.0220.0220.0000.0000.0000.000
156A157VAL00.0580.03037.4180.0250.0250.0000.0000.0000.000
157A158GLY0-0.003-0.01433.5430.1850.1850.0000.0000.0000.000
158A159GLU-1-0.878-0.95130.25110.32410.3240.0000.0000.0000.000
159A160ILE00.0060.00427.6390.3160.3160.0000.0000.0000.000
160A161SER00.0240.00526.906-0.107-0.1070.0000.0000.0000.000
161A162PRO00.0180.01024.4830.4070.4070.0000.0000.0000.000
162A163LEU0-0.010-0.01419.0930.0830.0830.0000.0000.0000.000
163A164PRO0-0.0230.00918.3450.1050.1050.0000.0000.0000.000
164A165SER0-0.041-0.03115.3441.0631.0630.0000.0000.0000.000
165A166LEU0-0.0500.00012.610-0.616-0.6160.0000.0000.0000.000
166A167PRO00.001-0.00714.1460.9670.9670.0000.0000.0000.000
167A168GLY00.0540.04717.3740.0080.0080.0000.0000.0000.000
168A169HIS00.0090.01220.512-0.342-0.3420.0000.0000.0000.000
169A170THR00.0260.00923.195-0.250-0.2500.0000.0000.0000.000
170A171ASP-1-0.818-0.92925.76610.61710.6170.0000.0000.0000.000
171A172GLU-1-1.004-1.00625.77211.01711.0170.0000.0000.0000.000
172A173ASP-1-0.816-0.90822.38913.55113.5510.0000.0000.0000.000
173A174VAL0-0.004-0.01425.479-0.065-0.0650.0000.0000.0000.000
174A175LYS10.8700.96928.577-10.356-10.3560.0000.0000.0000.000
175A176ASN00.020-0.01926.679-0.350-0.3500.0000.0000.0000.000
176A177ALA0-0.0140.00726.925-0.064-0.0640.0000.0000.0000.000
177A178ILE00.0000.00228.493-0.198-0.1980.0000.0000.0000.000
178A179GLY0-0.012-0.00131.860-0.211-0.2110.0000.0000.0000.000
179A180VAL0-0.038-0.03227.432-0.127-0.1270.0000.0000.0000.000
180A181LEU0-0.029-0.00730.704-0.100-0.1000.0000.0000.0000.000
181A182ILE00.0500.01132.268-0.177-0.1770.0000.0000.0000.000
182A183GLY0-0.0100.01434.558-0.153-0.1530.0000.0000.0000.000
183A184GLY0-0.035-0.02733.397-0.104-0.1040.0000.0000.0000.000
184A185LEU0-0.014-0.02834.363-0.083-0.0830.0000.0000.0000.000
185A186GLU-1-0.908-0.96637.0097.6027.6020.0000.0000.0000.000
186A187TRP0-0.100-0.04034.841-0.195-0.1950.0000.0000.0000.000
187A188ASN0-0.043-0.02036.332-0.133-0.1330.0000.0000.0000.000
188A189ASP-1-0.900-0.92340.2737.2307.2300.0000.0000.0000.000
189A190ASN00.021-0.00839.997-0.213-0.2130.0000.0000.0000.000
190A191THR0-0.033-0.00542.904-0.035-0.0350.0000.0000.0000.000
191A192VAL0-0.0130.00538.290-0.011-0.0110.0000.0000.0000.000
192A193ARG10.7970.90241.629-7.328-7.3280.0000.0000.0000.000
193A194VAL00.0180.02037.9560.1130.1130.0000.0000.0000.000
194A195SER0-0.031-0.05340.768-0.166-0.1660.0000.0000.0000.000
195A196GLU-1-0.801-0.92441.7897.3577.3570.0000.0000.0000.000
196A197THR0-0.043-0.03940.6850.0530.0530.0000.0000.0000.000
197A198LEU00.1030.03735.7920.1230.1230.0000.0000.0000.000
198A199GLN0-0.0110.02438.9680.0020.0020.0000.0000.0000.000
199A200ARG10.7990.90640.938-7.326-7.3260.0000.0000.0000.000
200A201PHE0-0.083-0.05737.452-0.094-0.0940.0000.0000.0000.000
201A202ALA0-0.0040.01835.3460.1300.1300.0000.0000.0000.000
202A203TRP0-0.021-0.01334.8030.2720.2720.0000.0000.0000.000